WorldWideScience

Sample records for changing molecular epidemiology

  1. Molecular epidemiology of ascariasis

    DEFF Research Database (Denmark)

    Betson, Martha; Halstead, Fennella; Nejsum, Peter;

      We are using molecular epidemiology techniques to study the population structure of Ascaris obtained from humans and pigs. Worms were obtained from human hosts on Zanzibar and in Uganda, Bangladesh, Guatemala and Nepal and Ascaris from pigs were collected from in Uganda, Tanzania, Denmark...

  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

    Directory of Open Access Journals (Sweden)

    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. Molecular epidemiology of giardiasis.

    Science.gov (United States)

    Cacciò, Simone M; Ryan, Una

    2008-08-01

    Giardia duodenalis is a widespread parasite of mammalian species, including humans. Due to its invariant morphology, investigation on aspects such as host specificity and transmission patterns requires a direct genetic characterization of cysts/trophozoites from host samples. A number of molecular assays have been developed to help unravel the complex epidemiology of this infection. A coherent picture has emerged from those studies, indicating the existence of seven genetic groups (or assemblages), two of which (A and B) are found in both humans and animals, whereas the remaining five (C-G) are host-specific. Sequence-based surveys have identified a number of genotypes within assemblages A and B in animal species, some of which may have zoonotic potential. Recently, however, molecular approaches have been complicated by the recognition of intra-isolate sequence heterogeneity (i.e., "mixed templates", that affects identification of subtypes within each assemblage), and by the unreliable assignment of isolates to G. duodenalis assemblages generated by different genetic markers. This raises concerns about previous interpretation of genotyping data, especially when single genetic markers have been used. The mechanisms that may be responsible for these findings, including allelic sequence heterozygosity and meiotic recombination, are discussed.

  5. 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.

  6. Molecular Epidemiology of Glanders, Pakistan

    OpenAIRE

    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

    2009-01-01

    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. [Future prospects of molecular epidemiology in tuberculosis].

    Science.gov (United States)

    Matsumoto, Tomoshige; Iwamoto, Tomotada

    2009-12-01

    )-VNTR system for developing discrimination power. By addition of 3 loci (ETR-A, VNTR-1982 and VNTR-2163 a) to JATA (12)-VNTR, we established new JATA (15)-VNTR. We found that the discrimination power of JATA (15)-VNTR was almost the same as that of RFLP analysis. 2. Molecular epidemiology of Mycobacterium tuberculosis reviewed by molecular epidemiology of other pathogenic bacteria: Eiji YOKOYAMA (Division of Bacteriology, Chiba Prefectural Institute of Public Health). Molecular epidemiology of M. tuberculosis should be progressed to two goals. First is the short-term goal that intends to elucidate the unapparent route of transmission of the organism. Second is the long-term goal that intends to ascertain the phylogeny of the organism. The combination of VNTR loci should be changed according to the goals of molecular epidemiology of the organism. 3. Progress of the research in molecular epidemiology of Mycobacterium tuberculosis: Tomotada IWAMOTO (Department of Microbiology, Kobe Institute of Health). In the past decade, molecular epidemiology of tuberculosis brought significant insights into the transmission of tuberculosis, genetic diversity of M. tuberculosis, population structure and geographical distribution of M. tuberculosis, etc. In the advanced stage of the molecular epidemiological study, we expect to change the current geno-typing based molecular epidemiology to whole genome-typing based molecular epidemiology on the basis of the rapid innovation of next-generation sequencing technology. 4. Clinical application of molecular epidemiology of tuberculosis: Tomoshige MATSUMOTO (Department of Clinical Research and Development, Osaka Prefectural Medical Center for Respiratory and Allergic Diseases). The molecular epidemiology can be applied in clinical practice. We showed some examples about usefulness of the clinical application of molecular epidemiology, especially using variable number of tandem repeats (VNTR) analysis. One example we showed: using VNTR, we can

  8. Web tools for molecular epidemiology of tuberculosis.

    Science.gov (United States)

    Shabbeer, Amina; Ozcaglar, Cagri; Yener, Bülent; Bennett, Kristin P

    2012-06-01

    In this study we explore publicly available web tools designed to use molecular epidemiological data to extract information that can be employed for the effective tracking and control of tuberculosis (TB). The application of molecular methods for the epidemiology of TB complement traditional approaches used in public health. DNA fingerprinting methods are now routinely employed in TB surveillance programs and are primarily used to detect recent transmissions and in outbreak investigations. Here we present web tools that facilitate systematic analysis of Mycobacterium tuberculosis complex (MTBC) genotype information and provide a view of the genetic diversity in the MTBC population. These tools help answer questions about the characteristics of MTBC strains, such as their pathogenicity, virulence, immunogenicity, transmissibility, drug-resistance profiles and host-pathogen associativity. They provide an integrated platform for researchers to use molecular epidemiological data to address current challenges in the understanding of TB dynamics and the characteristics of MTBC.

  9. 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

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

    Directory of Open Access Journals (Sweden)

    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.

  11. Molecular epidemiology of dengue viruses in Brazil

    Directory of Open Access Journals (Sweden)

    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.

  12. Molecular Epidemiology for Vector Research on Leishmaniasis

    Directory of Open Access Journals (Sweden)

    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.

  13. Evolution, phylogeny, and molecular epidemiology of Chlamydia.

    Science.gov (United States)

    Nunes, Alexandra; Gomes, João P

    2014-04-01

    The Chlamydiaceae are a family of obligate intracellular bacteria characterized by a unique biphasic developmental cycle. It encompasses the single genus Chlamydia, which involves nine species that affect a wide range of vertebral hosts, causing infections with serious impact on human health (mainly due to Chlamydia trachomatis infections) and on farming and veterinary industries. It is believed that Chlamydiales originated ∼700mya, whereas C. trachomatis likely split from the other Chlamydiaceae during the last 6mya. This corresponds to the emergence of modern human lineages, with the first descriptions of chlamydial infections as ancient as four millennia. Chlamydiaceae have undergone a massive genome reduction, on behalf of the deletional bias "use it or lose it", stabilizing at 1-1.2Mb and keeping a striking genome synteny. Their phylogeny reveals species segregation according to biological properties, with huge differences in terms of host range, tissue tropism, and disease outcomes. Genome differences rely on the occurrence of mutations in the >700 orthologous genes, as well as on events of recombination, gene loss, inversion, and paralogous expansion, affecting both a hypervariable region named the plasticity zone, and genes essentially encoding polymorphic and transmembrane head membrane proteins, type III secretion effectors and some metabolic pathways. Procedures for molecular typing are still not consensual but have allowed the knowledge of molecular epidemiology patterns for some species as well as the identification of outbreaks and emergence of successful clones for C. trachomatis. This manuscript intends to provide a comprehensive review on the evolution, phylogeny, and molecular epidemiology of Chlamydia.

  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.

  18. [TP53 mutations and molecular epidemiology].

    Science.gov (United States)

    Otsuka, Kazunori; Ishioka, Chikashi

    2007-05-01

    Tumor suppressor p53 protein is activated by a variety of cellular stresses through several pathways and transactivates its downstream genes, including regulators of cell cycle, apoptosis and DNA repair. The loss of p53 function by TP53 gene mutations therefore fails to activate these genes and is thought to be a critical cause of carcinogenesis and/or tumor progression. TP53 is one of the most frequently mutated genes in human cancer. TP53 mutations are found in about 50% of human cancers, although the frequency of TP53 mutations differs among tumor types. However, the degree of functional disorder of mutant p53 varies according to the type of TP53 mutation. And the effects of p53 on cancer formation and/or progression are influenced by the degree of p53 dysfunction. So it is important to analyze the effects of TP53 mutations carefully according to the oncogenicity of each mutation from the molecular epidemiological point of view. Here, together with some cautions needed for analyzing and interpreting the significance of TP53 gene mutations, we present some examples of the identified specific mutation spectrum and the correlation between the prognosis and TP53 mutation in some cancers.

  19. Molecular epidemiology: a multidisciplinary approach to understanding parasitic zoonoses.

    Science.gov (United States)

    Traub, R J; Monis, P T; Robertson, I D

    2005-10-01

    Sound application of molecular epidemiological principles requires working knowledge of both molecular biological and epidemiological methods. Molecular tools have become an increasingly important part of studying the epidemiology of infectious agents. Molecular tools have allowed the aetiological agent within a population to be diagnosed with a greater degree of efficiency and accuracy than conventional diagnostic tools. They have increased the understanding of the pathogenicity, virulence, and host-parasite relationships of the aetiological agent, provided information on the genetic structure and taxonomy of the parasite and allowed the zoonotic potential of previously unidentified agents to be determined. This review describes the concept of epidemiology and proper study design, describes the array of currently available molecular biological tools and provides examples of studies that have integrated both disciplines to successfully unravel zoonotic relationships that would otherwise be impossible utilising conventional diagnostic tools. The current limitations of applying these tools, including cautions that need to be addressed during their application are also discussed.

  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 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.

  2. 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.

  3. 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.

  4. Molecular epidemiology of Mycobacterium tuberculosis, Buenos Aires, Argentina.

    Science.gov (United States)

    Gonzalo, Ximena; Ambroggi, Marta; Cordova, Ezequiel; Brown, Tim; Poggi, Susana; Drobniewski, Francis

    2011-03-01

    To analyze the molecular epidemiology of Mycobacterium tuberculosis strains at a hospital in Buenos Aires, Argentina, and mutations related to multidrug-resistant and extensively drug-resistant tuberculosis, we conducted a prospective case-control study. Our findings reinforce the value of incorporating already standardized molecular methods for rapidly detecting resistance.

  5. Current molecular methods in epidemiological typing of Acinetobacter baumannii.

    Science.gov (United States)

    Rafei, Rayane; Kempf, Marie; Eveillard, Matthieu; Dabboussi, Fouad; Hamze, Monzer; Joly-Guillou, Marie-Laure

    2014-01-01

    The emergence of Acinetobacter baumannii during recent decades as an important nosocomial pathogen responsible of worldwide, intensively documented, outbreaks has resulted in a need for effective epidemiological typing methods. Throughout the years, many typing methods for A. baumannii epidemiological studies have been proposed from phenotypic to molecular methods. Currently, the use of phenotypic typing methods have declined considerably and been progressively replaced by molecular methods. In this review, we introduce the current molecular methods available for A. baumannii typing. Each method has its own advantages and disadvantages, and the selection of an appropriate genotyping method depends on studied objectives. This review sheds light on questions in different epidemiological settings and most molecular methods used to fit these objectives.

  6. 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

    2016-09-09

    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.

  7. 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

  8. Meningococcal disease: changes in epidemiology and prevention

    Directory of Open Access Journals (Sweden)

    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

  9. Dengue in Latin America: Systematic Review of Molecular Epidemiological Trends

    Science.gov (United States)

    Ramos-Castañeda, José; Barreto dos Santos, Flavia; Martínez-Vega, Ruth; Galvão de Araujo, Josélio Maria; Joint, Graham; Sarti, Elsa

    2017-01-01

    Dengue, the predominant arthropod-borne viral disease affecting humans, is caused by one of four distinct serotypes (DENV-1, -2, -3 or -4). A literature analysis and review was undertaken to describe the molecular epidemiological trends in dengue disease and the knowledge generated in specific molecular topics in Latin America, including the Caribbean islands, from 2000 to 2013 in the context of regional trends in order to identify gaps in molecular epidemiological knowledge and future research needs. Searches of literature published between 1 January 2000 and 30 November 2013 were conducted using specific search strategies for each electronic database that was reviewed. A total of 396 relevant citations were identified, 57 of which fulfilled the inclusion criteria. All four dengue virus serotypes were present and co-circulated in many countries over the review period (with the predominance of individual serotypes varying by country and year). The number of countries in which more than one serotype circulated steadily increased during the period under review. Molecular epidemiology data were found for Argentina, Bolivia, Brazil, the Caribbean region, Colombia, Ecuador, Mexico and Central America, Paraguay, Peru and Venezuela. Distinct lineages with different dynamics were found in each country, with co-existence, extinction and replacement of lineages occurring over the review period. Despite some gaps in the literature limiting the possibility for comparison, our review has described the molecular epidemiological trends of dengue infection. However, several gaps in molecular epidemiological information across Latin America and the Caribbean were identified that provide avenues for future research; in particular, sequence determination of the dengue virus genome is important for more precise phylogenetic classification and correlation with clinical outcome and disease severity. PMID:28068335

  10. 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.

  11. Molecular Epidemiology of Human Intestinal Amoebas in Iran

    Directory of Open Access Journals (Sweden)

    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.

  12. 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

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

    Directory of Open Access Journals (Sweden)

    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.

  14. Carbapenemases in Enterobacteriaceae: types and molecular epidemiology.

    Science.gov (United States)

    Martínez-Martínez, Luis; González-López, Juan José

    2014-12-01

    The most important mechanism of carbapenem resistance in Enterobacteriaceae is the production of carbapenemases, although resistance can also result from the synergistic activity between AmpC-type or (to a lesser extent) extended-spectrum beta-lactamases combined with decreased outer membrane permeability. Three major molecular classes of carbapenemases are recognized: A, B and D. Classes A and D are serine-beta-lactamases, whereas class B are metallo-beta-lactamases (their hydrolytic activity depends on the presence of zinc). In addition to carbapenems, carbapenemases also hydrolyze other beta-lactams, but the concrete substrate profile depends on the enzyme type. In general terms, class A enzymes are to some extent inhibited by clavulanic acid, and class B enzymes do not affect monobactams and are inhibited by zinc chelators. Given Enterobacteriaceae producing carbapenemases usually also contain gene coding for other mechanisms of resistance to beta-lactams, it is not unusual for the organisms to present complex beta-lactam resistance phenotypes. Additionally, these organisms frequently contain other genes that confer resistance to quinolones, aminoglycosides, tetracyclines, sulphonamides and other families of antimicrobial agents, which cause multiresistance or even panresistance. Currently, the most important type of class A carbapenemases are KPC enzymes, whereas VIM, IMP and (particularly) NDM in class B and OXA-48 (and related) in class D are the more relevant enzymes. Whereas some enzymes are encoded by chromosomal genes, most carbapenemases are plasmid-mediated (with genes frequently located in integrons), which favors the dissemination of the enzymes. Detailed information of the genetic platforms and the context of the genes coding for the most relevant enzymes will be presented in this review.

