WorldWideScience

Sample records for changing molecular epidemiology

  1. Molecular Epidemiology of Rotaviruses

    OpenAIRE

    Nakagomi, Osamu

    2004-01-01

    Molecular epidemiology of rotaviruses emerged a little over 25 years ago as a fascinating branch of science that utilized then cutting-edge technology of RNA polyacrylamide gel electrophoresis. Molecular epidemiology, as I have observed it closely almost since its dawn, is an ever-evolving discipline which has incorporated the advances of the related sciences including molecular evolutionary biology and ecology, while it is firmly and deeply rooted in the edifice of epidemiology of infectious...

  2. Molecular Epidemiology of Foodborne Pathogens

    Science.gov (United States)

    Chen, Yi; Brown, Eric; Knabel, Stephen J.

    The purpose of this chapter is to describe the basic principles and advancements in the molecular epidemiology of foodborne pathogens. Epidemiology is the study of the distribution and determinants of infectious diseases and/or the dynamics of disease transmission. The goals of epidemiology include the identification of physical sources, routes of transmission of infectious agents, and distribution and relationships of different subgroups. Molecular epidemiology is the study of epidemiology at the molecular level. It has been defined as "a science that focuses on the contribution of potential genetic and environmental risk factors, identified at the molecular level, to the etiology, distribution and prevention of diseases within families and across populations".

  3. The Changing Face of the Epidemiology of Tuberculosis due to Molecular Strain Typing: A Review

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    Philip N Suffys

    1997-05-01

    Full Text Available About one third of the world population is infected with tubercle bacilli, causing eight million new cases of tuberculosis (TB and three million deaths each year. After years of lack of interest in the disease, World Health Organization recently declared TB a global emergency and it is clear that there is need for more efficient national TB programs and newly defined research priorities. A more complete epidemiology of tuberculosis will lead to a better identification of index cases and to a more efficient treatment of the disease. Recently, new molecular tools became available for the identification of strains of Mycobacterium tuberculosis (M. tuberculosis, allowing a better recognition of transmission routes of defined strains. Both a standardized restriction-fragment-length-polymorphism-based methodology for epidemiological studies on a large scale and deoxyribonucleic acids (DNA amplification-based methods that allow rapid detection of outbreaks with multidrug-resistant (MDR strains, often characterized by high mortality rates, have been developed. This review comments on the existing methods of DNA-based recognition of M. tuberculosis strains and their peculiarities. It also summarizes literature data on the application of molecular fingerprinting for detection of outbreaks of M. tuberculosis, for identification of index cases, for study of interaction between TB and infection with the human immunodeficiency virus, for analysis of the behavior of MDR strains, for a better understanding of risk factors for transmission of TB within communities and for population-based studies of TB transmission within and between countries

  4. Changing epidemiology of AIDS.

    OpenAIRE

    Donovan, C. A.; Stratton, E.

    1994-01-01

    It has been 15 years since AIDS made its first appearance in North America, probably longer worldwide. In that time, our knowledge of the epidemiology of AIDS has grown and changed. This review highlights significant aspects of the epidemic with particular emphasis on the evolution of this disease in North America.

  5. [Opportunity and challenge on molecular epidemiology].

    Science.gov (United States)

    Duan, G C; Chen, S Y

    2016-08-10

    Molecular epidemiology, a branch of epidemiology, combines the theories and methods, both in epidemiology and molecular biology. Molecular epidemiology mainly focuses on biological markers, describing the distribution, occurrence, development and prognosis of diseases at the molecular level. The completion of Human Genome Project and rapid development of Precision Medicine and Big Data not only offer the new development opportunities but also bring about a higher demand and new challenge for molecular epidemiology. PMID:27539332

  6. Molecular epidemiology of glanders, Pakistan.

    Science.gov (United States)

    Hornstra, Heidie; Pearson, Talima; Georgia, Shalamar; Liguori, Andrew; Dale, Julia; Price, Erin; O'Neill, Matthew; Deshazer, David; Muhammad, Ghulam; Saqib, Muhammad; Naureen, Abeera; Keim, Paul

    2009-12-01

    We collected epidemiologic and molecular data from Burkholderia mallei isolates from equines in Punjab, Pakistan from 1999 through 2007. We show that recent outbreaks are genetically distinct from available whole genome sequences and that these genotypes are persistent and ubiquitous in Punjab, probably due to human-mediated movement of equines.

  7. Molecular epidemiology of Blastocystis

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    Fadime Eroğlu

    2015-12-01

    Full Text Available Blastocystis pathogenicity and classification was newly illuminated with molecular genetic studies and recently the parasite was found in the focus of many researchers. Several molecular methods such as; polymerase chain reaction (PCR, PCR-restriction fragment length polymorphism, random amplified polymorphic DNA, real-time polymerase chain reaction and DNA sequencing analyses can be used in genotyping of Blastocystis. Blastocystis parasites may cause diarrhea, abdominal pain, bloating, gas, irritability, anorexia, cramps, vomiting, dehydration, insomnia, nausea, loss of appetite, weight loss, fatigue symptoms and also could be asymptomatic cases. In this review, it was aimed to summarize the associations between Blastocystis subtypes and pathogenicity.

  8. [From molecular to genomic and metagenomic epidemiology].

    Science.gov (United States)

    Zhebrun, A B

    2014-01-01

    The notion "molecular epidemiology" was introduced into scientific literature by Kilburn E. et al. in 1973. The first period of development of infectious diseases molecular epidemiology may be called "genotypic" (1980-1990s). During this period methodology of molecular marking of pathogens for purposes of monitoring of their spread and outbreak detection (novel nomenclature of diphtheria corynebacteria based on ribotyping; international network PulseNet for monitoring food source infections; international database of tuberculosis mycobacteria spoligotypes) was created. The second--"genomic" period started in the 2000s. Molecular epidemiology rapidly went through single markers (genotypes or single genes) to deciphering the whole genome of pathoge "mobileome", "resistome", "virulome" etc. took an important place in the studies of emerging and pandemic infections. Knowledge on genetic mechanisms leading to emergence and global dissemination of novel pathogens give molecular epidemiology its own scientific content and transforms it from a methodical approach to an independent field of epidemiology. The third--"metagenomic" period starts nowadays based on meta-genomic approach that allows to determine the whole set ofgenomes in the studied sample without the cultivation procedure. In the short-term this would lead to a change of a century-long paradigm of diagnostics and control of infections: instead of search of separate (key) pathogens--characteristics of the full specter of microorganisms in the material from patients and environmental samples with its identification up to any taxonomic depth. In the systems of regional and global epidemiologic control a universal monitoring of all known and re-emerging pathogens with construction and maintenance of metagenomic passports of human habitats will be realized. PMID:25286516

  9. [From molecular to genomic and metagenomic epidemiology].

    Science.gov (United States)

    Zhebrun, A B

    2014-01-01

    The notion "molecular epidemiology" was introduced into scientific literature by Kilburn E. et al. in 1973. The first period of development of infectious diseases molecular epidemiology may be called "genotypic" (1980-1990s). During this period methodology of molecular marking of pathogens for purposes of monitoring of their spread and outbreak detection (novel nomenclature of diphtheria corynebacteria based on ribotyping; international network PulseNet for monitoring food source infections; international database of tuberculosis mycobacteria spoligotypes) was created. The second--"genomic" period started in the 2000s. Molecular epidemiology rapidly went through single markers (genotypes or single genes) to deciphering the whole genome of pathoge "mobileome", "resistome", "virulome" etc. took an important place in the studies of emerging and pandemic infections. Knowledge on genetic mechanisms leading to emergence and global dissemination of novel pathogens give molecular epidemiology its own scientific content and transforms it from a methodical approach to an independent field of epidemiology. The third--"metagenomic" period starts nowadays based on meta-genomic approach that allows to determine the whole set ofgenomes in the studied sample without the cultivation procedure. In the short-term this would lead to a change of a century-long paradigm of diagnostics and control of infections: instead of search of separate (key) pathogens--characteristics of the full specter of microorganisms in the material from patients and environmental samples with its identification up to any taxonomic depth. In the systems of regional and global epidemiologic control a universal monitoring of all known and re-emerging pathogens with construction and maintenance of metagenomic passports of human habitats will be realized.

  10. HCV and HCC molecular epidemiology

    Directory of Open Access Journals (Sweden)

    Flor H. Pujol

    2007-02-01

    Full Text Available

    iHepatitis C virus (HCV is a member of the family Flaviviridae, responsible for the majority of the non-A non-B post-transfusion hepatitis before 1990. Around 170 millions persons in the world are thought to be infected with this virus. A high number of HCV-infected people develop cirrhosis and from these, a significant proportion progresses to hepatocellular carcinoma (HCC. Six HCV genotypes and a large number of subtypes in each genotype have been described. Infections with HCV genotype 1 are associated with the lowest therapeutic success. HCV genotypes 1, 2, and 3 have a worldwide distribution. HCV subtypes 1a and 1b are the most common genotypes in the United States and are also are predominant in Europe, while in Japan, subtype 1b is predominant. Although HCV subtypes 2a and 2b are relatively common in America, Europe, and Japan, subtype 2c is found commonly in northern Italy. HCV genotype 3a is frequent in intravenous drug abusers in Europe and the United States. HCV genotype 4 appears to be prevalent in Africa and the Middle East, and genotypes 5 and 6 seem to be confined to South Africa and Asia, respectively. HCC accounts for approximately 6% of all human cancers. Around 500,000 to 1 million cases occur annually worldwide, with HCC being the fifth common malignancy in men and the ninth in women. HCC is frequently a consequence of infection by HBV and HCV. The first line of evidences comes from epidemiologic studies. While HBV is the most frequent cause of HCC in many countries of Asia and South America, both HBV and HCV are found at similar frequencies, and eventually HCV at a higher frequency than HBV, among HCC patients in Europe, North America, and Japan. The cumulative appearance rate of HCC might be higher for HCV

  11. Epidemiology, molecular epidemiology, and risk factors for renal cell carcinoma

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    Chiara Paglino

    2011-12-01

    Full Text Available Despite only accounting for approximately 2% of all new primary cancer cases, renal cell carcinoma (RCC incidence has dramatically increased over time. Incidence rates vary greatly according to geographic areas, so that it is extremely likely that exogenous risk factors could play an important role in the development of this cancer. Several risk factors have been linked with RCC, including cigarette smoking, obesity, hypertension (and antihypertensive drugs, chronic kidney diseases (also dialysis and transplantation, as well as the use of certain analgesics. Furthermore, although RCC has not generally been considered an occupational cancer, several types of occupationally-derived exposures have been implicated in its pathogenesis. These include exposure to asbestos, chlorinated solvents, gasoline, diesel exhaust fumes, polycyclic aromatic hydrocarbons, printing inks and dyes, cadmium and lead. Finally, families with a predisposition to the development of renal neoplasms were identified and the genes involved discovered and characterized. Therefore, there are now four well-characterized, genetically determined syndromes associated with an increased incidence of kidney tumors, i.e., Von Hippel Lindau (VHL, Hereditary Papillary Renal Carcinoma (HPRC, Birt-Hogg-Dubé Syndrome (BHD, and Hereditary Leiomyomatosis and Renal Cell Cancer (HLRCC. This review will address present knowledge about the epidemiology, molecular epidemiology and risk factors of RCC.

  12. Molecular epidemiology of dengue viruses in Brazil

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    Rita Maria Ribeiro Nogueira

    2000-01-01

    Full Text Available Dengue viruses (DEN are found as four antigenically distinct serotypes designated DEN-1, 2, 3, and 4. Laboratory evidence that strain-intratypical variation occurs among DEN viruses has been demonstrated since the 1970s, although only with the advances in molecular technologies has it been possible to determine the genetic variability of each serotype. Genotypical identification has proven to be a useful tool for determining the origin and spread of epidemics and to correlate virulence of strains. In this report we present the results of molecular epidemiological studies with the DEN-1 and DEN-2 viruses that caused dengue epidemics in Brazil during the last decade.

  13. Molecular Epidemiology for Vector Research on Leishmaniasis

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    Hirotomo Kato

    2010-03-01

    Full Text Available Leishmaniasis is a protozoan disease caused by the genus Leishmania transmitted by female phlebotomine sand flies. Surveillance of the prevalence of Leishmania and responsive vector species in endemic and surrounding areas is important for predicting the risk and expansion of the disease. Molecular biological methods are now widely applied to epidemiological studies of infectious diseases including leishmaniasis. These techniques are used to detect natural infections of sand fly vectors with Leishmania protozoa and are becoming powerful tools due to their sensitivity and specificity. Recently, genetic analyses have been performed on sand fly species and genotyping using PCR-RFLP has been applied to the sand fly taxonomy. In addition, a molecular mass screening method has been established that enables both sand fly species and natural leishmanial infections to be identified simultaneously in hundreds of sand flies with limited effort. This paper reviews recent advances in the study of sand flies, vectors of leishmaniasis, using molecular biological approaches.

  14. Applying molecular epidemiology in pediatric leukemia.

    Science.gov (United States)

    Schiffman, Joshua D

    2016-02-01

    Molecular epidemiology is the study of genetic and environmental risk for disease, with much effort centered on cancer. Childhood leukemia occurs in nearly a third of all patients newly diagnosed with pediatric cancer. only a small percentage of these new cases of childhood leukemia are associated with high penetrant hereditary cancer syndromes. Childhood leukemia, especially acute lymphoblastic leukemia, has been associated with a dysregulated immune system due to delayed infectious exposure at a young age. Identical twins with childhood leukemia suggest that acute lymphoblastic leukemia begins in utero and that the concordant presentation is due to a shared preleukemia subclone via placental transfer. Investigation of single nucleotide polymorphisms within candidate genes find that leukemia risk may be attributed to population-based polymorphisms affecting folate metabolism, xenobiotic metabolism, DNA repair, immunity, and B-cell development. More recently, genome-wide association studies for leukemia risk has led investigators to genes associated with B-cell development. When describing leukemia predisposition due to hereditary cancer syndromes, the following 6 categories become apparent on the basis of biology and clinical presentation: (1) genetic instability/DNA repair syndromes, (2) cell cycle/differentiation syndromes, (3) bone marrow failure syndromes, (4) telomere maintenance syndromes, (5) immunodeficiency syndromes, and (6) transcription factor syndromes and pure familial leukemia. understanding the molecular epidemiology of childhood leukemia can affect the treatment and tumor surveillance strategies for these high risk patients and their family members.

  15. Molecular epidemiology and evolution of fish Novirhabdoviruses

    Science.gov (United States)

    Kurath, Gael

    2014-01-01

    The genus Novirhabdoviridae contains several of the important rhabdoviruses that infect fish hosts. There are four established virus species: Infectious hematopoietic necrosis virus (IHNV), Viral hemorrhagic septicemia virus (VHSV), Hirame rhabdovirus(HIRRV), and Snakehead rhabdovirus (SHRV). Viruses of these species vary in host and geographic range, and they have all been studied at the molecular and genomic level. As globally significant pathogens of cultured fish, IHNV and VHSV have been particularly well studied in terms of molecular epidemiology and evolution. Phylogenic analyses of hundreds of field isolates have defined five major genogroups of IHNV and four major genotypes of VHSV worldwide. These phylogenies are informed by the known histories of IHNV and VHSV, each involving a series of viral emergence events that are sometimes associated with host switches, most often into cultured rainbow trout. In general, IHNV has relatively low genetic diversity and a narrow host range, and has been spread from its endemic source in North American to Europe and Asia due to aquaculture activities. In contrast, VHSV has broad host range and high genetic diversity, and the source of emergence events is virus in widespread marine fish reservoirs in the northern Atlantic and Pacific Oceans. Common mechanisms of emergence and host switch events include use of raw feed, proximity to wild fish reservoirs of virus, and geographic translocations of virus or naive fish hosts associated with aquaculture.

  16. Molecular and epidemiological studies of Porcine rubulavirus infection - an overview.

    Science.gov (United States)

    Cuevas-Romero, Julieta Sandra; Blomström, Anne-Lie; Berg, Mikael

    2015-01-01

    Porcine rubulavirus-La Piedad-Michoacan-Mexico virus (PorPV-LPMV) was identified as the causative agent of a viral disease that emerged spontaneously in Mexican swine in the 1980s. Since the report of the initial outbreak of the disease, only one full-length genome from a strain isolated in 1984 (PorPV-LPMV/1984) has been sequenced; sequence data are scarce from other isolates. The genetic variation of this virus that has spread throughout the main endemic region of Mexico is almost a complete mystery. The development of molecular techniques for improved diagnostics and to investigate the persistence, molecular epidemiology, and the possible reservoirs of PorPV are needed. Together, this will provide greater knowledge regarding the molecular genetic changes and useful data to establish new strategies in the control of this virus in Mexico.

  17. [Precision medicine: new opportunities and challenges for molecular epidemiology].

    Science.gov (United States)

    Song, Jing; Hu, Yonghua

    2016-04-01

    Since the completion of the Human Genome Project in 2003 and the announcement of the Precision Medicine Initiative by U.S. President Barack Obama in January 2015, human beings have initially completed the " three steps" of " genomics to biology, genomics to health as well as genomics to society". As a new inter-discipline, the emergence and development of precision medicine have relied on the support and promotion from biological science, basic medicine, clinical medicine, epidemiology, statistics, sociology and information science, etc. Meanwhile, molecular epidemiology is considered to be the core power to promote precision medical as a cross discipline of epidemiology and molecular biology. This article is based on the characteristics and research progress of medicine and molecular epidemiology respectively, focusing on the contribution and significance of molecular epidemiology to precision medicine, and exploring the possible opportunities and challenges in the future. PMID:27087232

  18. Molecular epidemiology, phylogeny and evolution of Legionella.

    Science.gov (United States)

    Khodr, A; Kay, E; Gomez-Valero, L; Ginevra, C; Doublet, P; Buchrieser, C; Jarraud, S

    2016-09-01

    Legionella are opportunistic pathogens that develop in aquatic environments where they multiply in protozoa. When infected aerosols reach the human respiratory tract they may accidentally infect the alveolar macrophages leading to a severe pneumonia called Legionnaires' disease (LD). The ability of Legionella to survive within host-cells is strictly dependent on the Dot/Icm Type 4 Secretion System that translocates a large repertoire of effectors into the host cell cytosol. Although Legionella is a large genus comprising nearly 60 species that are worldwide distributed, only about half of them have been involved in LD cases. Strikingly, the species Legionella pneumophila alone is responsible for 90% of all LD cases. The present review summarizes the molecular approaches that are used for L. pneumophila genotyping with a major focus on the contribution of whole genome sequencing (WGS) to the investigation of local L. pneumophila outbreaks and global epidemiology studies. We report the newest knowledge regarding the phylogeny and the evolution of Legionella and then focus on virulence evolution of those Legionella species that are known to have the capacity to infect humans. Finally, we discuss the evolutionary forces and adaptation mechanisms acting on the Dot/Icm system itself as well as the role of mobile genetic elements (MGE) encoding T4ASSs and of gene duplications in the evolution of Legionella and its adaptation to different hosts and lifestyles. PMID:27180896

  19. Molecular Epidemiology of Hemoglobinopathies in Cambodia.

    Science.gov (United States)

    Munkongdee, Thongperm; Tanakulmas, Jatuporn; Butthep, Punnee; Winichagoon, Pranee; Main, Barbara; Yiannakis, Miriam; George, Joby; Devenish, Robyn; Fucharoen, Suthat; Svasti, Saovaros

    2016-06-01

    Determining the magnitude of the thalassemia problem in a country is important for implementing a national prevention and control program. In order to acquire accurate thalassemia prevalence data, the gene frequency of α- and β-thalassemia (α- and β-thal) in different regions of a country should be determined. The molecular basis of thalassemia in Cambodia was performed by polymerase chain reaction (PCR)-based techniques in a community-based cross-sectional survey of 1631 unrelated individuals from three regions, Battambang, Preah Vihear and Phnom Penh. Thalassemia mutations were detected in 62.7% of the three studied population of Cambodia. Hb E (HBB: c.79G > A) was the most common β-globin gene mutation with a frequency ranging from 0.139 to 0.331, while the most frequent α-globin gene mutation was the -α(3.7) (rightward) deletion (0.098-0.255). The other frequencies were 0.001-0.003 for β-thal, 0.008-0.011 for α-thal-1 (- -(SEA)), 0.003-0.008 for α-thal-2 [-α(4.2) (leftward deletion)], 0.021-0.044 for Hb Constant Spring (Hb CS, HBA2: c.427T > C) and 0.009-0.036 for Hb Paksé (HBA2: c.429A > T). A regional specific thalassemia gene frequency was observed. Preah Vihear had the highest prevalence of Hb E (55.9%), α-thal-2 (24.0%) and nondeletional α-thal (15.1%), whereas Phnom Penh had the lowest frequency of thalassemia genes. Interestingly, in Preah Vihear, the frequency of Hb Paksé was extremely high (0.036), almost equivalent to that of Hb CS (0.044). Our results indicate the importance of micromapping and epidemiology studies of thalassemia, which will assist in establishing the national prevention and control program in Cambodia. PMID:27117566

  20. The Changing Epidemiology of Pediatric Endocarditis.

    Science.gov (United States)

    Elder, Robert W; Baltimore, Robert S

    2015-09-01

    The epidemiology of infective endocarditis (IE) appears to be related to changes in the management of children with congenital heart disease (CHD) and the virtual disappearance of rheumatic heart disease. To better understand these changes, we divide the history into: I. The pre-surgical era, II. The early years of CHD surgical intervention, correlated with introduction of antibiotics, III. The modern era of cardiac interventions. Microbiologic changes include an early predominance of viridans streptococci and an overtaking by staphylococci. Additionally, there have been advances in imaging that allow earlier detection of IE and a reduction in IE-related mortality.

  1. Molecular Epidemiology and its Role in Translational Medicine

    Institute of Scientific and Technical Information of China (English)

    Yeong Yeh Lee

    2016-01-01

    The primary deifnition of translational medicine is to develop new clinical therapeutic methods for the diagnosis, treatment and prognosis of diseases by the therapeutic mechanism and new pathological cognition obtained in laboratory. Since the 21st century, most developed countries worldwide have made great adjustment in the strategies of translational medicine, but so far, only a few basic research results have been successfully translated into clinical practice. Research of translational medicine requires the team work of interdisciplinary groups, including medical experts, molecular biologists, and epidemiologists. With the rapid development of biological techniques and extensive application of molecular biology, epidemiology has become a real interdisciplinary discipline from conventional population survey, and stepped into genetic and molecular era, an era of molecular epidemiology. Molecular epidemiology not only provides research ifndings to translational medicine, but also bridges between basic science and medical research, so as to improve the effective translation of basic scientiifc results. This article, focusing on molecular epidemiology and translational medicine, mainly summarized the history and current status of translational medicine and emphatically interpreted the importance of molecular epidemiology to translational medicine.

  2. Molecular Epidemiology and its Role in Translational Medicine

    Directory of Open Access Journals (Sweden)

    Yeh Lee Yeong

    2016-03-01

    Full Text Available The primary definition of translational medicine is to develop new clinical therapeutic methods for the diagnosis, treatment and prognosis of diseases by the therapeutic mechanism and new pathological cognition obtained in laboratory. Since the 21st century, most developed countries worldwide have made great adjustment in the strategies of translational medicine, but so far, only a few basic research results have been successfully translated into clinical practice. Research of translational medicine requires the team work of interdisciplinary groups, including medical experts, molecular biologists, and epidemiologists. With the rapid development of biological techniques and extensive application of molecular biology, epidemiology has become a real interdisciplinary discipline from conventional population survey, and stepped into genetic and molecular era, an era of molecular epidemiology. Molecular epidemiology not only provides research findings to translational medicine, but also bridges between basic science and medical research, so as to improve the effective translation of basic scientific results. This article, focusing on molecular epidemiology and translational medicine, mainly summarized the history and current status of translational medicine and emphatically interpreted the importance of molecular epidemiology to translational medicine.

  3. The Current Status of the Disease Caused by Enterovirus 71 Infections: Epidemiology, Pathogenesis, Molecular Epidemiology, and Vaccine Development.

    Science.gov (United States)

    Chang, Ping-Chin; Chen, Shou-Chien; Chen, Kow-Tong

    2016-01-01

    Enterovirus 71 (EV71) infections have a major public health impact in the Asia-Pacific region. We reviewed the epidemiology, pathogenesis, and molecular epidemiology of EV71 infection as well as EV71 vaccine development. Previous studies were found using the search terms "enterovirus 71" and "epidemiology" or "pathogenesis" or "molecular epidemiology" or "vaccine" in Medline and PubMed. Articles that were not published in the English language, manuscripts without an abstract, and opinion articles were excluded from the review. The reported epidemiology of cases caused by EV71 infection varied from country to country; seasonal variations in incidence were observed. Most cases of EV71 infection that resulted in hospitalization for complications occurred in children less than five years old. The brainstem was the most likely major target of EV71 infection. The emergence of the EV71 epidemic in the Asia-Pacific region has been associated with the circulation of different genetic lineages (genotypes B3, B4, C1, C2, and C4) that appear to be undergoing rapid evolutionary changes. The relationship between the gene structure of the EV71 virus and the factors that ensure its survival, circulation, and evasion of immunity is still unknown. EV71 infection has emerged as an important global public health problem. Vaccine development, including the development of inactivated whole-virus live attenuated, subviral particles, and DNA vaccines, has been progressing. PMID:27618078

  4. 2. Molecular Biology as a Tool in Cancer Epidemiology

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@There can be little doubt that we are entering a new era in our understanding of the origins of human cancer. Unfortunately from the point of view of the cancer epidemiology community, some of the more recent advances in the molecular biology of cancer (once fully assimilated) will tend to make the talk of the up-to-date cancer epidemiologist a great deal less straightforward than many of us had previously envisaged it to be, There may still be a few cancers that will prove to result from only a few distinctive types of mutation in a relatively small number of genes, but I strongly suspect that the great majority of human cancers that we wish to study will prove to have their origins in a complex set of DNA changes whose precise

  5. Molecular Epidemiology of Pulmonary Tuberculosis in Belgrade, Central Serbia

    OpenAIRE

    Vuković, Dragana; Rüsch-Gerdes, Sabine; Savić, Branislava; Niemann, Stefan

    2003-01-01

    In order to gain precise data on the actual epidemiology of tuberculosis (TB) in Belgrade, central Serbia, we conducted the molecular epidemiological investigation described herein. IS6110 restriction fragment length polymorphism (RFLP) typing of 176 Mycobacterium tuberculosis isolates was performed. These strains were obtained from 48.4% of all patients diagnosed with culture-proven pulmonary TB from April through September 1998 and from May through October 1999. Clusters containing strains ...

  6. Molecular Epidemiology and Emergence of Rift Valley Fever

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    Sall AA

    1998-01-01

    Full Text Available Rift Valley fever (RVF is a mosquito-borne viral disease which manifested itself during recent epidemics and revealed its significant potential of emergence. Studies on molecular epidemiology undertaken to better understand the factors leading to RVF emergence, have confirmed the mode of circulation of the virus and highlithted probable risks and obstacles for prevention and control. As for several other viral agents, molecular epidemiology is becoming a useful tool in the study of the emergence of RVF as a serious infectious disease.

  7. Meningococcal disease: changes in epidemiology and prevention

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    Chang Q

    2012-09-01

    Full Text Available Qiuzhi Chang,1 Yih-Ling Tzeng,2 David S Stephens1–31Department of Epidemiology, Rollins School of Public Health, Emory University, 2Department of Medicine, Emory University School of Medicine, 3Laboratories of Microbial Pathogenesis, Department of Veterans Affairs Medical Center, Atlanta, GAAbstract: The human bacterial pathogen Neisseria meningitidis remains a serious worldwide health threat, but progress is being made toward the control of meningococcal infections. This review summarizes current knowledge of the global epidemiology and the pathophysiology of meningococcal disease, as well as recent advances in prevention by new vaccines. Meningococcal disease patterns and incidence can vary dramatically, both geographically and over time in populations, influenced by differences in invasive meningococcal capsular serogroups and specific genotypes designated as ST clonal complexes. Serogroup A (ST-5, ST-7, B (ST-41/44, ST-32, ST-18, ST-269, ST-8, ST-35, C (ST-11, Y (ST-23, ST-167, W-135 (ST-11 and X (ST-181 meningococci currently cause almost all invasive disease. Serogroups B, C, and Y are responsible for the majority of cases in Europe, the Americas, and Oceania; serogroup A has been associated with the highest incidence (up to 1000 per 100,000 cases and large outbreaks of meningococcal disease in sub-Saharan Africa and previously Asia; and serogroups W-135 and X have emerged to cause major disease outbreaks in sub-Saharan Africa. Significant declines in meningococcal disease have occurred in the last decade in many developed countries. In part, the decline is related to the introduction of new meningococcal vaccines. Serogroup C polysaccharide-protein conjugate vaccines were introduced over a decade ago, first in the UK in a mass vaccination campaign, and are now widely used; multivalent meningococcal conjugate vaccines containing serogroups A, C, W-135, and/or Y were first used for adolescents in the US in 2005 and have now expanded

  8. Molecular Epidemiology of Mycobacterium bovis in Humans and Cattle.

    Science.gov (United States)

    El-Sayed, A; El-Shannat, S; Kamel, M; Castañeda-Vazquez, M A; Castañeda-Vazquez, H

    2016-06-01

    Bovine tuberculosis (bTB), caused by Mycobacterium bovis (M. bovis), is a serious re-emerging disease in both animals and humans. The evolution of the Multi- and Extensively drug-resistant M. bovis strains (MDR-TB and XDR-TB) represents a global threat to public health. Worldwide, the disease is responsible for great economic losses in the veterinary field, serious threat to the ecosystem, and about 3.1% of human TB cases, up to 16% in Tanzania. Only thorough investigation to understand the pathogen's epidemiology can help in controlling the disease and minimizing its threat. For this purpose, various tools have been developed for use in advanced molecular epidemiological studies of bTB, either alone or in combination with standard conventional epidemiological approaches. These techniques enable the analysis of the intra- and inter-species transmission dynamics of bTB. The delivered data can reveal detailed insights into the source of infection, correlations among human and bovine isolates, strain diversity and evolution, spread, geographical localization, host preference, tracing of certain virulence factors such as antibiotic resistance genes, and finally the risk factors for the maintenance and spread of M. bovis. They also allow for the determination of epidemic and endemic strains. This, in turn, has a significant diagnostic impact and helps in vaccine development for bTB eradication programs. The present review discusses many topics including the aetiology, epidemiology and importance of M. bovis, the prevalence of bTB in humans and animals in various countries, the molecular epidemiology of M. bovis, and finally applied molecular epidemiological techniques. PMID:26684712

  9. Molecular Epidemiology of Female Lung Cancer

    OpenAIRE

    Seon-Hee Yim; Yeun-Jun Chung

    2011-01-01

    Lung cancer is still a leading cause of cancer mortality in the world. The incidence of lung cancer in developed countries started to decrease mainly due to global anti-smoking campaigns. However, the incidence of lung cancer in women has been increasing in recent decades for various reasons. Furthermore, since the screening of lung cancer is not as yet very effective, clinically applicable molecular markers for early diagnosis are much required. Lung cancer in women appears to have differenc...

  10. Molecular epidemiological study of dengue virus type 1 in Taiwan.

    Science.gov (United States)

    Hwang, Kao-Pin; Chu, Pei-Yu; Tung, Yi-Ching; Wang, Heng-Lin; Yueh, Yi-Yun; Wu, Ying-Chang; Chin, Chuan; Lin, Kuei-Hsiang

    2003-07-01

    Taiwan has experienced several major outbreaks of dengue (DEN) virus since 1981. The predominant virus type involved has been dengue virus type one (DEN-1), which first appeared in 1987. To understand the molecular epidemiology of this virus, 15 strains of DEN-1 isolated during 1987-1991 and 1994-1995, including 11 epidemic strains, two sporadic strains, and two imported strains have been studied. Fragments of 490 nucleotides (nt) from the E/NS1 junction were amplified by reverse transcription-polymerase chain reaction and the nt sequences were determined. Of the 490 nt of the E/NS1 junction, 240 nt (nt 2282-2521) were aligned and compared. Nucleotide substitutions were found at 54 positions among 15 isolates. Most nt changes were synonymous substitutions, and only three amino acid changes were found. A total of 61 strains isolated worldwide were analyzed by the Neighbor-joining method, and separated phylogenetically into three distinct genotypes, I-III. Genotype I comprised isolates from Japan and Hawaii collected in the 1940s. Genotype II included most strains isolated from Asia in 1977-1995. Genotype III consisted of isolates from three continents in 1964-1995: Asia, the Americas, and Africa. Genotype III was divided further into two subgenotypes, IIIA and IIIB. Most recent isolates from Taiwan, except for the sporadic strain isolated in 1995, were similar genetically and have been classified as Genotype II. PMID:12767004

  11. Molecular epidemiology of human intestinal amoebas in iran.

    Science.gov (United States)

    Hooshyar, H; Rostamkhani, P; Rezaian, M

    2012-01-01

    Many microscopic-based epidemiological surveys on the prevalence of human intestinal pathogenic and non-pathogenic protozoa including intestinal amoeba performed in Iran show a high prevalence of human intestinal amoeba in different parts of Iran. Such epidemiological studies on amoebiasis are confusing, mainly due to recently appreciated distinction between the Entamoeba histolytica, E. dispar and E. moshkovskii. Differential diagnosis can be done by some methods such as PCR-based methods, monoclonal antibodies and the analysis of isoenzyme typing, however the molecular study of these protozoa in Iran is low. Based on molecular studies, it seems that E. dispar is predominant species especially in the central and northern areas of Iran and amoebiasis due to E. histolytica is a rare infection in the country. It is suggested that infection with E. moshkovskii may be common among Iranians. Considering the importance of molecular epidemiology of amoeba in Iran and also the current data, the present study reviews the data currently available on the molecular distribution of intestinal human amoeba in Iran.

  12. Molecular Epidemiology of Human Intestinal Amoebas in Iran

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    M Rezaian

    2012-09-01

    Full Text Available Many microscopic-based epidemiological surveys on the prevalence of human intestinal pathogenic and non-pathogenic protozoa including intestinal amoeba performed in Iran show a high prevalence of human intestinal amoeba in different parts of Iran. Such epidemiological studies on amoebiasis are confusing, mainly due to recently appreciated distinction between the Entamoeba histolytica, E. dispar and E. moshkovskii. Differential diagnosis can be done by some methods such as PCR-based methods, monoclonal antibodies and the analysis of isoenzyme typing, however the molecular study of these protozoa in Iran is low. Based on molecular studies, it seems that E. dispar is predominant species especially in the central and northern areas of Iran and amoebiasis due to E. histolytica is a rare infection in the country. It is suggested that infection with E. moshkovskii may be common among Iranians. Considering the importance of molecular epidemiology of amoeba in Iran and also the current data, the present study reviews the data currently available on the molecular distribution of intestinal human amoeba in Iran.

  13. Molecular epidemiology of respiratory viruses in virus-induced asthma

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    Hiroyuki eTsukagoshi

    2013-09-01

    Full Text Available Acute respiratory illness (ARI due to various viruses is not only the most common cause of upper respiratory infection in humans but is also a major cause of morbidity and mortality, leading to diseases such as bronchiolitis and pneumonia. Previous studies have shown that respiratory syncytial virus (RSV, human rhinovirus (HRV, human metapneumovirus (HMPV, human parainfluenza virus (HPIV, and human enterovirus (HEV infections may be associated with virus-induced asthma. For example, it has been suggested that HRV infection is detected in the acute exacerbation of asthma and infection is prolonged. Thus it is believed that the main etiological cause of asthma is ARI viruses. Furthermore, the number of asthma patients in most industrial countries has greatly increased, resulting in a morbidity rate of around 10-15% of the population. However, the relationships between viral infections, host immune response, and host factors in the pathophysiology of asthma remain unclear. To gain a better understanding of the epidemiology of virus-induced asthma, it is important to assess both the characteristics of the viruses and the host defense mechanisms. Molecular epidemiology enables us to understand the pathogenesis of microorganisms by identifying specific pathways, molecules, and genes that influence the risk of developing a disease. However, the epidemiology of various respiratory viruses associated with virus-induced asthma is not fully understood. Therefore, in this article, we review molecular epidemiological studies of RSV, HRV, HPIV, and HMPV infection associated with virus-induced asthma.

  14. Molecular epidemiology of rotavirus in black infants in South Africa.

    OpenAIRE

    Steele, A. D.; Alexander, J.J.

    1987-01-01

    The molecular epidemiology of rotavirus infections in black infants in Ga-Rankuwa, South Africa, was investigated by polyacrylamide gel electrophoresis. Between 1983 and 1986, 14 different RNA electrophoretic patterns were observed for children with acute gastroenteritis. These electrophoretypes showed a sequential pattern of appearance, with a limited number being present at any one time. In contrast, for neonates only one RNA electrophoretype was detected, which persisted for at least 3 years.

  15. Molecular epidemiology of dengue viruses from complete genome sequences

    OpenAIRE

    Ong, Swee Hoe

    2010-01-01

    The availability of the complete genetic blueprint of the dengue virus is essential in molecular epidemiological studies to uncover the role of the virus in dengue pathogenesis. During the course of this project, over two hundred complete genomes of the dengue virus were generated from clinical samples collected in three dengue-endemic Southeast Asian countries. In addition, a bioinformatics platform integrating a sequence database, sequence retrieval tools, sequence annotation data and a var...

  16. The Current Status of the Disease Caused by Enterovirus 71 Infections: Epidemiology, Pathogenesis, Molecular Epidemiology, and Vaccine Development

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    Ping-Chin Chang

    2016-09-01

    Full Text Available Enterovirus 71 (EV71 infections have a major public health impact in the Asia-Pacific region. We reviewed the epidemiology, pathogenesis, and molecular epidemiology of EV71 infection as well as EV71 vaccine development. Previous studies were found using the search terms “enterovirus 71” and “epidemiology” or “pathogenesis” or “molecular epidemiology” or “vaccine” in Medline and PubMed. Articles that were not published in the English language, manuscripts without an abstract, and opinion articles were excluded from the review. The reported epidemiology of cases caused by EV71 infection varied from country to country; seasonal variations in incidence were observed. Most cases of EV71 infection that resulted in hospitalization for complications occurred in children less than five years old. The brainstem was the most likely major target of EV71 infection. The emergence of the EV71 epidemic in the Asia-Pacific region has been associated with the circulation of different genetic lineages (genotypes B3, B4, C1, C2, and C4 that appear to be undergoing rapid evolutionary changes. The relationship between the gene structure of the EV71 virus and the factors that ensure its survival, circulation, and evasion of immunity is still unknown. EV71 infection has emerged as an important global public health problem. Vaccine development, including the development of inactivated whole-virus live attenuated, subviral particles, and DNA vaccines, has been progressing.

  17. The Current Status of the Disease Caused by Enterovirus 71 Infections: Epidemiology, Pathogenesis, Molecular Epidemiology, and Vaccine Development

    Science.gov (United States)

    Chang, Ping-Chin; Chen, Shou-Chien; Chen, Kow-Tong

    2016-01-01

    Enterovirus 71 (EV71) infections have a major public health impact in the Asia-Pacific region. We reviewed the epidemiology, pathogenesis, and molecular epidemiology of EV71 infection as well as EV71 vaccine development. Previous studies were found using the search terms “enterovirus 71” and “epidemiology” or “pathogenesis” or “molecular epidemiology” or “vaccine” in Medline and PubMed. Articles that were not published in the English language, manuscripts without an abstract, and opinion articles were excluded from the review. The reported epidemiology of cases caused by EV71 infection varied from country to country; seasonal variations in incidence were observed. Most cases of EV71 infection that resulted in hospitalization for complications occurred in children less than five years old. The brainstem was the most likely major target of EV71 infection. The emergence of the EV71 epidemic in the Asia-Pacific region has been associated with the circulation of different genetic lineages (genotypes B3, B4, C1, C2, and C4) that appear to be undergoing rapid evolutionary changes. The relationship between the gene structure of the EV71 virus and the factors that ensure its survival, circulation, and evasion of immunity is still unknown. EV71 infection has emerged as an important global public health problem. Vaccine development, including the development of inactivated whole-virus live attenuated, subviral particles, and DNA vaccines, has been progressing. PMID:27618078

  18. Preeclampsia: from epidemiological observations to molecular mechanisms

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    P. López-Jaramillo

    2001-10-01

    Full Text Available Preeclampsia is the main cause of maternal mortality and is associated with a five-fold increase in perinatal mortality in developing countries. In spite of this, the etiology of preeclampsia is unknown. The present article analyzes the contradictory results of the use of calcium supplementation in the prevention of preeclampsia, and tries to give an explanation of these results. The proposal of an integrative model to explain the clinical manifestations of preeclampsia is discussed. In this proposal we suggest that preeclampsia is caused by nutritional, environmental and genetic factors that lead to the creation of an imbalance between the free radicals nitric oxide, superoxide and peroxynitrate in the vascular endothelium. The adequate interpretation of this model would allow us to understand that the best way of preventing preeclampsia is the establishment of an adequate prenatal control system involving adequate antioxidant vitamin and mineral supplementation, adequate diagnosis and early treatment of asymptomatic urinary and vaginal infections. The role of infection in the genesis of preeclampsia needs to be studied in depth because it may involve a fundamental change in the prevention and treatment of preeclampsia.

  19. Molecular epidemiology of HIV-1 strains in the south-east and east of Turkey

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    Mustafa Kemal Çelen

    2015-09-01

    Conclusions: HIV molecular epidemiology studies are necessary to determine transmission patterns and spread. Subtype B and CRF01_AE, CRF02_AG are the most prevalent strains in the south-east of Turkey. However, subtype C, sub-subtypes A1 and F1 are of low prevalence but persist in the south-east of Turkey. In the near future, changing of HIV epidemiology will be possible in Turkey due to migration movement in border lines and resistance testing will play an important role in HIV management.

  20. The epidemiology and molecular mechanisms linking obesity, diabetes, and cancer.

    Science.gov (United States)

    Ferguson, Rosalyn D; Gallagher, Emily J; Scheinman, Eyal J; Damouni, Rawan; LeRoith, Derek

    2013-01-01

    The worldwide epidemic of obesity is associated with increasing rates of the metabolic syndrome and type 2 diabetes. Epidemiological studies have reported that these conditions are linked to increased rates of cancer incidence and mortality. Obesity, particularly abdominal obesity, is associated with insulin resistance and the development of dyslipidemia, hyperglycemia, and ultimately type 2 diabetes. Although many metabolic abnormalities occur with obesity and type 2 diabetes, insulin resistance and hyperinsulinemia appear to be central to these conditions and may contribute to dyslipidemia and altered levels of circulating estrogens and androgens. In this review, we will discuss the epidemiological and molecular links between obesity, type 2 diabetes, and cancer, and how hyperinsulinemia and dyslipidemia may contribute to cancer development. We will discuss how these metabolic abnormalities may interact with estrogen signaling in breast cancer growth. Finally, we will discuss the effects of type 2 diabetes medications on cancer risk. PMID:23810003

  1. Hepatitis A virus: host interactions, molecular epidemiology and evolution.

    Science.gov (United States)

    Vaughan, Gilberto; Goncalves Rossi, Livia Maria; Forbi, Joseph C; de Paula, Vanessa S; Purdy, Michael A; Xia, Guoliang; Khudyakov, Yury E

    2014-01-01

    Infection with hepatitis A virus (HAV) is the commonest viral cause of liver disease and presents an important public health problem worldwide. Several unique HAV properties and molecular mechanisms of its interaction with host were recently discovered and should aid in clarifying the pathogenesis of hepatitis A. Genetic characterization of HAV strains have resulted in the identification of different genotypes and subtypes, which exhibit a characteristic worldwide distribution. Shifts in HAV endemicity occurring in different parts of the world, introduction of genetically diverse strains from geographically distant regions, genotype displacement observed in some countries and population expansion detected in the last decades of the 20th century using phylogenetic analysis are important factors contributing to the complex dynamics of HAV infections worldwide. Strong selection pressures, some of which, like usage of deoptimized codons, are unique to HAV, limit genetic variability of the virus. Analysis of subgenomic regions has been proven useful for outbreak investigations. However, sharing short sequences among epidemiologically unrelated strains indicates that specific identification of HAV strains for molecular surveillance can be achieved only using whole-genome sequences. Here, we present up-to-date information on the HAV molecular epidemiology and evolution, and highlight the most relevant features of the HAV-host interactions.

  2. First molecular epidemiological study of cutaneous leishmaniasis in Libya.

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    Ahmad Amro

    Full Text Available BACKGROUND: Cutaneous leishmaniasis (CL is a major public health problem in Libya. The objective of this study was to investigate, for the first time, epidemiological features of CL outbreaks in Libya including molecular identification of parasites, the geographical distribution of cases and possible scenarios of parasite transmission. METHODOLOGY/PRINCIPAL FINDINGS: We studied 450 patients that came from 49 areas distributed in 12 districts in north-west Libya. The patients' ages ranged from 9 months to 87 years (median age 25 years; 54% of the cases were males. Skin scrapings spotted on glass slides were collected for molecular identification of causative agent. The ribosomal internal transcribed spacer 1 (ITS1 was amplified and subsequently characterized by restriction fragment length polymorphism (RFLP analysis. In total, 195 samples were successfully identified of which 148 (75.9% were Leishmania major, and 47 (24.1% Leishmania tropica. CL cases infected with L. major were found in all CL areas whereas L. tropica cases came mainly from Al Jabal Al Gharbi (46.4%, Misrata (17.8% and Tarhuna districts (10.7%. A trend of seasonality was noticed for the infections with L. major which showed a clear peak between November and January, but was less pronounced for infections by L. tropica. CONCLUSION: The first molecular study on CL in Libya revealed that the disease is caused by L. major and L. tropica and the epidemiological patterns in the different foci were the same as in other Mediterranean foci of CL.

  3. Molecular epidemiology of human oral Chagas disease outbreaks in Colombia.

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    Juan David Ramírez

    Full Text Available BACKGROUND: Trypanosoma cruzi, the causative agent of Chagas disease, displays significant genetic variability revealed by six Discrete Typing Units (TcI-TcVI. In this pathology, oral transmission represents an emerging epidemiological scenario where different outbreaks associated to food/beverages consumption have been reported in Argentina, Bolivia, Brazil, Ecuador and Venezuela. In Colombia, six human oral outbreaks have been reported corroborating the importance of this transmission route. Molecular epidemiology of oral outbreaks is barely known observing the incrimination of TcI, TcII, TcIV and TcV genotypes. METHODOLOGY AND PRINCIPAL FINDINGS: High-throughput molecular characterization was conducted performing MLMT (Multilocus Microsatellite Typing and mtMLST (mitochondrial Multilocus Sequence Typing strategies on 50 clones from ten isolates. Results allowed observing the occurrence of TcI, TcIV and mixed infection of distinct TcI genotypes. Thus, a majority of specific mitochondrial haplotypes and allelic multilocus genotypes associated to the sylvatic cycle of transmission were detected in the dataset with the foreseen presence of mitochondrial haplotypes and allelic multilocus genotypes associated to the domestic cycle of transmission. CONCLUSIONS: These findings suggest the incrimination of sylvatic genotypes in the oral outbreaks occurred in Colombia. We observed patterns of super-infection and/or co-infection with a tailored association with the severe forms of myocarditis in the acute phase of the disease. The transmission dynamics of this infection route based on molecular epidemiology evidence was unraveled and the clinical and biological implications are discussed.

  4. Changing Epidemiology of Pulmonary Nontuberculous Mycobacteria Infections

    OpenAIRE

    Thomson, Rachel M.; ,

    2010-01-01

    Nontuberculous mycobacteria (NTM) disease is a notifiable condition in Queensland, Australia. Mycobacterial isolates that require species identification are forwarded to the Queensland Mycobacterial Reference Laboratory, providing a central opportunity to capture statewide data on the epidemiology of NTM disease. We compared isolates obtained in 1999 and 2005 and used data from the Queensland notification scheme to report the clinical relevance of these isolates. The incidence of notified cas...

  5. Molecular techniques in foot-and-mouth disease epidemiology

    International Nuclear Information System (INIS)

    The study of the epidemiology of foot-and-mouth disease (FMD) has been revolutionized by the introduction of molecular biological techniques that can establish genetic relationships between the causative viruses. Early biochemical techniques such as sodiumdodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), electrofocusing and ribonuclease T1 oligonucleotide mapping were used to augment traditional antigenic comparisons to relate different FMD virus isolates and strains. FMD epidemiology using nucleotide sequencing has been studied since 1987, and there is an accumulated database of nearly 1500 partial VP1 sequences representing all seven serotypes of the virus. This has created a unique position for the study of the global epidemiology of the disease. Studies have shown that FMD viruses may be grouped into genetic types that correlate with geographical location. It has been proposed that these geographically distinct genotypes be termed 'topotypes'. For FMD type O, at least six topotypes have been defined, one of which is probably now extinct; for type A, four topotypes have so far been identified; for type C, about six genotypes; and, for Asia 1, only one genotype. Studies on the SAT 1 and SAT serotypes in southern Africa have shown the presence of three distinct topotypes for each serotype. These have probably arisen through the geographical isolation of wild buffalo herds and multiple introductions into domesticated cattle. The situation with the SAT 2 serotype was, however, different; only two genotypes were found, which did not correlate with the geographical origin. (author)

  6. Concordance and discordance of sequence survey methods for molecular epidemiology

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    Eduardo Castro-Nallar

    2015-02-01

    Full Text Available The post-genomic era is characterized by the direct acquisition and analysis of genomic data with many applications, including the enhancement of the understanding of microbial epidemiology and pathology. However, there are a number of molecular approaches to survey pathogen diversity, and the impact of these different approaches on parameter estimation and inference are not entirely clear. We sequenced whole genomes of bacterial pathogens, Burkholderia pseudomallei, Yersinia pestis, and Brucella spp. (60 new genomes, and combined them with 55 genomes from GenBank to address how different molecular survey approaches (whole genomes, SNPs, and MLST impact downstream inferences on molecular evolutionary parameters, evolutionary relationships, and trait character associations. We selected isolates for sequencing to represent temporal, geographic origin, and host range variability. We found that substitution rate estimates vary widely among approaches, and that SNP and genomic datasets yielded different but strongly supported phylogenies. MLST yielded poorly supported phylogenies, especially in our low diversity dataset, i.e., Y. pestis. Trait associations showed that B. pseudomallei and Y. pestis phylogenies are significantly associated with geography, irrespective of the molecular survey approach used, while Brucella spp. phylogeny appears to be strongly associated with geography and host origin. We contrast inferences made among monomorphic (clonal and non-monomorphic bacteria, and between intra- and inter-specific datasets. We also discuss our results in light of underlying assumptions of different approaches.

  7. Antimicrobial susceptibility and molecular epidemiology of Neisseria gonorrhoeae in Germany.

    Science.gov (United States)

    Horn, Nicole Nari; Kresken, Michael; Körber-Irrgang, Barbara; Göttig, Stephan; Wichelhaus, Cornelia; Wichelhaus, Thomas A

    2014-07-01

    Antimicrobial drug resistance in Neisseria gonorrhoeae has become an increasing public health problem. Hence, surveillance of resistance development is of crucial importance to implement adequate treatment guidelines. Data on the spread of antibiotic resistance among gonococcal isolates in Germany, however, is scarce. In a resistance surveillance study conducted by the Paul Ehrlich Society for Chemotherapy between October 2010 and December 2011, 23 laboratories all over Germany were requested to send N. gonorrhoeae isolates to the study laboratory in Frankfurt am Main. Species verification was performed biochemically using ApiNH and with Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS). Antimicrobial susceptibility testing was performed using the Etest method. For molecular epidemiological analysis, N. gonorrhoeae strains were genotyped by means of N. gonorrhoeae multi-antigen sequence typing. A total of 213 consecutive gonococcal isolates were analyzed in this nationwide study. Applying EUCAST breakpoints, high resistance rates were found for ciprofloxacin (74%) and tetracycline (41%). Penicillin non-susceptibility was detected in 80% of isolates. The rate of azithromycin resistance was 6%, while all strains were susceptible to spectinomycin, cefixime, and ceftriaxone. Molecular typing of gonococcal isolates revealed a great heterogeneity of 99 different sequence types (ST), but ST1407 predominated (n=39). This is the first comprehensive German multi-centre surveillance study on antibiotic susceptibility and molecular epidemiology of N. gonorrhoeae with implications for antibiotic choice for treatment of gonorrhoea. The World Health Organization supports the concept that an efficacious treatment of gonorrhoea results in at least 95% of infections being cured. Accordingly, as spectinomycin is not available on the German market, only the third generation cephalosporins cefixime and ceftriaxone are regarded as valuable drugs

  8. Initial data on the molecular epidemiology of cryptosporidiosis in Lebanon.

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    Marwan Osman

    Full Text Available Cryptosporidium spp. represent a major public health problem worldwide and infect the gastrointestinal tract of both immunocompetent and immunocompromised persons. The prevalence of these parasites varies by geographic region, and no data are currently available in Lebanon. To promote an understanding of the epidemiology of cryptosporidiosisin this country, the main aim of this study was to determine the prevalence Cryptosporidium in symptomatic hospitalized patients, and to analyze the genetic diversity of the corresponding isolates. Fecal specimens were collected in four hospitals in North Lebanon from 163 patients (77 males and 86 females, ranging in age from 1 to 88 years, with a mean age of 22 years presenting gastrointestinal disorders during the period July to December 2013. The overall prevalence of Cryptosporidium spp. infection obtained by modified Ziehl-Neelsen staining and/or nested PCR was 11%, and children <5 years old showed a higher rate of Cryptosporidium spp. The PCR products of the 15 positive samples were successfully sequenced. Among them, 10 isolates (66.7% were identified as C. hominis, while the remaining 5 (33.3% were identified as C. parvum. After analysis of the gp60 locus, C. hominis IdA19, a rare subtype, was found to be predominant. Two C. parvum subtypes were found: IIaA15G1R1 and IIaA15G2R1. The molecular characterization of Cryptosporidium isolates is an important step in improving our understanding of the epidemiology and transmission of the infection.

  9. Molecular epidemiological characteristics of norovirus gastroenteritis outbreaks in Guangdong province

    Institute of Scientific and Technical Information of China (English)

    HUI LI; LING FANG; LI RONG ZOU; CHANG WEN KE; PING HUANG; JI CHENG HUANG

    2006-01-01

    The purpose of this work is to study the molecular epidemiological characteristics of norovirus gastroenteritis outbreaks in Guangdong. During October 2003 and December 2004, fecal and anal swabs specimens collected from 13 outbreaks of non-bacterial gastroenteritis were tested for norovirus. Specimens were detected by RT-PCR and sequenced. The descriptive data were also collected. Eight in 13 outbreaks of gastroenteritis were positive for norovirus. All of 8 virus strains were identified as genogroup Ⅱ but belonged to 3 genotypes. Six strains were G Ⅱ-4 genotype. Norovirus is a major cause of outbreaks of nonbacterial gastroenteritis in Guangdong province and has a wide distribution. The illness happended from late autumn to winter. The prevalent strains were genogroup Ⅱ virus.

  10. [Molecular epidemiology of hepatitis B virus in Northern Cyprus].

    Science.gov (United States)

    Arıkan, Ayşe; Şanlıdağ, Tamer; Süer, Kaya; Sayan, Murat; Akçalı, Sinem; Güler, Emrah

    2016-01-01

    Identification of hepatitis B virus (HBV) strains and understanding of molecular epidemiological characteristics are important for the effective surveillance of HBV infections. Genotype D is dominant in studies performed in Turkey but it is known that cases infected with genotypes A, E, G and H also exists. In contrast, there are no data regarding the molecular epidemiologic characteristics of the HBV in Northern Cyprus. The aim of this study was to determine the distribution of genotypes and subgenotypes of HBV among the people living, educating and working in Northern Cyprus. A total of 160 cases (1.2%) who were HBsAg seropositive out of 13.892 subjects admitted to Nicosia, Near East University Hospital microbiology laboratory for the routine control and to blood center for donor screening tests between November 2011 to September 2014, were included in the study. HBV-DNA levels in the HBsAg positive cases were detected by real-time polymerase chain reaction and genotypes/subgenotypes were determined by sequence analysis of the viral pol gene (reverse transcriptase [rt] region, between 80-250. aminoacids). Sixty samples (60/160, 37.5%) were excluded from sequencing analysis due to negative and/or very low (mediterranean basin. The prevalences of genotype A (7/68, 10.3%) and E (8/68, 11.8%) were also remarkable. In conclusion, although Northern Cyprus is an island country the heterogeneous distribution of HBV genotype/subgenotype may be contributed to the cosmopolitan characteristics of various populations from different countries who have come here for education, work or touristic purposes. PMID:27058332

  11. Molecular epidemiology of DFNB1 deafness in France

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    Molinari Nicolas

    2004-03-01

    Full Text Available Abstract Background Mutations in the GJB2 gene have been established as a major cause of inherited non syndromic deafness in different populations. A high number of sequence variations have been described in the GJB2 gene and the associated pathogenic effects are not always clearly established. The prevalence of a number of mutations is known to be population specific, and therefore population specific testing should be a prerequisite step when molecular diagnosis is offered. Moreover, population studies are needed to determine the contribution of GJB2 variants to deafness. We present our findings from the molecular diagnostic screening of the GJB2 and GJB6 genes over a three year period, together with a population-based study of GJB2 variants. Methods and results Molecular studies were performed using denaturing High Performance Liquid Chromatograghy (DHPLC and sequencing of the GJB2 gene. Over the last 3 years we have studied 159 families presenting sensorineural hearing loss, including 84 with non syndromic, stable, bilateral deafness. Thirty families were genotyped with causative mutations. In parallel, we have performed a molecular epidemiology study on more than 3000 dried blood spots and established the frequency of the GJB2 variants in our population. Finally, we have compared the prevalence of the variants in the hearing impaired population with the general population. Conclusion Although a high heterogeneity of sequence variation was observed in patients and controls, the 35delG mutation remains the most common pathogenic mutation in our population. Genetic counseling is dependent on the knowledge of the pathogenicity of the mutations and remains difficult in a number of cases. By comparing the sequence variations observed in hearing impaired patients with those sequence variants observed in general population, from the same ethnic background, we show that the M34T, V37I and R127H variants can not be responsible for profound or severe

  12. Molecular and epidemiological studies of Porcine rubulavirus infection – an overview

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    Julieta Sandra Cuevas-Romero

    2015-11-01

    Full Text Available Porcine rubulavirus-La Piedad-Michoacan-Mexico virus (PorPV-LPMV was identified as the causative agent of a viral disease that emerged spontaneously in Mexican swine in the 1980s. Since the report of the initial outbreak of the disease, only one full-length genome from a strain isolated in 1984 (PorPV-LPMV/1984 has been sequenced; sequence data are scarce from other isolates. The genetic variation of this virus that has spread throughout the main endemic region of Mexico is almost a complete mystery. The development of molecular techniques for improved diagnostics and to investigate the persistence, molecular epidemiology, and the possible reservoirs of PorPV are needed. Together, this will provide greater knowledge regarding the molecular genetic changes and useful data to establish new strategies in the control of this virus in Mexico.

  13. Global Molecular Epidemiology of Cryptococcus neoformans and Cryptococcus gattii: An Atlas of the Molecular Types

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    Massimo Cogliati

    2013-01-01

    Full Text Available Cryptococcosis is a fungal disease affecting more than one million people per year worldwide. The main etiological agents of cryptococcosis are the two sibling species Cryptococcus neoformans and Cryptococcus gattii that present numerous differences in geographical distribution, ecological niches, epidemiology, pathobiology, clinical presentation and molecular characters. Genotyping of the two Cryptococcus species at subspecies level supplies relevant information to understand how this fungus has spread worldwide, the nature of its population structure, and how it evolved to be a deadly pathogen. At present, nine major molecular types have been recognized: VNI, VNII, VNB, VNIII, and VNIV among C. neoformans isolates, and VGI, VGII, VGIII, and VGIV among C. gattii isolates. In this paper all the information available in the literature concerning the isolation of the two Cryptococcus species has been collected and analyzed on the basis of their geographical origin, source of isolation, level of identification, species, and molecular type. A detailed analysis of the geographical distribution of the major molecular types in each continent has been described and represented on thematic maps. This study represents a useful tool to start new epidemiological surveys on the basis of the present knowledge.

  14. Molecular epidemiological research of Treponema pallidum infection in Haikou

    Institute of Scientific and Technical Information of China (English)

    Ke Han; Yong-Jiang Dai

    2015-01-01

    Objective: To discuss genotypes distribution and molecular epidemiological characters of Treponema pallidum (T. pallidum) infection in Haikou. Methods: A total of 102 specimens genital ulcers were collected from patients with suspected syphilitic chancre admitted during March 2012-February 2013, which were detected by dark-field microscope and PCR method. Acidic repeat protein (arp) gene of T. pallidum and T. pallidum repeat (tpr) gene families were amplified in PCR -positive samples by nested PCR. The number of repeats presented in the arp gene and the restriction fragment length polymorphism by Mse I in the tpr gene were analyzed by electrophoresis. Results: Out of 102 patients with suspected chancre, 55 cases (53.2%) were positive by dark-field microscopy and 89 cases (87.3%) by T. pallidum bmp PCR. Seven genotypes were found in 72 cases, including 14d (28, 38.9%), 12d (12, 16.7%), 13d (11, 15.3%), 14b (9, 12.5%), 14a (5, 6.9%), 12a (3, 4.2%), 15d (2, 2.8%) 10d (1, 1.4%), 12i (1, 1.4%). Conclusions: Genotype 14 d is the predominant type of T. pallidum in Haikou and bmp PCR has high sensitivity.

  15. Norovirus infection in Belarus: occurrence and molecular epidemiology.

    Science.gov (United States)

    Paklonskayal, Natallia Uladzimirauna; Amvrosieva, Tamara Vasil'evna; Dziadziulia, Kanstantsin Leanidavich; Baranouskaya, Natallia Mikalaeuna; Kishkurno, Elena Petrovna; Kluiko, Nina Leonidovna

    2015-03-01

    The objective of the study is to analyze molecular epidemiologic surveillance for norovirus infection in Belarus over the past five years (2009-2013). Laboratory diagnostics was carried out by RT-PCR in 684 patients. Two regions of norovirus genome, localized in RNA-polymerase and capsid protein genes, were used for phylogenetic analysis. Noroviruses were predominant causative agents in adults and second only to rotaviruses in children, they also prevailed among aetiological agents of outbreaks (66.7% of outbreaks). In 2009-2013, the major norovirus genotype was GII.4 (58.3% of all genotyped isolates). Genovariant GII.4 2006b circulated in 2009 and 2010, genovariant GII.4 2009 New Orleans - in 2010 and 2012. In addition to GII.4, genotypes GII.6 (16.6%), GII.2 (4.1%), GII.3 (2.2%), and recombinant genotypes GII.g-GII.12 and GII.g-GII.1 (10.4% and 8.3%, respectively) circulated in Belarus. The findings indicate a significant contribution of noroviruses in development of sporadic morbidity and outbreaks of acute gastroenteritis in Belarus. Outbreaks or prominent increases of sporadic morbidity were mostly due to the emergence of a new genotype, or an epidemic genovariant.

  16. Resistance to Tospoviruses in Vegetable Crops: Epidemiological and Molecular Aspects.

    Science.gov (United States)

    Turina, Massimo; Kormelink, Richard; Resende, Renato O

    2016-08-01

    During the past three decades, the economic impact of tospoviruses has increased, causing high yield losses in a variety of crops and ornamentals. Owing to the difficulty in combating thrips vectors with insecticides, the best way to limit/prevent tospovirus-induced diseases involves a management strategy that includes virus resistance. This review briefly presents current tospovirus taxonomy, diversity, molecular biology, and cytopathology as an introduction to a more extensive description of the two main resistance genes employed against tospoviruses: the Sw5 gene in tomato and the Tsw in pepper. Natural and experimental resistance-breaking (RB) isolates allowed the identification of the viral avirulence protein triggering each of the two resistance gene products; epidemiology of RB isolates is discussed to reinforce the need for allelic variants and the need to search for new/alternative resistance genes. Ongoing efforts for alternative resistance strategies are described not only for Tomato spotted wilt virus (TSWV) in pepper and tomato but also for other vegetable crops heavily impacted by tospoviruses. PMID:27296139

  17. Random Amplified Polymorphic DNA PCR in the Teaching of Molecular Epidemiology

    Science.gov (United States)

    Reinoso, Elina B.; Bettera, Susana G.

    2016-01-01

    In this article, we describe a basic practical laboratory designed for fifth-year undergraduate students of Microbiology as part of the Epidemiology course. This practice provides the students with the tools for molecular epidemiological analysis of pathogenic microorganisms using a rapid and simple PCR technique. The aim of this work was to assay…

  18. Epidemiologic Change of Patients With Spinal Cord Injury

    OpenAIRE

    Shin, Ji Cheol; Kim, Dae Hyun; Yu, Su Jin; Yang, Hea Eun; Yoon, Seo Yeon

    2013-01-01

    Objective To evaluate the epidemiologic change of patients with spinal cord injury who were admitted to a Rehabilitation Hospital, Yonsei University College of Medicine, during 1987-1996 and 2004-2008. Methods Medical records of 629 patients with spinal cord injury admitted to the Rehabilitation Hospital, Yonsei University College of Medicine, from 2004 to 2008 were collected and reviewed retrospectively. Results The male-to-female ratio decreased to 2.86:1, the mean age at injury increased, ...

  19. Molecular epidemiology of Mycobacterium tuberculosis in Gansu province of China

    Institute of Scientific and Technical Information of China (English)

    TIAN Li-li; ZHU Bing-dong; SI Hong-yan; MU Tao-jun; FAN Wen-bing; WANG Jing; JIANG Wei-min; LI Qing; YANG Biao; ZHANG Ying

    2012-01-01

    Background Mycobacterial interspersed repetitive units-variable number tandem repeat (MIRU-VNTR) and Beijing family typing based on detecting the deletion of RD105 sequence are two common genotyping methods used to study the molecular epidemiologic characteristics of Mycobacterium (M.) tuberculosis.We collected 218 strains of M.tuberculosis between 2004 and 2006 in the Linxia Hui Autonomous Prefecture of Gansu province in Northwest China.Methods MIRU-VNTR analysis and Beijing family typing based on detecting the deletion of RD105 sequence were used to type the 218 strains,and their typing power was evaluated to look for practical and efficient genotyping methods suitable for the region.Results The MIRU typing yielded 115 distinct genotypes,including 98 unique isolates and 17 different clusters containing 120 isolates (55.05%); the cluster rate was 47.25%.By detecting the deletion of RD105 sequence,188 of 218 (86.23%) isolates belonged to Beijing family.Combination of Beijing family typing and MIRU typing yielded 118 distinct patterns,including 101 unique isolates and 17 clusters containing 117 isolates (54.13%).The largest cluster contained 58 strains with MIRU genotype of 223325173533 which contained 50 strains belonging to Beijing family and 8 strains belonging to non-Beijing family.Conclusions The Beijing family strains occupied a large proportion and the Beijing family MIRU genotype 223325173533 is a dominant strain in Linxia of Gansu.Combining detecting the deletion of RD105 and MIRU typing together provides a simple,fast,and effective method which is low in cost and might be practical and suitable for M.tuberculosis genotyping in China.

  20. Molecular epidemiology study of Mycobacterium tuberculosis and its susceptibility to anti-tuberculosis drugs in Indonesia

    OpenAIRE

    Lisdawati, Vivi; Puspandari, Nelly; Rif’ati, Lutfah; Soekarno, Triyani; M, Melatiwati; K, Syamsidar; Ratnasari, Lies; Izzatun, Nur; Parwati, Ida

    2015-01-01

    Background Genotyping of Mycobacterium tuberculosis helps to understand the molecular epidemiology of tuberculosis and to address evolutionary questions about the disease spread. Certain genotypes also have implications for the spread of infection and treatment. Indonesia is a very diverse country with a population with multiple ethnicities and cultures and a history of many trade and tourism routes. This study describes the first attempt to map the molecular epidemiology of TB in the Indones...

  1. The changing epidemiology of group B streptococcus bloodstream infection

    DEFF Research Database (Denmark)

    Ballard, Mark S; Schønheyder, Henrik C; Lyytikäinen, Outi;

    2016-01-01

    Background Population-based studies conducted in single regions or countries have identified significant changes in the epidemiology of invasive group B streptococcus (GBS) infection. However, no studies have concurrently compared the epidemiology of GBS infections among multiple different regions......, Sweden, Finland and the UK during 2000-2010. Incidence rates were age- and gender-standardised to the EU population. Results During 114 million patient-years of observation, 3464 cases of GBS BSI were identified for an overall annual incidence of 3.4 patients per 100 000 persons. There were marked...... differences in the overall (range = 1.8-4.1 per 100 000 person-year) and neonatal (range = 0.19-0.83 per 1000 live births) incidences of GBS BSI observed among the study regions. The overall incidence significantly (p = 0.05) increased. Rates of neonatal disease were stable, while the incidence in individuals...

  2. Molecular detection of intestinal parasites for clinical diagnosis and epidemiology

    NARCIS (Netherlands)

    Hove, Robert Jan ten

    2009-01-01

    The detection of intestinal parasitic infections for routine diagnosis and for epidemiological research still depends mainly on microscopical examination of stool samples for the identification of helminth eggs and protozoan trophozoites and cysts. Because microscopy has several limitations, additio

  3. [Diagnosis and molecular epidemiology of viral gastroenteritis in the past, present and future].

    Science.gov (United States)

    Ushijima, Hiroshi

    2009-06-01

    Outline, history of research, diagnosis and molecular epidemiology of viral gastroenteritis were described. Rotavirus, adenovirus, norovirus, sapovirus, astrovirus, human parechovirus, Aichivirus, and human bocavirus are the major target viruses which cause acute gastroenteritis. The viruses were differentiated into genogroup, genotypes and subgenotypes/clusters/lineages. The changing of their genetic backgrounds was well recognized in different areas and years. Some reassortments or recombinations were observed not only between humans and humans but also between humans and animals. Viral gastroenteritis diseases were transmitted by food-borne and humans to humans contact. The environmental factors were also impacted on the infections. Recently, situation of the diseases in the natural ecosystem is becoming clearly. Diagnoses by immunological methods and gene technology are available for the known viruses. Further development of diagnosis and discovery of new viruses will be expected. Therefore, the research on molecular epidemiology is needed to be conducted continuously and then new findings will appear. We need to precede the research by using new techniques and we need to cope with the demand of society especially during acute gastroenteritis outbreak seasons. PMID:19927992

  4. Molecular epidemiology of cryptosporidiosis in cattle and other food animals [Spanish][Epidemiología molecular de cryptosporidiosis en el ganado vacuno y en otros animales de abasto

    Science.gov (United States)

    Molecular epidemiology of cryptosporidiosis in cattle and other food animals Cryptosporidium is an enteric protozoan parasite that infects a wide range of vertebrate hosts. Cryptosporidial infection is known now as one of the most common causes of diarrhea in humans and livestock. Worldwide prevale...

  5. Molecular epidemiology of rotavirus in cats in the United Kingdom.

    Science.gov (United States)

    German, A C; Iturriza-Gómara, M; Dove, W; Sandrasegaram, M; Nakagomi, T; Nakagomi, O; Cunliffe, N; Radford, A D; Morgan, K L

    2015-02-01

    Rotaviruses are leading causes of gastroenteritis in the young of many species. Molecular epidemiological studies in children suggest that interspecies transmission contributes to rotavirus strain diversity in people. However, population-based studies of rotaviruses in animals are few. We investigated the prevalence, risk factors for infection, and genetic diversity of rotavirus A in a cross-sectional survey of cats housed within 25 rescue catteries across the United Kingdom. Morning litter tray fecal samples were collected during the winter and summer in 2012 from all pens containing kittens and a random sample of those housing adult cats. Group A rotavirus RNA was detected by real-time reverse transcription-PCR, and positive samples were G and P genotyped using nested VP4 and VP7 PCR assays. A total of 1,727 fecal samples were collected from 1,105 pens. Overall, the prevalence of rotavirus was 3.0% (95% confidence interval [CI], 1.2 to 4.9%). Thirteen out of 25 (52%; 95% CI, 31.3 to 72.2%) centers housed at least one rotavirus-positive cat. The prevalence of rotavirus was associated with season (odds ratio, 14.8 [95% CI, 1.1 to 200.4]; P = 0.04) but not age or diarrhea. It was higher during the summer (4.7%; 95% CI, 1.2 to 8.3%) than in winter (0.8%; 95% CI, 0.2 to 1.5%). Asymptomatic epidemics of infection were detected in two centers. G genotypes were characterized for 19 (33.3%) of the 57 rotavirus-positive samples and P genotypes for 36 (59.7%). Two rotavirus genotypes were identified, G3P[9] and G6P[9]. This is the first population-based study of rotavirus in cats and the first report of feline G6P[9], which questions the previous belief that G6P[9] in people is of bovine origin. PMID:25411173

  6. Molecular epidemiology of salmonid alphavirus (SAV subtype 3 in Norway

    Directory of Open Access Journals (Sweden)

    Jansen Mona D

    2010-08-01

    by other researchers. Larger scale, full length sequence analyses should be instigated to allow further phylogenetic and molecular epidemiology investigations of SAV subtype 3.

  7. Molecular Epidemiology of Brucella abortus in Northern Ireland-1991 to 2012.

    Directory of Open Access Journals (Sweden)

    Adrian Allen

    Full Text Available Brucellosis is the most common bacterial zoonoses worldwide. Bovine brucellosis caused by Brucella abortus has far reaching animal health and economic impacts at both the local and national levels. Alongside traditional veterinary epidemiology, the use of molecular typing has recently been applied to inform on bacterial population structure and identify epidemiologically-linked cases of infection. Multi-locus variable number tandem repeat VNTR analysis (MLVA was used to investigate the molecular epidemiology of a well-characterised Brucella abortus epidemic in Northern Ireland involving 387 herds between 1991 and 2012.MLVA identified 98 unique B. abortus genotypes from disclosing isolates in the 387 herds involved in the epidemic. Clustering algorithms revealed the relatedness of many of these genotypes. Combined with epidemiological information on chronology of infection and geographic location, these genotype data helped to identify 7 clonal complexes which underpinned the outbreak over the defined period. Hyper-variability of some VNTR loci both within herds and individual animals led to detection of multiple genotypes associated with single outbreaks. However with dense sampling, these genotypes could still be associated with specific clonal complexes thereby permitting inference of epidemiological links. MLVA- based epidemiological monitoring data were congruent with an independent classical veterinary epidemiology study carried out in the same territory.MLVA is a useful tool in ongoing disease surveillance of B. abortus outbreaks, especially when combined with accurate epidemiological information on disease tracings, geographical clustering of cases and chronology of infection.

  8. STrengthening the Reporting of OBservational studies in Epidemiology - Molecular Epidemiology (STROBE-ME): An extension of the STROBE statement

    NARCIS (Netherlands)

    Gallo, V.; Egger, M.; McCormack, V.; Farmer, P.B.; Ioannidis, J.P.; Kirsch-Volders, M.; Matullo, G.; Phillips, D.H.; Schoket, B.; Stromberg, U.; Vermeulen, R.; Wild, C.; Porta, M.; Vineis, P.

    2012-01-01

    Advances in laboratory techniques have led to a rapidly increasing use of biomarkers in epidemiological studies. Biomarkers of internal dose, early biological change, susceptibility, and clinical outcomes are used as proxies for investigating the interactions between external and/or endogenous agent

  9. STrengthening the Reporting of OBservational studies in Epidemiology - Molecular Epidemiology (STROBE-ME): An extension of the STROBE statement

    NARCIS (Netherlands)

    Gallo, V.; Egger, M.; McCormack, V.; Farmer, P.B.; Ioannidis, J.P.; Kirsch-Volders, M.; Matullo, G.; Phillips, D.H.; Schoket, B.; Stromberg, U.; Vermeulen, R.; Wild, C.; Porta, M.; Vineis, P.

    2012-01-01

    Advances in laboratory techniques have led to a rapidly increasing use of biomarkers in epidemiological studies. Biomarkers of internal dose, early biological change, susceptibility and clinical outcomes are used as proxies for investigating interactions between external and / or endogenous agents a

  10. STrengthening the Reporting of OBservational studies in Epidemiology - Molecular Epidemiology (STROBE-ME): An extension of the STROBE statement

    NARCIS (Netherlands)

    Gallo, V.; Egger, M.; McCormack, V.; Farmer, P.B.; Ioannidis, J.P.; Kirsch-Volders, M.; Matullo, G.; Phillips, D.H.; Schoket, B.; Stromberg, U.; Vermeulen, R.; Wild, C.; Porta, M.; Vineis, P.

    2012-01-01

    Eur J Clin Invest 2012; 42 (1): 1-16 SUMMARY POINTS: Advances in laboratory techniques have led to a rapidly increasing use of biomarkers in epidemiological studies. Biomarkers of internal dose, early biological change, susceptibility and clinical outcomes are used as proxies for investigating inter

  11. Apocalypse... Now? Molecular epidemiology, predictive genetic tests, and social communication of genetic contents

    Directory of Open Access Journals (Sweden)

    Luis David Castiel

    1999-01-01

    Full Text Available The author analyzes the underlying theoretical aspects in the construction of the molecular watershed of epidemiology and the concept of genetic risk, focusing on issues raised by contemporary reality: new technologies, globalization, proliferation of communications strategies, and the dilution of identity matrices. He discusses problems pertaining to the establishment of such new interdisciplinary fields as molecular epidemiology and molecular genetics. Finally, he analyzes the repercussions of the social communication of genetic content, especially as related to predictive genetic tests and cloning of animals, based on triumphal, deterministic metaphors sustaining beliefs relating to the existence and supremacy of concepts such as 'purity', 'essence', and 'unification' of rational, integrated 'I's/egos'.

  12. Apocalypse...now? Molecular epidemiology, predictive genetic tests, and social communication of genetic contents.

    Science.gov (United States)

    Castiel, L D

    1999-01-01

    The author analyzes the underlying theoretical aspects in the construction of the molecular watershed of epidemiology and the concept of genetic risk, focusing on issues raised by contemporary reality: new technologies, globalization, proliferation of communications strategies, and the dilution of identity matrices. He discusses problems pertaining to the establishment of such new interdisciplinary fields as molecular epidemiology and molecular genetics. Finally, he analyzes the repercussions of the social communication of genetic content, especially as related to predictive genetic tests and cloning of animals, based on triumphal, deterministic metaphors sustaining beliefs relating to the existence and supremacy of concepts such as 'purity', 'essence', and 'unification' of rational, integrated 'I's/egos'. PMID:10089550

  13. Molecular epidemiology of Cryptosporidium and Giardia in cattle

    Science.gov (United States)

    Cryptosporidium spp. and Giardia duodenalis are enteric protozoan parasites that infect a wide range of vertebrate hosts including humans. Infections with both parasites are known as one of the most common causes of diarrhea in humans and livestock. The epidemiology of cryptosporidiosis and giardias...

  14. Epidemiological changes of respiratory syncytial virus (RSV infections in Israel.

    Directory of Open Access Journals (Sweden)

    Shira Hirsh

    Full Text Available RSV is the leading cause of lower respiratory-tract infections in infants and therefore demands in-depth epidemiological characterization. We investigated here the distribution of RSV types in Israel between the years 2005-2012. Clinical samples were collected from 11,018 patients hospitalized due to respiratory illnesses and were evaluated for the presence of various respiratory viruses, including RSV A and RSV B. Until 2008, each year was characterized by the presence of one dominant type of RSV. However, from 2008, both RSV A and B types were detected at significant levels, particularly among infants aged 0-2 years. Furthermore, significant changes in the RSV A and RSV B subtypes circulating in Israel since 2008 were observed. Finally, we demonstrate that, irrespectively of the changes observed in RSV epidemiology, when the pandemic H1N1pdm09 influenza virus appeared in 2009, RSV infections were delayed and were detected when infection with H1N1pdm09 had declined.

  15. Molecular epidemiology of Vibrio nigripulchritudo, a pathogen of cultured penaeid shrimp (Litopenaeus stylirostris) in New Caledonia

    OpenAIRE

    Goarant, Cyrille; Reynaud, Yann; Ansquer, Dominique; De Decker, Sophie; Saulnier, Denis; Leroux, Frederique

    2006-01-01

    A collection of 57 isolates of Vibrio nigripulchritudo from either diseased or healthy shrimp and from shrimp farms environment was studied in order to gain a better understanding of the epidemiology of this pathogen, notably isolated from two distinct shrimp disease complexes. Molecular typing using two different techniques, arbitrarily primed PCR (AP-PCR) and multi-locus sequence typing (MLST), studied together with experimental pathology data allowed a relevant epidemiological insight into...

  16. Molecular epidemiology of measles virus in Italy during 2008

    Directory of Open Access Journals (Sweden)

    Fabio Magurano

    2013-03-01

    Full Text Available INTRODUCTION. In view of the goal of measles elimination, it is of great importance to assess the circulation of wild-type measles virus (MV. Genetic analysis is indispensable to understand the epidemiology of measles. A large measles outbreak occurred in Italy in 2008, with over 4000 cases reported to the enhanced measles surveillance system introduced in 2007, 37% of which were laboratory confirmed. METHODS. Urine and saliva samples were collected during 2008. A phylogenetic analysis of measles sequences was performed in order to understand the epidemiological situation of wild-type (MV circulation in that period. RESULT AND DISCUSSION. Data showed predominant circulation of the genotype D4. Genotypes A, D8, D9 and H1 were also detected in a small number of samples, probably representing imported cases.

  17. Initial Data on the Molecular Epidemiology of Cryptosporidiosis in Lebanon

    OpenAIRE

    Osman, Marwan; El Safadi, Dima; Benamrouz, Sadia; Guyot, Karine; Dei-Cas, Eduardo; Aliouat, El Moukhtar; Creusy, Colette; Mallat, Hassan; Hamze, Monzer; Dabboussi, Fouad; Viscogliosi, Eric; Certad, Gabriela

    2015-01-01

    Cryptosporidium spp. represent a major public health problem worldwide and infect the gastrointestinal tract of both immunocompetent and immunocompromised persons. The prevalence of these parasites varies by geographic region, and no data are currently available in Lebanon. To promote an understanding of the epidemiology of cryptosporidiosisin this country, the main aim of this study was to determine the prevalence Cryptosporidium in symptomatic hospitalized patients, and to analyze the genet...

  18. Clinical, Epidemiologic, Histopathologic and Molecular Features of an Unexplained Dermopathy

    OpenAIRE

    Pearson, Michele L.; Selby, Joseph V.; Katz, Kenneth A; Cantrell, Virginia; Braden, Christopher R.; Parise, Monica E.; Paddock, Christopher D.; Michael R Lewin-Smith; Kalasinsky, Victor F.; Goldstein, Felicia C.; Hightower, Allen W.; Papier, Arthur; Lewis, Brian; Motipara, Sarita; Eberhard, Mark L.

    2012-01-01

    Background Morgellons is a poorly characterized constellation of symptoms, with the primary manifestations involving the skin. We conducted an investigation of this unexplained dermopathy to characterize the clinical and epidemiologic features and explore potential etiologies. Methods A descriptive study was conducted among persons at least 13 years of age and enrolled in Kaiser Permanente Northern California (KPNC) during 2006–2008. A case was defined as the self-reported emergence of fibers...

  19. Random amplified polymorphic DNA PCR in the teaching of molecular epidemiology.

    Science.gov (United States)

    Reinoso, Elina B; Bettera, Susana G

    2016-07-01

    In this article, we describe a basic practical laboratory designed for fifth-year undergraduate students of Microbiology as part of the Epidemiology course. This practice provides the students with the tools for molecular epidemiological analysis of pathogenic microorganisms using a rapid and simple PCR technique. The aim of this work was to assay RAPD-PCR technique in order to infer possible epidemiological relationships. The activity gives students an appreciation of the value of applying a simple molecular biological method as RAPD-PCR to a discipline-specific question. It comprises a three-session laboratory module to genetically assay DNAs from strains isolated from a food outbreak. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(4):391-396, 2016. PMID:26898662

  20. Integration of molecular pathology, epidemiology and social science for global precision medicine.

    Science.gov (United States)

    Nishi, Akihiro; Milner, Danny A; Giovannucci, Edward L; Nishihara, Reiko; Tan, Andy S; Kawachi, Ichiro; Ogino, Shuji

    2016-01-01

    The precision medicine concept and the unique disease principle imply that each patient has unique pathogenic processes resulting from heterogeneous cellular genetic and epigenetic alterations and interactions between cells (including immune cells) and exposures, including dietary, environmental, microbial and lifestyle factors. As a core method field in population health science and medicine, epidemiology is a growing scientific discipline that can analyze disease risk factors and develop statistical methodologies to maximize utilization of big data on populations and disease pathology. The evolving transdisciplinary field of molecular pathological epidemiology (MPE) can advance biomedical and health research by linking exposures to molecular pathologic signatures, enhancing causal inference and identifying potential biomarkers for clinical impact. The MPE approach can be applied to any diseases, although it has been most commonly used in neoplastic diseases (including breast, lung and colorectal cancers) because of availability of various molecular diagnostic tests. However, use of state-of-the-art genomic, epigenomic and other omic technologies and expensive drugs in modern healthcare systems increases racial, ethnic and socioeconomic disparities. To address this, we propose to integrate molecular pathology, epidemiology and social science. Social epidemiology integrates the latter two fields. The integrative social MPE model can embrace sociology, economics and precision medicine, address global health disparities and inequalities, and elucidate biological effects of social environments, behaviors and networks. We foresee advancements of molecular medicine, including molecular diagnostics, biomedical imaging and targeted therapeutics, which should benefit individuals in a global population, by means of an interdisciplinary approach of integrative MPE and social health science.

  1. HIV/AIDS in Asia: The Shape of Epidemics and Their Molecular Epidemiology

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The Asia-Pacific region is a home to 60% of the population in the world and to approximately one quarter of people with HIV/AIDS. Close to a million of people has been infected and a half million people died of AIDS annually in Asia, becoming the second largest epicenter of global AIDS epidemic. Molecular epidemiology has been useful tool to track a course of HIV spread. In-depth knowledge from the studies on molecular epidemiology elucidates the dynamics of HIV spread and the interrelationship of epidemics in the different regions in Asia.

  2. High-resolution molecular epidemiology and evolutionary history of HIV-1 subtypes in Albania.

    Directory of Open Access Journals (Sweden)

    Marco Salemi

    Full Text Available BACKGROUND: HIV-1 epidemic in Western Europe is largely due to subtype B. Little is known about the HIV-1 in Eastern Europe, but a few studies have shown that non-B subtypes are quite common. In Albania, where a recent study estimated a ten-fold increase of AIDS incidence during the last six years, subtype A and B account for 90% of the know infections. METHODOLOGY/PRINCIPAL FINDINGS: We investigated the demographic history of HIV-1 subtype A and B in Albania by using a statistical framework based on coalescent theory and phylogeography. High-resolution phylogenetic and molecular clock analysis showed a limited introduction to the Balkan country of subtype A during the late 1980s followed by an epidemic outburst in the early 1990 s. In contrast, subtype B was apparently introduced multiple times between the mid-1970s and mid-1980s. Both subtypes are growing exponentially, although the HIV-1A epidemic displays a faster growth rate, and a significantly higher basic reproductive number R(0. HIV-1A gene flow occurs primarily from the capital Tirane, in the center of the country, to the periphery, while HIV-1B flow is characterized by a balanced exchange between center and periphery. Finally, we calculated that the actual number of infections in Albania is at least two orders of magnitude higher than previously thought. CONCLUSIONS/SIGNIFICANCE: Our analysis demonstrates the power of recently developed computational tools to investigate molecular epidemiology of pathogens, and emphasize the complex factors involved in the establishment of HIV-1 epidemics. We suggest that a significant correlation exists between HIV-1 exponential spread and the socio-political changes occurred during the Balkan wars. The fast growth of a relatively new non-B epidemic in the Balkans may have significant consequences for the evolution of HIV-1 epidemiology in neighboring countries in Eastern and Western Europe.

  3. Strain typing methods and molecular epidemiology of Pneumocystis pneumonia

    DEFF Research Database (Denmark)

    Beard, Charles Ben; Roux, Patricia; Nevez, Gilles;

    2004-01-01

    Pneumocystis pneumonia (PCP) caused by the opportunistic fungal agent Pneumocystis jirovecii (formerly P. carinii) continues to cause illness and death in HIV-infected patients. In the absence of a culture system to isolate and maintain live organisms, efforts to type and characterize the organism...... have relied on polymerase chain reaction-based approaches. Studies using these methods have improved understanding of PCP epidemiology, shedding light on sources of infection, transmission patterns, and potential emergence of antimicrobial resistance. One concern, however, is the lack of guidance...

  4. Isoforms of thyroxine-binding globulin as a model for molecular epidemiology of human cancer risk

    International Nuclear Information System (INIS)

    The novel field of molecular epidemiology of human cancer risk has added a new branch to classical epidemiology by providing a direct link between human cancer and carcinogen exposure. It was estimated that about 80% of cancers are due to environmental factors. The blood proteins are almost certainly targets for modification in human cancer, and their identification and characterization will be of primary importance in the development of the new and rapidly evolving field of molecular epidemiology. Among blood proteins that are altered in human cancer, TBG occupies a special place because the level of human blood TBG is the most sensitive to intensification of biosynthesis and proliferation processes in organisms in different types of cancer. The increase of TBG concentration in cancer can be result from both activation of TBG biosynthesis in liver or altering of post translation glycosylation that prolongs protein survival time. The molecular basis for the change in the properties of TBG in cancer is unknown. These distinctive changes could have important consequences for the function of TBG in cancer and may help to develop more precise markers for monitoring pathological progression in this disease. Considerable variability and subtlety can occur in the carbohydrate composition and structure of serum glycoproteins in disease. This can be either as a major change, such as an increase in the number of oligosaccharide branches at a particular glycosylation site or as a minor change such as the addition of an extra fucose or sialic acid residue. Increased fucosylation has also been reported for transferrin and alpha-fetoprotein in liver cancer; thyroglobulin in thyroid cancer, IgG in myeloma, haptoglobin in ovarian cancer. The last own studies have shown that in clinically healthy teenagers born in Khojniki (137 Cs 185-555 kBq/m), we have found an unusual thyroid profile exhibiting increased levels of total triiodothyronine (T3), total thyroxine (T4), and thyroxine

  5. Molecular Epidemiology of Viral Gastroenteritis in Hajj pilgrimage

    KAUST Repository

    Padron Regalado, Eriko

    2014-05-01

    Hajj is the annual gathering of Islam practitioners in Mecca, Saudi Arabia. During the event, gastrointestinal infections are usually experienced and outbreaks have always been a concern; nevertheless, a deep and integrative study of the etiological agents has never been carried out. Here, I describe for the first time the epidemiology of pathogenic enteric viruses during Hajj 2011, 2012 and 2013. The focus of this study was the common enteric viruses Astrovirus, Norovirus, Rotavirus and Adenovirus. An enzyme Immunoassay established their presence in 14.9%, 15.0% and 6.6% of the reported cases of acute diarrhea for 2011, 2012 and 2013, respectively. For the three years of study, Astrovirus accounted for the majority of the viral infections. To our knowledge, this is the first time an epidemiological study depicts Astrovirus as the main viral agent of gastroenteritis in a mass gathering event. Hajj is rich in strains of Astrovirus, Norovirus and Rotavirus. A first screening by RT-PCR resulted in ten different genotypes. Strains HAstV 2, HAstV 1 and HAstV 5 were identified for Astrovirus. GI.6, GII.3, GII.4 and GII.1 were described for Norovirus and G1P[8], G4P[8] and G3P[8] were found for Rotavirus. The majority of the Astrovirus isolates could not be genotyped suggesting the presence of a new variant(s). Cases like this encourage the use of metagenomics (and nextgeneration sequencing) as a state-of-the-art technology in clinical diagnosis. A sample containing Adenovirus particles is being used to standardize a process for detection directly from stool samples and results will be obtained in the near future. The overall findings of the present study support the concept of Hajj as a unique mass gathering event that potentiates the transmission of infectious diseases. The finding of Norovirus GII.4 Sydney, a variant originated from Australia, suggests that Hajj is a receptor of infectious diseases worldwide. This work is part of the Hajj project, a collaborative

  6. Acute kidney injury: changing lexicography, definitions, and epidemiology.

    Science.gov (United States)

    Himmelfarb, J; Ikizler, T A

    2007-05-01

    In recent years, there have been numerous advances in understanding the molecular determinants of functional kidney injury after ischemic and/or toxic exposure. However, translation of successful novel therapies designed to attenuate kidney functional injury from animal models to the clinical sphere has had modest results. This lack of translatability is at least in part due to lack of sufficient standardization in definitions and classification of cases of acute kidney injury (AKI), an incomplete understanding of the natural history of human AKI, and a limited understanding of how kidney injury interacts with other organ system failure in the context of systemic metabolic abnormalities. A concerted effort is now being made by nephrologists and intensivists to arrive at standardized terminology and classification of AKI. There have also been dramatic advances in our understanding of the epidemiology and natural history of AKI, particularly in the hospital and intensive care unit setting. Promising strategies are now being developed which may ultimately lead to improved outcomes for patients at risk for or who have developed AKI, which should be readily testable in the coming decade.

  7. The changing landscape of rabies epidemiology and control

    OpenAIRE

    Sarah Cleaveland; Hawthorne Beyer; Katie Hampson; Daniel Haydon; Felix Lankester; Tiziana Lembo; Francois-Xavier Meslin; Michelle Morters; Zacharia Mtema; Maganga Sambo; Sunny Townsend

    2014-01-01

    Over the past 20 years, major progress has been made in our understanding of critical aspects of rabies epidemiology and control. This paper presents results of recent research, highlighting methodological advances that have been applied to burden of disease studies, rabies epidemiological modelling and rabies surveillance. These results contribute new insights and understanding with regard to the epidemiology of rabies and help to counteract misperceptions that currently hamper rabies contro...

  8. Molecular epidemiology, and possible real-world applications in breast cancer.

    Science.gov (United States)

    Ito, Hidemi; Matsuo, Keitaro

    2016-01-01

    Gene-environment interaction, a key idea in molecular epidemiology, has enabled the development of personalized medicine. This concept includes personalized prevention. While genome-wide association studies have identified a number of genetic susceptibility loci in breast cancer risk, however, the application of this knowledge to practical prevention is still underway. Here, we briefly review the history of molecular epidemiology and its progress in breast cancer epidemiology. We then introduce our experience with the trial combination of GWAS-identified loci and well-established lifestyle and reproductive risk factors in the risk prediction of breast cancer. Finally, we report our exploration of the cumulative risk of breast cancer based on this risk prediction model as a potential tool for individual risk communication, including genetic risk factors and gene-environment interaction with obesity.

  9. Dengue fever: new paradigms for a changing epidemiology

    Directory of Open Access Journals (Sweden)

    Schimmer Barbara

    2005-03-01

    Full Text Available Abstract Dengue is the most important arthropod-borne viral disease of public health significance. Compared with nine reporting countries in the 1950s, today the geographic distribution includes more than 100 countries worldwide. Many of these had not reported dengue for 20 or more years and several have no known history of the disease. The World Health Organization estimates that more than 2.5 billion people are at risk of dengue infection. First recognised in the 1950s, it has become a leading cause of child mortality in several Asian and South American countries. This paper reviews the changing epidemiology of the disease, focusing on host and societal factors and drawing on national and regional journals as well as international publications. It does not include vaccine and vector issues. We have selected areas where the literature raises challenges to prevailing views and those that are key for improved service delivery in poor countries. Shifts in modal age, rural spread, and social and biological determinants of race- and sex-related susceptibility have major implications for health services. Behavioural risk factors, individual determinants of outcome and leading indicators of severe illness are poorly understood, compromising effectiveness of control programmes. Early detection and case management practices were noted as a critical factor for survival. Inadequacy of sound statistical methods compromised conclusions on case fatality or disease-specific mortality rates, especially since the data were often based on hospitalised patients who actively sought care in tertiary centres. Well-targeted operational research, such as population-based epidemiological studies with clear operational objectives, is urgently needed to make progress in control and prevention.

  10. Molecular epidemiology of Enterococcus faecalis in liver transplant patients at University Hospital Groningen

    NARCIS (Netherlands)

    Waar, K; Slooff, MJH; Harmsen, HJM; Degener, JE; Willems, Rob J. L.

    2003-01-01

    We report the molecular epidemiology of Enterococcus faecalis in liver transplant patients transplanted at the University Hospital Groningen (The Netherlands) as determined by amplified fragment length polymorphism (AFLP) typing. A total of 133 E. faecalis isolates were cultured from the faeces and

  11. The Molecular Epidemiology and Genetic Environment of Carbapenemases Detected in Africa.

    Science.gov (United States)

    Sekyere, John Osei; Govinden, Usha; Essack, Sabiha

    2016-01-01

    Research articles describing carbapenemases and their genetic environments in Gram-negative bacteria were reviewed to determine the molecular epidemiology of carbapenemases in Africa. The emergence of resistance to the carbapenems, the last resort antibiotic for difficult to treat bacterial infections, affords clinicians few therapeutic options, with a resulting increase in morbidities, mortalities, and healthcare costs. However, the molecular epidemiology of carbapenemases throughout Africa is less described. Research articles and conference proceedings describing the genetic environment and molecular epidemiology of carbapenemases in Africa were retrieved from Google Scholar, Scifinder, Pubmed, Web of Science, and Science Direct databases. Predominant carbapenemase genes so far described in Africa include the blaOXA-48 type, blaIMP, blaVIM, and blaNDM in Acinetobacter baumannii, Klebsiella pneumoniae, Enterobacter cloacae, Citrobacter spp., and Escherichia coli carried on various plasmid types and sizes, transposons, and integrons. Class D and class B carbapenemases, mainly prevalent in A. baumannii, K. pneumoniae, E. cloacae, Citrobacter spp., and E. coli were the commonest carbapenemases. Carbapenemases are mainly reported in North and South Africa as under-resourced laboratories, lack of awareness and funding preclude the detection and reporting of carbapenemase-mediated resistance. Consequently, the true molecular epidemiology of carbapenemases and their genetic environment in Africa is still unknown.

  12. Molecular epidemiology of chronic Pseudomonas aeruginosa airway infections in cystic fibrosis

    DEFF Research Database (Denmark)

    Cramer, Nina; Wiehlmann, Lutz; Ciofu, Oana;

    2012-01-01

    The molecular epidemiology of the chronic airway infections with Pseudomonas aeruginosa in individuals with cystic fibrosis (CF) was investigated by cross-sectional analysis of bacterial isolates from 51 CF centers and by longitudinal analysis of serial isolates which had been collected at the CF...

  13. Molecular epidemiology of Neisseria gonorrhoeae in Amsterdam, The Netherlands, shows distinct heterosexual and homosexual networks

    NARCIS (Netherlands)

    M.E. Kolader; N.H.T.M. Dukers; A.K. van der Bij; M. Dierdorp; J.S.A. Fennema; R.A. Coutinho; S.A. Bruisten

    2006-01-01

    Molecular typing, added to epidemiological data, can better identify transmission patterns of gonorrhea in Western countries, where the incidence has recently been rising. From September 2002 to September 2003, patients with a laboratory-confirmed diagnosis of gonorrhea at the Clinic for Sexually Tr

  14. Molecular epidemiology of Neisseria gonorrhoeae in Amsterdam, The Netherlands, shows distinct heterosexual and homosexual networks.

    NARCIS (Netherlands)

    Kolader, Marion-Eliëtte; Dukers, Nicole H T M; Bij, Akke K van der; Dierdorp, Mirjam; Fennema, Johan S A; Coutinho, Roel A; Bruisten, Sylvia M

    2006-01-01

    Molecular typing, added to epidemiological data, can better identify transmission patterns of gonorrhea in Western countries, where the incidence has recently been rising. From September 2002 to September 2003, patients with a laboratory-confirmed diagnosis of gonorrhea at the Clinic for Sexually Tr

  15. Overview of molecular typing methods for outbreak detection and epidemiological surveillance.

    Science.gov (United States)

    Sabat, A J; Budimir, A; Nashev, D; Sá-Leão, R; van Dijl, J m; Laurent, F; Grundmann, H; Friedrich, A W

    2013-01-01

    Typing methods for discriminating different bacterial isolates of the same species are essential epidemiological tools in infection prevention and control. Traditional typing systems based on phenotypes, such as serotype, biotype, phage-type, or antibiogram, have been used for many years. However, more recent methods that examine the relatedness of isolates at a molecular level have revolutionised our ability to differentiate among bacterial types and subtypes. Importantly, the development of molecular methods has provided new tools for enhanced surveillance and outbreak detection. This has resulted in better implementation of rational infection control programmes and efficient allocation of resources across Europe. The emergence of benchtop sequencers using next generation sequencing technology makes bacterial whole genome sequencing (WGS) feasible even in small research and clinical laboratories. WGS has already been used for the characterisation of bacterial isolates in several large outbreaks in Europe and, in the near future, is likely to replace currently used typing methodologies due to its ultimate resolution. However, WGS is still too laborious and time-consuming to obtain useful data in routine surveillance. Also, a largely unresolved question is how genome sequences must be examined for epidemiological characterisation. In the coming years, the lessons learnt from currently used molecular methods will allow us to condense the WGS data into epidemiologically useful information. On this basis, we have reviewed current and new molecular typing methods for outbreak detection and epidemiological surveillance of bacterial pathogens in clinical practice, aiming to give an overview of their specific advantages and disadvantages. PMID:23369389

  16. Etiological and molecular-epidemiological analysis on enterovirus associated encephalitis in Zhejiang,2008-2012

    Institute of Scientific and Technical Information of China (English)

    严菊英

    2014-01-01

    Objective In order to investigate etiology and molecular-epidemiological characteristics of enterovirus associated encephalitis(EAE)in Zhejiang,2008—2012.Methods Cerebrospinal fluid and stool specimens were collected from suspected EAE patients,who were admitted to our hospitals.RD and Hep-2 cell lines were used to isolate

  17. Molecular epidemiological study of hand,foot and mouth disease in Shenzhen from 2010 to 2012

    Institute of Scientific and Technical Information of China (English)

    冼慧霞

    2014-01-01

    Objective To investigate the pathogen spectrum and molecular epidemiological characteristics of hand,foot and mouth disease(HFMD)in Shenzhen from 2010 to2012 and to provide scientific basis for HFMD control.Methods A total of 1 523 clinical stool specimens or anal swab from the sentinel surveillance systems of HFMD were obtained.Molecular evolutions of VP1 gene of causative agents were detected by real-time fluorescence

  18. The real ecological fallacy: epidemiology and global climate change.

    Science.gov (United States)

    Krieger, Nancy

    2015-08-01

    Prompted by my participation in the People's Climate March held in New York City on 21 September 2014, as part of the 'Harvard Divest' contingent, in this brief essay I reflect on the late 20th century development of--and debates over--the necessity of ecological thinking in epidemiology, and also the still limited engagement of our field with work on the health impact of global climate change. Revisiting critiques about the damaging influence of methodological individualism on our field, I extend critique of the still influential notion of 'ecological fallacy,' including its wilful disregard for ecology itself as being pertinent to people's ways of living--and dying. Indeed, the real 'ecological fallacy' is to think epidemiologists or others could ever understand the people's health except in societal and ecological, and hence historical, context. I conclude by urging all of us, as members of the broader scientific community, whether or not we directly study the health impacts of the planetary emergency of global climate change, to step up by joining the call for universities to divest from fossil fuels.

  19. Clinical, epidemiologic, histopathologic and molecular features of an unexplained dermopathy.

    Directory of Open Access Journals (Sweden)

    Michele L Pearson

    Full Text Available BACKGROUND: Morgellons is a poorly characterized constellation of symptoms, with the primary manifestations involving the skin. We conducted an investigation of this unexplained dermopathy to characterize the clinical and epidemiologic features and explore potential etiologies. METHODS: A descriptive study was conducted among persons at least 13 years of age and enrolled in Kaiser Permanente Northern California (KPNC during 2006-2008. A case was defined as the self-reported emergence of fibers or materials from the skin accompanied by skin lesions and/or disturbing skin sensations. We collected detailed epidemiologic data, performed clinical evaluations and geospatial analyses and analyzed materials collected from participants' skin. RESULTS: We identified 115 case-patients. The prevalence was 3.65 (95% CI = 2.98, 4.40 cases per 100,000 enrollees. There was no clustering of cases within the 13-county KPNC catchment area (p = .113. Case-patients had a median age of 52 years (range: 17-93 and were primarily female (77% and Caucasian (77%. Multi-system complaints were common; 70% reported chronic fatigue and 54% rated their overall health as fair or poor with mean Physical Component Scores and Mental Component Scores of 36.63 (SD = 12.9 and 35.45 (SD = 12.89, respectively. Cognitive deficits were detected in 59% of case-patients and 63% had evidence of clinically significant somatic complaints; 50% had drugs detected in hair samples and 78% reported exposure to solvents. Solar elastosis was the most common histopathologic abnormality (51% of biopsies; skin lesions were most consistent with arthropod bites or chronic excoriations. No parasites or mycobacteria were detected. Most materials collected from participants' skin were composed of cellulose, likely of cotton origin. CONCLUSIONS: This unexplained dermopathy was rare among this population of Northern California residents, but associated with significantly reduced health

  20. Molecular epidemiology of heteroresistant vancomycin-intermediate Staphylococcus aureus in Brazil

    Directory of Open Access Journals (Sweden)

    Alessandro Conrado de Oliveira Silveira

    2015-10-01

    Full Text Available ABSTRACTTo determine the epidemiological and molecular characteristics of 12 Staphylococcus aureus isolates presenting heteroresistance to vancomycin in laboratories of two cities in Santa Catarina, southern Brazil. Epidemiological data, including the city of isolation, health institution, and date of isolation were considered, as well as the associated clinical specimen. For molecular characterization, we analyzed the staphylococcal cassette chromosome types, the erm gene presence, and the genomic diversity of isolates using pulsed-field gel electrophoresis. The 12 isolates of S. aureus were previously confirmed as heteroresistance to vancomycin using the population analysis profile-area under curve. Regarding genetic variability, two clones were detected: the main one (clone A composed of four isolates and the clones B, with two isolates. For clone A, two isolates presented identical band patterns and were related to the same hospital, with an interval of 57 days between their isolation. The other isolates of this clone showed no epidemiological link between them because they were isolated in different hospitals and had no temporal relationship. The other clone showed no detectable epidemiological relationship. The heteroresistance to vancomycin recovered in Santa Catarina State from 2009 to 2012 had, in general, heterogeneous genomic patterns based on pulsed-field gel electrophoresis results, which is in accordance with the fact that these isolates had little or no epidemiological relationship among them. Due to the characteristic phenotypic instability and often prolonged vancomycin therapy for selection, clonal spread is not as common as for other resistance mechanisms disseminated through horizontal gene transfer.

  1. STrengthening the Reporting of OBservational studies in Epidemiology - Molecular Epidemiology (STROBE-ME): an extension of the STROBE Statement.

    OpenAIRE

    Gallo, Valentina; Egger, Matthias; McCormack, Valerie; Farmer, Peter B; Ioannidis, John P.A.; Kirsch-Volders, Micheline; Matullo, Giuseppe; Phillips, David H.; Schoket, Bernadette; Stromberg, Ulf; Vermeulen, Roel; Wild, Christopher; Porta, Miquel,; Vineis, Paolo

    2011-01-01

    Provenance: Not commissioned; externally peer reviewed by European Journal of Clinical Investigation, Journal of Clinical Epidemiology, Preventive Medicine, Mutagenesis, Journal of Epidemiology and Community Health, European Journal of Epidemiology. In order to encourage dissemination of this extension to the STROBE Statement, this article has also been published by European Journal of Clinical Investigation, Journal of Clinical Epidemiology, Preventive Medicine, Mutagenesis, Journal of Epide...

  2. Linking healthcare associated norovirus outbreaks: a molecular epidemiologic method for investigating transmission

    Directory of Open Access Journals (Sweden)

    Andrews Nick

    2006-07-01

    Full Text Available Abstract Background Noroviruses are highly infectious pathogens that cause gastroenteritis in the community and in semi-closed institutions such as hospitals. During outbreaks, multiple units within a hospital are often affected, and a major question for control programs is: are the affected units part of the same outbreak or are they unrelated transmission events? In practice, investigators often assume a transmission link based on epidemiological observations, rather than a systematic approach to tracing transmission. Here, we present a combined molecular and statistical method for assessing: 1 whether observed clusters provide evidence of local transmission and 2 the probability that anecdotally|linked outbreaks truly shared a transmission event. Methods 76 healthcare associated outbreaks were observed in an active and prospective surveillance scheme of 15 hospitals in the county of Avon, England from April 2002 to March 2003. Viral RNA from 64 out of 76 specimens from distinct outbreaks was amplified by reverse transcription-PCR and was sequenced in the polymerase (ORF 1 and capsid (ORF 2 regions. The genetic diversity, at the nucleotide level, was analysed in relation to the epidemiological patterns. Results Two out of four genetic and epidemiological clusters of outbreaks were unlikely to have occurred by chance alone, thus suggesting local transmission. There was anecdotal epidemiological evidence of a transmission link among 5 outbreaks pairs. By combining this epidemiological observation with viral sequence data, the evidence of a link remained convincing in 3 of these pairs. These results are sensitive to prior beliefs of the strength of epidemiological evidence especially when the outbreak strains are common in the background population. Conclusion The evidence suggests that transmission between hospitals units does occur. Using the proposed criteria, certain hypothesized transmission links between outbreaks were supported while

  3. The Molecular Epidemiology of Chronic Aflatoxin Driven Impaired Child Growth

    Science.gov (United States)

    Turner, Paul Craig

    2013-01-01

    Aflatoxins are toxic secondary fungal metabolites that contaminate dietary staples in tropical regions; chronic high levels of exposure are common for many of the poorest populations. Observations in animals indicate that growth and/or food utilization are adversely affected by aflatoxins. This review highlights the development of validated exposure biomarkers and their use here to assess the role of aflatoxins in early life growth retardation. Aflatoxin exposure occurs in utero and continues in early infancy as weaning foods are introduced. Using aflatoxin-albumin exposure biomarkers, five major studies clearly demonstrate strong dose response relationships between exposure in utero and/or early infancy and growth retardation, identified by reduced birth weight and/or low HAZ and WAZ scores. The epidemiological studies include cross-sectional and longitudinal surveys, though aflatoxin reduction intervention studies are now required to further support these data and guide sustainable options to reduce the burden of exposure. The use of aflatoxin exposure biomarkers was essential in understanding the observational data reviewed and will likely be a critical monitor of the effectiveness of interventions to restrict aflatoxin exposure. Given that an estimated 4.5 billion individuals live in regions at risk of dietary contamination the public health concern cannot be over stated. PMID:24455429

  4. Molecular epidemiology of HIV-1 strains in the south-east and east of Turkey

    Institute of Scientific and Technical Information of China (English)

    Mustafa; Kemal; ?elen; Murat; Sayan; Tuba; Dal; Celal; Ayaz; Alicem; Tekin; Tuncer; ?zekinci; Suda; Tekin; Koruk; Tunga; Barcin; Recep; Tekin; Mehmet; Sinan; Dal; Sevgi; Kalkanl?

    2015-01-01

    Objective:To detect the subtype characterization and drug-resistant mutations in HIV-1 strains after the refugee movement from Syria to Turkey between 2011 and 2014 in south east border lines. Methods: A total of 65 patients were included in this study, of which 57(88%) patients were antiretroviral therapy-naive patients. HIV-1 RNA was detected and quantii ed by realtime PCR assay. HIV-1 subtypes and circulating recombinant forms(CRFs) were identii ed by phylogenetic analysis(neighbor-joining method), and drug-resistant mutations were analyzed.Results: Three major HIV groups were indicated. Two of these groups were located in subtype B. The other group showed heterogeneity. Subtype B(48/65, 73.8%), followed by CRFs(12/65, 18.5%) was the most common strain. Subtype of CRFs consisted of CRF01_AE(9/65, 13.8%) and CRF02_AG(3/65, 4.6%). Subtype C(1/65, 1.5%), sub-subtypes A1(2/65, 3.1%) and F1(2/65, 3.1%) were also detected with low prevalence. The rate of overall primary antiretroviral resistance was 4.9%(3/61). Drug-resistant rate for non-nucleoside reverse transcriptase inhibitors was 4.9%. The thymidine analogue mutation rate was 13.1%(8/61).Conclusions: HIV molecular epidemiology studies are necessary to determine transmission patterns and spread. Subtype B and CRF01_AE, CRF02_AG are the most prevalent strains in the south-east of Turkey. However, subtype C, sub-subtypes A1 and F1 are of low prevalence but persist in the south-east of Turkey. In the near future, changing of HIV epidemiology will be possible in Turkey due to migration movement in border lines and resistance testing will play an important role in HIV management.

  5. Molecular epidemiology of HIV-1 strains in the south-east and east of Turkey

    Institute of Scientific and Technical Information of China (English)

    Mustafa Kemal elen; Mehmet Sinan Dal; Sevgi Kalkanl; Murat Sayan; Tuba Dal; Celal Ayaz; Alicem Tekin; Tuncer zekinci; Suda Tekin Koruk; Tunga Barcin; Recep Tekin

    2015-01-01

    To detect the subtype characterization and drug-resistant mutations in HIV-1 strains after the refugee movement from Syria to Turkey between 2011 and 2014 in south east border lines. Methods: A total of 65 patients were included in this study, of which 57 (88%) patients were antiretroviral therapy-naive patients. HIV-1 RNA was detected and quantified by real-time PCR assay. HIV-1 subtypes and circulating recombinant forms (CRFs) were identified by phylogenetic analysis (neighbor-joining method), and drug-resistant mutations were analyzed. Results: Three major HIV groups were indicated. Two of these groups were located in subtype B. The other group showed heterogeneity. Subtype B (48/65, 73.8%), followed by CRFs (12/65, 18.5%) was the most common strain. Subtype of CRFs consisted of CRF01_AE (9/65, 13.8%) and CRF02_AG (3/65, 4.6%). Subtype C (1/65, 1.5%), sub-subtypes A1 (2/65, 3.1%) and F1 (2/65, 3.1%) were also detected with low prevalence. The rate of overall primary antiretroviral resistance was 4.9% (3/61). Drug-resistant rate for non-nucleoside reverse transcriptase inhibitors was 4.9%. The thymidine analogue mutation rate was 13.1% (8/61). Conclusions: HIV molecular epidemiology studies are necessary to determine transmission patterns and spread. Subtype B and CRF01_AE, CRF02_AG are the most prevalent strains in the south-east of Turkey. However, subtype C, sub-subtypes A1 and F1 are of low prevalence but persist in the south-east of Turkey. In the near future, changing of HIV epidemiology will be possible in Turkey due to migration movement in border lines and resistance testing will play an important role in HIV management.

  6. Zoonotic Potential and Molecular Epidemiology of Giardia Species and Giardiasis†

    OpenAIRE

    Feng, Yaoyu; Xiao, Lihua

    2011-01-01

    Summary: Molecular diagnostic tools have been used recently in assessing the taxonomy, zoonotic potential, and transmission of Giardia species and giardiasis in humans and animals. The results of these studies have firmly established giardiasis as a zoonotic disease, although host adaptation at the genotype and subtype levels has reduced the likelihood of zoonotic transmission. These studies have also identified variations in the distribution of Giardia duodenalis genotypes among geographic a...

  7. Typing methods used in the molecular epidemiology of microbial pathogens: a how-to guide.

    Science.gov (United States)

    Ranjbar, Reza; Karami, Ali; Farshad, Shohreh; Giammanco, Giovanni M; Mammina, Caterina

    2014-01-01

    Microbial typing is often employed to determine the source and routes of infections, confirm or rule out outbreaks, trace cross-transmission of healthcare-associated pathogens, recognize virulent strains and evaluate the effectiveness of control measures. Conventional microbial typing methods have occasionally been useful in describing the epidemiology of infectious diseases. However, these methods are generally considered too variable, labour intensive and time-consuming to be of practical value in epidemiological investigations. Moreover, these approaches have proved to be insufficiently discriminatory and poorly reproducible. DNA-based typing methods rely on the analysis of the genetic material of a microorganism. In recent years, several methods have been introduced and developed for investigation of the molecular epidemiology of microbial pathogens. Each of them has advantages and limitations that make them useful in some studies and restrictive in others. The choice of a molecular typing method therefore will depend on the skill level and resources of the laboratory and the aim and scale of the investigation. This study reviews the most popular DNA-based molecular typing methods used in the epidemiology of bacterial pathogens together with their advantages and limitations. PMID:24531166

  8. The changing epidemiology of Staphylococcus aureus bloodstream infection

    DEFF Research Database (Denmark)

    Galbraith, J.C.; Valiquette, G.; Kennedy, K.J.;

    2013-01-01

    Clin Microbiol Infect ABSTRACT: Although the epidemiology of Staphylococcus aureus bloodstream infection (BSI) has been changing, international comparisons are lacking. We sought to determine the incidence of S. aureus BSI and assess trends over time and by region. Population-based surveillance...... episodes of S. aureus BSI were identified. The overall annual incidence rate for S. aureus BSI was 26.1 per 100 000 population, and those for methicillin-sensitive S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA) were 24.2 and 1.9 per 100 000, respectively. Although the overall incidence...... of community-onset MSSA BSI (15.0 per 100 000) was relatively similar across regions, the incidence rates of hospital-onset MSSA (9.2 per 100 000), community-onset MRSA (1.0 per 100 000) and hospital-onset MRSA (0.8 per 100 000) BSI varied substantially. Whereas the overall incidence of S. aureus BSI did...

  9. Children with medical complexity: the change in the pediatric epidemiology

    Directory of Open Access Journals (Sweden)

    Rino Agostiniani

    2014-06-01

    Full Text Available In the last years, epidemiological landscape of pediatric illness is changed; we are facing a progressive raising of the number of children affected by chronic illness (children with special health care needs [CSHCN], mainly due to the amelioration in surviving and in care. These patients have become the majority of the inpatients in some specialist hospitals, like the Meyer Children’s Hospital (Florence, Italy, in 2012. One important group of CSHCN is represented by the children who are most medically fragile and have the most intensive health care needs (children with medical complexity [CMC]. In these patients, the complexity of the pathological framework frequently results in a plenty of visits and tests, with high risk of redundant and expensive cares. They also need outside support networks such as advocacy and accommodations at school, at home, in social life. The CMC needs specific skill and new strategies that could involve pediatricians in hospital as in home care. The professional competencies are ready but a clear and shared strategy is lacking. Proceedings of the 10th International Workshop on Neonatology · Cagliari (Italy · October 22nd-25th, 2014 · The last ten years, the next ten years in Neonatology Guest Editors: Vassilios Fanos, Michele Mussap, Gavino Faa, Apostolos Papageorgiou

  10. -Thalassaemia in Tunisia: some epidemiological and molecular data

    Indian Academy of Sciences (India)

    H. Siala; F. Ouali; T. Messaoud; A. Bibi; S. Fattoum

    2008-12-01

    Unlike the other haemoglobinopathies, few researches have been published concerning -thalassaemia in Tunisia. The aim of the present work is to acquire further data concerning -thalassaemia prevalence and molecular defects spectrum in Tunisia, by collecting and studying several kinds of samples carrying -thalassaemia. The first survey conducted on 529 cord blood samples using cellulose acetate electrophoresis, have displayed the prevalence of 7.38% Hb Bart’s carriers at birth. Molecular analyses were conducted by PCR and DNA sequencing on 20 families’ cases from the above survey carrying the Hb Bart’s at birth and on 10 Hb H diseased patients. The results showed six -globin gene molecular defects and were responsible for -thalassaemia: -3.7, - -MedI, TSaudi, cd23GAG \\to Stop2, Hb Greone Hart: 119CCT \\to TCT1 corresponding to 11 genotypes out of which two are responsible for Hb H disease (--Med/$-$3.7) and (TSaudi/TSaudi) and a newly described polymorphism: +6 → G. The geographical repartition of -thal carriers showed that the $-$3.7 deletion is distributed all over the country, respectively the HphI and TSaudi seem to be more frequent in the central region of the northeast region. The haematological and clinical data showed a moderate phenotype with a late age of diagnosis for Hb H disease. This work had permitted, in addition to an overview on -thalassaemia in the country, the optimization of protocols for -thalassaemia detection in our lab, allowing further investigations concerning phenotype–genotype correlation in sickle cell disease or -thalassaemia.

  11. First approach to molecular epidemiology of bovine tuberculosis in Colombia

    Directory of Open Access Journals (Sweden)

    Jimena Jojoa-Jojoa

    2015-12-01

    Full Text Available Objective. To investigate the presence of Mycobacterium bovis and other Mycobacterium species in samples of cattle and buffalo in Colombia, to start the molecular characterization of M. bovis in the country. Material and methods. 492 samples were collected from herds identified with the presence of infected animals through the PPD, by the Group of Bovine Tuberculosis ICA Colombian Agricultural Institute in eight departments of Colombia. Lymph nodes of head, thorax and abdomen, gross lesions of tissues with tuberculosis, nasal swabs, milk, blood and fresh cheeses were included. Samples were subjected to detection of Mycobacterium bovis and other mycobacteria by conventional microbiological analysis and PCR-6110 and spoligotyping molecular assays. Results. In the samples analyzed especially in lymph nodes, Mycobacterium bovis was demonstrated with genotypes reported and not previously reported in the world, as well as M. tuberculosis in Antioquia, Cundinamarca, Boyacá and Magdalena departments. Conclusions. In Colombia there are at least 7 genotypes of M. bovis that are infected and sick cattle and buffalo from four different departments becoming serious threat to public health.

  12. Epidemiological and molecular characteristics of meticillin-resistant Staphylococcus aureus in Turkey: A multicentre study.

    Science.gov (United States)

    Dündar, Devrim; Willke, Ayse; Sayan, Murat; Koc, Meliha Meric; Akan, Ozay Arıkan; Sumerkan, Bulent; Saltoglu, Nese; Yaman, Akgun; Ayaz, Celal; Koksal, Iftihar

    2016-09-01

    The aim of this study was to investigate the epidemiological and molecular features of clinical meticillin-resistant Staphylococcus aureus (MRSA) isolates in Turkey. MRSA isolates were collected from six regions of Turkey. The mecA and nuc genes were detected by PCR. Antimicrobial susceptibilities were determined by the disk diffusion method. Staphylococcal cassette chromosome mec (SCCmec) and staphylococcal protein A (spa) typing were performed by the sequencing method for 270 randomly selected MRSA isolates. The US Centers for Disease Control and Prevention (CDC) definition was used for epidemiological diagnosis of community-associated MRSA (CA-MRSA). Resistance rates of MRSA to ciprofloxacin, gentamicin, clindamycin, erythromycin, rifampicin, trimethoprim/sulfamethoxazole and tetracycline were 93.4%, 81.2%, 38.5%, 57.8%, 93.9%, 1.1% and 93.1%, respectively. The most frequent SCCmec type was SCCmec III (91.1%). SCCmec type IV was found in 5.2% of the isolates. The most frequent spa type was t030 (81.1%). Five isolates were CA-MRSA if only the epidemiological definition was used (5/725; 0.7%). Two isolates were defined as CA-MRSA both by epidemiological features and SCCmec typing (2/270; 0.7%). Of 14 SCCmec type IV isolates, 12 were not defined as CA-MRSA by epidemiological features. In conclusion, this is the most comprehensive multicentre study in Turkey investigating MRSA using both epidemiological and genotypic features. The CA-MRSA rate is low in Turkey. Combined use of epidemiological and genotypic methods is the most accurate approach for the diagnosis of CA-MRSA. PMID:27530838

  13. Molecular epidemiology of HIV-1 variants in the global AIDS pandemic: an update.

    Science.gov (United States)

    Thomson, Michael M; Nájera, Rafael

    2005-01-01

    The picture of HIV-1 genetic diversity in the global pandemic continues to evolve. Identification of new variants, including circulating and unique recombinant forms, recognition of new outbreaks and of changes in established epidemics, and characterization of growing numbers of full-length genomes provide a view of high dynamism and increasing complexity. The pervasive role of recombination as a major driving force in the generation of diversity in the HIV-1 pandemic is becoming evident, and is particularly visible in areas in which different genetic forms meet, referred to as "geographic recombination hotspots". The importance of superinfection and its impact on HIV-1 diversification and propagation is surfacing, although restrictions to superinfection are also apparent. Genetic diversity within subtypes is increasing over time and new geographically localized lineages deriving from point introductions are being recognized. Characterization of such variants may be of relevance to vaccine development and may allow the detection of intrasubtype recombination and superinfection. Recent studies supporting the correlation of HIV-1 clades to immune responses and to drug resistance-associated mutations lend increasing relevance to the role of molecular epidemiology as an essential tool in combating the AIDS pandemic. However, knowledge on the global HIV-1 genetic diversity and its implications is still far from adequate and a major scaling up of efforts is needed. PMID:16425961

  14. Conventional and molecular epidemiology of Tuberculosis in Manitoba

    Directory of Open Access Journals (Sweden)

    Hershfield Earl S

    2003-08-01

    Full Text Available Abstract Background To describe the demographic and geographic distribution of tuberculosis (TB in Manitoba, thus determining risk factors associated with clustering and higher incidence rates in distinct subpopulations. Methods Data from the Manitoba TB Registry was compiled to generate a database on 855 patients with tuberculosis and their contacts from 1992–1999. Recovered isolates of M. tuberculosis were typed by IS6110 restriction fragment length polymorphisms. Bivariate and multivariate logistic regression models were used to identify risk factors involved in clustering. Results A trend to clustering was observed among the Canadian-born treaty Aboriginal subgroup in contrast to the foreign-born. The dominant type, designated fingerprint type 1, accounts for 25.8% of total cases and 75.3% of treaty Aboriginal cases. Among type 1 patients residing in urban areas, 98.9% lived in Winnipeg. In rural areas, 92.8% lived on Aboriginal reserves. Statistical models revealed that significant risk factors for acquiring clustered tuberculosis are gender, age, ethnic origin and residence. Those at increased risk are: males (p p p p Conclusion Molecular typing of isolates in conjunction with contact tracing data supports the notion of the largest ongoing transmission of a single strain of TB within the treaty-status population of Canada recorded to date. This data demonstrates the necessity of continued surveillance of countries with low prevalence of the disease in order to determine and target high-risk populations for concentrated prevention and control measures.

  15. Clinical and molecular epidemiology of neonatal leukemia in Brazil.

    Science.gov (United States)

    Moura, Suellen Valadares; Andrade, Francianne; Magalhães, Isis Q; Costa, Imaruí; Silva, Denise Bousfield; D'Andrea, Maria Lydia; Pinheiro, Vitória P; Lee, Maria Lucia M; Werneck, Fernando; Emerenciano, Mariana; Pombo-de-Oliveira, Maria S

    2015-04-01

    The clinical and molecular findings of 77 cases of neonatal leukemia (NL) and 380 of infant leukemia (IL) were selected to distinguish features between NL and IL. Somatic gene mutations associated with acute leukemia including FLT3, RAS and PTPN11 were revisited. There were 42 cases of congenital leukemia associated with Down syndrome (DS) and 39 of these cases presented features of acute myeloid leukemia (AML)-M7. Twenty-seven of the DS cases underwent spontaneous remission and were reclassified as a transient myeloproliferative disorder. GATA1 mutations were found in 70% of these cases. In non-DS, frequent abnormalities were MLL rearrangements, mainly MLL-AFF1 in acute lymphoblastic leukemia and MLL-MLLT3 in AML. The FLT3 mutation was not found, while RAS (n = 4) and PTPN11 (n = 2) mutations were identified and reported for the first time in NL. There was substantial evidence to support that somatic abnormalities occur in utero. Thus, congenital leukemia is a good model for understanding leukemogenesis.

  16. Molecular epidemiology of Mycobacterium tuberculosis clinical isolates in Southwest Ireland.

    LENUS (Irish Health Repository)

    Ojo, Olabisi O

    2010-10-01

    Tuberculosis has had significant effects on Ireland over the past two centuries, causing persistently higher morbidity and mortality than in neighbouring countries until the last decade. This study describes the results of genotyping and drug susceptibility testing of 171 strains of Mycobacterium tuberculosis complex isolated between January 2004 and December 2006 in a region of Ireland centred on the city of Cork. Spoligotype comparisons were made with the SpolDB4 database and clustered 130 strains in 23 groups, forty-one strains showed unique Spoligotyping patterns. The commonest spoligotypes detected were ST0137 (X2) (16.9%), and ST0351 (15.8%) (\\'U\\' clade). The major spoligotype clades were X (26.2%), U (19.3%), T (15.2%), Beijing (5.9%), Haarlem (4.7%), LAM (4.1%), BOVIS (1.75%), with 12.9% unassigned strains. A 24-locus VNTR genotyping produced 15 clusters containing 49 isolates, with high discrimination index (HGDI>0.99). A combination of Spoligotyping and VNTR reduced the number of clustered isolates to 47 in 15 clusters (27.5%). This study identified ST351 as common among Irish nationals, and found a low rate of drug resistance with little evidence of transmission of drug resistant strains. Strain clustering was significantly associated with age under 55 years and Irish nationality. Only strains of Euro-American lineage formed clusters. Molecular typing did not completely coincide with the results of contact investigations.

  17. AN EPIDEMIOLOGY AND MOLECULAR GENETIC STUDY ON BREAST CANCER SUSCEPTIBILITY

    Institute of Scientific and Technical Information of China (English)

    贾卫华; 王继先; 李本孝; 李征

    2000-01-01

    Objectives. To investigate the genetic susceptibility for breast cancer of Chinese, a hospital-based case-control study, pedigree survey and molecular genetic study were conducted. Methods. Logistic regression model and stratification methods were used in the risk factors analysis. Li-Mantel art and Falconer methods were used to analyze the segregation ratio and heritability. Polymerase chain reaction (PCR) and polyacrylamide gel electrophoresis were used to detect AI, G-banding technique was used to detect the chromosome aberration of peripheral blood lymphocyte. Results. Family history of breast cancer is related to enhanced breast cancer risk significartly, OR is 3.905 ( 95 % CI = 1.079 ~ 14.13), and it widely interacts with other risk factors. Accumulative incidence of breast cancer in first degree relatives is 9.99%, which is larger than that in second, third degree and non-blood relatives. Segregation ratio is 0.021, heritability among first degree relatives is 35.6 ± 5.8%. Frequencies of LOH at BRCA1 and BRCA2 loci in sporadic breast cancer are 6.12% and 5.77% respectively. In the sibs, both of them show LOH at D13S173 locus, and high frequencies of chromosome aberrations were observed. Conclusions. Genetic susceptibility contributes to breast cancer occurrence of Chinese, and its racial variation may be one of the important reasons for the large difference of incidence between western and eastern countries.

  18. AN EPIDEMIOLOGY AND MOLECULAR GENETIC STUDY ON BREAST CANCER SUSCEPTIBILITY

    Institute of Scientific and Technical Information of China (English)

    贾卫华; 王继先; 李本孝; 李征

    2000-01-01

    Obieaites. To investigate the genetic susceptibility for breast cancer of Chinese, a hospital-besed case-control study, pedigree survey and molecular genetic study were conducted. Methods. Logistic regression model and stratification methods were used in the risk factors analysis. Li-Mantel-Gart and Falconer methods were used to analyze the segregation ratio and heritability. Polymemse chain reaction (PCR) and polyacrylamide gel electrophoresis were used to detect AI, G-banding technique was used to detect the chromosome aberration of peripheral blood lymphocyte. Results. Family history of breast cancer is related to enhanced breast cancer risk significantly, OR is 3.905(95% CI = 1.079—14.13), and it widely interacts with other risk factors. Accumulative incidence of breast cancer in first degree relatives is 9.99%, which is larger than that in second, third degree and non-blnod relatives. Segregation ratio is 0.021, heritability among first degree relatives is 35.6 ± 5.8%. Frequencies of LDH at BRCA1 and BRCA2 loci in sporadic breast cancer are 6.12% and 5.77% respectively. In the sibs, both of them show LOH at D13S173 locus, and high frequencies of chromosome abermtions were observed.Condusions. Genetic susceptibility contributes to breast cancer occurrence of Chinese, and its racial variation may be one of the important reasons for the large difference of incidence between western and eastern countries.

  19. Molecular epidemiology of childhood leukemia with emphasis on chemical exposures

    Energy Technology Data Exchange (ETDEWEB)

    Buffler, P.A.; Smith, M.T.; Wood, S. [Univ. of California, Berkeley, CA (United States); Reynolds, P. [California Dept. of Health Services, Emeryville, CA (United States)

    1996-12-31

    Developing markets in the Pacific Basin depend heavily on the production and export of consumer goods. The generation of hazardous waste as a by-product of industrial production can be linked to adverse health outcomes, such as childhood leukemia, in ways that are presently unknown. In California, exposures resulting from hazardous waste disposal are of concern in the etiology of childhood cancer. Approximately 63% of the 57 hazardous waste sites that the U.S. Environmental Protection Agency (USEPA) included in the national priority list under the Comprehensive Environmental Response, Compensation and Liability Act (CERCLA) statute were in the six-county San Francisco Bay area. This area includes California`s Silicon Valley, where a disproportionate majority of these sites are located. Although only one study links hazardous waste disposal to childhood leukemia evidence is accumulating that in utero and maternal pesticide exposures as well as chemical exposures during childhood are important in the etiology of childhood leukemia. This study investigates whether children with leukemia have common genetic changes, whether children with genetic changes experience common chemical exposures, and whether the occurrences of these genetic changes correspond to the same temporal sequence as exposure. The purpose of this paper is to describe the study design and report on the status of research activity. 10 refs., 1 fig., 3 tabs.

  20. Molecular Epidemiology of Plasmodium falciparum Malaria Outbreak, Tumbes, Peru, 2010-2012.

    Science.gov (United States)

    Baldeviano, G Christian; Okoth, Sheila Akinyi; Arrospide, Nancy; Gonzalez, Rommell V; Sánchez, Juan F; Macedo, Silvia; Conde, Silvia; Tapia, L Lorena; Salas, Carola; Gamboa, Dionicia; Herrera, Yeni; Edgel, Kimberly A; Udhayakumar, Venkatachalam; Lescano, Andrés G

    2015-05-01

    During 2010-2012, an outbreak of 210 cases of malaria occurred in Tumbes, in the northern coast of Peru, where no Plasmodium falciparum malaria case had been reported since 2006. To identify the source of the parasite causing this outbreak, we conducted a molecular epidemiology investigation. Microsatellite typing showed an identical genotype in all 54 available isolates. This genotype was also identical to that of parasites isolated in 2010 in the Loreto region of the Peruvian Amazon and closely related to clonet B, a parasite lineage previously reported in the Amazon during 1998-2000. These findings are consistent with travel history of index case-patients. DNA sequencing revealed mutations in the Pfdhfr, Pfdhps, Pfcrt, and Pfmdr1 loci, which are strongly associated with resistance to chloroquine and sulfadoxine/pyrimethamine, and deletion of the Pfhrp2 gene. These results highlight the need for timely molecular epidemiology investigations to trace the parasite source during malaria reintroduction events.

  1. Molecular epidemiology of Vibrio nigripulchritudo, a pathogen of cultured penaeid shrimp (Litopenaeus stylirostris) in New Caledonia.

    Science.gov (United States)

    Goarant, Cyrille; Reynaud, Yann; Ansquer, Dominique; de Decker, Sophie; Saulnier, Denis; le Roux, Frédérique

    2006-11-01

    A collection of 57 isolates of Vibrio nigripulchritudo from either diseased or healthy shrimp and from shrimp farms environment was studied in order to gain a better understanding of the epidemiology of this pathogen, notably isolated from two distinct shrimp disease complexes. Molecular typing using two different techniques, arbitrarily primed PCR (AP-PCR) and multi-locus sequence typing (MLST), studied together with experimental pathology data allowed a relevant epidemiological insight into this possibly emerging pathogen. Additionally, results obtained with the two molecular typing techniques were congruent and allowed discriminating the strains associated with the "Summer Syndrome" from strains isolated from other contexts, especially the other shrimp vibriosis "Syndrome 93". These results highlight that the "Summer Syndrome" is most probably caused by an emergent clonal pathogen that therefore deserves surveillance and that AP-PCR can satisfactorily be used for that purpose. PMID:16413158

  2. Searching PubMed for molecular epidemiology studies: the case of chromosome aberrations

    DEFF Research Database (Denmark)

    Ugolini, Donatella; Neri, Monica; Knudsen, Lisbeth E;

    2006-01-01

    to environmental pollutants. The search, done on the PubMed/MedLine database, was based on a strategy combining descriptors listed in the PubMed Medical Subject Headings (MeSH) Thesaurus and other available tools (free text or phrase search tools). 178 articles were retrieved by searching the period from January 1......The available tools for searching literature in the field of Molecular Epidemiology are largely unsatisfactory. To identify major problems in retrieving information on this discipline, we comment here on the results of a literature search on cytogenetic biomarkers in children exposed......, 1980 to November 30, 2004. Only 2 of the 178 articles were indexed by the MeSH term "Epidemiology, molecular" (introduced in 1994) and 30 of 178 by the MeSH term "Biological markers" (introduced in 1989). The case of chromosome aberration (CA) was emblematic of the problem: 44 of 78 articles (56...

  3. Epidemiology and molecular characterization of multidrug-resistant Gram-negative bacteria in Southeast Asia

    OpenAIRE

    Suwantarat, Nuntra; Carroll, Karen C.

    2016-01-01

    Background Multidrug-resistant Gram-negative bacteria (MDRGN), including extended-spectrum β-lactamases (ESBLs) and multidrug-resistant glucose-nonfermenting Gram-negative bacilli (nonfermenters), have emerged and spread throughout Southeast Asia. Methods We reviewed and summarized current critical knowledge on the epidemiology and molecular characterization of MDRGN in Southeast Asia by PubMed searches for publications prior to 10 March 2016 with the term related to “MDRGN definition” combin...

  4. The changing landscape of rabies epidemiology and control

    Directory of Open Access Journals (Sweden)

    Sarah Cleaveland

    2014-04-01

    Full Text Available Over the past 20 years, major progress has been made in our understanding of critical aspects of rabies epidemiology and control. This paper presents results of recent research, highlighting methodological advances that have been applied to burden of disease studies, rabies epidemiological modelling and rabies surveillance. These results contribute new insights and understanding with regard to the epidemiology of rabies and help to counteract misperceptions that currently hamper rabies control efforts in Africa. The conclusion of these analyses is that the elimination of canine rabies in Africa is feasible, even in wildlife-rich areas, through mass vaccination of domestic dogs and without the need for indiscriminate culling to reduce dog population density. Furthermore, the research provides valuable practical insights that support the operational planning and design of dog vaccination campaigns and rabies surveillance measures.

  5. Taxonomy and molecular epidemiology of Echinococcus granulosus sensu lato.

    Science.gov (United States)

    Romig, T; Ebi, D; Wassermann, M

    2015-10-30

    Echinococcus granulosus, formerly regarded as a single species with a high genotypic and phenotypic diversity, is now recognised as an assemblage of cryptic species, which differ considerably in morphology, development, host specificity (including infectivity/pathogenicity for humans) and other aspects. This diversity is reflected in the mitochondrial and nuclear genomes and has led to the construction of phylogenetic trees and hypotheses on the origin and geographic dispersal of various taxa. Based on phenotypic characters and gene sequences, E. granulosus (sensu lato) has by now been subdivided into E. granulosus sensu stricto (including the formerly identified genotypic variants G1-3), Echinococcus felidis (the former 'lion strain'), Echinococcus equinus (the 'horse strain', genotype G4), Echinococcus ortleppi (the 'cattle strain', genotype G5) and Echinococcus canadensis. The latter species, as recognised here, shows the highest diversity and is composed of the 'camel strain', genotype G6, the 'pig strain', genotype G7, and two 'cervid strains', genotypes G8 and G10. There is debate whether the closely related G6 and G7 should be placed in a separate species, but more morphological and biological data are needed to support or reject this view. In this classification, the application of rules for zoological nomenclature led to the resurrection of old species names, which had before been synonymised with E. granulosus. This nomenclatural subdivision of the agents of cystic echinococcosis (CE) may appear inconvenient for practical applications, especially because molecular tools are needed for identification of the cyst stage, and because retrospective data on 'E. granulosus' are now difficult to interpret without examination of voucher specimens. However, the increased awareness for the diversity of CE agents - now emphasised by species names rather than genotype numbers - has led to a large number of recent studies on this issue and a rapid increase of knowledge

  6. EPIDEMIOLOGY AND MOLECULAR TYPING OF BRUCELLA STRAINS CIRCULATING IN GEORGIA.

    Science.gov (United States)

    Sidamonidze, K; Ramishvili, M; Kalandadze, I; Tsereteli, D; Nikolich, M P

    2015-10-01

    In 2009-2013, 851 cases of brucellosis were registered in Georgia. Most cases of brucellosis were found in eastern Georgia (91.3% of cases). Mainly men were infected with brucellosis (81.0%).The age group with the most frequent cases of brucellosis is 30-59 years (48.5%). Brucellosis is rarely found among children(0-4 years - 2.0%, 5-14 years - 8.0%). Brucellosis cases were linked to professional activity; mainly by farmers (33.0% of those infected) and shepherds (27.0%). Biotyping Brucella by microbiological methods alone has limitations, so molecular typing was implemented in this study to confirm species. Isolates from human blood and ruminant milk or blood were identified by a bacteriological algorithm and confirmed by real-time PCR (Brucella T1, Idaho Technology). Species identity was confirmed using the AMOS conventional PCR assay, which differentiates four human pathogenic species but cannot recognize certain biovars within them. This gap was addressed by using more universal species-specific Single Nucleotide Polymorphism (SNP) assays. Real-time PCR was used to confirm 86 Brucella strains (48 human, 38 animal isolates) obtained 2009-2011. AMOS PCR supported the biochemical test results for 53 B. melitensis and four B. abortus strains, but not for 29 suspected B. abortus human and animal isolates. SNP typing of all 86 isolates supported the AMOS PCR results but also confirmed the species of the 29 strains not amplified by AMOS PCR. In 2009-2013 years the prevalence of brucellosis was still high. Nowadays cases of brucellosis are higher in the western part of Georgia than in the 1991-2005 period by a factor of 2.62. Brucellosis continues to be mainly an infection in males, because men are mostly engaged in sheep and cattle care. Combined AMOS PCR and SNP typing in this study provided the first genetic confirmation that both B. abortus and B. melitensis are actively circulating in humans and animals in Georgia. PMID:26483376

  7. Taxonomy and molecular epidemiology of Echinococcus granulosus sensu lato.

    Science.gov (United States)

    Romig, T; Ebi, D; Wassermann, M

    2015-10-30

    Echinococcus granulosus, formerly regarded as a single species with a high genotypic and phenotypic diversity, is now recognised as an assemblage of cryptic species, which differ considerably in morphology, development, host specificity (including infectivity/pathogenicity for humans) and other aspects. This diversity is reflected in the mitochondrial and nuclear genomes and has led to the construction of phylogenetic trees and hypotheses on the origin and geographic dispersal of various taxa. Based on phenotypic characters and gene sequences, E. granulosus (sensu lato) has by now been subdivided into E. granulosus sensu stricto (including the formerly identified genotypic variants G1-3), Echinococcus felidis (the former 'lion strain'), Echinococcus equinus (the 'horse strain', genotype G4), Echinococcus ortleppi (the 'cattle strain', genotype G5) and Echinococcus canadensis. The latter species, as recognised here, shows the highest diversity and is composed of the 'camel strain', genotype G6, the 'pig strain', genotype G7, and two 'cervid strains', genotypes G8 and G10. There is debate whether the closely related G6 and G7 should be placed in a separate species, but more morphological and biological data are needed to support or reject this view. In this classification, the application of rules for zoological nomenclature led to the resurrection of old species names, which had before been synonymised with E. granulosus. This nomenclatural subdivision of the agents of cystic echinococcosis (CE) may appear inconvenient for practical applications, especially because molecular tools are needed for identification of the cyst stage, and because retrospective data on 'E. granulosus' are now difficult to interpret without examination of voucher specimens. However, the increased awareness for the diversity of CE agents - now emphasised by species names rather than genotype numbers - has led to a large number of recent studies on this issue and a rapid increase of knowledge

  8. Molecular epidemiology of mastitis pathogens of dairy cattle and comparative relevance to humans.

    Science.gov (United States)

    Zadoks, Ruth N; Middleton, John R; McDougall, Scott; Katholm, Jorgen; Schukken, Ynte H

    2011-12-01

    Mastitis, inflammation of the mammary gland, can be caused by a wide range of organisms, including gram-negative and gram-positive bacteria, mycoplasmas and algae. Many microbial species that are common causes of bovine mastitis, such as Escherichia coli, Klebsiella pneumoniae, Streptococcus agalactiae and Staphylococcus aureus also occur as commensals or pathogens of humans whereas other causative species, such as Streptococcus uberis, Streptococcus dysgalactiae subsp. dysgalactiae or Staphylococcus chromogenes, are almost exclusively found in animals. A wide range of molecular typing methods have been used in the past two decades to investigate the epidemiology of bovine mastitis at the subspecies level. These include comparative typing methods that are based on electrophoretic banding patterns, library typing methods that are based on the sequence of selected genes, virulence gene arrays and whole genome sequencing projects. The strain distribution of mastitis pathogens has been investigated within individual animals and across animals, herds, countries and host species, with consideration of the mammary gland, other animal or human body sites, and environmental sources. Molecular epidemiological studies have contributed considerably to our understanding of sources, transmission routes, and prognosis for many bovine mastitis pathogens and to our understanding of mechanisms of host-adaptation and disease causation. In this review, we summarize knowledge gleaned from two decades of molecular epidemiological studies of mastitis pathogens in dairy cattle and discuss aspects of comparative relevance to human medicine.

  9. Molecular Epidemiology of Human Rhinoviruses and Enteroviruses Highlights Their Diversity in Sub-Saharan Africa

    Directory of Open Access Journals (Sweden)

    Arnaud G. L’Huillier

    2015-12-01

    Full Text Available Human rhinoviruses (HRVs and enteroviruses (HEVs belong to the Enterovirus genus and are the most frequent cause of infection worldwide, but data on their molecular epidemiology in Africa are scarce. To understand HRV and HEV molecular epidemiology in this setting, we enrolled febrile pediatric patients participating in a large prospective cohort assessing the causes of fever in Tanzanian children. Naso/oropharyngeal swabs were systematically collected and tested by real-time RT-PCR for HRV and HEV. Viruses from positive samples were sequenced and phylogenetic analyses were then applied to highlight the HRV and HEV types as well as recombinant or divergent strains. Thirty-eight percent (378/1005 of the enrolled children harboured an HRV or HEV infection. Although some types were predominant, many distinct types were co-circulating, including a vaccinal poliovirus, HEV-A71 and HEV-D68. Three HRV-A recombinants were identified: HRV-A36/HRV-A67, HRV-A12/HRV-A67 and HRV-A96/HRV-A61. Four divergent HRV strains were also identified: one HRV-B strain and three HRV-C strains. This is the first prospective study focused on HRV and HEV molecular epidemiology in sub-Saharan Africa. This systematic and thorough large screening with careful clinical data management confirms the wide genomic diversity of these viruses, brings new insights about their evolution and provides data about associated symptoms.

  10. Molecular epidemiology of seal parvovirus, 1988-2014.

    Science.gov (United States)

    Bodewes, Rogier; Hapsari, Rebriarina; Rubio García, Ana; Sánchez Contreras, Guillermo J; van de Bildt, Marco W G; de Graaf, Miranda; Kuiken, Thijs; Osterhaus, Albert D M E

    2014-01-01

    A novel parvovirus was discovered recently in the brain of a harbor seal (Phoca vitulina) with chronic meningo-encephalitis. Phylogenetic analysis of this virus indicated that it belongs to the genus Erythroparvovirus, to which also human parvovirus B19 belongs. In the present study, the prevalence, genetic diversity and clinical relevance of seal parvovirus (SePV) infections was evaluated in both harbor and grey seals (Halichoerus grypus) that lived in Northwestern European coastal waters from 1988 to 2014. To this end, serum and tissue samples collected from seals were tested for the presence of seal parvovirus DNA by real-time PCR and the sequences of the partial NS gene and the complete VP2 gene of positive samples were determined. Seal parvovirus DNA was detected in nine (8%) of the spleen tissues tested and in one (0.5%) of the serum samples tested, including samples collected from seals that died in 1988. Sequence analysis of the partial NS and complete VP2 genes of nine SePV revealed multiple sites with nucleotide substitutions but only one amino acid change in the VP2 gene. Estimated nucleotide substitution rates per year were 2.00 × 10(-4) for the partial NS gene and 1.15 × 10(-4) for the complete VP2 gene. Most samples containing SePV DNA were co-infected with phocine herpesvirus 1 or PDV, so no conclusions could be drawn about the clinical impact of SePV infection alone. The present study is one of the few in which the mutation rates of parvoviruses were evaluated over a period of more than 20 years, especially in a wildlife population, providing additional insights into the genetic diversity of parvoviruses.

  11. Molecular epidemiology of seal parvovirus, 1988-2014.

    Directory of Open Access Journals (Sweden)

    Rogier Bodewes

    Full Text Available A novel parvovirus was discovered recently in the brain of a harbor seal (Phoca vitulina with chronic meningo-encephalitis. Phylogenetic analysis of this virus indicated that it belongs to the genus Erythroparvovirus, to which also human parvovirus B19 belongs. In the present study, the prevalence, genetic diversity and clinical relevance of seal parvovirus (SePV infections was evaluated in both harbor and grey seals (Halichoerus grypus that lived in Northwestern European coastal waters from 1988 to 2014. To this end, serum and tissue samples collected from seals were tested for the presence of seal parvovirus DNA by real-time PCR and the sequences of the partial NS gene and the complete VP2 gene of positive samples were determined. Seal parvovirus DNA was detected in nine (8% of the spleen tissues tested and in one (0.5% of the serum samples tested, including samples collected from seals that died in 1988. Sequence analysis of the partial NS and complete VP2 genes of nine SePV revealed multiple sites with nucleotide substitutions but only one amino acid change in the VP2 gene. Estimated nucleotide substitution rates per year were 2.00 × 10(-4 for the partial NS gene and 1.15 × 10(-4 for the complete VP2 gene. Most samples containing SePV DNA were co-infected with phocine herpesvirus 1 or PDV, so no conclusions could be drawn about the clinical impact of SePV infection alone. The present study is one of the few in which the mutation rates of parvoviruses were evaluated over a period of more than 20 years, especially in a wildlife population, providing additional insights into the genetic diversity of parvoviruses.

  12. Epidemiology.

    Science.gov (United States)

    Walsh, Kyle M; Ohgaki, Hiroko; Wrensch, Margaret R

    2016-01-01

    More than 250,000 new cases of primary malignant brain tumors are diagnosed annually worldwide, 77% of which are gliomas. A small proportion of gliomas are caused by the inheritance of rare high-penetrance genetic variants or high-dose radiation. Since 2009, inherited genetic variants in 10 regions near eight different genes have been consistently associated with glioma risk via genome-wide association studies. Most of these variants increase glioma risk by 20-40%, but two have higher relative risks. One on chromosome 8 increases risk of IDH-mutated gliomas sixfold and another that affects TP53 function confers a 2.5-fold increased risk of glioma. Functions of some of the other risk variants are known or suspected, but future research will determine functions of other risk loci. Recent progress also has been made in defining subgroups of glioma based on acquired alterations within tumors. Allergy history has been consistently associated with reduced glioma risk, though the mechanisms have not yet been clarified. Future studies will need to be large enough so that environmental and constitutive genetic risk factors can be examined within molecularly defined, etiologically homogeneous subgroups.

  13. Paper vs. electrons. Epidemiologic publishing in a changing world.

    Science.gov (United States)

    Rothenberg; Frank; Fitzmaurice

    2000-10-01

    PURPOSE: To present the parallel histories of epidemiologic and electronic publishing and consider positive and negative factors that might affect their amalgam.METHODS: We performed a quantitative assessment of the arc of epidemiologic publication from 1966-1999, using major self-designated epidemiologic journals as a sample, and of scholarly electronic publication from 1991-1997, based on current literature review. We use an online, paperless journal as a case study, and review selected information-technology opinion in the area.RESULTS: By traditional standards, growth in epidemiologic publication has been considerable, with the addition of six new journals since 1966. In contrast, scholarly electronic publication for the period 1991-1997 grew from 27 to 2459 journals (not all exclusively online). Positive features of electronic publishing include flexibility, shortened time to publication, freedom from fixed publication date, diversity in presentation, and instant linkage to relevant material. A case study of a new online journal illustrates the substantive power of the medium. Negative factors include restriction (or unrestricted expansion) of the audience, the potential for hasty peer review, pitfalls in establishing credibility, an emphasis on style over content, technologic dependence, and additions to the information explosion. Relative cost and archiving are still debated. In assessing the pros and cons, it is important to distinguish electronic mechanisms that facilitate publication from electronic publishing, and to appreciate the difference between moving an existing journal to the electronic medium, and creating a new online journal.CONCLUSIONS: The movement from print to internet is probably inexorable, but a headlong rush may be ill-advised. Several models for dual publishing now exist, with the expectation that many, including the journals that serve epidemiology, will do so. The ultimate configuration is difficult to predict, but likely to be

  14. Molecular epidemiology and phylogeny of Nipah virus infection: A mini review.

    Science.gov (United States)

    Angeletti, Silvia; Lo Presti, Alessandra; Cella, Eleonora; Ciccozzi, Massimo

    2016-07-01

    Nipah virus (NiV) is a member of the genus Henipavirus of the family Paramyxoviridae, characterized by high pathogenicity and endemic in South Asia. It is classified as a Biosafety Level-4 (BSL-4) agent. The case-fatality varies from 40% to 70% depending on the severity of the disease and on the availability of adequate healthcare facilities. At present no antiviral drugs are available for NiV disease and the treatment is just supportive. Phylogenetic and evolutionary analyses can be used to help in understanding the epidemiology and the temporal origin of this virus. This review provides an overview of evolutionary studies performed on Nipah viruses circulating in different countries. Thirty phylogenetic studies have been published from 2000 to 2015 years, searching on pub-med using the key words 'Nipah virus AND phylogeny' and twenty-eight molecular epidemiological studies from 2006 to 2015 have been performed, typing the key words 'Nipah virus AND molecular epidemiology'. Overall data from the published study demonstrated as phylogenetic and evolutionary analysis represent promising tools to evidence NiV epidemics, to study their origin and evolution and finally to act with effective preventive measure. PMID:27393089

  15. Molecular Epidemiologic Typing Systems of Bacterial Pathogens: Current Issues and Perpectives

    Directory of Open Access Journals (Sweden)

    Marc J Struelens

    1998-09-01

    Full Text Available The epidemiologic typing of bacterial pathogens can be applied to answer a number of different questions: in case of outbreak, what is the extent and mode of transmission of epidemic clone(s ? In case of long-term surveillance, what is the prevalence over time and the geographic spread of epidemic and endemic clones in the population? A number of molecular typing methods can be used to classify bacteria based on genomic diversity into groups of closely-related isolates (presumed to arise from a common ancestor in the same chain of transmission and divergent, epidemiologically-unrelated isolates (arising from independent sources of infection. Ribotyping, IS-RFLP fingerprinting, macrorestriction analysis of chromosomal DNA and PCR-fingerprinting using arbitrary sequence or repeat element primers are useful methods for outbreak investigations and regional surveillance. Library typing systems based on multilocus sequence-based analysis and strain-specific probe hybridization schemes are in development for the international surveillance of major pathogens like Mycobacterium tuberculosis. Accurate epidemiological interpretation of data obtained with molecular typing systems still requires additional research on the evolution rate of polymorphic loci in bacterial pathogens.

  16. Molecular epidemiology of isolates of the Cryptococcus neoformans species complex from Spain.

    Science.gov (United States)

    Frasés, Susana; Ferrer, Consuelo; Sánchez, Manuel; Colom-Valiente, María Francisca

    2009-06-30

    To study genetic diversity of Cryptococcus neoformans species complex in Spain, 97 isolates of the yeast recovered from human, animal and environmental samples have been analysed using three molecular epidemiological techniques. One of these, URA5 gene fragment length polymorphism (RFLP) analysis, has been previously described as a molecular epidemiology tool. Thus, standard profiles and reference strains have been defined for it. In addition, 5S rDNA/IGS RFLP and [GACA](4) microsatellite PCR fingerprinting were also used. Our results show five of the previously defined URA5 genotypes with a high frequency (33%) of the VNI type, which is in concordance with other studies. The high presence of VNIII pattern (28.9%) among our strains is remarkable and could be a specific feature of the isolates from our country. 5S rDNA/IGS RFLP showed a low intra-species discriminative power. Three different molecular profiles (S1-3), which showed a good correlation with the different species, varieties and genotypes, were obtained. [GACA](4) microsatellite PCR-fingerprinting analysis showed a high variability of patterns among the studied strains. Molecular profiles represented in a dendrogram clustered strains in four main groups related with the source of the yeast and also in concordance with some of the described genotypes (VNI-IV and VGI). PMID:19631160

  17. The changing epidemiology of smoking and lung cancer histology.

    OpenAIRE

    Wynder, E. L.; Muscat, J E

    1995-01-01

    In 1950, the first large-scale epidemiological studies demonstrated that lung cancer is causatively associated with cigarette smoking, a finding subsequently confirmed by the Royal College of Physicians in London, the U.S. Surgeon General, and the World Health Organization. Although cigarette consumption has gradually decreased in the United States from a high of about 3800 cigarettes per adult per year in 1965 to about 2800 cigarettes in 1993, death from lung cancer has reached a high among ...

  18. Epidemiological and molecular approaches for management of a measles outbreak in Liguria, Italy.

    Science.gov (United States)

    Orsi, A; Alicino, C; Patria, A G; Parodi, V; Carloni, R; Turello, V; Comaschi, M; Moscatelli, P; Orengo, G; Martini, M; De Florentiis, D

    2010-06-01

    Since March 2010 a measles outbreak has been occurred in Genoa, Liguria, an administrative Region in Northern Italy. Epidemiological and molecular data on the outbreak, obtained from the passive mandatory notification system, the laboratory surveillance and an innovative syndrome surveillance system, were investigated. Overall 39 cases were reported in the urban area. Information about demography, vaccination status, hospitalization and geographic distribution of measles cases are available. 19 cases (48.7%) were laboratory-confirmed and were characterized by sequence analysis: 18 strains belonged to genotype D8, so identifying a new measles variant within the Liguria population. Adopted control measures seem to have limited viral circulation. The outbreak allowed to test the efficacy of the 3 surveillance systems active in Liguria, highlighting their advantages and some important limitations. More efforts are needed to collect and integrate any epidemiological and virological available data in order to better describe the local measles transmission dynamics.

  19. Molecular epidemiology of Mannheimia haemolytica and Mannheimia glucosida associated with ovine mastitis.

    Science.gov (United States)

    Omaleki, Lida; Browning, Glenn F; Allen, Joanne L; Barber, Stuart R

    2012-07-01

    While Mannheimia haemolytica and Mannheimia glucosida have been recognized as causes of intramammary infection in sheep, there has been no investigation of the epidemiology of the strains involved. Pulsed field gel electrophoresis was used to study the molecular epidemiology of isolates of these 2 species associated with ovine mastitis. Ten distinct strains were recognized among 12 M. haemolytica isolates, and 7 distinct strains among 13 M. glucosida isolates. The results demonstrate a high diversity of isolates with the ability to cause ovine mastitis. However, the presence of some identical isolates may suggest the possibility of horizontal transmission of these species in some flocks, possibly through lamb sucking, and/or differences in the capacity of some isolates to cause mastitis in sheep. PMID:22621951

  20. Molecular Epidemiology of Norovirus in Outbreaks of Gastroenteritis in Southwest Germany from 2001 to 2004

    Science.gov (United States)

    Ike, Anthony C.; Brockmann, Stefan O.; Hartelt, Kathrin; Marschang, Rachel E.; Contzen, Matthias; Oehme, Rainer M.

    2006-01-01

    The identification and molecular epidemiology of norovirus in outbreaks of gastroenteritis were studied during a 3-year period in Germany. Specimens (n = 316) from 159 nonbacterial gastroenteritis outbreaks from March 2001 to June 2004 were analyzed for the presence of noroviruses by reverse transcriptase PCR. Outbreaks were most frequent in elderly people's homes and care centers (43%), followed by hospitals (24%). Molecular analyses of strains from 148 outbreaks showed that there were up to 12 genotypes involved in the outbreaks. Genogroup II noroviruses were responsible for 95% of the outbreaks. Cocirculation of more than one strain in the same outbreak and cocirculation of genogroup I and II strains in the same place were observed. Genogroup II4 (Grimsby-like) was the most prevalent strain, accounting for 48% and 67% of the outbreaks in 2002 and 2003, respectively. The genogroup IIb (Castell/Suria) genotype was observed in all the years of the study. Epidemiological and molecular data indicated that there was a major shift of the predominant strain that coincided with the appearance of a new variant of genogroup II4 in 2002. By the application of reverse transcriptase PCR, this study has demonstrated the importance and dynamism of noroviruses in Germany. PMID:16597849

  1. Molecular epidemiological analysis of three hepatitis C virus outbreaks in Jammu and Kashmir State, India.

    Science.gov (United States)

    Chadha, Sanjim; Sharma, Uma; Chaudhary, Artee; Prakash, Charu; Gupta, Sunil; Venkatesh, S

    2016-08-01

    Outbreaks of hepatitis C virus (HCV) infection are associated with unsafe injection practices, intravenous drug abuse and other exposure to blood and body fluids. We report here three outbreaks of HCV infection from Jammu and Kashmir (J&K) State, India, which occurred over a period of 3 years and in which molecular epidemiological investigations identified a presumptive common source of infection, most likely a single healthcare venue. Representative blood samples collected from cases of hepatitis C were sent to the National Centre for Disease Control (NCDC) for molecular characterization. These samples were positive by HCV ELISA. Subsequently, specimens were also tested for the presence of HCV RNA by RT-PCR. Sequencing was carried out for all positive samples. A total of 812 cases were laboratory confirmed by HCV ELISA; a total of 115 samples were sent to the NCDC for RT-PCR, and 77 were positive. Subtype 3a of HCV was found in all samples from Anantnag (February 2013); and for subtype 3b, in all samples from Srinagar (May 2015). Subtypes 3a and 3g were identified from two samples from the Kulgam outbreak (July 2014). A detailed epidemiological investigation should be conducted whenever a cluster of HCV cases is revealed, as this potentially allows for the identification of larger outbreaks. Epidemiological investigations of outbreaks should be further supported by inclusion of molecular tests. Efforts to limit therapeutic injections to only those cases having strong medical/surgical indications and to restrict the use of non-sterile needles are essential to prevent transmission of HCV.

  2. Molecular Epidemiology of Entamoeba: First Description of Entamoeba moshkovskii in a Rural Area from Central Colombia.

    Directory of Open Access Journals (Sweden)

    Myriam Consuelo López

    Full Text Available Entamoeba histolytica, E. dispar and E. moshkovskii are the most frequent species described in human infection where E. histolytica is the only true pathogen. The epidemiology of this infection is complex due to the absence of a routine exam that allows a correct discrimination of the Entamoeba species complex. Therefore, molecular methods appear as the unique epidemiological tool to accomplish the species discrimination. Herein, we conducted a cross-sectional study to determine the frequency of Entamoeba species infections in a group of asymptomatic individuals from a rural area in central Colombia.A total of 181 fecal samples from asymptomatic children under 16 years old from the hamlet La Vírgen, Cundinamarca (Colombia that voluntarily accepted to participate in the study were collected. The fecal samples were examined by light microscopy and DNA-extracted, subsequently submitted to molecular discrimination of E. dispar/E. histolytica/E. moshkovskii infection based on a multiplex PCR assay targeting the 18S rRNA fragment. To confirm the species description, twenty samples were randomly submitted to DNA sequencing of the aforementioned fragment. By direct microscopic examination, frequency of the complex E. histolytica/E. dispar/E. moshkovskii was 18.8% (34/181. PCR showed a frequency of 49.1% (89/181, discriminated as 23.2% (42/181 that were positive for E. dispar, 25.4% (46/181 for E. moshkovskii and 0.55% (1/ 181 for E. histolytica. Also, mixed infections were detected between E. dispar and E. moshkovskii at 4.42% (8/181 of the samples. Molecular barcoding confirmed the diagnosis depicted by the multiplex PCR assay.This is the first description of E. moshkovskii in Colombia and the second report in South-America to our knowledge. Our results suggest the need to unravel the true epidemiology of Entamoeba infections around the world, including the real pathogenic role that E. moshkovskii may have.