  15. Preeclampsia: from epidemiological observations to molecular mechanisms

    Directory of Open Access Journals (Sweden)

    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.

  16. 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.

  17. Standardised PCR-based molecular epidemiology of tuberculosis.

    Science.gov (United States)

    Allix-Béguec, C; Supply, P; Wanlin, M; Bifani, P; Fauville-Dufaux, M

    2008-05-01

    A population-based molecular epidemiology investigation has been undertaken to evaluate tuberculosis transmission and control in the Brussels-Capital Region (Belgium). All tuberculosis cases reported from January 2003 to December 2004 were investigated. In total, 536 Mycobacterium tuberculosis isolates (89% of culture-positive samples) were genotyped by the newly standardised 24 loci-based mycobacterial interspersed repetitive unit-variable number tandem-repeat typing, spoligotyping and IS6110 fingerprinting. Of all the patients, 30% were grouped based on strain clusters, suggesting a transmission index of 20%. An unsuspected outbreak entailing > or = 23 patients was evidenced by molecular typing analysis and confirmed by contact tracing. Foreign-born status accounted for 79% of the studied patients, including 37.9% illegal immigrants and asylum seekers. Among foreign-born patients, asylum seekers and illegal immigrants were significantly less abundant in strain clusters than settled residents. Tuberculosis in the Brussels-Capital Region is a bi-faceted problem, comprising both persisting recent transmission and "imported diseases". Molecular epidemiology based on real-time genotyping techniques has proven invaluable in better understanding tuberculosis transmission. However, it will most efficiently contribute to tuberculosis control when implemented in an integrated public health system.

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

    Directory of Open Access Journals (Sweden)

    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.

  19. Malignant Catarrhal Fever: Understanding Molecular Diagnostics in Context of Epidemiology

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    Hong Li

    2011-10-01

    Full Text Available Malignant catarrhal fever (MCF is a frequently fatal disease, primarily of ruminants, caused by a group of gammaherpesviruses. Due to complexities of pathogenesis and epidemiology in various species, which are either clinically-susceptible or reservoir hosts, veterinary clinicians face significant challenges in laboratory diagnostics. The recent development of specific assays for viral DNA and antibodies has expanded and improved the inventory of laboratory tests and opened new opportunities for use of MCF diagnostics. Issues related to understanding and implementing appropriate assays for specific diagnostic needs must be addressed in order to take advantage of molecular diagnostics in the laboratory.

  20. Epidemiología molecular de la tuberculosis en Asturias

    OpenAIRE

    Penedo Pallares, Ana

    2012-01-01

    La tuberculosis sigue siendo en la actualidad una de las enfermedades infecciosas con mayor tasa de mortalidad en el mundo. En España la incidencia de la tuberculosis se sitúa en torno a los 15-20 casos por 100.000 habitantes; esta tasa duplica o triplica a la de otros países de nuestro entorno. Asturias se encuentra situada dentro la media española. La epidemiología molecular de la tuberculosis pretende detectar y confirmar brotes; identificar cepas de importancia en salud pública; conocer l...

  1. Molecular approaches to epidemiology and clinical aspects of malaria.

    Science.gov (United States)

    Brown, G V; Beck, H P; Molyneux, M; Marsh, K

    2000-10-01

    Malaria is a problem of global importance, responsible for 1-2 million deaths per year, mainly in African children, as well as considerable morbidity manifested as severe anaemia and encephalopathy in young children. Fundamental to the development of new tools for malaria control in humans is an increased understanding of key features of malaria infection, such as the diversity of outcome in different individuals, the understanding of different manifestations of the disease and of the mechanisms of immunity that allow clinical protection in the face of ongoing low-grade infection (concomitant immunity or premunition). Here, Graham Brown and colleagues review some of the ways in which molecular approaches might be used to increase our understanding of the epidemiology and clinical manifestations of malaria, as discussed at the Molecular Approaches to Malaria conference (MAM2000), Lorne, Australia, 2-5 February 2000.

  2. The role of epidemiology in the era of molecular epidemiology and genomics: Summary of the 2013 AJE-sponsored Society of Epidemiologic Research Symposium.

    Science.gov (United States)

    Kuller, Lewis H; Bracken, Michael B; Ogino, Shuji; Prentice, Ross L; Tracy, Russell P

    2013-11-01

    On June 20, 2013, the American Journal of Epidemiology sponsored a symposium at the Society for Epidemiologic Research's 46th Annual Meeting in Boston, Massachusetts, entitled, "What Is the Role of Epidemiology in the Era of Molecular Biology and Genomics?" The future of epidemiology depends on innovation in generating interesting and important testable hypotheses that are relevant to population health. These new strategies will depend on new technology, both in measurement of agents and environment and in the fields of pathophysiology and outcomes, such as cellular epidemiology and molecular pathology. The populations to be studied, sample sizes, and study designs should be selected based on the hypotheses to be tested and include case-control, cohort, and clinical trials. Developing large mega cohorts without attention to specific hypotheses is inefficient, will fail to address many associations with high-quality data, and may well produce spurious results.

  3. Revitalization and Social Change: Contributions from Psychiatric Epidemiology.

    Science.gov (United States)

    Foulks, Edward F.

    The relationship between schizophrenia and social change is examined through a review of recent medical research in genetics, biology, and epidemiology. Those mental traits that today in our society characterize the schizoprenic, in a previous era or in another society may have provided a mechanism for cultural change during the periods of stress…

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

    Directory of Open Access Journals (Sweden)

    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.

  5. 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

  6. Proceedings of the third international molecular pathological epidemiology (MPE) meeting.

    Science.gov (United States)

    Campbell, Peter T; Rebbeck, Timothy R; Nishihara, Reiko; Beck, Andrew H; Begg, Colin B; Bogdanov, Alexei A; Cao, Yin; Coleman, Helen G; Freeman, Gordon J; Heng, Yujing J; Huttenhower, Curtis; Irizarry, Rafael A; Kip, N Sertac; Michor, Franziska; Nevo, Daniel; Peters, Ulrike; Phipps, Amanda I; Poole, Elizabeth M; Qian, Zhi Rong; Quackenbush, John; Robins, Harlan; Rogan, Peter K; Slattery, Martha L; Smith-Warner, Stephanie A; Song, Mingyang; VanderWeele, Tyler J; Xia, Daniel; Zabor, Emily C; Zhang, Xuehong; Wang, Molin; Ogino, Shuji

    2017-02-01

    Molecular pathological epidemiology (MPE) is a transdisciplinary and relatively new scientific discipline that integrates theory, methods, and resources from epidemiology, pathology, biostatistics, bioinformatics, and computational biology. The underlying objective of MPE research is to better understand the etiology and progression of complex and heterogeneous human diseases with the goal of informing prevention and treatment efforts in population health and clinical medicine. Although MPE research has been commonly applied to investigating breast, lung, and colorectal cancers, its methodology can be used to study most diseases. Recent successes in MPE studies include: (1) the development of new statistical methods to address etiologic heterogeneity; (2) the enhancement of causal inference; (3) the identification of previously unknown exposure-subtype disease associations; and (4) better understanding of the role of lifestyle/behavioral factors on modifying prognosis according to disease subtype. Central challenges to MPE include the relative lack of transdisciplinary experts, educational programs, and forums to discuss issues related to the advancement of the field. To address these challenges, highlight recent successes in the field, and identify new opportunities, a series of MPE meetings have been held at the Dana-Farber Cancer Institute in Boston, MA. Herein, we share the proceedings of the Third International MPE Meeting, held in May 2016 and attended by 150 scientists from 17 countries. Special topics included integration of MPE with immunology and health disparity research. This meeting series will continue to provide an impetus to foster further transdisciplinary integration of divergent scientific fields.

  7. Epidemiological and functional implications of molecular variants of human papillomavirus

    Directory of Open Access Journals (Sweden)

    L. Sichero

    2006-06-01

    Full Text Available Human papillomavirus genomes are classified into molecular variants when they present more than 98% of similarity to the prototype sequence within the L1 gene. Comparative nucleotide sequence analyses of these viruses have elucidated some features of their phylogenetic relationship. In addition, human papillomavirus intratype variability has also been used as an important tool in epidemiological studies of viral transmission, persistence and progression to clinically relevant cervical lesions. Until the present, little has been published concerning the functional significance of molecular variants. It has been shown that nucleotide variability within the long control region leads to differences in the binding affinity of some cellular transcriptional factors and to the enhancement of the expression of E6 and E7 oncogenes. Furthermore, in vivo and in vitro studies revealed differences in E6 and E7 biochemical and biological properties among molecular variants. Nevertheless, further correlation with additional functional information is needed to evaluate the significance of genome intratypic variability. These results are also important for the development of vaccines and to determine the extent to which immunization with L1 virus-like particles of one variant could induce antibodies that cross-neutralize other variants.

  8. 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.

  9. Molecular epidemiology of Pasteurella multocida in dairy and beef calves.

    Science.gov (United States)

    Hotchkiss, E J; Hodgson, J C; Schmitt-van de Leemput, E; Dagleish, M P; Zadoks, R N

    2011-08-05

    The molecular epidemiology of Pasteurella multocida has rarely been studied at the farm level in cattle. The aim of this study was to determine whether single or multiple strains of P. multocida tend to exist within farms. Molecular characterisation was carried out on isolates obtained from nasal swabs from 105 calves from 32 randomly selected beef and dairy farms located throughout Scotland, and from 131 calves from 20 farms in the Mayenne region of France, where sampling occurred in response to respiratory disease outbreaks. P. multocida isolates were characterised by random-amplified polymorphic DNA (RAPD) typing and pulsed-field gel electrophoresis (PFGE) using restriction enzyme ApaI. In addition, isolates representative of each farm/RAPD profile combination were typed by multilocus sequence typing (MLST). Among 105 Scottish isolates, 15 RAPD profiles were distinguished. The majority of farms (27/32) had indistinguishable profiles in all positive animals. Five farms had two profiles. Among 140 French isolates, 23 RAPD profiles were distinguished. More within-farm heterogeneity was observed although 10/20 farms had just one profile (E4) in sampled calves. Profile E4 accounted for 60% (84/140) of French isolates. PFGE was more discriminatory than RAPD but confirmed results with respect to within farm homogeneity or heterogeneity of strains, whereas MLST was not discriminatory enough for farm level epidemiology. As in other host species, either several strains or one dominant strain of P. multocida may exist within farms, with evidence for a role of management factors such as movements onto the farm in the number of strains detected.

  10. The changing epidemiology of Staphylococcus aureus bloodstream infection

    DEFF Research Database (Denmark)

    Laupland, K B; Lyytikäinen, O; Søgaard, M;

    2012-01-01

    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...

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

    OpenAIRE

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

    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 arti...

  13. 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. PMID:26584829

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

    Directory of Open Access Journals (Sweden)

    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.

  15. Changing epidemiology of Helicobacter pylori in Japan.

    Science.gov (United States)

    Inoue, Manami

    2017-03-01

    Helicobacter pylori (H. Pylori) is known as the most important cause of gastric cancer. The prevalence of H. pylori infection varies widely by geographic area, age, and socioeconomic status. In Japan, H. pylori infection has been highly correlated with the incidence rate of gastric cancer, and a reduction in H. pylori infection is therefore crucial for decreasing the incidence of gastric cancer, especially at the population level. Infection occurs during childhood, commonly before 5 years of age. In Japan, where gastric cancer has ranked as the most common cancer by incidence and mortality for the last several decades, the prevalence of H. pylori infection has dramatically declined by birth cohort effect, mainly due to improvements in the general hygiene environment in childhood. Older generations born before around 1950 show a high prevalence of around 80-90 %, decreasing with age to reach around 10 % or less in those born around the 1990s, and less than 2 % for children born after the year 2000. This change will have generational effects on gastric cancer prevention strategies, both primary and secondary. The risk-stratified approach to gastric cancer prevention should be considered in Japan and other countries which have similarly experienced rapid economic development.

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

    Directory of Open Access Journals (Sweden)

    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.

  17. 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.

  18. Molecular epidemiology, cancer-related symptoms, and cytokines pathway.

    Science.gov (United States)

    Reyes-Gibby, Cielito C; Wu, Xifeng; Spitz, Margaret; Kurzrock, Razelle; Fisch, Michael; Bruera, Eduardo; Shete, Sanjay

    2008-08-01

    The Human Genome Project and HapMap have led to a better appreciation of the importance of common genetic variation in determining cancer risk, created potential for predicting response to therapy, and made possible the development of targeted prevention and therapeutic interventions. Advances in molecular epidemiology can be used to explore the role of genetic variation in modulating the risk for severe and persistent symptoms, such as pain, depression, and fatigue, in patients with cancer. The same genes that are implicated in cancer risk might also be involved in the modulation of therapeutic outcomes. For example, polymorphisms in several cytokine genes are potential markers for genetic susceptibility both for cancer risk and for cancer-related symptoms. These genetic polymorphisms are stable markers and easily and reliably assayed to explore the extent to which genetic variation might prove useful in identifying patients with cancer at high-risk of symptom development. Likewise, they could identify subgroups who might benefit most from symptom intervention, and contribute to developing personalized and more effective therapies for persistent symptoms.

  19. 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.

  20. Molecular epidemiology studies on occupational and environmental exposure to mutagens and carcinogens, 1997-1999.

    OpenAIRE

    2000-01-01

    Molecular epidemiology is a new and evolving area of research, combining laboratory measurement of internal dose, biologically effective dose, biologic effects, and influence of individual susceptibility with epidemiologic methodologies. Biomarkers evaluated were selected according to basic scheme: biomarkers of exposure--metabolites in urine, DNA adducts, protein adducts, and Comet assay parameters; biomarkers of effect--chromosomal aberrations, sister chromatid exchanges, micronuclei, mutat...

  1. 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…

  2. The contribution of molecular epidemiology to the understanding and control of viral diseases of salmonid aquaculture

    Directory of Open Access Journals (Sweden)

    Snow Michael

    2011-04-01

    Full Text Available Abstract Molecular epidemiology is a science which utilizes molecular biology to define the distribution of disease in a population (descriptive epidemiology and relies heavily on integration of traditional (or analytical epidemiological approaches to identify the etiological determinants of this distribution. The study of viral pathogens of aquaculture has provided many exciting opportunities to apply such tools. This review considers the extent to which molecular epidemiological studies have contributed to better understanding and control of disease in aquaculture, drawing on examples of viral diseases of salmonid fish of commercial significance including viral haemorrhagic septicaemia virus (VHSV, salmonid alphavirus (SAV and infectious salmon anaemia virus (ISAV. Significant outcomes of molecular epidemiological studies include: Improved taxonomic classification of viruses A better understanding of the natural distribution of viruses An improved understanding of the origins of viral pathogens in aquaculture An improved understanding of the risks of translocation of pathogens outwith their natural host range An increased ability to trace the source of new disease outbreaks Development of a basis for ensuring development of appropriate diagnostic tools An ability to classify isolates and thus target future research aimed at better understanding biological function While molecular epidemiological studies have no doubt already made a significant contribution in these areas, the advent of new technologies such as pyrosequencing heralds a quantum leap in the ability to generate descriptive molecular sequence data. The ability of molecular epidemiology to fulfil its potential to translate complex disease pathways into relevant fish health policy is thus unlikely to be limited by the generation of descriptive molecular markers. More likely, full realisation of the potential to better explain viral transmission pathways will be dependent on the

  3. 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...

  4. Phylogeography and molecular epidemiology of Yersinia pestis in Madagascar.

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    Amy J Vogler

    2011-09-01

    Full Text Available BACKGROUND: Plague was introduced to Madagascar in 1898 and continues to be a significant human health problem. It exists mainly in the central highlands, but in the 1990s was reintroduced to the port city of Mahajanga, where it caused extensive human outbreaks. Despite its prevalence, the phylogeography and molecular epidemiology of Y. pestis in Madagascar has been difficult to study due to the great genetic similarity among isolates. We examine island-wide geographic-genetic patterns based upon whole-genome discovery of SNPs, SNP genotyping and hypervariable variable-number tandem repeat (VNTR loci to gain insight into the maintenance and spread of Y. pestis in Madagascar. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed a set of 262 Malagasy isolates using a set of 56 SNPs and a 43-locus multi-locus VNTR analysis (MLVA system. We then analyzed the geographic distribution of the subclades and identified patterns related to the maintenance and spread of plague in Madagascar. We find relatively high levels of VNTR diversity in addition to several SNP differences. We identify two major groups, Groups I and II, which are subsequently divided into 11 and 4 subclades, respectively. Y. pestis appears to be maintained in several geographically separate subpopulations. There is also evidence for multiple long distance transfers of Y. pestis, likely human mediated. Such transfers have resulted in the reintroduction and establishment of plague in the port city of Mahajanga, where there is evidence for multiple transfers both from and to the central highlands. CONCLUSIONS/SIGNIFICANCE: The maintenance and spread of Y. pestis in Madagascar is a dynamic and highly active process that relies on the natural cycle between the primary host, the black rat, and its flea vectors as well as human activity.

  5. 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.

  6. Molecular epidemiology of hepatitis A virus infection in Northeast India.

    Science.gov (United States)

    Bose, Moumita; Bose, Sujoy; Saikia, Anjan; Medhi, Subhash; Deka, Manab

    2015-07-01

    The present study was undertaken to screen the molecular epidemiology of Hepatitis A virus (HAV) in Northeast India (NEI) who are ethnically distinct, tribal dominated and of lower socio-economic status with almost no information available from NEI on these aspects. Briefly, 3 ml blood was collected from 324 random liver disease cases with jaundice, receiving care at Central Hospital, N.F. Railway, Guwahati, Assam with informed consent. The patients detected with HAV-IgM positive status were included and were stratified as acute viral hepatitis (AVH) and fulminant hepatitis (FHF) based on clinical profile. Viral RNA was isolated and HAV-RNA was detected by Real-time PCR using primers for the VP3-VP1 region. HAV genotyping was studied by PCR-direct sequencing-phylogenetic analysis approach using the VP1/2A region of HAV isolates. Statistical analysis was performed using SPSS13.0 software. A total of 69 cases were HAV infected with two HBV co-infected cases (n = 69 + 2 = 71), 62 cases and two co-infected cases were AVH and others were FHF cases. HAV infection was predominant in especially in the young and adult age group. HAV-RNA was detected in 28 cases, out of which 19 cases could be genotyped (12 AVH, 7 FHF); which showed the prevalence of genotype IIIA or IA only. Although HAV genotype IIIA was the major genotype in both the AVH (10/12, 83.33%) and FHF (5/7, 71.43%) group, but the difference in distribution of genotypes in AVH and FHF cases was statistically non-significant (P = 0.550). HAV genotype IIIA is associated with the majority of HAV infected cases and severity in NEI.

  7. Molecular epidemiology of hepatitis B virus in Misiones, Argentina.

    Science.gov (United States)

    Mojsiejczuk, Laura Noelia; Torres, Carolina; Sevic, Ina; Badano, Inés; Malan, Richard; Flichman, Diego Martin; Liotta, Domingo Javier; Campos, Rodolfo Hector

    2016-10-01

    Hepatitis B virus (HBV) infection is a major public health problem worldwide. The aims of this study were to describe the molecular epidemiology of HBV in the Province of Misiones, Argentina and estimate the phylodynamic of the main groups in a Bayesian coalescent framework. To this end, partial or complete genome sequences were obtained from 52 blood donor candidates. The phylogenetic analysis based on partial sequences of S/P region showed a predominance of genotype D (65.4%), followed by genotype F (30.8%) and genotype A as a minority (3.8%). At subgenotype level, the circulation of subgenotypes D3 (42.3%), D2 (13.5%), F1b (11.5%) and F4 (9.6%) was mainly identified. The Bayesian coalescent analysis of 29 complete genome sequences for the main groups revealed that the subgenotypes D2 and D3 had several introductions to the region, with ancestors dating back from 1921 to 1969 and diversification events until the late '70s. The genotype F in Misiones has a more recent history; subgenotype F4 isolates were intermixed with sequences from Argentina and neighboring countries and only one significant cluster dated back in 1994 was observed. Subgenotype F1b isolates exhibited low genetic distance and formed a closely related monophyletic cluster, suggesting a very recent introduction. In conclusion, the phylogenetic and coalescent analyses showed that the European genotype D has a higher circulation, a longer history of diversification and may be responsible for the largest proportion of chronic HBV infections in the Province of Misiones. Genotype F, especially subgenotype F1b, had a more recent introduction and its diversification in the last 20years might be related to its involvement in new transmission events.

  8. 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

  9. 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...

  10. 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.

  11. 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

  12. 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

  13. 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

  14. 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.

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

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    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.

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

    Directory of Open Access Journals (Sweden)

    Luis David Castiel

    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'.

  17. Malignant catarrhal fever: understanding molecular diagnostics in context of epidemiology

    Science.gov (United States)

    Malignant catarrhal fever (MCF) is a frequently fatal disease, primarily of ruminants, caused by a group of gammaherpesviruses. Due to complexities of pathogenesis and epidemiology in various species which are either clinically-susceptible or reservoir hosts, veterinary clinicians face significant ...

  18. Molecular Identification and Epidemiological Aspects of Dermatophytosis in Tehran, Iran

    Directory of Open Access Journals (Sweden)

    Aynaz Ghojoghi

    2015-07-01

    Conclusion: The survey showed that PCR-RFLP is a rapid and reliable method for discrimination of dermatophytes. We suggest using of PCR-RFLP as a valuable method along with morphological examination for diagnostic dermatophytes particularly in clinical and epidemiological settings.

  19. Strain typing methods and molecular epidemiology of Pneumocystis pneumonia

    DEFF Research Database (Denmark)

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

    2004-01-01

    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...... regarding the appropriateness of different methods and standardization of these methods, which would facilitate comparing results reported by different laboratories....

  20. 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...

  1. Molecular epidemiology of heartwater (Ehrlichia ruminantium infection) in The Gambia

    NARCIS (Netherlands)

    Faburay, B.

    2007-01-01

    Heartwater is caused by Ehrlichia ruminantium and transmitted by ticks of the genus Amblyomma. It occurs in sub-Saharan Africa and in the Caribbean and affects domestic ruminants. There is general lack of information on the epidemiology of the disease in The Gambia. Results of a countrywide serologi

  2. [Progress of the micronucleus test in the field of molecular cancer epidemiology].

    Science.gov (United States)

    Xu, Huadong; Jia, Guang

    2015-01-01

    The micronucleus test (MNT) can be used to detect multiple genetic end points simultaneously, including chromosome aberration, mis-repaired DNA damage, apoptosis, parts of mutation and so on, which MNT has been an important part of the study of cancer epidemiology.Here, we reviewed the progress of MNT in the field of molecular cancer epidemiology in recent years, including early detection and diagnosis of cancer, evaluation of carcinogenic substances, genetic susceptibility biomarkers, micronutrient and cohort studies.

  3. Molecular Epidemiology of Epidemic Severe Malaria Caused by Plasmodium vivax in the State of Amazonas, Brazil

    Science.gov (United States)

    2005-01-01

    Suarez, C.F., Florez, C., del Portillo, H.A.; Andrade, L.E. Direct Submission to NCBI gene bank. Submitted 03-JAN-1997. Laboratorio de Biologia Molecular ...display a currently valid OMB control number. 1. REPORT DATE 2005 2. REPORT TYPE 3. DATES COVERED - 4. TITLE AND SUBTITLE Molecular ...statement The author hereby certifies that the use of any copyrighted material in the thesis manuscript entitled: “ Molecular Epidemiology of

  4. 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.

  5. [Changes in the epidemiology of inflammatory bowel diseases].

    Science.gov (United States)

    Lakatos, László; Lakatos, Péter László

    2007-02-04

    Significant changes have been observed in the epidemiology of inflammatory bowel diseases (IBD) in the last two decades. Traditionally, the incidence of IBD was higher in the developed, industrialized countries, in contrast, nowadays it became more prevalent in the previously low incidence areas. In particular, the incidence of ulcerative colitis (UC) is similar to that observed in North America and Western Europe, while the incidence of Crohn's disease (CD) in developing countries is still low, suggesting that the environmental factors may act faster or differently in UC than in CD. In Europe, the North to South gradient disappeared, and also the West to East gradient is diminishing. Smoking and appendectomy may be considered as important environmental factors in both UC and CD, however, with opposite effects. In addition, the use of oral contraceptives is associated to disease susceptibility in both diseases. The role of diet, perinatal events, stress and nonsteroidal anti-inflammatory drugs in the pathogenesis is still controversial.

  6. The use of genetic markers in the molecular epidemiology of histoplasmosis: a systematic review.

    Science.gov (United States)

    Damasceno, L S; Leitão, T M J S; Taylor, M L; Muniz, M M; Zancopé-Oliveira, R M

    2016-01-01

    Histoplasmosis is a systemic mycosis caused by Histoplasma capsulatum, a dimorphic fungal pathogen that can infect both humans and animals. This disease has worldwide distribution and affects mainly immunocompromised individuals. In the environment, H. capsulatum grows as mold but undergoes a morphologic transition to the yeast morphotype under special conditions. Molecular techniques are important tools to conduct epidemiologic investigations for fungal detection, identification of infection sources, and determination of different fungal genotypes associated to a particular disease symptom. In this study, we performed a systematic review in the PubMed database to improve the understanding about the molecular epidemiology of histoplasmosis. This search was restricted to English and Spanish articles. We included a combination of specific keywords: molecular typing [OR] genetic diversity [OR] polymorphism [AND] H. capsulatum; molecular epidemiology [AND] histoplasmosis; and molecular epidemiology [AND] Histoplasma. In addition, we used the specific terms: histoplasmosis [AND] outbreaks. Non-English or non-Spanish articles, dead links, and duplicate results were excluded from the review. The results reached show that the main methods used for molecular typing of H. capsulatum were: restriction fragment length polymorphism, random amplified polymorphic DNA, microsatellites polymorphism, sequencing of internal transcribed spacers region, and multilocus sequence typing. Different genetic profiles were identified among H. capsulatum isolates, which can be grouped according to their source, geographical origin, and clinical manifestations.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Rationale and design of the Japan molecular epidemiology for lung cancer study.

    Science.gov (United States)

    Kawaguchi, Tomoya; Ando, Masahiko; Ito, Norimasa; Isa, Shun-Ichi; Tamiya, Akihiro; Shimizu, Shigeki; Saka, Hideo; Kubo, Akihito; Koh, Yasuhiro; Matsumura, Akihide

    2013-09-01

    We present the rationale for the Japan Molecular Epidemiology for Lung Cancer study designed to elucidate molecular mechanisms of carcinogenesis in smokers and never-smokers with non-small-cell lung cancer. This prospective, ongoing, multicenter study is being conducted nationwide in Japan. Although there is no doubt that active smoking is the major cause of lung cancer, the contribution of other possible factors, including environmental tobacco or wood smoke, human papilloma virus, radon, occupational exposures, and genetic susceptibility, is highly likely, based on studies of never-smokers with non-small-cell lung cancer. Because of the predominance of women in the never-smoker subgroup, the role of female hormones in lung cancer development has also been considered. We hypothesize that driver mutations, which are critical for the development of lung cancer, are triggered by the environmental factors with or without the influence of the hormone. The SWOG-led intergroup molecular epidemiology study S0424 was conducted to focus on these issues by using a detailed questionnaire and specimen collection in statistically significant cohorts of smokers and never-smokers from both sexes. The Japan Molecular Epidemiology for Lung Cancer study follows and extends the S0424 molecular epidemiology concept in principle by using a similar approach that will facilitate future comparisons between the studies but with a greater focus on more recently defined driver mutations and broad genomic sequencing.