  3. Molecular epidemiology of clonal diploids: a quick overview and a short DIY (do it yourself) notice.

    Science.gov (United States)

    De Meeûs, Thierry; Lehmann, Laurent; Balloux, François

    2006-03-01

    In this short review we report the basic notions needed for understanding the population genetics of clonal diploids. We focus on the consequences of clonality on the distribution of genetic diversity within individuals, between individuals and between populations. We then summarise how to detect clonality in mainly sexual populations, conversely, how to detect sexuality in mainly clonal populations and also how genetic differentiation between populations is affected by clonality in diploids. This information is then used for building recipes on how to analyse and interpret genetic polymorphism data in molecular epidemiology studies of clonal diploids. PMID:16290062

  4. Molecular epidemiology of current classical swine fever virus isolates of wild boar in Germany

    DEFF Research Database (Denmark)

    Leifer, I; Hoffmann, B; Höper, D;

    2010-01-01

    Classical swine fever (CSF) has caused significant economic losses in industrialized pig production, and is still present in some European countries. Recent CSF outbreaks in Europe were mainly associated with strains of genogroup 2 (subgroup 2.3). Although there are extensive datasets regarding 2.......3 strains, there is very little information available on longer fragments or whole classical swine fever virus (CSFV) genomes. Furthermore, there are no detailed analyses of the molecular epidemiology of CSFV wild boar isolates available. Nevertheless, complete genome sequences are supportive...

  5. Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees.

    Science.gov (United States)

    Kenah, Eben; Britton, Tom; Halloran, M Elizabeth; Longini, Ira M

    2016-04-01

    Recent work has attempted to use whole-genome sequence data from pathogens to reconstruct the transmission trees linking infectors and infectees in outbreaks. However, transmission trees from one outbreak do not generalize to future outbreaks. Reconstruction of transmission trees is most useful to public health if it leads to generalizable scientific insights about disease transmission. In a survival analysis framework, estimation of transmission parameters is based on sums or averages over the possible transmission trees. A phylogeny can increase the precision of these estimates by providing partial information about who infected whom. The leaves of the phylogeny represent sampled pathogens, which have known hosts. The interior nodes represent common ancestors of sampled pathogens, which have unknown hosts. Starting from assumptions about disease biology and epidemiologic study design, we prove that there is a one-to-one correspondence between the possible assignments of interior node hosts and the transmission trees simultaneously consistent with the phylogeny and the epidemiologic data on person, place, and time. We develop algorithms to enumerate these transmission trees and show these can be used to calculate likelihoods that incorporate both epidemiologic data and a phylogeny. A simulation study confirms that this leads to more efficient estimates of hazard ratios for infectiousness and baseline hazards of infectious contact, and we use these methods to analyze data from a foot-and-mouth disease virus outbreak in the United Kingdom in 2001. These results demonstrate the importance of data on individuals who escape infection, which is often overlooked. The combination of survival analysis and algorithms linking phylogenies to transmission trees is a rigorous but flexible statistical foundation for molecular infectious disease epidemiology. PMID:27070316

  6. Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees.

    Science.gov (United States)

    Kenah, Eben; Britton, Tom; Halloran, M Elizabeth; Longini, Ira M

    2016-04-01

    Recent work has attempted to use whole-genome sequence data from pathogens to reconstruct the transmission trees linking infectors and infectees in outbreaks. However, transmission trees from one outbreak do not generalize to future outbreaks. Reconstruction of transmission trees is most useful to public health if it leads to generalizable scientific insights about disease transmission. In a survival analysis framework, estimation of transmission parameters is based on sums or averages over the possible transmission trees. A phylogeny can increase the precision of these estimates by providing partial information about who infected whom. The leaves of the phylogeny represent sampled pathogens, which have known hosts. The interior nodes represent common ancestors of sampled pathogens, which have unknown hosts. Starting from assumptions about disease biology and epidemiologic study design, we prove that there is a one-to-one correspondence between the possible assignments of interior node hosts and the transmission trees simultaneously consistent with the phylogeny and the epidemiologic data on person, place, and time. We develop algorithms to enumerate these transmission trees and show these can be used to calculate likelihoods that incorporate both epidemiologic data and a phylogeny. A simulation study confirms that this leads to more efficient estimates of hazard ratios for infectiousness and baseline hazards of infectious contact, and we use these methods to analyze data from a foot-and-mouth disease virus outbreak in the United Kingdom in 2001. These results demonstrate the importance of data on individuals who escape infection, which is often overlooked. The combination of survival analysis and algorithms linking phylogenies to transmission trees is a rigorous but flexible statistical foundation for molecular infectious disease epidemiology.

  7. Molecular epidemiology of Acinetobacter baumannii in central intensive care unit in Kosova teaching hospital

    Directory of Open Access Journals (Sweden)

    Lul Raka

    2009-12-01

    Full Text Available Infections caused by bacteria of genus Acinetobacter pose a significant health care challenge worldwide. Information on molecular epidemiological investigation of outbreaks caused by Acinetobacter species in Kosova is lacking. The present investigation was carried out to enlight molecular epidemiology of Acinetobacterbaumannii in the Central Intensive Care Unit (CICU of a University hospital in Kosova using pulse field gel electrophoresis (PFGE. During March - July 2006, A. baumannii was isolated from 30 patients, of whom 22 were infected and 8 were colonised. Twenty patients had ventilator-associated pneumonia, one patient had meningitis, and two had coinfection with bloodstream infection and surgical site infection. The most common diagnoses upon admission to the ICU were politrauma and cerebral hemorrhage. Bacterial isolates were most frequently recovered from endotracheal aspirate (86.7%. First isolation occurred, on average, on day 8 following admission (range 1-26 days. Genotype analysis of A. baumannii isolates identified nine distinct PFGE patterns, with predominance of PFGE clone E represented by isolates from 9 patients. Eight strains were resistant to carbapenems. The genetic relatedness of Acinetobacter baumannii was high, indicating cross-transmission within the ICU setting. These results emphasize the need for measures to prevent nosocomial transmission of A. baumannii in ICU.

  8. Molecular epidemiology of Staphylococcus saprophyticus isolated from women with uncomplicated community-acquired urinary tract infection.

    Science.gov (United States)

    Widerström, Micael; Wiström, Johan; Ferry, Sven; Karlsson, Carina; Monsen, Tor

    2007-05-01

    Staphylococcus saprophyticus is a common cause of urinary tract infections (UTIs) in women. Little is known about the molecular epidemiology of S. saprophyticus UTIs. In the current study, we compared 76 isolates of S. saprophyticus prospectively isolated from women with uncomplicated UTI participating in a randomized placebo-controlled treatment trial performed in northern Sweden from 1995 to 1997 with 50 strains obtained in 2006 from five different locations in northern Europe with pulsed-field gel electrophoresis (PFGE). The aim was to elucidate the molecular epidemiology of this uropathogenic species and to investigate whether specific clones are associated with UTI in women. A total of 47 different PFGE profiles were detected among the 126 analyzed isolates. Ten clusters consisting of 5 to 12 isolates each showing PFGE DNA similarity of >85% were identified. Several clusters of genetically highly related isolates were detected in the original trial as well as among isolates obtained during 2006 from different locations. In the original trial, clonal persistence was found among 16 of 21 (76%) patients examined in the placebo group at follow-up 8 to 10 days after inclusion, indicating a low spontaneous short-time bacteriological cure rate. We conclude that multiple clones of S. saprophyticus were causing lower UTIs in women. The result suggests that some human-pathogenic clones of S. saprophyticus are spread over large geographical distances and that such clones may persist over long periods of time.

  9. Genetic characterisation and molecular epidemiology of Ascaris spp. from humans and pigs in Brazil.

    Science.gov (United States)

    Iñiguez, Alena M; Leles, Daniela; Jaeger, Lauren H; Carvalho-Costa, Filipe A; Araújo, Adauto

    2012-10-01

    The molecular epidemiology of Ascaris spp. of human and pig origin has been studied as a means to assess the potential of pigs as reservoirs for human ascariasis. In this study, human (H) and pig (P) Ascaris spp. haplotypes from two Brazilian regions were characterised based on two mitochondrial genes, nad1 and cox1. The results show six haplotypes of the cox1 gene, with two haplotypes (H9P9 and P3) corresponding to haplotypes previously characterised in China. Because P3 was found in humans in this study, it was designated as H14P3. Furthermore, five new Ascaris spp. nad1 haplotypes from humans (H12-H16) and five from pigs (P16-P20) were observed, with one being highly frequent and present in both hosts, here designated as H12P17. Phylogenetic and network analysis demonstrated that the molecular epidemiology of Ascaris spp. in Brazil is driven by the globally distributed haplotypes cox1 H14P3 and nad1 H12P17. In conclusion, in this study genetic characterisation of Ascaris spp. showed that humans and pigs share common haplotypes that are also present in two widely separated geographical regions of Brazil. PMID:22944771

  10. Molecular epidemiology of Acinetobacter baumannii in central intensive care unit in Kosova Teaching Hospital.

    Science.gov (United States)

    Raka, Lul; Kalenć, Smilja; Bosnjak, Zrinka; Budimir, Ana; Katić, Stjepan; Sijak, Dubravko; Mulliqi-Osmani, Gjyle; Zoutman, Dick; Jaka, Arbëresha

    2009-12-01

    Infections caused by bacteria of genus Acinetobacter pose a significant health care challenge worldwide. Information on molecular epidemiological investigation of outbreaks caused by Acinetobacter species in Kosova is lacking. The present investigation was carried out to enlight molecular epidemiology of Acinetobacter baumannii in the Central Intensive Care Unit (CICU) of a University hospital in Kosova using pulse field gel electrophoresis (PFGE). During March - July 2006, A. baumannii was isolated from 30 patients, of whom 22 were infected and 8 were colonised. Twenty patients had ventilator-associated pneumonia, one patient had meningitis, and two had coinfection with bloodstream infection and surgical site infection. The most common diagnoses upon admission to the ICU were politrauma and cerebral hemorrhage. Bacterial isolates were most frequently recovered from endotracheal aspirate (86.7%). First isolation occurred, on average, on day 8 following admission (range 1-26 days). Genotype analysis of A. baumannii isolates identified nine distinct PFGE patterns, with predominance of PFGE clone E represented by isolates from 9 patients. Eight strains were resistant to carbapenems. The genetic relatedness of Acinetobacter baumannii was high, indicating cross-transmission within the ICU setting. These results emphasize the need for measures to prevent nosocomial transmission of A. baumannii in ICU. PMID:20464330

  11. Human metapneumovirus: insights from a ten-year molecular and epidemiological analysis in Germany.

    Directory of Open Access Journals (Sweden)

    Janine Reiche

    Full Text Available Human metapneumovirus (HMPV is a cause of respiratory tract illness at all ages. In this study the epidemiological and molecular diversity among patients of different ages was investigated. Between 2000-2001 and 2009-2010, HMPV was detected in 3% (138/4,549 of samples from outpatients with influenza-like illness with a new, sensitive real-time RT-PCR assay. Several hundred (797 clinical specimens from hospitalized children below the age of 4 years with acute respiratory illness were investigated and HMPV was detected in 11.9% of them. Investigation of outpatients revealed that HMPV infections occurred in individuals of all ages but were most prevalent in children (0-4 years and the elderly (>60 years. The most present clinical features of HMPV infections were cough, bronchitis, fever/shivers and pneumonia. About two thirds of HMPV-positive samples were detected in February and March throughout the study period. Molecular characterization of HMPV revealed a complex cyclic pattern of group dominance where HMPV subgroup A and B viruses predominated in general for three consecutive seasons. German HMPV represented all genetic lineages including A1, A2, B1, B2, sub-clusters A2a and A2b. For Germany, not only time-dependent circulation of lineages and sub-clusters was observed but also co-circulation of two or three predominant lineages. Two newly emerging amino acid substitutions (positions 223 and 280 of lineage B2 were detected in seven German HMPV sequences. Our study gives new insights into the molecular epidemiology of HMPV in in- and outpatients over a time period of 10 years for the first time. It is one of only few long-term surveillance studies in Europe, and allows comparative molecular analyses of HMPV circulating worldwide.

  12. Genetic and molecular changes in ovarian cancer

    Science.gov (United States)

    Hollis, Robert L; Gourley, Charlie

    2016-01-01

    Epithelial ovarian cancer represents the most lethal gynecological malignancy in the developed world, and can be divided into five main histological subtypes: high grade serous, endometrioid, clear cell, mucinous and low grade serous. These subtypes represent distinct disease entities, both clinically and at the molecular level. Molecular analysis has revealed significant genetic heterogeneity in ovarian cancer, particularly within the high grade serous subtype. As such, this subtype has been the focus of much research effort to date, revealing molecular subgroups at both the genomic and transcriptomic level that have clinical implications. However, stratification of ovarian cancer patients based on the underlying biology of their disease remains in its infancy. Here, we summarize the molecular changes that characterize the five main ovarian cancer subtypes, highlight potential opportunities for targeted therapeutic intervention and outline priorities for future research.

  13. Reactive endplate marrow changes: a systematic morphologic and epidemiologic evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Karchevsky, Michael [Hahnemann University Hospital, Department of Radiology, Philadelphia (United States); Thomas Jefferson University Hospital, Department of Radiology, Philadelphia (United States); Schweitzer, Mark E. [Hospital for Joint Diseases, Department of Radiology, New York (United States); Carrino, John A.; Zoga, Adam; Montgomery, Douglas; Parker, Laurence [Thomas Jefferson University Hospital, Department of Radiology, Philadelphia (United States)

    2005-03-01

    To evaluate the morphology and location of vertebral endplate changes, and to analyze their association with age, gender, and body mass index (BMI). At 1.5 T (T1-weighted, T2-weighted/STIR) 100 lumbar spines were evaluated separately by three observers. The readers classified the endplate bone marrow abnormalities on sagittal MR images according to the definitions of Modic et al. Findings were localized by disc segment; whether in the upper and/or lower endplate; and within each endplate divided into 15 segments. Disc space narrowing, as well as disc desiccation, was also noted at each vertebral level. In addition, endplate changes were correlated with age, gender, and BMI (weight(kg)/height(m){sup 2}). A total of 15,000 data points were studied and 422 total changes recorded. A total of 99 vertebral levels were affected in 58 patients. Of these, 171 were of type I, 242 were of type II, and 9 were of type III. L4 - L5 and L5 - S1 vertebral levels were most commonly involved, having (142, 4.73%) and (116, 3.87%) changes respectively (P<0.0001). The upper and lower aspects of the endplate were affected similarly. Changes most frequently occurred at the anterior aspect of the endplate (P<0.0001). Endplate marrow changes were associated with increasing age (P<0.0001) and, surprisingly, male gender (P<0.0001). Endplate changes were not associated with BMI. The fatty pattern was most common, with the sclerotic pattern being rare. Endplate marrow changes most often occurred at the anterior aspect of the endplate, particularly at L4 - L5 and L5 - S1 levels. Modic changes occur more frequently with aging, evidence of their degenerative etiology. They were, however, not related to body habitus, but to weight and male gender. (orig.)

  14. Changing epidemiology of hepatitis A virus in Indian children

    Directory of Open Access Journals (Sweden)

    Arankalle V

    2014-01-01

    Full Text Available Vidya Arankalle,1 Monjori Mitra,2 Sheila Bhave,3 Apurba Ghosh,2 Sundaram Balasubramanian,4 Suparna Chatterjee,5 Jaydeep Choudhury,6 Amarjeet Chitkara,7 Ganesh Kadhe,8 Amey Mane,8 Sucheta Roy81Department of Virology, National Institute of Virology, Pashan, Pune, Maharashtra, India; 2Department of Pediatrics, Institute of Child Health, Kolkata, West Bengal, India; 3Department of Pediatrics, KEM Hospital and Research Center, Pune, Maharashtra, India; 4Department of Pediatrics, Kanchi Kamkodi Child Trust Hospital (KKCTH, Nungambakkam, Chennai, Tamil Nadu, India; 5Department of Pharmacology, Institute of Post Graduate Medical Education and Research (IPGMER and Seth Sukhlal Karnani Memorial (SSKM Hospital, Kolkata, West Bengal, India; 6Department of Pediatrics, Sri Aurobindo Seva Kendra (EEDF Hospital, Kolkata, West Bengal, India; 7Department of Pediatrics, Sarvodaya Childcare, Pitampura, Delhi, India; 8Medical Affairs Department, Wockhardt Ltd, Mumbai, Maharashtra, IndiaAbstract: Previous studies from India have observed an increased incidence of hepatitis A virus (HAV infection in the adult and adolescent population compared with children, indicating a shift in epidemiology of HAV. However, no HAV seroprevalence study has been conducted in India over the past decade. This prospective, multicenter, cross-sectional study was conducted in 928 children (aged 18 months to 10 years, to estimate the age-related seroprevalence of HAV across different regions of India. The present study also evaluated the impact of various factors such as age, socioeconomic class (SEC, education, source of drinking water, and excreta disposal on HAV seroprevalence. Overall, 348 (37.5% children were seropositive for anti-HAV antibodies. Seroprevalence of HAV in the 6- to 10-year age group (50.3% was higher (P=0.000 than in the 18-month to 6-year age group (30.3%. SEC and educational status of the parents were significantly associated with HAV seropositivity (P=0.000 for both

  15. Epidemiology and molecular characterization of hepatitis B virus in Luanda, Angola

    Directory of Open Access Journals (Sweden)

    Fatima Valente

    2010-12-01

    Full Text Available An estimated 360 million people are infected with hepatitis B virus (HBV worldwide. Among these, 65 million live in Africa. Despite the high levels of hepatitis B in Africa, HBV epidemiology is still poorly documented in most African countries. In this work, the epidemiological and molecular characteristics of HBV infection were evaluated among the staff, visitors and adult patients (n = 508 of a public hospital in Luanda, Angola. The overall prevalence of hepatitis B core antibody (anti-HBc and hepatitis B surface antigen was 79.7% and 15.1%, respectively. HBV infection was higher in males and was more prevalent in individuals younger than 50 years old. HBV-DNA was detected in 100% of HBV "e" antigen-positive serum samples and in 49% of anti-hepatitis Be antibody-positive samples. Thirty-five out of the 40 HBV genotypes belonged to genotype E. Circulation of genotypes A (4 samples and D (1 sample was also observed. The present study demonstrates that HBV infection is endemic in Luanda, which has a predominance of genotype E. This genotype is only sporadically found outside of Africa and is thought to have emerged in Africa at a time when the trans-Atlantic slave trade had stopped.

  16. A molecular epidemiology survey of respiratory adenoviruses circulating in children residing in Southern Palestine.

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    Lina Qurei

    Full Text Available A molecular epidemiology survey was performed in order to establish and document the respiratory adenovirus pathogen profiles among children in Southern Palestine. Three hundred and thirty-eight hospitalized pediatric cases with adenovirus-associated respiratory tract infections were analyzed. Forty four cases out of the 338 were evaluated in more detail for the adenoviruses types present. All of the children resided in Southern Palestine, that is, in city, village and refugee camp environments within the districts of Hebron and Bethlehem. Human adenoviruses circulated throughout 2005-2010, with major outbreaks occurring in the spring months. A larger percent of the children diagnosed with adenoviral infections were male infants. DNA sequence analysis of the hexon genes from 44 samples revealed that several distinct adenovirus types circulated in the region; these were HAdV-C1, HAdV-C2, HAdV-B3 and HAdV-C5. However, not all of these types were detected within each year. This is the first study ever conducted in Palestine of the genetic epidemiology of respiratory adenovirus infections.

  17. Tracking the molecular epidemiology of Brazilian Infectious bursal disease virus (IBDV) isolates.

    Science.gov (United States)

    Silva, Fernanda M F; Vidigal, Pedro M P; Myrrha, Luciana W; Fietto, Juliana L R; Silva, Abelardo; Almeida, Márcia R

    2013-01-01

    Infectious bursal disease is a highly contagious disease of young chickens caused by Infectious bursal disease virus (IBDV). Genome segment A encodes the capsid protein (VP2), while segment B encodes the RNA-dependent RNA polymerase (VP1). In the present study, we trace the molecular epidemiology of IBDV in Brazil by analyzing 29 isolates collected in the major regions of poultry production. To genetically characterize the isolates, phylogenetic and population dynamic analyses were conducted using 68 VP1 (2634 nt) and 102 VP2 (1356 nt) coding sequences from IBDV isolates from different regions of the world. Furthermore, the evolution of IBDV was analyzed by characterizing the selective forces that operated during the diversification of viral isolates. We show that IBDV isolates were introduced into Brazil mainly from the Netherlands and the USA. These introductions were associated with all Brazilian poultry production regions analyzed in this work. In addition, we show that the evolution of IBDV has been shaped by a combination of very low recombination rates and relatively high rates of nucleotide substitution (2.988×10(-4) for VP1 and 3.2937×10(-4) for VP2), which themselves are a function of purifying selection operating on VP1 and VP2. Furthermore, our extended Bayesian skyline plot suggests that the increase in the effective population size of isolates of IBDV is consistent with its epidemiological history, with a large increase during the emergence of acute outbreaks of IBD in the 1980s.

  18. Epidemiological and Molecular Characterization of Dengue Virus Circulating in Bhutan, 2013-2014.

    Science.gov (United States)

    Zangmo, Sangay; Klungthong, Chonticha; Chinnawirotpisan, Piyawan; Tantimavanich, Srisurang; Kosoltanapiwat, Nathamon; Thaisomboonsuk, Butsaya; Phuntsho, Kelzang; Wangchuk, Sonam; Yoon, In-Kyu; Fernandez, Stefan

    2015-01-01

    Dengue is one of the most significant public health problems in tropical and subtropical countries, and is increasingly being detected in traditionally non-endemic areas. In Bhutan, dengue virus (DENV) has only recently been detected and limited information is available. In this study, we analyzed the epidemiological and molecular characteristics of DENV in two southern districts in Bhutan from 2013-2014. During this period, 379 patients were clinically diagnosed with suspected dengue, of whom 119 (31.4%) were positive for DENV infection by NS1 ELISA and/or nested RT-PCR. DENV serotypes 1, 2 and 3 were detected with DENV-1 being predominant. Phylogenetic analysis of DENV-1 using envelope gene demonstrated genotype V, closely related to strains from northern India.

  19. A cautionary note on fecal sampling and molecular epidemiology in predatory wild great apes.

    Science.gov (United States)

    De Nys, Hélène Marie; Madinda, Nadège Freda; Merkel, Kevin; Robbins, Martha; Boesch, Christophe; Leendertz, Fabian Hubertus; Calvignac-Spencer, Sébastien

    2015-08-01

    Fecal samples are an important source of information on parasites (viruses, prokaryotes, or eukaryotes) infecting wild great apes. Molecular analysis of fecal samples has already been used for deciphering the origins of major human pathogens such as HIV-1 or Plasmodium falciparum. However, for apes that hunt (chimpanzees and bonobos), detection of parasite nucleic acids may reflect either true infection of the host of interest or ingestion of an infected prey, for example, another non-human primate. To determine the potential magnitude of this issue, we estimated the prevalence of prey DNA in fecal samples obtained from two wild chimpanzee communities. We observed values >15%, which are higher than or close to the fecal detection rates of many great ape parasites. Contamination of fecal samples with parasite DNA from dietary origin may therefore occasionally impact non-invasive epidemiological studies. This problem can be addressed (at least partially) by monitoring the presence of prey DNA. PMID:26031302

  20. Molecular epidemiology identifies HIV transmission networks associated with younger age and heterosexual exposure among Korean individuals.

    Science.gov (United States)

    Chin, Bum Sik; Chaillon, Antoine; Mehta, Sanjay R; Wertheim, Joel O; Kim, Gayeon; Shin, Hyoung-Shik; Smith, Davey M

    2016-10-01

    To evaluate if HIV transmission networks could be elucidated from data collected in a short time frame, 131 HIV-1 pol sequences were analyzed which were generated from treatment-naïve Korean individuals who were sequentially identified over 1 year. A transmission linkage was inferred when there was a genetic distance <1.5% and a total of 16 clusters, involving 39/131 (29.8%), were identified. Younger age and heterosexual exposure were independently related with clustering in the inferred network, which demonstrated that molecular epidemiology with currently generated data (i.e., drug resistance genotypes) can be used to identify local transmission networks, even over a short timeframe. J. Med. Virol. 88:1832-1835, 2016. © 2016 Wiley Periodicals, Inc. PMID:26990771

  1. Epidemiological-molecular evidence of metabolic reprogramming on proliferation, autophagy and cell signaling in pancreas cancer.

    Science.gov (United States)

    Søreide, Kjetil; Sund, Malin

    2015-01-28

    Pancreatic cancer remains one of the deadliest human cancers with little progress made in survival over the past decades, and 5-year survival usually below 5%. Despite this dismal scenario, progresses have been made in understanding of the underlying tumor biology through among other definition of precursor lesions, delineation of molecular pathways, and advances in genome-wide technology. Further, exploring the relationship between epidemiological risk factors involving metabolic features to that of an altered cancer metabolism may provide the foundation for new therapies. Here we explore how nutrients and caloric intake may influence the KRAS-driven ductal carcinogenesis through mediators of metabolic stress, including autophagy in presence of TP53, advanced glycation end products (AGE) and the receptors (RAGE) and ligands (HMGB1), as well as glutamine pathways, among others. Effective understanding the cancer metabolism mechanisms in pancreatic cancer may propose new ways of prevention and treatment. PMID:24704294

  2. Epidemiological and Molecular Characterization of Dengue Virus Circulating in Bhutan, 2013-2014.

    Directory of Open Access Journals (Sweden)

    Sangay Zangmo

    Full Text Available Dengue is one of the most significant public health problems in tropical and subtropical countries, and is increasingly being detected in traditionally non-endemic areas. In Bhutan, dengue virus (DENV has only recently been detected and limited information is available. In this study, we analyzed the epidemiological and molecular characteristics of DENV in two southern districts in Bhutan from 2013-2014. During this period, 379 patients were clinically diagnosed with suspected dengue, of whom 119 (31.4% were positive for DENV infection by NS1 ELISA and/or nested RT-PCR. DENV serotypes 1, 2 and 3 were detected with DENV-1 being predominant. Phylogenetic analysis of DENV-1 using envelope gene demonstrated genotype V, closely related to strains from northern India.

  3. Molecular epidemiology of sexually transmitted human papillomavirus in a self referred group of women in Ireland.

    LENUS (Irish Health Repository)

    Menton, John F

    2009-01-01

    BACKGROUND: Human papillomavirus (HPV) causes cervical cancer and external genital warts. The purpose of this study is to document the genotype distribution of HPV in females aged between 18 and 34 who self-referred to an STI clinic with visible external genital warts (EGW). Scrapings were taken from visible external genital warts (EGW). These scrapings were analysed by PCR for the presence of HPV DNA. Positive samples were then genotyped by means of a commercially available assay (LiPA). A comparison of genotyping results determined by the LiPA assay and direct amplicon DNA sequencing was also performed. RESULTS: Ninety-two patients out of 105 samples (88%) had detectable levels of HPV DNA. The majority of individuals with EGW (66%) showed the presence of two or more genotypes. The most common HPV genotypes present in the study population were HPV-6, HPV-11, HPV-16, HPV-18, HPV-33 and HPV-53. Potential effects of vaccination on HPV molecular epidemiology indicate that 40% of the patients could have been protected from the high risk genotypes HPV-16 and HPV-18. CONCLUSION: This is the first report of the molecular epidemiology of external genital warts in women aged between 18 and 34 from Ireland based on results from a LiPA assay. The study shows that most individuals are infected with multiple genotypes including those with high oncogenic potential and that the newly available HPV vaccines could have a significant impact on prevalence of the most common HPV genotypes in this study population.

  4. Molecular epidemiology of Cryptosporidium in HIV/AIDS patients in Malaysia.

    Science.gov (United States)

    Asma, I; Sim, B L H; Brent, R D; Johari, S; Yvonne Lim, A L

    2015-06-01

    Cryptosporidiosis is a particular concern in immunocompromised individuals where symptoms may be severe. The aim of this study was to examine the epidemiological and molecular characteristics of Cryptosporidium infections in HIV/AIDS patients in Malaysia in order to identify risk factors and facilitate control measures. A modified Ziehl-Neelsen acid fast staining method was used to test for the presence of Cryptosporidium oocysts in the stools of 346 HIV/AIDS patients in Malaysia. Standard coproscopical methods were used to identify infections with other protozoan or helminths parasites. To identify the species of Cryptosporidium, DNA was extracted and nested-PCR was used to amplify a portion of the SSU rRNA gene. A total of 43 (12.4%) HIV-infected patients were found to be infected with Cryptosporidium spp. Of the 43 Cryptosporidium-positive HIV patients, 10 (23.3%) also harboured other protozoa, and 15 (34.9%) had both protozoa and helminths. The highest rates of cryptosporidiosis were found in adult males of Malay background, intravenous drug users, and those with low CD4 T cell counts (i.e., parvum (84.3%), C. hominis (6.3%), C. meleagridis (6.3%), and C. felis (3.1%). The results of the present study revealed a high prevalence of Cryptosporidium infection in hospitalized HIV/AIDS patients. The results also confirmed the potential significance of zoonotic transmission of C. parvum in HIV infected patients, as it was the predominant species found in this study. However, these patients were found to be susceptible to a wide range of Cryptosporidium species. Epidemiological and molecular characterization of Cryptosporidium isolates provides clinicians and researchers with further information regarding the origin of the infection, and may enhance treatment and control strategies. PMID:26691260

  5. Diurnal Variation of Hormonal and Lipid Biomarkers in a Molecular Epidemiology-Like Setting.

    Directory of Open Access Journals (Sweden)

    Linda W M van Kerkhof

    Full Text Available Many molecular epidemiology studies focusing on high prevalent diseases, such as metabolic disorders and cancer, investigate metabolic and hormonal markers. In general, sampling for these markers can occur at any time-point during the day or after an overnight fast. However, environmental factors, such as light exposure and food intake might affect the levels of these markers, since they provide input for the internal time-keeping system. When diurnal variation is larger than the inter-individual variation, time of day should be taken into account. Importantly, heterogeneity in diurnal variation and disturbance of circadian rhythms among a study population might increasingly occur as a result of our increasing 24/7 economy and related variation in exposure to environmental factors (such as light and food.The aim of the present study was to determine whether a set of often used biomarkers shows diurnal variation in a setting resembling large molecular epidemiology studies, i.e., non-fasted and limited control possibilities for other environmental influences.We show that markers for which diurnal variation is not an issue are adrenocorticotropic hormone, follicle stimulating hormone, estradiol and high-density lipoprotein. For all other tested markers diurnal variation was observed in at least one gender (cholesterol, cortisol, dehydroepiandrosterone sulfate, free fatty acids, low-density lipoprotein, luteinizing hormone, prolactin, progesterone, testosterone, triglycerides, total triiodothyronine and thyroid-stimulating hormone or could not reliably be detected (human growth hormone.Thus, studies investigating these markers should take diurnal variation into account, for which we provide some options. Furthermore, our study indicates the need for investigating diurnal variation (in literature or experimentally before setting up studies measuring markers in routine and controlled settings, especially since time-of-day likely matters for many more

  6. A reassessment of the epidemiology of Rice yellow mottle virus following recent advances in field and molecular studies.

    Science.gov (United States)

    Traoré, O; Pinel-Galzi, A; Sorho, F; Sarra, S; Rakotomalala, M; Sangu, E; Kanyeka, Z; Séré, Y; Konaté, G; Fargette, D

    2009-05-01

    The available knowledge on the epidemiology of Rice yellow mottle virus (RYMV) is reassessed in the light of major advances in field and molecular studies of the disease it causes in rice. Previously un-described means of transmission by mammals and through leaf contact have been discovered recently. Several agricultural practices, including the use of seedbed nurseries, have also contributed to a massive build-up of RYMV inoculum. Phytosanitation is now known to be critical to reduce disease incidence in rice. A new model of the ecology of RYMV in which man plays a central role has emerged. Furthermore, estimates of the evolutionary rate of change of RYMV provided a time-frame for its epidemiology, the first attempt for a plant virus. Earlier interpretations of the patterns of virus diversity which assumed a long-term evolution, and assigned a major role to adaptive events had to be discarded. In contrast, a wave-like model of dispersal of RYMV, which postulates its initial diversification in East Africa, followed by westward spread across the continent, was developed, refined and dated. The most salient -- and largely unexpected -- finding is that RYMV emerged recently and subsequently spread rapidly throughout Africa in the last two centuries. Diversification and spread of RYMV has been concomitant with an extension of rice cultivation in Africa since the 19th century. This major agro-ecological change increased the encounters between primary hosts of RYMV and cultivated rice. It also modified the landscape ecology in ways that facilitated virus spread. PMID:19195488

  7. Changes in the epidemiology of sudden infant death syndrome in Sweden 1973-1996

    OpenAIRE

    Alm, B; Norvenius, S; Wennergren, G; Skjarven, R; Oyen, N; Milerad, J; Wennborg, M; Kjaerbeck, J; Helweg-Larsen, K.; Irgens, L.

    2001-01-01

    BACKGROUND—From the early 1970s to the early 1990s, there was a significant rise in the incidence of sudden infant death syndrome (SIDS) in Scandinavia. Following the risk reducing campaign, the incidence has fallen to about the same level as in 1973.
AIMS—To identify the changes that have occurred in the epidemiology of SIDS.
METHODS—We compared the Swedish part of the Nordic Epidemiological SIDS Study (NESS), covering the years 1992-1995, with two earlier, descriptive s...

  8. Gastric cancer in Scotland: changing epidemiology, unchanging workload.

    OpenAIRE

    Sedgwick, D M; Akoh, J A; Macintyre, I. M.

    1991-01-01

    OBJECTIVE--To determine the changes in incidence of and mortality from gastric cancer in Scotland between 1978 and 1987 and in the operative workload in Lothian between 1979 and 1988. DESIGN--Analysis of national incidence statistics for gastric cancer derived from the Scottish national cancer registry, deaths from gastric cancer recorded by the registrar general for Scotland, and Lothian surgical audit data. SETTING--Scotland and Lothian Health Board area. PATIENTS--Patients in Scotland with...

  9. An integrative analysis of foot-and-mouth disease virus carriers in Vietnam achieved through targeted surveillance and molecular epidemiology

    Science.gov (United States)

    A multidisciplinary, molecular and conventional epidemiological approach was applied to an investigation of endemic foot-and-mouth disease in Vietnam. Within the study space, it was found that 22.3 percent of sampled ruminants had previously been infected with FMD virus (FMDV) and that 2.4 percent w...

  10. Development of molecular methods for detection and epidemiological investigation of HIV-1, HIV-2, and HTLV-I/II infections

    NARCIS (Netherlands)

    Meijer A; Borleffs JCC; Roosendaal G; Loon AM van; VIR; AZU; Van Creveld Kliniek Utrecht

    1995-01-01

    The work presented here was initiated to determine the possibilities of molecular methods for the detection and epidemiological investigation of HIV and HTLV infections. We present the results of a literature research and describe the development and partial evaluation of a new PCR method for the am

  11. Changing trends in the epidemiology of hip fracture in Spain

    Science.gov (United States)

    Azagra, R.; López-Expósito, F.; Martin-Sánchez, JC.; Aguyé, A.; Moreno, N.; Cooper, C.; Díez-Pérez, A.; Dennison, EM.

    2016-01-01

    Summary Temporal trends in hip fracture incidence have recently been reported in some developed countries. Such data in Spain has previously been incomplete; this study reports the stratified incidence of hip fractures in people over 65 in Spain during the last 14 years. Introduction The main objective is to establish whether temporal trends in hip fracture incidence in Spain exist. Methods Ecological study with data from hospital discharges nationwide. The study includes patients aged ≥ 65 years during a 14-year period (1997-2010). The analysis compares two periods of four years: 1997-2000 (P1) and 2007-2010 (P2). Results There were 119,857 fractures in men and 415,421 in women. Comparing periods (P1 vs P2), over ten years the crude incidence rate/100,000 inhabitant/year increased an average of 2.3%/year in men and 1.4% in women. After adjustment, the rate increased an average of 0.4%/year in men (p<0.0001), but decreased 0.2%/year in women (p<0.0001). In men younger than 85, the decrease was not significant except in 70-74 years and from 80 years the adjusted rate increases significantly (p<0.0001). In women under 80 years of age, the decrease in adjusted rate was significant, there was no change in 80-84 years and the adjusted rate increased significantly in individuals 85 years and older (p<0.0001). Mortality rates declined by 22% in both sexes and the index of overaging population rises 30.1% in men and 25.2% in women. Conclusions This study supports other international studies by showing changes in the incidence of hip fractures after age-population adjustment, which denotes a decrease in the younger age groups and among women and shows an increase in both groups over 85 years. The increase in the crude incidence rate of hip fracture in Spain reflects changes in population structure. PMID:24322478

  12. Pacific paradigms of environmentally-induced neurological disorders: Clinical, epidemiological and molecular perspectives

    Energy Technology Data Exchange (ETDEWEB)

    Garruto, R.M. (Laboratory of Central Nervous System Studies, National Institutes of Health, Bethesda, MD (Unites States))

    During the past quarter century biomedical scientists have begun to recognize the unique opportunities for studying disease etiology and mechanisms of pathogenesis in non-Western anthropological populations with focal, endemic diseases. The systematic search for etiological factors and mechanisms of pathogenesis of neurodegenerative disorders is perhaps nowhere better exemplified than in the western Pacific. During the past three decades, the opportunistic and multidisciplinary study of hyperendemic foci of amyotrophic lateral sclerosis and parkinsonism-dementia which occur in different cultures, in different ecological zones and among genetically divergent populations have served as natural models that have had a major impact on our thinking and enhanced our understanding of these and other neurodegenerative disorders such as Alzheimer disease and the process of early neuronal aging. Our cross-disciplinary approach to these intriguing neurobiological problems and the accumulated epidemiological, genetic, cellular and molecular evidence strongly implicates environmental factors in their causation, specifically the role of aluminum and its interaction with calcium in neuronal degeneration. As a direct consequence of our studies in these Pacific populations, we have undertaken the long-term development of experimental models of neuronal degeneration, in an attempt to understand the cellular and molecular mechanisms by which these toxicants affect the central nervous system. Our experimental studies have resulted in the establishment of an aluminum-induced chronic myelopathy in rabbits and the development of neurofilamentous lesions after low-dose aluminum administration in cell culture.

  13. Resurgence of pertussis at the age of vaccination: clinical, epidemiological, and molecular aspects

    Directory of Open Access Journals (Sweden)

    Rosângela S.L.A. Torres

    2015-08-01

    Full Text Available OBJECTIVE: Report the incidence, epidemiology, clinical features, death, and vaccination status of patients with whooping cough and perform genotypic characterization of isolates of B. pertussis identified in the state of Paraná, during January 2007 to December 2013.METHODS: Cross-sectional study including 1,209 patients with pertussis. Data were obtained through the Notifiable Diseases Information System (Sistema de Informação de Agravos de Notificação - SINAN and molecular epidemiology was performed by repetitive sequence-based polymerase chain reaction (rep-PCR; DiversiLab(r, bioMerieux, France.RESULTS: The incidence of pertussis in the state of Paraná increased sharply from 0.15-0.76 per 100,000 habitants between 2007-2010 to 1.7-4.28 per 100,000 between 2011-2013. Patients with less than 1 year of age were more stricken (67.5%. Fifty-nine children (5% developed pertussis even after receiving three doses and two diphtheria-tetanus-pertussis (DTP boosters vaccine. The most common complications were pneumonia (14.5%, otitis (0.9%, and encephalopathy (0.7%. Isolates of B. pertussis were grouped into two groups (G1 and G2 and eight distinct patterns (G1: P1-P5 and G2: P6-P8.CONCLUSION: The resurgence of pertussis should stimulate new research to develop vaccines with greater capacity of protection against current clones and also encourage implementation of new strategies for vaccination in order to reduce the risk of disease in infants.

  14. Deciphering the origin of the 2012 cholera epidemic in Guinea by integrating epidemiological and molecular analyses.

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    Stanislas Rebaudet

    2014-06-01

    Full Text Available Cholera is typically considered endemic in West Africa, especially in the Republic of Guinea. However, a three-year lull period was observed from 2009 to 2011, before a new epidemic struck the country in 2012, which was officially responsible for 7,350 suspected cases and 133 deaths. To determine whether cholera re-emerged from the aquatic environment or was rather imported due to human migration, a comprehensive epidemiological and molecular survey was conducted. A spatiotemporal analysis of the national case databases established Kaback Island, located off the southern coast of Guinea, as the initial focus of the epidemic in early February. According to the field investigations, the index case was found to be a fisherman who had recently arrived from a coastal district of neighboring Sierra Leone, where a cholera outbreak had recently occurred. MLVA-based genotype mapping of 38 clinical Vibrio cholerae O1 El Tor isolates sampled throughout the epidemic demonstrated a progressive genetic diversification of the strains from a single genotype isolated on Kaback Island in February, which correlated with spatial epidemic spread. Whole-genome sequencing characterized this strain as an "atypical" El Tor variant. Furthermore, genome-wide SNP-based phylogeny analysis grouped the Guinean strain into a new clade of the third wave of the seventh pandemic, distinct from previously analyzed African strains and directly related to a Bangladeshi isolate. Overall, these results highly suggest that the Guinean 2012 epidemic was caused by a V. cholerae clone that was likely imported from Sierra Leone by an infected individual. These results indicate the importance of promoting the cross-border identification and surveillance of mobile and vulnerable populations, including fishermen, to prevent, detect and control future epidemics in the region. Comprehensive epidemiological investigations should be expanded to better understand cholera dynamics and improve

  15. Deciphering the origin of the 2012 cholera epidemic in Guinea by integrating epidemiological and molecular analyses.

    Science.gov (United States)

    Rebaudet, Stanislas; Mengel, Martin A; Koivogui, Lamine; Moore, Sandra; Mutreja, Ankur; Kande, Yacouba; Yattara, Ousmane; Sarr Keita, Véronique; Njanpop-Lafourcade, Berthe-Marie; Fournier, Pierre-Edouard; Garnotel, Eric; Keita, Sakoba; Piarroux, Renaud

    2014-06-01

    Cholera is typically considered endemic in West Africa, especially in the Republic of Guinea. However, a three-year lull period was observed from 2009 to 2011, before a new epidemic struck the country in 2012, which was officially responsible for 7,350 suspected cases and 133 deaths. To determine whether cholera re-emerged from the aquatic environment or was rather imported due to human migration, a comprehensive epidemiological and molecular survey was conducted. A spatiotemporal analysis of the national case databases established Kaback Island, located off the southern coast of Guinea, as the initial focus of the epidemic in early February. According to the field investigations, the index case was found to be a fisherman who had recently arrived from a coastal district of neighboring Sierra Leone, where a cholera outbreak had recently occurred. MLVA-based genotype mapping of 38 clinical Vibrio cholerae O1 El Tor isolates sampled throughout the epidemic demonstrated a progressive genetic diversification of the strains from a single genotype isolated on Kaback Island in February, which correlated with spatial epidemic spread. Whole-genome sequencing characterized this strain as an "atypical" El Tor variant. Furthermore, genome-wide SNP-based phylogeny analysis grouped the Guinean strain into a new clade of the third wave of the seventh pandemic, distinct from previously analyzed African strains and directly related to a Bangladeshi isolate. Overall, these results highly suggest that the Guinean 2012 epidemic was caused by a V. cholerae clone that was likely imported from Sierra Leone by an infected individual. These results indicate the importance of promoting the cross-border identification and surveillance of mobile and vulnerable populations, including fishermen, to prevent, detect and control future epidemics in the region. Comprehensive epidemiological investigations should be expanded to better understand cholera dynamics and improve disease control

  16. Molecular epidemiology and evolution of human enterovirus serotype 68 in Thailand, 2006-2011.

    Directory of Open Access Journals (Sweden)

    Piyada Linsuwanon

    Full Text Available BACKGROUND: Publications worldwide have reported on the re-occurrence of human enterovirus 68 (EV68, a rarely detected pathogen usually causing respiratory illness. However, epidemiological data regarding this virus in particular on the Asian continent has so far been limited. METHODOLOGY/FINDINGS: We investigated the epidemiology and genetic variability of EV68 infection among Thai children with respiratory illnesses from 2006-2011 (n = 1810. Semi-nested PCR using primer sets for amplification of the 5'-untranslated region through VP2 was performed for rhino-enterovirus detection. Altogether, 25 cases were confirmed as EV68 infection indicating a prevalence of 1.4% in the entire study population. Interestingly, the majority of samples were children aged >5 years (64%. Also, co-infection with other viruses was found in 28%, while pandemic H1N1 influenza/2009 virus was the most common co-infection. Of EV68-positive patients, 36% required hospitalizations with the common clinical presentations of fever, cough, dyspnea, and wheezing. The present study has shown that EV68 was extremely rare until 2009 (0.9%. An increasing annual prevalence was found in 2010 (1.6% with the highest detection frequency in 2011 (4.3%. Based on analysis of the VP1 gene, the evolutionary rate of EV68 was estimated at 4.93 × 10(-3 substitutions/site/year. Major bifurcation of the currently circulating EV68 strains occurred 66 years ago (1945.31 with (1925.95-1960.4695% HPD. Among the current lineages, 3 clusters of EV68 were categorized based on the different molecular signatures in the BC and DE loops of VP1 combined with high posterior probability values. Each cluster has branched off from their common ancestor at least 36 years ago (1975.78 with (1946.13-1984.9795% HPD. CONCLUSION: Differences in epidemiological characteristic and seasonal profile of EV68 have been found in this study. Results from Bayesian phylogenetic investigations also revealed that EV68 should be

  17. Enteroviruses and Rhinoviruses: Molecular Epidemiology of the Most Influenza-Like Illness Associated Viruses in Senegal.

    Science.gov (United States)

    Fall, Amary; Dia, Ndongo; Kébé, Ousmane; Sarr, Fatoumata Diene; Kiori, Davy E; Cissé, El Hadj Abdoul Khadir; Sy, Sara; Goudiaby, Deborah; Richard, Vincent; Diop, Ousmane Madiagne; Niang, Mbayame Ndiaye

    2016-08-01

    Different viruses have been identified as etiologic agents of respiratory tract infections, including severe cases. Among these, human rhinoviruses (HRVs) and human enteroviruses (HEVs) are recognized as leading causes. The present study describes the molecular epidemiology of HRVs and HEVs in Senegal over a 3-year surveillance period. From January 2012 to December 2014, nasopharyngeal and oropharyngeal swabs specimen were collected from patients with influenza-like illness (ILI). A real-time reverse transcription polymerase chain reaction was performed for HRV and HEV detection using the RV16 kit. Two regions were targeted for the molecular characterization of RVs: 5' untranslated region (5'UTR) and viral protein 4/viral protein 2 (VP4/VP2) transition region. For enteroviruses (EVs) phylogeny, VP1 gene was targeted. A total of 4,194 samples were collected. Children up to 5 years accounted for 52.9%. Among them, 1,415 (33.7%) were positive for HRV, 857 (20.4%) for HEV, and 437 cases of dual infections HRV/HEV. HRVs and HEVs were identified significantly in children aged 5 years or less. Only cough and vomiting signs were observed with significant association with viral infection. Both viruses co-circulated all year long with a marked increase of activity during rainy and cold period. All HRV types circulate in Senegal. HRV-A and C groups were the most common. HEV serotyping identified coxsackie B viruses (CBV) only. VP1 region revealed different CBV (CBV1, CBV2, CBV3, CBV4, and CBV5), echoviruses, coxsackieviruses A4-like strains and a poliovirus 2. The results suggest strong year-round respiratory picornavirus activity in children up to 5 years of age. Molecular studies identified a wide variety of RVs along with diverse EVs in samples from patients with ILI. PMID:27246444

  18. Molecular Epidemiology and Antimicrobial Susceptibility of Clostridium difficile Isolates from a University Teaching Hospital in China

    Science.gov (United States)

    Cheng, Jing-Wei; Xiao, Meng; Kudinha, Timothy; Kong, Fanrong; Xu, Zhi-Peng; Sun, Lin-Ying; Zhang, Li; Fan, Xin; Xie, Xiu-Li; Xu, Ying-Chun

    2016-01-01

    While the developed world has seen a significant increase in the number of scientific articles on Clostridium difficile infection (CDI), the developing world still lags behind on this subject due to limited laboratory capacity, low awareness, and limited surveillance of this problem. As such, CDI is considered a neglected but potentially huge problem in developing countries. The major aim of this study was to systemically evaluate the utility of several molecular typing tools for CDI, including their relevance in epidemiological studies in developing countries such as China. A total of 116 non-repetitive toxigenic C. difficile isolates from Chinese patients, were studied. The isolates comprised 83 (71.6%) A+B+CDT- isolates, 27 (23.3%) A-B+CDT- isolates, and 6 (5.1%) A+B+CDT+ isolates. Typing methods evaluated included multilocus variable-number tandem-repeat analysis, PCR ribotyping, multilocus sequence typing, and sequencing of slpA and tcdC genes, which identified 113, 30, 22, 18, and 8 genotypes each and exhibited discriminatory powers of 0.999, 0.916, 0.907, 0.883, and 0.765, respectively. Compared to A+B+ strains, A-B+ strains exhibited higher prevalence of drug resistance to clindamycin, erythromycin, levofloxacin, rifampicin, rifaximin, and tetracycline. Furthermore, drug resistance rates of strains with different PCR ribotypes differed, supporting the importance of molecular typing in management and control of CDI. Based on our earlier suggestion to improve the diagnostic laboratory capacity of CDI in developing countries, setting up efficient surveillance programs complemented by relevant molecular typing methods is warranted.

  19. Costs and epidemiological changes of chronic diseases: implications and challenges for health systems.

    Directory of Open Access Journals (Sweden)

    Armando Arredondo

    Full Text Available The need to integrate economic and epidemiological aspects in the clinical perspective leads to a proposal for the analysis of health disparities and to an evaluation of the health services and of the new challenges which are now being faced by health system reforms in middle income countries.To identify the epidemiological changes, the demand for health services and economic burden from chronic diseases (diabetes and hypertension in a middle income county.We conducted longitudinal analyses of costs and epidemiological changes for diabetes and hypertension in the Mexican health system. The study population included both the insured and uninsured populations. The cost-evaluation method was used, based on the instrumentation and consensus techniques. To estimate the epidemiological changes and financial consequences for 2014-2016, six models were constructed according to the Box-Jenkins technique, using confidence intervals of 95%, and the Box-Pierce test.Regarding epidemiological changes expected in both diseases for 2014 vs. 2016, an increase is expected, although results predict a greater increase for diabetes, 8-12% in all three studied institutions, (p < .05. Indeed, in the case of diabetes, the increase was 41469 cases for uninsured population (SSA and 65737 for the insured population (IMSS and ISSSTE. On hypertension cases the increase was 38109 for uninsured vs 62895 for insured. Costs in US$ ranged from $699 to $748 for annual case management per patient in the case of diabetes, and from $485 to $622 in patients with hypertension. Comparing financial consequences of health services required by insured and uninsured populations, the greater increase (23% will be for the insured population (p < .05. The financial requirements of both diseases will amount to 19.5% of the total budget for the uninsured and 12.5% for the insured population.If the risk factors and the different health care models remain as they currently are, the economic

  20. Serotype Distribution, Antimicrobial Susceptibility, and Molecular Epidemiology of Streptococcus pneumoniae Isolated from Children in Shanghai, China.

    Directory of Open Access Journals (Sweden)

    Fen Pan

    Full Text Available Streptococcus pneumoniae is a common pathogenic cause of pediatric infections. This study investigated the serotype distribution, antimicrobial susceptibility, and molecular epidemiology of pneumococci before the introduction of conjugate vaccines in Shanghai, China.A total of 284 clinical pneumococcal isolates (270, 5, 4,3, and 2 of which were isolated from sputum, bronchoalveolar lavage fluid, blood, cerebral spinal fluid, and ear secretions, respectively from children less than 14 years of age who had not been vaccinated with a conjugate vaccine, were collected between January and December in 2013. All isolates were serotyped by multiplex polymerase chain reaction or quellung reactions and antimicrobial susceptibility testing was performed using the broth microdilution method. The molecular epidemiology of S.pneumoniae was analyzed by multilocus sequence typing (MLST.Among the 284 pneumococcal isolates, 19F (33.5%, 19A (14.1%, 23F (12.0%, and 6A (8.8% were the most common serotypes and the coverage rates of the 7-, 10-, and 13-valent pneumococcal conjugate vaccines (PCV7, PCV10, and PCV13 were 58.6%, 59.4% and 85.1%, respectively. Antimicrobial susceptibility showed that the prevalence rates of S.pneumoniae resistance to penicillin were 11.3% (32/284. Approximately 88.0% (250/284 of the isolates exhibited multi-drug resistance. MLST analysis revealed a high level of diversity, with 65 sequence types (STs among 267 isolates. Specifically, the four predominant STs were ST271 (24.3%, 65/267, ST320 (11.2%, 30/267, ST81 (9.7%, 26/267, and ST3173 (5.2%, 14/267, which were mainly associated with serotypes 19F, 19A, 23F, and 6A, respectively.The prevalent serotypes among clinical isolates from children were 19F, 19A, 23F, and 6A and these isolates showed high resistance rates to β-lactams and macrolides. The Taiwan19F-14 clone played a predominant role in the dissemination of pneumococcal isolates in Shanghai, China. Therefore, continued and

  1. Molecular epidemiology of hospital-onset methicillin-resistant Staphylococcus aureus infections in Southern Chile.

    Science.gov (United States)

    Medina, G; Egea, A L; Otth, C; Otth, L; Fernández, H; Bocco, J L; Wilson, M; Sola, C

    2013-12-01

    Methicillin-resistant Staphylococcus aureus (MRSA) is a pathogen of public health importance. In Chile, the Cordobes/Chilean clone was the predominant healthcare-associated MRSA (HA-MRSA) clone in 1998. Since then, the molecular epidemiological surveillance of MRSA has not been performed in Southern Chile. We aimed to investigate the molecular epidemiology of HA-MRSA infections in Southern Chile to identify the MRSA clones involved, and their evolutionary relationships with epidemic international MRSA lineages. A total of 303 single inpatient isolates of S. aureus were collected in the Valdivia County Hospital (2007-2008), revealing 33% (100 MRSA/303) prevalence for HA-MRSA infections. The SCCmec types I and IV were identified in 97% and 3% of HA-MRSA, respectively. All isolates lacked the pvl genes. A random sample (n = 29) of all MRSA was studied by pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), SCCmec subtyping, agr and spa typing, and virulence genes profiling. PFGE analysis revealed the predominance (89%, 26/29) of pulsotype A and three additional pulsotypes, designated H1, I33, and G1. Pulsotype A (ST5-SCCmecI-spa-t149) is clonally related to the Cordobes/Chilean clone. Pulsotype H1 (ST5-SCCmecIVNT-spa-t002) is genetically related to the Pediatric clone (ST5-SCCmecIV). Pulsotype I33 (ST5-SCCmecIVc-spa-t002) is clonally related by PFGE to the community-associated MRSA (CA-MRSA) clone spread in Argentina, I-ST5-IVa-PVL(+). The G1 pulsotype (ST8-SCCmecIVc-spa-t024) is clonally related to the epidemic USA300 CA-MRSA. Here, we demonstrate the stability of the Cordobes/Chilean clone over time as the major HA-MRSA clone in Southern Chile. The identification of two CA-MRSA clones might suggest that these clones have entered into the healthcare setting from the community. These results emphasize the importance of the local surveillance of MRSA infections in the community and hospital settings.

  2. Molecular typing of Salmonella from Sergipe, Northeastern Brazil, showing the epidemiological relationship between poultry and human infection.

    Science.gov (United States)

    Góis, P B P; Carneiro, M R P; Jain, S; Santos, M I S; Batista, M V A; Cândido, A L

    2015-09-25

    Randomly amplified polymorphic DNA (RAPD) has been widely used for epidemiological and phylogenetic purposes ow-ing to its rapidity and efficiency. The aim of this study was to perform genome typing of Salmonella samples isolated from different sources by RAPD profiling. Thirty-three Salmonella samples from the bacterial collection of the Laboratório de Virologia Comparada, Departamento de Morfologia, Universidade Federal de Sergipe, Brazil, and two standard samples were used. RAPD profiling was conducted using six primers of the Ready-To-Go RAPD system. The amplified products were electro-phoresed on 5% polyacrylamide gel and silver-stained. RAPD analysis resulted in reproducible and stable banding patterns and showed high genetic diversity among the isolated strains. The Primer P1-generated dendrogram showed an epidemiologic relationship between the human and poultry isolated samples, highlighting the usefulness of RAPD for molecular typing and epidemiological studies.

  3. Changes in the epidemiology of acute appendicitis and appendectomy in Danish children 1996-2004

    DEFF Research Database (Denmark)

    Andersen, S B; Paerregaard, A; Larsen, K

    2009-01-01

    PURPOSE: Aim of the study was to describe changes in the epidemiology of acute appendicitis in Danish children between 0-19 years of age for the period 1996-2004. METHODS: The study was based on discharge diagnoses taken from the Danish National Patient Registry of all 28 274 patients with a diag......PURPOSE: Aim of the study was to describe changes in the epidemiology of acute appendicitis in Danish children between 0-19 years of age for the period 1996-2004. METHODS: The study was based on discharge diagnoses taken from the Danish National Patient Registry of all 28 274 patients...... with a diagnosis of acute uncomplicated or complicated appendicitis, and/or a registered procedure code of appendectomy. These data were computed together with data on the background population, and incidences were calculated. RESULTS: A significant decrease in the incidence of acute uncomplicated appendicitis...

  4. Immigration and changes in the epidemiology of hemoglobin disorders in Italy : an emerging public health burden

    Directory of Open Access Journals (Sweden)

    Cataldo Francesco

    2012-07-01

    Full Text Available Abstract Background In the last years Italy is confronting with massive migratory movements from developing countries where hemoglobinopathies are widespread. This is causing a large diffusion and a changing spectrum in the epidemiology of hemoglobin disorders in Italy. Methods Investigations recently published in Italy on hemoglobinopathies among immigrants were revised in order to appreciate the impact of immigration from developing countries on epidemiology of these pathologies and to outline adequate guidelines of prevention. Results Although in Italy there is a limited number of investigations regarding the relation between immigration and hemoglobin disorders, published data show that in our Nation there is a changing and increasing spectrum of hemoglobinopathies linked to immigration. Conclusions Prospective and retrospective actions of public healthy preventive policy are requested, based upon information (health educational programs for immigrants and caregivers, screenings among immigrants (school screening, pre-marital, preconception and early pregnancy screening, newborn screening, counseling for foreign at-risk couples and healthy carriers.

  5. Changing epidemiology of malaria in Sabah, Malaysia: increasing incidence of Plasmodium knowlesi

    OpenAIRE

    William, Timothy; Jelip, Jenarun; Menon, Jayaram; Anderios, Fread; Mohammad, Rashidah; Awang Mohammad, Tajul A; Grigg, Matthew J.; Tsin W Yeo; Anstey, Nicholas M.; Barber, Bridget E

    2014-01-01

    Background While Malaysia has had great success in controlling Plasmodium falciparum and Plasmodium vivax, notifications of Plasmodium malariae and the microscopically near-identical Plasmodium knowlesi increased substantially over the past decade. However, whether this represents microscopic misdiagnosis or increased recognition of P. knowlesi has remained uncertain. Methods To describe the changing epidemiology of malaria in Sabah, in particular the increasing incidence of P. knowlesi, a re...

  6. Changing Domesticity of Aedes aegypti in Northern Peninsular Malaysia: Reproductive Consequences and Potential Epidemiological Implications

    OpenAIRE

    Saifur, Rahman G. M.; Dieng, Hamady; Hassan, Ahmad Abu; Salmah, Md Rawi Che; Satho, Tomomitsu; Miake, Fumio; Hamdan, Ahmad

    2012-01-01

    Background The domestic dengue vector Aedes aegypti mosquitoes breed in indoor containers. However, in northern peninsular Malaysia, they show equal preference for breeding in both indoor and outdoor habitats. To evaluate the epidemiological implications of this peridomestic adaptation, we examined whether Ae. aegypti exhibits decreased survival, gonotrophic activity, and fecundity due to lack of host availability and the changing breeding behavior. Methodology/Principal Findings This yearlon...

  7. Climate change and epidemiology of human parasitoses in Saudi Arabia:A review

    Institute of Scientific and Technical Information of China (English)

    Wael Mohamed Lotfy; Souad Mohamed Alsaqabi

    2016-01-01

    Climate change is an emerging global problem. It has hazardous effects that vary across different geographic regions and populations. It is anticipated to have significant effects in Saudi Arabia. The present work reviews the future of human parasitoses in Saudi Arabia in response to the expected climate change. The key projections are increased precipitations, flash floods, unstable temperatures, sea-level rise and shoreline retreat. Such environmental changes could strongly influence the epidemiology of fly-borne, mosquito-borne, snail-borne and water-borne human parasitoses in the country.

  8. Climate change and epidemiology of human parasitoses in Saudi Arabia: A review

    Directory of Open Access Journals (Sweden)

    Wael Mohamed Lotfy

    2016-07-01

    Full Text Available Climate change is an emerging global problem. It has hazardous effects that vary across different geographic regions and populations. It is anticipated to have significant effects in Saudi Arabia. The present work reviews the future of human parasitoses in Saudi Arabia in response to the expected climate change. The key projections are increased precipitations, flash floods, unstable temperatures, sea-level rise and shoreline retreat. Such environmental changes could strongly influence the epidemiology of fly-borne, mosquito-borne, snail-borne and water-borne human parasitoses in the country.

  9. [Research advances in molecular epidemiology and vaccines of Coxsackievirus A16].

    Science.gov (United States)

    Chen, Xiang-Peng; Tan, Xiao-Juan; Xu, Wen-Bo

    2014-07-01

    Epidemics of hand, foot and mouth disease (HFMD) have mainly been caused by Coxsackievirus A16 (CVA16) and Enterovirus A 71 (EV-A71), which circulated alternatively or together in the affected area. CVA16 has caused numerous outbreaks and epidemics in multiple countries and geographical regions, and has become an important public health problem. Based on an analysis of the complete VP1 coding region, all CVA16 strains can be divided into genotypes A, B1, and B2. Furthermore, genotype B1 can be divided into subgenotypes B1a, B1b, and B1c. After 2000, no reports of genotype B2 virus strains have been reported. All of the CVA16 strains reported in mainland China have belonged to subgenotypes B1a and B1b. Most CVA16-associated infections cause only mild symptoms; however, some CVA16 infections can lead to severe complications and even death. Vaccination is considered to be the most effective method to control the transmission and infection rate of this virus. A number of research groups are studying various vaccine types, including inactivated vaccines, genetic engineering vaccines, and DNA vaccines, amongst others. In this review, an overview is provided of the research advances in molecular epidemiology and vaccines of CVA16.

  10. Molecular epidemiology of imported cases of leishmaniasis in Australia from 2008 to 2014.

    Directory of Open Access Journals (Sweden)

    Tamalee Roberts

    Full Text Available Leishmaniasis is a vector borne disease caused by protozoa of the genus Leishmania. Human leishmaniasis is not endemic in Australia though imported cases are regularly encountered. This study aimed to provide an update on the molecular epidemiology of imported leishmaniasis in Australia. Of a total of 206 biopsies and bone marrow specimens submitted to St Vincent's Hospital Sydney for leishmaniasis diagnosis by PCR, 55 were found to be positive for Leishmania DNA. All PCR products were subjected to restriction fragment length polymorphism analysis for identification of the causative species. Five Leishmania species/species complexes were identified with Leishmania tropica being the most common (30/55. Travel or prior residence in a Leishmania endemic region was the most common route of acquisition with ~47% of patients having lived in or travelled to Afghanistan. Cutaneous leishmaniasis was the most common manifestation (94% with only 3 cases of visceral leishmaniasis and no cases of mucocutaneous leishmaniasis encountered. This report indicates that imported leishmaniasis is becoming increasingly common in Australia due to an increase in global travel and immigration. As such, Australian clinicians must be made aware of this trend and consider leishmaniasis in patients with suspicious symptoms and a history of travel in endemic areas. This study also discusses the recent identification of a unique Leishmania species found in native kangaroos and a potential vector host which could create the opportunity for the establishment of a local transmission cycle within humans.

  11. Antimicrobial susceptibility/resistance and molecular epidemiological characteristics of Neisseria gonorrhoeae in 2009 in Belarus.

    Science.gov (United States)

    Glazkova, Slavyana; Golparian, Daniel; Titov, Leonid; Pankratova, Nataliya; Suhabokava, Nataliya; Shimanskaya, Irina; Domeika, Marius; Unemo, Magnus

    2011-08-01

    Increased antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a global concern, and ultimately gonorrhoea may become untreatable. Nonetheless, AMR data from East-Europe are scarce beyond Russia, and no AMR data or other characteristics of gonococci have been reported from Belarus for more than 20 years. The aim was to describe the prevalence of AMR, and report molecular epidemiological characteristics of gonococci circulating in 2009 in Belarus. In a sample of 80 isolates, resistance prevalences to antimicrobials used for gonorrhoea treatment in Belarus were: Ceftriaxone 0%, spectinomycin 0%, azithromycin 17.3%, tetracycline 25.9%, ciprofloxacin 34.6% and erythromycin 59.2%. The isolates displayed no penA mosaic alleles, 38 porB gene sequences and 35 N. gonorrhoeae multiantigen sequence types, of which 20 have not been described before worldwide. Due to the high levels of antimicrobial resistance, only ceftriaxone and spectinomycin can be recommended for empirical treatment of gonorrhoea in Belarus according to WHO recommendations. Continuous gonococcal AMR surveillance in Eastern Europe is crucial. This is now initiated in Belarus using WHO protocols.

  12. Evolving microbiology and molecular epidemiology of acute otitis media in the pneumococcal conjugate vaccine era.

    Science.gov (United States)

    Pichichero, Michael E; Casey, Janet R

    2007-10-01

    The addition of the 7-valent pneumococcal conjugate vaccine (PCV7) to the routine immunization schedule in the United States for infants has produced a much more favorable impact on the incidence of acute otitis media (AOM) than anticipated. Because the serotypes included in PCV7 were those most frequently expressing antibiotic resistance in 2001, predictions were made that up to 98% of pneumococcal AOM episodes would be caused by penicillin susceptible strains. However, recent studies have shown that the benefits of PCV7 are becoming eroded. Replacement serotypes of pneumococci have emerged, expressing polysaccharide capsules different from those included in PCV7, with increasing frequency. These replacement strains are coming to dominate in the nasopharynx and in AOM isolates (and in invasive disease). Expansion in the isolation of serotypes 3, 7F, 15B/C/F, 19A, 22F, 33F, and 38 has been described in various surveillance systems. Pneumococcal strains expressing non-PCV7 capsular serotypes also appear to be rapidly acquiring resistance to penicillin and other antibiotics. Emergence of strains of pneumococci expressing non-PCV7 capsular serotypes is occurring by multiple mechanisms including capsular switching as suggested by molecular epidemiology studies. Expansion of the number of serotypes included in pneumococcal conjugate vaccines is needed to sustain a long-term benefit from immunization against these bacteria.

  13. Recent advances and perspectives in molecular epidemiology of Taenia solium cysticercosis.

    Science.gov (United States)

    Ito, Akira; Yanagida, Tetsuya; Nakao, Minoru

    2016-06-01

    Cysticercosis caused by accidental ingestion of eggs of Taenia solium is spreading all over the world through globalization and is one of the most neglected, neglected tropical diseases (NTDs) or neglected zoonotic diseases (NZDs). In the present study, the reason why T. solium cysticercosis has been neglected is discussed at first, and followed with an overview on the most recent advances and perspectives in molecular approaches for epidemiology of T. solium taeniasis/cysticercosis, since although taeniasis does not constitute recognized zoonoses, transmission and complete development are dependent on human definitive hosts. Main topics are discussions on (1) the two, Asian and Afro/American, genotypes of T. solium, (2) comparative analysis of mitochondrial (haploid) and nuclear (diploid) genes, and (3) the presence of hybrids of these two genotypes which indicates out-crossing of two genotypes in hermaphrodite tapeworms in Madagascar. Additional topics are on (4) the usefulness of phylogeographic analyses to discuss where the infection was acquired from, and (5) miscellaneous unsolved topics around these genetic diversity of T. solium.

  14. Recent advances and perspectives in molecular epidemiology of Taenia solium cysticercosis.

    Science.gov (United States)

    Ito, Akira; Yanagida, Tetsuya; Nakao, Minoru

    2016-06-01

    Cysticercosis caused by accidental ingestion of eggs of Taenia solium is spreading all over the world through globalization and is one of the most neglected, neglected tropical diseases (NTDs) or neglected zoonotic diseases (NZDs). In the present study, the reason why T. solium cysticercosis has been neglected is discussed at first, and followed with an overview on the most recent advances and perspectives in molecular approaches for epidemiology of T. solium taeniasis/cysticercosis, since although taeniasis does not constitute recognized zoonoses, transmission and complete development are dependent on human definitive hosts. Main topics are discussions on (1) the two, Asian and Afro/American, genotypes of T. solium, (2) comparative analysis of mitochondrial (haploid) and nuclear (diploid) genes, and (3) the presence of hybrids of these two genotypes which indicates out-crossing of two genotypes in hermaphrodite tapeworms in Madagascar. Additional topics are on (4) the usefulness of phylogeographic analyses to discuss where the infection was acquired from, and (5) miscellaneous unsolved topics around these genetic diversity of T. solium. PMID:26112071

  15. Molecular epidemiology of KPC-2-producing Enterobacteriaceae (non-Klebsiella pneumoniae) isolated from Brazil.

    Science.gov (United States)

    Tavares, Carolina Padilha; Pereira, Polyana Silva; Marques, Elizabeth de Andrade; Faria, Celio; de Souza, Maria da Penha Araújo Herkenhoff; de Almeida, Robmary; Alves, Carlene de Fátima Morais; Asensi, Marise Dutra; Carvalho-Assef, Ana Paula D'Alincourt

    2015-08-01

    In Brazil, since 2009, there has been an ever increasing widespread of the bla(KPC-2) gene, mainly in Klebsiella pneumoniae. This study aims to assess the molecular epidemiology and genetic background of this gene in Enterobacteriaceae (non-K. pneumoniae) species from 9 Brazilian states between 2009 and 2011. Three hundred eighty-seven isolates were analyzed exhibiting nonsusceptibility to carbapenems, in which the bla(KPC-2) gene was detected in 21.4%. By disk diffusion and E-test, these isolates exhibited high rates of resistance to most of the antimicrobials tested, including tigecycline (45.6% nonsusceptible) and polymyxin B (16.5%), the most resistant species being Enterobacter aerogenes and Enterobacter cloacae. We found great clonal diversity and a variety of bla(KPC-2)-carrying plasmids, all of them exhibiting a partial Tn4401 structure. Therefore, this study demonstrates the dissemination of KPC-2 in 9 Enterobacteriaceae species, including species that were not previously described such as Pantoea agglomerans and Providencia stuartii. PMID:25935630

  16. Molecular Epidemiological Characterization and Health Burden of Thalassemias in the Chaoshan Region, People's Republic of China.

    Science.gov (United States)

    Zheng, Xiangbin; Lin, Min; Yang, Hui; Pan, Mei-Chen; Cai, Ying-Mu; Wu, Jiao-Ren; Lin, Fen; Zhan, Xiao-Fen; Luo, Zhao-Yun; Yang, Hui-Tian; Yang, Li-Ye

    2016-01-01

    Thalassemia is one of the most prevalent inherited disease in southern China. However, there have been only a few epidemiological studies of thalassemia in the Chaoshan region of Guangdong Province, People's Republic of China (PRC). A total of 6231 unrelated subjects in two main geographical cities of the Chaoshan region was analyzed for thalassemia. Seven hundred and thirty-six cases of suspected thalassemia carriers with microcytosis [mean corpuscular volume (MCV) T and HBB: c.126_129delCTTT, accounting for 69.81% of the β-thal defects in the studied individuals. In addition, a rare mutation, Cap +1 (A>C) (HBB: c.-50A>C) was described for the first time in the Chaoshan region. Our results gave a heterozygote frequency of 5.31% for common α- and β-thal in the Chaoshan region, and also indicated a higher prevalence of thalassemia with a heterozygote frequency of 6.29% in Chaozhou, followed by Shantou (3.37%). This study provided a detailed prevalence and molecular characterization of thalassemia in the Chaoshan region, and will be valuable for developing a strategy for prevention of thalassemia and reducing excessive health care costs in this area. PMID:26865073

  17. Spatial and Molecular Epidemiology of Giardia intestinalis Deep in the Amazon, Brazil

    Science.gov (United States)

    Coronato Nunes, Beatriz; Pavan, Márcio G.; Jaeger, Lauren H.; Monteiro, Kerla J. L.; Xavier, Samanta C. C.; Monteiro, Fernando A.; Bóia, Márcio N.; Carvalho-Costa, Filipe A.

    2016-01-01

    Background Current control policies for intestinal parasitosis focuses on soil-transmitted helminths, being ineffective against Giardia intestinalis, a highly prevalent protozoon that impacts children’s nutritional status in developing countries. The objective of this study was to explore spatial and molecular epidemiology of Giardia intestinalis in children of Amerindian descent in the Brazilian Amazon. Methodology/Principal Findings A cross sectional survey was performed in the Brazilian Amazon with 433 children aged 1 to 14 years. Fecal samples were processed through parasitological techniques and molecular characterization. Prevalence of G. intestinalis infection was 16.9% (73/433), reaching 22.2% (35/158) among children aged 2–5 years, and a wide distribution throughout the city with some hot spots. Positivity-rate was similar among children living in distinct socioeconomic strata (48/280 [17.1%] and 19/116 [16.4%] below and above the poverty line, respectively). Sequencing of the β-giardin gene revealed 52.2% (n = 12) of assemblage A and 47.8% (n = 11) of assemblage B with high haplotype diversity for the latter. The isolates clustered into two well-supported G. intestinalis clades. A total of 38 haplotypes were obtained, with the following subassemblages distribution: 5.3% (n = 2) AII, 26.3% (n = 10) AIII, 7.9% (n = 3) BIII, and 60.5% (n = 23) new B genotypes not previously described. Conclusions/Significance Giardia intestinalis infection presents a high prevalence rate among Amerindian descended children living in Santa Isabel do Rio Negro/Amazon. The wide distribution observed in a small city suggests the presence of multiple sources of infection, which could be related to environmental contamination with feces, possibly of human and animal origin, highlighting the need of improving sanitation, safe water supply and access to diagnosis and adequate treatment of infections. PMID:27392098

  18. Molecular epidemiology of human immunodeficiency virus type 1 in Guangdong province of southern China.

    Directory of Open Access Journals (Sweden)

    Song Chen

    Full Text Available BACKGROUND: Although the outbreak of human immunodeficiency virus type 1 (HIV-1 in Guangdong has been documented for more than a decade, the molecular characteristics of such a regional HIV-1 epidemic remained unknown. METHODOLOGY/PRINCIPAL FINDINGS: By sequencing of HIV-1 pol/env genes and phylogenetic analysis, we performed a molecular epidemiologic study in a representative subset (n  = 200 of the 508 HIV-1-seropositive individuals followed up at the center for HIV/AIDS care and treatment of Guangzhou Hospital of Infectious Diseases. Of 157 samples (54.1% heterosexual acquired adults, 20.4% needle-sharing drug users, 5.7% receivers of blood transfusion, 1.3% men who have sex with men, and 18.5% remained unknown with successful sequencing for both pol and env genes, 105 (66.9% HIV-1 subtype CRF01_AE and 24 (15.3% CRF07_BC, 9 (5.7% B', 5 (3.2% CRF08_BC, 5 (3.2% B, 1 (0.6% C, 3 (1.9% CRF02_AG, and 5 (3.2% inter-region recombinants were identified within pol/env sequences. Thirteen (8.3% samples (3 naïves, 6 and 5 received with antiretroviral treatment [ART] 1-21 weeks and ≥24 weeks respectively showed mutations conferring resistance to nucleoside/nonnucleoside reverse transcriptase inhibitors or protease inhibitors. Among 63 ART-naïve patients, 3 (4.8% showed single or multiple drug resistant mutations. Phylogenetic analysis showed 8 small clusters (2-3 sequences/cluster with only 17 (10.8% sequences involved. CONCLUSION/SIGNIFICANCE: This study confirms that sexual transmission with dominant CRF01_AE strain is a major risk for current HIV-1 outbreak in the Guangdong's general population. The transmission with drug-resistant variants is starting to emerge in this region.

  19. Spatial and Molecular Epidemiology of Giardia intestinalis Deep in the Amazon, Brazil.

    Directory of Open Access Journals (Sweden)

    Beatriz Coronato Nunes

    Full Text Available Current control policies for intestinal parasitosis focuses on soil-transmitted helminths, being ineffective against Giardia intestinalis, a highly prevalent protozoon that impacts children's nutritional status in developing countries. The objective of this study was to explore spatial and molecular epidemiology of Giardia intestinalis in children of Amerindian descent in the Brazilian Amazon.A cross sectional survey was performed in the Brazilian Amazon with 433 children aged 1 to 14 years. Fecal samples were processed through parasitological techniques and molecular characterization. Prevalence of G. intestinalis infection was 16.9% (73/433, reaching 22.2% (35/158 among children aged 2-5 years, and a wide distribution throughout the city with some hot spots. Positivity-rate was similar among children living in distinct socioeconomic strata (48/280 [17.1%] and 19/116 [16.4%] below and above the poverty line, respectively. Sequencing of the β-giardin gene revealed 52.2% (n = 12 of assemblage A and 47.8% (n = 11 of assemblage B with high haplotype diversity for the latter. The isolates clustered into two well-supported G. intestinalis clades. A total of 38 haplotypes were obtained, with the following subassemblages distribution: 5.3% (n = 2 AII, 26.3% (n = 10 AIII, 7.9% (n = 3 BIII, and 60.5% (n = 23 new B genotypes not previously described.Giardia intestinalis infection presents a high prevalence rate among Amerindian descended children living in Santa Isabel do Rio Negro/Amazon. The wide distribution observed in a small city suggests the presence of multiple sources of infection, which could be related to environmental contamination with feces, possibly of human and animal origin, highlighting the need of improving sanitation, safe water supply and access to diagnosis and adequate treatment of infections.

  20. New insights into the molecular epidemiology and population genetics of Schistosoma mansoni in Ugandan pre-school children and mothers.

    Directory of Open Access Journals (Sweden)

    Martha Betson

    Full Text Available Significant numbers of pre-school children are infected with Schistosoma mansoni in sub-Saharan Africa and are likely to play a role in parasite transmission. However, they are currently excluded from control programmes. Molecular phylogenetic studies have provided insights into the evolutionary origins and transmission dynamics of S. mansoni, but there has been no research into schistosome molecular epidemiology in pre-school children. Here, we investigated the genetic diversity and population structure of S. mansoni in pre-school children and mothers living in lakeshore communities in Uganda and monitored for changes over time after praziquantel treatment. Parasites were sampled from children (<6 years and mothers enrolled in the longitudinal Schistosomiasis Mothers and Infants Study at baseline and at 6-, 12- and 18-month follow-up surveys. 1347 parasites from 35 mothers and 45 children were genotyped by direct sequencing of the cytochrome c oxidase (cox1 gene. The cox1 region was highly diverse with over 230 unique sequences identified. Parasite populations were genetically differentiated between lakes and non-synonymous mutations were more diverse at Lake Victoria than Lake Albert. Surprisingly, parasite populations sampled from children showed a similar genetic diversity to those sampled from mothers, pointing towards a non-linear relationship between duration of exposure and accumulation of parasite diversity. The genetic diversity six months after praziquantel treatment was similar to pre-treatment diversity. Our results confirm the substantial genetic diversity of S. mansoni in East Africa and provide significant insights into transmission dynamics within young children and mothers, important information for schistosomiasis control programmes.

  1. Molecular Epidemiology of Pneumococcal Colonization in Response to Pneumococcal Conjugate Vaccination in Children with Recurrent Acute Otitis Media

    OpenAIRE

    Bogaert, D.; Veenhoven, R.H.; Sluijter, M.; Wannet, W. J. W.; Rijkers, G.T.; Mitchell, T J; Clarke, S. C.; Goessens, W.H.F.; Schilder, A. G.; Sanders, E. A. M.; de Groot, R.; Hermans, P. W. M.

    2005-01-01

    A randomized double-blind trial with a 7-valent pneumococcal conjugate vaccine was conducted in The Netherlands among 383 children, aged 1 to 7 years, with a history of recurrent acute otitis media. No effect of vaccination on the pneumococcal colonization rate was found. However, a shift in serotype distribution was clearly observed (R. Veenhoven et al., Lancet 361:2189-2195, 2003). We investigated the molecular epidemiology of 921 pneumococcal isolates retrieved from both the pneumococcal v...

  2. A reassessment of the epidemiology of Rice yellow mottle virus following recent advances in field and molecular studies

    OpenAIRE

    Traoré, O.; Pinel Galzi, Agnès; Sorho, F.; Sarra, S.; Rakotomalala, M.; Sangu, E.; Kanyeka, Z.; Séré, Y.; Konaté, G.; Fargette, Denis

    2009-01-01

    The available knowledge on the epidemiology of Rice yellow mottle virus (RYMV) is reassessed in the light of major advances in field and molecular studies of the disease it causes in rice. Previously undescribed means of transmission by mammals and through leaf contact have been discovered recently. Several agricultural practices, including the use of seedbed nurseries, have also contributed to a massive build-up of RYMV inoculum. Phytosanitation is now known to be critical to reduce disease ...

  3. Molecular Epidemiological Investigation of Porcine kobuvirus and Its Coinfection Rate with PEDV and SaV in Northwest China

    OpenAIRE

    Chen Wang,; Xi Lan; Bin Yang

    2016-01-01

    Porcine kobuvirus (PKV) has circulated throughout China in recent years. Although many studies have detected it throughout the world, its molecular epidemiology has not been characterized in northwest China. To understand its prevalence, 203 fecal samples were collected from different regions of Gansu Province and tested with reverse transcription-polymerase chain reaction. In this study, we tested these samples for PKV, porcine epidemic diarrhea virus (PEDV), and sapovirus and analyzed the a...