  12. Molecular epidemiology of Mycobacterium tuberculosis complex in Brussels, 2010–2013

    Science.gov (United States)

    Vluggen, Christelle; Soetaert, Karine; Groenen, Guido; Wanlin, Maryse; Spitaels, Martine; Arrazola de Oñate, Wouter; Fauville-Dufaux, Maryse; Saegerman, Claude

    2017-01-01

    The tuberculosis (TB) incidence rate in Brussels-Capital Region is 3-fold higher than in Belgium as a whole. Eight years after the realization of initial prospective population-based molecular epidemiology investigations in this Region, a similar study over the period 2010–2013 was conducted. TB strains isolated from 945 patients were submitted to genotyping by standardized 24-locus-MIRU-VNTR typing and spoligotyping. The phylogenetic analysis showed that the LAM (16.7%) and Haarlem (15.7%) branches are the two most prevalent TB lineages circulating in Brussels. Analysis of the MDR subgroup showed an association with Beijing strains (39.9%) and patients native of Eastern Europe (40.7%). Genotyping detected 113 clusters involving 321 patients, giving a recent transmission index of 22.9%. Molecular-guided epidemiological investigations and routine surveillance activities revealed family transmission or social contact for patients distributed over 34 clusters. Most of the patients were foreign-born (75.7%). However, cluster analysis revealed only limited trans-national transmission. Comparison with the previous study shows a stable epidemiological situation except for the mean age difference between Belgian-born and foreign-born patients which has disappeared. This study confirms that molecular epidemiology has become an important determinant for TB control programs. However, sufficient financial means need to be available to perform all required epidemiological investigations. PMID:28222189

  13. Welcome to epidemiology and health.

    Science.gov (United States)

    Choi, Bo Youl

    2009-10-29

    The Korean Society of Epidemiology publishes a scholarly journal titled 'Korean Journal of Epidemiology', which announces and discusses the results of epidemiological studies from the past 30 yr. Since its first publication in 1979, the journal has contributed to the advancement of epidemiology as well as the prevention and control of disease, and the promotion of health in Korea.In 2009, the editorial board has decided to publish the journal in English to contribute internationally, and change the journal's name. The new name of the journal is 'Epidemiology and Health'.The abstract and full text of articles will be published as an open access online journal, which will be posted onto the homepage (http://www.e-epih.org/) in real time for anyone in the world to access free of charge. Our editorial policy is that 'Epidemiology and Health' is open to every researcher in fields related to epidemiology, regardless of membership, his or her major and nationality.Editorials, lectures, review papers, original articles, epidemic and case investigations, brief communications and letters will be published to generate active discussion through the journal along with the publication of the papers.'Epidemiology and Health' welcomes articles from various fields of epidemiology, such as 1) infectious diseases epidemiology, 2) chronic diseases epidemiology, 3) nutritional epidemiology, 4) clinical epidemiology, 5) pharmacoepidemiology, 6) genetic or molecular epidemiology, 7) social epidemiology, 8) environmental or occupational epidemiology, 9) epidemiological methods and biostatistics, 10) disease prevention and control, 11) health promotion and, 12) all other fields related to epidemiology.

  14. 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

  15. Alcohol and breast cancer: reconciling epidemiological and molecular data.

    Science.gov (United States)

    Zakhari, Samir; Hoek, Jan B

    2015-01-01

    Breast cancer is the most diagnosed cancer in women worldwide. Epidemiological studies have suggested a possible causative role of alcohol consumption as a risk factor for breast cancer. However, such conclusions should be interpreted with considerable caution for several reasons. While epidemiological studies can help identify the roots of health problems and disease incidence in a community, they are by necessity associative and cannot determine cause and effect relationships. In addition, all these studies rely on self-reporting to determine the amount and type of alcoholic beverage consumed, which introduces recall bias. This is documented in a recent study which stated that the apparent increased risk of cancer among light-moderate drinkers may be "substantially due to underreporting of intake." Another meta-analysis about alcohol and breast cancer declared "the modest size of the association and variation in results across studies leave the causal role of alcohol in question." Furthermore, breast cancer develops over decades; thus, correlations between alcohol consumption and breast cancer cannot be determined in epidemiological studies with windows of alcohol exposure that captures current or recent alcohol intake, after clinical diagnosis. Numerous risk factors are involved in breast carcinogenesis; some are genetic and beyond the control of a woman; others are influenced by lifestyle factors. Breast cancer is a heterogeneous and polygenic disease which is further influenced by epigenetic mechanisms that affect the transciptomes, proteomes and metabolomes, and ultimately breast cancer evolution. Environmental factors add another layer of complexity by their interactions with the susceptibility genes for breast cancer and metabolic diseases. The current state-of-knowledge about alcohol and breast cancer association is ambiguous and confusing to both a woman and her physician. Confronting the huge global breast cancer issue should be addressed by sound

  16. 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.

  17. 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.

  18. [Survey of Trichophyton tonsurans infection in Japan. Molecular epidemiology and factors affecting adequate hairbrush sampling].

    Science.gov (United States)

    Mochizuki, Takashi; Tanabe, Hiroshi; Wakasa, Asako; Kawasaki, Masako; Anzawa, Kazushi; Ishizaki, Hiroshi

    2006-01-01

    At the 48th Annual Meeting of The Society for Japanese Medical Mycology, held in October, 2004, we reported our findings from a survey on Trichophyton tonsurans infections in the Hokuriku and Kinki regions of Japan. The survey revealed that a few epidemics had occurred across these regions. In this article, we introduce our subsequent studies relating to 1) molecular epidemiology of isolates taken from people in many parts of Japan and 2) factors affecting adequate sampling of the scalp with hairbrushes, essential for surveying and monitoring the infection. In total, 198 isolates of Trichophyton tonsurans were analyzed using restriction fragment length polymorphisms of the non-transcribed spacer regions of ribosomal RNA genes. The restriction enzyme Mva I indicated two molecular types of strains, implying that the causative agents of the epidemic had different origins. None of the isolates obtained from the epidemic showed the same restriction profile as that of isolates from aged and sporadic cases. The published hairbrush method suitable for obtaining samples from the scalp of Judo trainees was reevaluated by changing several factors. We found that sampling should not be done soon after the students' physical training because other fungal elements may give a false positive, samples should not be obtained from students who have recently applied topical antimycotics, and samples should be taken under the guidance of qualified instructors familiar with the sampling method.

  19. 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

  20. 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.

  1. 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...

  2. 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

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

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    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.

  4. Molecular and Genetic Research in Tuberculosis Clinical Practice and Epidemiology

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    Bahytkul Zhakipbayeva

    2014-12-01

    Full Text Available Introduction. Tuberculosis (TB remains a global public health problem. In order for multi-drug resistant tuberculosis (MDR-TB to be more effectively managed, there is a need for better tools for diagnosis, treatment, and prevention. The decline of TB incidence and mortality in Kazakhstan during last decade was accompanied with consistent growth of MDR-TB. This study aimed to investigate genotype characteristics of Mycobacterium tuberculosis (MT isolated from TB patients from different regions of the country and its clinical and epidemiological significance.Methods. Over 500 clinical MT isolates from pulmonary TB patients between 2003-2008 were genotyped using spoligotyping, MIRU-VNTR, IS6110 RFLP, and hybridization on an oligonucleotide biochip “TB–biochip.”Results. Out of  250 isolates with interpretable results, 31 different spoligopatterns were detected. The Beijing genotype was the most predominant lineage detected (71.6%, characterized by heterogenicity on ETR A, B, C, D, and E markers, and 56.6% of them had an allelic profile 42435. The Beijing genotype and dominating variant strains have a high transmission rate, a high rate of primary MDR (associated with infiltrating lung TB and complications, and a high level resistance to rifampicin and izoniazid due to mutation of rpoB531TTG and katG315ACC. MIRU-VNTR–typing by 15 loci of 33 isolates from 13 family TB foci revealed that strains from supposed sources and contact persons completely coincide in only 5 foci in the genomic structure.Conclusion. There is a heterogeneous pool of genotypes that circulate in Kazakhstan, with the Beijing lineage being the most predominant. It appears that at the present stage of circulation , MT Beijing genotype has an endemic character. However, clonal spreading of epidemiologically and clinically significant MDR strains of this genotype is also a serious threat to the population. To increase TB control efficiency and prevent further transmission

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

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    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

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

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    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

  7. The changing clinical picture and epidemiology of spondyloarthritis.

    Science.gov (United States)

    van Tubergen, Astrid

    2015-02-01

    In the past decade, major progress has been made in the recognition, classification and treatment of spondyloarthritis (SpA). Classification criteria have been developed for axial and peripheral SpA by the Assessment of SpondyloArthritis international Society (ASAS) as a response to new insight into the clinical picture and unmet needs. The ASAS criteria have contributed to a better understanding of the full spectrum of axial and peripheral SpA and of the potential for treatment. However, whether all patients fulfilling these criteria should be considered as having true SpA is a matter of debate. Furthermore, the implementation of the ASAS criteria might lead to an increase in the reported prevalence of SpA, as patients who were previously unidentified could now be classified as having the disease, which might have consequences for healthcare budgets. In this Review, the changes in the clinical picture and epidemiology of SpA are discussed in light of the ASAS classification criteria for SpA.

  8. The changing epidemiology of dengue in Delhi, India

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    Kapoor Geetanjali

    2006-11-01

    Full Text Available Abstract Background A major DHF outbreak occurred in Delhi in 1996. Following this another outbreak was reported in the year 2003. In the years 2004 and 2005, though no outbreak was reported, a definitely higher number of samples were received in the virology laboratory of A.I.I.M.S. from suspected cases of dengue infection. This study was designed to compare the serological and virological profiles of confirmed dengue cases in the years 2003, 2004 and 2005. Results Out of 1820 serum samples received from suspected cases in all three years, 811 (44.56% were confirmed as dengue infection serologically. Out of these confirmed dengue cases maximum cases, in all three years, were seen in the age group 21–30 years. There was an increase in the number of samples received in the post monsoon period (September to November with a peak in the second and third week of October. More samples were received from DHF cases in the year 2005 than 2004 and 2003. All four dengue serotypes were seen co-circulating in the year 2003, followed by complete predominance of dengue serotype 3 in 2005. Conclusion Epidemiology of dengue is changing rapidly in Delhi. Dengue infections are seen every year thus making it an endemic disease. After co-circulation of all serotypes in 2003, now dengue serotype 3 is emerging as the predominant serotype.

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

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    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

  10. 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

  11. Molecular Epidemiology of Human Metapneumovirus in Riyadh Province, Saudi Arabia.

    Science.gov (United States)

    Amer, Haitham Mohamed

    2016-01-01

    Human metapneumovirus (HMPV) is an important cause of respiratory tract illness in children. Two HMPV subgroups, A and B, and four genotypes, A1, A2, B1 and B2, have been identified. Concurrent circulation of the different genotypes in yearly epidemics has been recorded globally, but not in Saudi Arabia. The current report was designed to study HMPV epidemiology in Saudi children and to analyze the genetic diversity and circulation patterns. Nasopharyngeal aspirates (n = 174) were collected from hospitalized children in Riyadh (2008-2009). The screening of samples using real-time RT-PCR identified 19 HMPV strains. The majority of the strains belonged to subgroup B, while all strains of subgroup A were members of genotype A2. In 2008, only subgroup B was recognized, whereas in 2009 both subgroups were identified to be cocirculating at similar rates. The full-length attachment (G) gene and a partial sequence of the fusion (F) gene of positive samples were sequenced. The G gene showed a high degree of genetic diversity and exhibited a variable number of positively selected sites in different lineages. In contrast, the F gene demonstrated an extensive genetic stability with a higher tendency toward purifying selection. This is the first report on HMPV genotype circulation in Saudi Arabia; however, the exact circulation kinetics requires further retrospective and prospective study.

  12. Molecular epidemiology and genotyping of Mycobacterium tuberculosis isolated in Baghdad.

    Science.gov (United States)

    Mustafa Ali, Ruqaya; Trovato, Alberto; Couvin, David; Al-Thwani, Amina N; Borroni, Emanuele; Dhaer, Fahim H; Rastogi, Nalin; Cirillo, Daniela M

    2014-01-01

    Tuberculosis (TB) remains a major health problem in Iraq but the strains responsible for the epidemic have been poorly characterized. Our aim was to characterize the TB strains circulating in Bagdad (Iraq). A total of 270 Mycobacterium tuberculosis complex (MTBC) strains isolated between 2010 and 2011 from TB patients attending the Center of Chest and Respiratory diseases in Baghdad were analyzed by Spoligotyping. The analysis indicated that 94.1% of the isolates belong to known genotype clades: CAS 39.6%, ill-defined T clade 29.6%, Manu 7.4%, Haarlem 7%, Ural 4.1%, LAM 3.3%, X 0.7%, LAM7-TUR 0.7%, EAI 0.7%, S 0.7%, and unknown 5.9%. Comparison with the international multimarker database SITVIT2 showed that SIT 309 (CAS1-Delhi) and SIT1144 (T1) were the most common types. In addition, 44 strains were included in SITVIT2 database under 16 new Spoligotype International Types (SITs); of these, 6 SITs (SIT3346, SIT3497, SIT3708, SIT3790, SIT3791, and SIT3800) (n = 32 strains) were created within the present study and 10 were created after a match with an orphan in the database. By using 24-loci MIRU-VNTR-typing on a subset of 110 samples we found a high recent transmission index (RTI) of 33.6%. In conclusion, we present the first unifying framework for both epidemiology and evolutionary analysis of M. tuberculosis in Iraq.

  13. 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.

  14. 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.

  15. A Molecular Epidemiologic Case-Case Study of Prostate Cancer

    Science.gov (United States)

    2002-03-01

    Receptor Polymorphism and Prostate Cancer Risk 1 Sara S. Strom 2, Qiang Zhang, Yun Gu, Margaret R. Spitz, Peter T. Scardino 3, Christopher J. Logothetis...Taylor, J. A. Vitamin D receptor polymorphisms and prostate cancer. Molecular Carcinogenesis, 27: 18-23, 2000. 6. Ma, J., Stampfer , M. J., Gann, P. H...Margaret R. Spitz, Richard J. Babaian, Christopher Logothetis, Sara S. Strom, University of Texas M.D. Anderson Cancer Center, Houston, TX; The University

  16. Molecular epidemiology of measles in India, 2005-2010.

    Science.gov (United States)

    Wairagkar, Niteen; Chowdhury, Deepika; Vaidya, Sunil; Sikchi, Sarika; Shaikh, Naseem; Hungund, Laxman; Tomar, R S; Biswas, D; Yadav, K; Mahanta, J; Das, V N R; Yergolkar, Prasanna; Gunasekaran, P; Raja, D; Jadi, R; Ramamurty, Nalini; Mishra, A C

    2011-07-01

    Measles is a childhood disease that causes great morbidity and mortality in India and worldwide. Because measles surveillance in India is in its infancy, there is a paucity of countrywide data on circulating Measles virus genotypes. This study was conducted in 21 of 28 States and 2 of 7 Union Territories of India by MeaslesNetIndia, a national network of 27 centers and sentinel practitioners. MeaslesNetIndia investigated 52 measles outbreaks in geographically representative areas from 2005 through June 2010. All outbreaks were serologically confirmed by detection of antimeasles virus immunoglobulin M (IgM) antibodies in serum or oral fluid samples. Molecular studies, using World Health Organization (WHO)-recommended protocols obtained 203 N-gene, 40 H-gene, and 4 M-gene sequences during this period. Measles genotypes D4, D7, and D8 were found to be circulating in various parts of India during the study period. Further phylogenetic analysis revealed 4 lineages of Indian D8 genotypes: D8a, D8b, D8c, and D8d. This study generated a large, countrywide sequence database that can form the baseline for future molecular studies on measles virus transmission pathways in India. This study has created support and capabilities for countrywide measles molecular surveillance that must be carried forward.