  4. Epidemiología molecular del dengue en las Américas

    Directory of Open Access Journals (Sweden)

    Francisco Javier Díaz Castrillón

    2004-03-01

    Full Text Available

    Después de varias décadas de erradicación, el dengue se ha hecho endémico en la mayor parte de la América tropical y presenta tendencia al crecimiento en la mayoría de los países. La enfermedad ha sufrido un cambio en su expresión clínica en las últimas dos décadas. Una forma grave inexistente hasta los años 80 conocida como fiebre hemorrágica dengue (FHD se ha diseminado primero por las Antillas, luego en Suramérica y más tarde en Centroamérica y Méjico, convirtiéndose en un problema significativo para la salud pública del continente. Las causas del aumento en la virulencia de la enfermedad producida por el virus del dengue (DENV solo se conocen parcialmente. La potenciación de la enfermedad por acción de la inmunidad previa a serotipos diferentes al causante de la infección actual fue demostrada en el sureste asiático, pero no ha sido muy estudiada en las Américas. Además, este mecanismo no provee una explicación completa, puesto que FHD se ha observado también en personas que se infectan por primera vez, y la infección secundaria no siempre resulta en un cuadro severo.

    La epidemiología molecular permite correlacionar la variación genética del agente infeccioso con los eventos epidemiológicos en un marco espacio-temporal. Utilizando técnicas moleculares es posible clasificar las diferentes cepas de cada serotipo del DENV en tres a seis subtipos o “genotipos”. Estos genotipos generalmente están segregados geográficamente pero ocasionalmente son introducidos en países o continentes que no los habían detectado previamente. Estos episodios migratorios pueden o no ir acompañados de cambios en la frecuencia y en la expresión clínica de la enfermedad.

    En las Américas, sólo se ha detectado

  5. Burkholderia cepacia complex in Serbian patients with cystic fibrosis: prevalence and molecular epidemiology.

    Science.gov (United States)

    Vasiljevic, Z V; Novovic, K; Kojic, M; Minic, P; Sovtic, A; Djukic, S; Jovcic, B

    2016-08-01

    The Burkholderia cepacia complex (Bcc) organisms remain significant pathogens in patients with cystic fibrosis (CF). This study was performed to evaluate the prevalence, epidemiological characteristics, and presence of molecular markers associated with virulence and transmissibility of the Bcc strains in the National CF Centre in Belgrade, Serbia. The Bcc isolates collected during the four-year study period (2010-2013) were further examined by 16 s rRNA gene, pulsed-field gel electrophoresis of genomic DNA, multilocus sequence typing analysis, and phylogenetic analysis based on concatenated sequence of seven alleles. Fifty out of 184 patients (27.2 %) were colonized with two Bcc species, B. cenocepacia (n = 49) and B. stabilis (n = 1). Thirty-four patients (18.5 %) had chronic colonization. Typing methods revealed a high level of similarity among Bcc isolates, indicating a person-to-person transmission or acquisition from a common source. New sequence types (STs) were identified, and none of the STs with an international distribution were found. One centre-specific ST, B. cenocepacia ST856, was highly dominant and shared by 48/50 (96 %) patients colonized by Bcc. This clone was characterized by PCR positivity for both the B. cepacia epidemic strain marker and cable pilin, and showed close genetic relatedness to the epidemic strain CZ1 (ST32). These results indicate that the impact of Bcc on airway colonization in the Serbian CF population is high and virtually exclusively limited to a single clone of B. cenocepacia. The presence of a highly transmissible clone and probable patient-to-patient spread was observed. PMID:27177755

  6. Taxonomy, phylogeny and molecular epidemiology of Echinococcus multilocularis: From fundamental knowledge to health ecology.

    Science.gov (United States)

    Knapp, Jenny; Gottstein, Bruno; Saarma, Urmas; Millon, Laurence

    2015-10-30

    Alveolar echinococcosis, caused by the tapeworm Echinococcus multilocularis, is one of the most severe parasitic diseases in humans and represents one of the 17 neglected diseases prioritised by the World Health Organisation (WHO) in 2012. Considering the major medical and veterinary importance of this parasite, the phylogeny of the genus Echinococcus is of considerable importance; yet, despite numerous efforts with both mitochondrial and nuclear data, it has remained unresolved. The genus is clearly complex, and this is one of the reasons for the incomplete understanding of its taxonomy. Although taxonomic studies have recognised E. multilocularis as a separate entity from the Echinococcus granulosus complex and other members of the genus, it would be premature to draw firm conclusions about the taxonomy of the genus before the phylogeny of the whole genus is fully resolved. The recent sequencing of E. multilocularis and E. granulosus genomes opens new possibilities for performing in-depth phylogenetic analyses. In addition, whole genome data provide the possibility of inferring phylogenies based on a large number of functional genes, i.e. genes that trace the evolutionary history of adaptation in E. multilocularis and other members of the genus. Moreover, genomic data open new avenues for studying the molecular epidemiology of E. multilocularis: genotyping studies with larger panels of genetic markers allow the genetic diversity and spatial dynamics of parasites to be evaluated with greater precision. There is an urgent need for international coordination of genotyping of E. multilocularis isolates from animals and human patients. This could be fundamental for a better understanding of the transmission of alveolar echinococcosis and for designing efficient healthcare strategies. PMID:26260408

  7. Surveillance of Canine Rabies in the Central African Republic: Impact on Human Health and Molecular Epidemiology.

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    Vianney Tricou

    2016-02-01

    Full Text Available Although rabies represents an important public health threat, it is still a neglected disease in Asia and Africa where it causes tens of thousands of deaths annually despite available human and animal vaccines. In the Central African Republic (CAR, an endemic country for rabies, this disease remains poorly investigated.To evaluate the extent of the threat that rabies poses in the CAR, we analyzed data for 2012 from the National Reference Laboratory for Rabies, where laboratory confirmation was performed by immunofluorescence and PCR for both animal and human suspected cases, and data from the only anti-rabies dispensary of the country and only place where post-exposure prophylaxis (PEP is available. Both are located in Bangui, the capital of the CAR. For positive samples, a portion of the N gene was amplified and sequenced to determine the molecular epidemiology of circulating strains.In 2012, 966 exposed persons visited the anti-rabies dispensary and 632 received a post-exposure rabies vaccination. More than 90% of the exposed persons were from Bangui and its suburbs and almost 60% of them were under 15-years of age. No rabies-related human death was confirmed. Of the 82 samples from suspected rabid dogs tested, 69 were confirmed positive. Most of the rabid dogs were owned although unvaccinated. There was a strong spatiotemporal correlation within Bangui and within the country between reported human exposures and detection of rabid dogs (P<0.001. Phylogenetic analysis indicated that three variants belonging to Africa I and II lineages actively circulated in 2012.These data indicate that canine rabies was endemic in the CAR in 2012 and had a detrimental impact on human health as shown by the hundreds of exposed persons who received PEP. Implementation of effective public health interventions including mass dog vaccination and improvement of the surveillance and the access to PEP are urgently needed in this country.

  8. Molecular epidemiology of dengue viruses in southern China from 1978 to 2006

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    Liu Jinhua

    2011-06-01

    Full Text Available Abstract To investigate molecular epidemiology of dengue viruses (DENV in southern China, a total of 14 dengue isolates were collected in southern China during each epidemic year between 1978 and 2006 and their full-length genome sequences were obtained by using RT-PCR method. The E gene sequences from additional 6 dengue fever patients in Guangzhou in 2006 were also obtained by using RT-PCR method. Combined with DENVs sequences published in GenBank, phylogenetic analysis and recombination analysis were performed. One hundred and twenty-five E gene sequences and 60 complete genome sequences published in the GenBank were also involved. Phylogenetic analysis showed that there was a wide genetic diversity of DENVs isolated in southern China. DENV-1 strains exist in almost all of the clades of genotype I and IV except the Asia 1 clade of genotype I; DENV-2 stains are grouped into four of the five genotypes except American genotype. DENV-4 strains are grouped into 2 genotypes (I and II. Phylogenetic analysis also showed that all DENV-4 isolates and two DENV-2 isolates were closely related to the prior isolates from neighboring Southeast Asia countries. The DENV-1 strain isolated during the 2006 epidemic is highly homologous to the strains isolated during the 2001 epidemic. Recombination analysis showed no inter-serotype recombination, but 22 intra-serotype recombination events were found across the 32 complete genomes of all Chinese isolates. The study suggested that dengue fever epidemic in Southern China over the past 30 years presented two important modes, 1 imported-cases-induced endemic prevalence; 2 endogenous epidemic outbreak with natural epidemic focus. Recombination may play an important role in dengue virus evolution and adaptation.

  9. Molecular epidemiology of FMDV in Isfahan province of Iran (2006-2009

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    Nabinejad, A.

    2014-05-01

    Full Text Available It is about 50 years that FMD affected the ruminants of Isfahan. Last outbreaks of FMD were happened at 2005 even vaccinated animals, so in current work using RT-PCR, sequencing and regression "r" values, the isolated strains in Isfahan were identified. The aim of this study was molecular epidemiology of FMDV in Isfahan province as the central part of Iran in 2006-2009. According to the result , a highly pathogen A05 strain was isolated from west (Najafabad city about 2 months after the entrance of this virus to Iran through the west and north west margins toward central part and then distributed around 10 cities of Isfahan province. Here it is obvious that the A05 strain of Isfahan just showed 1% difference with A05IR (vaccine strain, in which for A22 were 65 %. Also based on the alignment of 600 bp of 3΄ end of the VP1 sequences of isolated type O comparing with representative of type O Shabestar vaccine strain and the other provinces of Iran, the Isfahan O isolate was 3% distinct from O shabestar vaccine strain. In a random "r" value detection of west isolate strain (A /Najafabad/Isfahan/Iran/ 05 against A87IR were 0.35 and against A05IR were 0.73; For O strain, randomly "r" value of center isolate (O/Isfahan/Isfahan/Iran obtained against Iranian O vaccine strain (O Shabestar were 0.76 and with O 967 (Panasia were 0.88. Regarding to the conclusion, the FMD lived vaccine for Isfahan was improved with A05/Ir FMDV by Razi Vaccine and Serum Research Institute (RVSRI.

  10. Molecular Epidemiology of Oral Treponemes in Patients with Periodontitis and in Periodontitis-Resistant Subjects

    Science.gov (United States)

    Moter, Annette; Riep, Birgit; Haban, Vesna; Heuner, Klaus; Siebert, Gerda; Berning, Moritz; Wyss, Chris; Ehmke, Benjamin; Flemmig, Thomas F.; Göbel, Ulf B.

    2006-01-01

    The etiologic role of oral treponemes in human periodontitis is still under debate. Although seen by dark-field microscopy in large numbers, their possible role is still unclear since they comprise some 60 different phylotypes, most of which are still uncultured. To determine their status as mere commensals or opportunistic pathogens, molecular epidemiological studies are required that include both cultured and as-yet-uncultured organisms. Here we present such data, comparing treponemal populations from chronic periodontitis (CP) or generalized aggressive periodontitis (GAP) patients. As a periodontitis-resistant (PR) control group, we included elderly volunteers with more than 20 natural teeth and no history of periodontal treatment and no or minimal clinical signs of periodontitis. Almost every treponemal phylotype was present in all three groups. For most treponemes, the proportion of subjects positive for a certain species or phylotype was higher in both periodontitis groups than in the PR group. This difference was pronounced for treponemes of the phylogenetic groups II and IV and for Treponema socranskii and Treponema lecithinolyticum. Between the periodontitis groups the only significant differences were seen for T. socranskii and T. lecithinolyticum, which were found more often in periodontal pockets of GAP patients than of CP patients. In contrast, no difference was found for Treponema denticola. Our findings, however, strengthen the hypothesis of treponemes being opportunistic pathogens. It appears that T. socranskii, T. lecithinolyticum and group II and IV treponemes may represent good indicators for periodontitis and suggest the value of the respective probes for microbiological diagnosis in periodontitis subjects. PMID:16954230

  11. Taxonomy, phylogeny and molecular epidemiology of Echinococcus multilocularis: From fundamental knowledge to health ecology.

    Science.gov (United States)

    Knapp, Jenny; Gottstein, Bruno; Saarma, Urmas; Millon, Laurence

    2015-10-30

    Alveolar echinococcosis, caused by the tapeworm Echinococcus multilocularis, is one of the most severe parasitic diseases in humans and represents one of the 17 neglected diseases prioritised by the World Health Organisation (WHO) in 2012. Considering the major medical and veterinary importance of this parasite, the phylogeny of the genus Echinococcus is of considerable importance; yet, despite numerous efforts with both mitochondrial and nuclear data, it has remained unresolved. The genus is clearly complex, and this is one of the reasons for the incomplete understanding of its taxonomy. Although taxonomic studies have recognised E. multilocularis as a separate entity from the Echinococcus granulosus complex and other members of the genus, it would be premature to draw firm conclusions about the taxonomy of the genus before the phylogeny of the whole genus is fully resolved. The recent sequencing of E. multilocularis and E. granulosus genomes opens new possibilities for performing in-depth phylogenetic analyses. In addition, whole genome data provide the possibility of inferring phylogenies based on a large number of functional genes, i.e. genes that trace the evolutionary history of adaptation in E. multilocularis and other members of the genus. Moreover, genomic data open new avenues for studying the molecular epidemiology of E. multilocularis: genotyping studies with larger panels of genetic markers allow the genetic diversity and spatial dynamics of parasites to be evaluated with greater precision. There is an urgent need for international coordination of genotyping of E. multilocularis isolates from animals and human patients. This could be fundamental for a better understanding of the transmission of alveolar echinococcosis and for designing efficient healthcare strategies.

  12. Genotype Distribution and Molecular Epidemiology of Hepatitis C Virus in Hubei, Central China.

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    Jing Peng

    Full Text Available Little is known about the molecular epidemiology of hepatitis C virus (HCV infection in Central China.A total of 570 patients from Hubei Province in central China were enrolled. These patients were tested positive for HCV antibody prior to blood transfusion. Among them, 177 were characterized by partial NS5B and/or Core-E1 sequences and classified into five subtypes: 1b, 83.0% (147/177; 2a, 13.0% (23/177; 3b, 2.3% (4/177; 6a, 1.1% (2/177; 3a, 0.6% (1/177. Analysis of genotype-associated risk factors revealed that paid blood donation and transfusion before 1997 were strongly associated with subtypes 1b and 2a, while some subtype 2a cases were also found in individuals with high risk sexual behaviors; subtypes 3b, 6a, and 3a were detected only in intravenous drug users. Phylogeographic analyses based on the coalescent datasets demonstrated that 1b, 2a, 3b, and 6a were locally epidemic in Hubei Province. Among them, subtype 1b Hubei strains may have served as the origins of this subtype in China, and 2a and 3b Hubei strains may have descended from the northwest and southwest of China, respectively, while 6a Hubei strains may have been imported from the central south and southwest.The results suggest that the migration patterns of HCV in Hubei are complex and variable among different subtypes. Implementation of mandatory HCV screening before donation has significantly decreased the incidence of transfusion-associated HCV infection since 1997. More attention should be paid to intravenous drug use and unsafe sexual contact, which may have become new risk factors for HCV infection in Hubei Province.

  13. Recent changes in bacteremia in patients with cancer: a systematic review of epidemiology and antibiotic resistance.

    Science.gov (United States)

    Montassier, E; Batard, E; Gastinne, T; Potel, G; de La Cochetière, M F

    2013-07-01

    Bacteremia remains a major cause of life-threatening complication in patients with cancer. Significant changes in the spectrum of microorganisms isolated from blood culture have been reported in cancer patients over the past years. The aim of our systematic review was to inventory the recent trends in epidemiology and antibiotic resistance of microorganisms causing bacteremia in cancer patients. Data for this review was identified by searches of Medline, Scopus and Cochrane Library for indexed articles and abstracts published in English since 2008. The principal search terms were: "antimicrobial resistance", "bacteremia", "bacterial epidemiology", "bloodstream infection", "cancer patients", "carbapenem resistance", "Escherichia coli resistance", "extended-spectrum β-lactamase producing E. coli", "febrile neutropenia", "fluoroquinolone resistance", "neutropenic cancer patient", "vancomycin-resistant Enterococcus", and "multidrug resistance". Boolean operators (NOT, AND, OR) were also used in succession to narrow and widen the search. Altogether, 27 articles were selected to be analyzed in the review. We found that Gram-negative bacteria were the most frequent pathogen isolated, particularly in studies with minimal use of antibiotic prophylaxis. Another important trend is the extensive emergence of antimicrobial-resistant strains associated with increased risk of morbidity, mortality and cost. This increasing incidence of antibiotic resistance has been reported in Gram-negative bacteria as well as in Gram-positive bacteria. This exhaustive review, reporting the recent findings in epidemiology and antibiotic resistance of bacteremia in cancer patients, highlights the necessity of local continuous surveillance of bacteremia and stringent enforcement of antibiotic stewardship programs in cancer patients. PMID:23354675

  14. Changing health in China: re-evaluating the epidemiological transition model.

    Science.gov (United States)

    Cook, Ian G; Dummer, Trevor J B

    2004-03-01

    This paper reviews the changing health situation in China, which has shown remarkable improvement in the 50 years since the founding of the People's Republic of China (PRC) in 1949. At first sight this improving health situation follows the classical epidemiological transition model. Just three decades ago health in China was characterised by high rates of infectious disease and early mortality (diseases of poverty) in a mainly peasant society. More recently infectious disease rates have decreased, with corresponding and extended morbidity and mortality associated with an aging population in a rapidly urbanising society. This process has given rise to new health problems, including chronic and degenerative diseases (diseases of affluence). Nonetheless, while there is some validity in the application of the epidemiological transition concept, further analysis demonstrates that China faces a new epidemiological phase, characterised by increasing life expectancy and diseases of affluence coupled with the emergence and re-emergence of infectious diseases. We demonstrate that China's state policy plays a major role in defining the parameters of health in a Chinese context. We conclude that, today, China is faced with a new set of health issues, including the impact of smoking, hypertension, the health effects of environmental pollution and the rise of HIV/AIDS; however, state policy remains vital to the health of China's vast population. The challenge for policy is to maintain health reform whilst tackling the problems associated with rapid urbanisation, widening social and spatial inequalities and the emergence of HIV/AIDS and other infectious diseases.

  15. Prevalence and Molecular Epidemiology of Staphylococcus aureus among Residents of Seven Nursing Homes in Shanghai.

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    Ji Zhang

    Full Text Available Residents in nursing homes (NHs always represent potential reservoirs for Staphylococcus aureus and methicillin-resistant S. aureus (MRSA. To our knowledge, there is no epidemiological information up till now that describes the prevalence and molecular characteristics of S. aureus in nursing home residents in Shanghai, China.Four hundred and ninety-one unique residents from 7 NHs were enrolled in this study. Specimens were collected among these residents including 491 nasal swabs, 487 axillary swabs and 119 skin swabs. S. aureus isolated and identified from the swabs was characterized according to antimicrobial susceptibility profiling, toxin gene prevalence, and multilocus sequence typing (MLST, spa and SCCmec typing.Among the 491 residents screened, S. aureus was isolated in 109 residents from 90 nasal swabs (90/491, 18.3%, 29 axillary swabs (29/487, 6.0%, and 22 skin swabs (22/119, 18.5%. Sixty-eight MRSA isolates were detected in 52 residents from 41 nasal carriers, 15 axillary carriers and 12 skin carriers. The overall prevalence rate of S. aureus and MRSA colonization was 22.2% and 10.6% respectively. Ten residents presented S. aureus in all three sample types and 12 residents presented S. aureus in two of the three sample types collected. Molecular analysis revealed CC1 (29.1% to be the dominant clone in this study, followed by CC398 (19.9%, CC188 (13.5% and CC5 (12.8%. The most common spa type was t127 (22.0%, followed by t14383 (12.8% and t002 (10.6%.A high prevalence of S. aureus and MRSA colonization was revealed in nursing home residents in Shanghai. CC1 was the most common clonal complex and t127 was the most common spa type among NH residents. The data provides an important baseline for future surveillance of S. aureus in NHs in Shanghai and other highly urbanized regions in China. Implementation of infection control strategies must be given high priority in NHs to fight such high prevalence of both MRSA and methicillin

  16. Molecular epidemiology of nonencapsulated Streptococcus pneumoniae among Japanese children with acute otitis media.

    Science.gov (United States)

    Hotomi, Muneki; Nakajima, Kouji; Hiraoka, Masanobu; Nahm, Moon H; Yamanaka, Noboru

    2016-02-01

    The introduction of pneumococcal conjugate vaccine may change the epidemiology of Streptococcus pneumoniae. The increased prevalence of non-vaccine serotypes as the cause of pneumococcal diseases has already reported in the United States and Europe. However, little attention has been focused on the S. pneumoniae. In this study, nonencapsulated S. pneumoniae were identified in 15 isolates (6.4%) out of 236 pneumococcal strains obtained from the nasopharynges of children with acute otitis media (AOM), in 3 isolates (14.3%) out of 21 strains from acute rhinosinusitis, and in 2 isolates (12.5%) out of 16 nasopharyngeal carriage strains obtained from normal healthy children. Among the 20 nonencapsulated S. pneumoniae isolates, 15 (75.0%) isolates had the pspK gene. Seven sequence types (STs) were identified: ST7502 (5 strains), ST1106 (2 strains), ST7803 (2 strains), ST7786 (1 strain), ST6741 (1 strain), ST7496 (1 strain), and ST8642 (1 strain). Because nonencapsulated S. pneumoniae strains are not targeted by the current available pneumococcal vaccines, these strains will gradually become more common in nasopharyngeal carriage. The increase in colonization and dissemination of these strains would increase the risk of AOM and other systemic pneumococcal diseases against which current vaccines cannot provide protection. Nonencapsulated S. pneumoniae may thus become more prevalent as human pathogen.

  17. Changing epidemiology and clinical issues arising in an ageing cystic fibrosis population.

    Science.gov (United States)

    Parkins, Michael D; Parkins, Vicky M; Rendall, Jackie C; Elborn, Stuart

    2011-04-01

    Improvements in the quality and implementation of medical care for individuals with cystic fibrosis (CF) have resulted in a dramatic improvement in survival. Many of these strategies have focused on the effective management of pulmonary disease which has delayed its manifestations into later years. With an increasing number of patients surviving to later years the impact of chronic inflammation and nutritional compromise on other organ systems over a lifetime are increasingly manifest. This review highlights the changing epidemiology of the ageing CF population and the complications that may ensue.

  18. Molecular epidemiology of bovine tuberculosis in wild animals in Spain: a first approach to risk factor analysis.

    Science.gov (United States)

    Parra, A; Larrasa, J; García, A; Alonso, J M; de Mendoza, J Hermoso

    2005-10-31

    In human tuberculosis (Mycobacterium tuberculosis), molecular epidemiology has accurately indicated the risk factors involved in active transmission of the disease, by comparing individuals whose isolates belong to a cluster with patients whose strains are considered unique. Nevertheless, this application has not been used in bovine tuberculosis (Mycobacterium bovis). Our study describes the integration of epidemiological data into molecular classification data on M. bovis isolates. These were isolated from wild ungulates in Extremadura (western Spain) with the objective of detecting the risk factors linked to the association of strains in clades, which are indicators of the active spread of the disease. The molecular markers used were spoligotyping + VNTR typing (loci: VNTR 2165, VNTR 2461, VNTR 0577, VNTR 0580, VNTR 3192 VNTR 2163a and VNTR 2163b) on a population of 59 M. bovis strains isolated from deer (Cervus elaphus), 112 from wild boar (Sus scrofa), six from bovines, 28 from pigs and 2 from goats (n=207). Epidemiological variables included the animal species from which the strain was isolated, pathological condition of the host (incipient lesion, early and late generalisation), date of sampling (during or after the reproductive period) and hunting season. Bivariant analysis was used to establish the risk factors connected to the association of strains and later, the variables were evaluated by means of logistic regression. Molecular typing grouped a total of 131 strains (64.21%) in 28 clusters and 76 isolates shows unique profiles. The association of strains was connected to the appearance of macroscopic lesions during the reproductive period (O.R. 4.80; 95% CI 1.09-22.99, PActive spread was not connected to any species in particular, or to any concrete pathological condition. PMID:16143470

  19. Sankara Nethralaya Diabetic Retinopathy Epidemiology and Molecular Genetic Study (SN--DREAMS III: Study design and research methodology

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    Sahu Chinmaya

    2011-03-01

    Full Text Available Abstract Background To describe the methodology of the Sankara Nethralaya Diabetic Retinopathy Epidemiology and Molecular Genetic Study III, an ongoing epidemiological study to estimate the prevalence of Diabetes and Diabetic Retinopathy in rural population of Kanchipuram and Thiravallur districts of Tamil Nadu, India and to elucidate the clinical, anthropometric, biochemical and genetic risk factors associated with diabetic retinopathy in this rural population. Methods Sankara Nethralaya Diabetic Retinopathy Epidemiology and Molecular Genetic Study III will be a mobile van based epidemiological study; 11,760 participants aged ≥ 40 years will be recruited from the study areas. Eligible subjects will undergo blood sugar estimation to diagnose Diabetes. Oral Glucose Tolerance Test will be done to conform diabetes. All subjects with diabetes will undergo complete information of knowledge, aptitude and practice of diabetes and diabetic retinopathy, Diet questionnaire, demographic data, socioeconomic status, physical activity, anthropometric measurements, and risk of sleep apnoea. A detailed medical and ocular history, a comprehensive eye examination including refraction, slit lamp biomicroscopy examination, indirect ophthalmoscopy, slit lamp biomicroscopy, digital stereo fundus photography and ultrasound of eye will be done in the mobile van. Blood will be collected for biochemical investigations including blood hemoglobin, glycosylated hemoglobin, lipid profile, urea and creatinine, genetic study. Urine will be collected for microalbuminuria. All fundus photographs will be graded at base hospital. Participants who need treatment will be sent to the base hospital. A computerized database is created for the records. Conclusion The study is expected to provide an estimate of the prevalence of Diabetes and Diabetic Retinopathy and also a better understanding of the genetic, anthropometric and socio-economic risk factors associated with Diabetic

  20. Molecular biology, epidemiology, and the demise of the linear no-threshold (LNT) hypothesis

    International Nuclear Information System (INIS)

    The prime concern of radiation protection policy since 1959 has been protecting DNA from damage. The 1995 NCRP Report 121 on collective dose stases that since no human data provides direct support for the linear no threshold hypothesis (LNT), and some studies provide quantitative data that, with statistical significance, contradict LNT, ultimately, confidence in LNT is based on the biophysical concept that the passage of a single charged particle could cause damage to DNA that would result in cancer. Current understanding of the basic molecular biologic mechanisms involved and recent data are examined before presenting several statistically significant epidemiologic studies that contradict the LNT hypothesis. Over eons of time a complex bio-system evolved to control the DNA alterations (oxidative adducts) produced by about 1010 free radicals/cell/d derived from 2-3 % of all metabolized oxygen. Antioxidant prevention, enzymatic repair of DNA damage, and removal of persistent DNA alterations by apoptosis, differentiation, necrosis, and the immune system, sequentially reduce DNA damage from about 106 DNA alterations/cell/d to about 1 mutation/cell/d. These mutations accumulate in stem cells during a lifetime with progressive DNA damage-control impairment associated with aging and malignant growth. A comparatively negligible number of mutations, an average of about 10-7 mutations/cell/d, is produced by low LET radiation background of 0.1 cGy/y. The remarkable efficiency of this bio-system is increased by the adaptive responses to low-dose ionizing radiation. Each of the sequential functions that prevent, repair, and remove DNA damage are adaptively stimulated by long-dose ionizing radiation in contrast to their impairment by high-dose radiation. The biologic effect of radiation is not determined by the number of mutations it creates, but by its effect on the bio-system that controls the relentless enormous burden of oxidative DNA damage. At low doses, radiation

  1. Molecular Epidemiology of Streptococcus pneumoniae Isolates from Children with Recurrent Upper Respiratory Tract Infections.

    Science.gov (United States)

    Korona-Glowniak, Izabela; Maj, Maciej; Siwiec, Radosław; Niedzielski, Artur; Malm, Anna

    2016-01-01

    A total of 125 isolates were recovered from adenoids and/or nasopharynx of 170 children aged 2 to 5 from south-east Poland; they had undergone adenoidectomy for recurrent and/or persistent symptoms of upper respiratory tract infections. Pneumococcal isolates were analyzed by phenotyping (serotyping and antimicrobial resistance tests) and genotyping together with the clonality of the pneumococcal isolates based on resistance determinants, transposon distribution and multilocus sequence typing (MLST). Serotypes 19F, 6B and 23F constituted 44.8% of the isolates. Among all of the strains, 44.8% showed decreased susceptibility to penicillin and resistance to co-trimoxazole (52.8%), tetracycline (38.4%), erythromycin (53.6%), clindamycin (52.8%) and chloramphenicol (27.2%) was observed. Tn6002 was found in 34.8% of erythromycin-resistant isolates while composite Tn2010-in 16.7% of erm(B)-carrying isolates that harboured also mef(E) gene. Tn3872-related elements were detected in 27.3% of erythromycin-resistant strains. In the majority of chloramphenicol-resistant catpC194-carrying isolates (79.4%), ICESp23FST81-family elements were detected. The genotyping showed that pneumococcal population was very heterogeneous; 82 sequence types (STs) were identified, and the most frequent contributed to not more than 8% of the isolates. Nearly 44% STs were novel, each of them was recovered only from one child. Four STs belonged to one of the 43 worldwide spread resistant pneumococcal clones currently accepted by Pneumococcal Molecular Epidemiology Network (PMEN), i.e. Spain 9V-3, Spain 23F-1, Norway NT-42 and Poland 6B-20, accounting for 12 (16.7%) of the 75 nonususceptible isolates, and five STs were single-locus variants of PMEN resistant clones (England 14-9, Spain 9V-3, Spain 23F-1, Greece 21-30, Denmark 14-32), accounting 9 (12%) of nonsusceptible isolates. A few MDR clones belonging to 6B and 19F serotypes found among preschool children emphasizes rather the role of clonal

  2. Molecular epidemiology and genetic diversity of human rhinovirus affecting hospitalized children in Rome.

    Science.gov (United States)

    Pierangeli, Alessandra; Ciccozzi, Massimo; Chiavelli, Stefano; Concato, Carlo; Giovanetti, Marta; Cella, Eleonora; Spano, Lucia; Scagnolari, Carolina; Moretti, Corrado; Papoff, Paola; Muraca, Maurizio; Midulla, Fabio; Antonelli, Guido

    2013-08-01

    Human rhinoviruses (HRV) have been re-classified into three species (A-C), but the recently discovered HRV-C strains are not fully characterized yet. This study aimed to undertake a molecular and epidemiological characterization of HRV strains infecting children hospitalized over one year in two large research hospitals in Rome. Nasal washings from single HRV infections were retrospectively subjected to phylogenetic analysis on two genomic regions: the central part of the 5'Untranslated Region (5'UTR) and the Viral Protein (VP) 4 gene with the 5' portion of the VP2 gene (VP4/2). Forty-five different strains were identified in 73 HRV-positive children: 55 % of the cases were HRV-A, 38 % HRV-C and only 7 % HRV-B. HRV-C cases were less frequent than HRV-A during summer months and more frequent in cases presenting wheezing with respect to HRV-A. Species distribution was similar with respect to patient age, and seasonality differed during summer months with fewer HRV-C than HRV-A cases. On admission, a significantly higher number of HRV-C cases presented with wheezing with respect to HRV-A. The inter- and intra-genotype variability in VP4/2 was higher than in 5'UTR; in particular, HRV-A patient VP4/2 sequences were highly divergent (8-14 %) at the nucleotide level from those of their reference strains, but VP4 amino acid sequence was highly conserved. In HRV-C isolates, the region preceding the initiator AUG, the amino acids involved in VP4 myristoylation, the VP4-VP2 cleavage site and the cis-acting replication element were highly conserved. Differently, VP4 amino acid conservation was significantly lower in HRV-C than in HRV-A strains, especially in the transiently exposed VP4 N-terminus. This study confirmed the high number of different HRV genotypes infecting hospitalized children over one year and reveals a greater than expected variability in HRV-C VP4 protein, potentially suggestive of differences in replication.

  3. Molecular epidemiology of enterovirus 71 infection in the central region of Taiwan from 2002 to 2012.

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    Wen-Hao Wu

    Full Text Available Enterovirus 71 (EV71, a causative agent of hand, foot, and mouth disease can be classified into three genotypes and many subtypes. The objectives of this study were to conduct a molecular epidemiological study of EV71 in the central region of Taiwan from 2002-2012 and to test the hypothesis that whether the alternative appearance of different EV71 subtypes in Taiwan is due to transmission from neighboring countries or from re-emergence of pre-existing local strains. We selected 174 EV71 isolates and used reverse transcription-polymerase chain reaction to amplify their VP1 region for DNA sequencing. Phylogenetic analyses were conducted using Neighbor-Joining, Maximum Likelihood and Bayesian methods. We found that the major subtypes of EV71 in Taiwan were B4 for 2002 epidemic, C4 for 2004-2005 epidemic, B5 for 2008-2009 epidemic, C4 for 2010 epidemic and B5 for 2011-2012 epidemic. Phylogenetic analysis demonstrated that the 2002 and 2008 epidemics were associated with EV71 from Malaysia and Singapore; while both 2010 and 2011-2012 epidemics originated from different regions of mainland China including Shanghai, Henan, Xiamen and Gong-Dong. Furthermore, minor strains have been identified in each epidemic and some of them were correlated with the subsequent outbreaks. Therefore, the EV71 infection in Taiwan may originate from pre-existing minor strains or from other regions in Asia including mainland China. In addition, 101 EV71 isolates were selected for the detection of new recombinant strains using the nucleotide sequences spanning the VP1-2A-2B region. No new recombinant strain was found. Analysis of clinical manifestations showed that patients infected with C4 had significantly higher rates of pharyngeal vesicles or ulcers than patients infected with B5. This is the first study demonstrating that different EV 71 genotypes may have different clinical manifestations and the association of EV71 infections between Taiwan and mainland China.

  4. Molecular Epidemiology of Streptococcus pneumoniae Isolates from Children with Recurrent Upper Respiratory Tract Infections.

    Science.gov (United States)

    Korona-Glowniak, Izabela; Maj, Maciej; Siwiec, Radosław; Niedzielski, Artur; Malm, Anna

    2016-01-01

    A total of 125 isolates were recovered from adenoids and/or nasopharynx of 170 children aged 2 to 5 from south-east Poland; they had undergone adenoidectomy for recurrent and/or persistent symptoms of upper respiratory tract infections. Pneumococcal isolates were analyzed by phenotyping (serotyping and antimicrobial resistance tests) and genotyping together with the clonality of the pneumococcal isolates based on resistance determinants, transposon distribution and multilocus sequence typing (MLST). Serotypes 19F, 6B and 23F constituted 44.8% of the isolates. Among all of the strains, 44.8% showed decreased susceptibility to penicillin and resistance to co-trimoxazole (52.8%), tetracycline (38.4%), erythromycin (53.6%), clindamycin (52.8%) and chloramphenicol (27.2%) was observed. Tn6002 was found in 34.8% of erythromycin-resistant isolates while composite Tn2010-in 16.7% of erm(B)-carrying isolates that harboured also mef(E) gene. Tn3872-related elements were detected in 27.3% of erythromycin-resistant strains. In the majority of chloramphenicol-resistant catpC194-carrying isolates (79.4%), ICESp23FST81-family elements were detected. The genotyping showed that pneumococcal population was very heterogeneous; 82 sequence types (STs) were identified, and the most frequent contributed to not more than 8% of the isolates. Nearly 44% STs were novel, each of them was recovered only from one child. Four STs belonged to one of the 43 worldwide spread resistant pneumococcal clones currently accepted by Pneumococcal Molecular Epidemiology Network (PMEN), i.e. Spain 9V-3, Spain 23F-1, Norway NT-42 and Poland 6B-20, accounting for 12 (16.7%) of the 75 nonususceptible isolates, and five STs were single-locus variants of PMEN resistant clones (England 14-9, Spain 9V-3, Spain 23F-1, Greece 21-30, Denmark 14-32), accounting 9 (12%) of nonsusceptible isolates. A few MDR clones belonging to 6B and 19F serotypes found among preschool children emphasizes rather the role of clonal

  5. MOLECULAR EPIDEMIOLOGY FEATURES OF HBV/HDV CO-INFECTION IN KYRGYZSTAN

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    A. V. Semenov

    2016-01-01

    Full Text Available One of the most serious health problems in the world are hepatotropic viruses that cause chronic liver disease. Hepatitis B virus is distributed globally; around 5% of the carriers are also infected with hepatitis delta virus. Co-infection or superinfection of hepatitis viruses B and D significantly associated with a much more severe liver disease, compared with infection only hepatitis B virus. However, examination of hepatitis virus B carriers for the presence of hepatitis D virus in most regions of the world is not mandatory. It should be noted that the complete genotype mapping of viruses hepatitis B and D isolated on the territory of the CIS and the countries of the former Soviet Union, there is not yet, despite the constantly ongoing works devoted genotyping hepatotropic virus in the territory of the Russian Federation and neighboring countries. Due to the fact that one of the prospective ways of spreading viruses is the “labor migration” the inhabitants of Central Asia in other countries, including the Russian Federation, there is a need to pay attention to the situation of viral hepatitis in the region. The aim of our study was to estimate the prevalence of genetic variants and characteristics of molecular epidemiology of chronic viral hepatitis co-infection B + D in Kyrgyzstan. The study involved 30 plasma samples from patients with chronic viral hepatitis B and D from different regions of Kyrgyzstan. Based on the phylogenetic analysis of the isolates showed that among patients examined HBV identified only D genotype. Based on the phylogenetic analysis of the isolates indicated that among the examined patients with chronic viral hepatitis B revealed only genotype D. It is shown prevalence of HBV subtype D1 (73.34% compared to the HBV subtype D2 (3.33% and D3 (23.33%. Revealed HDV genotype I with highly variable region of the gene encoding the delta antigen. The high similarity of some isolates with strains specific to neighboring

  6. The molecular epidemiological characteristics of streptococci isolated from primary school children in Vietnam

    Directory of Open Access Journals (Sweden)

    A. G. Nosik

    2015-01-01

    Full Text Available Objectives. The goal of the study was to isolate group A, С, and G streptococci from children and characterize them by the methods of molecular epidemiology.Materials and methods. Group A, С, and G streptococci were isolated from tonsils and back wall of pharynx of Vietnamese children during 2012–2014. сpn60 gene based PCR approach and rnpB gene sequencing were used to identify streptococcal species belonging to group С and G streptococci. The presence of scpA, lmb, nga, slo virulence genes was analyzed in S. anginosus and S. dysgalactiae subsp. equisimilis strainS. emm-typing of S. pyogenes was done as published (http://www.cdc.gov/ncidod/biotech/strep/MProteinGene_typing.htm. Antibiotic resistance of the strains was tested by the disk diffusion method.Results. A total of 1359 children were examined. Group A streptococci (S. pyogenes were isolated from 49 children, group C streptococci – from 8 children (4 stains – S. anginosus, 1 strain – S. dysgalactiae subsp. equisimilis, 1 strain – S. parasanguinis, 1 strain – S. gordonii, 1 strain – S. constellatus, and group G streptococci – from 75 children (55 stains – S. anginosus, 8 stains – S. dysgalactiae subsp. equisimilis, 4 stains – S. sanguinis, 3 stains – S. parasanguinis, 2 stains – S. australis, 2 stains – S. constellatus, 1 stain – S. mitis. emm-typing of 47 S. pyogenes strains revealed 15 different emm-subtypes belonging to 11 different emm-typeS. The subtypes emm104.0 and emm109.1 were found to be predominant. S. anginosus strains under study were genetically heterogeneous for the presence of virulence genes. All tested strains were susceptible to cephalosporins and vancomycin, and resistant to amikacine. A total of 70% and 52,5% of S. pyogenes were resistant to tetracycline and erythromycin, respectively.

  7. Molecular epidemiology and phylogenetic analyses of influenza B virus in Thailand during 2010 to 2014.

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    Nipaporn Tewawong

    Full Text Available Influenza B virus remains a major contributor to the seasonal influenza outbreak and its prevalence has increased worldwide. We investigated the epidemiology and analyzed the full genome sequences of influenza B virus strains in Thailand between 2010 and 2014. Samples from the upper respiratory tract were collected from patients diagnosed with influenza like-illness. All samples were screened for influenza A/B viruses by one-step multiplex real-time RT-PCR. The whole genome of 53 influenza B isolates were amplified, sequenced, and analyzed. From 14,418 respiratory samples collected during 2010 to 2014, a total of 3,050 tested positive for influenza virus. Approximately 3.27% (471/14,418 were influenza B virus samples. Fifty three isolates of influenza B virus were randomly chosen for detailed whole genome analysis. Phylogenetic analysis of the HA gene showed clusters in Victoria clades 1A, 1B, 3, 5 and Yamagata clades 2 and 3. Both B/Victoria and B/Yamagata lineages were found to co-circulate during this time. The NA sequences of all isolates belonged to lineage II and consisted of viruses from both HA Victoria and Yamagata lineages, reflecting possible reassortment of the HA and NA genes. No significant changes were seen in the NA protein. The phylogenetic trees generated through the analysis of the PB1 and PB2 genes closely resembled that of the HA gene, while trees generated from the analysis of the PA, NP, and M genes showed similar topology. The NS gene exhibited the pattern of genetic reassortment distinct from those of the PA, NP or M genes. Thus, antigenic drift and genetic reassortment among the influenza B virus strains were observed in the isolates examined. Our findings indicate that the co-circulation of two distinct lineages of influenza B viruses and the limitation of cross-protection of the current vaccine formulation provide support for quadrivalent influenza vaccine in this region.

  8. Molecular epidemiology of lung cancer and geographic variations with special reference to EGFR mutations.

    Science.gov (United States)

    Mitsudomi, Tetsuya

    2014-08-01

    Lung cancer is a leading cause of cancer-related mortality in many countries. Although recent advances in targeted therapy against driver oncogenes have significantly improved patient outcome, cure of this disease is still exceptional. Although tobacco is a known cause of lung cancer, not all smokers develop lung cancer, and conversely many patients, especially Asian female patients with lung cancer, are lifetime never-smokers. Therefore, efforts to understand the basis for different susceptibilities to lung cancer among individuals with different genetic, biologic, ethnic, and social backgrounds are important to help develop effective preventive measures. Lung cancer in never-smokers has many different characteristics to lung cancer in smokers, such as adenocarcinoma predominance and high frequency of epidermal growth factor receptor (EGFR) mutation yet low number of genetic changes. Epidemiologic studies suggest that East Asians are more susceptible to smoking-unrelated lung cancer but less susceptible to smoking-related lung cancer compared with Caucasians. Mutations in the EGFR gene are more common in Asian females and never-smokers. Our case-control study suggests that EGFR mutation occurs independent of smoking, and that the apparent low frequency of EGFR mutations in smokers may be the result of dilution by smoking-related lung cancer. The frequencies of three EGFR gene polymorphisms associated with increased protein expression are significantly different between East Asians and Caucasians, favoring lower protein expression in East Asians. Although these may be associated with preferred expression of the EGFR mutant allele, it is difficult to explain the frequent EGFR mutation in Asian patients. Genome wide association studies (GWAS) revealed several loci related to lung cancer susceptibility. In the future, GWAS may identify loci that are specifically related to EGFR-targeted carcinogenesis, leading to identification of carcinogens that induce EGFR

  9. Molecular epidemiological and serological studies of bovine leukemia virus (BLV) infection in Thailand cattle.

    Science.gov (United States)

    Lee, EunJung; Kim, Eun-Ju; Ratthanophart, Jadsada; Vitoonpong, Ratchaneekorn; Kim, Bo-Hye; Cho, In-Soo; Song, Jae-Young; Lee, Kyoung-Ki; Shin, Yeun-Kyung

    2016-07-01

    BLV is the etiological agent of enzootic bovine leucosis. BLV has negative effects on animal health and causes economic losses worldwide. However, epidemiological studies on BLV are relatively unknown in many parts of Asian countries. Thus, this study sought to explore BLV infections in cattle in Thailand to determine the extent of the geographic distribution of BLV and to measure its prevalence rates. For this study, 744 cattle from 11 farms in 9 provinces of Thailand were screened in 2013 and 2014 by ELISA and nested PCR. Of those cattle, 41 BLVs were genetically characterized using 188 BLV gp51 env gene sequences available in GenBank. The BLV prevalence in Thailand was high, ranging from 5.3% to 87.8%, as determined by PCR and 11.0% to 100% as determined by ELISA, according to geographical region. Phylogenetic analysis showed that Thailand BLVs belonged to genotypes 1 and 6 and a new genotype 10, which are sporadically observed across Thailand with a prevalence of 31.7%, 19.5%, and 48.8%, respectively. A significant number of amino acid substitutions were also found in the gp51 sequences, of which unique changes in genotype 10 have not been reported previously. Briefly, the majority of substitutions were confined to CD4+/CD8+ T-cell epitopes, neutralizing domains, and E-D-A epitopes. Those observations indicate that BLV infections in Thailand cattle are prevalent and that the geographic distribution of BLV is dynamic, with a high level of genetic diversity. This distribution implies a long-term BLV infection in cattle populations and the movement of infected cattle. In sum, this study suggests that intensive surveillance and effective prevention strategies are required to determine the prevalence of BLV in Thailand and control continuous infections with BLVs.

  10. The changing epidemiology of meningococcal disease in Quebec, Canada, 1991-2011: potential implications of emergence of new strains.

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    Rodica Gilca

    Full Text Available BACKGROUND: In order to inform meningococcal disease prevention strategies, we analysed the epidemiology of invasive meningococcal disease (IMD in the province of Quebec, Canada, 10 years before and 10 years after the introduction of serogroup C conjugate vaccination. METHODOLOGY: IMD cases reported to the provincial notifiable disease registry in 1991-2011 and isolates submitted for laboratory surveillance in 1997-2011 were analysed. Serogrouping, PCR testing and assignment of isolates to sequence types (ST by using multilocus sequence typing (MLST were performed. RESULTS: Yearly overall IMD incidence rates ranged from 2.2-2.3/100,000 in 1991-1992 to 0.49/100,000 in 1999-2000, increasing to 1.04/100,000 in 2011. Among the 945 IMD cases identified by laboratory surveillance in 1997-2011, 68%, 20%, 8%, and 3% were due to serogroups B, C, Y, and W135, respectively. Serogroup C IMD almost disappeared following the implementation of universal childhood immunization with monovalent C conjugate vaccines in 2002. Serogroup B has been responsible for 88% of all IMD cases and 61% of all IMD deaths over the last 3 years. The number and proportion of ST-269 clonal complex has been steadily increasing among the identified clonal complexes of serogroup B IMD since its first identification in 2003, representing 65% of serogroup B IMD in 2011. This clonal complex was first introduced in adolescent and young adults, then spread to other age groups. CONCLUSION: Important changes in the epidemiology of IMD have been observed in Quebec during the last two decades. Serogroup C has been virtually eliminated. In recent years, most cases have been caused by the serogroup B ST-269 clonal complex. Although overall burden of IMD is low, the use of a vaccine with potential broad-spectrum coverage could further reduce the burden of disease. Acceptability, feasibility and cost-effectiveness studies coupled with ongoing clinical and molecular surveillance are necessary in

  11. Molecular epidemiology of endemic human T-lymphotropic virus type 1 in a rural community in Guinea-Bissau.

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    Carla van Tienen

    Full Text Available Human T-Lymphotropic Virus Type 1 (HTLV-1 infection causes lethal adult T-cell leukemia (ATL and severely debilitating HTLV-associated myelopathy/tropical spastic paraparesis (HAM/TSP in up to 5% of infected adults. HTLV-1 is endemic in parts of Africa and the highest prevalence in West Africa (5% has been reported in Caio, a rural area in the North-West of Guinea-Bissau. It is not known which HTLV-1 variants are present in this community. Sequence data can provide insights in the molecular epidemiology and help to understand the origin and spread of HTLV-1.To gain insight into the molecular diversity of HTLV-1 in West Africa.HTLV-1 infected individuals were identified in community surveys between 1990-2007. The complete Long Terminal Repeat (LTR and p24 coding region of HTLV-1 was sequenced from infected subjects. Socio-demographic data were obtained from community census and from interviews performed by fieldworkers. Phylogenetic analyses were performed to characterize the relationship between the Caio HTLV-1 and HTLV-1 from other parts of the world.LTR and p24 sequences were obtained from 72 individuals (36 LTR, 24 p24 only and 12 both. Consistent with the low evolutionary change of HTLV-1, many of the sequences from unrelated individuals showed 100% nucleotide identity. Most (45 of 46 of the LTR sequences clustered with the Cosmopolitan HTLV-1 subtype 1a, subgroup D (1aD. LTR and p24 sequences from two subjects were divergent and formed a significant cluster with HTLV-1 subtype 1g, and with the most divergent African Simian T-cell Lymphotropic Virus, Tan90.The Cosmopolitan HTLV-1 1aD predominates in this rural West African community. However, HTLV-1 subtype 1g is also present. This subtype has not been described before in West Africa and may be more widespread than previously thought. These data are in line with the hypothesis that multiple monkey-to-man zoonotic events are contributing to HTLV-1 diversity.

  12. Climate change and health: new challenges for epidemiology and public health

    International Nuclear Information System (INIS)

    Climate change contributes to a rapid and deep modification of the environment. In the same time, other factors such as population increase, ageing or urbanization increase the vulnerability to various environmental and health risks. Chains of complex interactions are impacting populations' health and well-being. Developing prevention measures is an asset to reduce the health impacts of present climate change (through adaptation measures) and to limit the intensity of future impacts (through mitigation measures). Mitigation will result in major changes in several sectors, for instance housing, transports or agriculture. Taking into account the potential health impacts is important to avoid choices impairing human health, and to maximize health co-benefits. In this paper we propose a reflection on how present and future climate change in France challenges epidemiology and public health in the next few years. While many questions remain unanswered, there is a consensus on the importance of the links between climate change and human health, that can be summarized into three points: 1) climate change already impacts human health, 2) adaptation and mitigation are needed to reduce those impacts, 3) adaptation and mitigation can rely on immediate measures that would be beneficial for health and for climate. An integrated and interdisciplinary approach is essential to tackle the complexity of the issue, of its implications for public health, for research, surveillance and intervention. (authors)

  13. Application of PCR-mediated DNA typing in the molecular epidemiology of medically important microorganisms

    NARCIS (Netherlands)

    A.F. van Belkum (Alex)

    1996-01-01

    textabstractThis thesis describes the development, application and validation of the newer DNA analysis techniques within the field of microbiological epidemiology. Emphasis is placed on the use of the polymerase chain reaction (PCR), a test-tube technique enabling the amplification of (parts of) DN

  14. Molecular epidemiology of acute hepatitis B in the Netherlands in 2004 : nationwide survey

    NARCIS (Netherlands)

    van Houdt, R; Bruisten, S M; Koedijk, F D H; Dukers, N H T M; Op de Coul, E L M; Mostert, M C; Niesters, H G M; Richardus, J H; de Man, R A; van Doornum, G J J; van den Hoek, J A R; Coutinho, R A; van de Laar, M J W; Boot, H J

    2007-01-01

    To gain insight into hepatitis B virus (HBV) transmission in the Netherlands, epidemiological data and sera were collected from reported cases of acute HBV infections in the Netherlands in 2004. Cases were classified according to mode of transmission. A fragment of the S-gene of HBV (648 bp) was amp

  15. Molecular Epidemiology Study in Xuanwei: the Relationship among
Coal Type, Genotype and Lung Cancer Risk

    Directory of Open Access Journals (Sweden)

    Jihua LI

    2015-01-01

    Full Text Available Background and objective It has been proven that the lung cancer mortality rate in Xuanwei County, China was among the highest in the country and has been associated with exposure to indoor smoky coal emissions that contain high levels of polycyclic aromatic hydrocarbons. This risk may be modified by variation in genetic polymorphisms and coal subtypes. Our objective was to use molecular epidemiological techniques to investigate the relationship among genetic polymorphisms, coal subtype and lung cancer risk in Xuanwei County. Methods On the basis of two population-based case-control studies in residents of Xuanwei County, China, questionnaires covering demographic information, smoking history, family and personal medical history, and information on other variables were administered and buccal cells and sputum samples were collected separately from each subject enrolled to extract DNA. GST superfamily, AKR1C3 superfamily, OGG1 superfamily and other genotype were scanned by useing PCR method. ORs and 95%CIs were used to estimate the association between genotypes, coal subtypes and lung cancer risk factors by conditional Logistic regression using Statistical Analysis Software. Results Compared with subjects who using smokeless coal or wood, smoky coal use was statistically significantly associated with lung cancer risk (OR=7.7, 95%CI: 4.5-13.3. There was marked heterogeneity in risk estimates for specific subtypes of smoky coal. Estimates were highest for coal from the Laibin (OR=24.8, Longtan (OR=11.6 and Baoshan (OR=6.0 coal types, and lower for coal from other types; the risk within the same subtype of coal in male and female were similar. The GSTM1-null genotype, the AKR1C3 (Ex1-70C>G, OGG1 (Ex6-315C>G genotypes were closely associated with increased risk of lung cancer in Xuanwei County, and their odds ratios (95%CI were 2.3 (1.3-4.2, 1.8 (1.0-3.5 and 1.9 (1.1-3.3, respectively. Compared to subjects who with GSTM1-positive and used less than

  16. Review on the Molecular Tools for the Understanding of the Epidemiology of Animal Trypanosomosis in West Africa

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    Duvallet G

    1999-01-01

    Full Text Available The epidemiology of animal trypanosomosis around Bobo-Dioulasso (Burkina Faso, West Africa benefited a lot in the last years from the progress of molecular tools. The two most used molecular techniques were the polymerase chain reaction for the diagnosis of the disease in cattle and the characterization of the trypanosomes in the host and the vector on one hand, and the microsatellite DNA polymorphism in tsetse flies to study the intraspecific genetic variability of the vector on the other hand. The results obtained in the Sideradougou area during a recent two year survey with these techniques, associated with many other georeferenced informations concerning vector and cattle distribution, natural environment, landuse, ground occupation, livestock management, were combined in a Geographical Information System. This new approach of a complex pathogenic system led to a better evaluation of the risk of trypanosome transmission.

  17. Molecular epidemiology of simian immunodeficiency virus SIVsm in U.S. primate centers unravels the origin of SIVmac and SIVstm.

    Science.gov (United States)

    Apetrei, Cristian; Kaur, Amitinder; Lerche, Nicholas W; Metzger, Michael; Pandrea, Ivona; Hardcastle, Johnny; Falkenstein, Shelley; Bohm, Rudolf; Koehler, Jeffrey; Traina-Dorge, Vicki; Williams, Tessa; Staprans, Silvija; Plauche, Gail; Veazey, Ronald S; McClure, Harold; Lackner, Andrew A; Gormus, Bobby; Robertson, David L; Marx, Preston A

    2005-07-01

    Retrospective molecular epidemiology was performed on samples from four sooty mangabey (SM) colonies in the United States to characterize simian immunodeficiency virus SIVsm diversity in SMs and to trace virus circulation among different primate centers (PCs) over the past 30 years. The following SIVsm sequences were collected from different monkeys: 55 SIVsm isolates from the Tulane PC sampled between 1984 and 2004, 10 SIVsm isolates from the Yerkes PC sampled in 2002, 7 SIVsm isolates from the New Iberia PC sampled between 1979 and 1986, and 8 SIVsm isolates from the California PC sampled between 1975 and 1977. PCR and sequencing were done to characterize the gag, pol, and env gp36 genes. Phylogenetic analyses were correlated with the epidemiological data. Our analysis identified nine different divergent phylogenetic lineages that cocirculated in these four SM colonies in the Unites States in the past 30 years. Lineages 1 to 5 have been identified previously. Two of the newly identified SIVsm lineages found in SMs are ancestral to SIVmac251/SIVmac239/SIVmne and SIVstm. We further identified the origin of these two macaque viruses in SMs from the California National Primate Research Center. The diversity of SIVsm isolates in PCs in the United States mirrors that of human immunodeficiency virus type 1 (HIV-1) group M subtypes and offers a model for the molecular epidemiology of HIV and a new approach to vaccine testing. The cocirculation of divergent SIVsm strains in PCs resulted in founder effects, superinfections, and recombinations. This large array of SIVsm strains showing the same magnitude of diversity as HIV-1 group M subtypes should be extremely useful for modeling the efficacy of vaccination strategies under the real-world conditions of HIV-1 diversity. The genetic variability of SIVsm strains among PCs may influence the diagnosis and monitoring of SIVsm infection and, consequently, may bias the results of pathogenesis studies. PMID:15994793

  18. Meningococcal meningitis: vaccination outbreak response and epidemiological changes in the African meningitis belt.

    Science.gov (United States)

    Carod Artal, Francisco Javier

    2015-07-01

    The main approach to controlling epidemics of meningococcal meningitis in the African meningitis belt has been reactive vaccination campaigns with serogroup A polysaccharide vaccine once the outbreak reached an incidence threshold. Early reactive vaccination is effective in reducing morbidity and mortality. A recent paper in International Health has shown that earlier reactive vaccination campaigns may be even more effective than increasing the coverage area of vaccination. Monovalent serogroup A conjugate vaccine programs have recently been launched to prevent transmission in endemic areas in the African meningitis belt. Conjugate vaccines can induce immunological memory and have impact on pharyngeal carriage. However, reactive vaccination still has a role to play taking into account the dynamic changes in the epidemiology of meningitis in this area. PMID:25878213

  19. Dengue fever in Pakistan: a paradigm shift; changing epidemiology and clinical patterns.

    Science.gov (United States)

    Haider, Zahra; Ahmad, Farina Zia; Mahmood, Asif; Waseem, Tariq; Shafiq, Irfan; Raza, Tanzeem; Qazi, Javaria; Siddique, Nasir; Humayun, Malik Asif

    2015-11-01

    Dengue fever has huge public health implications and affects over 100 million people worldwide. This review pictures the current situation of Dengue in Pakistan and presents a review of published literature. Pakistan has seen recurrent epidemics of Dengue Fever recently. Unfortunately, these epidemics are becoming more severe in their clinical manifestation. Pakistan experienced large epidemics of dengue fever during 2008, 2010 and 2011 affecting thousands of people and claiming hundreds of deaths. A comparison of data during these epidemics indicates a shift from mild to a more severe disease, which could be interpreted as an epidemiologic transition pattern in the country. Expansion of Dengue in Pakistan seems to be multifactorial, including the climate change, frequent natural disasters, vector resistance to insecticides and lack of resources. This highlights the need for rigorous vector control. Continuing education of primary care physicians is crucial for early appropriate management to reduce mortality.

  20. Visceral leishmaniasis epidemiologic evolution in timeframes, based on demographic changes and scientific achievements in Brazil.

    Science.gov (United States)

    Conti, Renata Vivas; Moura Lane, Viviane Fragoso; Montebello, Lucia; Pinto Junior, Vitor Laerte

    2016-01-01

    Visceral leishmaniasis (VL) is a disease of chronic evolution which could be uniformly fatal, if left untreated. Human VL was first described in the Americas in 1913 and in 1936 in Brazil. The number of VL cases in Brazil is increasing steadily in the last three decades. Medical literature highlights this change in the disease epidemiology as a recent urbanization phenomenon, with most of the cases occurring in large cities since 1981, different to that observed previously, like a typical rural endemic. The aim of this study was to create a narrative review of the evolution of VL epidemiology since its first description in Brazil. To describe the process of urbanization of VL, timeframes were created historically consistent with the scientific and public health knowledge obtained about the VL and the demographics changes in Brazil, especially considering the extensive migratory movements in the country due to political or economic events. The first phase of VL was the decades of 30-50 when industrialization triggered internal migration process from countryside to the cities; during this period VL was studied for the first time and described as a rural endemic disease with no relevance to public health. Until the second phase, between the 50s and 80s of the 20th century, demography was characterized by expansion of immigration to the large cities and increase in population density in the suburbs with poor living standards. In this period, there was an advancement in the knowledge of the transmission of the disease being described as the first case acquired in the urban environment. The third phase was characterized by the explosion of cases in Brazilian cities and consolidation of urban endemic transmission. The possibility of urban transmission has been known since the 50s; however, the current phenomenon was due to the creation of ideal conditions for the establishment of transmission cycle in Brazilian cities.

  1. To what extent has climate change contributed to the recent epidemiology of tick-borne diseases?

    Science.gov (United States)

    Randolph, Sarah E

    2010-02-10

    There is no doubt that all vector-borne diseases are very sensitive to climatic conditions. Many such diseases have shown marked increases in both distribution and incidence during the past few decades, just as human-induced climate change is thought to have exceeded random fluctuations. This coincidence has led to the general perception that climate change has driven disease emergence, but climate change is the inevitable backdrop for all recent events, without implying causality. Coincidence and causality can be disentangled using tick-borne encephalitis (TBE) as a test case, based on the excellent long-term data for this medically significant European disease system. Detailed analysis of climate records since 1970 has revealed abrupt temperature increases just prior to the dramatic upsurge in TBE incidence in many parts of central and eastern Europe. Furthermore, the seasonal patterns of this temperature change are such as might have favoured the transmission of TBE virus between co-feeding ticks. Nevertheless, the pattern of climate change is too uniform to explain the marked heterogeneity in the timing and degree of TBE upsurge, for example in different counties within each of the Baltic countries. Recent decreases as well as increases in TBE incidence must also be taken into account. Instead of a single cause, a network of interacting factors, acting synergistically but with differential force in space and time, would generate this epidemiological heterogeneity. From analysis of past and present events, it appears that human behavioural factors have played a more significant role than purely biological enzootic factors, although there is an explicit causal linkage from one to the other. This includes a range of abiotic and biotic environmental factors, together with human behaviour determined by socio-economic conditions. Many of the abrupt changes followed from the shift from planned to market economies with the fall of Soviet rule. Comparisons between eight

  2. Epidemiology in a changing world: implications for population-based research on mental disorders.

    Science.gov (United States)

    Cooper, B

    2014-06-01

    Introduction and objectives. Population-based research on mental disorders needs to keep pace with trends in general epidemiology. At present, this requirement is complicated by uncertainty within the parent discipline about its future development. The present study examines proposals for new directions in strategy and methods and considers their significance for psychiatric epidemiology. Method. Narrative review, cross-checked by search of English-language journals of epidemiology for new trends and developments reported in the years from 2000 onwards. Results. The proposals reviewed here are divided into three groups: 1. A new research paradigm of 'eco-epidemiology', which includes both individual risk factors and macro-environmental systems that mediate population levels of health and sickness. 2. Improved 'translation' of research findings - i.e. more rapid and effective implementation of epidemiological evidence into health policy and practice. 3. Adaptation of epidemiology to a globalised economy, with firmer regulation of funding and resources. Conclusions. Each of these proposals has implications for psychiatric epidemiology. Workers in this field, however, are still preoccupied by relatively specific problems of definition, measurement and classification, and so far the current debates in general epidemiology are scarcely reflected. The proposals outlined above call for: • a working model of eco-epidemiology as it relates to psychiatric disorders; • implementation strategies to encourage more active participation in epidemiological research by community health services and caregiver organisations; • international collaborative projects that offer practical benefits in training and service facilities for the countries taking part. PMID:24345606

  3. Carcinoma of the stomach: A review of epidemiology, pathogenesis, molecular genetics and chemoprevention

    OpenAIRE

    Nagini, Siddavaram

    2012-01-01

    Carcinoma of the stomach is still the second most common cause of cancer death worldwide, although the incidence and mortality have fallen dramatically over the last 50 years in many regions. The incidence of gastric cancer varies in different parts of the world and among various ethnic groups. Despite advances in diagnosis and treatment, the 5-year survival rate of stomach cancer is only 20 per cent. Stomach cancer can be classified into intestinal and diffuse types based on epidemiological ...

  4. Molecular epidemiological study of Cryptococcus neoformans and Cryptococcus gattii in Shenzhen

    Institute of Scientific and Technical Information of China (English)

    梁训宏

    2014-01-01

    Objective To study the epidemiological features of Cryptococcus neoformans and Cryptococcus gattii isolated from clinical samples in Shenzhen and to elucidate the distribution of species,varieties,genotypes and mating types within the strains tested.Methods The strains involved in this study were 55 cryptococcal strains isolated from our clinical samples.The canavanine-glycine bromthymolblue(CGB)culture was performed to distinguish Cryptococcus neoformans from Cryptococcus gattii.The

  5. Epidemiology, clinical, immune, and molecular profiles of microsporidiosis and cryptosporidiosis among HIV/AIDS patients

    Directory of Open Access Journals (Sweden)

    Wumba R

    2012-07-01

    Full Text Available Roger Wumba,1 Benjamin Longo-Mbenza,2 Jean Menotti,3,4 Madone Mandina,5 Fabien Kintoki,5 Nani Hippolyte Situakibanza,1,5 Marie Kapepela Kakicha,6 Josue Zanga,1 Kennedy Mbanzulu-Makola,1 Tommy Nseka,1 Jean Pierre Mukendi,1 Eric Kendjo,7 Jean Sala,1 Marc Thellier7,81Department of Tropical Medicine, Infectious and Parasitic Diseases, Department of Parasitology, University Clinic of Kinshasa, Faculty of Medicine, University of Kinshasa, Kinshasa, Congo; 2Faculty of Health Sciences, Walter Sisulu University, Eastern Cape, South Africa; 3Laboratory of Parasitology and Mycology, Saint-Louis Hospital, Public Assistance-Hospitals of Paris, Paris, France; 4Faculty of Medicine, Lariboisière-Saint-Louis, University of Paris VII, Paris, France; 5Department of Internal Medicine, University Clinic of Kinshasa, Faculty of Medicine, University of Kinshasa, Kinshasa, Congo; 6Department of Pediatrics, University Clinic of Kinshasa, Faculty of Medicine, University of Kinshasa, Kinshasa, Congo; 7National Center for Malaria Research, AP-HP, CHU Pitie Salpêtrière, Paris, France; 8Laboratory of Parasitology and Mycology, Pitié Salpêtrière Hospital, Public Assistance-Hospitals of Paris, Pierre and Marie Curie University, Paris, FranceBackground: The objective of this study was to determine the prevalence of intestinal parasites, with special emphasis on microsporidia and Cryptosporidium, as well as their association with human immunodeficiency virus (HIV symptoms, risk factors, and other digestive parasites. We also wish to determine the molecular biology definitions of the species and genotypes of microsporidia and Cryptosporidium in HIV patients.Methods: In this cross-sectional study, carried out in Kinshasa, Democratic Republic of the Congo, stool samples were collected from 242 HIV patients (87 men and 155 women with referred symptoms and risk factors for opportunistic intestinal parasites. The analysis of feces specimen were performed using Ziehl

  6. Prevalence and Trends of Staphylococcus aureus Bacteraemia in Hospitalized Patients in South Africa, 2010 to 2012: Laboratory-Based Surveillance Mapping of Antimicrobial Resistance and Molecular Epidemiology.

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    Olga Perovic

    Full Text Available We aimed to obtain an in-depth understanding on recent antimicrobial resistance trends and molecular epidemiology trends of S. aureus bacteraemia (SAB.Thirteen academic centres in South Africa were included from June 2010 until July 2012. S. aureus susceptibility testing was performed on the MicroScan Walkaway. Real-time PCR using the LightCycler 480 II was done for mecA and nuc. SCCmec and spa-typing were finalized with conventional PCR. We selected one isolate per common spa type per province for multilocus sequence typing (MLST.S. aureus from 2709 patients were included, and 1231 (46% were resistant to methicillin, with a significant decline over the three-year period (p-value = 0.003. Geographical distribution of MRSA was significantly higher in Gauteng compared to the other provinces (P<0.001. Children <5 years were significantly associated with MRSA with higher rates compared to all other age groups (P = 0.01. The most prevalent SCCmec type was SCCmec type III (531 [41%] followed by type IV (402 [31%]. Spa-typing discovered 47 different spa-types. The five (87% most common spa-types were t037, t1257, t045, t064 and t012. Based on MLST, the commonest was ST612 clonal complex (CC8 (n = 7 followed by ST5 (CC5 (n = 4, ST36 (CC30 (n = 4 and ST239 (CC8 (n = 3.MRSA rate is high in South Africa. Majority of the isolates were classified as SCCmec type III (41% and type IV (31%, which are typically associated with hospital and community- acquired infections, respectively. Overall, this study reveals the presence of a variety of hospital-acquired MRSA clones in South Africa dominance of few clones, spa 037 and 1257. Monitoring trends in resistance and molecular typing is recommended to detect changing epidemiological trends in AMR patterns of SAB.

  7. Prevalence and Trends of Staphylococcus aureus Bacteraemia in Hospitalized Patients in South Africa, 2010 to 2012: Laboratory-Based Surveillance Mapping of Antimicrobial Resistance and Molecular Epidemiology

    Science.gov (United States)

    Perovic, Olga; Iyaloo, Samantha; Kularatne, Ranmini; Lowman, Warren; Bosman, Noma; Wadula, Jeannette; Seetharam, Sharona; Duse, Adriano; Mbelle, Nontombi; Bamford, Colleen; Dawood, Halima; Mahabeer, Yesholata; Bhola, Prathna; Abrahams, Shareef; Singh-Moodley, Ashika

    2015-01-01

    Introduction We aimed to obtain an in-depth understanding on recent antimicrobial resistance trends and molecular epidemiology trends of S. aureus bacteraemia (SAB). Methods Thirteen academic centres in South Africa were included from June 2010 until July 2012. S. aureus susceptibility testing was performed on the MicroScan Walkaway. Real-time PCR using the LightCycler 480 II was done for mecA and nuc. SCCmec and spa-typing were finalized with conventional PCR. We selected one isolate per common spa type per province for multilocus sequence typing (MLST). Results S. aureus from 2709 patients were included, and 1231 (46%) were resistant to methicillin, with a significant decline over the three-year period (p-value = 0.003). Geographical distribution of MRSA was significantly higher in Gauteng compared to the other provinces (P<0.001). Children <5 years were significantly associated with MRSA with higher rates compared to all other age groups (P = 0.01). The most prevalent SCCmec type was SCCmec type III (531 [41%]) followed by type IV (402 [31%]). Spa-typing discovered 47 different spa-types. The five (87%) most common spa-types were t037, t1257, t045, t064 and t012. Based on MLST, the commonest was ST612 clonal complex (CC8) (n = 7) followed by ST5 (CC5) (n = 4), ST36 (CC30) (n = 4) and ST239 (CC8) (n = 3). Conclusions MRSA rate is high in South Africa. Majority of the isolates were classified as SCCmec type III (41%) and type IV (31%), which are typically associated with hospital and community- acquired infections, respectively. Overall, this study reveals the presence of a variety of hospital-acquired MRSA clones in South Africa dominance of few clones, spa 037 and 1257. Monitoring trends in resistance and molecular typing is recommended to detect changing epidemiological trends in AMR patterns of SAB. PMID:26719975

  8. Molecular and epidemiological profiles of hepatitis C virus genotype 4 in Denmark

    DEFF Research Database (Denmark)

    Eriksen, Mette Brandt; Jørgensen, Louise Bruun; Krarup, Henrik;

    2010-01-01

    patients (22%) were infected with subtypes 4h, 4k, 4l, 4n, 4o, or 4Unclassified. Three epidemiological profiles were identified: (1) patients infected with HCV by intravenous drug use were infected solely with subtype 4d. They were all of European origin, and 15 of the 16 patients were ethnic Danes...... East. (3) Patients from Southern Africa dominated among patients infected with subtype 4r (10 of 12 patients). This study demonstrates that HCV genotype 4d has been introduced in and spread among Danish intravenous drug users. The remaining subtypes show restricted distribution, infecting almost...

  9. Molecular tools for epidemiological investigations into Legionella pneumophila environmental diffusion: applications for the prevention

    Directory of Open Access Journals (Sweden)

    Stefania Boccia

    2004-12-01

    Full Text Available

    Microbiological typing is a useful tool in the epidemiological investigations of infectious diseases, given that it allows for the identification of specific clones among a set of isolates.

     In the last ten years several studies have demonstrated how genotyping methods can be useful in Legionella spp investigations in hospital setting (e.g., epidemic events. Pulsed field gel electrophoresis and amplified fragment length polymorphisms are the current typing methods of choice, even though multilocus sequence typing will probably be the gold standard of the future.

  10. A large-scale genomic approach affords unprecedented resolution for the molecular epidemiology and evolutionary history of contagious caprine pleuropneumonia.

    Science.gov (United States)

    Dupuy, Virginie; Verdier, Axel; Thiaucourt, François; Manso-Silván, Lucía

    2015-01-01

    Contagious caprine pleuropneumonia (CCPP), caused by Mycoplasma capricolum subsp. capripneumoniae (Mccp), is a devastating disease of domestic goats and of some wild ungulate species. The disease is currently spreading in Africa and Asia and poses a serious threat to disease-free areas. A comprehensive view of the evolutionary history and dynamics of Mccp is essential to understand the epidemiology of CCPP. Yet, analysing the diversity of genetically monomorphic pathogens, such as Mccp, is complicated due to their low variability. In this study, the molecular epidemiology and evolution of CCPP was investigated using a large-scale genomic approach based on next-generation sequencing technologies, applied to a sample of strains representing the global distribution of this disease. A highly discriminatory multigene typing system was developed, allowing the differentiation of 24 haplotypes among 25 Mccp strains distributed in six genotyping groups, which showed some correlation with geographic origin. A Bayesian approach was used to infer the first robust phylogeny of the species and to date the principal events of its evolutionary history. The emergence of Mccp was estimated only at about 270 years ago, which explains the low genetic diversity of this species despite its high mutation rate, evaluated at 1.3 × 10(-6) substitutions per site per year. Finally, plausible scenarios were proposed to elucidate the evolution and dynamics of CCPP in Asia and Africa, though limited by the paucity of Mccp strains, particularly in Asia. This study shows how combining large-scale genomic data with spatial and temporal data makes it possible to obtain a comprehensive view of the epidemiology of CCPP, a precondition for the development of improved disease surveillance and control measures. PMID:26149260

  11. Molecular epidemiology of C. diphtheriae strains during different phases of the diphtheria epidemic in Belarus

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    Grimont Patrick AD

    2006-08-01

    Full Text Available Abstract Background The reemergence of epidemic diphtheria in Belarus in 1990s has provided us with important information on the biology of the disease and the diversity of the causative agent Corynebacterium diphtheriae. Molecular investigations were conducted with the aim to analyze the genetic variability of C diphtheriae during the post-epidemic period. Methods The biotype and toxigenicity status of 3513 C. diphtheriae strains isolated from all areas in Belarus during a declining period of diphtheria morbidity (1996–2005 was undertaken. Of these, 384 strains were isolated from diphtheria cases, 1968 from tonsillitis patients, 426 from contacts and 735 from healthy carriers. Four hundred and thirty two selected strains were ribotyped. Results The C diphtheriae gravis biotype, which was prevalent during 1996–2000, was "replaced" by the mitis biotype during 2001–2005. The distribution of toxigenic C. diphtheriae strains also decreased from 47.1% (1996 to 5.8% (2005. Changes in the distribution of the epidemic ribotypes Sankt-Peterburg and Rossija were also observed. During 2001–2005 the proportion of the Sankt-Peterburg ribotype decreased from 24.3% to 2.3%, in contrast to the Rossija ribotype, that increased from 25.1% to 49.1%. The circulation of other toxigenic ribotypes (Otchakov, Lyon, Bangladesh, which were prevalent during the period of high diphtheria incidence, also decreased. But at the same time, the proportion of non-toxigenic strains with the Cluj and Rossija ribotypes dramatically increased and accounted for 49.3% and 30.1%, respectively. Conclusion The decrease in morbidity correlated with the dramatic decrease in the isolation of the gravis biotype and Sankt Peterburg ribotype, and the prevalence of the Rossija ribotype along with other rare ribotypes associated with non-toxigenic strains (Cluj and Rossija, in particular.

  12. Age-Related Change in Mobility: Perspectives From Life Course Epidemiology and Geroscience.

    Science.gov (United States)

    Ferrucci, Luigi; Cooper, Rachel; Shardell, Michelle; Simonsick, Eleanor M; Schrack, Jennifer A; Kuh, Diana

    2016-09-01

    Mobility is the most studied and most relevant physical ability affecting quality of life with strong prognostic value for disability and survival. Natural selection has built the "engine" of mobility with great robustness, redundancy, and functional reserve. Efficient patterns of mobility can be acquired during development even by children affected by severe impairments. Analogously, age-associated impairments in mobility-related physiological systems are compensated and overt limitations of mobility only occur when the severity can no longer be compensated. Mobility loss in older persons usually results from multiple impairments in the central nervous system, muscles, joints, and energetic and sensory physiological systems. Early preclinical changes in these physiological systems that precede mobility loss have been poorly studied. Peak performance, rate of decline, compensatory behaviors, or subclinical deterioration of physiological resources may cumulatively influence both timing of mobility loss and chances of recovery, but their role as risk factors has not been adequately characterized. Understanding the natural history of these early changes and intervening on them would likely be the most effective strategy to reduce the burden of disability in the population. For example, young women with low bone peak mass could be counseled to start strength resistance exercise to reduce their high risk of developing osteoporosis and fracture later in life. Expanding this approach to other physiological domains requires collecting and interpreting data from life course epidemiological studies, establishing normative measures of mobility, physical function, and physical activity, and connecting them with life course trajectories of the mobility-relevant physiological domains.

  13. Age-Related Change in Mobility: Perspectives From Life Course Epidemiology and Geroscience.

    Science.gov (United States)

    Ferrucci, Luigi; Cooper, Rachel; Shardell, Michelle; Simonsick, Eleanor M; Schrack, Jennifer A; Kuh, Diana

    2016-09-01

    Mobility is the most studied and most relevant physical ability affecting quality of life with strong prognostic value for disability and survival. Natural selection has built the "engine" of mobility with great robustness, redundancy, and functional reserve. Efficient patterns of mobility can be acquired during development even by children affected by severe impairments. Analogously, age-associated impairments in mobility-related physiological systems are compensated and overt limitations of mobility only occur when the severity can no longer be compensated. Mobility loss in older persons usually results from multiple impairments in the central nervous system, muscles, joints, and energetic and sensory physiological systems. Early preclinical changes in these physiological systems that precede mobility loss have been poorly studied. Peak performance, rate of decline, compensatory behaviors, or subclinical deterioration of physiological resources may cumulatively influence both timing of mobility loss and chances of recovery, but their role as risk factors has not been adequately characterized. Understanding the natural history of these early changes and intervening on them would likely be the most effective strategy to reduce the burden of disability in the population. For example, young women with low bone peak mass could be counseled to start strength resistance exercise to reduce their high risk of developing osteoporosis and fracture later in life. Expanding this approach to other physiological domains requires collecting and interpreting data from life course epidemiological studies, establishing normative measures of mobility, physical function, and physical activity, and connecting them with life course trajectories of the mobility-relevant physiological domains. PMID:26975983

  14. epiPATH: an information system for the storage and management of molecular epidemiology data from infectious pathogens

    Science.gov (United States)

    Amadoz, Alicia; González-Candelas, Fernando

    2007-01-01

    Background Most research scientists working in the fields of molecular epidemiology, population and evolutionary genetics are confronted with the management of large volumes of data. Moreover, the data used in studies of infectious diseases are complex and usually derive from different institutions such as hospitals or laboratories. Since no public database scheme incorporating clinical and epidemiological information about patients and molecular information about pathogens is currently available, we have developed an information system, composed by a main database and a web-based interface, which integrates both types of data and satisfies requirements of good organization, simple accessibility, data security and multi-user support. Results From the moment a patient arrives to a hospital or health centre until the processing and analysis of molecular sequences obtained from infectious pathogens in the laboratory, lots of information is collected from different sources. We have divided the most relevant data into 12 conceptual modules around which we have organized the database schema. Our schema is very complete and it covers many aspects of sample sources, samples, laboratory processes, molecular sequences, phylogenetics results, clinical tests and results, clinical information, treatments, pathogens, transmissions, outbreaks and bibliographic information. Communication between end-users and the selected Relational Database Management System (RDMS) is carried out by default through a command-line window or through a user-friendly, web-based interface which provides access and management tools for the data. Conclusion epiPATH is an information system for managing clinical and molecular information from infectious diseases. It facilitates daily work related to infectious pathogens and sequences obtained from them. This software is intended for local installation in order to safeguard private data and provides advanced SQL-users the flexibility to adapt it to their

  15. epiPATH: an information system for the storage and management of molecular epidemiology data from infectious pathogens

    Directory of Open Access Journals (Sweden)

    González-Candelas Fernando

    2007-04-01

    Full Text Available Abstract Background Most research scientists working in the fields of molecular epidemiology, population and evolutionary genetics are confronted with the management of large volumes of data. Moreover, the data used in studies of infectious diseases are complex and usually derive from different institutions such as hospitals or laboratories. Since no public database scheme incorporating clinical and epidemiological information about patients and molecular information about pathogens is currently available, we have developed an information system, composed by a main database and a web-based interface, which integrates both types of data and satisfies requirements of good organization, simple accessibility, data security and multi-user support. Results From the moment a patient arrives to a hospital or health centre until the processing and analysis of molecular sequences obtained from infectious pathogens in the laboratory, lots of information is collected from different sources. We have divided the most relevant data into 12 conceptual modules around which we have organized the database schema. Our schema is very complete and it covers many aspects of sample sources, samples, laboratory processes, molecular sequences, phylogenetics results, clinical tests and results, clinical information, treatments, pathogens, transmissions, outbreaks and bibliographic information. Communication between end-users and the selected Relational Database Management System (RDMS is carried out by default through a command-line window or through a user-friendly, web-based interface which provides access and management tools for the data. Conclusion epiPATH is an information system for managing clinical and molecular information from infectious diseases. It facilitates daily work related to infectious pathogens and sequences obtained from them. This software is intended for local installation in order to safeguard private data and provides advanced SQL-users the

  16. Epidemiological changes with potential implication for antifungal prescription recommendations for fungaemia

    DEFF Research Database (Denmark)

    Arendrup, M C; Dzajic, E; Jensen, R H;

    2013-01-01

    .7%, itraconazole 69.6%, posaconazole 64.2% and voriconazole 85.0%. Acquired echinocandin resistance was molecularly confirmed in three isolates. The use of systemic antifungals doubled over the last decade (2002-2011) (from 717 000 to 1 450 000 defined daily doses/year) of which the vast majority (96.9%) were...... azoles. The incidence of fungaemia continues to increase in Denmark and is associated with a decreasing proportion being susceptible to fluconazole. Changes in demography, higher incidence in the elderly and higher antifungal consumption can at least in part explain the changes. © 2013 The Authors...

  17. Molecular epidemiology of norovirus in asymptomatic food handlers in Busan, Korea, and emergence of genotype GII.17.

    Science.gov (United States)

    Koo, Hee Soo; Lee, Mi Ok; Ku, Pyeong Tae; Hwang, Su Jeong; Park, Dong Ju; Baik, Hyung Suk

    2016-10-01

    The molecular epidemiology of norovirus infections was studied in food handlers without any symptoms from January to December 2015 in Busan city, Korea. A total of 2,174 fecal specimens from asymptomatic food handlers were analyzed, and 2.3% (49/2,174) were norovirus-positive. Fourteen of 335 samples (4.2%) were positive in January; fifteen of 299 samples (5.0%) in February, and seven of 189 samples (3.7%) in December. However, norovirus was rarely detected in other months. From sequencing analysis, 11 genotypes (five GI and six GII genotypes) were detected. Among the 42 capid gene sequences identified, 14 were from the GI genogroup, while 28 were from the GII genogroup. The most commonly detected genotype was GII.17, comprising 15 (35.7%) of positive samples. From January 2012 to December 2015, 5,138 samples were collected from gastroenteritis patients and outbreaks in Busan. The most detected genotype in 2012, 2013, and 2014 was GII.4 (121, 24, and 12 cases, respectively), but in 2015, GII.17 (25 cases) was the most common. The GII.4 genotype was the major cause of acute gastroenteritis from 2012 to 2014, but the GII.17 genotype became the most prevalent cause in 2015. Continued epidemiological surveillance of GII.17 is needed, together with assessment of the risk of norovirus infection. PMID:27687231

  18. Integrated Bioinformatics, Environmental Epidemiologic and Genomic Approaches to Identify Environmental and Molecular Links between Endometriosis and Breast Cancer

    Directory of Open Access Journals (Sweden)

    Deodutta Roy

    2015-10-01

    Full Text Available We present a combined environmental epidemiologic, genomic, and bioinformatics approach to identify: exposure of environmental chemicals with estrogenic activity; epidemiologic association between endocrine disrupting chemical (EDC and health effects, such as, breast cancer or endometriosis; and gene-EDC interactions and disease associations. Human exposure measurement and modeling confirmed estrogenic activity of three selected class of environmental chemicals, polychlorinated biphenyls (PCBs, bisphenols (BPs, and phthalates. Meta-analysis showed that PCBs exposure, not Bisphenol A (BPA and phthalates, increased the summary odds ratio for breast cancer and endometriosis. Bioinformatics analysis of gene-EDC interactions and disease associations identified several hundred genes that were altered by exposure to PCBs, phthalate or BPA. EDCs-modified genes in breast neoplasms and endometriosis are part of steroid hormone signaling and inflammation pathways. All three EDCs–PCB 153, phthalates, and BPA influenced five common genes—CYP19A1, EGFR, ESR2, FOS, and IGF1—in breast cancer as well as in endometriosis. These genes are environmentally and estrogen responsive, altered in human breast and uterine tumors and endometriosis lesions, and part of Mitogen Activated Protein Kinase (MAPK signaling pathways in cancer. Our findings suggest that breast cancer and endometriosis share some common environmental and molecular risk factors.

  19. Molecular epidemiology of canine norovirus in dogs from Portugal, 2007–2011

    Directory of Open Access Journals (Sweden)

    Mesquita João

    2012-07-01

    Full Text Available Abstract Background Canine noroviruses (NoVs have been recently described in south European countries and associated with outbreaks of diarrhea in kennels. Unlike human NoV which are known as an important cause of acute gastroenteritis, little is known about the role of canine NoV as pathogens in dogs as well as its epidemiological features. Results From 2007–2011, 256 stool samples were collected from dogs across Portugal and tested by RT-PCR for canine NoV. Viral fecal shedding was found to be 23% (60/256. All sequences contained the GLPSG amino acid motif characteristic of the RNA-dependent RNA-polymerase gene of NoVs and had a high nucleotide identity (range 98%–100% to the canine NoV first described in Portugal. The highest shedding rate was detected during the winter months. Conclusions This study shows that canine NoV infection is endemic in the dog population of Portugal. Peak shedding was detected in the winter months, a well-known epidemiologic feature of human NoV infections.

  20. The Molecular and Spatial Epidemiology of Typhoid Fever in Rural Cambodia.

    Science.gov (United States)

    Pham Thanh, Duy; Thompson, Corinne N; Rabaa, Maia A; Sona, Soeng; Sopheary, Sun; Kumar, Varun; Moore, Catrin; Tran Vu Thieu, Nga; Wijedoru, Lalith; Holt, Kathryn E; Wong, Vanessa; Pickard, Derek; Thwaites, Guy E; Day, Nicholas; Dougan, Gordon; Turner, Paul; Parry, Christopher M; Baker, Stephen

    2016-06-01

    Typhoid fever, caused by the bacterium Salmonella Typhi, is an endemic cause of febrile disease in Cambodia. The aim of this study was to better understand the epidemiology of pediatric typhoid fever in Cambodia. We accessed routine blood culture data from Angkor Hospital for Children (AHC) in Siem Reap province between 2007 and 2014, and performed whole genome sequencing (WGS) on the isolated bacteria to characterize the S. Typhi population. The resulting phylogenetic information was combined with conventional epidemiological approaches to investigate the spatiotemporal distribution of S. Typhi and population-level risk factors for reported disease. During the study period, there were 262 cases of typhoid within a 100 km radius of AHC, with a median patient age of 8.2 years (IQR: 5.1-11.5 years). The majority of infections occurred during the rainy season, and commune incidences as high as 11.36/1,000 in children aged typhoid fever in rural communes in Cambodia. Our data provide a platform for additional population-based typhoid fever studies in this location, and suggest that this would be a suitable setting in which to introduce a school-based vaccination programme with Vi conjugate vaccines.

  1. The Molecular and Spatial Epidemiology of Typhoid Fever in Rural Cambodia.

    Science.gov (United States)

    Pham Thanh, Duy; Thompson, Corinne N; Rabaa, Maia A; Sona, Soeng; Sopheary, Sun; Kumar, Varun; Moore, Catrin; Tran Vu Thieu, Nga; Wijedoru, Lalith; Holt, Kathryn E; Wong, Vanessa; Pickard, Derek; Thwaites, Guy E; Day, Nicholas; Dougan, Gordon; Turner, Paul; Parry, Christopher M; Baker, Stephen

    2016-06-01

    Typhoid fever, caused by the bacterium Salmonella Typhi, is an endemic cause of febrile disease in Cambodia. The aim of this study was to better understand the epidemiology of pediatric typhoid fever in Cambodia. We accessed routine blood culture data from Angkor Hospital for Children (AHC) in Siem Reap province between 2007 and 2014, and performed whole genome sequencing (WGS) on the isolated bacteria to characterize the S. Typhi population. The resulting phylogenetic information was combined with conventional epidemiological approaches to investigate the spatiotemporal distribution of S. Typhi and population-level risk factors for reported disease. During the study period, there were 262 cases of typhoid within a 100 km radius of AHC, with a median patient age of 8.2 years (IQR: 5.1-11.5 years). The majority of infections occurred during the rainy season, and commune incidences as high as 11.36/1,000 in children aged fever in rural communes in Cambodia. Our data provide a platform for additional population-based typhoid fever studies in this location, and suggest that this would be a suitable setting in which to introduce a school-based vaccination programme with Vi conjugate vaccines. PMID:27331909

  2. Genetic and Molecular Epidemiological Characterization of a Novel Adenovirus in Antarctic Penguins Collected between 2008 and 2013

    Science.gov (United States)

    Lee, Sook-Young; Kim, Jeong-Hoon; Seo, Tae-Kun; No, Jin Sun; Kim, Hankyeom; Kim, Won-keun; Choi, Han-Gu; Kang, Sung-Ho; Song, Jin-Won

    2016-01-01

    Antarctica is considered a relatively uncontaminated region with regard to the infectious diseases because of its extreme environment, and isolated geography. For the genetic characterization and molecular epidemiology of the newly found penguin adenovirus in Antarctica, entire genome sequencing and annual survey of penguin adenovirus were conducted. The entire genome sequences of penguin adenoviruses were completed for two Chinstrap penguins (Pygoscelis antarctica) and two Gentoo penguins (Pygoscelis papua). The whole genome lengths and G+C content of penguin adenoviruses were found to be 24,630–24,662 bp and 35.5–35.6%, respectively. Notably, the presence of putative sialidase gene was not identified in penguin adenoviruses by Rapid Amplification of cDNA Ends (RACE-PCR) as well as consensus specific PCR. The penguin adenoviruses were demonstrated to be a new species within the genus Siadenovirus, with a distance of 29.9–39.3% (amino acid, 32.1–47.9%) in DNA polymerase gene, and showed the closest relationship with turkey adenovirus 3 (TAdV-3) in phylogenetic analysis. During the 2008–2013 study period, the penguin adenoviruses were annually detected in 22 of 78 penguins (28.2%), and the molecular epidemiological study of the penguin adenovirus indicates a predominant infection in Chinstrap penguin population (12/30, 40%). Interestingly, the genome of penguin adenovirus could be detected in several internal samples, except the lymph node and brain. In conclusion, an analysis of the entire adenoviral genomes from Antarctic penguins was conducted, and the penguin adenoviruses, containing unique genetic character, were identified as a new species within the genus Siadenovirus. Moreover, it was annually detected in Antarctic penguins, suggesting its circulation within the penguin population. PMID:27309961

  3. Genetic and Molecular Epidemiological Characterization of a Novel Adenovirus in Antarctic Penguins Collected between 2008 and 2013.

    Directory of Open Access Journals (Sweden)

    Sook-Young Lee

    Full Text Available Antarctica is considered a relatively uncontaminated region with regard to the infectious diseases because of its extreme environment, and isolated geography. For the genetic characterization and molecular epidemiology of the newly found penguin adenovirus in Antarctica, entire genome sequencing and annual survey of penguin adenovirus were conducted. The entire genome sequences of penguin adenoviruses were completed for two Chinstrap penguins (Pygoscelis antarctica and two Gentoo penguins (Pygoscelis papua. The whole genome lengths and G+C content of penguin adenoviruses were found to be 24,630-24,662 bp and 35.5-35.6%, respectively. Notably, the presence of putative sialidase gene was not identified in penguin adenoviruses by Rapid Amplification of cDNA Ends (RACE-PCR as well as consensus specific PCR. The penguin adenoviruses were demonstrated to be a new species within the genus Siadenovirus, with a distance of 29.9-39.3% (amino acid, 32.1-47.9% in DNA polymerase gene, and showed the closest relationship with turkey adenovirus 3 (TAdV-3 in phylogenetic analysis. During the 2008-2013 study period, the penguin adenoviruses were annually detected in 22 of 78 penguins (28.2%, and the molecular epidemiological study of the penguin adenovirus indicates a predominant infection in Chinstrap penguin population (12/30, 40%. Interestingly, the genome of penguin adenovirus could be detected in several internal samples, except the lymph node and brain. In conclusion, an analysis of the entire adenoviral genomes from Antarctic penguins was conducted, and the penguin adenoviruses, containing unique genetic character, were identified as a new species within the genus Siadenovirus. Moreover, it was annually detected in Antarctic penguins, suggesting its circulation within the penguin population.

  4. Preliminary molecular epidemiology of the Staphylococcus aureus in lower respiratory tract infections: a multicenter study in China

    Institute of Scientific and Technical Information of China (English)

    LI De-zhi; HU Ke; CAI Shao-xi; WAN Huan-ying; WANG Qiu-yue; WEI Li-ping; DU Juan; YU Qin; ZHONG Xiao-ning; WANG Rui-qin; MA Jian-jun; CHEN Yu-sheng; TIAN Gui-zhen; WANG Si-qin; GAO Zhan-cheng; YANG Jing-ping; ZHANG Wei; HU Cheng-ping; LI Jia-shu; MU Lan; HU Ying-hui; GENG Rong

    2011-01-01

    Background Staphylococcus aureus (S.aureus) remains as an important microbial pathogen resulting in community and nosocomial acquired infections with significant morbidity and mortality. Few reports for S. aureus in lower respiratory tract infections (LRTIs) have been documented. The aim of this study was to explore the molecular epidemiology of S.aureus in LRTIs in China.Methods A multicenter study of the molecular epidemiology of S. aureus in LRTIs was conducted in 21 hospitals in Beijing, Shanghai and twelve other provinces from November 2007 to February 2009. All the collected S. aureus strains were classified as minimum inhibitory concentration (MIC), mecA gene, virulence genes Panton-Valentine Leukocidin (PVL)and y-hemolysin (hlg), staphylococcal cassette chromosome mec (SCCmec) type, agr type, and Multilocus Sequence Typing (MLST).Results Totally, nine methicillin-sensitive S. aureus (MSSA) and 29 methicillin-resistant S. aureus (MRSA) strains were isolated after culture from a total of 2829 sputums or bronchoalveolar lavages. The majority of MRSA strains (22/29) had a MIC value of ≥512 μg/ml for cefoxitin. The mecA gene acting as the conservative gene was carried by all MRSA strains.PVL genes were detected in only one S. aureus strain (2.63%, 1/38). The hlg gene was detected in almost the all S.aureus (100% in MSSA and 96.56% in MRSA strains). About 75.86% of MRSA strains carried SCCmec Ⅲ. Agr type 1 was predominant (78.95%) among the identified three agr types (agr types 1,2, and 3). Totally, ten sequence type (ST) of S. aureus strains were detected. A new sequence type (ST1445) was found besides confirming ST239 as the major sequence type (60.53%). A dendrogram generated from our own MLST database showed all the bootstrap values≤50%.Conclusion Our preliminary epidemiology data show SCCmec Ⅲ, ST239 and agr type 1 of S. aureus as the predominant strains in LRTIs in Mainland of China.

  5. Toxigenicity in Staphylococcus aureus and Coagulase-Negative Staphylococci: Epidemiological and Molecular Aspects

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    M.L.R.S. Cunha

    2008-01-01

    Full Text Available Representatives of the Staphylococcus genus are the most common pathogens found in hospital environments, and they are etiological agents for a large variety of infections. Various virulence factors are responsible for the symptoms and severity of infections caused by Staphylococcus aureus. Among them are staphylococcal enterotoxins (SEs, which cause staphylococcal food poisoning, and toxic shock syndrome toxin-1 (TSST-1. Some reports indicate that TSST-1 and staphylococcal enterotoxins are also produced by coagulase-negative staphylococci (CNS. The present review aimed to discuss general aspects of staphylococcal toxins as well as the epidemiology, genetics and detection of toxins in Staphylococcus aureus and coagulase-negative staphylococci, since these microorganisms are becoming more and more frequent in nosocomial infections.

  6. Comparative molecular epidemiology provides new insights into Zucchini yellow mosaic virus occurrence in France.

    Science.gov (United States)

    Lecoq, H; Wipf-Scheibel, C; Nozeran, K; Millot, P; Desbiez, C

    2014-06-24

    Zucchini yellow mosaic virus (ZYMV, genus Potyvirus) causes important crop losses in cucurbits worldwide. In France, ZYMV epidemics are sporadic but occasionally very severe. This contrasts with Watermelon mosaic virus (WMV, genus Potyvirus) which causes regular and early epidemics. Factors influencing ZYMV epidemiology are still poorly understood. In order to gain new insights on the ecology and epidemiology of this virus, a 5-year multilocation trial was conducted in which ZYMV spread and populations were studied in each of the 20 plot/year combinations and compared with WMV. Search for ZYMV alternative hosts was conducted by testing weeds growing naturally around one plot and also by checking ZYMV natural infections in selected ornamental species. Although similar ZYMV populations were observed occasionally in the same plot in two successive years suggesting the occurrence of overwintering hosts nearby, only two Lamium amplexicaule plants were found to be infected by ZYMV of 3459 weed samples that were tested. The scarcity of ZYMV reservoirs contrasts with the frequent detection of WMV in the same samples. Since ZYMV and WMV have many aphid vectors in common and are transmitted with similar efficiencies, the differences observed in ZYMV and WMV reservoir abundances could be a major explanatory factor for the differences observed in the typology of ZYMV and WMV epidemics in France. Other potential ZYMV alternative hosts have been identified in ornamental species including begonia. Although possible in a few cases, exchanges of populations between different plots located from 500 m to 4 km apart seem uncommon. Therefore, the potential dissemination range of ZYMV by its aphid vectors seems to be rather limited in a fragmented landscape. PMID:24486486

  7. The Molecular and Spatial Epidemiology of Typhoid Fever in Rural Cambodia.

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    Duy Pham Thanh

    2016-06-01

    Full Text Available Typhoid fever, caused by the bacterium Salmonella Typhi, is an endemic cause of febrile disease in Cambodia. The aim of this study was to better understand the epidemiology of pediatric typhoid fever in Cambodia. We accessed routine blood culture data from Angkor Hospital for Children (AHC in Siem Reap province between 2007 and 2014, and performed whole genome sequencing (WGS on the isolated bacteria to characterize the S. Typhi population. The resulting phylogenetic information was combined with conventional epidemiological approaches to investigate the spatiotemporal distribution of S. Typhi and population-level risk factors for reported disease. During the study period, there were 262 cases of typhoid within a 100 km radius of AHC, with a median patient age of 8.2 years (IQR: 5.1-11.5 years. The majority of infections occurred during the rainy season, and commune incidences as high as 11.36/1,000 in children aged <15 years were observed over the study period. A population-based risk factor analysis found that access to water within households and increasing distance from Tonle Sap Lake were protective. Spatial mapping and WGS provided additional resolution for these findings, and confirmed that proximity to the lake was associated with discrete spatiotemporal disease clusters. We confirmed the dominance of MDR H58 S. Typhi in this population, and found substantial evidence of diversification (at least seven sublineages within this single lineage. We conclude that there is a substantial burden of pediatric typhoid fever in rural communes in Cambodia. Our data provide a platform for additional population-based typhoid fever studies in this location, and suggest that this would be a suitable setting in which to introduce a school-based vaccination programme with Vi conjugate vaccines.

  8. Molecular epidemiology, evolution and phylogeny of Chikungunya virus: An updating review.

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    Lo Presti, Alessandra; Cella, Eleonora; Angeletti, Silvia; Ciccozzi, Massimo

    2016-07-01

    Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus belonging to the Togaviridae family, causing a febrile illness associated with severe arthralgia and rash. In this review, we summarized a series of articles published from 2013 to 2016 concerning CHIKV epidemiology, phylogeny, vaccine and therapies, to give an update of our most recent article written in 2014 (Lo Presti et al.,2014). CHIKV infection was first reported in 1952 from Makonde plateaus and since this time caused many outbreaks worldwide, involving the Indian Ocean region, African countries, American continent and Italy. CHIKV infection is still underestimated and it is normally associated with clinical symptoms overlapping with dengue virus, recurring epidemics and mutations within the viral genome. These characteristics promote the geographical spread and the inability to control vector-mediated transmission of the virus. For these reasons, the majority of studies were aimed to describe outbreaks and to enhance knowledge on CHIKV biology, pathogenesis, infection treatment, and prevention. In this review, 16 studies on CHIKV phylogenetic and phylodinamics were considered, during the years 2013-2016. Phylogenetic and phylodinamic analysis are useful tools to investigate how the genealogy of a pathogen population is influenced by pathogen's demographic history, host immunological milieu and environmental/ecological factors. Phylogenetic tools were revealed important to reconstruct the geographic spread of CHIKV during the epidemics wave and to have information on the circulating strains of the virus, that are important for the prediction and control of the epidemics, as well as for vaccines and antiviral drugs development. In conclusion, this updating review can give a critical appraisal of the epidemiology, therapeutic and phylogenesis of CHIKV, reinforcing the need to monitor the geographic spread of virus and vectors. PMID:27085290

  9. Molecular Epidemiological Analysis of Echovirus 19 Isolated From an Outbreak Associated With Hand, Foot, and Mouth Disease (HFMD) in Shandong Province of China

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Objective To elucidate the genetic characterization and molecular epidemiological features of Echovirus 19 (E19) isolates collected from an outbreak associated with hand, foot and mouth disease (HFMD) in Tai'an city of Shandong Province of China from July to September, 2003. Methods Thirty seven Echovirus 19 isolates were isolated from stool specimens and throat swabs collected during the outbreak, then major capsid (VP1) genomic sequence was determined, and phylogenetic tree was done based on the VP1 sequences among these 37 and other E19 viruses deposited in the Genbank. Also a representative strain named CHN-SD03-TN12 was selected for sequencing of 5'-untranslated regions (5'-UTR). Results The identity rate was about 98.9%-100% among all these 37 El9 viruses. The genetic relationships between these 37 E19 isolates and other strains reported were also depicted. The identity rate was about 78.4%-78.9% compared with E19 reference strain Burke. The substitutions in the sequence of 5'-UTR resulted in changes in the conjectural properties of 5'-UTR of E19 viruses.Conclusion The genetic features of E19 viruses isolated during the outbreak in Shandong Province in 2003 may be associated with a genetic and antigenic drift that changes the virulence of the Shandong isolates, but the molecular changes in Shandong E19 viruses contributing to their phenotype remain to be further illuminated. However, the sequences described in this paper substantiate the changes taken place in capsid VP1 and 5'UTR regions. These substitutions may contribute to their tropism and virulence, and play a significant role in pathogenesis and clinical manifestations of the disease.

  10. Changing domesticity of Aedes aegypti in northern peninsular Malaysia: reproductive consequences and potential epidemiological implications.

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    Rahman G M Saifur

    Full Text Available BACKGROUND: The domestic dengue vector Aedes aegypti mosquitoes breed in indoor containers. However, in northern peninsular Malaysia, they show equal preference for breeding in both indoor and outdoor habitats. To evaluate the epidemiological implications of this peridomestic adaptation, we examined whether Ae. aegypti exhibits decreased survival, gonotrophic activity, and fecundity due to lack of host availability and the changing breeding behavior. METHODOLOGY/PRINCIPAL FINDINGS: This yearlong field surveillance identified Ae. aegypti breeding in outdoor containers on an enormous scale. Through a sequence of experiments incorporating outdoors and indoors adapting as well as adapted populations, we observed that indoors provided better environment for the survival of Ae. aegypti and the observed death patterns could be explained on the basis of a difference in body size. The duration of gonotrophic period was much shorter in large-bodied females. Fecundity tended to be greater in indoor acclimated females. We also found increased tendency to multiple feeding in outdoors adapted females, which were smaller in size compared to their outdoors breeding counterparts. CONCLUSION/SIGNIFICANCE: The data presented here suggest that acclimatization of Ae. aegypti to the outdoor environment may not decrease its lifespan or gonotrophic activity but rather increase breeding opportunities (increased number of discarded containers outdoors, the rate of larval development, but small body sizes at emergence. Size is likely to be correlated with disease transmission. In general, small size in Aedes females will favor increased blood-feeding frequency resulting in higher population sizes and disease occurrence.

  11. Identification and molecular epidemiology of Campylobacter coli isolates from human gastroenteritis, food, and animal sources by amplified fragment length polymorphism analysis and Penner serotyping

    DEFF Research Database (Denmark)

    Siemer, B.L.; Nielsen, Elsa; On, Stephan L.w.

    2005-01-01

    Campylobacter coli is an infrequently studied but important food-borne pathogen with a wide natural distribution. We investigated its molecular epidemiology by use of amplified fragment length polymorphism (AFLP)-based genotyping and Penner serotyping. Serotype reference strains and 177 Danish...

  12. Evolution, molecular epidemiology and perspectives on the research of taeniid parasites with special emphasis on Taenia solium.

    Science.gov (United States)

    Bobes, Raúl J; Fragoso, Gladis; Fleury, Agnès; García-Varela, Martín; Sciutto, Edda; Larralde, Carlos; Laclette, Juan P

    2014-04-01

    Human cysticercosis is known since old historical times in Greece and China; however, human infections by tapeworms have accompanied human beings for more that hundred thousand years. The disease is tightly bound to poverty and lack of hygiene, and has been eradicated in developed countries, but continues being a public health problem in developing countries of Latin-American, Sub-Saharan Africa and Asia, and is also remerging in a number of non endemic countries. It is considered a neglected disease. Here we revise a number of key scientific contributions on taeniid biology that open new avenues for more effective approaches to the control of cysticercosis. The evolution of flatworms and class Cestoda is analyzed, with special emphasis on the emergence of taeniid parasites and the colonization of the human species by tapeworms. The complex molecular host-parasite interplay in this relationship as result of co-evolution between two distantly related organisms. The relevant host and parasite's factors, in the prospect of identifying species-specific molecular markers useful in epidemiological studies carried out in endemic countries. The new possibilities arising with the characterization of the genomes for several species of tapeworms, including a deeper understanding of these organisms, as well as improved tools for diagnosis, vaccination and drug treatment. The need to revise the current control and management strategies for this tropical neglected disease.

  13. Molecular epidemiology of influenza A/H3N2 viruses circulating in Mexico from 2003 to 2012.

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    Marina Escalera-Zamudio

    Full Text Available In this work, nineteen influenza A/H3N2 viruses isolated in Mexico between 2003 and 2012 were studied. Our findings show that different human A/H3N2 viral lineages co-circulate within a same season and can also persist locally in between different influenza seasons, increasing the chance for genetic reassortment events. A novel minor cluster was also identified, named here as Korea, that circulated worldwide during 2003. Frequently, phylogenetic characterization did not correlate with the determined antigenic identity, supporting the need for the use of molecular evolutionary tools additionally to antigenic data for the surveillance and characterization of viral diversity during each flu season. This work represents the first long-term molecular epidemiology study of influenza A/H3N2 viruses in Mexico based on the complete genomic sequences and contributes to the monitoring of evolutionary trends of A/H3N2 influenza viruses within North and Central America.

  14. Long-term molecular epidemiology of Staphylococcus epidermidis blood culture isolates from patients with hematological malignancies.

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    Erik Ahlstrand

    Full Text Available Staphylococcus epidermidis is an important cause of bloodstream infections in patients with hematological malignancies. Knowledge of the long-term epidemiology of these infections is limited. We surveyed all S. epidermidis blood culture isolates from patients treated for hematological malignancies at the University Hospital of Örebro, Sweden from 1980 to 2009. A total of 373 S. epidermidis isolates were identified and multilocus sequence typing, staphylococcal chromosome cassette mec (SCCmec typing and standard antibiotic susceptibility testing were employed to characterize these isolates. The majority of the isolates 361/373 (97% belonged to clonal complex 2, and the 373 isolates were divided into 45 sequence types (STs; Simpson's Diversity Index was 0.56. The most prevalent STs were ST2 (243/373, 65% and ST215 (28/373, 8%. Ninety three percent (226/243 of the ST2 isolates displayed either SCCmec type III or IV. ST2 and 215 were isolated during the entire study period, and together these STs caused temporal peaks in the number of positive blood cultures of S. epidermidis. Methicillin resistance was detected in 213/273 (78% of all isolates. In the two predominating STs, ST2 and ST215, methicillin resistance was detected in 256/271 isolates (95%, compared with 34/100 (34% in other STs (p<0.001. In conclusion, in this long-term study of patients with hematological malignancies, we demonstrate a predominance of methicillin-resistant ST2 among S. epidermidis blood culture isolates.

  15. Molecular Epidemiology of Enteric Adenovirus Gastroenteritis in under-Five-Year-Old Children in Iran

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    Anahita Sanaei Dashti

    2016-01-01

    Full Text Available Background. Acute gastroenteritis is one of the major sources of morbidity and mortality among young children in developed and developing countries. The aim of this study was to determine the prevalence of human adenovirus- (HAdV- 40 and HAdV-41 in children hospitalized with gastroenteritis in five different health centers of Iran. Methods. In a cross-sectional epidemiological study, we studied 2682 fecal specimens that were collected from children under the age of 5 years in five educational and therapeutic pediatric centers in Iran from February 2012 to February 2013. Samples were tested for HAdV-40 and HAdV-41, using a specific pair of primers in polymerase chain reaction (PCR method. Results. HAdV-40 and HAdV-41 were detected in 132 (5.18% of the patients with diarrhea. A significantly higher prevalence of HAdV-40 and HAdV-41 (58.3% was observed in children under 12 months of age, compared to other age groups. The male to female ratio was 1.7. Conclusion. The results of this study demonstrated that HAdV-40 and HAdV-41 could be considered etiological agents for acute gastroenteritis among children in Iran. The PCR as a rapid test may increase the chance for a relatively mild course of the disease followed by a complete recovery and avoiding administration of unnecessary antibiotics.

  16. Molecular epidemiology of rotavirus in four provinces of Angola before vaccine introduction.

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    Esteves, Aida; Nordgren, Johan; Pereira, Joana; Fortes, Filomeno; Dimbu, Rafael; Saraiva, Nilton; Mendes, Cristina; Istrate, Claudia

    2016-09-01

    Angola is a sub-Saharan country in southern Africa highly affected by diarrhoeal disease with limited epidemiological data regarding etiologic agents. This study was performed during 2012-2013, prior to rotavirus vaccine introduction, with the objective to detect and characterize the rotavirus strains circulating in four provinces of the country: Huambo, Luanda, Zaire, and Cabinda. A high rotavirus detection rate (35%, 117/334) was observed. G1 was the most common G-genotype (83.6%), whereas P[8] (50.9%) followed by P[6] (38.8%) were the most common P-types. G1P[8] was identified as the predominant combination (50%), followed by the unusual G1P[6] (29.3%). Strains such G2P[4], G8P[6], G9P[6], and G12P[6] were also found in lower frequencies (5.2-1.7%). The P[6] strains did not cluster in the phylogenetic trees according to their geographic origin or even the corresponding G-genotype, suggesting a limited number of recent introductions and extensive reassortment events. Our results represent the first report on rotavirus genotype profiles in Angola, showing a wide circulation of the unusual genotype G1P[6], and underline the importance of RV surveillance after the vaccine introduction. J. Med. Virol. 88:1511-1520, 2016. © 2016 Wiley Periodicals, Inc. PMID:26946356

  17. Molecular epidemiology of Staphylococcus aureus isolates at different sites in the milk producing dairy farms.

    Science.gov (United States)

    Souza, Viviane; Nader Filho, Antonio; de Castro Melo, Poliana; Ferraudo, Guilherme Moraes; Antônio Sérgio, Ferraudo; de Oliveira Conde, Sandra; Fogaça Junior, Flavio Augusto

    2012-10-01

    The epidemiological relationships between isolated Staphylococcus aureus strains in milk samples of dairy cows, reagent to California Mastitis Test, individual and group milk was demonstrated in different sites of the production fluxogram, in 12 milk-producing farms in the Gameleira region, municipality of Sacramento MG Brazil, so that localization and transmission modes may be identified. Two hundred and forty-four strains out of 446 samples collected at several sites were isolated and bio-chemically characterized as coagulase-positive staphylococcus. Specific chromosome DNA fragment of the species Staphylococcus aureus was amplified to 106 strains and 103 underwent (PFGE). Samples' collection sites with the highest isolation frequency of Staphylococcus aureus strains comprised papillary ostia (31.1%), CMT-reagent cow milk (21.7%), mechanical milking machines' insufflators (21,7%), milk in milk pails (6.6%) and the milk in community bulk tanks (5.6%). Genetic heterogeneity existed among the isolated 103 Staphylococcus aureus strains, since 32 different pulse-types were identified. Pulse-type 1 had the highest similarity among the isolated strains within the different sites of the milk-production fluxogram. Highest occurrence of pulsetype 1 isolates of Staphylococcus aureus strains was reported in samples collected from the papillary ostia (10.6%), followed by milk samples from CMT-reagent dairy cows (5.8%) and mechanical milking machine insufflators (3.8%). The above shows the relevance of these sites in the agents' transmission mechanism within the context of the farms investigated. PMID:24031997

  18. Molecular epidemiology of an outbreak of clinical mastitis in sheep caused by Mannheimia haemolytica.

    Science.gov (United States)

    Omaleki, Lida; Browning, Glenn F; Allen, Joanne L; Markham, Philip F; Barber, Stuart R

    2016-08-15

    The aetiology and epidemiology of outbreaks of clinical mastitis in sheep under extensive pastoral conditions are incompletely understood. The objective of this study was to conduct a detailed investigation of a clinical mastitis outbreak that affected more than 10% of 230 at-risk ewes on a sheep and grain producing property in south east Australia during drought conditions in 2009. Milk samples were collected aseptically from all affected ewes and plated on sheep blood agar for bacterial identification. M. haemolytica was isolated from 80% of the samples that yielded cultivable microorganisms and thus was the main microorganism responsible for the outbreak. Analysis of the restriction endonuclease cleavage patterns of the isolates using pulsed field gel electrophoresis revealed some evidence of clonality, suggesting the possibility of horizontal transmission, but there was also considerable diversity between the clusters of closely related isolates. Multilocus sequence typing of the M. haemolytica isolates revealed most of the isolates belonged to ST1 with no association between the PFGE and MLST fingerprints of the isolates. Resistance to neomycin, streptomycin and sulphafurazole was detected in some of the isolates, but they were all susceptible to penicillin, ampicillin, ceftiofur, amoxycillin/clavulanic acid, ciprofloxacin, tetracycline, erythromycin and trimethoprim. This is the first published record of a comparison of the strains of M. haemolytica involved in a clinical mastitis outbreak in sheep and demonstrates the importance of this pathogen in sheep production systems, particularly during adverse climatic conditions and increased stocking rate. PMID:27374911

  19. Cardiac pathology and molecular epidemiology by avian leukosis viruses in Japan.

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    Sayuri Nakamura

    Full Text Available Epidemiological studies suggest that retroviruses, including human immunodeficiency virus type 1, are associated with cardiomyopathy and myocarditis, but a causal relationship remains to be established. We encountered unusual cardiomyocyte hypertrophy and mitosis in Japanese native fowls infected with subgroup A of the avian leukosis viruses (ALVs-A, which belong to the genus Alpharetrovirus of the family Retroviridae and mainly induce lymphoid neoplasm in chickens. The affected hearts were evaluated by histopathology and immunohistochemistry, viral isolation, viral genome sequencing and experimental infection. There was non-suppurative myocarditis in eighteen fowls and seven of them had abnormal cardiomyocytes, which were distributed predominantly in the left ventricular wall and showed hypertrophic cytoplasm and atypical large nuclei. Nuclear chains and mitosis were frequently noted in these cardiomyocytes and immunohistochemistry for proliferating cell nuclear antigen supported the enhancement of mitotic activity. ALVs were isolated from all affected cases and phylogenic analysis of envSU genes showed that the isolates were mainly classified into two different clusters, suggesting viral genome diversity. In ovo experimental infection with two of the isolates was demonstrated to cause myocarditis and cardiomyocyte hypertrophy similar to those in the naturally occurring lesions and cardiac hamartoma (rhabdomyoma in a shorter period of time (at 70 days of age than expected. These results indicate that ALVs cause myocarditis as well as cardiomyocyte abnormality in chickens, implying a pathogenetic mechanism different from insertional mutagenesis and the existence of retrovirus-induced heart disorder.

  20. A molecular epidemiological study of rabies epizootics in kudu (Tragelaphus strepsiceros in Namibia

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    Nel Louis H

    2006-01-01

    Full Text Available Abstract Background A panel of 37 rabies virus isolates were collected and studied, originating mainly from the northern and central regions of Namibia, between 1980 and 2003. Results These virus isolates demonstrated a high degree of genetic similarity with respect to a 400 bp region of the nucleoprotein gene, with the virus isolates originating from kudu antelope (n = 10 sharing 97.2–100% similarity with jackal isolates, and 97–100% similarity with those isolated from domestic dogs. Phylogenetic analysis suggested that these viruses were all of the canid rabies biotype of southern Africa. The viruses from kudu were closely associated with jackal isolates (n = 6, bat-eared fox isolates (n = 2 and domestic dog isolates (n = 2 at the genetic level and identical at the amino acid level, irrespective of the year of isolation. Conclusion These data suggest that jackal and kudu may form part of the same epidemiological cycle of rabies in Namibian wildlife, and might demonstrate the close-relationship between rabies virus strains that circulate within Namibia and those that circulate between Namibia and its neighbouring countries such as Botswana and South Africa.

  1. Changing Pattern of Clinical Epidemiology on Hepatitis C Virus Infection in Southwest China

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    Zehui Yan

    2012-03-01

    Full Text Available Background: The changing pattern of hepatitis C virus (HCV infection could have a significant impact on future medical prevention practices and therapies.Objectives: The purpose of this study was to describe the changing pattern of HCV infection in southwest China using clinical epidemiology, and to assess the association between the genotypes distribution and certain potential risk factors.Patients and Methods: A retrospective analysis which included 1 208 subjects with chronic HCV registered at the Southwest Hospital (Chongqing, Southwest China was performed. The information was reviewed and the data collected from clinical records and short telephone interviews when necessary. HCV genotypes were determined by nucleotide sequencing of the CE1 regions followed by phylogenic analysis with the published HCV genotype. HCV genotype distribution was analyzed according to the patients' age, gender, risk exposure, and the initial risk exposure.Results: Among the 1 208 patients, the HCV subtype 1b was the most prevalent (32.9%, followed by subtype 3b (18.9%, 6a (18.0%, 3a (12.8% and 2a (10.4%, while subtypes 1a and 6k accounted for cases of HCV infection in only 9 and 3 cases respectively. Individuals older than 40 years were mainly infected with subtypes 1b and 2a, whereas younger patients were predominantly infected with genotypes 3 and 6. Subtypes 1b and 2a were observed more frequently among 44.4% and 16.0% patients respectively, with a history of invasive operations. Subtypes 3b and 6a constituted the majority of HCV infections among intravenous drug users (IDUs (28.7% and 34.9%, respectively. A significant difference (P < 0.001 was observed between the HCV genotype distributions, according to the potential route of infection.Conclusion: In southwest China, the most common remaining subtype is the 1b genotype, but this has declined significantly among young patients. This is followed by subtype 3b and 6a which has increased significantly

  2. Investigación sobre epidemiología convencional y molecular de tuberculosis en Orizaba, Veracruz, 1995-2008 Research on conventional and molecular epidemiology of tuberculosis in Orizaba, Veracruz, 1995-2008

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    Ma Eugenia Jiménez-Corona

    2009-01-01

    Full Text Available Se describen los resultados de investigación del Consorcio Mexicano contra la Tuberculosis, en la Jurisdicción Sanitaria de Orizaba, Veracruz, entre 1995 y 2008. Las aportaciones principales de los trabajos se refieren a los siguientes rubros: 1. Epidemiología convencional y molecular (medición de la carga de la enfermedad, tendencias, factores de riesgo y grupos vulnerables; descripción de las consecuencias de la farmacorresistencia e identificación de factores que favorecen la transmisión en la comunidad y en los hospitales. 2. Desarrollo de técnicas rápidas para conservación de muestras respiratorias que permitan el aislamiento y diagnóstico de farmacorresistencia de M. tuberculosis en campo. 3. Evaluación de la prueba tuberculínica, respuesta inmunológica al Bacilo de Calmette-Guerin (BCG, biomarcadores de la respuesta inmunitaria y medidas de control. 4. Comentarios en torno a aspectos éticos de la investigación en tuberculosis. Además se describe el impacto en políticas públicas, la transferencia de tecnología, la formación de recursos humanos y las perspectivas a futuro.This study describes the achievements of the Mexican Consortium against Tuberculosis, in the Sanitary District of Orizaba, Veracruz, Mexico between 1995 and 2008. In brief, the main results can be classified as follows: 1 Conventional and molecular epidemiology (measurement of burden of disease, trends, risk factors and vulnerable groups, consequences of drug resistance, identification of factors that favor nosocomial and community transmission; 2 Development of diagnostic techniques to detect drug resistance, description of circulating clones and adaptation of simple techniques to be used in the field; 3 Evaluation of usefulness of tuberculin skin test, immunologic responses to BCG, impact of directly observed therapy for tuberculosis (DOTS, and study of immunological biomarkers and 4 Comments on ethical aspects of tuberculosis research. Additionally

  3. Evaluation and utilization as a public health tool of a national molecular epidemiological tuberculosis outbreak database within the United Kingdom from 1997 to 2001.

    Science.gov (United States)

    Drobniewski, F A; Gibson, A; Ruddy, M; Yates, M D

    2003-05-01

    The aim of this study was to develop a national model and analyze the value of a molecular epidemiological Mycobacterium tuberculosis DNA fingerprint-outbreak database. Incidents were investigated by the United Kingdom PHLS Mycobacterium Reference Unit (MRU) from June 1997 to December 2001, inclusive. A total of 124 incidents involving 972 tuberculosis cases, including 520 patient cultures from referred incidents and 452 patient cultures related to two population studies, were examined by using restriction fragment length polymorphism IS6110 fingerprinting and rapid epidemiological typing. Investigations were divided into the following three categories, reflecting different operational strategies: retrospective passive analysis, retrospective active analysis, and retrospective prospective analysis. The majority of incidents were in the retrospective passive analysis category, i.e., the individual submitting isolates has a suspicion they may be linked. Outbreaks were examined in schools, hospitals, farms, prisons, and public houses, and laboratory cross-contamination events and unusual clinical presentations were investigated. Retrospective active analysis involved a major outbreak centered on a high school. Contact tracing of a teenager with smear-positive pulmonary tuberculosis matched 14 individuals, including members of his class, and another 60 cases were identified in schools clinically and radiologically and by skin testing. Retrospective prospective analysis involved an outbreak of 94 isoniazid-resistant tuberculosis cases in London, United Kingdom, that began after cases were identified at one hospital in January 2000. Contact tracing and comparison with MRU databases indicated that the earliest matched case had occurred in 1995. Subsequently, the MRU changed to an active prospective analysis targeting linked isoniazid-monoresistant isolates for follow up. The patients were multiethnic, born mainly in the United Kingdom, and included professionals

  4. Multicentre study highlighting clinical relevance of new high-throughput methodologies in molecular epidemiology of Pneumocystis jirovecii pneumonia.

    Science.gov (United States)

    Esteves, F; de Sousa, B; Calderón, E J; Huang, L; Badura, R; Maltez, F; Bassat, Q; de Armas, Y; Antunes, F; Matos, O

    2016-06-01

    Pneumocystis jirovecii causes severe interstitial pneumonia (PcP) in immunosuppressed patients. This multicentre study assessed the distribution frequencies of epidemiologically relevant genetic markers of P. jirovecii in different geographic populations from Portugal, the USA, Spain, Cuba and Mozambique, and the relationship between the molecular data and the geographical and clinical information, based on a multifactorial approach. The high-throughput typing strategy for P. jirovecii characterization consisted of DNA pooling using quantitative real-time PCR followed by multiplex-PCR/single base extension. The frequencies of relevant P. jirovecii single nucleotide polymorphisms (mt85, SOD110, SOD215, DHFR312, DHPS165 and DHPS171) encoded at four loci were estimated in ten DNA pooled samples representing a total of 182 individual samples. Putative multilocus genotypes of P. jirovecii were shown to be clustered due to geographic differences but were also dependent on clinical characteristics of the populations studied. The haplotype DHFR312T/SOD110C/SOD215T was associated with severe AIDS-related PcP and high P. jirovecii burdens. The frequencies of this genetic variant of P. jirovecii were significantly higher in patients with AIDS-related PcP from Portugal and the USA than in the colonized patients from Portugal, and Spain, and children infected with P. jirovecii from Cuba or Mozambique, highlighting the importance of this haplotype, apparently associated with the severity of the disease and specific clinical groups. Patients from the USA and Mozambique showed higher rates of DHPS mutants, which may suggest the circulation of P. jirovecii organisms potentially related with trimethoprim-sulfamethoxazole resistance in those geographical regions. This report assessed the worldwide distribution of P. jirovecii haplotypes and their epidemiological impact in distinct geographic and clinical populations.

  5. Multicentre study highlighting clinical relevance of new high-throughput methodologies in molecular epidemiology of Pneumocystis jirovecii pneumonia.

    Science.gov (United States)

    Esteves, F; de Sousa, B; Calderón, E J; Huang, L; Badura, R; Maltez, F; Bassat, Q; de Armas, Y; Antunes, F; Matos, O

    2016-06-01

    Pneumocystis jirovecii causes severe interstitial pneumonia (PcP) in immunosuppressed patients. This multicentre study assessed the distribution frequencies of epidemiologically relevant genetic markers of P. jirovecii in different geographic populations from Portugal, the USA, Spain, Cuba and Mozambique, and the relationship between the molecular data and the geographical and clinical information, based on a multifactorial approach. The high-throughput typing strategy for P. jirovecii characterization consisted of DNA pooling using quantitative real-time PCR followed by multiplex-PCR/single base extension. The frequencies of relevant P. jirovecii single nucleotide polymorphisms (mt85, SOD110, SOD215, DHFR312, DHPS165 and DHPS171) encoded at four loci were estimated in ten DNA pooled samples representing a total of 182 individual samples. Putative multilocus genotypes of P. jirovecii were shown to be clustered due to geographic differences but were also dependent on clinical characteristics of the populations studied. The haplotype DHFR312T/SOD110C/SOD215T was associated with severe AIDS-related PcP and high P. jirovecii burdens. The frequencies of this genetic variant of P. jirovecii were significantly higher in patients with AIDS-related PcP from Portugal and the USA than in the colonized patients from Portugal, and Spain, and children infected with P. jirovecii from Cuba or Mozambique, highlighting the importance of this haplotype, apparently associated with the severity of the disease and specific clinical groups. Patients from the USA and Mozambique showed higher rates of DHPS mutants, which may suggest the circulation of P. jirovecii organisms potentially related with trimethoprim-sulfamethoxazole resistance in those geographical regions. This report assessed the worldwide distribution of P. jirovecii haplotypes and their epidemiological impact in distinct geographic and clinical populations. PMID:27021425

  6. Molecular Typing of Borrelia burgdorferi Sensu Lato: Taxonomic, Epidemiological, and Clinical Implications

    OpenAIRE

    Wang, Guiqing; Dam, Alje P. van; Schwartz, Ira; Dankert, Jacob

    1999-01-01

    Borrelia burgdorferi sensu lato, the spirochete that causes human Lyme borreliosis (LB), is a genetically and phenotypically divergent species. In the past several years, various molecular approaches have been developed and used to determine the phenotypic and genetic heterogeneity within the LB-related spirochetes and their potential association with distinct clinical syndromes. These methods include serotyping, multilocus enzyme electrophoresis, DNA-DNA reassociation analysis, rRNA gene res...

  7. Molecular epidemiology of zoonotic streptococcosis/lactococcosis in rainbow trout (Oncorhynchus mykiss) aquaculture in Iran

    DEFF Research Database (Denmark)

    Karsidani, S. Haghighi; Soltani, M.; Nikbakhat-Brojeni, G.;

    2010-01-01

    ."nMaterials and Methods: 108 Gram positive cocci isolates were obtained from diseased trout in seven provinces with major trout production during 2008 till 2009. These bacterial isolates were characterized using phenotypic and molecular studies. The isolates were also analysed phylogeneticaly and compared...... similarity values with all other recorded strains."nConculsion: The results of this study clearly show that trout farming in Iran is severely affected by both species of S. iniae and L. garvieae and requires serious preventive criteria....

  8. Molecular epidemiology of giardiasis among Orang Asli in Malaysia: application of the triosephosphate isomerase gene

    OpenAIRE

    Anuar, Tengku Shahrul; Nor Azreen, Siti; Salleh, Fatmah Md; Moktar, Norhayati

    2014-01-01

    Background Giardia duodenalis is a flagellate parasite which has been considered the most common protozoa infecting human worldwide. Molecular characterization of G. duodenalis isolates have revealed the existence of eight groups (Assemblage A to H) which differ in their host distribution. Assemblages A and B are found in humans and in many other mammals. Methods This cross-sectional study was conducted to identify assemblage’s related risk factors of G. duodenalis among Orang Asli in Malaysi...

  9. Modelling refractive index changes due to molecular interactions

    Science.gov (United States)

    Varma, Manoj

    2016-03-01

    There are a large number of sensing techniques which use optical changes to monitor interactions between molecules. In the absence of fluorophores or other labels, the basic signal transduction mechanism relies on refractive index changes arising from the interactions of the molecules involved. A quantitative model incorporating molecular transport, reaction kinetics and optical mixing is presented which reveals important insights concerning the optimal detection of molecular interactions optically. Although conceptually simple, a comprehensive model such as this has not been reported anywhere. Specifically, we investigate the pros and cons of detecting molecular interactions in free solution relative to detecting molecular interactions on surfaces using surface bound receptor molecules such as antibodies. The model reveals that the refractive index change produced in surface based sensors is 2-3 orders of magnitude higher than that from interactions in free solution. On the other hand, the model also reveals that it is indeed possible to distinguish specific molecular interactions from non-specific ones based on free-solution bulk refractometry without any washing step necessary in surface based sensors. However, the refractive index change for free solution interactions predicted by the model is smaller than 10-7 RIU, even for large proteins such as IgG in sufficiently high concentrations. This value is smaller than the typical 10-6 RIU detection limit of most state of the art optical sensing techniques therefore requiring techniques with substantially higher index sensitivity such as Back Scattering Interferometry.

  10. The Changing Epidemiology of Herpes Simplex Virus Type 1 Infection: The Associated Effects on the Incidence of Ocular Herpes

    Directory of Open Access Journals (Sweden)

    Abedi Kiasari, B.

    2016-07-01

    Full Text Available Herpes simplex virus type 1 (HSV-1 with a worldwide distribution has been reported in all human populations, resulting in a clinical spectrum of infections. Although HSV type 2 (HSV-2 is known as the most common cause of genital herpes, an increasing number of cases with genital herpes are caused by HSV-1. The present study aimed to discuss the changes in the epidemiology of HSV-1 infection including the decline in the general incidence of HSV-1 infection in childhood and the increased rate of genital herpes, caused by HSV-1. Moreover, changes in the epidemiology of ocular herpes, i.e., the reduced rate of primary ocular herpes in children and increased incidence of ocular HSV infection in adults, were discussed.

  11. Molecular Epidemiology of Staphylococcus aureus among Patients with Skin and Soft Tissue Infections in Two Chinese Hospitals

    Science.gov (United States)

    Gu, Fei-Fei; Chen, Ye; Dong, De-Ping; Song, Zhen; Guo, Xiao-Kui; Ni, Yu-Xing; Han, Li-Zhong

    2016-01-01

    Background: Staphylococcus aureus is one of the predominant causes of skin and soft tissue infections (SSTIs), but limited data were available regarding the characterization of S. aureus from SSTIs patients in Jiangsu Province in China. We aimed to investigate the molecular epidemiology of S. aureus among SSTIs patients in two hospitals of Jiangsu Province. Methods: Sixty-two patients with SSTIs from two Chinese hospitals in Jiangsu Province were enrolled in this study, and 62 S. aureus isolates were collected from February 2014 to January 2015. S. aureus isolates were characterized by antimicrobial susceptibility testing, toxin gene detection, and molecular typing with sequence type, Staphylococcus protein A gene type, accessory gene regulator (agr) group, and Staphylococcal cassette chromosome mec type. Results: Sixteen (25.8%) methicillin-resistant S. aureus (MRSA) isolates were detected, and there was no isolate found resistant to vancomycin, teicoplanin, sulfamethoxazole-trimethoprim, and linezolid. The sei was the toxin gene most frequently found, and no lukS/F-PV-positive isolates were detected among the SSTIs’ patients. Molecular analysis revealed that ST398 (10/62, 16.1%; 2 MRSA and 8 methicillin-susceptible S. aureus) to be the dominant clone, followed by ST5 (8/62, 12.9%) and ST7 (8/62, 12.9%). Conclusions: The livestock ST398 was the most common clone among patients with S. aureus SSTIs in Jiangsu Province, China. Surveillance and further studies on the important livestock ST398 clone in human infections are necessarily requested. PMID:27647191

  12. Molecular Epidemiology and Phylogenetic Analysis of Human Adenovirus Caused an Outbreak in Taiwan during 2011.

    Directory of Open Access Journals (Sweden)

    Yung-Cheng Lin

    Full Text Available An outbreak of adenovirus has been surveyed in Taiwan in 2011. To better understand the evolution and epidemiology of adenovirus in Taiwan, full-length sequence of hexon and fiber coapsid protein was analyzed using series of phylogenetic and dynamic evolution tools. Six different serotypes were identified in this outbreak and the species B was predominant (HAdV-3, 71.50%; HAdV-7, 15.46%. The most frequent diagnosis was acute tonsillitis (54.59% and bronchitis (47.83%. Phylogenetic analysis revealed that hexon protein gene sequences were highly conserved for HAdV-3 and HAdV-7 circulation in Taiwan. However, comparison of restriction fragment length polymorphism (RFLP analysis and phylogenetic trees of fiber gene in HAdV-7 clearly indicated that the predominant genotype in Taiwan has shifted from 7b to 7d. Several positive selection sites were observed in hexon protein. The estimated nucleotide substitution rates of hexon protein of HAdV-3 and HAdV-7 were 0.234×10-3 substitutions/site/year (95% HPD: 0.387~0.095×10-3 and 1.107×10-3 (95% HPD: 0. 541~1.604 respectively; those of the fiber protein of HAdV-3 and HAdV-7 were 1.085×10-3 (95% HPD: 1.767~0.486 and 0.132×10-3 (95% HPD: 0.283~0.014 respectively. Phylodynamic analysis by Bayesian skyline plot (BSP suggested that using individual gene to evaluate the effective population size might possibly cause miscalculation. In summary, the virus evolution is ongoing, and continuous surveillance of this virus evolution will contribute to the control of the epidemic.

  13. Molecular epidemiology of Staphylococcus aureus isolates at different sites in the milk producing dairy farms

    Directory of Open Access Journals (Sweden)

    Viviane Souza

    2012-12-01

    Full Text Available The epidemiological relationships between isolated Staphylococcus aureus strains in milk samples of dairy cows, reagent to California Mastitis Test, individual and group milk was demonstrated in different sites of the production fluxogram, in 12 milk-producing farms in the Gameleira region, municipality of Sacramento MG Brazil, so that localization and transmission modes may be identified. Two hundred and forty-four strains out of 446 samples collected at several sites were isolated and bio-chemically characterized as coagulase-positive staphylococcus. Specific chromosome DNA fragment of the species Staphylococcus aureus was amplified to 106 strains and 103 underwent (PFGE. Samples' collection sites with the highest isolation frequency of Staphylococcus aureus strains comprised papillary ostia (31.1%, CMT-reagent cow milk (21.7%, mechanical milking machines' insufflators (21,7%, milk in milk pails (6.6% and the milk in community bulk tanks (5.6%. Genetic heterogeneity existed among the isolated 103 Staphylococcus aureus strains, since 32 different pulse-types were identified. Pulse-type 1 had the highest similarity among the isolated strains within the different sites of the milk-production fluxogram. Highest occurrence of pulsetype 1 isolates of Staphylococcus aureus strains was reported in samples collected from the papillary ostia (10.6%, followed by milk samples from CMT-reagent dairy cows (5.8% and mechanical milking machine insufflators (3.8%. The above shows the relevance of these sites in the agents' transmission mechanism within the context of the farms investigated.

  14. [Molecular epidemiologic surveillance and antifungal agent sensitivity of Candida albicans isolated from anesthesia intensive care units].

    Science.gov (United States)

    Gülay, Zeynep; Ergon, Cem; Ozkütük, Aydan; Yücesoy, Mine; Biçmen, Meral

    2002-01-01

    Patients in intensive care units (ICU) are at risk of nosocomial infections. The incidence of nosocomial fungal infections has increased in parallel with the increase of nosocomial infections. Candida albicans is the most frequent pathogenic species among the fungi. The aim of this study was to make an epidemiological surveillance of C. albicans urine isolates which were isolated from patients who were hospitalized in ICU between June 2000 and October 2001 by antifungal susceptibility testing and Randomly Amplified Polymorphic DNA (RAPD) analysis. For this purpose, 38 C. albicans which were isolated from 29 patients were investigated for amphotericin B and fluconazole susceptibility with the microdilution method. The range of minimal inhibitory concentration (MIC) of amphotericin B was between 0.25-1 microgram/ml and MIC50 value was 0.5 microgram/ml and none of the isolates had high (MIC > 1 microgram/ml) MIC values. The MIC values for fluconazole varied between 0.25-16 micrograms/ml and MIC50 value was 1 microgram/ml. While none of the isolates was resistant to fluconazole, two isolates were detected as dose dependent susceptible. RAPD analysis was performed with two different primers in order to investigate clonal relationship, and 22 patterns were detected with one of the primers and 24 patterns were detected with the other. In conclusion, it is thought that the origin of the C. albicans urine isolates were mostly endogenous but exogenous spread might also be considered as isolates that were clonally related were isolated from different patients at the same time interval.

  15. Molecular epidemiology of Candida species isolated from urine at an intensive care unit.

    Science.gov (United States)

    Ergon, M C; Gülay, Z

    2005-03-01

    Candida spp. has been the leading microorganism isolated from the urine specimens of patients hospitalized at the Anesthesiology and Reanimation intensive care unit (ICU) of Dokuz Eylul University Hospital, Izmir, since 1998. This study was undertaken to investigate the clonal relationship of Candida urine isolates in order to find the mode of spread among the patients. Epidemiological surveillance of 38 Candida albicans, 15 Candida tropicalis and 12 Candida glabrata recovered from the urine specimens of patients who were hospitalized in the ICU between June 11, 2000 and October 15, 2001 was carried out by antifungal susceptibility testing and randomly amplified polymorphic DNA (RAPD) analysis. Two short primers [Cnd3 (5'-CCAGATGCAC-3') and Cnd4 (5'-ACGGTACACT-3')] were used for RAPD. None of the isolates had high minimal inhibitory concentration (MIC) values (>1 microg ml(-1)) against amphotericin B with MIC50 values of 0.5 microg ml(-1), 0.5 microg ml(-1) and 0.125 microg ml(-1) for C. albicans, C. tropicalis and C. glabrata isolates, respectively. However, three C. glabrata isolates were resistant and one C. albicans and five C. glabrata isolates were dose-dependent susceptible (D-DS) to fluconazole. Among C. albicans isolates 19 and 20 patterns were detected with primers Cnd3 and Cnd4, respectively. When primers Cnd3 and Cnd4 were evaluated together, three and four genotypes were identified for C. tropicalis and C. glabrata isolates, respectively. Our results suggest that the source of C. albicans isolates was mostly endogenous. It is difficult to interpret the mode of spread of C. tropicalis and C. glabrata urine isolates as we obtained insufficient banding patterns for these species.

  16. Prevalence and molecular epidemiology of human papillomavirus infection in Italian women with cervical cytological abnormalities

    Directory of Open Access Journals (Sweden)

    Angelo Meloni

    2014-03-01

    Full Text Available Background. Human papillomavirus (HPV infection is the most common sexually transmitted infection and high-risk HPV types are a necessary cause for the development of cervical cancer. The present study investigated the HPV-type specific prevalence in 650 women, aged 15-76 years, with cytological abnormalities and the association between HPV infection and cervical disease in a subset of 160 women for whom cytological results for Pap-Test were available, during the period 2008-2011 in Cagliari (Southern Italy.Design and Methods. HPV-DNA extraction was performed by lysis and digestion with proteinase K and it was typed by using the INNOLiPA HPV Genotyping Assay.Results. Overall the HPV prevalence was 52.6%; high-risk genotypes were found in 68.9% of women and multiple-type infection in 36.1% of HPV-positive women. The commonest types were HPV-52 (23.4%, HPV-53 (15.7%, HPV-16 (15.4% and HPV-6 (12.4%. Among the women with cytological diagnosis, any-type of HPV DNA was found in 49.4% of the samples and out of these 93.7% were high-risk genotypes. Genotype HPV 53 was the commonest type among women affected by ASCUS lesions (21.4%, genotype 52 in positive L-SIL cases (22.5%, genotype 16 H-SIL (27.3%.Conclusions. This study confirmed the high prevalence of HPV infection and high-risk genotypes among women with cervical abnormalities while, unlike previously published data, genotype HPV-52 was the most common type in our series. These data may contribute to increase the knowledge of HPV epidemiology and designing adequate vaccination strategies.

  17. Changing Epidemiology of Common Cancers in Southern Iran, 2007-2010: A Cross Sectional Study.

    Directory of Open Access Journals (Sweden)

    Seyed Masoom Masoompour

    Full Text Available We have evaluated the ever changing epidemiology of cancers in Fars province, Iran since the re-establishment of Fars cancer registry. Based on the collected data from all related sources in Fars province from 2007-2010 we calculated the cancer age-standardized rates per 100,000 person-years (ASRs. The results are presented as incidence rates of cases by site according to the International Classification of Diseases for Oncology (ICD-O, sex, age, crude rate, and ASRs. In women the total ASR was 41.70 per 100,000 from 1985-1989 which had increased to 55.50 and 95.46 during 1998-2002 and 2007-2010. The incidence of breast cancer in women during 2007-2010 was about two and four times higher than 1998-2002 and 1985-1989. The incidence of colorectal cancer in women during 2007-2010 was about three and five times higher than 1998-2002 and 1985-1989. In men the total ASR was 62.9 per 100,000 in 1985-1989 that increased to 64.50 and 101.48 during 1998-2002 and 2007-2010. Although stomach cancer was the most common cancer among men during 1985-1989 and 1998-2002, but in recent study bladder cancer was the most common cancer among men in Fars province. The incidence of colorectal cancer in men during 2007-2010 was about three times higher than 1998-2002 and 1985-1989. This study shows growing incidence of cancer in southern Iran. The colorectal cancer in both genders had increased and its pattern is similar to western countries. In men, bladder and prostate cancers had a growing rate and the incidences of these cancers in the present study were greater than stomach cancer.

  18. Changing Pattern of Hepatitis A Virus Epidemiology in an Area of High Endemicity

    Directory of Open Access Journals (Sweden)

    Marcello Campagna

    2012-06-01

    Full Text Available Background: Continuous assessment of hepatitis A virus (HAV seroepidemiology is a useful tool to control the risk of infection.Objectives:This study aimed to evaluate the changing patterns of anti-HAV seroprevalence in a population,which isgenerally considered to be anarea ofhigh endemicity.Patients and Methods: Overall, the results of 3349 sera collected during the period 2005-2008 from patients attending the University Hospital of Cagliari, Italy were studied; their mean age was 52.7 years, (s + 16.22. Patients with liver disease were excluded from the study. Age specific seroprevalence results were compared with those observed in similar previous studies carried out in the same area.Results: The overall prevalence of anti-HAV was 74.6% with consistently lower values in subjects younger than 40 years (17.5%; P < 0.0001 particularly in those under 30 years of age (8.9%, CI 5.8-11.9. A significant declining trend in age specific seroprevalence has been foundin people under 30 years;61% in 1988, 33% in 1995 and 8.9% in 2005-2008.Conclusions: Our findings show that a significant decline inherd immunity has occurred in the last 20 years as a consequence of lower HAV circulation due to improvementsin socio-economical and hygienic conditions. Adolescents and young adults are becoming increasingly susceptible to HAV infections, as recent outbreaks of acute HAV hepatitis have occurred. Persistent environmental monitoring and the implementation of prevention measures must be considered in order to contain the risk related to this epidemiological shift..

  19. Changes in seroprevalence of hepatitis B surface antigen and epidemiologic characteristics in the Republic of Korea, 1998-2013

    OpenAIRE

    Lee, Hyerin; Lee, Hyungmin; Cho, Yumi; Oh, Kyungwon; Ki, Moran

    2015-01-01

    OBJECTIVES: This study investigated changes in hepatitis B seroprevalence from 1998 to 2013, and to identify differences in epidemiologic characteristics between hepatitis B surface antigen (HBsAg)-positive and HBsAg-negative people. METHODS: HBsAg seropositive rates were compared by year, sex, and age using the blood test data from the periods I to VI (1998-2013) of the Korea National Health and Nutrition Examination Survey. Interviews and self-administered surveys were conducted to collect ...

  20. [Molecular epidemiology and antifungal susceptibility of Candida species isolated from urine samples of patients in intensive care unit].

    Science.gov (United States)

    Yüksekkaya, Serife; Fındık, Duygu; Arslan, Uğur

    2011-01-01

    The aims of this study were to analyse the amphotericin B and fluconazole susceptibility and molecular epidemiology of Candida strains (Candida albicans, Candida tropicalis and Candida glabrata) isolated from the urine samples of patients hospitalized in the intensive care unit. Identification of the isolates was done according to microscopic morphology (chlamydospor, blastospor, pseudohyphae and true hyphae) on cornmeal agar, germ tube formation and carbohydrate assimilation patterns (API ID 32C bioMérieux, France). Antifungal susceptibilities of the isolates were determined by in vitro broth microdilution method recommended by Clinical and Laboratory Standards Institute (CLSI). To investigate the clonal relationship of the isolates, randomly amplified polymorphic DNA (RAPD) analysis was performed by using Cnd3 primer. Of the 56 Candida isolates minimum inhibitory concentration (MIC) ranges, MIC50 and MIC90 values for amphotericin B were 0.125-1 µg/ml, 0.125 and 0.5 µg/ml for C.albicans, 0.125-1 µg/ml, 0.25 and 1 µg/ml for C.tropicalis and 0.125-1 µg/ml, 0.25 and 1 µg/ml for C.glabrata, respectively. Fluconazole MIC ranges, MIC50 and MIC90 values were 0.25-4 µg/ml, 0.25 and 0.5 µg/ml for C.albicans, 0.25-16 µg/ml, 0.5 and 1 µg/ml for C.tropicalis and 0.5-64 µg/ml, 8 and 16 µg/ml for C.glabrata, respectively. For amphotericin B, none of the isolates had high MIC values (MIC > 1 µg/ml). While one of the C.glabrata isolates was resistant to fluconazole (MIC ≥ 64 µg/ml), one C.tropicalis and two C.glabrata isolates were dose-dependent susceptible (MIC: 16-32 µg/ml). The results of RAPD analysis indicated an exogenous spread from two clones for C.albicans, one clone for C.glabrata and one clone for C.tropicalis. This study underlines the importance of molecular epidemiological analysis of clinical samples together with hospital environmental samples in terms of Candida spp. To determine the exogenous origin for the related strains and to prevent

  1. Analysis on drug-resistance and molecular epidemiology of Acinetobacter baumannii isolated from the clinical samples in two Chinese hospitals

    Institute of Scientific and Technical Information of China (English)

    WEI FENG SHI; ZHI MI HUANG; NING XU

    2006-01-01

    In the present study, the drug-resistance genes encoding β-lactamases, aminoglycoside modifying enzymes, DNA topoisomerases and integron as well as their molecular epidemiology were investigated by means of analyzing the drug-resistance and molecular epidemiology of Acinebacter baumannii isolated from the clinical samples in two hospitals in Changzhou and Huzhou city of Jiangsu and Zhejiang province from July 2000 to March 2005. The minimal inhibitory concentrations (MICs) of these 307 isolates were detected by automatic microbiological system, and 35 strains against 5-fluoroquinolones were performed by agar dilution assay. Meanwhile, the resistant genes in 80 isolates were amplified by PCR with identification by DNA sequencer. It was found that most of the 307 isolates of A. baumannii were resistant to multiple antibiotics tested, in which the resistance rates of the isolates against piperacillin, piperacillin/tazobactam, amoxacillin/clavulanic acid, cefotaxime, ceftazidime,cefepime, gentamicin, amikacin, ciprofloxacin, chloramphenicol and sulfamethoxazole/trimethoprim were all above 35%, but those of imipenem and meropenem were quite low, ranged only 2.6% and 3.3 %. In addition, it was also demonstrated that the positive rates of TEM and SHV β-lactamase genes accounted for 93.8% and 22.5% respectively, and those of the aminoglycoside-modifying enzyme genes including aacC1, aacC2, aacC3, aacC4, aacC4A, aphA6, ant(2")-Ⅰ and ant(3")-Ⅰ were 58.8%, 8.8%, 7.5%, 28.8%, 45.0%, 2.5%, 28.8% and 65.0% respectively. The mutations in the quinolone-resistant determining region (QRDR) of gyrA and parC genes indicated that substitution in Ser-83 residue of GyrA protein was most frequently occurred among strains with MIC for ciprofloxacin of more than 4 μg/ml, whereas a double mutation at Ser-83 residue of gyrA and Ser-80 of parC was found in strains with MIC of ciprofloxacin of more than 8 μg/ml. As to the positive rates of class 1 integron (Int Ⅰ -1) and qacE△1-sul

  2. Methicillin-resistant Staphylococcus aureus in Spain: molecular epidemiology and utility of different typing methods.

    Science.gov (United States)

    Vindel, Ana; Cuevas, Oscar; Cercenado, Emilia; Marcos, Carmen; Bautista, Verónica; Castellares, Carol; Trincado, Pilar; Boquete, Teresa; Pérez-Vázquez, Maria; Marín, Mercedes; Bouza, Emilio

    2009-06-01

    use of spa typing and PFGE typing for epidemiological surveillance, since this combination is useful for both long-term and short-term studies. PMID:19339473

  3. Molecular and epidemiologic findings of childhood acute leukemia in Costa Rica.

    Science.gov (United States)

    Santamaría-Quesada, Carlos; Vargas, Mario; Venegas, Patricia; Calvo, Melvin; Obando, Catalina; Valverde, Berta; Cartín, Walter; Carrillo, Juan Manuel; Jimenez, Rafael; González, Marcos

    2009-02-01

    In Central America, nearly 70% of pediatric cancer is related to hemato-oncologic disorders, especially acute lymphoblastic leukemia (ALL). Preliminary studies have described a high incidence of childhood leukemia in these countries; however, no molecular analyses of these malignancies have yet been carried out. We studied diagnostic samples from 84 patients from the National Children's Hospital in San Jose, Costa Rica (65 precursor B-ALL, 5 T-cell ALL, and 14 acute myeloblastic leukemia). Our methodology included cytogenetic, fluorescent in situ hybridization, and polymerase chain reaction approaches. The observed rate of leukemia was 52.2 cases per million children per year. Twelve out of 65 (18.4%) precursor B-ALL tested positive for TEL-AML1 and 3 cases for BCR-ABL (4.6%). In addition, we detected 2 patients carrying an E2A-PBX1 transcript (3.1%) and 1 patient with an MLL-AF4 fusion gene (1.5%). None of the T-cell ALL cases were positive for either SIL-TAL1 or HOX11L2. Within 14 acute myeloblastic leukemia patients, we confirmed 2 cases with FLT3-internal tandem duplication+, 1 patient with AML1-ETO, and only 1 case carrying a PML-RARalpha rearrangement. The present study confirms the relatively high incidence of pediatric leukemia in Costa Rica and constitutes the first report regarding the incidence of the main molecular alterations of childhood leukemia in our region.

  4. Prevalence and molecular epidemiology of Cryptosporidium parvum in dairy calves in Punjab (India).

    Science.gov (United States)

    Joute, J R; Gill, J P S; Singh, B B

    2016-09-01

    Cryptosporidium parvum is an important zoonotic protozoan parasite that infects the gastrointestinal tract of vertebrate animals and man. The current study was contemplated for molecular detection of Cryptosporidium species prevalent in dairy calves in Punjab, India. A total of 302 faecal samples were screened by modified Ziehl-Neelsen staining technique for the detection of Cryptosporidium oocysts. Molecular characterisation was done using PCR followed by sequence analysis of the representative isolates. An overall prevalence of 26.15 % was obtained with the highest prevalence obtained in 0-30 day old calves in both diarrhoeic and non-diarrhoeic animals. PCR analysis revealed the expected bands at 1,325 and 835 bp from all the isolates for primary and secondary/nested PCR respectively. Ten representative samples were sequenced in both directions. Phylogenetic analysis revealed the presence of C. parvum in all the samples. The high rate of calves infected with C. parvum can act as a great source of zoonotic cryptosporidiosis which indicates a potential risk of zoonotic transmission from animal to human beings in Punjab (India). PMID:27605777

  5. A Molecular Epidemiology Analysis of HIV in Shenzhen and HIV Env Gene Variation Replication Analysis

    Institute of Scientific and Technical Information of China (English)

    CHEN Lin(陈琳); FENG Tiejian(冯铁建); LI Liangcheng(李良成); HE Jianfan(何建凡)

    2002-01-01

    Objective: To analyze molecular trends of the HIV epidemic in Shenzhen.Methods: Serum collected from Shenzhen AIDS patientsbetween 1992-1999 was analyzed using molecular techniques.DNA fragments of the HIV-1 Env gene were amplified bynested PCR from uncultured peripheral blood mononuclearcells (PBMCs) from these serum samples. The C2-C3 region ofthe Env gene was sequenced and analyzed. Specific high-riskbehaviors were also analyzed.Results: We found that the transmission of HIV in the citywas mainly through sexual behaviors (46.0%). There werefour HIV-1 subtypes: B', B, C and E with 6.31%, 7.95%,3.09% and 8.92% gene divergence inside each subtype inShenzhen. These results suggested that epidemic times were 6,8, 3 and 9 respectively. The main epidemic subtypes were Eand B strains. AIDS patient's antigenic variation was slightlyhigher than that of HIV infected individuals.Conclusion: Surveillance data reflect trends and theepidemic time of HIV, which will be useful for policy makersto formulate effective strategies of HIV/AIDS prevention andcontrol in Shenzhen.

  6. MOLECULAR ION DETECTION BY A LASER INDUCED CHANGE IN MOBILITY

    OpenAIRE

    Walkup, R.; Dreyfus, R.; Avouris, Ph.

    1983-01-01

    We report the optogalvanic detection of molecular ions (N+2, CO+) via a laser induced change in ion mobility. The technique relies on a difference in collision limited transport of excited vs. ground state ions, and provides a uniquely sensitive probe of ions in the cathode sheath region of glow discharges.

  7. Prevalence and molecular epidemiology of porcine cysticercosis in naturally infected pigs (Sus scrofa) in Punjab, India.

    Science.gov (United States)

    Chawhan, P; Singh, B; Sharma, R; Gill, P S

    2015-12-01

    Porcine cysticercosis is a serious zoonosis in resource-poor countries. Despite the evidence showing that the disease is endemic in the Punjab region of India, molecular characterisation of Taenia solium cysticercosis from naturally infected pigs has not been carried out. The authors examined a total of 519 pigs slaughtered in small slaughter shops (shops that sell meat from animals that are slaughtered on the premises as the customer waits) in the urban slums of Punjab state in northern India. The expected polymerase chain reaction products with molecular sizes of 286 bp, 420 bp, 1150 bp and 333 bp corresponding to the targeted large subunit ribosomal RNA (rRNA), cytochrome oxidase 1, internal transcribed spacer 1, and diagnostic antigen Ts14 genes, respectively, were amplified from the cysts collected from all 22 infected carcasses. The detection limits for the respective primers (except those targeting the Ts14 gene) were estimated. The analytical sensitivities of both the TBR and JB primers (targeting the rRNA and cytochrome oxidase genes, respectively) were found to be higher (10 pg) than that of the internal transcribed spacer 1 gene (1 ng) primers. Ten representative samples from cytochrome oxidase 1 gene amplified products were sequenced in both directions for phylogenetic analysis. Sequencing demonstrated that all cysticerci were of the Asian genotype of T. solium and not of the African/Latin American genotype or T. asiatica. The results confirm the presence of T. solium porcine cysticercosis in Punjab state and there is therefore an urgent need for science-based policies for prevention and control of this serious zoonosis. PMID:27044164

  8. Molecular epidemiology and antimicrobial resistance of methicillin-resistant Staphylococcus aureus bloodstream isolates in Taiwan, 2010.

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    Chih-Jung Chen

    Full Text Available The information of molecular characteristics and antimicrobial susceptibility pattern of methicillin-resistant Staphylococcus aureus (MRSA is essential for control and treatment of diseases caused by this medically important pathogen. A total of 577 clinical MRSA bloodstream isolates from six major hospitals in Taiwan were determined for molecular types, carriage of Panton-Valentine leukocidin (PVL and sasX genes and susceptibilities to 9 non-beta-lactam antimicrobial agents. A total of 17 genotypes were identified in 577 strains by pulsotyping. Five major pulsotypes, which included type A (26.2%, belonging to sequence type (ST 239, carrying type III staphylococcal chromosomal cassette mec (SCCmec, type F (18.9%, ST5-SCCmecII, type C (18.5%, ST59-SCCmecIV, type B (12.0%, ST239-SCCmecIII and type D (10.9%, ST59-SCCmecVT/IV, prevailed in each of the six sampled hospitals. PVL and sasX genes were respectively carried by ST59-type D strains and ST239 strains with high frequencies (93.7% and 99.1%, respectively but rarely detected in strains of other genotypes. Isolates of different genotypes and from different hospitals exhibited distinct antibiograms. Multi-resistance to ≥3 non-beta-lactams was more common in ST239 isolates (100% than in ST5 isolates (97.2%, P = 0.0347 and ST59 isolates (8.2%, P<0.0001. Multivariate analysis further indicated that the genotype, but not the hospital, was an independent factor associated with muti-resistance of the MRSA strains. In conclusion, five common MRSA clones with distinct antibiograms prevailed in the major hospitals in Taiwan in 2010. The antimicrobial susceptibility pattern of invasive MRSA was mainly determined by the clonal distribution.

  9. Neuronal ceroid lipofuscinosis in Border Collie dogs in Japan: clinical and molecular epidemiological study (2000-2011).

    Science.gov (United States)

    Mizukami, Keijiro; Kawamichi, Takuji; Koie, Hiroshi; Tamura, Shinji; Matsunaga, Satoru; Imamoto, Shigeki; Saito, Miyoko; Hasegawa, Daisuke; Matsuki, Naoaki; Tamahara, Satoshi; Sato, Shigenobu; Yabuki, Akira; Chang, Hye-Sook; Yamato, Osamu

    2012-01-01

    Neuronal ceroid lipofuscinosis (NCL) is an inherited, neurodegenerative lysosomal disease that causes premature death. The present study describes the clinical and molecular epidemiologic findings of NCL in Border Collies in Japan for 12 years, between 2000 and 2011. The number of affected dogs was surveyed, and their clinical characteristics were analyzed. In 4 kennels with affected dogs, the dogs were genotyped. The genetic relationships of all affected dogs and carriers identified were analyzed. The survey revealed 27 affected dogs, but there was a decreasing trend at the end of the study period. The clinical characteristics of these affected dogs were updated in detail. The genotyping survey demonstrated a high mutant allele frequency in examined kennels (34.8%). The pedigree analysis demonstrated that all affected dogs and carriers in Japan are related to some presumptive carriers imported from Oceania and having a common ancestor. The current high prevalence in Japan might be due to an overuse of these carriers by breeders without any knowledge of the disease. For NCL control and prevention, it is necessary to examine all breeding dogs, especially in kennels with a high prevalence. Such endeavors will reduce NCL prevalence and may already be contributing to the recent decreasing trend in Japan. PMID:22919312

  10. Neuronal Ceroid Lipofuscinosis in Border Collie Dogs in Japan: Clinical and Molecular Epidemiological Study (2000–2011

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    Keijiro Mizukami

    2012-01-01

    Full Text Available Neuronal ceroid lipofuscinosis (NCL is an inherited, neurodegenerative lysosomal disease that causes premature death. The present study describes the clinical and molecular epidemiologic findings of NCL in Border Collies in Japan for 12 years, between 2000 and 2011. The number of affected dogs was surveyed, and their clinical characteristics were analyzed. In 4 kennels with affected dogs, the dogs were genotyped. The genetic relationships of all affected dogs and carriers identified were analyzed. The survey revealed 27 affected dogs, but there was a decreasing trend at the end of the study period. The clinical characteristics of these affected dogs were updated in detail. The genotyping survey demonstrated a high mutant allele frequency in examined kennels (34.8%. The pedigree analysis demonstrated that all affected dogs and carriers in Japan are related to some presumptive carriers imported from Oceania and having a common ancestor. The current high prevalence in Japan might be due to an overuse of these carriers by breeders without any knowledge of the disease. For NCL control and prevention, it is necessary to examine all breeding dogs, especially in kennels with a high prevalence. Such endeavors will reduce NCL prevalence and may already be contributing to the recent decreasing trend in Japan.

  11. Molecular Epidemiology of HIV Type 1 CRF02_AG in Cameroon and African Patients Living in Italy

    Science.gov (United States)

    Véras, Nazle Mendonca Collaço; Santoro, Maria Mercedes; Gray, Rebecca R.; Tatem, Andrew J.; Presti, Alessandra Lo; Olearo, Flaminia; Cappelli, Giulia; Colizzi, Vittorio; Takou, Desiré; Torimiro, Judith; Russo, Gianluca; Callegaro, Annapaola; Salpini, Romina; D'Arrigo, Roberta; Perno, Carlo-Federico; Goodenow, Maureen M.; Ciccozzi, Massimo

    2011-01-01

    Abstract HIV-1 CRF02_AG accounts for >50% of infected individuals in Cameroon. CRF02_AG prevalence has been increasing both in Africa and Europe, particularly in Italy because of migrations from the sub-Saharan region. This study investigated the molecular epidemiology of CRF02_AG in Cameroon by employing Bayesian phylodynamics and analyzed the relationship between HIV-1 CRF02_AG isolates circulating in Italy and those prevalent in Africa to understand the link between the two epidemics. Among 291 Cameroonian reverse transcriptase sequences analyzed, about 70% clustered within three distinct clades, two of which shared a most recent common ancestor, all related to sequences from Western Africa. The major Cameroonian clades emerged during the mid-1970s and slowly spread during the next 30 years. Little or no geographic structure was detected within these clades. One of the major driving forces of the epidemic was likely the high accessibility between locations in Southern Cameroon contributing to the mobility of the population. The remaining Cameroonian sequences and the new strains isolated from Italian patients were interspersed mainly within West and Central African sequences in the tree, indicating a continuous exchange of CRF02_AG viral strains between Cameroon and other African countries, as well as multiple independent introductions in the Italian population. The evaluation of the spread of CRF02_AG may provide significant insight about the future dynamics of the Italian and European epidemic. PMID:21453131

  12. Molecular Epidemiological Investigation of Porcine kobuvirus and Its Coinfection Rate with PEDV and SaV in Northwest China.