  17. -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.

  18. 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.

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

    Science.gov (United States)

    Ojo, Olabisi O; Sheehan, Stella; Corcoran, Daniel G; Nikolayevsky, Vladyslav; Brown, Timothy; O'Sullivan, Margaret; O'Sullivan, Kathleen; Gordon, Stephen V; Drobniewski, Francis; Prentice, Michael B

    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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Molecular epidemiology of Mycobacterium tuberculosis in the United States-Affiliated Pacific Islands.

    Science.gov (United States)

    Bamrah, Sapna; Desmond, Edward; Ghosh, Smita; France, Anne Marie; Kammerer, J Steve; Cowan, Lauren S; Heetderks, Andrew; Forbes, Alstead; Moonan, Patrick K

    2014-01-01

    The United States-Affiliated Pacific Islands (USAPI) are part of the US National Tuberculosis (TB) Surveillance System and use laboratory services contracted through a cooperative agreement with the Centers for Disease Control and Prevention (CDC). In 2004, the CDC established the National Tuberculosis Genotyping Service, a system to genotype 1 isolate from each culture-confirmed case of TB. To describe the molecular epidemiology of TB in the region, we examined all Mycobacterium tuberculosis isolates submitted for genotyping from January 1, 2004, to December 31, 2008. Over this time period, the USAPI jurisdictions reported 1339 verified TB cases to the National Tuberculosis Surveillance System. Among 419 (31%) reported culture-confirmed TB cases, 352 (84%) had complete genotype results. Routine TB genotyping allowed, for the first time, an exploration of the molecular epidemiology of TB in the USAPI.

  5. 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.

  6. A molecular epidemiological survey of Babesia, Hepatozoon, Ehrlichia and Anaplasma infections of dogs in Japan

    OpenAIRE

    2015-01-01

    Tick-borne diseases are often encountered in canine clinical practice. In the present study, a molecular epidemiological survey of dogs in Japan was conducted to understand the prevalence and geographical distribution of Babesia spp., Hepatozoon spp., Ehrlichia spp. and Anaplasma spp. Pathogen-derived DNA in blood samples obtained from 722 dogs with a history of exposure to ticks and/or fleas was examined by PCR. The prevalence of Babesia gibsoni, Babesia odocoilei-like species, Hepatozoon ca...

  7. Cutaneous Pythiosis in calves: An epidemiologic, pathologic, serologic and molecular characterization

    Directory of Open Access Journals (Sweden)

    Guilherme Konradt

    2016-12-01

    Full Text Available This study reports the epidemiological, pathological and mycological findings of cutaneous pythiosis in cattle in southern Brazil. 23 calves, that were kept next to a river with extensive marshy regions, presented ulcerated cutaneous lesions in thoracic and pelvic limbs, sometimes extending to the ventral thoracic region. Histopathological examination revealed multifocal pyogranulomas in the superficial and deep dermis. The Grocott-Methenamine silver, immunohistochemistry anti-Pythium insidiosum, ELISA serology and molecular characterization demonstrated the agent P. insidiosum in these cases.

  8. MOLECULAR-EPIDEMIOLOGICAL FEATURES OF HEPATITIS B VIRUS

    Directory of Open Access Journals (Sweden)

    V. V. Gerasimova

    2015-01-01

    Full Text Available Abstract. Hepatitis B virus is a serious issue of public health services all over the world, particularly in Russia and its regions. The cause can be determined due to its higher incidence rate in different ethnic and geographical groups, variety of manifestation of clinical forms as well as outcomes. According to WHO data, about 50 million people in the world are annually infected with hepatitis B virus. Development of molecular-genetic methods of research has allowed to expand representations about the activator biology. Genetic variability of hepatitis B virus genome has been subject to identification of 10 various geographically widespread genotypes designated by letters from A to J. In a number of genotypes subgenotypes differing from one another on 4–8% full genome sequences are revealed. In the work a table of geographical prevalence of various genotypes of hepatitis B virus in the world is presented. The geographic distribution of genotypes of hepatitis B virus is closely connected with endemic regions and indigenous population, living there. So the genotypes B and C are connected with the population of Asian countries, genotypes A and D are extended among European countries and in the USA. The genotype D is considered to be a prevailing type among patients with hepatitis B in several regions of Turkey. The phylogenetic analysis of nucleotide sequences of hepatitis B virus isolates in African regions has shown presence of three subgenotypes — А1, А2, А3. In the countries of Asia the following six subgenotypes B are noted: В1 in Japan, В2–В5 and В7 in East Asia Subgenotip B6 is found among indigenous population living in the Arctic regions, including Alaska, northern Canada and Greenland. The genotype C has five serotypes (С1–С5 which are extended in East and South East Asia. The genotype D, also has five subgenotypes (D1–D5 which are extended in Africa, India, the Mediterranean region, Europe. Genotype F has four

  9. 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

  10. 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.

  11. Molecular epidemiology is becoming complex under the dynamic HIV prevalence: The perspective from Harbin, China.

    Science.gov (United States)

    Shao, Bing; Song, Bo; Cao, Lijun; Du, Juan; Sun, Dongying; Lin, Yuanlong; Wang, Binyou; Wang, Fuxiang; Wang, Sunran

    2016-05-01

    Unlike most areas of China, HIV transmission via men who have sex with men (MSM) is increasing rapidly, and has become the main route of HIV transmission in Harbin city. The purpose of the current study was to elaborate the molecular epidemiologic characteristics of the new HIV epidemic. Eighty-one HIV-1 gag gene sequences (HXB2:806-1861) from local HIV infections were isolated; CRF01_AE predominated among HIV infections (71.6%), followed by subtype B (16.5%), CRF07_BC (6.2%), and unique recombinant strains (URFs; 6.2%). URFs were most often identified in the MSM population, which consisted of a recombination of CRF01_AE with subtype B or CRF07_BC. Six clusters were formed in this analysis; clusters I and II mainly circulated in southwest China. Clusters III and IV mainly circulated in southwest, southeast, and central China. Clusters V and VI mainly circulated in north and northeast China. Clusters III and IV may facilitate the transmission of the CRF01_AE strain from the southwest to the north and northeast regions of China. HIV subtypes are becoming diverse with the persistent epidemic in this geographic region. In brief, our results indicate that the molecular epidemiology of HIV is trending to be more complex. Thus, timely molecular epidemiologic supervision of HIV is necessary, especially for the MSM population.

  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. 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.

  14. 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.

  15. 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 ...

  16. 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.

  17. 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.

  18. An overview of molecular epidemiology of hepatitis B virus (HBV in India

    Directory of Open Access Journals (Sweden)

    Datta Sibnarayan

    2008-12-01

    Full Text Available Abstract Hepatitis B virus (HBV is one of the major global public health problems. In India, HBsAg prevalence among general population ranges from 2% to 8%, placing India in intermediate HBV endemicity zone and the number of HBV carriers is estimated to be 50 million, forming the second largest global pool of chronic HBV infections. India is a vast country, comprised of multiracial communities with wide variations in ethnicity and cultural patterns, which is attributable to its geographical location, gene influx due to invasion and/or anthropological migrations in the past. Moreover, recent increase in trade, trafficking and use of illicit drugs has also considerably influenced the epidemiology of HBV, specifically in the eastern and north eastern parts of India. However, data on the molecular epidemiology of HBV in India is scanty. HBV genotypes A and D have been well documented from different parts of mainland India. Interestingly, in addition to genotypes A and D, genotype C having high nucleotide similarity with south East Asian subgenotype Cs/C1 strain, have been detected exclusively from eastern Indian HBV carriers, suggesting a recent introduction. Thus, compared to other parts of India, the molecular epidemiology of HBV is naturally distinct in eastern India. Very recently, taking the advantage of circulation of three distinct HBV genotypes within the population of eastern India, different aspects of HBV molecular epidemiology was studied that revealed very interesting results. In this study, the clinical significance of HBV genotypes, core promoter and precore mutations, possible routes of introduction of HBV genotype C in eastern India, the clinical implications of x gene variability, prevalence of the AFB1 induced p53 gene codon 249 mutation, the transmission potentiality of HBV among asymptomatic/inactive or occult HBV carriers and the genetic variability of HBV persisting in the PBL was investigated. In this manuscript, the

  19. Molecular epidemiology of hepatitis C infection in Cyprus within the general population and high-risk cohorts

    Directory of Open Access Journals (Sweden)

    Kostrikis Leondios G

    2011-10-01

    Full Text Available Abstract Background Initial data on the molecular epidemiology of HCV infection in Cyprus showed a highly polyphyletic infection and multiple points of introduction into the general population. The continuation and expansion of this investigation is presented here including high risk groups. Findings The samples include additional subjects from the general population, a group of inmates and HIV/HCV coinfected individuals, whose strains were amplified by RT-PCR and sequenced in partial Core-E1 and NS5B regions. The results confirm the broad genotype distribution and polyphyletic infection on the island, and no new subtypes were found. Monophyletic clusters between strains of the prisoners and the injecting drug users imply sharing of infected equipment, and highlight the risk of widespread transmission in these cohorts, although no spill-over to the general population was observed. Conclusions The results of this study underline the impact of population movements and high-risk population groups on the changing molecular epidemiology of HCV, with strains moving to Europe from Asia, Africa and Eastern Europe by means of immigration and modern transmission routes.

  20. Molecular epidemiology of Crimean-Congo hemorrhagic fever in Bulgaria--An update.

    Science.gov (United States)

    Papa, Anna; Pappa, Styliani; Panayotova, Elitsa; Papadopoulou, Elpida; Christova, Iva

    2016-05-01

    Crimean-Congo hemorrhagic fever (CCHF) is endemic in Bulgaria. During 2013-2014, 11 confirmed CCHF cases have been reported in the country (seven in 2013 and four in 2014). The present study provides the CCHF molecular epidemiology in Bulgaria based on all currently available S, M, and L RNA segment nucleotide sequences spanning the years 1978-2014. A relatively low genetic difference (0-6%, the maximum seen in the M RNA segment) was seen among the CCHFV sequences suggesting that a slow evolving CCHFV strain belonging to "Europe 1" clade is present in Bulgaria. Although the virus emerged in new foci during the recent years, it is more active in the established endemic foci which seem to offer the most suitable ecosystem and environment. Understanding the CCHF epidemiology and virus evolution is the basis for public health programs and vaccine design.

  1. Molecular epidemiology of betanodavirus-sequence analysis strategies and quasispecies influence outbreak source attribution.

    Science.gov (United States)

    Hick, Paul; Gore, Kylie; Whittington, Richard

    2013-02-05

    The quasispecies structure of nervous necrosis virus (NNV) was determined to investigate an outbreak of viral nervous necrosis disease at a barramundi (Lates calcarifer) hatchery. A traditional epidemiological investigation indicated horizontal transmission of infection between two cohorts of fish. However, variation in the viral capsid protein gene sequence from cell culture-derived viral populations and from individual fish suggested that each cohort was infected with a different virus. Molecular support for the correct epidemiological conclusion was provided by determining the consensus NNV sequence directly from multiple fish, to show that each cohort was infected with the same quasispecies. Variation in the capsid gene of isolates obtained from this quasispecies was up to 3.3% compared with sequences determined directly from fish tissue, and ≤1.7% between individual fish within each cohort. Determination of the NNV quasispecies structure supported implementation of biosecurity measures to protect fish in the hatchery from environmental sources of infection.

  2. 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.

  3. Potencial de desarrollo de la epidemiología molecular en América Latina

    OpenAIRE

    Sotelo, Juan Manuel

    2013-01-01

    Todo proyecto de desarrollo en Salud Pública, a mi juicio debe sustentarse en las características de la región o país en donde será realizado, además de otras cuestiones políticas y sociales. Por ello me permito hacer, de entrada, un somero análisis epidemiológico de la situación, con el fin de asociar, mediante la comprensión de esta problemática social, a las ricas opciones que ofrecen la biología y la epidemiología, esto es: la epidemiología molecular.

  4. Interdisciplinary education to integrate pathology and epidemiology: towards molecular and population-level health science.

    Science.gov (United States)

    Ogino, Shuji; King, Emily E; Beck, Andrew H; Sherman, Mark E; Milner, Danny A; Giovannucci, Edward

    2012-10-15

    In recent decades, epidemiology, public health, and medical sciences have been increasingly compartmentalized into narrower disciplines. The authors recognize the value of integration of divergent scientific fields in order to create new methods, concepts, paradigms, and knowledge. Herein they describe the recent emergence of molecular pathological epidemiology (MPE), which represents an integration of population and molecular biologic science to gain insights into the etiologies, pathogenesis, evolution, and outcomes of complex multifactorial diseases. Most human diseases, including common cancers (such as breast, lung, prostate, and colorectal cancers, leukemia, and lymphoma) and other chronic diseases (such as diabetes mellitus, cardiovascular diseases, hypertension, autoimmune diseases, psychiatric diseases, and some infectious diseases), are caused by alterations in the genome, epigenome, transcriptome, proteome, metabolome, microbiome, and interactome of all of the above components. In this era of personalized medicine and personalized prevention, we need integrated science (such as MPE) which can decipher diseases at the molecular, genetic, cellular, and population levels simultaneously. The authors believe that convergence and integration of multiple disciplines should be commonplace in research and education. We need to be open-minded and flexible in designing integrated education curricula and training programs for future students, clinicians, practitioners, and investigators.