    Science.gov (United States)

    Wang, Chen; Lan, Xi; Yang, Bin

    2016-01-01

    Porcine kobuvirus (PKV) has circulated throughout China in recent years. Although many studies have detected it throughout the world, its molecular epidemiology has not been characterized in northwest China. To understand its prevalence, 203 fecal samples were collected from different regions of Gansu Province and tested with reverse transcription-polymerase chain reaction. In this study, we tested these samples for PKV, porcine epidemic diarrhea virus (PEDV), and sapovirus and analyzed the amplified 2C gene fragments of PKV. Overall, 126 (62.1%) samples were positive for PKV. Of the 74 piglets samples among the 203 fecal samples, 65 (87.8%) were positive for PKV. PKV infection was often accompanied by PEDV, but the relationship between the two viruses must be confirmed. A phylogenetic analysis indicated that the PKV strains isolated from the same regions clustered on the same branches. This investigation shows that PKV infections are highly prevalent in pigs in northwest China, especially in piglets with symptoms of diarrhea. PMID:27294133

  13. Molecular Epidemiological Investigation of Porcine kobuvirus and Its Coinfection Rate with PEDV and SaV in Northwest China

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    Chen Wang

    2016-01-01

    Full Text Available Porcine kobuvirus (PKV has circulated throughout China in recent years. Although many studies have detected it throughout the world, its molecular epidemiology has not been characterized in northwest China. To understand its prevalence, 203 fecal samples were collected from different regions of Gansu Province and tested with reverse transcription-polymerase chain reaction. In this study, we tested these samples for PKV, porcine epidemic diarrhea virus (PEDV, and sapovirus and analyzed the amplified 2C gene fragments of PKV. Overall, 126 (62.1% samples were positive for PKV. Of the 74 piglets samples among the 203 fecal samples, 65 (87.8% were positive for PKV. PKV infection was often accompanied by PEDV, but the relationship between the two viruses must be confirmed. A phylogenetic analysis indicated that the PKV strains isolated from the same regions clustered on the same branches. This investigation shows that PKV infections are highly prevalent in pigs in northwest China, especially in piglets with symptoms of diarrhea.

  14. Molecular epidemiology of canine picornavirus in Hong Kong and Dubai and proposal of a novel genus in Picornaviridae.

    Science.gov (United States)

    Woo, Patrick C Y; Lau, Susanna K P; Choi, Garnet K Y; Huang, Yi; Sivakumar, Saritha; Tsoi, Hoi-Wah; Yip, Cyril C Y; Jose, Shanty V; Bai, Ru; Wong, Emily Y M; Joseph, Marina; Li, Tong; Wernery, Ulrich; Yuen, Kwok-Yung

    2016-07-01

    Previously, we reported the discovery of a novel canine picornavirus (CanPV) in the fecal sample of a dog. In this molecular epidemiology study, CanPV was detected in 15 (1.11%) of 1347 canine fecal samples from Hong Kong and one (0.76%) of 131 canine fecal samples from Dubai, with viral loads 1.06×10(3) to 6.64×10(6) copies/ml. Complete genome sequencing and phylogenetic analysis showed that CanPV was clustered with feline picornavirus (FePV), bat picornavirus (BatPV) 1 to 3, Ia io picornavirus 1 (IaioPV1) and bovine picornavirus (BoPV), and this cluster was most closely related to the genera Enterovirus and Sapelovirus. The Ka/Ks ratios of all the coding regions were <0.1. According to the definition of the Picornavirus Study Group of ICTV, CanPV, FePV, BatPV 1 to 3, IaioPV1 and BoPV should constitute a novel genus in Picornaviridae. BEAST analysis showed that this genus diverged from its most closely related genus, Sapelovirus, about 49 years ago.

  15. Molecular Epidemiology and Sequencing of the G-L Intergenic Region of Rabies Viruses Isolated in China

    Institute of Scientific and Technical Information of China (English)

    Sheng-Li MENG; QI-You XIAO; Guan-Mu DONG; Ge-Lin XU; Jia-Xin YAN; Ping-Gang MING; Jie WU; Xiao-Ming YANG; He-Tian MING; Feng-Cai ZHU; Dun-Jin ZHOU

    2007-01-01

    A group of 25 rabies viruses (RABVs),recovered from 24 dogs and one human case,were collected from various areas in China between 2004 and 2006.Genetic and phylogenetic analyses of the G-L intergenic region were carried out in 25 street RABV isolates and CTN vaccine strains of 7 generations.The study was based on the comparison of a 519 bp nucleotide sequence,encompassing the G-L intergenic region.The nucleotide sequence homologies of Chinese street strains were from 95.5% to 100%.The phylogenetic analysis showed that all Chinese isolates clearly supported the placement of all Chinese viruses in Lyssavirus genotype 1 and they were distributed according to their geographical origins.All of the Chinese strains were closely related but they could still be divided into two groups:group of street strains and group of CTN strains.This study presents details about the molecular epidemiology of rabies viruses based on the sequences of the G-L Intergenic region.

  16. Evolution and molecular epidemiology of classical swine fever virus during a multi-annual outbreak amongst European wild boar.

    Science.gov (United States)

    Goller, Katja V; Gabriel, Claudia; Dimna, Mireille Le; Le Potier, Marie-Frédérique; Rossi, Sophie; Staubach, Christoph; Merboth, Matthias; Beer, Martin; Blome, Sandra

    2016-03-01

    Classical swine fever is a viral disease of pigs that carries tremendous socio-economic impact. In outbreak situations, genetic typing is carried out for the purpose of molecular epidemiology in both domestic pigs and wild boar. These analyses are usually based on harmonized partial sequences. However, for high-resolution analyses towards the understanding of genetic variability and virus evolution, full-genome sequences are more appropriate. In this study, a unique set of representative virus strains was investigated that was collected during an outbreak in French free-ranging wild boar in the Vosges-du-Nord mountains between 2003 and 2007. Comparative sequence and evolutionary analyses of the nearly full-length sequences showed only slow evolution of classical swine fever virus strains over the years and no impact of vaccination on mutation rates. However, substitution rates varied amongst protein genes; furthermore, a spatial and temporal pattern could be observed whereby two separate clusters were formed that coincided with physical barriers. PMID:26684209

  17. Recent advances and prospective researches on molecular epidemiology of dengue viruses

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    Vincent Deubel

    1992-01-01

    Full Text Available The determination of amino acid changes in the envelop protein by direct sequencing of either genomic RNA or PCR-amplified cDNA fragments provides useful informations for assessing the genetic variability and the geographic distribution of the actually most widespread dengue-2 serotype. The possible link of variations in the envelope protein-gene and virus virulence is discussed.

  18. Targeted exon sequencing successfully discovers rare causative genes and clarifies the molecular epidemiology of Japanese deafness patients.

    Science.gov (United States)

    Miyagawa, Maiko; Naito, Takehiko; Nishio, Shin-ya; Kamatani, Naoyuki; Usami, Shin-ichi

    2013-01-01

    Target exon resequencing using Massively Parallel DNA Sequencing (MPS) is a new powerful strategy to discover causative genes in rare Mendelian disorders such as deafness. We attempted to identify genomic variations responsible for deafness by massive sequencing of the exons of 112 target candidate genes. By the analysis of 216randomly selected Japanese deafness patients (120 early-onset and 96 late-detected), who had already been evaluated for common genes/mutations by Invader assay and of which 48 had already been diagnosed, we efficiently identified causative mutations and/or mutation candidates in 57 genes. Approximately 86.6% (187/216) of the patients had at least one mutation. Of the 187 patients, in 69 the etiology of the hearing loss was completely explained. To determine which genes have the greatest impact on deafness etiology, the number of mutations was counted, showing that those in GJB2 were exceptionally higher, followed by mutations in SLC26A4, USH2A, GPR98, MYO15A, COL4A5 and CDH23. The present data suggested that targeted exon sequencing of selected genes using the MPS technology followed by the appropriate filtering algorithm will be able to identify rare responsible genes including new candidate genes for individual patients with deafness, and improve molecular diagnosis. In addition, using a large number of patients, the present study clarified the molecular epidemiology of deafness in Japanese. GJB2 is the most prevalent causative gene, and the major (commonly found) gene mutations cause 30-40% of deafness while the remainder of hearing loss is the result of various rare genes/mutations that have been difficult to diagnose by the conventional one-by-one approach. In conclusion, target exon resequencing using MPS technology is a suitable method to discover common and rare causative genes for a highly heterogeneous monogenic disease like hearing loss.

  19. Molecular epidemiology of enterovirus B77 isolated from non polio acute flaccid paralytic patients in Pakistan during 2013.

    Science.gov (United States)

    Angez, Mehar; Shaukat, Shahzad; Zahra, Rabaab; Khurshid, Adnan; Sharif, Salmaan; Alam, Muhammad Masroor; Zaidi, Syed Sohail Zahoor

    2015-01-01

    Human enteroviruses are associated with various clinical syndromes and severe neurological disorders. The aim of this study was to determine the molecular epidemiology of non polio enteroviruses and their correlation with acute flaccid paralysis (AFP) patients living in Khyber Pakhtunkhwa (KP) and Federally Administered Tribal Areas (FATA) of Pakistan. The stool samples collected from these patients were used for isolation of non polio enteroviruses (NPEVs). Out of 38 samples, 29 (76.3%) were successfully typed by microneutralization assay into eleven serotypes including echovirus (E)-3 (5.3%), E-7 (2.6%), E-11 (13.2%), E-12 (7.9%), E-13 (10.5%), E-20 (7.9%), E-27 (5.3%), E-29 (10.5%), E-30 (7.9%), E-33 (2.6%), coxsackievirus (CV) B5 (2.6%) and nine isolates (23.7%) remained untyped which were confirmed as NPEVs by real time RT-PCR. Complete VP1 genetic sequencing data characterized untypeable isolates into enterovirus B77 (EV-B77). Moreover, molecular phylogenetic analysis classified these viruses into two new genotypes having high genetic diversity (at least 17.7%) with prototype. This study provides valuable information on extensive genetic diversity of EV-B77 genotypes. Although, its association with neurological disorder has not yet been known but isolation of nine EV-B77 viruses from AFP cases highlights the fact that they may have a contributing role in the etiology of AFP. In addition, it is needed to establish enterovirus surveillance system and laboratory diagnostic facilities for early detection of NPEVs that may cause poliomyelitis like paralysis especially in the situation when we are at the verge of polio eradication. PMID:25433133

  20. Epidemiology and molecular characterisation of metallo-β-lactamase-producing Enterobacteriaceae in a university hospital Intensive Care Unit in Greece.

    Science.gov (United States)

    Koratzanis, Evangelos; Souli, Maria; Galani, Irene; Chryssouli, Zoi; Armaganidis, Apostolos; Giamarellou, Helen

    2011-11-01

    The molecular epidemiology of VIM-producing Enterobacteriaceae isolated at the beginning of an epidemic in the Intensive Care Unit (ICU) of a university hospital in Athens, Greece, was studied. All Gram-negative organisms isolated from March 2004 to November 2005 positive for metallo-β-lactamase (MBL) production were submitted to polymerase chain reaction (PCR) and sequencing, to repetitive sequence-based PCR (Rep-PCR) for molecular typing, and to S1 nuclease digestion for plasmid DNA characterisation. Conjugation experiments and isoelectric focusing were performed to identify co-existing β-lactamases. Amongst 23 patients, 12 suffered one or more clinical infections. Eighty-two isolates representing one isolate per clone, source and ICU patient were studied, including Klebsiella pneumoniae (77), Enterobacter cloacae (2), Citrobacter freundii (1) and Pseudomonas aeruginosa (2). High clonal diversity was detected amongst the K. pneumoniae, with 10 distinct clones identified. Conjugation was successful in 54.5% of K. pneumoniae, and five different-sized plasmids were detected. All K. pneumoniae and both E. cloacae isolates shared the same bla(VIM-1)-containing class 1 integron structure also carrying aacA7, dhfrI and aadA1 gene cassettes. The C. freundii isolate carried a different integron that included bla(VIM-1) and aac(6')-IIc. Both P. aeruginosa isolates were positive for bla(VIM-2). It was not possible to identify specific clones with the potential to cause clinical infections. In conclusion, a multiclonal cluster of MBL-producers was responsible for the first cases of colonisation and/or infection in the ICU. A single integron structure, common in Greek hospitals, efficiently disseminated between clones and species, suggesting that the epidemic was mainly the result of successful horizontal transfer of mobile genetic material rather than the result of horizontal transfer of one or a few clones. PMID:21873034

  1. Molecular epidemiology of a hepatitis C virus epidemic in a haemodialysis unit: outbreak investigation and infection outcome

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    Lanini Simone

    2010-08-01

    Full Text Available Abstract Background HCV is a leading cause of liver chronic diseases all over the world. In developed countries the highest prevalence of infection is reported among intravenous drug users and haemodialysis (HD patients. The present report is to identify the pathway of HCV transmission during an outbreak of HCV infection in a privately run haemodialysis (HD unit in Italy in 2005. Methods Dynamics of the outbreak and infection clinical outcomes were defined through an ambi-directional cohort study. Molecular epidemiology techniques were used to define the relationships between the viral variants infecting the patients and confirm the outbreak. Risk analysis and auditing procedures were carried out to define the transmission pathway(s. Results Of the 50 patients treated in the HD unit 5 were already anti-HCV positive and 13 became positive during the study period (AR = 28.9%. Phylogenic analysis identified that, all the molecularly characterized incident cases (10 out of 13, were infected with the same viral variant of one of the prevalent cases. The multivariate analysis and the auditing procedure disclosed a single event of multi-dose vials heparin contamination as the cause of transmission of the infection in 11 out of the 13 incident cases; 2 additional incident cases occurred possibly as a result of inappropriate risk management. Discussion More than 30% of all HCV infections in developed countries results from poor application of standard precautions during percutaneous procedures. Comprehensive strategy which included: educational programmes, periodical auditing on standard precaution, use of single-dose vials whenever possible, prospective surveillance for blood-borne infections (including a system of prompt notification and risk assessment/management dedicated staff are the cornerstone to contain and prevent outbreaks in HD Conclusions The outbreak described should serve as a reminder to HD providers that patients undergoing dialysis are

  2. Molecular epidemiology of Vibrio cholerae associated with flood in Brahamputra River valley, Assam, India.

    Science.gov (United States)

    Bhuyan, Soubhagya K; Vairale, Mohan G; Arya, Neha; Yadav, Priti; Veer, Vijay; Singh, Lokendra; Yadava, Pramod K; Kumar, Pramod

    2016-06-01

    Cholera is often caused when drinking water is contaminated through environmental sources. In recent years, the drastic cholera epidemics in Odisha (2007) and Haiti (2010) were associated with natural disasters (flood and Earthquake). Almost every year the state of Assam India witnesses flood in Brahamputra River valley during reversal of wind system (monsoon). This is often followed by outbreak of diarrheal diseases including cholera. Beside the incidence of cholera outbreaks, there is lack of experimental evidence for prevalence of the bacterium in aquatic environment and its association with cholera during/after flood in the state. A molecular surveillance during 2012-14 was carried out to study prevalence, strain differentiation, and clonality of Vibrio cholerae in inland aquatic reservoirs flooded by Brahamputra River in Assam. Water samples were collected, filtered, enriched in alkaline peptone water followed by selective culturing on thiosulfate bile salt sucrose agar. Environmental isolates were identified as V. cholerae, based on biochemical assays followed by sero-grouping and detailed molecular characterization. The incidence of the presence of the bacterium in potable water sources was higher after flood. Except one O1 isolate, all of the strains were broadly grouped under non-O1/non-O139 whereas some of them did have cholera toxin (CT). Surprisingly, we have noticed Haitian ctxB in two non-O1/non-O139 strains. MLST analyses based on pyrH, recA and rpoA genes revealed clonality in the environmental strains. The isolates showed varying degree of antimicrobial resistance including tetracycline and ciprofloxacin. The strains harbored the genetic elements SXT constins and integrons responsible for multidrug resistance. Genetic characterization is useful as phenotypic characters alone have proven to be unsatisfactory for strain discrimination. An assurance to safe drinking water, sanitation and monitoring of the aquatic reservoirs is of utmost importance for

  3. Molecular epidemiology of Vibrio cholerae associated with flood in Brahamputra River valley, Assam, India.

    Science.gov (United States)

    Bhuyan, Soubhagya K; Vairale, Mohan G; Arya, Neha; Yadav, Priti; Veer, Vijay; Singh, Lokendra; Yadava, Pramod K; Kumar, Pramod

    2016-06-01

    Cholera is often caused when drinking water is contaminated through environmental sources. In recent years, the drastic cholera epidemics in Odisha (2007) and Haiti (2010) were associated with natural disasters (flood and Earthquake). Almost every year the state of Assam India witnesses flood in Brahamputra River valley during reversal of wind system (monsoon). This is often followed by outbreak of diarrheal diseases including cholera. Beside the incidence of cholera outbreaks, there is lack of experimental evidence for prevalence of the bacterium in aquatic environment and its association with cholera during/after flood in the state. A molecular surveillance during 2012-14 was carried out to study prevalence, strain differentiation, and clonality of Vibrio cholerae in inland aquatic reservoirs flooded by Brahamputra River in Assam. Water samples were collected, filtered, enriched in alkaline peptone water followed by selective culturing on thiosulfate bile salt sucrose agar. Environmental isolates were identified as V. cholerae, based on biochemical assays followed by sero-grouping and detailed molecular characterization. The incidence of the presence of the bacterium in potable water sources was higher after flood. Except one O1 isolate, all of the strains were broadly grouped under non-O1/non-O139 whereas some of them did have cholera toxin (CT). Surprisingly, we have noticed Haitian ctxB in two non-O1/non-O139 strains. MLST analyses based on pyrH, recA and rpoA genes revealed clonality in the environmental strains. The isolates showed varying degree of antimicrobial resistance including tetracycline and ciprofloxacin. The strains harbored the genetic elements SXT constins and integrons responsible for multidrug resistance. Genetic characterization is useful as phenotypic characters alone have proven to be unsatisfactory for strain discrimination. An assurance to safe drinking water, sanitation and monitoring of the aquatic reservoirs is of utmost importance for

  4. Immunohistochemistry and molecular epidemiology of avian paramyxovirus 1 from formalin-fixed and paraffin-embedded sections of Japanese doves (Columba livia) affected with neurological signs.

    Science.gov (United States)

    Nakamura, Kikuyasu; Fujimori, Hideo; Koyama, Akiko; Dai, Trinh Quang; Imai, Kunitoshi; Ikezawa, Mitsutaka; Yamamoto, Yu

    2015-07-01

    Four doves (Nos. 1-4 birds) affected with neurological signs (ataxia, circling and torticollis) were investigated pathologically and microbiologically. Viral isolation was tried from the tracheal and cloacal swabs of all 4 birds and from liver, spleen, kidney, heart, lung and brain of Nos. 1 and 2 birds. No viruses were isolated from 4 birds, but they had high serum antibody titers against avian paramyxovirus 1 (APMV-1). Histologically, they had the characteristic histological changes of pigeon APMV-1 infection; nonpurulent encephalitis and interstitial nephritis. Immununohistochemically, APMV-1 antigens were detected in the necrotic renal tubular epithelial cells of 1 bird of them (No. 3 bird). Detection of APMV-1 ribonucleic acid (RNA) from formalin-fixed and paraffin-embedded (FFPE) sections was attempted by reverse transcription-polymerase chain reaction (RT-PCR). Sequencing the RT-PCR product showed the virus RNA belonged to the same APMV-1 genotype (VI) as the strains isolated from the world previous cases of pigeon APMV-1 infection. The RT-PCR of FFPE sections and sequencing of RT-PCR products are useful for molecular epidemiology of the virus when viral isolation from fresh samples is unsuccessful.

  5. Molecular epidemiology of a Pseudomonas aeruginosa hospital outbreak driven by a contaminated disinfectant-soap dispenser.

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    Simone Lanini

    Full Text Available BACKGROUND AND OBJECTIVE: Pseudomonas aeruginosa infection represents a main cause of morbidity and mortality among immunocompromised patients. This study describes a fatal epidemic of P. aeruginosa that occurred in a hematology unit in Italy. METHODS: Retrospective cohort study, prospective surveillance, auditing, extensive testing on healthcare workers and environmental investigation were performed to define the dynamics and potential causes of transmission. RAPD, macrorestriction analyses and sequence typing were used to define relationships between P. aeruginosa isolates. RESULTS: Eighteen cases of infection were identified in the different phases of the investigation. Of these, five constitute a significant molecular cluster of infection. A P. aeruginosa strain with the same genetic fingerprint and sequence type (ST175 as clinical isolates strain was also isolated from a heavily contaminated triclosan soap dispenser. DISCUSSION AND CONCLUSIONS: Our results are consistent with the hypothesis that patients became indirectly infected, e.g., during central venous catheter handling through contaminated items, and that the triclosan soap dispenser acted as a common continuous source of P. aeruginosa infection. Since P. aeruginosa is intrinsically unsusceptible to triclosan, the use of triclosan-based disinfectant formulations should be avoided in those healthcare settings hosting patients at high risk of P. aeruginosa infection.

  6. Enterocytozoon bieneusi in human and animals, focus on laboratory identification and molecular epidemiology

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    Thellier M.

    2008-09-01

    Full Text Available Human microsporidian infections have emerged following the onset of the AIDS pandemic. Microsporidia are unicellular eukaryotic parasites that form spores. They are an exceptionally diverse group of parasites that infect a wide range of eukaryotic cells in numerous invertebrate and vertebrate hosts. Of the 14 species newly described as pathogens in human, Enterocytozoon bieneusi, which causes gastrointestinal diseases, is the most common agent of human infections. In the past fifteen years, E. bieneusi was also identified in environmental sources, especially in surface water, as well as in wild, domestic and farm animals. These findings raised concerns for waterborne, foodborne and zoonotic transmission. Molecular analyses of the 243-bp internal Transcribed spacer-(ITS of the rRNA gene have revealed a considerable genetic variation within E. bieneusi isolates of human and animal origins, supporting the potential for zoonotic transmission. The focus of this revue is to present and discuss recent advances in diagnosis and zoonotic potential of E. bieneusi infections.

  7. Molecular epidemiology of serotype 19A Streptococcus pneumoniae isolated from children in Beijing, 1997-2006

    Institute of Scientific and Technical Information of China (English)

    XUE Lian; YAO Kai-hu; YU Sang-jie; LIU Zun-jie; QIAN Jing; SHEN Xu-zhuang; YANG Yong-hong

    2011-01-01

    Background Despite the prevalence of Streptococcus pneumoniae serotype 19A, the molecular characteristics of this serotype are yet to be fully elucidated. The aim of this study was therefore to determine the homology of the serotype 19A in China.Methods Pulsed-field gel electrophoresis and multilocus sequence typing were done to these forty-nine serotype 19A isolates to investigate the relationship between the strains prevalent in Beijing and other regions. Results From 1997 to 2006, the percentage of serotype 19A isolates increased. The susceptibility rate to penicillin and amoxicillin decreased and the resistance rate to cefuroxime increased. ST320 was the most prevalent ST, followed by ST3546. There were six new STs identified in our study. The serotype 19A strains were classified into six different pulsed-field gel electrophoresis (PFGE) patterns. ST320, which was associated with two different PFGE patterns (A and D), accounted for 32 isolates, and ST3546, which was associated with two PFGE patterns (B and E), accounted for eightConclusions From 2003 onwards, ST320 was the most common ST and the rate of resistance to cefuroxime increased significantly. Further long-term surveys of Streptococcus pneumoniae serotype 19A are required to monitor ST prevalence and antimicrobial resistance in this important human pathogen.

  8. Molecular epidemiology of Malassezia globosa and Malassezia restricta in Sudanese patients with pityriasis versicolor.

    Science.gov (United States)

    Saad, M; Sugita, T; Saeed, H; Ahmed, A

    2013-02-01

    Pityriasis versicolor is a superficial infection of the stratum corneum caused by Malassezia yeasts. The cutaneous Malassezia globosa and Malassezia restricta in Sudanese patients with pityriasis versicolor were elucidated using a molecular-based, culture-independent method and compared with that in healthy individuals. Scale samples were collected by applying an Opsite™ transparent dressing to lesional and non-lesional sites on 29 Sudanese patients with pityriasis versicolor and 54 healthy individuals. Malassezia DNA was extracted directly from the samples. The overall level of colonization by Malassezia globosa and Malassezia restricta was analyzed by real-time PCR using a TaqMan probe. The overall level of colonization by Malassezia at the lesional sites was higher than that at the non-lesional sites for all body sites, including the face, neck, cheeks, and trunk (2.7- to 6.0-fold increase). Both M. globosa and M. restricta were detected in patients and healthy individuals. However, M. globosa predominated at lesional sites, whereas the level of colonization by both species was similar in healthy individuals.

  9. Molecular epidemiology of Trichinella spp. in three Baltic countries: Lithuania, Latvia, and Estonia.

    Science.gov (United States)

    Malakauskas, A; Paulauskas, V; Järvis, T; Keidans, P; Eddi, C; Kapel, C M O

    2007-03-01

    Meat of domestic pigs and wild boars has been the significant source of emerged human trichinellosis in Lithuania, Latvia, and Estonia over the past two decades. However, there is very little known on the occurrence of Trichinella spp. in main wildlife reservoirs and its transmission in domestic and sylvatic cycles in these countries. The present study demonstrated considerably higher endemicity of Trichinella spp. in main sylvatic reservoirs (28.9-42% in foxes (Vulpes vulpes) and raccoon dogs (Nyctereutes procyonoides) in all three countries than previously reported. Molecular identification of Trichinella larvae from more than 500 sylvatic and domestic animals revealed four Trichinella species (Trichinella spiralis, Trichinella britovi, Trichinella nativa, and Trichinella pseudospiralis) sympatric in a relatively small area and several as the first records for the respective countries. The nonencapsulating T. pseudospiralis is found for the first time in the Eastern Europe. Sylvatic T. britovi was found in domestic pigs in Lithuania and Latvia (16 and 57.1%, respectively) and only in these countries, domestic T. spiralis was detected in sylvatic animals in areas where domestic trichinellosis was registered. The study suggests that transmission of Trichinella between domestic and sylvatic cycles in Lithuania and Latvia is favored by improper human behavior, e.g., pig and slaughter waste management. PMID:17013647

  10. Molecular epidemiology of Echinococcosis from food producing animals in north India.

    Science.gov (United States)

    Singh, Balbir Bagicha; Sharma, Jagdish Kamal; Ghatak, Sandeep; Sharma, Rajnish; Bal, Mandeep Singh; Tuli, Aashuma; Gill, Jatinder Paul Singh

    2012-05-25

    Echinococcosis is an important medical, veterinary and economic concern in India. Ten cysts were randomly selected from each intermediate host species (cattle, buffalo, sheep, goat and pigs). Either the germinal layer (sterile cysts) or protoscoleces (fertile cysts) were collected for molecular characterization. A 434 base pair fragment of the mitochondrial cytochrome oxidase-1 gene was amplified using PCR from each isolate. Ten representative samples (2 from each intermediate host species) were sequenced in both the directions from which readable sequences were obtained from nine for phylogenetic analysis (NCBI, Blast). Phylogenetic analysis of cytochrome oxidase I gene revealed that seven (77.7%) isolates, from cattle (2), pigs (2), buffaloes (1) and goat (2) were clustered with the Indian Buffalo (G3) strain of Echinococcus granulosus, while two (22.2%) isolates from sheep were clustered with the sheep strain (G1) of E. granulosus. Phylogenetic analysis of the cytochrome oxidase-1 gene revealed that the buffalo strain (G3) and common sheep strain (G1) are cycling among livestock in north India and that these strains are highly adapted to cattle, buffalo, sheep, goats and pigs.

  11. Enthalpy-Entropy Compensation upon Molecular Conformational Changes.

    Science.gov (United States)

    Ahmad, Mazen; Helms, Volkhard; Lengauer, Thomas; Kalinina, Olga V

    2015-04-14

    The change in free energy is the dominant factor in all chemical processes; it usually encompasses enthalpy-entropy compensation (EEC). Here, we use the free energy perturbation formalism to show that EEC is influenced by the molecular conformational changes (CCs) of the entire system comprising the solute and by the already known solvent reorganization. The internal changes of enthalpy and the entropy due to CCs upon modifying the interactions (perturbation) cancel each other exactly. The CCs influence the dissipation of the modified interactions and their contributions to the free energy. Using molecular simulations, we show that, for solvation of six different HIV-1 protease inhibitors, CCs in the solute cause EEC as large as 10-30 kcal/mol. Moreover, the EEC due to CCs in HIV-1 protease is shown to vary significantly upon modifying its bound ligand. These findings have important implications for understanding of EEC phenomena and for interpretation of thermodynamic measurements.

  12. Staphylococcal Toxic Shock Syndrome 2000–2006: Epidemiology, Clinical Features, and Molecular Characteristics

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    DeVries, Aaron S.; Lindsey Lesher; Patrick M Schlievert; Tyson Rogers; Lourdes G Villaume; Richard Danila; Ruth Lynfield

    2011-01-01

    INTRODUCTION: Circulating strains of Staphylococcus aureus (SA) have changed in the last 30 years including the emergence of community-associated methicillin-resistant SA (MRSA). A report suggested staphylococcal toxic shock syndrome (TSS) was increasing over 2000-2003. The last population-based assessment of TSS was 1986. METHODS: Population-based active surveillance for TSS meeting the CDC definition using ICD-9 codes was conducted in the Minneapolis-St. Paul area (population 2,642,056) fro...

  13. Molecular Epidemiology of Mycoplasma pneumoniae: Genotyping Using Single Nucleotide Polymorphisms and SNaPshot Technology

    Science.gov (United States)

    Touati, A.; Blouin, Y.; Sirand-Pugnet, P.; Renaudin, H.; Oishi, T.; Vergnaud, G.; Bébéar, C.

    2015-01-01

    Molecular typing of Mycoplasma pneumoniae is an important tool for identifying grouped cases and investigating outbreaks. In the present study, we developed a new genotyping method based on single nucleotide polymorphisms (SNPs) selected from the whole-genome sequencing of eight M. pneumoniae strains, using the SNaPshot minisequencing assay. Eight SNPs, localized in housekeeping genes, predicted lipoproteins, and adhesin P1 genes were selected for genotyping. These SNPs were evaluated on 140 M. pneumoniae clinical isolates previously genotyped by multilocus variable-number tandem-repeat analysis (MLVA-5) and adhesin P1 typing. This method was also adapted for direct use with clinical samples and evaluated on 51 clinical specimens. The analysis of the clinical isolates using the SNP typing method showed nine distinct SNP types with a Hunter and Gaston diversity index (HGDI) of 0.836, which is higher than the HGDI of 0.583 retrieved for the MLVA-4 typing method, where the nonstable Mpn1 marker was removed. A strong correlation with the P1 adhesin gene typing results was observed. The congruence was poor between MLVA-5 and SNP typing, indicating distinct genotyping schemes. Combining the results increased the discriminatory power. This new typing method based on SNPs and the SNaPshot technology is a method for rapid M. pneumoniae typing directly from clinical specimens, which does not require any sequencing step. This method is based on stable markers and provides information distinct from but complementary to MLVA typing. The combined use of SNPs and MLVA typing provides powerful discrimination of strains. PMID:26202117

  14. Molecular epidemiology of human enterovirus associated with aseptic meningitis in Shandong Province, China, 2006-2012.

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    Zexin Tao

    Full Text Available BACKGROUND: Human enteroviruses (HEVs are common causes of acute meningitis. However, there is limited information about HEV associated with aseptic meningitis in mainland China because it has not been classified as a notifiable disease. OBJECTIVES: To characterize the HEVs associated with sporadic aseptic meningitis in China and to analyze their genetic features. STUDY DESIGN: Cerebrospinal fluid, throat swab and feces specimens were collected from patients with aseptic meningitis in 5 sentinel hospitals in Shandong Province, China between 2006 and 2012. Virological investigation (viral isolation and molecular identification and phylogenetic analysis were performed. RESULTS: A total of 437 hospitalized patients were reported, and enteroviruses were detected in the specimens from 84 patients (19.2% and were identified into 17 serotypes. The nine main serotypes were echovirus (E 30 (27.4%, EV71 (13.1%, coxsackievirus (CV B1 (9.5%, CVB3 (7.1%, CVB5 (7.1%, E6 (7.1%, E9 (7.1%, CVA9 (6.0%, and CVA10 (3.6%. Monthly distribution of isolated enteroviruses revealed a major peak in summer-fall season and a small second peak in winter constituted totally by EV71. Sequence analysis on VP1 coding region suggested Shandong strains had great genetic divergence with isolates from other countries. CONCLUSIONS: Multiple serotypes were responsible for enterovirus meningitis in mainland China. Aseptic meningitis caused by EV71 and coxsackie A viruses-the predominant pathogens for the hand, foot, and mouth disease-is currently an important concern in mainland China.

  15. Molecular epidemiology and complete genome characterization of H1N1pdm virus from India.

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    Shashi Sharma

    Full Text Available BACKGROUND: Influenza A virus is one of world's major uncontrolled pathogen, causing seasonal epidemic as well as global pandemic. This was evidenced by recent emergence and continued prevalent 2009 swine origin pandemic H1N1 Influenza A virus, provoking first true pandemic in the past 40 years. In the course of its evolution, the virus acquired many mutations and multiple unidentified molecular determinants are likely responsible for the ability of the 2009 H1N1 virus to cause increased disease severity in humans. Availability of limited data on complete genome hampers the continuous monitoring of this type of events. Outbreaks with considerable morbidity and mortality have been reported from all parts of the country. METHODS/RESULTS: Considering a large number of clinical cases of infection complete genome based sequence characterization of Indian H1N1pdm virus and their phylogenetic analysis with respect to circulating global viruses was undertaken, to reveal the phylodynamic pattern of H1N1pdm virus in India from 2009-2011. The Clade VII was observed as a major circulating clade in phylogenetic analysis. Selection pressure analysis revealed 18 positively selected sites in major surface proteins of H1N1pdm virus. CONCLUSIONS: This study clearly revealed that clade VII has been identified as recent circulating clade in India as well globally. Few clade VII specific well identified markers undergone positive selection during virus evolution. Continuous monitoring of the H1N1pdm virus is warranted to track of the virus evolution and further transmission. This study will serve as a baseline data for future surveillance and also for development of suitable therapeutics.

  16. Assessing the HIV-1 Epidemic in Brazilian Drug Users: A Molecular Epidemiology Approach.

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    Monick Lindenmeyer Guimarães

    Full Text Available Person who inject illicit substances have an important role in HIV-1 blood and sexual transmission and together with person who uses heavy non-injecting drugs may have less than optimal adherence to anti-retroviral treatment and eventually could transmit resistant HIV variants. Unfortunately, molecular biology data on such key population remain fragmentary in most low and middle-income countries. The aim of the present study was to assess HIV infection rates, evaluate HIV-1 genetic diversity, drug resistance, and to identify HIV transmission clusters in heavy drug users (DUs. For this purpose, DUs were recruited in the context of a Respondent-Driven Sampling (RDS study in different Brazilian cities during 2009. Overall, 2,812 individuals were tested for HIV, and 168 (6% of them were positive, of which 19 (11.3% were classified as recent seroconverters, corresponding to an estimated incidence rate of 1.58%/year (95% CI 0.92-2.43%. Neighbor joining phylogenetic trees from env and pol regions and bootscan analyses were employed to subtype the virus from132 HIV-1-infected individuals. HIV-1 subtype B was prevalent in most of the cities under analysis, followed by BF recombinants (9%-35%. HIV-1 subtype C was the most prevalent in Curitiba (46% and Itajaí (86% and was also detected in Brasília (9% and Campo Grande (20%. Pure HIV-1F infections were detected in Rio de Janeiro (9%, Recife (6%, Salvador (6% and Brasília (9%. Clusters of HIV transmission were assessed by Maximum likelihood analyses and were cross-compared with the RDS network structure. Drug resistance mutations were verified in 12.2% of DUs. Our findings reinforce the importance of the permanent HIV-1 surveillance in distinct Brazilian cities due to viral resistance and increasing subtype heterogeneity all over Brazil, with relevant implications in terms of treatment monitoring, prophylaxis and vaccine development.

  17. Pattern and molecular epidemiology of Hepatitis B virus genotypes circulating in Pakistan.

    Science.gov (United States)

    Awan, Zunaira; Idrees, Muhammad; Amin, Irum; Butt, Sadia; Afzal, Samia; Akbar, Haji; Rehman, Irshad-ur; Younas, Saima; Shahid, Muhammad; Lal, Amreek; Saleem, Sana; Rauff, Bisma

    2010-12-01

    The continuously mutating nature of Hepatitis B virus (HBV) is responsible for the emergence of varying genotypes in different regions of the world affecting the disease outcome. The objective of the current study was to find out the pattern of HBV genotypes circulating in Pakistan. HBV genotypes were determined in HBV chronic patients of different age and gender from all the four different geographical regions (provinces) of Pakistan for a period of 2 years (2007-2009). Out of the total 3137 consecutive patients, 300 (175; 58.3% males and 125; 41.7% females) were randomly selected for HBV genotype A through H determination using molecular genotyping methods. Total 269 (89.6%) isolates were successfully genotyped where as 31 (10.3%) samples failed to generate a type-specific PCR band and were found untypable. Out of the successfully genotyped samples, 43 (14.3%) were with type A, 54 (18%) were with type B, 83 (27.6%) were with type C, 39 (13%) were with type D, 2 (0.6%) were with type E, 4 (1.3%) were with genotype F and total 44 (14.6%) were with mixed HBV infections. Of the mixed genotype infection cases, 16 were with genotypes A/D, 9 were B/C, six were A/D/F, five were with genotypes A/F, two were with A/B/D and B/E and one each for A/C as well as A/E genotypes. Four common genotypes of HBV found worldwide (A, B, C & D) were isolated from Pakistan along with uncommon genotypes E and F for the first time in Pakistan. Overall Genotype C is the most prevalent genotype. Genotypes B and C are predominant in Punjab & Balochistan and Khyber Pakhtoonkhwa, respectively whereas genotype A in Sindh.

  18. Molecular epidemiology, genotype-phenotype correlation and BH4 responsiveness in Spanish patients with phenylketonuria.

    Science.gov (United States)

    Aldámiz-Echevarría, Luis; Llarena, Marta; Bueno, María A; Dalmau, Jaime; Vitoria, Isidro; Fernández-Marmiesse, Ana; Andrade, Fernando; Blasco, Javier; Alcalde, Carlos; Gil, David; García, María C; González-Lamuño, Domingo; Ruiz, Mónica; Ruiz, María A; Peña-Quintana, Luis; González, David; Sánchez-Valverde, Felix; Desviat, Lourdes R; Pérez, Belen; Couce, María L

    2016-08-01

    Phenylketonuria (PKU), the most common inborn error of amino acid metabolism, is caused by mutations in the phenylalanine-4-hydroxylase (PAH) gene. This study aimed to assess the genotype-phenotype correlation in the PKU Spanish population and the usefulness in establishing genotype-based predictions of BH4 responsiveness in our population. It involved the molecular characterization of 411 Spanish PKU patients: mild hyperphenylalaninemia non-treated (mild HPA-NT) (34%), mild HPA (8.8%), mild-moderate (20.7%) and classic (36.5%) PKU. BH4 responsiveness was evaluated using a 6R-BH4 loading test. We assessed genotype-phenotype associations and genotype-BH4 responsiveness in our population according to literature and classification of the mutations. The mutational spectrum analysis showed 116 distinct mutations, most missense (70.7%) and located in the catalytic domain (62.9%). The most prevalent mutations were c.1066-11G>A (9.7%), p.Val388Met (6.6%) and p.Arg261Gln (6.3%). Three novel mutations (c.61-13del9, p.Ile283Val and p.Gly148Val) were reported. Although good genotype-phenotype correlation was observed, there was no exact correlation for some genotypes. Among the patients monitored for the 6R-BH4 loading test: 102 were responders (87, carried either one or two BH4-responsive alleles) and 194 non-responders (50, had two non-responsive mutations). More discrepancies were observed in non-responders. Our data reveal a great genetic heterogeneity in our population. Genotype is quite a good predictor of phenotype and BH4 responsiveness, which is relevant for patient management, treatment and follow-up.

  19. Development and evaluation of double locus sequence typing for molecular epidemiological investigations of Clostridium difficile.

    Science.gov (United States)

    Stojanov, M; Magalhaes, B; Terletsky, V; Basset, P; Prod'hom, G; Greub, G; Senn, L; Blanc, D S

    2016-02-01

    Despite the development of novel typing methods based on whole genome sequencing, most laboratories still rely on classical molecular methods for outbreak investigation or surveillance. Reference methods for Clostridium difficile include ribotyping and pulsed-field gel electrophoresis, which are band-comparing methods often difficult to establish and which require reference strain collections. Here, we present the double locus sequence typing (DLST) scheme as a tool to analyse C. difficile isolates. Using a collection of clinical C. difficile isolates recovered during a 1-year period, we evaluated the performance of DLST and compared the results to multilocus sequence typing (MLST), a sequence-based method that has been used to study the structure of bacterial populations and highlight major clones. DLST had a higher discriminatory power compared to MLST (Simpson's index of diversity of 0.979 versus 0.965) and successfully identified all isolates of the study (100 % typeability). Previous studies showed that the discriminatory power of ribotyping was comparable to that of MLST; thus, DLST might be more discriminatory than ribotyping. DLST is easy to establish and provides several advantages, including absence of DNA extraction [polymerase chain reaction (PCR) is performed on colonies], no specific instrumentation, low cost and unambiguous definition of types. Moreover, the implementation of a DLST typing scheme on an Internet database, such as that previously done for Staphylococcus aureus and Pseudomonas aeruginosa ( http://www.dlst.org ), will allow users to easily obtain the DLST type by submitting directly sequencing files and will avoid problems associated with multiple databases. PMID:26581425

  20. Molecular epidemiological analysis of Mycoplasma bovis isolates from the Pennsylvania Animal Diagnostic Laboratory showing genetic diversity.

    Science.gov (United States)

    Soehnlen, M K; Kariyawasam, S; Lumadue, J A; Pierre, T A; Wolfgang, D R; Jayarao, B M

    2011-04-01

    We have examined the genetic variability of Mycoplasma bovis strains submitted to the Pennsylvania Animal Diagnostics Laboratory, University Park (PA-ADL), between December 2007 and December 2008. Of 4,868 total samples submitted for Mycoplasma testing, 302 were determined to be culture positive. Mycoplasma bovis (63.6%), Mycoplasma californicum (7.3%), Mycoplasma bovirhinis (2.7%), Mycoplasma bovigenitalium (0.7%), Mycoplasma alkalescens (4.9%), Mycoplasma putrefaciens (0.3%), and Mycoplasma dispar (1.3%) and unidentified Mycoplasma sp. (19.2%) were identified using PCR. Mycoplasma bovis represented the largest portion of the positive samples submitted. Each of the 192 M. bovis isolates was examined for variations in the BglII and MfeI restriction sites of the DNA using amplified fragment length polymorphism fingerprinting and subsequently compared with the M. bovis type strain PG45 (ATCC 25523). Similarity between strains was calculated using the Dice similarity coefficient, which ranged from approximately 0.7 to 1.0. When clustering the isolates at greater than 95% similarity, it was determined that 11 distinct clusters were present. The results are consistent with the existence of at least 2 clonally distinct groups. No clear geographical, month of isolation, or source origination relationship was identified, indicating that a currently unclassified characteristic is responsible for the strain heterogeneity. These data indicate strong heterogeneity of M. bovis isolates submitted to PA-ADL. Additionally, multiple sites throughout Pennsylvania had isolates of separate clonal lineages present concomitantly, indicating the ability of multiple overlapping outbreaks to occur at a single location. Mycoplasma bovis represents the largest portion of Mycoplasma species isolated from PA-ADL samples. We propose that amplified fragment length polymorphism may serve as a valuable tool for molecular characterization of M. bovis strains from the United States. PMID:21426978

  1. Molecular and Epidemiological Analysis of a Campylobacter jejuni Outbreak in Northern Italy in November 2013.

    Science.gov (United States)

    Lucarelli, Claudia; Dionisi, Anna Maria; Trezzi, Livia; Farina, Claudio; Passera, Marco; Kärki, Tommi; D'Ancona, Fortunato; Luzzi, Ida

    2016-09-01

    Campylobacter spp. is the most common gastrointestinal pathogen worldwide with a very low reported incidence in Italy. In November of 2013, local and national public health authorities investigated an outbreak caused by Campylobacter jejuni among children in a kindergarten in Northern Italy. A case was defined as a child who had diarrhea with a laboratory-confirmed diagnosis of C. jejuni between 11 and 30 November. Stool samples from the kindergarten kitchen staff and environmental samples from the kitchen were examined for enteric pathogens. As food leftovers were not available, the menu logbook of the refectory was reviewed to identify a possible source of the outbreak. C. jejuni strains were tested for antimicrobial susceptibility and subtyped by pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). We identified 20 cases among 247 schoolchildren (attack rate = 8%), all who reported having lunch in the kindergarten. The stools from the kitchen staff as well as the environmental samples were negative for enteric pathogens. The identified outbreak strains (n = 5) were sensitive to all of the antimicrobials tested; the first four strains showed an identical PFGE profile, whereas the fifth strain showed a PFGE pattern similarity of 89%. Using MLST, all five strains were assigned to a single sequence type (ST), ST451 (clonal complex, CC21); this was the first identification of ST and the third reported outbreak of C. jejuni in Italy. Molecular typing confirmed that most of the cases belonged to a clonal cluster supporting the hypothesis of a common source; however, the source was not identified. Due to a delayed start of the investigation, it was not possible to perform any microbiological evaluation of the food consumed. PMID:27455195

  2. Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study.

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    Andreas Roetzer

    Full Text Available BACKGROUND: Understanding Mycobacterium tuberculosis (Mtb transmission is essential to guide efficient tuberculosis control strategies. Traditional strain typing lacks sufficient discriminatory power to resolve large outbreaks. Here, we tested the potential of using next generation genome sequencing for identification of outbreak-related transmission chains. METHODS AND FINDINGS: During long-term (1997 to 2010 prospective population-based molecular epidemiological surveillance comprising a total of 2,301 patients, we identified a large outbreak caused by an Mtb strain of the Haarlem lineage. The main performance outcome measure of whole genome sequencing (WGS analyses was the degree of correlation of the WGS analyses with contact tracing data and the spatio-temporal distribution of the outbreak cases. WGS analyses of the 86 isolates revealed 85 single nucleotide polymorphisms (SNPs, subdividing the outbreak into seven genome clusters (two to 24 isolates each, plus 36 unique SNP profiles. WGS results showed that the first outbreak isolates detected in 1997 were falsely clustered by classical genotyping. In 1998, one clone (termed "Hamburg clone" started expanding, apparently independently from differences in the social environment of early cases. Genome-based clustering patterns were in better accordance with contact tracing data and the geographical distribution of the cases than clustering patterns based on classical genotyping. A maximum of three SNPs were identified in eight confirmed human-to-human transmission chains, involving 31 patients. We estimated the Mtb genome evolutionary rate at 0.4 mutations per genome per year. This rate suggests that Mtb grows in its natural host with a doubling time of approximately 22 h (400 generations per year. Based on the genome variation discovered, emergence of the Hamburg clone was dated back to a period between 1993 and 1997, hence shortly before the discovery of the outbreak through epidemiological

  3. Monitoring the long-term molecular epidemiology of the pneumococcus and detection of potential 'vaccine escape' strains.

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    Gagan A Pandya

    within research and clinical laboratories in both monitoring the molecular epidemiology of the pneumococcus and detecting 'vaccine escape' strains among vaccine-candidate genes.

  4. Full-Genome Sequencing as a Basis for Molecular Epidemiology Studies of Bluetongue Virus in India.

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    Sushila Maan

    Full Text Available Since 1998 there have been significant changes in the global distribution of bluetongue virus (BTV. Ten previously exotic BTV serotypes have been detected in Europe, causing severe disease outbreaks in naïve ruminant populations. Previously exotic BTV serotypes were also identified in the USA, Israel, Australia and India. BTV is transmitted by biting midges (Culicoides spp. and changes in the distribution of vector species, climate change, increased international travel and trade are thought to have contributed to these events. Thirteen BTV serotypes have been isolated in India since first reports of the disease in the country during 1964. Efficient methods for preparation of viral dsRNA and cDNA synthesis, have facilitated full-genome sequencing of BTV strains from the region. These studies introduce a new approach for BTV characterization, based on full-genome sequencing and phylogenetic analyses, facilitating the identification of BTV serotype, topotype and reassortant strains. Phylogenetic analyses show that most of the equivalent genome-segments of Indian BTV strains are closely related, clustering within a major eastern BTV 'topotype'. However, genome-segment 5 (Seg-5 encoding NS1, from multiple post 1982 Indian isolates, originated from a western BTV topotype. All ten genome-segments of BTV-2 isolates (IND2003/01, IND2003/02 and IND2003/03 are closely related (>99% identity to a South African BTV-2 vaccine-strain (western topotype. Similarly BTV-10 isolates (IND2003/06; IND2005/04 show >99% identity in all genome segments, to the prototype BTV-10 (CA-8 strain from the USA. These data suggest repeated introductions of western BTV field and/or vaccine-strains into India, potentially linked to animal or vector-insect movements, or unauthorised use of 'live' South African or American BTV-vaccines in the country. The data presented will help improve nucleic acid based diagnostics for Indian serotypes/topotypes, as part of control strategies.

  5. Molecular epidemiology of CTX-M producing Enterobacteriaceae isolated from bloodstream infections in Rio de Janeiro, Brazil: emergence of CTX-M-15

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    Liliane Miyuki Seki

    2013-12-01

    Full Text Available OBJECTIVE: The present studywas designed to evaluate the molecular epidemiology of CTX-M producing Klebsiella pneumoniae, Enterobacter cloacae and Escherichia coli isolated from bloodstream infections at tertiary care hospitals in the State of Rio de Janeiro, Brazil. MATERIAL AND METHODS: A total of 231 nonduplicate Enterobacteriaceae were isolated from five Brazilian hospitals between September 2007 and September 2008. The antimicrobial susceptibility testing was performed by disk diffusion method according to the Clinical Laboratory Standard Institute. Isolates showing resistance to third-generation cephalosporins were screened for ESBL activity by the double-disk synergy test. The presence of blaCTX-M , blaCTX-M-15 and blaKPC genes was determined by Polymerase Chain Reaction (PCR amplification andDNA sequencing. The molecular typing of CTX-M producing isolateswas performed by pulsed-field gel electrophoresis (PFGE. RESULTS AND DISCUSSION: Ninety-three isolates were screened as ESBL positive and 85 (91% were found to carry CTX-M-type, as follows: K. pneumoniae 59 (49%, E. cloacae 15 (42%, and E. coli 11 (15%. Ten isolates resistant for carbapenems in K. pneumoniae were blaKPC-2 gene positive. Among CTX-M type isolates, CTX-M-15 was predominant in more than 50% of isolates for K. pneumoniae, E. coli, and E. cloacae. PFGE analysis of CTX-M producing isolates showed the predominance of CTX-M-15 in 10 of 24 pulsotypes in K. pneumoniae, 6 of 13 in E. cloacae and 3 of 6 in E. coli. CTX-M-15 was also predominant among KPC producing isolates. In conclusion, this study showed that CTX-M-15 was circulating in Rio de Janeiro state in 2007-2008. This data reinforce the need for continuing surveillance because this scenario may have changed over the years.

  6. Impairment of Colour Vision in Diabetes with No Retinopathy: Sankara Nethralaya Diabetic Retinopathy Epidemiology and Molecular Genetics Study (SNDREAMS- II, Report 3)

    OpenAIRE

    Gella, Laxmi; Raman, Rajiv; Kulothungan, Vaitheeswaran; Pal, Swakshyar Saumya; Ganesan, Suganeswari; Sharma, Tarun

    2015-01-01

    Purpose To assess impairment of colour vision in type 2 diabetics with no diabetic retinopathy and elucidate associated risk factors in a population-based cross-sectional study. Methods This is part of Sankara Nethralaya Diabetic Retinopathy Epidemiology and Molecular-genetics Study (SN-DREAMS II) which was conducted between 2007–2010. FM 100 hue-test was performed in 253 subjects with no clinical evidence of diabetic retinopathy. All subjects underwent detailed ophthalmic evaluation includin...

  7. Molecular epidemiology of Crimean-Congo hemorrhagic fever virus in Kosovo.

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    Luka Fajs

    Full Text Available Crimean-Congo hemorrhagic fever virus (CCHFV is a zoonotic agent that causes severe, life-threatening disease, with a case fatality rate of 10-50%. It is the most widespread tick-borne virus in the world, with cases reported in Africa, Asia and Eastern Europe. CCHFV is a genetically diverse virus. Its genetic diversity is often correlated to its geographical origin. Genetic variability of CCHFV was determined within few endemic areas, however limited data is available for Kosovo. Furthermore, there is little information about the spatiotemporal genetic changes of CCHFV in endemic areas. Kosovo is an important endemic area for CCHFV. Cases were reported each year and the case-fatality rate is significantly higher compared to nearby regions. In this study, we wanted to examine the genetic variability of CCHFV obtained directly from CCHF-confirmed patients, hospitalized in Kosovo from 1991 to 2013. We sequenced partial S segment CCHFV nucleotide sequences from 89 patients. Our results show that several viral variants are present in Kosovo and that the genetic diversity is high in relation to the studied area. We also show that variants are mostly uniformly distributed throughout Kosovo and that limited evolutionary changes have occurred in 22 years. Our results also suggest the presence of a new distinct lineage within the European CCHF phylogenetic clade. Our study provide the largest number of CCHFV nucleotide sequences from patients in 22 year span in one endemic area.

  8. Molecular epidemiology of Crimean-Congo hemorrhagic fever virus in Kosovo.

    Science.gov (United States)

    Fajs, Luka; Jakupi, Xhevat; Ahmeti, Salih; Humolli, Isme; Dedushaj, Isuf; Avšič-Županc, Tatjana

    2014-01-01

    Crimean-Congo hemorrhagic fever virus (CCHFV) is a zoonotic agent that causes severe, life-threatening disease, with a case fatality rate of 10-50%. It is the most widespread tick-borne virus in the world, with cases reported in Africa, Asia and Eastern Europe. CCHFV is a genetically diverse virus. Its genetic diversity is often correlated to its geographical origin. Genetic variability of CCHFV was determined within few endemic areas, however limited data is available for Kosovo. Furthermore, there is little information about the spatiotemporal genetic changes of CCHFV in endemic areas. Kosovo is an important endemic area for CCHFV. Cases were reported each year and the case-fatality rate is significantly higher compared to nearby regions. In this study, we wanted to examine the genetic variability of CCHFV obtained directly from CCHF-confirmed patients, hospitalized in Kosovo from 1991 to 2013. We sequenced partial S segment CCHFV nucleotide sequences from 89 patients. Our results show that several viral variants are present in Kosovo and that the genetic diversity is high in relation to the studied area. We also show that variants are mostly uniformly distributed throughout Kosovo and that limited evolutionary changes have occurred in 22 years. Our results also suggest the presence of a new distinct lineage within the European CCHF phylogenetic clade. Our study provide the largest number of CCHFV nucleotide sequences from patients in 22 year span in one endemic area. PMID:24416468

  9. Transient Changes in Molecular Geometries and How to Model Them

    DEFF Research Database (Denmark)

    Dohn, Asmus Ougaard

    by the solvent. The simulations has also served as benchmarks on this newly developed implementation First, we establish that the chosen model provides a trustworthy description of the systems; since transition metals are heavier than purely organic systems, we test a range of approximations to relativistic...... changes in molecular structure, vibrations and solvation. In this thesis, we employ our recently developed Quantum-/Molecular -Mechanical Direct Dynamics method to do simulations of transition metal complexes in solution, to uncover their energy dissipation channels, and how they are affected...... quantum mechanic descriptions, to ascertain the accuracy of the quantum model in the Direct Dynamics simulations. We then test - and improve - the framework for calculating the experimental X-ray Diffuse Scattering Difference signal from (any kind of) Molecular Dynamics (MD) simulations. Comparisons...

  10. The molecular epidemiology of the highly virulent ST93 Australian community Staphylococcus aureus strain.

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    Geoffrey W Coombs

    Full Text Available In Australia the PVL-positive ST93-IV [2B], colloquially known as "Queensland CA-MRSA" has become the dominant CA-MRSA clone. First described in the early 2000s, ST93-IV [2B] is associated with skin and severe invasive infections including necrotizing pneumonia. A singleton by multilocus sequence typing (MLST eBURST analysis ST93 is distinct from other S. aureus clones. To determine if the increased prevalence of ST93-IV [2B] is due to the widespread transmission of a single strain of ST93-IV [2B] the genetic relatedness of 58 S. aureus ST93 isolated throughout Australia over an extended period were studied in detail using a variety of molecular methods including pulsed-field gel electrophoresis, spa typing, MLST, microarray DNA, SCCmec typing and dru typing. Identification of the phage harbouring the lukS-PV/lukF-PV Panton Valentine leucocidin genes, detection of allelic variations in lukS-PV/lukF-PV, and quantification of LukF-PV expression was also performed. Although ST93-IV [2B] is known to have an apparent enhanced clinical virulence, the isolates harboured few known virulence determinants. All PVL-positive isolates carried the PVL-encoding phage ΦSa2USA and the lukS-PV/lukF-PV genes had the same R variant SNP profile. The isolates produced similar expression levels of LukF-PV. Although multiple rearrangements of the spa sequence have occurred, the core genome in ST93 is very stable. The emergence of ST93-MRSA is due to independent acquisitions of different dru-defined type IV and type V SCCmec elements in several spa-defined ST93-MSSA backgrounds. Rearrangement of the spa sequence in ST93-MRSA has subsequently occurred in some of these strains. Although multiple ST93-MRSA strains were characterised, little genetic diversity was identified for most isolates, with PVL-positive ST93-IVa [2B]-t202-dt10 predominant across Australia. Whether ST93-IVa [2B] t202-dt10 arose from one PVL-positive ST93-MSSA-t202, or by independent acquisitions of

  11. Molecular epidemiology of zoonotic streptococcosis/lactococcosis in rainbow trout (Oncorhynchus mykiss aquaculture in Iran

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    G Nikbakhat-Brojeni

    2010-12-01

    Full Text Available Background and Objectives: Streptococcosis/lactococcosis is a hyperacute systemic disease that can occur in marine and fresh waters of many species of fish. The aim of this work was to study the disease outbreak in the major rainbow trout (Oncorhynchus mykiss production of Iran."nMaterials and Methods: 108 Gram positive cocci isolates were obtained from diseased trout in seven provinces with major trout production during 2008 till 2009. These bacterial isolates were characterized using phenotypic and molecular studies. The isolates were also analysed phylogeneticaly and compared with the available data."nResults: 49 samples (45.37% were identified as Streptococcus iniae, 37 samples (35.2% matched with Lactococcus garvieae; and 22 samples (19.43% were identified as members of Streptooccus genus by culture-based and biochemical tests of API 50 CH, API 20 STREP and rapid 32 STREP systems. Using universal primers for differentiation of Streptococcus sp. and Enterococcus sp, all 108 samples were identified as Streptococcus sp. with a target region of 500 bp. Single specific PCR resulted in identification of 64 (59.2% isolates as S. iniae and 44 (40.8% isolates as L. garvieae. The phylogenetic analysis of the S. iniae isolates resulted in maximal similarity to some strains reported from Taiwan and to all Brazilian strains. Also, one strain showed less sequence similarity values with other tested strains although this strain has high similarity with ATCC 29178 strain, all reported Chinese, and some Taiwanian strains. Also, analysis of S. iniae LctO gene sequence showed that this isolate clustered within the S. iniae group. The sequence analysis of L. garvieae strains also showed that they have maximum similarity to all Japanese and Chinese strains, but one strain has lower sequence similarity values with all other recorded strains."nConculsion: The results of this study clearly show that trout farming in Iran is severely affected by both species of S

  12. Molecular epidemiology of nontuberculous mycobacteria isolates from clinical and environmental sources of a metropolitan city.

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    Ali Akbar Velayati

    Full Text Available While NTM infection is mainly acquired from environmental exposure, monitoring of environmental niches for NTM is not a routine practice. This study aimed to find the prevalence of environmental NTM in soil and water in four highly populated suburbs of Tehran, Iran.A total of 4014 samples from soil and water resources were collected and studied. Sediments of each treated sample were cultured in Lowenstein-Jensen medium and observed twice per week for growth rate, colony morphology, and pigmentation. Colonies were studied with phenotypic tests. Molecular analysis was performed on single colonies derived from subculture of original isolates. Environmental samples were compared with 34 NTM isolates from patients who were residents of the study locations.Out of 4014 samples, mycobacteria were isolated from 862 (21.4% specimens; 536 (62.1% belonged to slow growing mycobacteria (SGM and 326 (37.8% were rapid growing mycobacteria (RGM. The five most frequent NTM were M. farcinogens (105/862; 12.1%, M. fortuitum (72/862; 8.3%, M. senegalense (58/862; 6.7%, M. kansasii (54/862; 6.2%, and M. simiae (46/862; 5.3%. In total, 62.5% (539/862 of mycobacterial positive samples were isolated from water and only 37.4% (323/862 of them were isolated from soil samples (P<0.05. Out of 5314 positive clinical samples for mycobacteria, 175 (3.2% isolates were NTM. The trend of NTM isolates increased from 1.2% (13 out of 1078 in 2004 to 3.8% (39 out of 1005 in 2014 (P = 0.0001. The major clinical isolates were M. simiae (51; 29.1%, M. kansasii (26; 14.8%, M. chelonae (28; 16%, and M. fortuitum (13; 7.4%.Comparing the distribution pattern of environmental NTM isolates with clinical isolates suggests a possible transmission link, but this does not apply to all environmental NTM species. Our study confirms an increasing trend of NTM isolation from clinical samples that needs further investigation.

  13. Full-Genome Sequencing as a Basis for Molecular Epidemiology Studies of Bluetongue Virus in India

    Science.gov (United States)

    Maan, Sushila; Maan, Narender S.; Belaganahalli, Manjunatha N.; Rao, Pavuluri Panduranga; Singh, Karam Pal; Hemadri, Divakar; Putty, Kalyani; Kumar, Aman; Batra, Kanisht; Krishnajyothi, Yadlapati; Chandel, Bharat S.; Reddy, G. Hanmanth; Nomikou, Kyriaki; Reddy, Yella Narasimha; Attoui, Houssam; Hegde, Nagendra R.; Mertens, Peter P. C.

    2015-01-01

    Since 1998 there have been significant changes in the global distribution of bluetongue virus (BTV). Ten previously exotic BTV serotypes have been detected in Europe, causing severe disease outbreaks in naïve ruminant populations. Previously exotic BTV serotypes were also identified in the USA, Israel, Australia and India. BTV is transmitted by biting midges (Culicoides spp.) and changes in the distribution of vector species, climate change, increased international travel and trade are thought to have contributed to these events. Thirteen BTV serotypes have been isolated in India since first reports of the disease in the country during 1964. Efficient methods for preparation of viral dsRNA and cDNA synthesis, have facilitated full-genome sequencing of BTV strains from the region. These studies introduce a new approach for BTV characterization, based on full-genome sequencing and phylogenetic analyses, facilitating the identification of BTV serotype, topotype and reassortant strains. Phylogenetic analyses show that most of the equivalent genome-segments of Indian BTV strains are closely related, clustering within a major eastern BTV ‘topotype’. However, genome-segment 5 (Seg-5) encoding NS1, from multiple post 1982 Indian isolates, originated from a western BTV topotype. All ten genome-segments of BTV-2 isolates (IND2003/01, IND2003/02 and IND2003/03) are closely related (>99% identity) to a South African BTV-2 vaccine-strain (western topotype). Similarly BTV-10 isolates (IND2003/06; IND2005/04) show >99% identity in all genome segments, to the prototype BTV-10 (CA-8) strain from the USA. These data suggest repeated introductions of western BTV field and/or vaccine-strains into India, potentially linked to animal or vector-insect movements, or unauthorised use of ‘live’ South African or American BTV-vaccines in the country. The data presented will help improve nucleic acid based diagnostics for Indian serotypes/topotypes, as part of control strategies. PMID

  14. Integrated Bioinformatics, Environmental Epidemiologic and Genomic Approaches to Identify Environmental and Molecular Links between Endometriosis and Breast Cancer

    OpenAIRE

    Deodutta Roy; Marisa Morgan; Changwon Yoo; Alok Deoraj; Sandhya Roy; Vijay Kumar Yadav; Mohannad Garoub; Hamza Assaggaf; Mayur Doke

    2015-01-01

    We present a combined environmental epidemiologic, genomic, and bioinformatics approach to identify: exposure of environmental chemicals with estrogenic activity; epidemiologic association between endocrine disrupting chemical (EDC) and health effects, such as, breast cancer or endometriosis; and gene-EDC interactions and disease associations. Human exposure measurement and modeling confirmed estrogenic activity of three selected class of environmental chemicals, polychlorinated biphenyls (PC...

  15. Minimum Cost Estimation of a Baseline Survey for a Molecular Epidemiology Cohort Study: Collecting Participants in a Model Region in Japan

    Science.gov (United States)

    Sawada, Norie; Iwasaki, Motoki; Ohashi, Kayo; Tsugane, Shoichiro

    2016-01-01

    Background Some recent molecular epidemiology studies of the effects of genetic and environmental factors on human health have required the enrollment of more than 100 000 participants and the involvement of regional study offices across the country. Although regional study office investigators play a critical role in these studies, including the acquisition of funds, this role is rarely discussed. Methods We first differentiated the functions of the regional and central study offices. We then investigated the minimum number of items required and approximate cost of a molecular epidemiology study enrolling 7400 participants from a model region with a population of 100 000 for a 4-year baseline survey using a standard protocol developed based on the protocol of Japan Public Health Center-based Prospective Study for the Next Generation. Results The functions of the regional study office were identified, and individual expenses were itemized. The total cost of the 4-year baseline survey was 153 million yen, excluding consumption tax. Accounting difficulties in conducting the survey were clarified. Conclusions We investigated a standardized example of the tasks and total actual costs of a regional study office. Our approach is easy to utilize and will help improve the management of regional study offices in future molecular epidemiology studies. PMID:27001116

  16. Patogénesis molecular, epidemiología y diagnóstico de Escherichia coli enteropatógena Molecular pathogenesis, epidemiology and diagnosis of enteropathogenic Escherichia coli

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    Jorge E. Vidal

    2007-10-01

    Full Text Available Escherichia coli enteropatógena (EPEC es una de las principales causas de diarrea en niños menores de dos años en países en vías de desarrollo. La principal característica histopatológica de la infección es una lesión que induce la EPEC en el intestino conocida como la lesión A/E (adherencia y eliminación. Las bacterias se adhieren a los enterocitos y permiten la acumulación de la actina del citoesqueleto en la región apical de la célula, hasta formar una estructura de tipo "pedestal" y causar la eliminación de las microvellosidades intestinales. A pesar de que se conoce de modo detallado el proceso de formación de los pedestales de actina, aún no se ha esclarecido el mecanismo global de la diarrea que induce EPEC. La diarrea se ha vinculado con: a la destrucción de las microvellosidades del enterocito, b la salida masiva de iones hacia la luz intestinal y c la secreción de alguna enterotoxina. En estudios realizados en países en vías de desarrollo se ha demostrado que EPEC es uno de los principales agentes participantes en la diarrea infantil, con elevadas tasas de morbilidad y mortalidad. El diagnóstico microbiológico de la infección se realiza con metodologías adicionales a las utilizadas con regularidad en el laboratorio de microbiología clínica, entre ellas las siguientes: a serotipificación, b ensayo de adherencia, c prueba de FAS (tinción fluorescente para actina y d detección específica de genes que codifican a proteínas incluidas en la patogénesis, como el bfpA y eae. Un objetivo de esta revisión es actualizar los avances observados en la patogénesis molecular de la infección por EPEC, las metodologías para el diagnóstico microbiológico y la epidemiología en México y otros países en vías de desarrollo.Enteropathogenic Escherichia coli (EPEC is a leading cause of diarrhea in infants less than two years of age in developing countries. To induce diarrhea EPEC uses several virulence factors acting

  17. Evaluation of a Phylogenetic Marker Based on Genomic Segment B of Infectious Bursal Disease Virus: Facilitating a Feasible Incorporation of this Segment to the Molecular Epidemiology Studies for this Viral Agent.

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    Abdulahi Alfonso-Morales

    Full Text Available Infectious bursal disease (IBD is a highly contagious and acute viral disease, which has caused high mortality rates in birds and considerable economic losses in different parts of the world for more than two decades and it still represents a considerable threat to poultry. The current study was designed to rigorously measure the reliability of a phylogenetic marker included into segment B. This marker can facilitate molecular epidemiology studies, incorporating this segment of the viral genome, to better explain the links between emergence, spreading and maintenance of the very virulent IBD virus (vvIBDV strains worldwide.Sequences of the segment B gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank Database; Cuban sequences were obtained in the current work. A phylogenetic marker named B-marker was assessed by different phylogenetic principles such as saturation of substitution, phylogenetic noise and high consistency. This last parameter is based on the ability of B-marker to reconstruct the same topology as the complete segment B of the viral genome. From the results obtained from B-marker, demographic history for both main lineages of IBDV regarding segment B was performed by Bayesian skyline plot analysis. Phylogenetic analysis for both segments of IBDV genome was also performed, revealing the presence of a natural reassortant strain with segment A from vvIBDV strains and segment B from non-vvIBDV strains within Cuban IBDV population.This study contributes to a better understanding of the emergence of vvIBDV strains, describing molecular epidemiology of IBDV using the state-of-the-art methodology concerning phylogenetic reconstruction. This study also revealed the presence of a novel natural reassorted strain as possible manifest of change in the genetic structure and stability of the vvIBDV strains. Therefore, it highlights the need to obtain information about both genome segments of IBDV for

  18. Coagulase-negative staphylococci: update on the molecular epidemiology and clinical presentation, with a focus on Staphylococcus epidermidis and Staphylococcus saprophyticus.

    Science.gov (United States)

    Widerström, M; Wiström, J; Sjöstedt, A; Monsen, T

    2012-01-01

    Coagulase-negative staphylococci (CoNS), originally described as ubiquitous commensals of the healthy human skin and mucosa, have emerged as important opportunistic pathogens primarily causing healthcare-associated infections in patients with indwelling medical devices. Recent studies, utilizing new molecular typing methods, particularly on Staphylococcus epidermidis, have increased our understanding of the mechanisms that contribute to the evolutionary success of these extremely versatile microorganisms. In the following mini-review, we summarize recent research in this area focusing on the molecular methods and epidemiology of S. epidermidis and S. saprophyticus.

  19. Epidemiology and molecular genotyping of echinostome metacercariae in Filopaludina snails in Lamphun Province, Thailand

    Institute of Scientific and Technical Information of China (English)

    Waraporn Noikong; Chalobol Wongsawad

    2014-01-01

    Objective: To analyze the prevalence of echinostome metacercariae in Filopaludina dorliaris (F. dorliaris) and Filopaludina martensi martensi (F. martensi martensi) and genotype variation of echinostome metacercariae by using random amplified polymorphic DNA (RAPD) analysis. Methods: Filopaludina sp. snails were collected from eight localities of Lamphun Province, Northern Thailand and examined for echinostome metacercariae. RAPD-PCR was used to analyze genotype variation of echinostome metacercariae. Results: A total of 3 226 F. dorliaris and F. martensi martensi snails were collected from eight localities. The overall prevalences of echinostome metacercariae in F. dorliaris and F. martensi martensi were 40.89% and 36.27%, while the intensity of infection was 20.37 and 12.04, respectively. The dendrogram constructed base on RAPD profiles, 4 well supported domains were generated; (i) group of metacercariae from Ban Hong, Mae Ta, Meaung, Pa Sang, Toong Hua Chang, and Weang Nong that were clustered in the group of E. revolutum, (ii) Ban Thi, (iii) Lee, and (iv) 3 adults of an out group. Conclusions:This research demonstrated RAPD profiling has been a useful tool to detect DNA polymorphisms to determine genetic relationship between echinostome metacercariae in Lamphun Province, Northern Thailand.

  20. Molecular epidemiology of influenza A/H3N2 viruses circulating in Uganda.

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    Denis K Byarugaba

    Full Text Available The increasing availability of complete influenza virus genomes is deepening our understanding of influenza evolutionary dynamics and facilitating the selection of vaccine strains. However, only one complete African influenza virus sequence is available in the public domain. Here we present a complete genome analysis of 59 influenza A/H3N2 viruses isolated from humans in Uganda during the 2008 and 2009 season. Isolates were recovered from hospital-based sentinel surveillance for influenza-like illnesses and their whole genome sequenced. The viruses circulating during these two seasons clearly differed from each other phylogenetically. They showed a slow evolution away from the 2009/10 recommended vaccine strain (A/Brisbane/10/07, instead clustering with the 2010/11 recommended vaccine strain (A/Perth/16/09 in the A/Victoria/208/09 clade, as observed in other global regions. All of the isolates carried the adamantane resistance marker S31N in the M2 gene and carried several markers of enhanced transmission; as expected, none carried any marker of neuraminidase inhibitor resistance. The hemagglutinin gene of the 2009 isolates differed from that of the 2008 isolates in antigenic sites A, B, D, and to a lesser extent, C and E indicating evidence of an early phylogenetic shift from the 2008 to 2009 viruses. The internal genes of the 2009 isolates were similar to those of one 2008 isolate, A/Uganda/MUWRP-050/2008. Another 2008 isolate had a truncated PB1-F2 protein. Whole genome sequencing can enhance surveillance of future seasonal changes in the viral genome which is crucial to ensure that selected vaccine strains are protective against the strains circulating in Eastern Africa. This data provides an important baseline for this surveillance. Overall the influenza virus activity in Uganda appears to mirror that observed in other regions of the southern hemisphere.

  1. Molecular epidemiology of novel swine origin influenza virus (S-OIV from Gwalior, India, 2009

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    Shukla Jyoti

    2011-06-01

    Full Text Available Abstract Background The H1N1pandemic virus is a newly emergent human influenza A virus that is closely related to a number of currently circulating pig viruses in the 'classic North American' and 'Eurasian' swine influenza virus lineages and thus referred as S-OIV. Since the first reports of the virus in humans in April 2009, H1N1 virus has spread to 168 countries and overseas territories. India also witnessed severe H1N1 pandemic virus epidemic with considerable morbidity and mortality in different parts starting from May 2009. Findings The suspected swine flu outbreak from Gwalior India during October- December 2009 was confirmed through S-OIV HA gene specific RT-LAMP and real time RT-PCR. Positive samples through CDC real time and Lamp assay were further processed for isolation of the virus. Full HA gene sequencing of the H1N1 isolates of Gwalior, India revealed 99% homology with California and other circulating novel swine flu viruses. Three major changes were observed at nucleotide level, while two major amino acid shifts were observed at the position C9W and I30M corresponding to the ORF with prototype strain. The HA gene sequence phylogeny revealed the circulation of two genetically distinct lineages belonging to Clade VII and Clade I of S-OIV. Conclusions Our findings also supported the earlier report about circulation of mixed genogroups of S-OIV in India. Therefore continuous monitoring of the genetic makeup of this newly emergent virus is essential to understand its evolution within the country.

  2. Staphylococcal toxic shock syndrome 2000-2006: epidemiology, clinical features, and molecular characteristics.

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    Aaron S DeVries

    Full Text Available INTRODUCTION: Circulating strains of Staphylococcus aureus (SA have changed in the last 30 years including the emergence of community-associated methicillin-resistant SA (MRSA. A report suggested staphylococcal toxic shock syndrome (TSS was increasing over 2000-2003. The last population-based assessment of TSS was 1986. METHODS: Population-based active surveillance for TSS meeting the CDC definition using ICD-9 codes was conducted in the Minneapolis-St. Paul area (population 2,642,056 from 2000-2006. Medical records of potential cases were reviewed for case criteria, antimicrobial susceptibility, risk factors, and outcome. Superantigen PCR testing and PFGE were performed on available isolates from probable and confirmed cases. RESULTS: Of 7,491 hospitalizations that received one of the ICD-9 study codes, 61 TSS cases (33 menstrual, 28 non-menstrual were identified. The average annual incidence per 100,000 of all, menstrual, and non-menstrual TSS was 0.52 (95% CI, 0.32-0.77, 0.69 (0.39-1.16, and 0.32 (0.12-0.67, respectively. Women 13-24 years had the highest incidence at 1.41 (0.63-2.61. No increase in incidence was observed from 2000-2006. MRSA was isolated in 1 menstrual and 3 non-menstrual cases (7% of TSS cases; 1 isolate was USA400. The superantigen gene tst-1 was identified in 20 (80% of isolates and was more common in menstrual compared to non-menstrual isolates (89% vs. 50%, p = 0.07. Superantigen genes sea, seb and sec were found more frequently among non-menstrual compared to menstrual isolates [100% vs 25% (p = 0.4, 60% vs 0% (p<0.01, and 25% vs 13% (p = 0.5, respectively]. DISCUSSION: TSS incidence remained stable across our surveillance period of 2000-2006 and compared to past population-based estimates in the 1980s. MRSA accounted for a small percentage of TSS cases. tst-1 continues to be the superantigen associated with the majority of menstrual cases. The CDC case definition identifies the most severe cases and has

  3. Molecular Epidemiology and Clinical Impact of Acinetobacter calcoaceticus-baumannii Complex in a Belgian Burn Wound Center

    Science.gov (United States)

    Bilocq, Florence; Jennes, Serge; Verbeken, Gilbert; Rose, Thomas; Keersebilck, Elkana; Bosmans, Petra; Pieters, Thierry; Hing, Mony; Heuninckx, Walter; De Pauw, Frank; Soentjens, Patrick; Merabishvili, Maia; Deschaght, Pieter; Vaneechoutte, Mario; Bogaerts, Pierre; Glupczynski, Youri; Pot, Bruno; van der Reijden, Tanny J.; Dijkshoorn, Lenie

    2016-01-01

    Multidrug resistant Acinetobacter baumannii and its closely related species A. pittii and A. nosocomialis, all members of the Acinetobacter calcoaceticus-baumannii (Acb) complex, are a major cause of hospital acquired infection. In the burn wound center of the Queen Astrid military hospital in Brussels, 48 patients were colonized or infected with Acb complex over a 52-month period. We report the molecular epidemiology of these organisms, their clinical impact and infection control measures taken. A representative set of 157 Acb complex isolates was analyzed using repetitive sequence-based PCR (rep-PCR) (DiversiLab) and a multiplex PCR targeting OXA-51-like and OXA-23-like genes. We identified 31 rep-PCR genotypes (strains). Representatives of each rep-type were identified to species by rpoB sequence analysis: 13 types to A. baumannii, 10 to A. pittii, and 3 to A. nosocomialis. It was assumed that isolates that belonged to the same rep-type also belonged to the same species. Thus, 83.4% of all isolates were identified to A. baumannii, 9.6% to A. pittii and 4.5% to A. nosocomialis. We observed 12 extensively drug resistant Acb strains (10 A. baumannii and 2 A. nosocomialis), all carbapenem-non-susceptible/colistin-susceptible and imported into the burn wound center through patients injured in North Africa. The two most prevalent rep-types 12 and 13 harbored an OXA-23-like gene. Multilocus sequence typing allocated them to clonal complex 1 corresponding to EU (international) clone I. Both strains caused consecutive outbreaks, interspersed with periods of apparent eradication. Patients infected with carbapenem resistant A. baumannii were successfully treated with colistin/rifampicin. Extensive infection control measures were required to eradicate the organisms. Acinetobacter infection and colonization was not associated with increased attributable mortality. PMID:27223476

  4. Molecular, ethno-spatial epidemiology of leprosy in China: novel insights for tracing leprosy in endemic and non endemic provinces.