  5. 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.

  6. 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.

  7. Molecular Epidemiological Survey of Theileria orientalis in Thua Thien Hue Province, Vietnam

    OpenAIRE

    2011-01-01

    Theileria orientalis is a benign bovine protozoan parasite that occasionally causes serious economic loss in the livestock industry.We report the findings of a molecular epidemiological survey of T. orientalis in 94 Vietnamese yellow cattle, 43 water buffaloes,21 sheep, 21 goats and 85 blood-sucking ticks of cattle in the Thua Thien Hue province of Vietnam. The major piroplasm surface protein(MPSP) gene of T. orientalis was detected using polymerase chain reaction from 13 cattle (13.8%), 11 w...

  8. Real-time molecular epidemiology of tuberculosis by direct genotyping of smear-positive clinical specimens.

    Science.gov (United States)

    Alonso, María; Herranz, Marta; Martínez Lirola, Miguel; González-Rivera, Milagros; Bouza, Emilio; García de Viedma, Darío

    2012-05-01

    We applied MIRU-VNTR (mycobacterial interspersed repetitive-unit-variable-number tandem-repeat typing) to directly analyze the bacilli present in 61 stain-positive specimens from tuberculosis patients. A complete MIRU type (24 loci) was obtained for all but one (no amplification in one locus) of the specimens (98.4%), and the allelic values fully correlated with those obtained from the corresponding cultures. Our study is the first to demonstrate that real-time genotyping of Mycobacterium tuberculosis can be achieved, fully transforming the way in which molecular epidemiology techniques can be integrated into control programs.

  9. Molecular epidemiology studies on occupational and environmental exposure to mutagens and carcinogens, 1997-1999.

    Science.gov (United States)

    Srám, R J; Binková, B

    2000-03-01

    Molecular epidemiology is a new and evolving area of research, combining laboratory measurement of internal dose, biologically effective dose, biologic effects, and influence of individual susceptibility with epidemiologic methodologies. Biomarkers evaluated were selected according to basic scheme: biomarkers of exposure--metabolites in urine, DNA adducts, protein adducts, and Comet assay parameters; biomarkers of effect--chromosomal aberrations, sister chromatid exchanges, micronuclei, mutations in the hypoxanthine-guanine phosphoribosyltransferase gene, and the activation of oncogenes coding for p53 or p21 proteins as measured on protein levels; biomarkers of susceptibility--genetic polymorphisms of genes CYP1A1, GSTM1, GSTT1, NAT2. DNA adducts measured by 32P-postlabeling are the biomarker of choice for the evaluation of exposure to polycyclic aromatic hydrocarbons. Protein adducts are useful as a biomarker for exposure to tobacco smoke (4-aminobiphenyl) or to smaller molecules such as acrylonitrile or 1,3-butadiene. Of the biomarkers of effect, the most common are cytogenetic end points. Epidemiologic studies support the use of chromosomal breakage as a relevant biomarker of cancer risk. The use of the Comet assay and methods analyzing oxidative DNA damage needs reliable validation for human biomonitoring. Until now there have not been sufficient data to interpret the relationship between genotypes, biomarkers of exposure, and biomarkers of effect for assessing the risk of human exposure to mutagens and carcinogens.

  10. Bioinformatics in bacterial molecular epidemiology and public health : databases, tools and the next-generation sequencing revolution

    NARCIS (Netherlands)

    Carrico, J. A.; Sabat, A. J.; Friedrich, A. W.; Ramirez, M.

    2013-01-01

    Advances in typing methodologies have been the driving force in the field of molecular epidemiology of pathogens. The development of molecular methodologies, and more recently of DNA sequencing methods to complement and improve phenotypic identification methods, was accompanied by the generation of

  11. 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

    Significant changes in the management of fungaemia have occurred over the last decade with increased use of fluconazole prophylaxis, of empirical treatment and of echinocandins as first-line agents for documented disease. These changes may impact the epidemiology of fungaemia. We present nationwide...

  12. 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.

  13. Molecular epidemiology of tuberculosis in India: moving forward with a systems biology approach.

    Science.gov (United States)

    Ahmed, Niyaz; Hasnain, Seyed E

    2011-09-01

    Tuberculosis (TB), caused by Mycobacterium tuberculosis, continues to be the leading source of mortality and morbidity across the world with India fast emerging as the TB capital of the world. In order to develop effective intervention strategies it is equally important to focus not only on a system of information and efficient methods for localizing sources of infection, but also highlight tools that enable enhanced understanding of the dynamics of spreading of disease. Accurate identification of the underlying strains in an epidemiological setting is therefore of paramount significance. There is no scientific evidence to explain that some strains of the TB bacilli spread faster and transmit more aggressively than others although strains such as M. tuberculosis Beijing/W have been widely reported to cause large scale and fatal outbreaks perhaps linked to their postulated propensity to transmit faster. We provide an overview of the present scenario of molecular epidemiology and dissemination dynamics of M. tuberculosis and discuss how systematic, genome sequence based methods allow decipherment of the population genetic structure of M. tuberculosis in India which was not achievable with traditional fingerprinting methods. We discuss the prevalence of ancestral genotypes in India which perhaps represent less disseminating and more controllable lineages that infect a majority of TB patients in this high burden country. Further, we suggest 'functional molecular infection epidemiology' as a new discipline to guide investigation of the impact of pathogen diversity (as juxtaposed to the host response) on the disease phenotype. We also propose systems biology to be a powerful new science to holistically analyze the epidemic through integration of high-throughput multi-omics data to understand the dynamic interactions that occur at the level of host-pathogen cross-talks and to identify potentially novel drivers of the future control strategies.

  14. Genetic and molecular changes in ovarian cancer

    Institute of Scientific and Technical Information of China (English)

    Robert L Hollis; Charlie Gourley

    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.

  15. Phylogeography and molecular epidemiology of hepatitis C virus genotype 2 in Africa.

    Science.gov (United States)

    Markov, Peter V; Pepin, Jacques; Frost, Eric; Deslandes, Sylvie; Labbé, Annie-Claude; Pybus, Oliver G

    2009-09-01

    Understanding the origin and nature of hepatitis C virus (HCV) genetic diversity is critical for improving treatment and vaccine design, and such diversity is the sole source of information about the virus' epidemic history prior to its identification 20 years ago. In this paper, we study the molecular epidemiology of HCV genotype 2 in its region of endemic origin, west and central Africa. Our analysis includes 56 new and highly diverse HCV isolates sampled from infected individuals in Guinea-Bissau. By combining phylogenetic, geographical and epidemiological information, we find a previously unappreciated geographical structure in the diversity of HCV genotype 2, pointing to a history of eastwards spatial spread from the west African coast to Cameroon that took place over several centuries. Molecular clock analysis dates the common ancestor of HCV in Guinea-Bissau to 1470 (1414-1582). The phylogenetic position of isolates from Madagascar and Martinique suggests a role for the historical slave trade in the global dissemination of HCV and of the epidemic subtypes 2a and 2c. Coalescent-based estimates of epidemic growth indicate a rapid 20th-century spread of HCV genotype 2 in Cameroon that is absent in Guinea-Bissau. We discuss this contrast in the context of possible parenteral HCV exposure during public-health campaigns undertaken during the colonial era.

  16. Impact of immigration on HIV-1 molecular epidemiology in West Africa, Maghreb and Southern Europe.

    Science.gov (United States)

    Miri, Lamia; Wakrim, Lahcen; Kassar, Hassène; Hemminki, Kari; Khyatti, Meriem

    2014-01-01

    There is global concern about the relation between international migration and the course of the AIDS epidemic. Maghreb is a North African region, which lies between sub-Saharan Africa and Europe. It has been turned recently into a region of immigration, since there are more and more flows of West African migrants hoping to reach European countries. Here we provide an overview on HIV-1 molecular epidemiology particularly in West African countries, Maghreb (Morocco, Algeria, Tunisia) and southern European countries (Spain, France, and Italy). The studies conducted in several countries of the region revealed different features of HIV-1 molecular epidemiology, especially for the distribution of viral subtypes and for transmitted drug resistance profiles. Furthermore, migration from West Africa to Europe seems to be a potential source of non-B subtype mobility to Maghreb and eventually to southern Europe, where HIV-1 non-B variants significantly increased in the last 10 to 15 years. As genetic differences between subtypes might impact the drug resistance pathways, it is important to provide continuous surveillance programs for the early detection of new variants spreading in the population before they become more prevalent, and to identify resistance profiles in different infected populations, especially migrants.

  17. First insight into the molecular epidemiology of Mycobacterium tuberculosis in Santa Catarina, southern Brazil.

    Science.gov (United States)

    Nogueira, Christiane Lourenço; Prim, Rodrigo Ivan; Senna, Simone Gonçalves; Rovaris, Darcita Büerger; Maurici, Rosemeri; Rossetti, Maria Lúcia; Couvin, David; Rastogi, Nalin; Bazzo, Maria Luiza

    2016-03-01

    Molecular epidemiology of Mycobacterium tuberculosis is useful for understanding disease transmission dynamics, and to establish strategic measures for TB control and prevention. The aim of this study was to analyze clinical, epidemiological and molecular characteristics of MTBC clinical isolates from Santa Catarina state, southern Brazil. During one-year period, 406 clinical isolates of MTBC were collected from Central Laboratory of Public Health and typed by spoligotyping. Demographic and clinical data were collected from the Brazilian National Mandatory Disease Reporting System. The majority of cases occurred in highest population densities regions and about 50% had some condition associated with TB. Among all isolates, 5.7% were MDR, which showed association with drug addiction. LAM was the most predominant lineage with 47.5%, followed by the T superfamily with 25.9% and Haarlem with 12.3%. The MST showed two major groups: the first was formed mainly by the LAM lineage and the second was mainly formed by the T and Haarlem lineages. Others lineages were distributed in peripheral positions. This study provides the first insight into the population structure of M. tuberculosis in SC State. Spoligotyping and other genotyping analyses are important to establish strategic measures for TB control and prevention.

  18. Molecular epidemiology of rabies in bat-eared foxes (Otocyon megalotis) in South Africa.

    Science.gov (United States)

    Sabeta, C T; Mansfield, K L; McElhinney, L M; Fooks, A R; Nel, L H

    2007-10-01

    A panel of 124 rabies viruses from wildlife host species (principally the bat-eared fox, Otocyon megalotis) and domestic carnivore species were collected between 1980 and 2005 from a region of South Africa associated with endemic bat-eared fox rabies. We have studied the molecular epidemiology of bat-eared fox rabies by virtue of nucleotide sequence analyses of PCR amplicons specific to the variable G-L intergenic region as well as the conserved nucleoprotein gene of each of the rabies viruses in this South African panel. Although it was demonstrated that all of these viruses were very closely related, they could be segregated into two major phylogenetic groups. The data presented in this paper complement antigenic and surveillance data on rabies in this host species in South Africa. Most importantly our data support a hypothesis that the bat-eared fox independently maintains rabies cycles in specific geographical loci. This is the first molecular epidemiological investigation describing rabies transmission dynamics in this wildlife carnivore host species in South Africa.

  19. 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.

  20. 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.

  1. Exploring the use of molecular epidemiology to track bovine tuberculosis in Nigeria: an overview from 2002 to 2004.

    Science.gov (United States)

    Cadmus, S I B; Gordon, S V; Hewinson, R G; Smith, N H

    2011-07-05

    Tuberculosis remains a major public health problem in Nigeria. While human to human transmission of Mycobacterium tuberculosis is clearly of major importance in driving the tuberculosis epidemic in Nigeria, the impact of Mycobacterium bovis transmission from infected cattle is largely unknown. Molecular epidemiology of M. bovis in Nigeria will increase our understanding of this endemic disease and provide tools to assess cattle-to-human transmission. Between 2002 and 2004, molecular techniques including spoligotyping, variable number of tandem repeats (VNTR) typing and deletion typing were used to track and analyze a sample of strains of the M. tuberculosis complex circulating in the cattle population in Ibadan, Southwestern Nigeria. In all, 180 isolates were typed with a view to elucidating epidemiological information on circulating strains, occurrence of transborder transmission and molecular diversity of the M. bovis strains. Results obtained showed that 99% (178/180) of the isolates were M. bovis, while the remaining were M. tuberculosis and M. africanum. In all, strains of M. bovis had 34 different spoligotypes: strains with spoligotype pattern SB0944 (as designated by www.mbovis.org) were the most common (46% of strains). This molecular type is also common in countries neighbouring Nigeria. Strains with this spoligotype pattern could be further divided into 40 different VNTR types. This analysis shows the value of simple molecular epidemiological techniques applied to strains of M. bovis and suggests that further epidemiological studies will shed more light on the transmission dynamics of bovine tuberculosis locally and across neighbouring African countries.

  2. 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.

  3. The re-emergence of tuberculosis: what have we learnt from molecular epidemiology?

    Science.gov (United States)

    Borgdorff, M W; van Soolingen, D

    2013-10-01

    Tuberculosis (TB) has re-emerged over the past two decades: in industrialized countries in association with immigration, and in Africa owing to the human immunodeficiency virus epidemic. Drug-resistant TB is a major threat worldwide. The variable and uncertain impact of TB control necessitates not only better tools (diagnostics, drugs, and vaccines), but also better insights into the natural history and epidemiology of TB. Molecular epidemiological studies over the last two decades have contributed to such insights by answering long-standing questions, such as the proportion of cases attributable to recent transmission, risk factors for recent transmission, the occurrence of multiple Mycobacterium tuberculosis infection, and the proportion of recurrent TB cases attributable to re-infection. M. tuberculosis lineages have been identified and shown to be associated with geographical origin. The Beijing genotype is strongly associated with multidrug resistance, and may have escaped from bacille Calmette-Guérin-induced immunity. DNA fingerprinting has quantified the importance of institutional transmission and laboratory cross-contamination, and has helped to focus contact investigations. Questions to be answered in the near future with whole genome sequencing include identification of chains of transmission within clusters of patients, more precise quantification of mixed infection, and transmission probabilities and rates of progression from infection to disease of various M. tuberculosis lineages, as well as possible variations in vaccine efficacy by lineage. Perhaps most importantly, dynamics in the population structure of M. tuberculosis in response to control measures in high-prevalence areas should be better understood.