    Science.gov (United States)

    Weng, Xiaoman; Xing, Yan; Liu, Jian; Wang, Yonghong; Ning, Yong; Li, Ming; Wu, Wenbin; Zhang, Lianhua; Li, Wei; Vander Heiden, Jason; Vissa, Varalakshmi

    2013-03-01

    Leprosy continues to be detected at near stable rates in China even with established control programs, necessitating new knowledge and alternative methods to interrupt transmission. A molecular epidemiology investigation of 190 patients was undertaken to define Mycobacterium leprae strain types and discern genetic relationships and clusters in endemic and non-endemic regions spanning seventeen provinces and two autonomous regions. The findings support multiple locus variable number of tandem repeat (VNTR) analysis as a useful tool in uncovering characteristic patterns across the multiethnic and divergent geographic landscape of China. Several scenarios of clustering of leprosy from township to provincial to regional levels were recognized, while recent occupational or remote migration showed geographical separation of certain strains. First, prior studies indicated that of the four major M. leprae subtypes defined by single nucleotide polymorphisms (SNPs), only type 3 was present in China, purportedly entering from Europe/West/Central Asia via the Silk Road. However, this study revealed VNTR linked strains that are of type 1 in Guangdong, Fujian and Guangxi in southern China. Second, a subset of VNTR distinguishable strains of type 3, co-exist in these provinces. Third, type 3 strains with rpoT VNTR allele of 4, detected in Japan and Korea were discovered in Jiangsu and Anhui in the east and in western Sichuan bordering Tibet. Fourth, considering the overall genetic diversity, strains of endemic counties of Qiubei, Yunnan; Xing Yi, Guizhou; and across Sichuan in southwest were related. However, closer inspection showed distinct local strains and clusters. Altogether, these insights, primarily derived from VNTR typing, reveal multiple and overlooked paths for spread of leprosy into, within and out of China and invoke attention to historic maritime routes in the South and East China Sea. More importantly, new concepts and approaches for prospective case finding and

  5. Are glutathione S transferases involved in DNA damage signalling? Interactions with DNA damage and repair revealed from molecular epidemiology studies

    Energy Technology Data Exchange (ETDEWEB)

    Dusinska, Maria, E-mail: Maria.DUSINSKA@nilu.no [CEE-Health Effects Group, NILU - Norwegian Institute for Air Research, Kjeller (Norway); Staruchova, Marta; Horska, Alexandra [Department of Experimental and Applied Genetics, Slovak Medical University, Bratislava (Slovakia); Smolkova, Bozena [Laboratory of Cancer Genetics, Cancer Research Institute of the Slovak Academy of Sciences, Bratislava (Slovakia); Collins, Andrew [Department of Nutrition, Faculty of Medicine, University of Oslo (Norway); Bonassi, Stefano [Unit of Clinical and Molecular Epidemiology, IRCCS San Raffaele Pisana, Rome (Italy); Volkovova, Katarina [Department of Experimental and Applied Genetics, Slovak Medical University, Bratislava (Slovakia)

    2012-08-01

    Glutathione S-transferases (GSTs) are members of a multigene family of isoenzymes that are important in the control of oxidative stress and in phase II metabolism. Acting non-enzymically, GSTs can modulate signalling pathways of cell proliferation, cell differentiation and apoptosis. Using a molecular epidemiology approach, we have investigated a potential involvement of GSTs in DNA damage processing, specifically the modulation of DNA repair in a group of 388 healthy adult volunteers; 239 with at least 5 years of occupational exposure to asbestos, stone wool or glass fibre, and 149 reference subjects. We measured DNA damage in lymphocytes using the comet assay (alkaline single cell gel electrophoresis): strand breaks (SBs) and alkali-labile sites, oxidised pyrimidines with endonuclease III, and oxidised purines with formamidopyrimidine DNA glycosylase. We also measured GST activity in erythrocytes, and the capacity for base excision repair (BER) in a lymphocyte extract. Polymorphisms in genes encoding three GST isoenzymes were determined, namely deletion of GSTM1 and GSTT1 and single nucleotide polymorphism Ile105Val in GSTP1. Consumption of vegetables and wine correlated negatively with DNA damage and modulated BER. GST activity correlated with oxidised bases and with BER capacity, and differed depending on polymorphisms in GSTP1, GSTT1 and GSTM1. A significantly lower BER rate was associated with the homozygous GSTT1 deletion in all asbestos site subjects and in the corresponding reference group. Multifactorial analysis revealed effects of sex and exposure in GSTP1 Ile/Val heterozygotes but not in Ile/Ile homozygotes. These variants affected also SBs levels, mainly by interactions of GSTP1 genotype with exposure, with sex, and with smoking habit; and by an interaction between sex and smoking. Our results show that GST polymorphisms and GST activity can apparently influence DNA stability and repair of oxidised bases, suggesting a potential new role for these

  6. Antimicrobial Resistance and Molecular Epidemiology of Escherichia coli Causing Bloodstream Infections in Three Hospitals in Shanghai, China.

    Directory of Open Access Journals (Sweden)

    Su Wang

    Full Text Available Escherichia coli (E. coli is one of the most frequent and lethal causes of bloodstream infections (BSIs. We carried out a retrospective multicenter study on antimicrobial resistance and phylogenetic background of clinical E. coli isolates recovered from bloodstream in three hospitals in Shanghai. E. coli isolates causing BSIs were consecutively collected between Sept 2013 and Sept 2014. Ninety isolates randomly selected (30 from each hospital were enrolled in the study. Antimicrobial susceptibility testing was performed by disk diffusion. PCR was used to detect antimicrobial resistance genes coding for β-lactamases (TEM, CTX-M, OXA, etc., carbapenemases (IMP, VIM, KPC, NDM-1 and OXA-48, and phylogenetic groups. eBURST was applied for analysis of multi-locus sequence typing (MLST. The resistance rates for penicillins, second-generation cephalosporins, fluoroquinolone and tetracyclines were high (>60%. Sixty-one of the 90 (67.8% strains enrolled produced ESBLs and no carbapenemases were found. Molecular analysis showed that CTX-M-15 (25/61, CTX-M-14 (18/61 and CTX-M-55 (9/61 were the most common ESBLs. Phylogenetic group B2 predominated (43.3% and exhibited the highest rates of ESBLs production. ST131 (20/90 was the most common sequence type and almost assigned to phylogenetic group B2 (19/20. The following sequence types were ST405 (8/90 and ST69 (5/90. Among 61 ESBL-producers isolates, B2 (26, 42.6% and ST131 (18, 29.5% were also the most common phylogenetic group and sequence type. Genetic diversity showed no evidence suggesting a spread of these antimicrobial resistant isolates in the three hospitals. In order to provide more comprehensive and reliable epidemiological information for preventing further dissemination, well-designed and continuous surveillance with more hospitals participating was important.

  7. Antimicrobial Resistance and Molecular Epidemiology of Escherichia coli Causing Bloodstream Infections in Three Hospitals in Shanghai, China.

    Science.gov (United States)

    Wang, Su; Zhao, Sheng-Yuan; Xiao, Shu-Zhen; Gu, Fei-Fei; Liu, Qing-Zhong; Tang, Jin; Guo, Xiao-Kui; Ni, Yu-Xing; Han, Li-Zhong

    2016-01-01

    Escherichia coli (E. coli) is one of the most frequent and lethal causes of bloodstream infections (BSIs). We carried out a retrospective multicenter study on antimicrobial resistance and phylogenetic background of clinical E. coli isolates recovered from bloodstream in three hospitals in Shanghai. E. coli isolates causing BSIs were consecutively collected between Sept 2013 and Sept 2014. Ninety isolates randomly selected (30 from each hospital) were enrolled in the study. Antimicrobial susceptibility testing was performed by disk diffusion. PCR was used to detect antimicrobial resistance genes coding for β-lactamases (TEM, CTX-M, OXA, etc.), carbapenemases (IMP, VIM, KPC, NDM-1 and OXA-48), and phylogenetic groups. eBURST was applied for analysis of multi-locus sequence typing (MLST). The resistance rates for penicillins, second-generation cephalosporins, fluoroquinolone and tetracyclines were high (>60%). Sixty-one of the 90 (67.8%) strains enrolled produced ESBLs and no carbapenemases were found. Molecular analysis showed that CTX-M-15 (25/61), CTX-M-14 (18/61) and CTX-M-55 (9/61) were the most common ESBLs. Phylogenetic group B2 predominated (43.3%) and exhibited the highest rates of ESBLs production. ST131 (20/90) was the most common sequence type and almost assigned to phylogenetic group B2 (19/20). The following sequence types were ST405 (8/90) and ST69 (5/90). Among 61 ESBL-producers isolates, B2 (26, 42.6%) and ST131 (18, 29.5%) were also the most common phylogenetic group and sequence type. Genetic diversity showed no evidence suggesting a spread of these antimicrobial resistant isolates in the three hospitals. In order to provide more comprehensive and reliable epidemiological information for preventing further dissemination, well-designed and continuous surveillance with more hospitals participating was important.

  8. New insights into the molecular epidemiology of Trichinella infection in domestic pigs, wild boars, and bears in Romania.

    Science.gov (United States)

    Nicorescu, Isabela Madalina Dragoi; Ionita, Mariana; Ciupescu, Laurentiu; Buzatu, Cristian Vasile; Tanasuica, Rodica; Mitrea, Ioan Liviu

    2015-09-15

    Trichinellosis is a food-borne zoonosis caused by the parasitic nematode Trichinella, characterized by an extremely wide host range and geographical distribution. In Romania, it is recognized as one of the most serious zoonotic diseases. A cross-sectional study, covering all regions of Romania, was conducted in 2014 to investigate and update the prevalence of Trichinella infection among domestic pigs, wild boars, and bears. Additional, molecular identification of Trichinella species circulating among these animals was performed in order to establish the biogeography of Trichinella species within the seven geographical regions of Romania. For this, a total of 113,383 pigs raised in non-controlled housing conditions (backyards), 5596 hunted wild boars and 147 hunted bears were subjected to Trichinella analysis. The highest prevalence of Trichinella infections was found in bears (12.93%), followed by wild boars (1.66%) and domestic pigs (0.20%). Of 294 Trichinella isolates that tested positive by multiplex PCR, 219 (74.49%) were identified as Trichinella spiralis, 66 (22.45%) as Trichinella britovi, and 9 isolates (3.06%) as mixed infections of T. spiralis and T. britovi. T. spiralis was more prevalent in domestic pigs (165/228; 72.37%) than in game (63/228; 27.63%), while T. britovi showed a higher prevalence in game (50/75; 66.66%) than in domestic pigs (25/75; 33.33%). Moreover, the present study revealed a significant host- and area- related distribution of Trichinella species within the seven regions of Romania. Therefore, these findings are of epidemiological relevance, updating data on the prevalence and distribution of Trichinella species circulating among domestic and wild animals in South-Eastern Europe. PMID:26238657

  9. Molecular Epidemiology of Oxacillin-resistant Staphylococcus aureus and in vitro Activity of Glycopeptides against Staphylococcus species

    Institute of Scientific and Technical Information of China (English)

    王辉; 孙宏莉; 陈民钧

    2004-01-01

    The purpose of this subject was to investigate molecular epidemiology of oxacillin-resistant Staphylococcus aureus (MRSA) isolated from hospitalized patients, and to survey the in vitro activity of teicoplanin, vancomycin and other 9 antibiotics against Staphylococcus species. MRSA were detected by oxacillin-NaCl-containing screen agar. The homology of nosocomial MRSA from ICU and RCU was determined by pulse-field gel electrophoresis. Agar diffusion, E test and agar dilution were used to compare the in vitro activity of teicoplanin and vancomycin against Staphylococcus spp from 2001 to 2003 at Peking Union Medical College Hospital. WHONET-5.3 software was used to analyze the antimicrobial susceptibility data. From 2001 to 2003, the prevalences of MRSA were 56.5%, 65.3%, 64.7%, respectively. PFGE found most of MRSA from ICU and RCU were closely related. All of S. aureus and S. epidimidis isolates were susceptible to teicoplanin and vancomycin from 2001 to 2003. However, 1 isolate of S. haemolyticus was resistant and 9 isolates intermediate to teicoplanin. The minimal inhibitory concentration of teicoplanin did not correlate well with zone diameter, when inoculum increased by 100 folds, the zone diameters of teicoplanin decreased more greatly than those of vancomycin. In 2002, severe outbreaks caused by MRSA strains had been found in ICU and RCU wards. Teicoplanin and vancomycin had good activity against clinical isolates of Staphylococci spp. Teicoplanin was less active than vancomycin against S. haemolyticus. Most of S. haemolyticus isolates were intermediate to teicoplanin. Antimicrobial susceptibility testing of teicoplanin was influenced by the diffusion speed in the agar and inoculum size.

  10. Changing epidemiology of methicillin-resistant Staphylococcus aureus in Iceland from 2000 to 2008: a challenge to current guidelines

    DEFF Research Database (Denmark)

    Holzknecht, B.J.; Hardardottir, H.; Haraldsson, Gustav Helgi;

    2010-01-01

    The epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) is continuously changing. Iceland has a low incidence of MRSA. A "search and destroy" policy (screening patients with defined risk factors and attempting eradication in carriers) has been implemented since 1991. Clinical......, and screening for the Panton-Valentine leukocidin (PVL) gene. Two hundred twenty-six infected (60%) or colonized (40%) individuals were detected (annual incidence 2.5 to 16/100,000). From 2000 to 2003, two health care-associated outbreaks dominated (spa types t037 and t2802), which were successfully controlled...

  11. Review Article: The Role of Molecular Pathological Epidemiology in the Study of Neoplastic and Non-neoplastic Diseases in the Era of Precision Medicine.

    Science.gov (United States)

    Ogino, Shuji; Nishihara, Reiko; VanderWeele, Tyler J; Wang, Molin; Nishi, Akihiro; Lochhead, Paul; Qian, Zhi Rong; Zhang, Xuehong; Wu, Kana; Nan, Hongmei; Yoshida, Kazuki; Milner, Danny A; Chan, Andrew T; Field, Alison E; Camargo, Carlos A; Williams, Michelle A; Giovannucci, Edward L

    2016-07-01

    Molecular pathology diagnostics to subclassify diseases based on pathogenesis are increasingly common in clinical translational medicine. Molecular pathological epidemiology (MPE) is an integrative transdisciplinary science based on the unique disease principle and the disease continuum theory. While it has been most commonly applied to research on breast, lung, and colorectal cancers, MPE can investigate etiologic heterogeneity in non-neoplastic diseases, such as cardiovascular diseases, obesity, diabetes mellitus, drug toxicity, and immunity-related and infectious diseases. This science can enhance causal inference by linking putative etiologic factors to specific molecular biomarkers as outcomes. Technological advances increasingly enable analyses of various -omics, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, metagenomics, microbiome, immunomics, interactomics, etc. Challenges in MPE include sample size limitations (depending on availability of biospecimens or biomedical/radiological imaging), need for rigorous validation of molecular assays and study findings, and paucities of interdisciplinary experts, education programs, international forums, and standardized guidelines. To address these challenges, there are ongoing efforts such as multidisciplinary consortium pooling projects, the International Molecular Pathological Epidemiology Meeting Series, and the Strengthening the Reporting of Observational Studies in Epidemiology-MPE guideline project. Efforts should be made to build biorepository and biobank networks, and worldwide population-based MPE databases. These activities match with the purposes of the Big Data to Knowledge (BD2K), Genetic Associations and Mechanisms in Oncology (GAME-ON), and Precision Medicine Initiatives of the United States National Institute of Health. Given advances in biotechnology, bioinformatics, and computational/systems biology, there are wide open opportunities in MPE to contribute to public

  12. Molecular epidemiology of HIV-1 subtypes in India: origin and evolutionary history of the predominant subtype C.

    Directory of Open Access Journals (Sweden)

    Ujjwal Neogi

    Full Text Available BACKGROUND: India has the third largest HIV-1 epidemic with 2.4 million infected individuals. Molecular epidemiological analysis has identified the predominance of HIV-1 subtype C (HIV-1C. However, the previous reports have been limited by sample size, and uneven geographical distribution. The introduction of HIV-1C in India remains uncertain due to this lack of structured studies. To fill the gap, we characterised the distribution pattern of HIV-1 subtypes in India based on data collection from nationwide clinical cohorts between 2007 and 2011. We also reconstructed the time to the most recent common ancestor (tMRCA of the predominant HIV-1C strains. METHODOLOGY/PRINCIPAL FINDINGS: Blood samples were collected from 168 HIV-1 seropositive subjects from 7 different states. HIV-1 subtypes were determined using two or three genes, gag, pol, and env using several methods. Bayesian coalescent-based approach was used to reconstruct the time of introduction and population growth patterns of the Indian HIV-1C. For the first time, a high prevalence (10% of unique recombinant forms (BC and A1C was observed when two or three genes were used instead of one gene (p<0.01; p = 0.02, respectively. The tMRCA of Indian HIV-1C was estimated using the three viral genes, ranged from 1967 (gag to 1974 (env. Pol-gene analysis was considered to provide the most reliable estimate [1971, (95% CI: 1965-1976]. The population growth pattern revealed an initial slow growth phase in the mid-1970s, an exponential phase through the 1980s, and a stationary phase since the early 1990s. CONCLUSIONS/SIGNIFICANCE: The Indian HIV-1C epidemic originated around 40 years ago from a single or few genetically related African lineages, and since then largely evolved independently. The effective population size in the country has been broadly stable since the 1990s. The evolving viral epidemic, as indicated by the increase of recombinant strains, warrants a need for continued molecular

  13. The changing epidemiology of Asian digestive cancers: From etiologies and incidences to preventive strategies.

    Science.gov (United States)

    Wu, Chun-Ying; Lin, Jaw-Town

    2015-12-01

    Digestive cancers are a major health burden in Asia. Due to the presence of similar "infection-inflammation-cancer" pathways in the carcinogenesis process, eradicating infective pathogens or attenuating relevant inflammatory signaling pathways may reduce digestive cancer incidences and improve patient outcomes. The aim of this paper is to review the recent evidence regarding the epidemiology of three major digestive cancers in Asia: stomach cancer, liver cancer, and colorectal cancer. We focused on the incidence trends, the major etiologies, and especially the potential preventive strategies.

  14. Molecular Epidemiology of Amebiasis

    OpenAIRE

    Ali, Ibne Karim M.; Clark, C. Graham; Petri, William A.

    2008-01-01

    Entamoeba histolytica, the causative agent of human amebiasis, remains a significant cause of morbidity and mortality in developing countries and is responsible for up to 100,000 deaths worldwide each year. Entamoeba dispar, morphologically indistinguishable from E. histolytica, is more common in humans in many parts of the world. Similarly Entamoeba moshkovskii, which was long considered to be a free-living ameba, is also morphologically identical to E. histolytica and E. dispar, and is high...

  15. Molecular epidemiology of ascariasis

    DEFF Research Database (Denmark)

    Betson, Martha; Nejsum, Peter; Bendall, Richard P.;

    2014-01-01

    BACKGROUND: The roundworm Ascaris lumbricoides infects 0.8 billion people worldwide, and Ascaris suum infects innumerable pigs across the globe. The extent of natural cross-transmission of Ascaris between pig and human hosts in different geographical settings is unknown, warranting investigation....... METHODS: Adult Ascaris organisms were obtained from humans and pigs in Europe, Africa, Asia, and Latin America. Barcodes were assigned to 536 parasites on the basis of sequence analysis of the mitochondrial cytochrome c oxidase I gene. Genotyping of 410 worms was also conducted using a panel...... of microsatellite markers. Phylogenetic, population genetic, and Bayesian assignment methods were used for analysis. RESULTS: There was marked genetic segregation between worms originating from human hosts and those originating from pig hosts. However, human Ascaris infections in Europe were of pig origin...

  16. Molecular epidemiology of ascariasis

    DEFF Research Database (Denmark)

    Betson, Martha; Halstead, Fennella; Nejsum, Peter;

    , Guatemala and the Philippines. Genomic DNA was extracted from each worm and a 450 base pair fragment of the mitochondrial cytochrome oxidase gene subunit 1 (COI) was PCR amplified. The products were sequenced from both strands and sequences were manually edited. Fifty different Ascaris CO1 haplotypes were...

  17. Sex Change in Clownfish: Molecular Insights from Transcriptome Analysis

    KAUST Repository

    Casas, Laura

    2016-10-17

    Sequential hermaphroditism is a unique reproductive strategy among teleosts that is displayed mainly in fish species living in the coral reef environment. The reproductive biology of hermaphrodites has long been intriguing; however, very little is known about the molecular pathways underlying their sex change. Here, we provide the first de novo transcriptome analyses of a hermaphrodite teleost´s undergoing sex change in its natural environment. Our study has examined relative gene expression across multiple groups—rather than just two contrasting conditions— and has allowed us to explore the differential expression patterns throughout the whole process. Our analysis has highlighted the rapid and complex genomic response of the brain associated with sex change, which is subsequently transmitted to the gonads, identifying a large number of candidate genes, some well-known and some novel, involved in the process. The present study provides strong evidence of the importance of the sex steroidogenic machinery during sex change in clownfish, with the aromatase gene playing a central role, both in the brain and the gonad. This work constitutes the first genome-wide study in a social sex-changing species and provides insights into the genetic mechanism governing social sex change and gonadal restructuring in protandrous hermaphrodites.

  18. Sex Change in Clownfish: Molecular Insights from Transcriptome Analysis

    Science.gov (United States)

    Casas, Laura; Saborido-Rey, Fran; Ryu, Taewoo; Michell, Craig; Ravasi, Timothy; Irigoien, Xabier

    2016-01-01

    Sequential hermaphroditism is a unique reproductive strategy among teleosts that is displayed mainly in fish species living in the coral reef environment. The reproductive biology of hermaphrodites has long been intriguing; however, very little is known about the molecular pathways underlying their sex change. Here, we provide the first de novo transcriptome analyses of a hermaphrodite teleost´s undergoing sex change in its natural environment. Our study has examined relative gene expression across multiple groups—rather than just two contrasting conditions— and has allowed us to explore the differential expression patterns throughout the whole process. Our analysis has highlighted the rapid and complex genomic response of the brain associated with sex change, which is subsequently transmitted to the gonads, identifying a large number of candidate genes, some well-known and some novel, involved in the process. The present study provides strong evidence of the importance of the sex steroidogenic machinery during sex change in clownfish, with the aromatase gene playing a central role, both in the brain and the gonad. This work constitutes the first genome-wide study in a social sex-changing species and provides insights into the genetic mechanism governing social sex change and gonadal restructuring in protandrous hermaphrodites. PMID:27748421

  19. [Reactive changes in psychological condition and behaviour in children of parents with cancer--results of an epidemiological survey].

    Science.gov (United States)

    Bergelt, Corinna; Ernst, Johanna Christine; Beierlein, Volker; Inhestern, Laura; Holes, Sarah; Möller, Birgit; Romer, Georg; Koch, Uwe

    2012-01-01

    Children of cancer patients are at risk for developing psychological symptoms. The parental appraisal of the child's psychological condition is a key variable for the utilization of child-centred psychosocial services. This study aimed at the systematic analysis of parental appraisals of changes in the emotional condition or behaviour of their children. We conducted an epidemiologic survey with a sample size of 1,809 patients with different cancer diagnoses, giving information about 2,581 children aged 21 years or younger at time of diagnosis. Quantitative information on children's distress during the disease and on changes in psychological condition or behaviour and qualitative information on the kind of changes were analysed. About half of the children were considered to be psychologically strongly affected during the disease. For about 25 % negative changes in psychological condition or behaviour are reported, positive changes are reported for 20 % of the children. Negative changes are most frequently described in young children (up to five years), positive changes are most frequently described in young adults (18 to 21 years). The results indicate that from the cancer parent's view many children are substantially distressed. Thus, the implementation of additional preventive psychosocial services seems reasonable and necessary. PMID:22950334

  20. Impairment of Colour Vision in Diabetes with No Retinopathy: Sankara Nethralaya Diabetic Retinopathy Epidemiology and Molecular Genetics Study (SNDREAMS- II, Report 3.

    Directory of Open Access Journals (Sweden)

    Laxmi Gella

    Full Text Available To assess impairment of colour vision in type 2 diabetics with no diabetic retinopathy and elucidate associated risk factors in a population-based cross-sectional study.This is part of Sankara Nethralaya Diabetic Retinopathy Epidemiology and Molecular-genetics Study (SN-DREAMS II which was conducted between 2007-2010. FM 100 hue-test was performed in 253 subjects with no clinical evidence of diabetic retinopathy. All subjects underwent detailed ophthalmic evaluation including cataract grading using LOCS III and 45° 4-field stereoscopic fundus photography. Various ocular and systemic risk factors for impairment of colour vision (ICV were assessed in subjects with diabetes but no retinopathy. P value of < 0.05 was considered statistically significant.The mean age of the study sample was 57.08 ± 9.21 (range: 44-86 years. Gender adjusted prevalence of ICV among subjects with diabetes with no retinopathy was 39.5% (CI: 33.5-45.5. The mean total error score in the study sample was 197.77 ± 100 (range: 19-583. The risk factors for ICV in the study were women OR: 1.79 (1.00-3.18, increased resting heart rate OR: 1.04 (1.01-1.07 and increased intraocular pressure OR: 1.12 (1.00-1.24. Significant protective factor was serum high-density lipoprotein OR: 0.96 (0.93-0.99.Acquired ICV is an early indicator of neurodegenerative changes in the retina. ICV found in diabetic subjects without retinopathy may be of non-vascular etiology.

  1. The Changing Epidemiology of Bloodstream Infections and Resistance in Hematopoietic Stem Cell Transplantation Recipients

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    Mücahit Yemişen

    2016-08-01

    Full Text Available Objective: Patients receiving hematopoietic stem cell transplantation (HSCT are exposed to highly immunosuppressive conditions and bloodstream infections (BSIs are one of the most common major complications within this period. Our aim, in this study, was to evaluate the epidemiology of BSIs in these patients retrospectively. Materials and Methods: The epidemiological properties of 312 patients with HSCT were retrospectively evaluated. Results: A total of 312 patients, followed between 2000 and 2011, who underwent autologous (62% and allogeneic (38% HSCT were included in the study. The most common underlying malignancies were multiple myeloma (28% and Hodgkin lymphoma (21.5%. A total of 142 (45% patients developed at least 1 episode of BSI and 193 separate pathogens were isolated from the blood cultures. There was a trend of increase in the numbers of BSIs in 2005-2008 and a relative increase in the proportion of gram-positive infections in recent years (2009-2011, and central venous catheter-related BSI was found to be most common source. Coagulase-negative staphylococci (49.2% and Acinetobacter baumannii (8.8% were the most common pathogens. Extended-spectrum beta-lactamase-producing strains were 23% and 22% among Escherichia coli and Klebsiella spp. isolates, respectively. Quinolone resistance was detected in 10% of Enterobacteriaceae. Resistance to carbapenems was not detected in Enterobacteriaceae, while it was seen at 11.1% and 23.5% in Pseudomonas and Acinetobacter strains, respectively. Conclusion: A shift was detected from gram-negative bacteria to gram-positive in the etiology over the years and central lines were the most common sources of BSIs.

  2. A Multi-Site Study of Norovirus Molecular Epidemiology in Australia and New Zealand, 2013-2014

    Science.gov (United States)

    Lim, Kun Lee; Hewitt, Joanne; Sitabkhan, Alefiya; Eden, John-Sebastian; Lun, Jennifer; Levy, Avram; Merif, Juan; Smith, David; Rawlinson, William D.; White, Peter A.

    2016-01-01

    Background Norovirus (NoV) is the major cause of acute gastroenteritis across all age groups. In particular, variants of genogroup II, genotype 4 (GII.4) have been associated with epidemics globally, occurring approximately every three years. The pandemic GII.4 variant, Sydney 2012, was first reported in early 2012 and soon became the predominant circulating NoV strain globally. Despite its broad impact, both clinically and economically, our understanding of the fundamental diversity and mechanisms by which new NoV strains emerge remains limited. In this study, we describe the molecular epidemiological trends of NoV-associated acute gastroenteritis in Australia and New Zealand between January 2013 and June 2014. Methodology Overall, 647 NoV-positive clinical faecal samples from 409 outbreaks and 238 unlinked cases of acute gastroenteritis were examined by RT-PCR and sequencing. Phylogenetic analysis was then performed to identify NoV capsid genotypes and to establish the temporal dominance of circulating pandemic GII.4 variants. Recombinant viruses were also identified based on analysis of the ORF1/2 overlapping region. Findings Peaks in NoV activity were observed, however the timing of these epidemics varied between different regions. Overall, GII.4 NoVs were the dominant cause of both outbreaks and cases of NoV-associated acute gastroenteritis (63.1%, n = 408/647), with Sydney 2012 being the most common GII.4 variant identified (98.8%, n = 403/408). Of the 409 reported NoV outbreaks, aged-care facilities were the most common setting in both Western Australia (87%, n = 20/23) and New Zealand (58.1%, n = 200/344) while most of the NoV outbreaks were reported from hospitals (38%, n = 16/42) in New South Wales, Australia. An analysis of a subset of non-GII.4 viruses from all locations (125/239) showed the majority (56.8%, n = 71/125) were inter-genotype recombinants. These recombinants were surprisingly diverse and could be classified into 18 distinct recombinant

  3. Molecular epidemiology of clinical and carrier strains of methicillin resistant Staphylococcus aureus (MRSA in the hospital settings of north India

    Directory of Open Access Journals (Sweden)

    Dar Mohammad J

    2006-09-01

    Full Text Available Abstract Background The study was conducted between 2000 and 2003 on 750 human subjects, yielding 850 strains of staphylococci from clinical specimens (575, nasal cultures of hospitalized patients (100 and eye & nasal sources of hospital workers (50 & 125 respectively in order to determine their epidemiology, acquisition and dissemination of resistance genes. Methods Organisms from clinical samples were isolated, cultured and identified as per the standard routine procedures. Susceptibility was measured by the agar diffusion method, as recommended by the Nat ional Committee for Clinical Laboratory Standards (NCCLS. The modified method of Birnboin and Takahashi was used for isolation of plasmids from staphylococci. Pulsed-field gel electrophoresis (PFGE typing of clinical and carrier Methicillin resistant Staphylococcus aureus (MRSA strains isolated during our study was performed as described previously. Results It was shown that 35.1% of Staphylococcus aureus and 22.5% of coagulase-negative staphylococcal isolates were resistant to methicillin. Highest percentage of MRSA (35.5% was found in pus specimens (n = 151. The multiple drug resistance of all MRSA (n = 180 and Methicillin resistant Coagulase-negative Staphylococcus aureus (MRCNS (n = 76 isolates was detected. In case of both methicillin-resistant as well as methicillin-sensitive Saphylococcal isolates zero resistance was found to vancomycin where as highest resistance was found to penicillin G followed by ampicillin. It was shown that the major reservoir of methicillin resistant staphylococci in hospitals are colonized/infected inpatients and colonized hospital workers, with carriers at risk for developing endogenous infection or transmitting infection to health care workers and patients. The results were confirmed by molecular typing using PFGE by SmaI-digestion. It was shown that the resistant markers G and T got transferred from clinical S. aureus (JS-105 to carrier S. aureus (JN-49

  4. Molecular Epidemiology of HIV-1 Infection among Men who Have Sex with Men in Taiwan in 2012.

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    Szu-Wei Huang

    Full Text Available The number of men who have sex with men (MSM infected with HIV-1 in Taiwan has increased rapidly in the past few years. The goal of this study was to conduct a molecular epidemiological study of HIV-1 infection among MSM in Taiwan to identify risk factors for intervention. Voluntary counseling program and anonymous testing were provided to patrons at 1 gay bar, 7 night clubs and 3 gay saunas in Taipei and New Taipei Cities in 2012. HIV-1 subtypes were determined using gag subtype-specific PCR and phylogenetic analysis by env sequences. Recent HIV-1 infection was determined using LAg-Avidity EIA. In-depth interviews and questionnaires were used to identify risk factors. The prevalence and incidence of HIV-1 among MSM in Taiwan were 4.38% (53/1,208 and 3.29 per 100 person-years, respectively. Of 49 cases genotyped, 48 (97.9% were infected with subtype B and 1 with CRF01_AE (2%. Phylogenetic analysis of 46 HIV-1 strains showed that 25 (54.4% subtype B strains formed 9 clusters with each other or with other local strains. The CRF01_AE case clustered with a reference strain from a Thai blood donor with bootstrap value of 99. Multivariate logistic regression analysis showed that risk factors associated with HIV-1 infection included use of oil-based solution as lubricant (vs. saliva or water-based lubricants, OR= 4.23; p <0.001; exclusively receptive role (vs. insertive role, OR= 9.69; p <0.001; versatile role (vs. insertive role, OR= 6.45; p= 0.003; oral sex (vs. insertive role, OR= 11.93; p= 0.044; times of sexual contact per week (2-3 vs. zero per week, OR= 3.41; p= 0.021; illegal drug use (OR= 4.12; p <0.001; and history of sexually transmitted diseases (OR= 3.65; p= 0.002. In conclusion, there was no new HIV-1 subtype or circulating recombinant form responsible for the increase of HIV-1 among MSM in Taiwan in 2012. Misuse of oil-based solution as lubricant is a new risk factor identified among MSM in Taiwan. The Taiwan's Centers for Disease

  5. Molecular epidemiology of invasive Candida albicans at a tertiary hospital in northern Taiwan from 2003 to 2011.

    Science.gov (United States)

    Wang, Shao-Hung; Shen, Mandy; Lin, Hsin-Chieh; Sun, Pei-Lun; Lo, Hsiu-Jung; Lu, Jang-Jih

    2015-11-01

    Candida albicans is a common cause of bloodstream fungal infections in hospitalized patients. To investigate its epidemiology, multilocus sequence typing (MLST) was performed on 285 C. albicans bloodstream isolates from patients in Chang Gung Memorial Hospital at Linkou (CGMHL), Taiwan from 2003 to 2011. Among these isolates, the three major diploid sequence types (DSTs) were 693, 659, and 443 with 19, 16, and 13 isolates, respectively. The 179 DSTs were classified into 16 clades by unweighted pair-group method using arithmetic averages (UPGMA). The major ones were clades 1, 4, 3, and 17 (54, 49, 31, and 31 isolates, respectively). Further analyses with eBURST clustered the 285 isolates into 28 clonal complexes (CC). The most common complexes were CC8, CC20, and CC9. DST 693 that had the highest number of isolates was determined to be the cluster founder of CC20, which belonged to clade 3. So far, 33 isolates worldwide including 29 from Taiwan and 4 from Korea, are CC20, suggesting that CC20 is an Asian cluster. Two fluconazole-resistant isolates belonging to CC12 and CC19 were detected. All other CGMHL isolates were susceptible to 5-flucytosine, amphotericin B, anidulfungin, caspofungin, fluconazole, itraconazole, micafungin, posaconazole, and voriconazole. However, CC20 isolates exhibited significantly lower susceptibility to fluconazole. In conclusion, the 285 CGMHL C. albicans isolates displayed geographically clustering with Asian isolates, and most of them are susceptible to common antifungal drugs. Isolates of DST 693, a Taiwanese major genotype belonging to MLST clade 3, were more resistant to fluconazole than other isolates.

  6. Molecular changes of DOM cycling in forest ecosystem

    Science.gov (United States)

    Hara, M.; Ohashi, M.; Piirainen, S.; Kortelainen, P.; Finer, L.; Kumagai, T.; Takahashi, K.; Sugiyama, Y.

    2011-12-01

    Fresh water is essential for sustaining all the life on the earth. Most of the fresh water available for human is stored in forest ecosystem in the forms of soil and ground water. Therefore, the chemical compositions of fresh water could be controlled by the forest ecosystem. Dissolved Organic Matter (DOM) is one of the main dissolved components of water. Since it controls the cycling processes of both organic and inorganic matters in water by variety of physical, chemical, and biochemical interactions, chatacterization of DOM in both qualitatively and quantitatively is very important. However, molecular-level study in DOM has been behind due to technological difficulties. Over the past years, high resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) which enables us to identify individual molecular species of DOM had been hugely developed and brought radical changes to the analysis of many different substances in molecular level. The purpose of this study is to observe the cycling and alteration process of DOM in the forest ecosystem substantially using FT-ICR MS. We analyzed DOM samples by FT-ICR MS to determine the molecular-level characteristics of DOM. We also analyzed dissolved organic carbon (DOC) and characteristics of fluorescence spectra to elucidate the bulk characteristics of DOM in the forest ecosystem. In forest ecosystem, DOC increased from bulk deposition (1.0~3.3 mgC/L) and throughfall (0.8~3.6 mgC/L) to soil water of the A- (4.7~28.6 mgC/L) and B-horizon (4.5~29.2 mgC/L). DOC decreased as the water percolated through the soil deeper to ground water (0.3~1.7 mgC/L). In the whole forest ecosystem, fluorescence spectra showed strong humic-like fluorescence peaks rather than protein-like peaks. Each sample's result of FT-ICR MS including bulk deposition, throughfall, soil waters in different depths, and groundwater showed different molecular characteristics between one another. These results suggest that DOM in water is

  7. Subtype-independent near full-length HIV-1 genome sequencing and assembly to be used in large molecular epidemiological studies and clinical management

    Directory of Open Access Journals (Sweden)

    Sebastian Grossmann

    2015-06-01

    Full Text Available Introduction: HIV-1 near full-length genome (HIV-NFLG sequencing from plasma is an attractive multidimensional tool to apply in large-scale population-based molecular epidemiological studies. It also enables genotypic resistance testing (GRT for all drug target sites allowing effective intervention strategies for control and prevention in high-risk population groups. Thus, the main objective of this study was to develop a simplified subtype-independent, cost- and labour-efficient HIV-NFLG protocol that can be used in clinical management as well as in molecular epidemiological studies. Methods: Plasma samples (n=30 were obtained from HIV-1B (n=10, HIV-1C (n=10, CRF01_AE (n=5 and CRF01_AG (n=5 infected individuals with minimum viral load >1120 copies/ml. The amplification was performed with two large amplicons of 5.5 kb and 3.7 kb, sequenced with 17 primers to obtain HIV-NFLG. GRT was validated against ViroSeqTM HIV-1 Genotyping System. Results: After excluding four plasma samples with low-quality RNA, a total of 26 samples were attempted. Among them, NFLG was obtained from 24 (92% samples with the lowest viral load being 3000 copies/ml. High (>99% concordance was observed between HIV-NFLG and ViroSeqTM when determining the drug resistance mutations (DRMs. The N384I connection mutation was additionally detected by NFLG in two samples. Conclusions: Our high efficiency subtype-independent HIV-NFLG is a simple and promising approach to be used in large-scale molecular epidemiological studies. It will facilitate the understanding of the HIV-1 pandemic population dynamics and outline effective intervention strategies. Furthermore, it can potentially be applicable in clinical management of drug resistance by evaluating DRMs against all available antiretrovirals in a single assay.

  8. 乙型肝炎分子流行病学研究进展%Study advance in molecular epidemiology of hepatitis B virus

    Institute of Scientific and Technical Information of China (English)

    纪惠玲; 郭燕; 郑能雄

    2008-01-01

    Molecular epidemiology of hepatitis B is the epidemiological study of hepatitis B in molecular biological approach. It can clarify the pathogen, progression and mechanism of hepatitis B virus infection. Molecular epidemiology of hepatitis B is vital important for the early diagnosis, infection assesement, illness prediction, observing antiviral therapies, monitoring disease progression and understanding the natural infectious history of hepatitis B. This review focuses on some hot topics on molecular epidemiology of hepatitis Bin recent years , such as viral detection, genotyping, phylogenetic analysis, gene variation and gene polymorphism, aimed at introducing the present studies briefly. Although the researches on this aspect are increasing quickly , many are in groping status. There are still challenges ahead on the mechanism of viral infection, elimination and so on.%乙肝的分子流行病学是运用先进的分子生物学技术研究乙肝流行病学的诸多问题,能够进一步从分子水平阐明乙型肝炎病毒感染的病因、致病过程及发病机制,对于疾病早期诊断、传染性的评估、病情的预测、抗病毒药物疗效的观察、疾病发展进程的监测和乙肝感染自然史的研究等方面均有重要的指导意义.针对近几年乙肝分子流行病学研究的几个热点即乙型肝炎病毒的检测、基因分型、基因系统进化分析、基因变异、基因多态性的研究进展作一回顾.虽然近年来该领域的研究迅速增多,但多数仍处于探索阶段,乙肝病毒感染、清除等诸多机制的研究仍任重而道远.

  9. Molecular epidemiological study of Arctic rabies virus isolates from Greenland and comparison with isolates from throughout the Arctic and Baltic regions

    DEFF Research Database (Denmark)

    Mansfield, K.L.; Racloz, V.; McElhinney, L.M.;

    2006-01-01

    We report a Molecular epidemiological study of rabies in Arctic Countries by comparing a panel of novel Greenland isolates to a larger cohort of viral sequences from both Arctic and Baltic regions. Rabies Virus isolates originating from wildlife (Arctic/red foxes, raccoon-dogs and reindeer), from...... domestic animals (dogs/cats) and from two human cases were investigated. The resulting 400 bp N-gene sequences were compared with isolates representing neighbouring Arctic or Baltic Countries from North America, the former Soviet Union and Europe. Phylogenetic analysis demonstrated similarities between...

  10. The changing epidemiology of pediatric aseptic meningitis in Daejeon, Korea from 1987 to 2003

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    Lee Mi-Hee

    2005-11-01

    Full Text Available Abstract Background Aseptic meningitis is a relatively frequent childhood disease and virologic data suggest that enteroviruses are the commonest etiologic agents. We evaluated the epidemiologic characteristics of aseptic meningitis in Daejeon, South Korea from 1987 to 2003. Methods 2201 medical records of children with aseptic meningitis admitted to The Catholic University of Korea, Daejeon St Mary's Hospital were retrospectively analyzed. Results Outbreaks of aseptic meningitis were observed in 1990, 1993, 1996, 1997, 2001 and 2002. The age distribution of cases was relatively uniform, with a higher incidence in those aged P = 0.001. Neurologic sequelae were observed in 0.7% of the patients. Conclusion Aseptic meningitis, rare before the 1980s in Korea, has since become a common clinical entity. Since 1990, outbreaks of aseptic meningitis have occurred every 1 to 3 years in Daejeon in keeping with Korea-wide epidemics. The frequency of disease affecting children less than one year of age may reflect herd immunity to the epidemic strain.

  11. Molecular changes after shockwave therapy in osteoarthritic knee in rats

    Science.gov (United States)

    Wang, C.-J.; Sun, Y.-C.; Wu, C.-T.; Weng, L.-H.; Wang, F.-S.

    2016-01-01

    This study investigated the molecular changes of DKK-1, MMP13, Wnt-5a and \\upbeta -catenin after extracorporeal shockwave therapy (ESWT) in anterior cruciate ligament transected (ACLT) osteoarthritic (OA) knee in rats. 27 male Spraque-Dawley rats were divided into three groups. Group I was the control one and received sham knee arthrotomy but no ACLT or ESWT. Group II underwent ACLT, but no ESWT. Group III underwent ACLT and received ESWT. The animals were killed at 12 weeks, and the harvested knee specimens were subjected to histopathological examination and immunohistochemical analysis. Radiographs of the knees were obtained at 0 and 12 weeks. At 12 weeks, radiographs of group II showed more arthritic changes with formation of osteochondral fragments, whereas very subtle arthritis was noted in groups I and III. In histopathological examination, group II showed a significant increase of Mankin score and a decrease of subchondral bone as compared to groups I and III. Group III showed a significant decrease of Mankin score and an increase of subchondral bone, with the data comparable to group I. In immunohistochemical analysis, group II showed significant increases of DKK-1 and MMP13 and decreases of Wnt-5a and \\upbeta -catenin in articular cartilage and subchondral bone as compared to groups I and III. Group III showed significant decreases of DKK-1 and MMP13 and increases of Wnt-5a and \\upbeta -catenin, with the data comparable to group I. In conclusion, the application of ESWT causes molecular changes that are consistent with the improvement in subchondral bone remodeling and chondroprotective effect in ACLT OA knees in rats.

  12. Changes of the molecular structure in polyelectrolyte multilayers under stress.

    Science.gov (United States)

    Früh, Johannes; Köhler, Ralf; Möhwald, Helmuth; Krastev, Rumen

    2010-10-01

    Polyelectrolyte multilayers (PEMs) produced by layer-by-layer (LbL) self-assembly find different applications. Often the PEMs are exposed to mechanical stress which they have to sustain. A correlation of the mechanical properties of PEM on macroscopic level with the ordering of polyelectrolyte molecules on molecular level is of interest. Our study is focused on the changes of orientation of the polyelectrolyte molecules when the PEM is under lateral mechanical stress. The PEM was prepared from pyrene (PY) labeled polystyrene sulfonate (PSS-PY) and poly(diallyldimethylammonium) chloride (PDDA) on sheets of polydimethylsiloxane (PDMS) rubber used as substrates. The LbL dipping technique was used for the formation of PEMs. A special stretching device was constructed which allows the fluorescence of the films under stress to be observed. The change in the fluorescence spectra which can be attributed to a PY ordering change from the PEM under stress of up to 10% was monitored. We observed that PEMs undergo a plastic deformation under external mechanical stretching. We conclude that under mechanical stress the polyelectrolyte molecules organized in polyelectrolyte multilayers experience an irreversible transition from the coiled to decoiled state. PMID:20809658

  13. Mutational myriad of tumor suppressor p53 in Filipino breast cancer: results and perspectives in molecular pathology and epidemiology

    International Nuclear Information System (INIS)

    The p53 tumor suppressor is by far the most widely mutated gene in human cancers. p53 encodes a 53-kDa phosphoprotein, transcription-activator whose targets include genes and gene products that orchestrate genomic stability, cellular response to DNA damage, cell cycle progression apoptosis and aging (senescence). Analysis of the p53 gene profile has previously resulted in identifying several cancer-causative factors in the human setting, as well as, in creating a unique molecular profile of a tumor useful in the design of tailored-therapies for individual cancer patients. Our results in screening for p53 abnormalities in 140 Filipino patients with primary breast lesions confined from 1997-1998 in 5 major hospitals in Manila reveal that p53 plays an important role in the development and progression of breast cancer in at least 48% of all cases. Two methods of p53 analysis are employed, enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction-temporal temperature gradient electrophoresis (PCR-TTGE). Inter-comparisons of method exhibit 63.3% concordance in 21 fresh breast carcinoma samples, with ELISA demonstrating 14% false-positives and 10% false-negatives. Only mutations in exon 7 (p=0.063) in the tumor samples how significant correlation with abnormal cellular elevation of p53. PCR-TTGE screening in a large series of 140 patients show that most genetic lesions are localized in exons 5 (41% of the total cases) and 6 (27% of the total cases). No mutations are, however, detected in the transactivation (exons 2-4) and oligomerization (exons 10-11) domains. Invasive carcinomas (stages II and III) are characterized with more frequent and diverse genetic alterations compared with benign tumors, most significantly at exon 5B (p=0.066) and at independently multiple sites (p=0.066). Earlier-onset cases (age of diagnosis < 50 yrs), known to be more clinico-pathologically aggressive, are diagnosed harboring more frequent p53 mutations centered at exon 7 (p=0

  14. Molecular Epidemiology of Invasive Listeriosis due to Listeria monocytogenes in a Spanish Hospital over a Nine-Year Study Period, 2006–2014

    Directory of Open Access Journals (Sweden)

    Jaime Ariza-Miguel

    2015-01-01

    Full Text Available We investigated the pathogenicity, invasiveness, and genetic relatedness of 17 clinical Listeria monocytogenes stains isolated over a period of nine years (2006–2014. All isolates were phenotypically characterised and growth patterns were determined. The antimicrobial susceptibility of L. monocytogenes isolates was determined in E-tests. Invasion assays were performed with epithelial HeLa cells. Finally, L. monocytogenes isolates were subtyped by PFGE and MLST. All isolates had similar phenotypic characteristics (β-haemolysis and lecithinase activity, and three types of growth curve were observed. Bacterial recovery rates after invasion assays ranged from 0.09% to 7.26% (1.62 ± 0.46. MLST identified 11 sequence types (STs, and 14 PFGE profiles were obtained, indicating a high degree of genetic diversity. Genetic studies unequivocally revealed the occurrence of one outbreak of listeriosis in humans that had not previously been reported. This outbreak occurred in October 2009 and affected three patients from neighbouring towns. In conclusion, the molecular epidemiological analysis clearly revealed a cluster (three human cases, all ST1 of not previously reported listeriosis cases in northwestern Spain. Our findings indicate that molecular subtyping, in combination with epidemiological case analysis, is essential and should be implemented in routine diagnosis, to improve the tracing of the sources of outbreaks.

  15. Climate change and epidemiology of human parasitosis in Egypt: A review.

    Science.gov (United States)

    Lotfy, Wael M

    2014-11-01

    Climate change is an emerging global issue. It is expected to have significant impacts both in Egypt and around the world. Thus, the country is in need for taking action to prepare for the unavoidable effects of climate change, including the increase in water stress, the rise in sea level, and the rapidly increasing gap between the limited water availability and the escalating demand for water in the country. Also, weather and climate play a significant role in people's health. Direct impacts of climate change on the Egyptians public health may include also increased prevalence of human parasitic diseases. Climate could strongly influence parasitic diseases transmitted through intermediate hosts. The present work reviews the future of such parasitic diseases in the view of the current available evidence and scenarios for climate change in the Egypt.

  16. Molecular Epidemiology of Uropathogenic Escherichia coli in North West England and Characterisation of the ST131 clone in the Region

    OpenAIRE

    Gibreel, Tarek Mohamed

    2011-01-01

    Multilocus Sequence-Typing (MLST) is a phylogenetic technique based on the detection of differences in multiple conserved housekeeping genes. Together with powerful evaluation software, MLST provides an extensive classification scheme for highly diverse species. However, despite the increasing use of MLST as a trusted epidemiological tool, the population structure of UPEC has been poorly studied using this technique, as most of the previous studies conducted have been limited either by bias t...

  17. Abattoir-based study on the epidemiology of caprine tuberculosis in Ethiopia using conventional and molecular tools

    OpenAIRE

    Deresa, Benti; Conraths, Franz J.; Ameni, Gobena

    2013-01-01

    Background Despite the important role of goats for meat and milk production in Ethiopia, little information is available on the epidemiology of caprine tuberculosis (TB). Caprine TB is important as milk is usually consumed raw particularly by Ethiopian pastoralists. The objectives of the present study were to estimate the prevalence of TB in goats at an abattoir, to evaluate associated risk factors and to characterize the causative mycobacteria. Methods A cross-sectional study was conducted o...

  18. Climate change and epidemiology of human parasitosis in Egypt: A review

    OpenAIRE

    Lotfy, Wael M.

    2014-01-01

    Climate change is an emerging global issue. It is expected to have significant impacts both in Egypt and around the world. Thus, the country is in need for taking action to prepare for the unavoidable effects of climate change, including the increase in water stress, the rise in sea level, and the rapidly increasing gap between the limited water availability and the escalating demand for water in the country. Also, weather and climate play a significant role in people’s health. Direct impacts...

  19. AIDS molecular epidemiological survey in Laibin%来宾市艾滋病分子流行病学调查

    Institute of Scientific and Technical Information of China (English)

    周方; 骆安德; 蒋就喜; 陶田秀; 黄甲清; 胡婷停; 李赫伟

    2011-01-01

    Objective To make the molecular epidemiological survey on the populations affected with HIV-1 to provide experimental basis for prevention and control of AIDS in Laibin. Methods Combined epidemiological methods with molecular biological methods,the AIDS strains in Laibin were sequenced and its subtype was analyzed. Meanwhile,the way of transmission and the relationship between the characteristics of the epidemiological strains and the various strains of AIDS were analyzed. Result The main transmission way of AIDS is through sex in Laibin among the infected populations,with the epidemical strains B,01-AE, and CRF-BC subtypes, in which CRF-BC strain was the major one. Conclusions AIDS epidemic situation becomes critical in Laibin, and the main subtype is epidemiological reconstruction-type CRF-BC in HIV-1 affected populations,so we should strengthen the monitor of the variation of HIV-1 subtype strains,actively conduct behavioral intervention and make new prevention and therapy strategy timely.%目的 对来宾市HIV-1感染者进行分子流行病学调查,为来宾市艾滋病的防治工作提供实验依据.方法 将流行病学方法 与分子生物学方法 相结合,对来宾市HIV株进行序列测定和亚型分析,总结其传播途径,分析流行毒株特点及各个流行毒株间的关系.结果 来宾市HIV感染者以性传播为主,流行毒株存在B、01-AE、CRF-BC 3种亚型,其中以CRF-BC流行毒株为主.结论 来宾市艾滋病流行形势严峻,HIV-1感染者中以流行重组型亚型CRF-BC为主,应加强对HIV-1毒株亚型变异的监测,积极进行行为干预,及时制定新的防治策略.

  20. Continued emergence and changing epidemiology of oseltamivir-resistant influenza A(H1N1)2009 virus, United Kingdom, winter 2010/11.

    Science.gov (United States)

    Lackenby, A; Moran Gilad, J; Pebody, R; Miah, S; Calatayud, L; Bolotin, S; Vipond, I; Muir, P; Guiver, M; McMenamin, J; Reynolds, A; Moore, C; Gunson, R; Thompson, C; Galiano, M; Bermingham, A; Ellis, J; Zambon, M

    2011-01-01

    During the winter period 2010/11 27 epidemiologically unlinked, confirmed cases of oseltamivir-resistant influenza A(H1N1)2009 virus infection have been detected in multiple, geographically dispersed settings. Three of these cases were in community settings, with no known exposure to oseltamivir. This suggests possible onward transmission of resistant strains and could be an indication of a possibility of changing epidemiology of oseltamivir-resistant influenza A(H1N1)2009 virus. PMID:21315056

  1. Molecular epidemiology of Theileria annulata and identification of 18S rRNA gene and ITS regions sequences variants in apparently healthy buffaloes and cattle in Pakistan.

    Science.gov (United States)

    Khan, Muhammad Kasib; He, Lan; Hussain, Altaf; Azam, Sabita; Zhang, Wen-Jie; Wang, Li-Xia; Zhang, Qing-Li; Hu, Min; Zhou, Yan-Qin; Zhao, Junlong

    2013-01-01

    A molecular epidemiological survey was conducted to determine the prevalence of piroplasms in buffaloes and cattle from Sheikhupura and Okara districts of Punjab, Pakistan using reverse line blot (RLB) hybridization assay. The genetic diversity within 18S rRNA gene and ITS regions sequences of various obtained Theileria species (spp.) was also investigated. Briefly, 102 blood samples from buffaloes and cattle in the study districts were collected on blood collection cards and brought to the laboratory. DNA was extracted; the V4 hypervariable region of 18S rRNA was amplified and analyzed using RLB. Out of total samples analyzed, 61 (59.8%) were hybridized with Babesia/Theileria (B/T) genus-specific probe. Only one species of piroplasm was detected in buffaloes and cattle in study districts, i.e. Theileria (T.) annulata. Six samples only hybridized with B/T genus-specific and Theileria genus-specific probes but not with any species-specific probe indicating the presence of novel species or variants. The sequences of 18S rRNA gene and ITS regions of these six samples revealed the presence of T. annulata variants as confirmed through sequence identity estimation and phylogenetic analyses. Meanwhile, an unexpected sequence variation was observed within the 18S rRNA gene and ITS regions sequences of T. annulata identified in the present study. This is the first report on the simultaneous detection of species of piroplasms infecting buffaloes and cattle in Pakistan and molecular characterization of T. annulata 18S rRNA gene and ITS regions. The present study may address the new insights into the epidemiology of theileriosis which will help researches in designing control strategies and developing various molecular diagnostic tools at national level.

  2. Developing Measures of Pathways that May Link Macro Social/Structural Changes with HIV Epidemiology.

    Science.gov (United States)

    Pouget, Enrique R; Sandoval, Milagros; Nikolopoulos, Georgios K; Mateu-Gelabert, Pedro; Rossi, Diana; Smyrnov, Pavlo; Jones, Yolanda; Friedman, Samuel R

    2016-08-01

    Macro-social/structural events ("big events") such as wars, disasters, and large-scale changes in policies can affect HIV transmission by making risk behaviors more or less likely or by changing risk contexts. The purpose of this study was to develop new measures to investigate hypothesized pathways between macro-social changes and HIV transmission. We developed novel scales and indexes focused on topics including norms about sex and drug injecting under different conditions, involvement with social groups, helping others, and experiencing denial of dignity. We collected data from 300 people who inject drugs in New York City during 2012-2013. Most investigational measures showed evidence of validity (Pearson correlations with criterion variables range = 0.12-0.71) and reliability (Cronbach's alpha range = 0.62-0.91). Research is needed in different contexts to evaluate whether these measures can be used to better understand HIV outbreaks and help improve social/structural HIV prevention intervention programs. PMID:26796384

  3. Statistico epidemiological study of changes in the vaginal flora of contraceptive pill users in Alexandria.

    Science.gov (United States)

    Fares, E; El-Ghazzawi, E; Bedwani, R N

    1979-01-01

    A stratified random sample of 1000 women with proportionate allocation according to district of residence was taken from normal females living in Alexandria, Egypt, and attending family planning centers in order to understand social-pathological changes in the vaginal flora of oral contraceptive (OC) users. Cases were examined over 18 months, and all cases were given a combined OC. Bacteriology and pH changes in vaginal flora were determined after 18 months. Results of the bacteriological examination revealed a positive correlation between those having a vaginal discharge and pH above 5, mixed infection, and illiteracy. As the duration of pill use increased, so did the incidence of monilla, staphylococcus aureus, anaerobic streptococci, gram negative bacilli, trichomonas vaginalis, and hemophilus vaginalis, whereas lactobacilli decreased. Duration of pill use also corresponded to increase in vaginal pH. Longer duration of OC use, practice of bad hygiene, and illiteracy were factors associated with an alkaline pH, changed pattern of vaginal flora, and greater susceptibility to infection by staph aureus and E. coli. PMID:44312

  4. 10-year epidemiological profile changes for cervical and endometrial cancer patients treated by radiotherapy in the Pernambuco state, Brazil

    Energy Technology Data Exchange (ETDEWEB)

    Cantinha, Rebeca S.; Santos, Mariana L.O.; Franca, Elvis J., E-mail: ejfranca@yahoo.com.br, E-mail: marianasantos_ufpe@hotmail.com, E-mail: rebecanuclear@gmail.com [Centro Regional de Ciencias Nucleares do Nordeste (CRCN-NE/CNEN-PE), Recife, PE (Brazil); Pessoa, Juanna G.; Melo, Ana M.M.A.; Amancio, Francisco F., E-mail: amdemelo@hotmail.com, E-mail: amanciobike@gmail.com, E-mail: juannapessoa@gmail.com, E-mail: marianasantos_ufpe@hotmail.com [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Departamento de Biofisica e Radiobiologia; Oliveira Neto, Aristides M.; Melo, Jonathan A., E-mail: aristidesoliveira466@hotmail.com, E-mail: jonathan@truenet.com.br [Centro de Radioterapia de Pernambuco (CERAPE), Santo Amaro, PE (Brazil)

    2014-07-01

    Cancer is a worldwide public health problem, its prevention and control are included within 16 strategic objectives of the Brazilian Ministry of Health for the period 2011-2015. Cervical cancer is the fourth most common tumor in the female population, being new 15,590 cases estimated for 2014 according to the Brazilian National Cancer Institute (INCA). Pernambuco is the fifth state with the highest number of cases of cervical cancer and the seventh in cases of endometrial ones, both estimative for 2014. The understanding of the epidemiological profile of these pathologies corroborates strategies for prevention, control and treatment. As Pernambuco has implemented the radiotherapy for cancer treatment since 1998-1999, this work encompassed the comparison of the 1998-1999 epidemiological profile of patients treated by radiotherapy for cervical and endometrial cancer in the State of Pernambuco, Brazil, with 2008-2009 profile - ten years after. Medical record of 490 patients treated at the Center of Radiotherapy of Pernambuco (CERAPE) were compiled according to the patient origin, the affected uterus region, the staging of disease, the type and cell differentiation of the tumor, the age group, and, finally, the realization of hysterectomy as part of the treatment. More than 90% of the patients were affected by cervical cancer in the two investigated periods. For the interval of 1998-1999 the proportion of patients submitted to hysterectomy was quite higher compared to those after ten years. The results also showed a change in the origin of the patients, in which, in 1999, most of the patients were from the capital and the metropolitan area, while, after ten years, patients were mostly from the interior of the State. There was a predominance of squamous cell type tumors in both periods evaluated. For the 1998-1999 interval, tumors were stage 2, moderately differentiated type. Differently, the tumors were mostly stage 3, not differentiated type, for the 2008-2009 period

  5. The Concept and the Epidemiology of Diabetic Nephropathy Have Changed in Recent Years

    Directory of Open Access Journals (Sweden)

    Alberto Martínez-Castelao

    2015-05-01

    Full Text Available Diabetes Mellitus (DM is a growing worldwide epidemic. It was estimated that more than 366 million people would be affected. DM has spread its presence over the world due to lifestyle changes, increasing obesity and ethnicities, among others. Diabetic nephropathy (DN is one of the most important DM complications. A changing concept has been introduced from the classical DN to diabetic chronic kidney disease (DCKD, taking into account that histological kidney lesions may vary from the nodular or diffuse glomerulosclerosis to tubulointerstitial and/or vascular lesions. Recent data showed how primary and secondary prevention were the key to reduce cardiovascular episodes and improve life expectancy in diabetic patients. A stabilization in the rate of end stage kidney disease has been observed in some countries, probably due to the increased awareness by primary care physicians about the prognostic importance of chronic kidney disease (CKD, better control of blood pressure and glycaemia and the implementation of protocols and clinical practice recommendations about the detection, prevention and treatment of CKD in a coordinated and multidisciplinary management of the DM patient. Early detection of DM and DCKD is crucial to reduce morbidity, mortality and the social and economic impact of DM burden in this population.

  6. Molecular epidemiology of HIV-1 in Panama: origin of non-B subtypes in samples collected from 2007 to 2013.

    Directory of Open Access Journals (Sweden)

    Yaxelis Mendoza

    Full Text Available Phylogenetic studies have suggested that the HIV-1 epidemic in the Americas is mainly dominated by HIV subtype B. However, countries of South America and the Caribbean have recently reported changes in their circulating HIV-1 genetic profiles. The aim of this study was to characterize the molecular profile of the HIV-1 epidemic in Panama by the analysis of 655 polymerase gene (pol sequences that were obtained from HIV-infected Panamanians diagnosed between 1987 and 2013. Blood samples were collected from recently infected, antiretroviral drug-naïve and treatment-experienced subjects since mid-2007 to 2013. Viral RNA from plasma was extracted and sequences of HIV protease and reverse transcriptase genes were obtained. Bootscanning and phylogenetic methods were used for HIV subtyping and to trace the putative origin of non-B subtype strains. Our results showed that HIV-1 infections in Panama are dominated by subtype B (98.9%. The remaining 1.1% is represented by a diverse collection of recombinant variants including: three URFs_BC, one CRF20_BG, and one CRF28/29_BF, in addition to one subtype F1 and one subtype C, none of which were previously reported in Panama. The non-B subtype variants detected in Panama were probably introduced from Brazil (subtype F1 and CRF28/29_BF, Cuba (CRF20_BG, Dominican Republic (URFs_BC and India (subtype C. Panama is the geographical vertex that connects the North with South America and the Caribbean through trade and cultural relations, which may explain the observed introductions of non-B subtype HIV-1 variants from both the Caribbean and South America into this Central American country.

  7. Molecular epidemiology of HIV-1 in Panama: origin of non-B subtypes in samples collected from 2007 to 2013.

    Science.gov (United States)

    Mendoza, Yaxelis; Bello, Gonzalo; Castillo Mewa, Juan; Martínez, Alexander A; González, Claudia; García-Morales, Claudia; Avila-Ríos, Santiago; Reyes-Terán, Gustavo; Pascale, Juan M

    2014-01-01

    Phylogenetic studies have suggested that the HIV-1 epidemic in the Americas is mainly dominated by HIV subtype B. However, countries of South America and the Caribbean have recently reported changes in their circulating HIV-1 genetic profiles. The aim of this study was to characterize the molecular profile of the HIV-1 epidemic in Panama by the analysis of 655 polymerase gene (pol) sequences that were obtained from HIV-infected Panamanians diagnosed between 1987 and 2013. Blood samples were collected from recently infected, antiretroviral drug-naïve and treatment-experienced subjects since mid-2007 to 2013. Viral RNA from plasma was extracted and sequences of HIV protease and reverse transcriptase genes were obtained. Bootscanning and phylogenetic methods were used for HIV subtyping and to trace the putative origin of non-B subtype strains. Our results showed that HIV-1 infections in Panama are dominated by subtype B (98.9%). The remaining 1.1% is represented by a diverse collection of recombinant variants including: three URFs_BC, one CRF20_BG, and one CRF28/29_BF, in addition to one subtype F1 and one subtype C, none of which were previously reported in Panama. The non-B subtype variants detected in Panama were probably introduced from Brazil (subtype F1 and CRF28/29_BF), Cuba (CRF20_BG), Dominican Republic (URFs_BC) and India (subtype C). Panama is the geographical vertex that connects the North with South America and the Caribbean through trade and cultural relations, which may explain the observed introductions of non-B subtype HIV-1 variants from both the Caribbean and South America into this Central American country.

  8. Molecular epidemiology and antimicrobial susceptibility of extended- and broad-spectrum beta-lactamase-producing Klebsiella pneumoniae isolated in Portugal.

    Science.gov (United States)

    Mendonça, Nuno; Ferreira, Eugénia; Louro, Deolinda; Caniça, Manuela

    2009-07-01

    All 187 Klebsiella pneumoniae isolated over six consecutive months of 1999 in 17 Portuguese health institutions were studied: 89% were resistant to ampicillin, 31% to trimethoprim/sulfamethoxazole, 17% to aminoglycosides and 3% to fluoroquinolones; 16% were multidrug-resistant and 14% expressed an extended-spectrum beta-lactamase (ESBL) phenotype confirmed by genotyping. Molecular methods identified: 11 isolates possessing bla(ESBL-SHV) genes (bla(SHV-2A), bla(SHV-5), bla(SHV-12) and bla(SHV-55)), 9 isolates with bla(ESBL-TEM) (bla(TEM-3), bla(TEM-10) and bla(TEM-24)) and 7 isolates with bla(GES-1), encoding ESBL enzymes; and 160 isolates with bla(SHV-1) and bla(SHV-type) encoding non-ESBL enzymes. Overall, 15 new beta-lactamases were detected: SHV-60 to SHV-62, SHV-71 and SHV-73 to SHV-83. The genetic relatedness of 108 isolates was studied by pulsed-field gel electrophoresis (PFGE) analysis. The isolates were diverse and 18 clusters were defined, the largest including 12 isolates of different specimens, 6 of which expressed GES-1 enzymes. Twenty additional strains isolated during a second period (March-November 2006) in three of the participating hospitals contained ESBL-encoding genes, whereas none of the isolates in the same hospitals in 1999 carried such genes: bla(SHV-5), bla(SHV-12), bla(TEM-10), bla(TEM-52), bla(CTX-M-15), bla(CTX-M-32) and bla(CTX-M-61) (first described in the country). In this period, three new enzymes were detected: SHV-106 to SHV-108. We provide evidence that the genotypes of K. pneumoniae isolates is changing towards the emergence of ESBL enzymes. PMID:19272757

  9. Molecular epidemiology of livestock rabies viruses isolated in the northeastern Brazilian states of Paraíba and Pernambuco from 2003 - 2009

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    Mochizuki Nobuyuki

    2012-01-01

    Full Text Available Abstract Background Limited or no epidemiological information has been reported for rabies viruses (RABVs isolated from livestock in the northeastern Brazilian states of Paraíba (PB and Pernambuco (PE. The aim of this study was to clarify the molecular epidemiology of RABVs circulating in livestock, especially cattle, in these areas between 2003 and 2009. Findings Phylogenetic analysis based on 890 nt of the nucleoprotein (N gene revealed that the 52 livestock-derived RABV isolates characterized here belonged to a single lineage. These isolates clustered with a vampire bat-related RABV lineage previously identified in other states in Brazil; within PB and PE, this lineage was divided between the previously characterized main lineage and a novel sub-lineage. Conclusions The occurrences of livestock rabies in PB and PE originated from vampire bat RABVs, and the causative RABV lineage has been circulating in this area of northeastern Brazil for at least 7 years. This distribution pattern may correlate to that of a vampire bat population isolated by geographic barriers.

  10. Molecular Epidemiology of Avian Malaria in Wild Breeding Colonies of Humboldt and Magellanic Penguins in South America.

    Science.gov (United States)

    Sallaberry-Pincheira, Nicole; Gonzalez-Acuña, Daniel; Herrera-Tello, Yertiza; Dantas, Gisele P M; Luna-Jorquera, Guillermo; Frere, Esteban; Valdés-Velasquez, Armando; Simeone, Alejandro; Vianna, Juliana A

    2015-06-01

    Avian malaria is a disease caused by species of the genera Haemoproteus, Leucocytozoon, and Plasmodium. It affects hundreds of bird species, causing varied clinical signs depending on the susceptibility of the host species. Although high mortality has been reported in captive penguins, limited epidemiological studies have been conducted in wild colonies, and isolated records of avian malaria have been reported mostly from individuals referred to rehabilitation centers. For this epidemiological study, we obtained blood samples from 501 adult Humboldt and 360 adult Magellanic penguins from 13 colonies throughout South America. To identify malaria parasitaemia, we amplified the mtDNA cytochrome b for all three parasite genera. Avian malaria was absent in most of the analyzed colonies, with exception of the Punta San Juan Humboldt penguin colony, in Peru, where we detected at least two new Haemoproteus lineages in three positive samples, resulting in a prevalence of 0.6% for the species. The low prevalence of avian malaria detected in wild penguins could be due to two possible causes: A low incidence, with high morbidity and mortality in wild penguins or alternatively, penguins sampled in the chronic stage of the disease (during which parasitaemia in peripheral blood samples is unlikely) would be detected as false negatives.

  11. Molecular Epidemiology of Avian Malaria in Wild Breeding Colonies of Humboldt and Magellanic Penguins in South America.

    Science.gov (United States)

    Sallaberry-Pincheira, Nicole; Gonzalez-Acuña, Daniel; Herrera-Tello, Yertiza; Dantas, Gisele P M; Luna-Jorquera, Guillermo; Frere, Esteban; Valdés-Velasquez, Armando; Simeone, Alejandro; Vianna, Juliana A

    2015-06-01

    Avian malaria is a disease caused by species of the genera Haemoproteus, Leucocytozoon, and Plasmodium. It affects hundreds of bird species, causing varied clinical signs depending on the susceptibility of the host species. Although high mortality has been reported in captive penguins, limited epidemiological studies have been conducted in wild colonies, and isolated records of avian malaria have been reported mostly from individuals referred to rehabilitation centers. For this epidemiological study, we obtained blood samples from 501 adult Humboldt and 360 adult Magellanic penguins from 13 colonies throughout South America. To identify malaria parasitaemia, we amplified the mtDNA cytochrome b for all three parasite genera. Avian malaria was absent in most of the analyzed colonies, with exception of the Punta San Juan Humboldt penguin colony, in Peru, where we detected at least two new Haemoproteus lineages in three positive samples, resulting in a prevalence of 0.6% for the species. The low prevalence of avian malaria detected in wild penguins could be due to two possible causes: A low incidence, with high morbidity and mortality in wild penguins or alternatively, penguins sampled in the chronic stage of the disease (during which parasitaemia in peripheral blood samples is unlikely) would be detected as false negatives. PMID:25492695

  12. The molecular epidemiological study of colistin-only-sensitive strains in multi-drug resistant Acinetobacter baumannii

    Institute of Scientific and Technical Information of China (English)

    YANG Li; HAN Lizhong; SUN Jingyong; YU Yunsong; NI Yuxing

    2007-01-01

    This paper reported the epidemiology of the colistin-only-sensitive Acinetobacter baumannii(COS-AB)in a tertiary teaching hospital in China.We analyzed the clinical data of 136 COS-AB isolates from June 2004 to May 2005 and collected 66 A.baumannii isolates in which 33 strains were COS-AB,and the rest were non-COS-AB.Random amplified polymorphic DNA(RAPD)analysis (primer ERIC2 and 272)showed that all COS-AB were identical,while pulsed-field gel electrophotesis(PFGE)analysis showed two separate genotypes of these COS-ABwhich were distinctly different from that of non-COS-AB.The COS-AB from burn wards showed the identical PFGE pattern which was distinguished from the genotype of COS-AB in other departments,mainly surgical systems.The cross-infection was severe and strict methods of disinfection and sterilization should be implemented.Meanwhile,the epidemiology of COS-AB in environment and patients should be closely monitored.The PFGE analysis is a reliable method of A.baumannii typing.

  13. Impact of vaccination on the molecular epidemiology and evolution of group A rotaviruses in Latin America and factors affecting vaccine efficacy.

    Science.gov (United States)

    Bucardo, Filemón; Nordgren, Johan

    2015-08-01

    Despite high rotavirus (RV) vaccine coverage (∼83%) and good effectiveness (∼77%) against RV-diarrhea hospitalization, RV is still contributing to the burden of diarrhea that persists in hospital settings in several Latin American countries, where RV vaccination is being implemented. Due to the extensive genomic and antigenic diversity, among co-circulating human RV, a major concern has been that the introduction of RV vaccination could exert selection pressure leading to higher prevalence of strains not included in the vaccines and/or emergence of new strains, thus, reducing the efficacy of vaccination. Here we review the molecular epidemiology of RV in Latin America and explore issues of RV evolution and selection in light of vaccination. We further explore etiologies behind the large burden of diarrhea remaining after vaccination in some countries and discuss plausible reasons for vaccine failures.

  14. Epidemic and Maintenance of Rabies in Chinese Ferret Badgers (Melogale moschata) indicated by Epidemiology and the Molecular Signatures of Rabies Viruses

    Institute of Scientific and Technical Information of China (English)

    Shoufeng Zhang; Ye Liu; Yanli Hou; Jinghui Zhao; Fei Zhang; Ying Wang; Rongliang Hu

    2013-01-01

    An epidemic of Chinese ferret badger-associated human rabies was investigated in Wuyuan county,Jiangxi province and rabies viruses isolates from ferret badgers in different districts in Jiangxi and Zhejiang provinces were sequenced with their nucleotides and amino acids and aligned for epidemiological analysis.The results showed that the human rabies in Wuyuan are only associated with ferret badger bites; the rabies virus can be isolated in a high percentage of ferret badgers in the epidemic areas in Jiangxi and Zhejiang provinces; the isolates share the same molecular features in nucleotides and have characteristic amino acid signatures,i.e.,2 sites in the nucleoprotein and 3 sites in the glycoprotein,that are distinct from virus isolates from dogs in the same region.We conclude that rabies in Chinese ferret badgers has formed an independent transmission cycle and ferret badgers may serve as another important rabies reservoir independent of dog rabies in China.

  15. The Aging of the Global Population: The Changing Epidemiology of Disease and Spinal Disorders.

    Science.gov (United States)

    Fehlings, Michael G; Tetreault, Lindsay; Nater, Anick; Choma, Ted; Harrop, James; Mroz, Tom; Santaguida, Carlo; Smith, Justin S

    2015-10-01

    The global population is currently undergoing an upward shift in its age structure due to decreasing fertility rates and increasing life expectancy. As a result, clinicians worldwide will be required to manage an increasing number of spinal disorders specific to the elderly and the aging of the spine. Elderly individuals pose unique challenges to health care systems and to spinal physicians as these patients typically have an increased number of medical comorbidities, reduced bone density mass, more severe spinal degeneration and a greater propensity to falls. In anticipation of the aging of the population, we undertook this project to heighten physicians' awareness of age-related spinal disorders, including geriatric odontoid fractures, central cord syndrome, osteoporotic compression fractures, degenerative cervical myelopathy, lumbar spinal stenosis and degenerative spinal deformity. This introductory article provides an overview of the changing demographics of the global population; discusses the age-related alterations that may occur to the spine; and summarizes the purpose and contents of this focus issue. PMID:26378347

  16. Changes in the EU legislation on Trichinella inspection--new challenges in the epidemiology.

    Science.gov (United States)

    Kapel, C M O

    2005-09-01

    The European Union (EU) countries are searching for new ways to certify meat free of Trichinella; however, with the expansion of the EU, the acceptance of a unilateral method is complicated by the variability of pig and human trichinellosis among EU countries, where significantly higher prevalence rates have been observed in the newly added eastern countries. Several attempts have been made to define Trichinella-free areas, but certification of Trichinella-free pig production farms appears to be the only feasible approach. The increasing prevalence of the non-encapsulating species, Trichinella pseudospiralis, in game, domestic pigs and humans has eliminated the compression technique from the new EU legislation to be enacted in 2006. Also, the observation that several species of Trichinella tolerate freezing in horse meat for up to 4 weeks has forced a change in legislation as well where freezing is no longer an option for certifying horse meat. Because current serological detection methods are not suited for meat inspection, classical direct detection methods and inactivation by freezing remain the methods of choice for pork. It has been proposed, therefore, to automate direct inspection methods as a cost effective alternative to certify pig farms free of Trichinella. PMID:16039781

  17. An overview of molecular epidemiologic studies in biliary tract cancer%肝外胆道癌分子流行病学研究的新进展

    Institute of Scientific and Technical Information of China (English)

    孟令勤; 刘金钢

    2012-01-01

    胆道癌是一种生存率极低的高致死性疾病,在世界范围内,胆道癌的发病率呈上升趋势.胆道癌不良的预后源于缺乏早期诊断和有效治疗的手段,因此,明确胆道癌的发病机制显得至关重要.基因多态性的关联分析将有助于阐明胆道癌的发生机制,有望发现有价值的肿瘤标记物以确定胆道癌高危人群并进行早期诊断和预后评估,进而成为基因治疗的新靶点.本文从分子流行病学角度对胆道癌基因多态性方面的最新研究进展进行综述.%Biliary tract cancer is a rare but highly fatal malignancy,with world -wide increasing incidence in recent years. The prognosis of biliary tract cancer is grim due to lack of early diagnostic modalities and effective treatments. It is important to explore the pathogenesis of biliary tract cancer. Molecular epidemiologic studies examining the associations between polymorphisms in several gene pathways and biliary tract cancer risk may provide insight into the etiology of this kind of cancer, and be helpful to discover validated biomarkers for early detection in asymptomatic individuals and present new targets of gene therepy in biliary tract cancer in the future. We present a broad overview of molecular epidemiologic studies that have addressed the relationship between biliary tract cancer risk and genetic polymorphisms in several candidate genes and suggest avenues for future research.

  18. Molecular epidemiology of methicillin resistant staphylococcus aureus colonizing the anterior Nares of school children of Udupi Taluk

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    S Govindan

    2015-01-01

    Full Text Available Context: Community associated methicillin resistant Staphylococcus aureus (CA-MRSA cause serious skin and soft tissue infections including necrotizing fasciitis and necrotizing pneumonia. Production of Panton Valentine Leucocidine (PVL toxin is implicated in its enhanced virulence. A variant of epidemic MRSA-15 (EMRSA-15 which produces PVL toxin has been isolated and characterized by pulsed-field gel electrophoresis (PFGE method from the Indian population both in hospital and community settings. Aims: Identify the epidemiological type of MRSA colonizing the anterior nares of school children in Udupi taluk. Settings and Design: The study population included children of the age group of 5-16 years belonging to the Udupi taluk of Karnataka, India. A total of 1503 children were screened for MRSA colonization during July 2009 to December 2010. Materials and Methods: PVL assay, Staphylococcal Cassette Chromosome (SCC mec typing and PFGE typing were carried out with all the MRSA isolates. Statistical Analysis Used: Frequency distribution of different variables was assessed by SPSS. Results: Among the 1.1% of MRSA, 58.8% (10/17 of isolates were positive for pvl and 41.7% (7/17 were identified as SCC mec type IV. PFGE patterns of all the strains were identical with Indian variant EMRSA-15; however they were different from classical EMRSA-15 in 3-4 bands. Conclusions: The Indian variant EMRSA-15 gains much epidemiological relevance owing to the acquisition of pvl gene. In spite of low prevalence of nasal colonization of MRSA, emergence of the virulent Indian variant EMRSA-15 in our community is a worrisome fact to be reckoned with.

  19. Epidemiology, molecular characterization and antibiotic resistance of Neisseria meningitidis from patients ≤15 years in Manhica, rural Mozambique.

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    Ana Belén Ibarz-Pavón

    Full Text Available BACKGROUND: The epidemiology of meningococcal disease in Mozambique and other African countries located outside the "meningitis belt" remains widely unknown. With the event of upcoming vaccines microbiological and epidemiological information is urgently needed. METHODS: Prospective surveillance for invasive bacterial infections was conducted at the Manhiça District hospital (rural Mozambique among hospitalized children below 15 years of age. Available Neisseria meningitidis isolates were serogrouped and characterized by Multilocus Sequence Typing (MLST. Antibiotic resistance was also determined. RESULTS: Between 1998 and 2008, sixty-three cases of confirmed meningococcal disease (36 meningitis, 26 sepsis and 1 conjunctivitis were identified among hospitalized children. The average incidence rate of meningococcal disease was 11.6/100,000 (8/100,000 for meningitis and 3.7/100,000 for meningococcemia, respectively. There was a significant rise on the number of meningococcal disease cases in 2005-2006 that was sustained till the end of the surveillance period. Serogroup was determined for 43 of the 63 meningococcal disease cases: 38 serogroup W-135, 3 serogroup A and 2 serogroup Y. ST-11 was the most predominant sequence type and strongly associated with serogroup W-135. Two of the three serogroup A isolates were ST-1, and both serogroup Y isolates were ST-175. N. meningitidis remained highly susceptible to all antibiotics used for treatment in the country, although the presence of isolates presenting intermediate resistance to penicillin advocates for continued surveillance. CONCLUSIONS: Our data show a high rate of meningococcal disease in Manhiça, Mozambique, mainly caused by serogroup W-135 ST-11 strains, and advocates for the implementation of a vaccination strategy covering serogroup W-135 meningococci in the country.

  20. A conundrum in molecular toxicology: molecular and biological changes during neoplastic transformation of human cells.

    Science.gov (United States)

    Milo, G E; Shuler, C F; Lee, H; Casto, B C

    1995-12-01

    , the populations exhibit phenotypic diversity in that many of the transformed cells differentiate and fail to continue to divide in culture. Historically, we have assumed only a limited role for epigenetic modulation of molecular changes that occur during progression; however, our data suggest quite strongly that nonmalignant tumor populations can be converted to a more malignant phenotype without additional mutations taking place and, conversely, malignant populations can be downregulated to a nontumorigenic phenotype. Tumor cell plasticity is not only a fundamental characteristic of diverse types of human tumors, but also appears as an integral characteristic of carcinogen-transformed cells in vitro. PMID:8788209

  1. Systematics and epidemiology of trichinella.

    Science.gov (United States)

    Pozio, Edoardo; Darwin Murrell, K

    2006-01-01

    In this review, we describe the current knowledge on the systematics, ecology and epidemiology of Trichinella and trichinellosis, and the impact of recent research discoveries on the understanding of this zoonosis. The epidemiology of this zoonosis has experienced important changes over the past two decades, especially with regard to the importance of the sylvatic cycle and the sylvatic species. Outbreaks of trichinellosis due to Trichinella spiralis from domestic swine, while still frequent, increasingly are caused by other Trichinella spp. infecting hosts such as horses, dogs, wild boars, bears and walruses. The latter revelations have occurred as a result of a series of discoveries on the systematics of Trichinella spp., facilitated by new molecular tools. As a consequence, the genus is now composed of two clades, an encapsulated group (five species and three genotypes) and a non-encapsulated one (three species). This has sparked renewed investigations on the host range of these parasites and their epidemiological features. Most dramatic, perhaps, is the recognition that reptiles may also serve as hosts for certain species. This new knowledge base, in addition to having an important relevance for food safety policies and protection measures, is raising important questions on the phylogeny of Trichinella spp., the ecological characteristics of the species and their geographic histories. Answers to these questions may have great value for the understanding of the evolutionary biology for other parasitic helminths, and may increase the value of this genus as models for research on parasitism in general. PMID:17134656

  2. 10 years of prophylaxis with nebulized liposomal amphotericin B and the changing epidemiology of Aspergillus spp. infection in lung transplantation.