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

    Directory of Open Access Journals (Sweden)

    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.

  5. Acute hepatitis C: changing epidemiology and association with HIV infection.

    Science.gov (United States)

    Brejt, Nick; Gilleece, Yvonne; Fisher, Martin

    2007-03-01

    Over the past 6 to 7 years an increasing incidence of acute hepatitis C virus (AHCV) has been fuelled by two different changing epidemics: (1) a new resurgence of AHCV amongst intravenous drug users (IVDU); and (2) presumed sexually transmitted AHCV amongst predominantly HIV-positive men who have sex with men (MSM). Increasing incidence amongst IVDUs is likely to be a consequence of changing injecting behaviour, possibly related to changes in perception of HIV as well as HCV risk and consequences. Increasing incidence amongst MSM is likely to be a consequence of changing sexual practices, for example number of sexual partners and type of sexual behaviour, as well as increasing availability of recreational drugs associated with sexual risk-taking, and wider availability of casual sexual partners via the internet or sex-on-premises venues. It remains unclear whether the current outbreaks in MSM, predominantly seen in HIV-positive individuals, reflect a predisposition to AHCV secondary to HIV status per se, or whether this reflects differences in behaviour amongst HIV-positive versus HIV-negative MSM, or potentially increased screening (either routine or secondary to abnormal liver function tests) in HIV-positive MSM. The majority of individuals with AHCV are asymptomatic and therefore routine screening of individuals in at-risk groups with abnormal liver function tests should be considered. Previous historical studies suggest that individuals with concomitant HIV infection are far less likely than those without to spontaneously clear HCV. It is currently recommended that such individuals acutely infected with HCV should undergo monitoring of HCV viral load levels to determine whether spontaneous clearance is likely or whether the opportunity for early treatment should be considered.

  6. Giardia duodenalis: genetic recombination and its implications for taxonomy and molecular epidemiology.

    Science.gov (United States)

    Cacciò, Simone M; Sprong, Hein

    2010-01-01

    Traditionally, species within the Giardia genus have been considered as eukaryotic organisms that show an absence of sexual reproduction in their simple life cycles. This apparent lack of sex has been challenged by a number of studies that have demonstrated (i) the presence in the Giardia duodenalis genome of true homologs of genes specifically involved in meiosis in other eukaryotes, and their stage-specific expression; (ii) the exchange of genetic material in different chromosomal regions among human isolates of the parasite; (iii) the fusion between cyst nuclei (karyogamy) and the transfer of genetic material (episomal plasmids) between them. These results are pivotal for the existence of sexual recombination. However, many details of the process remain elusive, and experimental data are still scarce. This review summarizes the experimental approaches and the results obtained, and discusses the implications of recombination from the standpoint of the taxonomy and molecular epidemiology of this widespread pathogen.

  7. Molecular epidemiology of human immunodeficiency virus-infected individuals in Medellin, Colombia.

    Science.gov (United States)

    Sanchez, Gloria I; Bautista, Christian T; Eyzaguirre, Lindsay; Carrion, Gladys; Arias, Sonia; Sateren, Warren B; Negrete, Monica; Montano, Silvia M; Sanchez, Jose L; Carr, Jean K

    2006-04-01

    To study the molecular epidemiology of human immunodeficiency virus type 1 (HIV-1) strains in Medellín, Colombia, 115 HIV-1-positive individuals who were recruited from an HIV outpatient hospital (Universitario San Vicente de Paul) during the period from July 2001 to January 2002 were genotyped. All samples were analyzed by envelope heteroduplex mobility assay and found to be subtype B. Twenty-four samples were randomly selected for sequencing of the protease and the reverse transcriptase regions; all isolates were found to be subtype B. Phylogenetic analysis of seven nearly full-length genomes showed that all samples were subtype B. This study shows that the HIV epidemic in Colombia continues to be dominated by the subtype B virus. The predominance of subtype B genotypes of HIV-1 strains in Medellín resembles what is seen in the nearby countries of Peru, Ecuador, and Venezuela.

  8. Implications and challenges of tuberculosis in wildlife ungulates in Portugal: a molecular epidemiology perspective.

    Science.gov (United States)

    Cunha, Mónica V; Matos, Filipa; Canto, Ana; Albuquerque, Teresa; Alberto, João R; Aranha, José M; Vieira-Pinto, Madalena; Botelho, Ana

    2012-04-01

    Mycobacterium bovis and, more rarely, Mycobacterium caprae, may cause zoonotic bovine tuberculosis (bTB) in an extensive range of animal species. In Portugal, during 2009, a remarkable raise of bTB incidence was registered in cattle along with an increase of new cases in wildlife. In this work, we reassess and update the molecular epidemiology of bTB in wild ungulates by including 83 new M. bovis and M. caprae isolates from wild boar and red deer obtained during 2008-2009. Spoligotyping identified 27 patterns in wild ungulates, including 11 patterns exclusive from deer and five from wild boar. The genetic relatedness of wildlife and livestock isolates is confirmed. However, the relative prevalence of the predominant genotypes is different between the two groups. Contrasting with the disease in livestock, which is widespread in the territory, the isolation of bTB in wildlife is, apparently, geographically localized and genotypic similarities of strains are observed at the Iberian level.

  9. [Research on conventional and molecular epidemiology of tuberculosis in Orizaba, Veracruz, 1995-2008].

    Science.gov (United States)

    Jiménez-Corona, Ma Eugenia; García-García, Lourdes; León, Alfredo Ponce de; Bobadilla-del Valle, Miriam; Torres, Martha; Canizales-Quintero, Sergio; Palacios-Merino, Carmen; Molina-Hernández, Susana; Martínez-Gamboa, Rosa Areli; Juárez-Sandino, Luis; Cano-Arellano, Bulmaro; Ferreyra-Reyes, Leticia; Cruz-Hervert, Luis Pablo; Báez-Saldaña, Renata; Ferreira-Guerrero, Elizabeth; Sada, Eduardo; Marquina, Brenda; Sifuentes-Osornio, José

    2009-01-01

    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, we describe the impact on public policies, transference of technology, capacity building and future perspectives.

  10. 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.

  11. A molecular epidemiological survey of Babesia, Hepatozoon, Ehrlichia and Anaplasma infections of dogs in Japan.

    Science.gov (United States)

    Kubo, Shotaro; Tateno, Morihiro; Ichikawa, Yasuaki; Endo, Yasuyuki

    2015-10-01

    Tick-borne diseases are often encountered in canine clinical practice. In the present study, a molecular epidemiological survey of dogs in Japan was conducted to understand the prevalence and geographical distribution of Babesia spp., Hepatozoon spp., Ehrlichia spp. and Anaplasma spp. Pathogen-derived DNA in blood samples obtained from 722 dogs with a history of exposure to ticks and/or fleas was examined by PCR. The prevalence of Babesia gibsoni, Babesia odocoilei-like species, Hepatozoon canis and Ehrlichia spp./Anaplasma spp. was 2.4% (16/722), 0.1% (1/722), 2.5% (18/722) and 1.5% (11/722), respectively. While B. gibsoni and Ehrlichia spp./Anaplasma spp. were detected in the western part of Japan, H. canis was detected in Tohoku area in addition to western and central parts of Japan.

  12. Vancomycin-resistant enterococcal bacteremia in a hematology unit: molecular epidemiology and analysis of clinical course.

    Science.gov (United States)

    Yoo, Jin-Hong; Lee, Dong-Gun; Choi, Su Mi; Choi, Jung-Hyun; Shin, Wan-Shik; Kim, Myungshin; Yong, Dongeun; Lee, Kyungwon; Min, Woo-Sung; Kim, Chun-Choo

    2005-04-01

    An increase in vancomycin-resistant enterococcal (VRE) bacteremia in hemato-oncological patients (n=19) in our institution from 2000 through 2001 led us to analyze the molecular epidemiologic patterns and clinical features unique to our cases. The pulsed field gel electrophoresis of the isolates revealed that the bacteremia was not originated from a single clone but rather showed endemic pattern of diverse clones with small clusters. A different DNA pattern of blood and stool isolates from one patient suggested exogenous rather than endogenous route of infection. Enterococcus faecium carrying vanA gene was the causative pathogen in all cases. Patients with VRE bacteremia showed similar clinical courses compared with those with vancomycin-susceptible enterococcal (VSE) bacteremia. Vancomycin resistance did not seem to be a poor prognostic factor because of similar mortality (5/8, 62.5%) noted in VSE bacteremia. Initial disease severity and neutropenic status may be major determinants of prognosis in patients with VRE bacteraemia.

  13. 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.

  14. Syphilis epidemiology in 1994-2013, molecular epidemiological strain typing and determination of macrolide resistance in Treponema pallidum in 2013-2014 in Tuva Republic, Russia.

    Science.gov (United States)

    Khairullin, Rafil; Vorobyev, Denis; Obukhov, Andrey; Kuular, Ural-Herel; Kubanova, Anna; Kubanov, Alexey; Unemo, Magnus

    2016-07-01

    The incidence of syphilis in the Tuva Republic (geographical centre of Asia), Russia has been exceedingly high historically. No detailed examinations and no molecular investigations of Treponema pallidum strains transmitted in the Tuva Republic, or in general, in Russia, were published internationally. We examined the syphilis epidemiology in 1994-2013, and the molecular epidemiology and macrolide resistance in T. pallidum strains in 2013-2014 in the Tuva Republic. Among 95 mainly primary or secondary syphilis patients, the arp, tpr, tp0548 and 23S rRNA genes in 85 polA gene-positive genital ulcer specimens were characterized. The syphilis incidence in Tuva Republic peaked in 1998 (1562), however declined to 177 in 2013. Among the 70 (82%) completely genotyped specimens, six molecular strain types were found. Strain type 14d/f accounted for 91%, but also 14c/f, 14d/g, 14b/f, 14i/f, 9d/f, and 4d/f were identified. Two (2.4%) specimens contained the 23S rRNA A2058G macrolide resistance mutation. This is the first internationally published typing study regarding T. pallidum in Russia, performed in the Tuva Republic with the highest syphilis incidence in Russia. The two molecular strain types 4d/f and 9d/f have previously been described only in Eastern and Northern China and for the first time, macrolide-resistant syphilis was described in Russia.

  15. 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.

  16. 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

  17. 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., < 200 cells/mm3). Most were asymptomatic and had concurrent opportunistic infections mainly with Mycobacterium tuberculosis. DNA sequence analysis of 32 Cryptosporidium isolates identified C. 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

  18. 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

  19. Education in epidemiology: "The Times They Are a-Changin'".

    Science.gov (United States)

    Samet, Jonathan M; Savitz, David A

    2008-03-01

    "The Changing Face of Epidemiology" is a series of symposia sponsored by Epidemiology for the purpose of addressing topical issues that cut across specialty areas. We comment here on 3 papers presented last summer at a symposium ("Education in Epidemiology: Changing needs for changing times") at the 2007 meeting of the Society for Epidemiologic Research. These papers address current challenges in training epidemiologists, including the rise of molecular epidemiology, the ongoing need to redefine core epidemiologic methods and develop optimum approaches, and the increasing difficulty of assuring competency in primary data collection. We offer suggestions for educational programs and professional organizations on approaching these ongoing challenges.

  20. 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

  1. 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...

  2. Changing Epidemiology of Human Brucellosis, China, 1955–2014

    Science.gov (United States)

    Lai, Shengjie; Zhou, Hang; Xiong, Weiyi; Gilbert, Marius; Huang, Zhuojie; Yu, Jianxing; Yin, Wenwu; Wang, Liping; Chen, Qiulan; Li, Yu; Mu, Di; Zeng, Lingjia; Ren, Xiang; Geng, Mengjie; Zhang, Zike; Cui, Buyun; Li, Tiefeng; Wang, Dali; Li, Zhongjie; Wardrop, Nicola A.; Tatem, Andrew J.

    2017-01-01

    Brucellosis, a zoonotic disease, was made statutorily notifiable in China in 1955. We analyzed the incidence and spatial–temporal distribution of human brucellosis during 1955–2014 in China using notifiable surveillance data: aggregated data for 1955–2003 and individual case data for 2004–2014. A total of 513,034 brucellosis cases were recorded, of which 99.3% were reported in northern China during 1955–2014, and 69.1% (258, 462/374, 141) occurred during February–July in 1990–2014. Incidence remained high during 1955–1978 (interquartile range 0.42–1.0 cases/100,000 residents), then decreased dramatically in 1979–1994. However, brucellosis has reemerged since 1995 (interquartile range 0.11–0.23 in 1995–2003 and 1.48–2.89 in 2004–2014); the historical high occurred in 2014, and the affected area expanded from northern pastureland provinces to the adjacent grassland and agricultural areas, then to southern coastal and southwestern areas. Control strategies in China should be adjusted to account for these changes by adopting a One Health approach. PMID:28098531

  3. 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.

  4. Molecular Epidemiology and Characterization of Genotypes of Acinetobacter baumannii Isolates from Regions of South China.

    Science.gov (United States)

    Ying, Jun; Lu, Junwan; Zong, Li; Li, Ailing; Pan, Ruowang; Cheng, Cong; Li, Kunpeng; Chen, Liqiang; Ying, Jianchao; Tou, Huifen; Zhu, Chuanxin; Xu, Teng; Yi, Huiguang; Li, Jinsong; Ni, Liyan; Xu, Zuyuan; Bao, Qiyu; Li, Peizhen

    2016-05-20

    The aim of this study was to analyze the molecular epidemiologic characteristics of Acinetobacter baumannii. A total of 398 isolates were collected in 7 regions of South China from January to June of 2012. Drug sensitivity was tested toward 15 commonly used antibiotics; thus, 146 multi-drug-resistant strains (resistant to more than 7 drugs) were identified, representing 36.7% of all isolates. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were used for molecular subtyping. According to the PFGE results (with a cutoff of 70% similarity for the DNA electrophoretic bands), 146 strains were subdivided into 15 clusters, with cluster A being the largest (33.6%, distributed in all districts except Jiaxing). Cluster B was also widespread and included 14.4% of all strains. In addition, MLST results revealed 11 sequence types (ST), with ST208 being the most prevalent, followed by ST191 and ST729. Furthermore, 4 novel alleles and 6 novel STs were identified. Our results showed that multi-drug-resistant A. baumannii in South China shares the origin with other widespread strains in other countries. The nosocomial infections caused by A. baumannii have been severe in South China. Continuous monitoring and judicious antibiotic use are required.