    Science.gov (United States)

    Peghin, Maddalena; Monforte, Victor; Martin-Gomez, Maria-Teresa; Ruiz-Camps, Isabel; Berastegui, Cristina; Saez, Berta; Riera, Jordi; Ussetti, Piedad; Solé, Juan; Gavaldá, Joan; Roman, Antonio

    2016-01-01

    The aim of this study was to assess the outcome and tolerability of prophylactic nebulized liposomal amphotericin B (n-LAB) in lung transplant recipients (LTR) and the changing epidemiology of Aspergillus spp. infection and colonization. We performed an observational study including consecutive LTR recipients (2003-2013) undergoing n-LAB prophylaxis lifetime. A total of 412 patients were included (mean postoperative follow-up 2.56 years; IQR 1.01-4.65). Fifty-three (12.8%) patients developed 59 Aspergillus spp. infections, and 22 invasive aspergillosis (overall incidence 5.3%). Since 2009, person-time incidence rates of Aspergillus spp. colonization and infection decreased (2003-2008, 0.19; 2009-2014, 0.09; P = 0.0007), but species with reduced susceptibility or resistance to amphotericin significantly increased (2003-2008, 38.1% vs 2009-2014, 58.1%; P = 0.039). Chronic lung allograft dysfunction (CLAD) was associated with Aspergillus spp. colonization and infection (HR 24.4, 95% CI 14.28-41.97; P = 0.00). Only 2.9% of patients presented adverse effects, and 1.7% required discontinuation. Long-term administration of prophylaxis with n-LAB has proved to be tolerable and can be used for preventing Aspergillus spp. infection in LTR. Over the last years, the incidence of Aspergillus spp. colonization and infection has decreased, but species with reduced amphotericin susceptibility or resistance are emerging. CLAD is associated with Aspergillus spp. colonization and infection.

  3. Molecular epidemiology of J-subgroup avian leukosis virus isolated from meat-type chickens in southern China between 2013 and 2014.

    Science.gov (United States)

    Lin, Wencheng; Li, Xinjian; Dai, Zhenkai; Zhang, Xinheng; Chang, Shuang; Zhao, Peng; Zhang, Huanmin; Chen, Feng; Xie, Qingmei

    2016-11-01

    Members of avian leukosis virus subgroup J (ALV-J) cause various diseases associated with tumor formation and decreased fertility, resulting in major economic losses in the poultry industry worldwide. To assess the status of ALV-J infection in meat-type chickens in southern China, the molecular epidemiology of ALV-J strains was investigated. A total of 265 clinical samples collected from southern China from 2013 to 2014 were investigated in this study for the presence of ALV-J, which resulted in 12 virus isolates. Phylogenetic analysis showed that 91.7 % (11/12) of the ALV-J isolates have possessed high homology to Chinese layer isolates and belong to one subgroup. One of the ALV isolates (designated GD1411-1) was relatively closely related to the ALV-J broiler isolates, indicating that the GD1411-1 isolate might be a transition strain. Several unique nucleotide substitutions in gp85 and the U3 region were detected in all 12 ALV-J isolates. This study provides some interesting information on the molecular characterization of ALV-J isolates. These findings will be beneficial for understanding of the pathogenic mechanism of ALV-J infection.

  4. Molecular epidemiology of J-subgroup avian leukosis virus isolated from meat-type chickens in southern China between 2013 and 2014.

    Science.gov (United States)

    Lin, Wencheng; Li, Xinjian; Dai, Zhenkai; Zhang, Xinheng; Chang, Shuang; Zhao, Peng; Zhang, Huanmin; Chen, Feng; Xie, Qingmei

    2016-11-01

    Members of avian leukosis virus subgroup J (ALV-J) cause various diseases associated with tumor formation and decreased fertility, resulting in major economic losses in the poultry industry worldwide. To assess the status of ALV-J infection in meat-type chickens in southern China, the molecular epidemiology of ALV-J strains was investigated. A total of 265 clinical samples collected from southern China from 2013 to 2014 were investigated in this study for the presence of ALV-J, which resulted in 12 virus isolates. Phylogenetic analysis showed that 91.7 % (11/12) of the ALV-J isolates have possessed high homology to Chinese layer isolates and belong to one subgroup. One of the ALV isolates (designated GD1411-1) was relatively closely related to the ALV-J broiler isolates, indicating that the GD1411-1 isolate might be a transition strain. Several unique nucleotide substitutions in gp85 and the U3 region were detected in all 12 ALV-J isolates. This study provides some interesting information on the molecular characterization of ALV-J isolates. These findings will be beneficial for understanding of the pathogenic mechanism of ALV-J infection. PMID:27503348

  5. Progress towards understanding the ecology and epidemiology of malaria in the western Kenya highlands: opportunities and challenges for control under climate change risk

    OpenAIRE

    Githeko, AK; Ototo, EN; Guiyun, Yan

    2011-01-01

    Following severe malaria epidemics in the western Kenya highlands after the late 1980s it became imperative to undertake eco-epidemiological assessments of the disease and determine its drivers, spatial-temporal distribution and control strategies. Extensive research has indicated that the major biophysical drivers of the disease are climate change and variability, terrain, topography, hydrology and immunity. Vector distribution is focalized at valley bottoms and abundance is closely related ...

  6. Tumor-based case-control studies of infection and cancer: muddling the when and where of molecular epidemiology.

    Science.gov (United States)

    Engels, Eric A; Wacholder, Sholom; Katki, Hormuzd A; Chaturvedi, Anil K

    2014-10-01

    We describe the "tumor-based case-control" study as a type of epidemiologic study used to evaluate associations between infectious agents and cancer. These studies assess exposure using diseased tissues from affected individuals (i.e., evaluating tumor tissue for cancer cases), but they must utilize nondiseased tissues to assess control subjects, who do not have the disease of interest. This approach can lead to exposure misclassification in two ways. First, concerning the "when" of exposure assessment, retrospective assessment of tissues may not accurately measure exposure at the key earlier time point (i.e., during the etiologic window). Second, concerning the "where" of exposure assessment, use of different tissues in cases and controls can have different accuracy for detecting the exposure (i.e., differential exposure misclassification). We present an example concerning the association of human papillomavirus with various cancers, where tumor-based case-control studies likely overestimate risk associated with infection. In another example, we illustrate how tumor-based case-control studies of Helicobacter pylori and gastric cancer underestimate risk. Tumor-based case-control studies can demonstrate infection within tumor cells, providing qualitative information about disease etiology. However, measures of association calculated in tumor-based case-control studies are prone to over- or underestimating the relationship between infections and subsequent cancer risk. PMID:25063520

  7. Genomic Epidemiology and Molecular Resistance Mechanisms of Azithromycin-Resistant Neisseria gonorrhoeae in Canada from 1997 to 2014.

    Science.gov (United States)

    Demczuk, Walter; Martin, Irene; Peterson, Shelley; Bharat, Amrita; Van Domselaar, Gary; Graham, Morag; Lefebvre, Brigitte; Allen, Vanessa; Hoang, Linda; Tyrrell, Greg; Horsman, Greg; Wylie, John; Haldane, David; Archibald, Chris; Wong, Tom; Unemo, Magnus; Mulvey, Michael R

    2016-05-01

    The emergence of Neisseria gonorrhoeae strains with decreased susceptibility to cephalosporins and azithromycin (AZM) resistance (AZM(r)) represents a public health threat of untreatable gonorrhea infections. Genomic epidemiology through whole-genome sequencing was used to describe the emergence, dissemination, and spread of AZM(r) strains. The genomes of 213 AZM(r) and 23 AZM-susceptible N. gonorrhoeae isolates collected in Canada from 1989 to 2014 were sequenced. Core single nucleotide polymorphism (SNP) phylogenomic analysis resolved 246 isolates into 13 lineages. High-level AZM(r) (MICs ≥ 256 μg/ml) was found in 5 phylogenetically diverse isolates, all of which possessed the A2059G mutation (Escherichia coli numbering) in all four 23S rRNA alleles. One isolate with high-level AZM(r) collected in 2009 concurrently had decreased susceptibility to ceftriaxone (MIC = 0.125 μg/ml). An increase in the number of 23S rRNA alleles with the C2611T mutations (E. coli numbering) conferred low to moderate levels of AZM(r) (MICs = 2 to 4 and 8 to 32 μg/ml, respectively). Low-level AZM(r) was also associated with mtrR promoter mutations, including the -35A deletion and the presence of Neisseria meningitidis-like sequences. Geographic and temporal phylogenetic clustering indicates that emergent AZM(r) strains arise independently and can then rapidly expand clonally in a region through local sexual networks. PMID:26935729

  8. Molecular Identification and Epidemiological Features of Human Adenoviruses Associated with Acute Respiratory Infections in Hospitalized Children in Southern China, 2012-2013.

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    Yi Chen

    Full Text Available Acute respiratory infections (ARI are the major worldwide health problem associated with high morbidity and mortality rates. Human adenovirus (HAdV is one of the most common pathogens associated with viral ARI, and thus calls for specific diagnosis and better understanding of the epidemiology and clinical characteristics.Total 4,130 children with ARI requiring hospitalization from 2012 to 2013 were retrospectively studied. Throat swab specimens were collected from each patient. Fluorescence Quantitative PCR was performed to detect adenovirus as well as other common ARI-related pathogens. The seven HAdV hypervariable regions (HVRs of the hexon gene from fifty-seven HAdVs-positive samples collected in the seasonal peaks were sequenced. Phylogenetic analysis of HVRs was also conducted to confirm the molecular types and genetic variation. In addition, epidemiological features and co-infection with other human respiratory pathogens were investigated and analyzed.Of 4,130 hospitalized pediatric patients tested, the positive rates of respiratory syncytial virus (RSV, Mycoplasma pneumoniae (MP, and HAdV were 13.7%, 13.2%, and 12.0%, respectively. The HAdV positive patients accounted for 7.9%, 17.2%, 17.5% and 10.7% in age groups <1, 1-3, 3-6 and 6-14 years, respectively. Eighty-four HAdV positive children were co-infected with other respiratory pathogens (84/495, 17.0%. The most common co-infection pathogens with HAdV were MP (57.1% and Human Bocavirus (HBoV (16.7%. The majority of HAdV infected patients were totally recovered (96.9%, 480/495; However, four (0.8% patients, who were previously healthy and at the age of 2 years or younger died of pneumonia. Seasonal peaks of HAdV infection occurred in the summer season of 2012 and 2013; the predominant HAdV type was HAdV-3 (70%, followed by HAdV-7 (28%. These epidemiological features were different from those in Northern China. The HAdV-55 was identified and reported for the first time in Guangzhou

  9. Changes in molecular species of triacylglycerols during frying

    Directory of Open Access Journals (Sweden)

    Dobson, Gary

    1996-04-01

    Full Text Available The loss of specific molecular species of triacylglycerols from sunflower, high-oleate sunflower and palm oils has been investigated in commercial frying operations and simulated frying experiments. The non-oxidized triacylglycerols were isolated and molecular species separated by silver ion highperformance liquid chromatography. Linoleate-containing species were lost more rapidly than those containing oleate, as expected. However, all species were liable to oxidation and those containing oleate were lost more rapidly than might have been anticipated. It is suggested that oxidation of linoleate is the probable initiation step, but then the reaction can be propagated readily to all unsaturated species.

  10. Geographic and Temporal Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance: An Individual-Patient- and Sequence-Level Meta-Analysis

    Science.gov (United States)

    Rhee, Soo-Yon; Blanco, Jose Luis; Jordan, Michael R.; Taylor, Jonathan; Lemey, Philippe; Varghese, Vici; Hamers, Raph L.; Bertagnolio, Silvia; de Wit, Tobias F. Rinke; Aghokeng, Avelin F.; Albert, Jan; Avi, Radko; Avila-Rios, Santiago; Bessong, Pascal O.; Brooks, James I.; Boucher, Charles A. B.; Brumme, Zabrina L.; Busch, Michael P.; Bussmann, Hermann; Chaix, Marie-Laure; Chin, Bum Sik; D’Aquin, Toni T.; De Gascun, Cillian F.; Derache, Anne; Descamps, Diane; Deshpande, Alaka K.; Djoko, Cyrille F.; Eshleman, Susan H.; Fleury, Herve; Frange, Pierre; Fujisaki, Seiichiro; Harrigan, P. Richard; Hattori, Junko; Holguin, Africa; Hunt, Gillian M.; Ichimura, Hiroshi; Kaleebu, Pontiano; Katzenstein, David; Kiertiburanakul, Sasisopin; Kim, Jerome H.; Kim, Sung Soon; Li, Yanpeng; Lutsar, Irja; Morris, Lynn; Ndembi, Nicaise; NG, Kee Peng; Paranjape, Ramesh S.; Peeters, Martine; Poljak, Mario; Price, Matt A.; Ragonnet-Cronin, Manon L.; Reyes-Terán, Gustavo; Rolland, Morgane; Sirivichayakul, Sunee; Smith, Davey M.; Soares, Marcelo A.; Soriano, Vincent V.; Ssemwanga, Deogratius; Stanojevic, Maja; Stefani, Mariane A.; Sugiura, Wataru; Sungkanuparph, Somnuek; Tanuri, Amilcar; Tee, Kok Keng; Truong, Hong-Ha M.; van de Vijver, David A. M. C.; Vidal, Nicole; Yang, Chunfu; Yang, Rongge; Yebra, Gonzalo; Ioannidis, John P. A.; Vandamme, Anne-Mieke; Shafer, Robert W.

    2015-01-01

    Background Regional and subtype-specific mutational patterns of HIV-1 transmitted drug resistance (TDR) are essential for informing first-line antiretroviral (ARV) therapy guidelines and designing diagnostic assays for use in regions where standard genotypic resistance testing is not affordable. We sought to understand the molecular epidemiology of TDR and to identify the HIV-1 drug-resistance mutations responsible for TDR in different regions and virus subtypes. Methods and Findings We reviewed all GenBank submissions of HIV-1 reverse transcriptase sequences with or without protease and identified 287 studies published between March 1, 2000, and December 31, 2013, with more than 25 recently or chronically infected ARV-naïve individuals. These studies comprised 50,870 individuals from 111 countries. Each set of study sequences was analyzed for phylogenetic clustering and the presence of 93 surveillance drug-resistance mutations (SDRMs). The median overall TDR prevalence in sub-Saharan Africa (SSA), south/southeast Asia (SSEA), upper-income Asian countries, Latin America/Caribbean, Europe, and North America was 2.8%, 2.9%, 5.6%, 7.6%, 9.4%, and 11.5%, respectively. In SSA, there was a yearly 1.09-fold (95% CI: 1.05–1.14) increase in odds of TDR since national ARV scale-up attributable to an increase in non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance. The odds of NNRTI-associated TDR also increased in Latin America/Caribbean (odds ratio [OR] = 1.16; 95% CI: 1.06–1.25), North America (OR = 1.19; 95% CI: 1.12–1.26), Europe (OR = 1.07; 95% CI: 1.01–1.13), and upper-income Asian countries (OR = 1.33; 95% CI: 1.12–1.55). In SSEA, there was no significant change in the odds of TDR since national ARV scale-up (OR = 0.97; 95% CI: 0.92–1.02). An analysis limited to sequences with mixtures at less than 0.5% of their nucleotide positions—a proxy for recent infection—yielded trends comparable to those obtained using the complete dataset. Four

  11. Geographic and temporal trends in the molecular epidemiology and genetic mechanisms of transmitted HIV-1 drug resistance: an individual-patient- and sequence-level meta-analysis.

    Directory of Open Access Journals (Sweden)

    Soo-Yon Rhee

    2015-04-01

    Full Text Available Regional and subtype-specific mutational patterns of HIV-1 transmitted drug resistance (TDR are essential for informing first-line antiretroviral (ARV therapy guidelines and designing diagnostic assays for use in regions where standard genotypic resistance testing is not affordable. We sought to understand the molecular epidemiology of TDR and to identify the HIV-1 drug-resistance mutations responsible for TDR in different regions and virus subtypes.We reviewed all GenBank submissions of HIV-1 reverse transcriptase sequences with or without protease and identified 287 studies published between March 1, 2000, and December 31, 2013, with more than 25 recently or chronically infected ARV-naïve individuals. These studies comprised 50,870 individuals from 111 countries. Each set of study sequences was analyzed for phylogenetic clustering and the presence of 93 surveillance drug-resistance mutations (SDRMs. The median overall TDR prevalence in sub-Saharan Africa (SSA, south/southeast Asia (SSEA, upper-income Asian countries, Latin America/Caribbean, Europe, and North America was 2.8%, 2.9%, 5.6%, 7.6%, 9.4%, and 11.5%, respectively. In SSA, there was a yearly 1.09-fold (95% CI: 1.05-1.14 increase in odds of TDR since national ARV scale-up attributable to an increase in non-nucleoside reverse transcriptase inhibitor (NNRTI resistance. The odds of NNRTI-associated TDR also increased in Latin America/Caribbean (odds ratio [OR] = 1.16; 95% CI: 1.06-1.25, North America (OR = 1.19; 95% CI: 1.12-1.26, Europe (OR = 1.07; 95% CI: 1.01-1.13, and upper-income Asian countries (OR = 1.33; 95% CI: 1.12-1.55. In SSEA, there was no significant change in the odds of TDR since national ARV scale-up (OR = 0.97; 95% CI: 0.92-1.02. An analysis limited to sequences with mixtures at less than 0.5% of their nucleotide positions—a proxy for recent infection—yielded trends comparable to those obtained using the complete dataset. Four NNRTI SDRMs—K101E, K103N, Y181C, and

  12. [Dose-Response Dependences for Frequency of RET/PTC Gene Rearrangements in Papillary Thyroid Carcinoma after Irradiation. Simple Pooling Analysis of Molecular Epidemiological Data].

    Science.gov (United States)

    Koterov, A N; Ushenkova, L N; Biryukov, A P

    2016-01-01

    On the basis of all possible publications on the theme included in the previously formed base of sources on molecular epidemiology of RET/PTC rearrangements in thyroid papillary carcinoma a pooled analysis ("simple pooling data") on determination of the dose-effect dependences for RET/PTC frequency in radiogenic carcinomas of various irradiated groups was performed. (They are groups subjected to radiotherapeutic exposure, residents near the Chernobyl nuclear power plant (CNPP) and victims of nuclear bombing). The tendency to Pearson linear correlation (r = 0.746; p = 0.148) between the frequency of RET/PTC and the estimated dose on thyroid in the regions affected by the CNPP accident was revealed. But this tendency was recognized to be random owing to abnormally low values of the indicator for the most contaminated Gomel region. The method tentatively called "case-control" showed reliable differences in thyroid dose values for carcinomas with RET/PTC and without those. The versatility of changes was found: the lack of RET/PTC for radiotherapeutic impacts was associated with higher doses, whereas in case of the CNPP accident and for nuclear bombing victims it was the opposite. Probably, in the first case the "cellular cleaning" phenomenon after exposure to very high doses took place. Search of direct Pearson correlations between average/median thyroid doses on groups and RET/PTC frequency in carcinomas of these groups showed a high reliability for the dose-effect dependences- at the continuous dose scale (for RET/PTC in total and RET/PTC1 respectively: r = 0.830; p = 0.002 and r = 0.906; p = 0.0003); while there was no significant correlation received for RET/PTC3. When using the weighting least square regression analysis (proceeding from the number of carcinomas in samples), the specified regularities remained. Attempts to influence the strength of correlation by exception ofthe data of all the samples connected with the accident on the CNPP did not significantly

  13. Molecular and epidemiologic analysis of a county-wide outbreak caused by Salmonella enterica subsp. enterica serovar Enteritidis traced to a bakery

    Directory of Open Access Journals (Sweden)

    Lu Po-Liang

    2004-11-01

    Full Text Available Abstract Background An increase in the number of attendees due to acute gastroenteritis and fever was noted at one hospital emergency room in Taiwan over a seven-day period from July to August, 2001. Molecular and epidemiological surveys were performed to trace the possible source of infection. Methods An epidemiological investigation was undertaken to determine the cause of the outbreak. Stool and blood samples were collected according to standard protocols per Center for Disease Control, Taiwan. Typing of the Salmonella isolates from stool, blood, and food samples was performed with serotyping, antibiotypes, and pulsed field gel electrophoresis (PFGE following XbaI restriction enzyme digestion. Results Comparison of the number of patients with and without acute gastroenteritis (506 and 4467, respectively during the six weeks before the outbreak week revealed a significant increase in the number of patients during the outbreak week (162 and 942, respectively (relative risk (RR: 1.44, 95% confidence interval (CI: 1.22–1.70, P value Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis was isolated from the stool samples of 28 of 32 individuals and from a recalled bread sample. All S. Enteritidis isolates were of the same antibiogram. PFGE typing revealed that all except two of the clinical isolates and the bread isolates were of the same DNA macrorestriction pattern. Conclusions The egg-covered bread contaminated with S. Enteritidis was confirmed as the vehicle of infection. Alertness in the emergency room, surveillance by the microbiology laboratory, prompt and thorough investigation to trace the source of outbreaks, and institution of appropriate control measures provide effective control of community outbreaks.

  14. Molecular methods for the detection of human papillomavirus infection: new insights into their role in diagnostics and epidemiological surveillance

    Directory of Open Access Journals (Sweden)

    Andrea Piana

    2009-06-01

    Full Text Available Human papillomaviruses (HPVs comprise more than 180 genotypes. HPV infection is mainly diagnosed by molecular methods. The aim of our study was to review the main molecular methods used to diagnose HPV infection, underscoring their characteristics. Several methods have been developed for molecular diagnosis of Papilloma infection, such as those based on PCR technique. Another commercial non-PCR based diagnostic method is Hybrid Capture test; it is the only commercially available HPV DNA detection test approved by the FDA. Several Authors have suggested that viral load and E6/E7 transcripts could be used as surrogate markers of persistent HPV infection, being more specific predictors of progressive disease than the simple presence of HPV DNA. Validating clinical sensitivity and specificity of each technique and improving the interpretation of the results are essential; consequently, there is a clear need for well characterized international quality control panels to compare the various diagnostic methods. HPV DNA testing could be useful both as a primary screening test, alone or in combination with a Pap smear, for the early detection of cervical cancer precursors, and as triage test to select women with minor cytological abnormalities who will need further follow-up and to predict possible treatment failure in women with diagnosed high-grade intraepithelial lesions who have undergone excisional therapy. In the next future surveillance for HPV infections, based on these molecular methods, could represent an important step for the development of primary and secondary prophylactic interventions, such as new vaccines targeted to genotypes who might replace those previously prevalent.

  15. Molecular Epidemiology of Aspergillus fumigatus Isolates Recovered from Water, Air, and Patients Shows Two Clusters of Genetically Distinct Strains

    OpenAIRE

    Warris, Adilia; Klaassen, Corné H. W.; Meis, Jacques F. G. M.; de Ruiter, Maaike T.; de Valk, Hanneke A.; Abrahamsen, Tore G.; Gaustad, Peter; Verweij, Paul E.

    2003-01-01

    There has been an increase in data suggesting that besides air, hospital water is a potential source of transmission of filamentous fungi, and in particular Aspergillus fumigatus. Molecular characterization of environmental and clinical A. fumigatus isolates, collected prospectively during an 18-month period, was performed to establish if waterborne fungi play a role in the pathogenesis of invasive aspergillosis. Isolates recovered from water (n = 54) and air (n = 21) at various locations ins...

  16. Molecular Recognition: Detection of Colorless Compounds Based on Color Change

    Science.gov (United States)

    Khalafi, Lida; Kashani, Samira; Karimi, Javad

    2016-01-01

    A laboratory experiment is described in which students measure the amount of cetirizine in allergy-treatment tablets based on molecular recognition. The basis of recognition is competition of cetirizine with phenolphthalein to form an inclusion complex with ß-cyclodextrin. Phenolphthalein is pinkish under basic condition, whereas it's complex form…

  17. Molecular epidemiology and phylogenetic analysis of diverse bovine astroviruses associated with diarrhea in cattle and water buffalo calves in China.

    Science.gov (United States)

    Alfred, Niyokwishimira; Liu, Huan; Li, Mu Lan; Hong, Shao Feng; Tang, Hai Bo; Wei, Zu Zhang; Chen, Ying; Li, Fa Kai; Zhong, Yi Zhi; Huang, Wei Jian

    2015-06-01

    Astroviruses are the principal causative agents of gastroenteritis in humans and have been associated with diarrhea in other mammals as well as birds. However, astroviral infection of animals had been poorly studied. In the present study, 211 rectal swabs collected from cattle and water buffalo calves with mild to severe diarrhea were tested for bovine astrovirus (BAstV) by RT-PCR. Results: 92/211 (43.6%) samples were positive for BAstV, at a rate of 46.10% (71/154) in cattle and 36.84% (21/57) in water buffalo. Phylogenetic analysis based on the partial and full-length of 25 ORF2 amino acid sequences obtained in this study classified the Guangxi BAstVs isolates into five subgroups under the genus of Mamastrovirus, genotype MAstV33, which suggested that the water buffalo was a new host of this genogroup that previously included only cattle and roe deer. Despite the origin of the host, the Guangxi BAstV isolates were closely related to the BAstV Hong Kong isolates (B18/HK and B76-2/HK), but highly divergent from the BAstV NeuroS1 isolate previously associated with neurologic disease in cattle in the U.S.A. Nucleotide sequence-based characterization of the ORF1b/ORF2 junction and corresponding overlapping regions showed distinctive properties, which may be common to BAstVs. Our results suggested that cattle and water buffalo are prone to infection of closely related astroviruses, which probably evolved from the same ancestor. The current study described astroviruses in water buffalo for the first time and is thus far among the largest epidemiological investigations of BAstV infection in cattle conducted in China.

  18. Endodontic Epidemiology

    OpenAIRE

    Shahravan, Arash; Haghdoost, Ali Akbar

    2014-01-01

    Epidemiology is the study of disease distribution and factors determining or affecting it. Likewise, endodontic epidemiology can be defined as the science of studying the distribution pattern and determinants of pulp and periapical diseases; specially apical periodontitis. Although different study designs have been used in endodontics, researchers must pay more attention to study designs with higher level of evidence such as randomized clinical trials.

  19. Inflammatory breast cancer in North Africa: Comparison of clinical and molecular epidemiologic characteristics of patients from Egypt, Tunisia, and Morocco

    OpenAIRE

    Soliman, Amr S; Kleer, Celina G.; Mrad, Karima; Karkouri, Mehdi; Omar, Sherif; Khaled, Hussein M.; Benider, Abdel-Latif; Ayed, Farhat Ben; Eissa, Saad S.; Eissa, Mohab S.; McSpadden, Erin J.; Lo, An-Chi; Toy, Kathy; Kantor, Elizabeth D.; Xiao, Quin

    2011-01-01

    Understanding molecular characteristics that distinguish inflammatory breast cancer (IBC) from non-IBC is crucial for elucidating breast cancer etiology and management. We included 3 sets of patients from Egypt (48 IBC and 64 non-IBC), Tunisia (24 IBC and 40 non-IBC), and Morocco (42 IBC and 41 non-IBC). Egyptian IBC patients had the highest combined erythema, edema, peau d'orange, and metastasis among the 3 IBC groups. Egyptian IBC tumors had the highest RhoC expression than Tunisians and Mo...

  20. Profile of the HIV epidemic in Cape Verde: molecular epidemiology and drug resistance mutations among HIV-1 and HIV-2 infected patients from distinct islands of the archipelago.

    Science.gov (United States)

    de Pina-Araujo, Isabel Inês M; Guimarães, Monick L; Bello, Gonzalo; Vicente, Ana Carolina P; Morgado, Mariza G

    2014-01-01

    HIV-1 and HIV-2 have been detected in Cape Verde since 1987, but little is known regarding the genetic diversity of these viruses in this archipelago, located near the West African coast. In this study, we characterized the molecular epidemiology of HIV-1 and HIV-2 and described the occurrence of drug resistance mutations (DRM) among antiretroviral therapy naïve (ARTn) patients and patients under treatment (ARTexp) from different Cape Verde islands. Blood samples, socio-demographic and clinical-laboratory data were obtained from 221 HIV-positive individuals during 2010-2011. Phylogenetic and bootscan analyses of the pol region (1300 bp) were performed for viral subtyping. HIV-1 and HIV-2 DRM were evaluated for ARTn and ARTexp patients using the Stanford HIV Database and HIV-GRADE e.V. Algorithm Homepage, respectively. Among the 221 patients (169 [76.5%] HIV-1, 43 [19.5%] HIV-2 and 9 [4.1%] HIV-1/HIV-2 co-infections), 67% were female. The median ages were 34 (IQR = 1-75) and 47 (IQR = 12-84) for HIV-1 and HIV-2, respectively. HIV-1 infections were due to subtypes G (36.6%), CRF02_AG (30.6%), F1 (9.7%), URFs (10.4%), B (5.2%), CRF05_DF (3.0%), C (2.2%), CRF06_cpx (0.7%), CRF25_cpx (0.7%) and CRF49_cpx (0.7%), whereas all HIV-2 infections belonged to group A. Transmitted DRM (TDRM) was observed in 3.4% (2/58) of ARTn HIV-1-infected patients (1.7% NRTI, 1.7% NNRTI), but not among those with HIV-2. Among ARTexp patients, DRM was observed in 47.8% (33/69) of HIV-1 (37.7% NRTI, 37.7% NNRTI, 7.4% PI, 33.3% for two classes) and 17.6% (3/17) of HIV-2-infections (17.6% NRTI, 11.8% PI, 11.8% both). This study indicates that Cape Verde has a complex and unique HIV-1 molecular epidemiological scenario dominated by HIV-1 subtypes G, CRF02_AG and F1 and HIV-2 subtype A. The occurrence of TDRM and the relatively high level of DRM among treated patients are of concern. Continuous monitoring of patients on ART, including genotyping, are public policies to be implemented

  1. Profile of the HIV epidemic in Cape Verde: molecular epidemiology and drug resistance mutations among HIV-1 and HIV-2 infected patients from distinct islands of the archipelago.

    Directory of Open Access Journals (Sweden)

    Isabel Inês M de Pina-Araujo

    Full Text Available HIV-1 and HIV-2 have been detected in Cape Verde since 1987, but little is known regarding the genetic diversity of these viruses in this archipelago, located near the West African coast. In this study, we characterized the molecular epidemiology of HIV-1 and HIV-2 and described the occurrence of drug resistance mutations (DRM among antiretroviral therapy naïve (ARTn patients and patients under treatment (ARTexp from different Cape Verde islands. Blood samples, socio-demographic and clinical-laboratory data were obtained from 221 HIV-positive individuals during 2010-2011. Phylogenetic and bootscan analyses of the pol region (1300 bp were performed for viral subtyping. HIV-1 and HIV-2 DRM were evaluated for ARTn and ARTexp patients using the Stanford HIV Database and HIV-GRADE e.V. Algorithm Homepage, respectively. Among the 221 patients (169 [76.5%] HIV-1, 43 [19.5%] HIV-2 and 9 [4.1%] HIV-1/HIV-2 co-infections, 67% were female. The median ages were 34 (IQR = 1-75 and 47 (IQR = 12-84 for HIV-1 and HIV-2, respectively. HIV-1 infections were due to subtypes G (36.6%, CRF02_AG (30.6%, F1 (9.7%, URFs (10.4%, B (5.2%, CRF05_DF (3.0%, C (2.2%, CRF06_cpx (0.7%, CRF25_cpx (0.7% and CRF49_cpx (0.7%, whereas all HIV-2 infections belonged to group A. Transmitted DRM (TDRM was observed in 3.4% (2/58 of ARTn HIV-1-infected patients (1.7% NRTI, 1.7% NNRTI, but not among those with HIV-2. Among ARTexp patients, DRM was observed in 47.8% (33/69 of HIV-1 (37.7% NRTI, 37.7% NNRTI, 7.4% PI, 33.3% for two classes and 17.6% (3/17 of HIV-2-infections (17.6% NRTI, 11.8% PI, 11.8% both. This study indicates that Cape Verde has a complex and unique HIV-1 molecular epidemiological scenario dominated by HIV-1 subtypes G, CRF02_AG and F1 and HIV-2 subtype A. The occurrence of TDRM and the relatively high level of DRM among treated patients are of concern. Continuous monitoring of patients on ART, including genotyping, are public policies to be implemented.

  2. Sero-epidemiological evaluation of changes in Plasmodium falciparum and Plasmodium vivax transmission patterns over the rainy season in Cambodia

    DEFF Research Database (Denmark)

    Cook, Jackie; Speybroeck, Nico; Sochanta, Tho;

    2012-01-01

    In Cambodia, malaria transmission is low and most cases occur in forested areas. Sero-epidemiological techniques can be used to identify both areas of ongoing transmission and high-risk groups to be targeted by control interventions. This study utilizes repeated cross-sectional data to assess...

  3. Molecular epidemiology of HIV-1 transmission in a cohort of HIV-1 concordant heterosexual couples from Dakar, Senegal.

    Directory of Open Access Journals (Sweden)

    Wim Jennes

    Full Text Available BACKGROUND: A large number of HIV-1 infections in Africa occur in married couples. The predominant direction of intracouple transmission and the principal external origins of infection remain important issues of debate. METHODS: We investigated HIV-1 transmission in 46 HIV-1 concordant positive couples from Dakar, Senegal. Intracouple transmission was confirmed by maximum-likelihood phylogenetic analysis and pairwise distance comparisons of HIV-1 env gp41 sequences from both partners. Standardized interview data were used to deduce the direction as well as the external sources of the intracouple transmissions. RESULTS: Conservative molecular analyses showed linked viruses in 34 (74% couples, unlinked viruses in 6 (13% couples, and indeterminate results for 6 (13% couples. The interview data corresponded completely with the molecular analyses: all linked couples reported internal transmission and all unlinked couples reported external sources of infection. The majority of linked couples (93% reported the husband as internal source of infection. These husbands most frequently (82% reported an occasional sexual relationship as external source of infection. Pairwise comparisons of the CD4 count, antiretroviral therapy status, and the proportion of gp41 ambiguous base pairs within transmission pairs correlated with the reported order of infection events. CONCLUSIONS: In this suburban Senegalese population, a majority of HIV-1 concordant couples showed linked HIV-1 transmission with the husband as likely index partner. Our data emphasize the risk of married women for acquiring HIV-1 as a result of the occasional sexual relationships of their husbands.

  4. Molecular Epidemiology of Carbapenem-Resistant Acinetobacter Baumannii Complex Isolates from Patients that were Injured During the Eastern Ukrainian Conflict.

    Science.gov (United States)

    Granzer, Heike; Hagen, Ralf Matthias; Warnke, Philipp; Bock, Wolfgang; Baumann, Tobias; Schwarz, Norbert Georg; Podbielski, Andreas; Frickmann, Hagen; Koeller, Thomas

    2016-06-24

    This study addressed carbapenem-resistant Acinetobacter baumannii complex (ABC) isolates from patients that were injured during the military conflict in the Eastern Ukraine and treated at German Armed Forces Hospitals in 2014 and 2015. Clonal diversity of the strains and potential ways of transmission were analyzed. Patients with one or several isolation events of carbapenem-resistant ABC were included. Isolates were characterized by VITEK II-based identification and resistance testing, molecular screening for frequent carbapenemase genes, and DiversiLab rep-PCR-based typing. Available clinical information of the patients was assessed. From 21 young male Ukrainian patients with battle injuries, 32 carbapenem- and fluoroquinolone-resistant ABC strains were isolated. Four major clonal clusters were detected. From four patients (19%), ABC isolates from more than one clonal cluster were isolated. The composition of the clusters suggested transmission events prior to the admission to the German hospitals. The infection and colonization pressure in the conflict regions of the Eastern Ukraine with ABC of low clonal diversity is considerable. Respective infection risks have to be considered in case of battle-related injuries in these regions. The low number of local clones makes any molecular exclusion of transmission events difficult. PMID:27429793

  5. Malnutrition in a Modernising Economy: The Changing Aetiology and Epidemiology of Malnutrition in an African Kingdom, Buganda c.1940-73.

    Science.gov (United States)

    Nott, John

    2016-04-01

    The ecological fecundity of the northern shore of Lake Victoria was vital to Buganda's dominance of the interlacustrine region during the pre-colonial period. Despite this, protein-energy malnutrition was notoriously common throughout the twentieth century. This paper charts changes in nutritional illness in a relatively wealthy, food-secure area of Africa during a time of vast social, economic and medical change. In Buganda at least, it appears that both the causation and epidemiology of malnutrition moved away from the endemic societal causes described by early colonial doctors and became instead more defined by individual position within a rapidly modernising economy. PMID:26971598

  6. Malnutrition in a Modernising Economy: The Changing Aetiology and Epidemiology of Malnutrition in an African Kingdom, Buganda c.1940–73

    Science.gov (United States)

    Nott, John

    2016-01-01

    The ecological fecundity of the northern shore of Lake Victoria was vital to Buganda’s dominance of the interlacustrine region during the pre-colonial period. Despite this, protein-energy malnutrition was notoriously common throughout the twentieth century. This paper charts changes in nutritional illness in a relatively wealthy, food-secure area of Africa during a time of vast social, economic and medical change. In Buganda at least, it appears that both the causation and epidemiology of malnutrition moved away from the endemic societal causes described by early colonial doctors and became instead more defined by individual position within a rapidly modernising economy. PMID:26971598

  7. Sero-epidemiological evaluation of changes in Plasmodium falciparum and Plasmodium vivax transmission patterns over the rainy season in Cambodia

    Directory of Open Access Journals (Sweden)

    Cook Jackie

    2012-03-01

    Full Text Available Abstract Background In Cambodia, malaria transmission is low and most cases occur in forested areas. Sero-epidemiological techniques can be used to identify both areas of ongoing transmission and high-risk groups to be targeted by control interventions. This study utilizes repeated cross-sectional data to assess the risk of being malaria sero-positive at two consecutive time points during the rainy season and investigates who is most likely to sero-convert over the transmission season. Methods In 2005, two cross-sectional surveys, one in the middle and the other at the end of the malaria transmission season, were carried out in two ecologically distinct regions in Cambodia. Parasitological and serological data were collected in four districts. Antibodies to Plasmodium falciparum Glutamate Rich Protein (GLURP and Plasmodium vivax Merozoite Surface Protein-119 (MSP-119 were detected using Enzyme Linked Immunosorbent Assay (ELISA. The force of infection was estimated using a simple catalytic model fitted using maximum likelihood methods. Risks for sero-converting during the rainy season were analysed using the Classification and Regression Tree (CART method. Results A total of 804 individuals participating in both surveys were analysed. The overall parasite prevalence was low (4.6% and 2.0% for P. falciparum and 7.9% and 6.0% for P. vivax in August and November respectively. P. falciparum force of infection was higher in the eastern region and increased between August and November, whilst P. vivax force of infection was higher in the western region and remained similar in both surveys. In the western region, malaria transmission changed very little across the season (for both species. CART analysis for P. falciparum in the east highlighted age, ethnicity, village of residence and forest work as important predictors for malaria exposure during the rainy season. Adults were more likely to increase their antibody responses to P. falciparum during the

  8. Epidemiología molecular de la rabia urbana en Colombia, 1994-2004. La rabia en ecosistemas silvestres como amenaza para la población humana

    Directory of Open Access Journals (Sweden)

    Jorge Boshell

    2004-03-01

    Full Text Available

    En Colombia la rabia ocurre en dos ciclos epidemiológicos principales: la rabia urbana con el perro como principal reservorio y transmisor principalmente a humanos, y la rabia silvestre con especies animales de la vida silvestre como los quirópteros y zorros entre otros, como reservorios y transmisores principalmente a especies ganaderas y eventualmente a humanos que se convierten en víctimas accidentales. Durante los últimos años la rabia silvestre en Colombia ha cobrado mayor relevancia como problema de salud pública que la rabia urbana, a juzgar por el número de víctimas humanas. Con el fin de perfeccionar el diagnóstico y la tipificación del virus de la rabia en Colombia, el Laboratorio Nacional de Referencia del Instituto Nacional de Salud estandarizó técnicas para amplificar y secuenciar un fragmento de ADN complementario (cADN a una fracción de 902 nucleótidos seleccionados del ARN del virus, con el fin de adelantar estudios de epidemiología molecular. La fracción mencionada contiene secuencias que codifican para los aminoácidos 447-525 de la glicoproteína y 1-35 de la proteína L. Además contiene la región intergénica no codificante conocida como Pseudogen Psi.

    Las técnicas estandarizadas fueron las siguientes: a extracción de ARN total a partir de cerebro de ratón infectado. b amplificación molecular por transcripción reversa y reacción en cadena de la polimerasa. c secuenciación del fragmento amplificado.

    Mediante estas técnicas de epidemiología molecular viral se determinó que durante 1994-2004, la rabia urbana se concentró en tres regiones geográficas definidas, con epizootias en el antiplano cundiboyacense, departamento de Arauca y la región Caribe. Las dos primeras se controlaron

  9. Recognition of Conformational Changes in β-Lactoglobulin by Molecularly Imprinted Thin Films

    OpenAIRE

    Turner, Nicholas W.; Liu, Xiao; Piletsky, Sergey A.; Hlady, Vladimir; Britt, David W

    2007-01-01

    Pathogenesis in protein conformational diseases is initiated by changes in protein secondary structure. This molecular restructuring presents an opportunity for novel shape-based detection approaches, as protein molecular weight and chemistry are otherwise unaltered. Here we apply molecular imprinting to discriminate between distinct conformations of the model protein β-lactoglobulin (BLG). Thermal- and fluoro-alcohol-induced BLG isoforms were imprinted in thin films of 3-aminophenylboronic a...

  10. Retrospective epidemiological evaluation of molecular and animal husbandry data within the bovine viral diarrhoea virus (BVDV) control programme in Western Austria during 2009-2014.

    Science.gov (United States)

    Schoepf, Karl; Revilla-Fernández, Sandra; Steinrigl, Adolf; Fuchs, Reinhard; Sailer, Andreas; Weikel, Joachim; Schmoll, Friedrich

    2016-01-01

    A retrospective epidemiological investigation of molecular and animal husbandry data collected over an observation period of five years (2009-2014) within the compulsory bovine viral diarrhoea virus (BVDV) control programme in Western Austria, covering the federal provinces of Tyrol and Vorarlberg is presented in this study. Samples collected from 232 infected calves were phylogenetically classified based on the 5' untranslated region (5'UTR). All but 13 samples, which were typed as border disease virus subtype 3 (BDV-3), belonged to the bovine viral diarrhoea virus genotype 1 (BVDV-1) and clustered within six different subtypes (1b, 1e, 1f, 1h, 1d and 1k). Movement data and survival times from infected individual animals were analysed because of their potential of passing on infection to naive herds. From the moment of submission of the laboratory results, 180 animals were culled within the first month, 13 lived longer than two but not longer than six months and seven infected animals lived longer than one year. 13 of the infected animals were born on alpine pastures and eleven infected animals were grazed on mountain pastures during summer. The movement of infected animals and the role of trade in alpine areas are a possible source for spreading the infection, thus hampering the progress of eradication.

  11. Evaluation of two PCR-based techniques for molecular epidemiology in Finland, a high-endemic area with four sympatric Trichinella species

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    Kapel C.M.O.

    2001-06-01

    Full Text Available Trichinella larvae collected from wildlife, domestic and synanthropic animals in Finland were identified to species by two molecular techniques: Random amplified polymorphic DNA (RAPD polymerase chain reaction (PCR and the recently described multiplex PCR. The RAPD-PCR was very sensitive to the sub-optimal preservation muscle larvae and resulting in weak and smeared bands on the gels for such material. However, the same samples yielded easily recognizable bands in the multiplex PCR; this latter technique is then recommended for epidemiological studies, especially when the preservation of the samples is sub-optimal. For larvae in good condition the unequivocal bands obtained by multiplex was the easiest identifiable. Four species of Trichinella were identified in the material: T. spiralis, T. nativa, T. britovi, and T. pseudospiralis. Trichinella britovi is a new record for Finland, and T. pseudospiralis is a new record for Northern Europe. Mixed infections between T. britovi and T. spiralis, T. nativa and T. spiralis, and between T. britovi and T. nativa were detected; this is the first record of a mixed infection between T. spiralis and T. nativa in a naturally infected host. Raccoon dogs were the only host species from which all of the four Trichinella species were detected. Trichinella spiralis was found in both domestic animals and wildlife, but none of the sylvatic Trichinella species were detected in domestic pig.

  12. Rapid detection of Acinetobacter baumannii and molecular epidemiology of carbapenem-resistant A.baumannii in two comprehensive hospitals of Beijing, China

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    Puyuan eLi

    2015-09-01

    Full Text Available Acinetobacter baumannii is an important opportunistic pathogen associated with a variety of nosocomial infections. A rapid and sensitive molecular detection in clinical isolates is quite needed for the appropriate therapy and outbreak control of A. baumannii. Group 2 carbapenems have been considered the agents of choice for the treatment of multiple drug resistant A. baumannii. But the prevalence of carbapenem-resistant A. baumannii (CRAB has been steadily increasing in recent years. Here, we developed a loop-mediated isothermal amplification (LAMP assay for the rapid detection of A. baumannii in clinical samples by using high-specificity primers of the blaOXA-51 gene. Then we investigated the OXA-carbapenemases molecular epidemiology of A. baumannii isolates in 2 comprehensive hospitals in Beijing. The results showed that the LAMP assay could detect target DNA within 60 min at 65°C. The detection limit was 50 pg/μl, which was about 10-fold greater than that of PCR. Furthermore, this method could distinguish A. baumannii from the homologous A. nosocomialis and A. pittii. A total of 228 positive isolates were identified by this LAMP-based method for A. baumannii from 335 ICU patients with clinically suspected multi-resistant infections in 2 hospitals in Beijing. The rates of CRAB are on the rise and are slowly becoming a routine phenotype for A. baumannii. Among the CRABs, 92.3% harbored both the blaOXA-23 and blaOXA-51 genes. Thirty-three pulsotypes were identified by pulsed-field gel electrophoresis, and the majority belonged to clone C. In conclusion, the LAMP method developed for detecting A. baumannii was faster and simpler than conventional PCR and has great potential for both point-of-care testing and basic research. We further demonstrated a high distribution of class D carbapenemase-encoding genes, mainly OXA-23, which presents an emerging threat in hospitals in China.

  13. Clinical and Molecular Epidemiology of Multidrug-Resistant P. aeruginosa Carrying aac(6')-Ib-cr, qnrS1 and blaSPM Genes in Brazil.

    Science.gov (United States)

    Araujo, Bruna Fuga; Ferreira, Melina Lorraine; Campos, Paola Amaral de; Royer, Sabrina; Batistão, Deivid William da Fonseca; Dantas, Raquel Cristina Cavalcanti; Gonçalves, Iara Rossi; Faria, Ana Luiza Souza; Brito, Cristiane Silveira de; Yokosawa, Jonny; Gontijo-Filho, Paulo Pinto; Ribas, Rosineide Marques

    2016-01-01

    We described a comprehensive analysis of the molecular epidemiology of multidrug-resistant (MDR) P. aeruginosa. Molecular analysis included typing by Pulsed Field Gel Electrophoresis, identification of genes of interest through PCR-based assays and sequencing of target genes. Case-control study was conducted to better understand the prognostic of patients and the impact of inappropriate therapy in patients with bacteremia, as well as the risk factors of MDR infections. We observed a high rate of MDR isolates (40.7%), and 51.0% of them was independently associated with inappropriate antibiotic therapy. Bacteremia was detected in 66.9% of patients, and prolonged hospital stay was expressive in those resistant to fluoroquinolone. Plasmid-mediated quinolone resistance genes (PMQR), qnrS1 and aac(6')Ib-cr, were detected in two different nosocomial isolates (5.3%), and the aac(6')-Ib7 variant was detected at a high frequency (87.5%) in those negative to PMQR. The presence of mutations in gyrA and parC genes was observed in 100% and 85% of selected isolates, respectively. Isolates harboring PMQR genes or mutations in gyrA and parC were not closely related, except in those containing SPM (São Paulo metallo-β-lactamase) clone. In addition, there is no study published in Brazil to date reporting the presence of Pseudomonas aeruginosa isolates harboring both qnrS1 and aac(6')Ib-cr genes, with alarming frequency of patients with inappropriate therapy. PMID:27219003

  14. Extensive transmission of isoniazid resistant M. tuberculosis and its association with increased multidrug-resistant TB in two rural counties of eastern China: A molecular epidemiological study

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    Wang Weibing

    2010-02-01

    Full Text Available Abstract Background The aim of this study was to investigate the molecular characteristics of isoniazid resistant Mycobacterium tuberculosis (MTB, as well as its contribution to the dissemination of multi-drug resistant TB (MDR-TB in rural areas of eastern China. Methods A population-based epidemiological study was conducted in two rural counties of eastern China from 2004 to 2005. In total, 131 isoniazid resistant MTB isolates were molecularly characterized by DNA sequencing and genotyped by IS6110 restriction fragment length polymorphism (RFLP and spoligotyping. Results The katG315Thr mutation was observed in 74 of 131 isoniazid resistant isolates and more likely to be MDR-TB (48.6% and have mutations in rpoB gene (47.3%. Spoligotyping identified 80.2% of isoniazid resistant MTB isolates as belonging to the Beijing family. Cluster analysis by genotyping based on IS6110 RFLP, showed that 48.1% isoniazid resistant isolates were grouped into 26 clusters and katG315Thr mutants had a significantly higher clustering proportion compared to those with katG wild type (73%.vs.18%; OR, 12.70; 95%CI, 6.357-14.80. Thirty-one of the 53 MDR-TB isolates were observed in 19 clusters. Of these clusters, isoniazid resistance in MDR-TB isolates was all due to the katG315Thr mutation; 18 clusters also contained mono-isoniazid resistant and other isoniazid resistant isolates. Conclusions These results highlighted that isoniazid resistant MTB especially with katG315Thr is likely to be clustered in a community, develop extra resistance to rifampicin and become MDR-TB in Chinese rural settings.

  15. An outbreak of infections caused by extensively drug-resistant Klebsiella pneumoniae strains during a short period of time in a Chinese teaching hospital: epidemiology study and molecular characteristics.

    Science.gov (United States)

    Zhou, Tieli; Zhang, Yapei; Li, Meimei; Yu, Xiao; Sun, Yao; Xu, Jiru

    2015-07-01

    In this study, we comprehensively described the clinical risk factors, outcome, epidemiology, and molecular basis associated with an outbreak of extensively drug-resistant KPC-2-producing Klebsiella pneumoniae involving 15 patients in a teaching hospital from May 1 to June 27, 2013. Most of the patients were elderly and received long-term hospital treatment, and 40.0% (6/15) of them were dead. All strains carried bla(KPC-2), rmtB, bla(CTX-M-65), bla(SHV-11), oqxA, oqxB, and aac(6')-Ib-cr and even harbored additional other resistance genes, such as armA, bla(CTX-M-1), bla(TEM-1). bla(KPC-2), rmtB, and bla(CTX-M-65) were located on the same ~54.2-kb plasmid, and conjugation experiments further proved the cotransferable characteristic. Alterations of outer membrane proteins were confirmed by sodium dodecyl sulfate--olyacrylamide gelelectrophoresis and sequencing, which can lead to a drastic change in the permeability of cells. All isolates belonged to the clone complex 258, spreading rapidly across the world. Our study demonstrated that a high degree of awareness and surveillance of those drug resistance determinants is urgently needed. PMID:25865067

  16. Molecular Epidemiological Characteristics of Streptococcus pyogenes Strains Involved in an Outbreak of Scarlet Fever in China, 2011

    Institute of Scientific and Technical Information of China (English)

    YOU Yuan Hai; ZHANG Bing Hua; ZHOU Hao; XIAO Di; JIN Lian Mei; FENG Zi Jian; LUO Feng Ji; ZHANG Jian Zhong; SONG Yan Yang; YAN Xiao Mei; WANG Hai Bin; ZHANG Meng Han; TAO Xiao Xia; LI Lei Lei; ZHANG Yu Xin; JIANG Xi Hong

    2013-01-01

    Objective To investigate molecular characterization of streptococcus pyogenes isolates involved in an outbreak of scarlet fever in China in 2011. Methods Seventy-four Streptococcal pyogenes involved in an outbreak of scarlet fever were isolated from pediatric patients in the areas with high incidence in China from May to August of 2011. Emm genotyping, pulsed-field gel electrophoresis (PFGE), superantigen (SAg) genes and antimicrobial susceptibility profiling were analyzed for these isolates. Results A total of 4 different emm types were identified. Emm12 was the most prevalent type which contained four predominating PFGE patterns corresponding to four different virulence and superantigen profiles. Emm12 (79.7%) and emml (14.90 accounted for approximately 94} of all the isolates. The speA gene was all negative in emm12 isolates and positive in emml isolates. All strains were resistant to erythromycin, and 89.4% of them were resistant to erythromycin, tracycline, and clindamycin simultaneously. Conclusion Several highly diversified clones with a high macrolide resistance rate comprise a predominant proportion of circulating strains, though no new emm type was found in this outbreak. The data provide a baseline for further surveillance of scarlet fever, which may contribute to the explanation of the outbreak and development of a GAS vaccine in China.

  17. Circulation of HIV-1 CRF02_AG among MSM Population in Central Italy: A Molecular Epidemiology-Based Study

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    Massimo Giuliani

    2013-01-01

    Full Text Available Introduction. The evolutionary and demographic history of the circular recombinant form CRF02_AG in a selected retrospective group of HIV-1 infected men who have sex with men (MSM resident in Central Italy was investigated. Methods. A total of 55 HIV-1 subtype CRF02_AG pol sequences were analyzed using Bayesian methods and a relaxed molecular clock to reconstruct their dated phylogeny and estimate population dynamics. Results. Dated phylogeny indicated that the HIV-1 CRF02_AG strains currently circulating in Central Italy originated in the early 90's. Bayesian phylogenetic analysis revealed the existence of a main HIV-1 CRF02_AG clade, introduced in the area of Rome before 2000 and subsequently differentiated in two different subclades with a different date of introduction (2000 versus 2005. All the sequences within clusters were interspersed, indicating that the MSM analyzed form a close and restricted network where the individuals, also moving within different clinical centers, attend the same places to meet and exchange sex. Conclusions. It was suggested that the HIV-1 CRF02_AG epidemic entered central Italy in the early 1990s, with a similar trend observed in western Europe.

  18. INSIGHT INTO THE MOLECULAR AND GENETIC CHANGES IN HEART FAILURE

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    Sergio Dalla–Volta, MD, PhD

    2010-01-01

    Full Text Available n the last fifteen years much progress has been made on the knowledge of the mechanisms controlling the genetic and molecular activities of the mammalian (with special emphasis on the human heart in chronic cardiac insufficiency.This increased knowledge has greatly influenced the understanding and treatment of heart failure, helping to prolong duration of life; even if clear evidence of a long lasting improvement of the syndrome is lacking.The causes of heart failure are numerous and different, but the common feature depends on the modest regenerative capacity of the human heart after any important injury damaging the myocardium. Therefore, the more frequent consequence is the appearance of scar tissue, with collagen deposition and tissue remodelling. Even is some proliferation of cardiac myocites has been noted, this process is unable to overcome the destruction of normal cells observed in the several cardiac disorders, so that the only efficient response is usually the cellular hypertrophy.

  19. A molecular organic carbon isotope record of Miocene climate changes

    OpenAIRE

    Schoell, M.; Schouten, S.; Sinninghe Damsté, J.S.; J. W. de Leeuw; Summons, R. E.

    1994-01-01

    The difference in carbon-13 (13C) contents of hopane and sterane biomarkers in the Monterey formation (Naples Beach, California) parallels the Miocene inorganic record of the change in 18O (δ18O), reflecting the Miocene evolution from a well-mixed to a highly stratified photic zone (upper 100 meters) in the Pacific. Steranes (δ13C = 25.4 ± 0.7 per mil versus the Pee Dee belemnite standard) from shallow photic-zone organisms do not change isotopically throughout the Miocene. In contrast, sulfu...

  20. Risk factors, molecular epidemiology and outcomes of ertapenem-resistant, carbapenem-susceptible Enterobacteriaceae: a case-case-control study.

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    Jocelyn Teo

    Full Text Available BACKGROUND: Increasing prevalence of ertapenem-resistant, carbapenem-susceptible Enterobacteriaceae (ERE in Singapore presents a major therapeutic problem. Our objective was to determine risk factors associated with the acquisition of ERE in hospitalized patients; to assess associated patient outcomes; and to describe the molecular characteristics of ERE. METHODS: A retrospective case-case-control study was conducted in 2009 at a tertiary care hospital. Hospitalized patients with ERE and those with ertapenem-sensitive Enterobacteriaceae (ESE were compared with a common control group consisting of patients with no prior gram-negative infections. Risk factors analyzed included demographics; co-morbidities; instrumentation and antibiotic exposures. Two parallel multivariate logistic regression models were performed to identify independent variables associated with ERE and ESE acquisition respectively. Clinical outcomes were compared between ERE and ESE patients. RESULTS: Twenty-nine ERE cases, 29 ESE cases and 87 controls were analyzed. Multivariate logistic regression showed that previous hospitalization (Odds ratio [OR], 10.40; 95% confidence interval [CI], 2.19-49.20 and duration of fluoroquinolones exposure (OR, 1.18 per day increase; 95% CI, 1.05-1.34 were unique independent predictors for acquiring ERE. Duration of 4(th-generation cephalosporin exposure was found to predict for ESE acquisition (OR, 1.63 per day increase; 95% CI, 1.05-2.54. In-hospital mortality rates and clinical response rates were significantly different between ERE and ESE groups, however ERE infection was not a predictor of mortality. ERE isolates were clonally distinct. Ertapenem resistance was likely to be mediated by the presence of extended-spectrum β-lactamases or plasmid-borne AmpC in combination with impermeability due to porin loss and/or efflux pumps. CONCLUSION: Prior hospitalization and duration of fluoroquinolone treatment were predictors of ERE acquisition

  1. Epidemiological situation and molecular identification of cercarial stage in freshwater snails in Chao-Phraya Basin, Central Thailand

    Institute of Scientific and Technical Information of China (English)

    Sothorn Anucherngchai; Thanawan Tejangkura; Thapana Chontananarth

    2016-01-01

    Objective: To investigate the prevalence of cercarial trematode infection in snails and to examine the reconstruction of the phylogenetic relationship to explain the molecular system of cercarial stage trematodes to estimate the infection rate of in the definite host from the Chao-Phraya Basin. Methods: The snails were collected from 10 provinces of the Chao-Phraya Basin, Thailand by stratified sampling method. The snails were examined for cercarial infection by the crushing method. All DNA specimens were amplified with internal transcribed spacer 3 (ITS3) and ITS4 primer based on PCR technique. The sequence data were aligned and used to reconstruct the phylogenetic tree by unweighted pair-group method with arithmetic means with 10 000 bootstraps. Results: The overall rate of cercarial infection was found to be 5.90%(122/2 067). Snails in the family Thiaridae were found to be in the highest prevalence followed by Lym-naeidae, Bithyniidae, Planorbidae, Viviparidae, and Ampullariidae, respectively, while the Buccinidae family (Clea helena) did not reveal any infections. The frequently found species of cercariae were parapleurolophocercous cercariae, cercariae and megarulous cercariae. The monophyletic tree separated the snails into five groups comprised of Heterophyidae, Strigeidae, Lecithodendriidae, Philophthalmidae and Echinostomatidae using the sequence of Angiostrongylus cantonensis as an out-group. Conclusions: This study was the first to report on cercarial infection in the Chao-Phraya Basin, Thailand. This revealed that a high variety of freshwater snails were infected by cercariae stage trematodes with a high prevalence. The sequence data of ITS2 can be used to investigate the phylogenetic relationships of trematodes at the family level and in each clade of different families separated by the definitive hosts.

  2. Molecular epidemiology of extended-spectrum β-lactamase-producing Escherichia coli in the community and hospital in Korea: emergence of ST131 producing CTX-M-15

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    Park Sun

    2012-06-01

    Full Text Available Abstract Background The prevalence of extended-spectrum β-lactamase (ESBL-producing Escherichia coli has been increased not only in the hospital but also in the community worldwide. This study was aimed to characterize ESBL- producing E. coli isolates and to investigate the molecular epidemiology of community isolates in comparison with hospital isolates at a single center in Korea. Methods A total of 142 ESBL-producing E. coli isolates were collected at Daejeon St Mary’s Hospital in Korea from January 2008 to September 2009. The ESBLs were characterized by PCR sequencing using specific primers. The genetic relatedness was determined by pulsed field gel electrophoresis (PFGE and multilocus sequence typing (MLST. Results Of 142 isolates, 139 were positive for CTX-M type ESBLs; CTX-M-14 (n = 69, 49.6 %, CTX-M-15 (n = 53, 38.1 % and both CTX-M-14 and -15 (n = 17, 12.2 %. CTX-M-14 and CTX-M-15 were detected in both community and hospital isolates whereas isolates producing both CTX-M14 and-15 were mainly identified in the hospital. CTX-M producing E. coli isolates were genetically heterogeneous, revealing 75 distinct PFGE types. By MLST, 21 distinctive STs including 5 major STs (ST131, ST405, ST38, ST10, and ST648 were identified. Major STs were distributed in both community and hospital isolates, and ST131 was the predominant clone regardless of the locations of acquisition. No specific major STs were confined to a single type of ESBLs. However, ST131 clones were significantly associated with CTX-M-15 and the majority of them were multidrug-resistant. Distinctively, we identified a hospital epidemic caused by the dissemination of an epidemic strain, ST131-PFGE type 10, characterized by multidrug resistance and co-producing both CTX-Ms with OXA-1 or TEM-1b. Conclusions The epidemiology of ESBL-producing E. coli is a complex and evolving phenomenon attributed to the horizontal transfer of genetic elements and clonal spread of

  3. Epidemiological criminology

    OpenAIRE

    Ignjatović Đorđe

    2015-01-01

    Paper deals with one of so-called „new criminologies“ - specific amalgam composed by criminological and epidemiological experiences. First of all, the author points the main characteristics of these two sciences and their connections. After such explanations, he give examples of famous research in the field of ‘epidemiological criminology’. They show how many important issues in criminology has been neglected until the end of the twentieth century (evaluati...

  4. Endodontic Epidemiology

    Science.gov (United States)

    Shahravan, Arash; Haghdoost, Ali Akbar

    2014-01-01

    Epidemiology is the study of disease distribution and factors determining or affecting it. Likewise, endodontic epidemiology can be defined as the science of studying the distribution pattern and determinants of pulp and periapical diseases; specially apical periodontitis. Although different study designs have been used in endodontics, researchers must pay more attention to study designs with higher level of evidence such as randomized clinical trials. PMID:24688577

  5. Plant molecular stress responses face climate change. Trends in Plants

    NARCIS (Netherlands)

    Ahuja, I.; Vos, de R.C.H.; Bones, A.M.; Hall, R.D.

    2010-01-01

    Environmental stress factors such as drought, elevated temperature, salinity and rising CO2 affect plant growth and pose a growing threat to sustainable agriculture. This has become a hot issue due to concerns about the effects of climate change on plant resources, biodiversity and global food secur

  6. A molecular organic carbon isotope record of Miocene climate changes

    NARCIS (Netherlands)

    Schoell, M.; Schouten, S.; Sinninghe Damsté, J.S.; Leeuw, J.W. de; Summons, R.E.

    1994-01-01

    The difference in carbon-13 (13C) contents of hopane and sterane biomarkers in the Monterey formation (Naples Beach, California) parallels the Miocene inorganic record of the change in 18O (δ18O), reflecting the Miocene evolution from a well-mixed to a highly stratified photic zone (upper 100 meters

  7. A molecular organic carbon isotope record of miocene climate changes.

    Science.gov (United States)

    Schoell, M; Schouten, S; Damsté, J S; de Leeuw, J W; Summons, R E

    1994-02-25

    The difference in carbon-13 ((13)C) contents of hopane and sterane biomarkers in the Monterey formation (Naples Beach, California) parallels the Miocene inorganic record of the change in (18)O (delta(18)O), reflecting the Miocene evolution from a well-mixed to a highly stratified photic zone (upper 100 meters) in the Pacific. Steranes (delta(13)C = 25.4 +/- 0.7 per mil versus the Pee Dee belemnite standard) from shallow photic-zone organisms do not change isotopically throughout the Miocene. In contrast, sulfur-bound C(35) hopanes (likely derived from bacterial plankton living at the base of the photic zone) have systematically decreasing (13)C concentrations in Middle and Late Miocene samples (delta(13)C = -29.5 to -31.5 per mil), consistent with the Middle Miocene formation of a carbon dioxide-rich cold water mass at the base of the photic zone. PMID:17831625

  8. Use of Case Studies to Introduce Undergraduate Students to Principles of Food Microbiology, Molecular Biology, and Epidemiology of Food-Borne Disease

    Science.gov (United States)

    Ponder, Monica A.; Sumner, Susan

    2009-01-01

    Mock outbreaks of infectious disease offer the ability to introduce principles of food microbiology, ecology, and epidemiology to undergraduate students using an inquiry driven process. Students were presented with an epidemiological case study detailing patient history, clinical presentation, and foods recently consumed. The students then had to…

  9. Molecular epidemiology of influenza A(H1N1pdm09 viruses from Pakistan in 2009-2010.

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    Uzma Bashir Aamir

    Full Text Available BACKGROUND: In early 2009, a novel influenza A(H1N1 virus that emerged in Mexico and United States rapidly disseminated worldwide. The spread of this virus caused considerable morbidity with over 18000 recorded deaths. The new virus was found to be a reassortant containing gene segments from human, avian and swine influenza viruses. METHODS/RESULTS: The first case of human infection with A(H1N1pdm09 in Pakistan was detected on 18(th June 2009. Since then, 262 laboratory-confirmed cases have been detected during various outbreaks with 29 deaths (as of 31(st August 2010. The peak of the epidemic was observed in December with over 51% of total respiratory cases positive for influenza. Representative isolates from Pakistan viruses were sequenced and analyzed antigenically. Sequence analysis of genes coding for surface glycoproteins HA and NA showed high degree of high levels of sequence identity with corresponding genes of regional viruses circulating South East Asia. All tested viruses were sensitive to Oseltamivir in the Neuraminidase Inhibition assays. CONCLUSIONS: Influenza A(H1N1pdm09 viruses from Pakistan form a homogenous group of viruses. Their HA genes belong to clade 7 and show antigenic profile similar to the vaccine strain A/California/07/2009. These isolates do not show any amino acid changes indicative of high pathogenicity and virulence. It is imperative to continue monitoring of these viruses for identification of potential variants of high virulence or drug resistance.

  10. Peat molecular fossils recording paleoclimatic change and organism replacement

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The occurrence of the dominant C23 n-alkane derived from bryophyte was demonstrated to be related to the cold climate, based on the GC and GC/MS analyses on a 40-cm long peat core, in which this compound exponentially varies in abundance with the depth corresponding to the well-known second Little Ice Age. Both the variation of the chemical components of modern bryophyte resulted from climatic change and the ecological data about the biological growth influenced by climate shed light on the point that the variation of this compound in the peat was related to the cold climate. This was also evidenced by the previously-reported lacustrine data. In addition, the variations of the ratios of ketones/esters and C24 n-alkene/n-alkane (C24: t/C24: 0) display the trend identical with that of organisms, implicating the replacement between bryophyte and monocotyledon occurring in the peatcore.

  11. Molecular Epidemiology of Nosocomial Infection: Analysis of chro­mosomal Restriction Fragment Patterns by Pulsed-Field Gel Electro­phoresis

    Directory of Open Access Journals (Sweden)

    Afaf I Shehata

    2010-04-01

    Full Text Available Acinetobacter baumannii is a species of non-fermentative gram-negative coccobacilli commonly found in soil, water and other environmental samples. This bacterium is defined as being strict aerobes, nonmotile, catalase-positive and oxidase-negative. This organism was susceptible to most antibiotics in the 1970s. A. baumannii is an opportunistic pathogen that may be an important threat due to its increasing multidrug resistance and is involved in nosocomial infections that are often severe. The objective of this study was undertaken to elucidate the molecular epidemiology of A. baumannii using the most widely applicable DNA – based typing methods namely Pulsed-Field Gel Electrophoresis (PFGE. These strains comprised isolates from environmental samples, blood, wound, urine, cerebrospinal fluid and tracheal aspirates. PFGE analysis of 81 clinical isolates has been carried out by using CHEF–DR III systems from Bio – Rad and following the protocol of Gautom with some modifications. A 2.00% band tolerance and an optimization of 4.00% were selected for use during comparisons of generated fingerprints or pulsotypes after digestion with Apa I restriction enzyme. Similarity values have been generated using BioNumerics software, cluster analysis was performed by the unweighted pair – group method using arithmetic averages and DNA relatedness was calculated based on Dice coefficient. An interlinkage homology level of 80% between patterns was assumed as the cutoff for defining a close genetic relationship between strains and was used to define the cluster. As per the generated dendogram, isolates were categorized into 18 major groups designated as Strain I to Strain xvIII. Overall, PFGE was able to discriminate the 81 different Acinetobacter baumannii isolates with similarity levels of 63.63%.

  12. Molecular epidemiology of Rift Valley fever virus based on genetic analysis of the virus isolates recovered in 1944-2008 from distinct geographic regions

    International Nuclear Information System (INIS)

    Full text: Rift Valley fever (RVF) is an emerging mosquito-borne viral zoonosis caused by a RNA virus named Rift Valley fever virus (RVFV), a Phlebovirus member of the Bunyaviridae family. Historically the disease was present in Africa and Madagascar where outbreaks occur at irregular intervals when heavy rains facilitate the breeding of vector competent mosquito vectors. The occurrence of the first confirmed outbreaks of RVF in 2000-2001 among humans and livestock outside Africa, in the Arabian Peninsula, carries the implication of further spread of infection into non-endemic areas since the virus is capable of utilizing a wide range of mosquito vectors. This work undertook investigation of the molecular epidemiology of the disease (1944-2008) with special reference to South Africa where the first documented outbreak of RVF occurred in 1951 and the most recent in 2008. A total of 149 isolates of RVF recovered over a period of 65 years from various hosts and during endemic and epidemic periods of disease in 15 African countries, Madagascar and Saudi Arabia were characterised by partial genomic sequencing of a 535-nucleotide segment of the G2 glycoprotein coding region of the M segment and the genetic relatedness determined using MEGA software. Pair-wise comparison of RVF isolates revealed divergences ranging from 0-5.6% at the nucleotide level, corresponding to 0-2.8% at the amino acid level. Most isolates are compartmentalized geographically and belong to one of 16 genotypes within three main lineages. Isolates from South Africa collected over 57 years belong to one of 4 genotypes. The 2008 South African isolates were closely related to isolates from the recent east African outbreak in 2006 and a 2003 Mauritanian isolate. Phylogenetic analysis indicates that circulation of RVFV is highly compartmentalized but with favourable climatic conditions a single genotype can rapidly spread from endemic areas over vast distances to cause outbreaks in susceptible human and

  13. Molecular epidemiology and distribution of serotypes, genotypes, and antibiotic resistance genes of Streptococcus agalactiae clinical isolates from Guelma, Algeria and Marseille, France.

    Science.gov (United States)

    Bergal, A; Loucif, L; Benouareth, D E; Bentorki, A A; Abat, C; Rolain, J-M

    2015-12-01

    This study describes, for the first time, the genetic and phenotypic diversity among 93 Streptococcus agalactiae (group B Streptococcus, GBS) isolates collected from Guelma, Algeria and Marseille, France. All strains were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The molecular support of antibiotic resistance and serotyping were investigated by polymerase chain reaction (PCR). The phylogenetic lineage of each GBS isolate was determined by multilocus sequence typing (MLST) and grouped into clonal complexes (CCs) using eBURST. The isolates represented 37 sequence types (STs), 16 of which were novel, grouped into five CCs, and belonging to seven serotypes. Serotype V was the most prevalent serotype in our collection (44.1%). GBS isolates of each serotype were distributed among multiple CCs, including cps III/CC19, cps V/CC1, cps Ia/CC23, cps II/CC10, and cps III/CC17. All isolates presented susceptibility to penicillin, whereas resistance to erythromycin was detected in 40% and tetracycline in 82.2% of isolates. Of the 37 erythromycin-resistant isolates, 75.7% showed the macrolide-lincosamide-streptogramin B (MLSB)-resistant phenotype and 24.3% exhibited the macrolide (M)-resistant phenotype. Constitutive MLSB resistance (46%) mediated by the ermB gene was significantly associated with the Guelma isolates, whereas the M resistance phenotype (24.3%) mediated by the mefA/E gene dominated among the Marseille isolates and belonged to ST-23. Tetracycline resistance was predominantly due to tetM, which was detected alone (95.1%) or associated with tetO (3.7%). These results provide epidemiological data in these regions that establish a basis for monitoring increased resistance to erythromycin and also provide insight into correlations among clones, serotypes, and resistance genes. PMID:26415872

  14. Foveal slope measurements in diabetic retinopathy: Can it predict development of sight-threatening retinopathy? Sankara Nethralaya Diabetic Retinopathy Epidemiology and Molecular Genetics Study (SN-DREAMS II, Report no 8

    Directory of Open Access Journals (Sweden)

    Laxmi Gella

    2015-01-01

    Full Text Available Aim: The aim was to assess the foveal slope configuration in subjects with type 2 diabetes in a population-based study. Materials and Methods: A subset of 668 subjects from Sankara Nethralaya Diabetic Retinopathy (DR Epidemiology and Molecular Genetics Study II, a population-based study, were included in the current study. All the subjects underwent comprehensive ophthalmic evaluation including spectral domain optical coherence tomography. Foveal thickness was assessed in five central early treatment DR study quadrants from the three-dimensional scan and foveal slope was calculated in all the four quadrants. Results: Subjects with sight-threatening DR (STDR had significantly shallow foveal slope in inferior quadrant (STDR: 7.33 ± 6.26 vs. controls: 10.31 ± 3.44; P = 0.021 when compared to controls and in superior (STDR: 7.62 ± 5.81 vs. no DR: 9.11 ± 2.82; P = 0.033, inferior (STDR: 7.33 ± 6.26 vs. no DR: 8.81 ± 2.81; P = 0.048, and temporal quadrants (STDR: 6.69 ± 5.70 vs. no DR: 7.97 ± 2.33; P = 0.030 when compared to subjects with no DR. Foveal slope was significantly shallow among the older age groups in subjects with no DR (P < 0.001 and non-STDR (P = 0.027. Average foveal slope in the diabetic subjects was independently and significantly correlated with increase in age (r = −0.241; P < 0.001 and central subfield thickness (r = −0.542; P < 0.001. Conclusion: Changes in foveal slope were seen with increasing age; however, in diabetes these segmental slope changes can be seen in late DR (STDR.

  15. Structural Changes of a Doubly Spin-Labeled Chemically Driven Molecular Shuttle Probed by PELDOR Spectroscopy.

    Science.gov (United States)

    Franchi, Paola; Bleve, Valentina; Mezzina, Elisabetta; Schäfer, Christian; Ragazzon, Giulio; Albertini, Marco; Carbonera, Donatella; Credi, Alberto; Di Valentin, Marilena; Lucarini, Marco

    2016-06-20

    Gaining detailed information on the structural rearrangements associated with stimuli-induced molecular movements is of utmost importance for understanding the operation of molecular machines. Pulsed electron-electron double resonance (PELDOR) was employed to monitor the geometrical changes arising upon chemical switching of a [2]rotaxane that behaves as an acid-base-controlled molecular shuttle. To this aim, the rotaxane was endowed with stable nitroxide radical units in both the ring and axle components. The combination of PELDOR data and molecular dynamic calculations indicates that in the investigated rotaxane, the ring displacement along the axle, caused by the addition of a base, does not alter significantly the distance between the nitroxide labels, but it is accompanied by a profound change in the geometry adopted by the macrocycle. PMID:27123774

  16. Gynaekologisk epidemiologi

    DEFF Research Database (Denmark)

    Lidegaard, Øjvind

    2006-01-01

    Epidemiological research has good possibilities in Denmark due to the fact that all people have a personal PIN code and due to our many National health registers. In gynaecology the National Register of Patients, the Birth Registry, IVF-registry, Cancer Registry and latest the National Prescription...... Database offer unique possibilities of linking exposure data with many clinical outcomes. Danish epidemiology has contributed with morbidity analyses on children concieved by in vitro fertilisation, pharmacoepidemiological studies on short and long term effects of oral contraceptives and hormone therapy...

  17. Current-Driven Conformational Changes, Charging and Negative Differential Resistance in Molecular Wires

    OpenAIRE

    Emberly, Eldon; Kirczenow, George

    2001-01-01

    We introduce a theoretical approach based on scattering theory and total energy methods that treats transport non-linearities, conformational changes and charging effects in molecular wires in a unified way. We apply this approach to molecular wires consisting of chain molecules with different electronic and structural properties bonded to metal contacts. We show that non-linear transport in all of these systems can be understood in terms of a single physical mechanism and predict that negati...

  18. Molecular Epidemiology of Koi Herpesvirus

    NARCIS (Netherlands)

    Kurita, J.; Yuasa, K.; Ito, T.; Sano, M.; Hedrick, R.P.; Engelsma, M.Y.; Haenen, O.L.M.; Sunarto, A.; Kholidin, E.B.; Chou, H.Y.; Tung, M.C.; Pena, de la L.; Lio-Po, G.; Tu, C.; Way, K.; Iida, T.

    2009-01-01

    Three regions of koi herpesvirus (KHV) genomic DNA were compared for 34 samples from Japan, six from Indonesia, two from Taiwan, one from the Philippines, 13 from the Netherlands, one from the UK, one from the USA and one from Israel. The analyzed genomic regions included known PCR-detection targets

  19. Molecular epidemiology of Chlamydia trachomatis

    NARCIS (Netherlands)

    R.J.M. Bom

    2014-01-01

    Chlamydia trachomatis infections are the most prevalent bacterial sexually transmitted infections (STT) worldwide. A better understand of the transmission of C. trachomatis may contribute to improved screening and prevention programs in the future and ultimately alleviate this burden. Through the us

  20. Molecular epidemiology of Fonsecaea species.

    Science.gov (United States)

    Najafzadeh, Mohammad Javad; Sun, Jiufeng; Vicente, Vania A; Klaassen, Corne H W; Bonifaz, Alexandro; Gerrits van den Ende, A H G; Menken, Steph B J; de Hoog, G Sybren

    2011-03-01

    To assess population diversities among 81 strains of fungi in the genus Fonsecaea that had been identified down to species level, we applied amplified fragment-length polymorphism (AFLP) technology and sequenced the internal transcribed spacer regions and the partial cell division cycle, beta-tubulin, and actin genes. Many species of the genus Fonsecaea cause human chromoblastomycosis. Strains originated from a global sampling of clinical and environmental sources in the Western Hemisphere, Asia, Africa, and Europe. According to AFLP fingerprinting, Fonsecaea isolates clustered in 5 groups corresponding with F. pedrosoi, F. monophora, and F. nubica: the latter 2 species each comprised 2 groups, and F. pedrosoi appeared to be of monophyletic origin. F. pedrosoi was found nearly exclusively in Central and South America. F. monophora and F. nubica were distributed worldwide, but both showed substantial geographic structuring. Clinical cases outside areas where Fonsecaea is endemic were probably distributed by human migration.

  1. Molecular Epidemiology of Fonsecaea Species

    Science.gov (United States)

    Najafzadeh, Mohammad Javad; Sun, Jiufeng; Vicente, Vania A.; Klaassen, Corne H.W.; Bonifaz, Alexandro; van den Ende, A.H.G. Gerrits; Menken, Steph B.J.

    2011-01-01

    To assess population diversities among 81 strains of fungi in the genus Fonsecaea that had been identified down to species level, we applied amplified fragment-length polymorphism (AFLP) technology and sequenced the internal transcribed spacer regions and the partial cell division cycle, β-tubulin, and actin genes. Many species of the genus Fonsecaea cause human chromoblastomycosis. Strains originated from a global sampling of clinical and environmental sources in the Western Hemisphere, Asia, Africa, and Europe. According to AFLP fingerprinting, Fonsecaea isolates clustered in 5 groups corresponding with F. pedrosoi, F. monophora, and F. nubica: the latter 2 species each comprised 2 groups, and F. pedrosoi appeared to be of monophyletic origin. F. pedrosoi was found nearly exclusively in Central and South America. F. monophora and F. nubica were distributed worldwide, but both showed substantial geographic structuring. Clinical cases outside areas where Fonsecaea is endemic were probably distributed by human migration. PMID:21392438

  2. Epidemiological causality.

    Science.gov (United States)

    Morabia, Alfredo

    2005-01-01

    Epidemiological methods, which combine population thinking and group comparisons, can primarily identify causes of disease in populations. There is therefore a tension between our intuitive notion of a cause, which we want to be deterministic and invariant at the individual level, and the epidemiological notion of causes, which are invariant only at the population level. Epidemiologists have given heretofore a pragmatic solution to this tension. Causal inference in epidemiology consists in checking the logical coherence of a causality statement and determining whether what has been found grossly contradicts what we think we already know: how strong is the association? Is there a dose-response relationship? Does the cause precede the effect? Is the effect biologically plausible? Etc. This approach to causal inference can be traced back to the English philosophers David Hume and John Stuart Mill. On the other hand, the mode of establishing causality, devised by Jakob Henle and Robert Koch, which has been fruitful in bacteriology, requires that in every instance the effect invariably follows the cause (e.g., inoculation of Koch bacillus and tuberculosis). This is incompatible with epidemiological causality which has to deal with probabilistic effects (e.g., smoking and lung cancer), and is therefore invariant only for the population.

  3. The evolving epidemiology of inflammatory bowel disease.

    LENUS (Irish Health Repository)

    Shanahan, Fergus

    2009-07-01

    Epidemiologic studies in inflammatory bowel disease (IBD) include assessments of disease burden and evolving patterns of disease presentation. Although it is hoped that sound epidemiologic studies provide aetiological clues, traditional risk factor-based epidemiology has provided limited insights into either Crohn\\'s disease or ulcerative colitis etiopathogenesis. In this update, we will summarize how the changing epidemiology of IBD associated with modernization can be reconciled with current concepts of disease mechanisms and will discuss studies of clinically significant comorbidity in IBD.

  4. Combining directed acyclic graphs and the change-in-estimate procedure as a novel approach to adjustment-variable selection in ep