  5. 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

  6. 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

  7. Porcine deltacoronavirus infection: Etiology, cell culture for virus isolation and propagation, molecular epidemiology and pathogenesis.

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    Jung, Kwonil; Hu, Hui; Saif, Linda J

    2016-12-02

    Porcine deltacoronavirus (PDCoV) (family Coronaviridae, genus Deltacoronavirus) is a novel swine enteropathogenic coronavirus that causes acute diarrhea/vomiting, dehydration and mortality in seronegative neonatal piglets. PDCoV diarrhea was first reported in the US in early 2014, concurrently with co-circulation of porcine epidemic diarrhea virus (PEDV) (family Coronaviridae, genus Alphacoronavirus). The origin of PDCoV in pigs and also its sudden emergence or route of introduction into the US still remains unclear. In the US, since 2013-2014, the newly emerged PDCoV and PEDV have spread nationwide, causing a high number of pig deaths and significant economic impacts. The current US PDCoV strains are enteropathogenic and infect villous epithelial cells of the entire small and large intestines although the jejunum and ileum are the primary sites of infection. Similar to PEDV infections, PDCoV infections also cause acute, severe atrophic enteritis accompanied by transient viremia (viral RNA) that leads to severe diarrhea and/or vomiting, followed by dehydration as the potential cause of death in nursing piglets. At present, differential diagnosis of PDCoV, PEDV, and transmissible gastroenteritis virus (TGEV) is essential to control viral diarrheas in US swine. Cell culture-adapted US PDCoV (TC-PDCoV) strains have been isolated and propagated by us and in several other laboratories. TC-PDCoV strains will be useful to develop serologic assays and to evaluate if serial cell-culture passage attenuates TC-PDCoV as a potential vaccine candidate strain. A comprehensive understanding of the pathogenesis and epidemiology of epidemic PDCoV strains is currently needed to prevent and control the disease in affected regions and to develop an effective vaccine. This review focuses on the etiology, cell culture isolation and propagation, molecular epidemiology, disease mechanisms and pathogenesis of PDCoV infection.

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

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    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.

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

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    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

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

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    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.

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

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    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.

  12. 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.

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

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    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.

  14. Molecular Epidemiology of Giardia, Blastocystis and Cryptosporidium among Indigenous Children from the Colombian Amazon Basin

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    Sánchez, Angie; Munoz, Marina; Gómez, Natalia; Tabares, Juan; Segura, Laura; Salazar, Ángela; Restrepo, Cristian; Ruíz, Miguel; Reyes, Patricia; Qian, Yuchen; Xiao, Lihua; López, Myriam C.; Ramírez, Juan D.

    2017-01-01

    The incidence and prevalence of intestinal parasites in children is most likely due to lack of natural or acquired resistance and differences in behavior and habits closely related to environmental and socioeconomic determinants. The most important protozoa that parasitize humans are Giardia, Entamoeba, Blastocystis, and Cryptosporidium. These parasites present wide intraspecific genetic diversity and subsequently classified into assemblages and subtypes. The Amazon basin is the largest in the world and is the fifth freshwater reserve on the planet. Contradictorily, people living in these areas (Indigenous populations) have poor quality of life, which favors the infection of diseases of fecal-oral transmission. The aim of this work was to unravel the molecular epidemiology of Giardia, Blastocystis and Cryptosporidium across four communities (Puerto Nariño, San Juan del Soco, Villa Andrea and Nuevo Paraíso). We obtained 284 fecal samples from children under 15 years old that were analyzed by direct microscopy (261 samples) and Real Time PCR (qPCR) (284 samples). The positive samples for these protozoa were further characterized by several molecular markers to depict assemblages and subtypes. We observed a frequency of Giardia infection by microscopy of 23.7% (62 samples) and by qPCR of 64.8% (184 samples); for Blastocystis by microscopy of 35.2% (92 samples) and by qPCR of 88.7% (252 samples) and for Cryptosporidium only 1.9% (5 samples) were positive by microscopy and qPCR 1.8% (5 samples). Regarding the Giardia assemblages, using the glutamate dehydrogenase (gdh) marker we observed AI, BIII and BIV assemblages and when using triose phosphate isomerase (tpi) we observed assemblages AI, AII, BIII and BIV. In contrast, Blastocystis STs detected were 1, 2, 3, 4, and 6. Lastly, the species C. viatorum, C. hominis (with the subtypes IdA19 and IaA12R8) and C. parvum (with the subtype IIcA5G3c) were identified. We observed a high profile of zoonotic transmission

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

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    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

  16. 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.

  17. Molecular Epidemiology of Amoebiasis: A Cross-Sectional Study among North East Indian Population.

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    Joyobrato Nath

    2015-12-01

    Full Text Available Epidemiological studies carried out using culture or microscopy in most of the amoebiasis endemic developing countries, yielded confusing results since none of these could differentiate the pathogenic Entamoeba histolytica from the non-pathogenic Entamoeba dispar and Entamoeba moshkovskii. The Northeastern part of India is a hot spot of infection since the climatic conditions are most conducive for the infection and so far no systemic study has been carried out in this region.Following a cross-sectional study designed during the period 2011-2014, a total of 1260 fecal samples collected from the Northeast Indian population were subjected to microscopy, fecal culture and a sensitive and specific DNA dot blot screening assay developed in our laboratory targeting the Entamoeba spp. Further species discrimination using PCR assay performed in microscopy, culture and DNA dot blot screening positive samples showed E. histolytica an overall prevalence rate of 11.1%, 8.0% and 13.7% respectively. In addition, infection rates of nonpathogenic E. dispar and E. moshkovskii were 11.8% (95% CI = 10.2, 13.8 and 7.8% (95% CI = 6.4, 9.4 respectively. The spatial distributions of infection were 18.2% (107/588 of Assam, 11.7% (23/197 of Manipur, 10.2% (21/207 of Meghalaya, and 8.2% (22/268 of Tripura states. Association study of the disease with demographic features suggested poor living condition (OR = 3.21; 95% CI = 1.83, 5.63, previous history of infection in family member (OR = 3.18; 95% CI = 2.09, 4.82 and unhygienic toilet facility (OR = 1.79; 95% CI = 1.28, 2.49 as significant risk factors for amoebiasis. Children in age group <15 yr, participants having lower levels of education, and daily laborers exhibited a higher infection rate.Despite the importance of molecular diagnosis of amoebiasis, molecular epidemiological data based on a large sample size from endemic countries are rarely reported in the literature. Improved and faster method of diagnosis

  18. Molecular epidemiology of tuberculosis in the Tula area, Central Russia, before the introduction of the Directly Observed Therapy Strategy.

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    Dubiley, S; Ignatova, A; Mukhina, T; Nizova, A; Blagodatskikh, S; Stepanshina, V; Shemyakin, I

    2010-09-01

    Tuberculosis remains a major public health concern in Russia and worldwide. Given the great geographical, ethnic, and socio-economic heterogeneities between Russian regions, epidemiological data cannot be generalized from a regional to a country-wide level. We present data on the epidemiology of tuberculosis in Central Russia. We report a high level of resistance to major antitubercular drugs in both new and previously treated patients in the region. The level of drug resistance in new cases was almost twice as high as the estimated average national level. The Mycobacterium tuberculosis strains that circulated in the region were predominantly represented by LAM-RUS and Beijing genotypes. These two lineages were strongly associated with drug resistance and clustering. Using molecular epidemiology techniques, we showed a high interpenetration by M. tuberculosis strains between the prison and civilian populations. A limited number of identical strains were responsible for the majority of drug-resistant tuberculosis cases in both settings.

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

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    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.

  20. Impact of climate change in the epidemiology of vector-borne diseases in domestic carnivores.

    Science.gov (United States)

    Beugnet, F; Chalvet-Monfray, K

    2013-12-01

    Vector-borne diseases are medically important in humans and animals but were long considered tropical and known to first affect production animals. This is no longer true and we can see today that they are common in domestic animals and that they are also present in temperate countries, especially in Europe. In recent years, an increase in the diagnosis of vector borne diseases among humans and animals has been observed, which may partly due to the development of diagnostic tools. Their study requires exchanges and collaborations between the many actors involved, especially since the epidemiology seems to be constantly evolving. The veterinary practitioner is the first one to notice the emergence of cases and to implement prevention measures. He also acts as a sentinel to alert epidemiologists. Many factors can explain the epidemiological changes, i.e. all human factors, such as the increase in commercial transportation, but also owners traveling with their pet during the holidays, the development of "outdoor" activities, the increase of individual housings with gardens; to these human factors must be added the ignorance of the risks, linked to animals in general and to wildlife in particular; then the environmental changes: forest fragmentation, establishment of parks; the increase of wild mammal populations (deer, carnivores, rodents, etc.); finally, climate changes. Climate change is a reality which may explain the increase of density of arthropod vectors, but also of their hosts, changes in periods of activity and variations in geographical distribution. The authors show the proof of the climate modifications and then explain how it has an impact in Europe on ticks, mosquitoes, sandflies and even fleas. They conclude on the practical consequences for veterinary practitioners, especially with the diagnosis of parasitic diseases or diseases in areas where they usually do not occur. However, not any epidemiological modification should be linked to climate change

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

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    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.

  2. A molecular epidemiological study of respiratory viruses detected in Japanese children with acute wheezing illness

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    Noda Masahiro

    2011-06-01

    Full Text Available Abstract Background Recent studies strongly suggest that some respiratory viruses are associated with the induction of acute wheezing and/or exacerbation of bronchial asthma. However, molecular epidemiology of these viruses is not exactly known. Methods Using PCR technology, we attempted to detect various respiratory viruses from 115 Japanese children. Furthermore, the detected viruses were subjected to homology, pairwise distance, and phylogenetic analysis. Results Viruses were detected from 99 (86.1% patients. Respiratory syncytial virus (RSV alone and human rhinovirus (HRV alone were detected in 47 (40.9% and 36 (31.3% patients, respectively. Both RSV and HRV were detected in 14 (12.2% patients. Human metapneumovirus (HMPV alone and human parainfluenza virus (HPIV alone were detected in 1 (0.9% patient each, respectively. Homology and phylogenetic analyses showed that the RSV and HRV strains were classified into genetically diverse species or subgroups. In addition, RSV was the dominant virus detected in patients with no history of wheezing, whereas HRV was dominant in patients with a history of wheezing. Conclusions The results suggested that these genetically diverse respiratory viruses, especially RSV and HRV, might be associated with wheezing in Japanese children.

  3. Impact of immigration on the molecular epidemiology of tuberculosis in Rhode Island.

    Science.gov (United States)

    Vanhomwegen, Jessica; Kwara, Awewura; Martin, Melissa; Gillani, Fizza S; Fontanet, Arnaud; Mutungi, Peninnah; Crellin, Joyce; Obaro, Stephen; Gosciminski, Michael; Carter, E Jane; Rastogi, Nalin

    2011-03-01

    While foreign-born persons constitute only 11% of the population in the state of Rhode Island, they account for more than 65% of incident tuberculosis (TB) annually. We investigated the molecular-epidemiological differences between foreign-born and U.S.-born TB patients to estimate the degree of recent transmission and identify predictors of clustering. A total of 288 isolates collected from culture-confirmed TB cases in Rhode Island between 1995 and 2004 were fingerprinted by spoligotyping and 12-locus mycobacterial interspersed repetitive units. Of the 288 fingerprinted isolates, 109 (37.8%) belonged to 36 genetic clusters. Our findings demonstrate that U.S.-born patients, Hispanics, Asian/Pacific islanders, and uninsured patients were significantly more likely to be clustered. Recent transmission among the foreign-born population was restricted and occurred mostly locally, within populations originating from the same region. Nevertheless, TB transmission between the foreign-born and U.S.-born population should not be neglected, since 80% of the mixed clusters of foreign- and U.S.-born persons arose from a foreign-born source case. We conclude that timely access to routine screening and treatment for latent TB infection for immigrants is vital for disease elimination in Rhode Island.

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

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    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.

  5. [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.

  6. Molecular epidemiology of porcine Cytomegalovirus (PCMV in Sichuan Province, China: 2010-2012.

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    Xiao Liu

    Full Text Available Porcine cytomegalovirus (PCMV is an immunosuppressive virus that mainly inhibits the immune function of the macrophage and T-cell lymphatic systems, and has caused huge economic losses to the porcine breeding industry. Molecular epidemiological investigation of PCMV is important for prevention and treatment, and this study is the first such investigation in Sichuan Province, Southwest China. A PCMV positive infection rate of 84.4% (865/1025 confirmed that PCMV is widely distributed in Sichuan Province. A phylogenetic tree was constructed based on the PCMV glycoprotein B gene (gB nucleotide and amino acid sequences from 24 novel Sichuan isolates and 18 other PCMV gB sequences from Genbank. PCMV does not appear to have evolved into different serotypes, and two distinct sequence groups were identified (A and B. However, whether PCMV from this region has evolved into different genotypes requires further research. Analysis of the amino acid sequences confirmed the conservation of gB, but amino acid substitutions in the major epitope region have caused antigenic drift, which may have altered the immunogenicity of PCMV.

  7. 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.

  8. Acanthamoeba keratitis update-incidence, molecular epidemiology and new drugs for treatment.

    Science.gov (United States)

    Seal, D V

    2003-11-01

    A reliable figure for the expected incidence of Acanthamoeba keratitis of one per 30000 contact lens wearers per year has now been obtained from a combination of three cohort and three Questionnaire Reporting Surveys; 88% of cases wore hydrogel lenses and 12% wore rigid lenses. This figure now provides a basis for the expected number of cases against which to judge either epidemic outbreaks or effects of prevention with disinfecting solutions, better hygiene, or the use of disposable lenses. Molecular biology of Acanthamoeba has advanced considerably in the last 10 years with new automated sequencing technology. This has allowed the construction of a genotype identification scheme with 13 different genotypes against which to compare clinical isolates for epidemiological investigations or pathogenicity markers. So far, only four genotypes have been associated with keratitis of which the majority have been T4 but T3, T6, and T11 have each caused individual cases. Each genotype is heterogenous and can be further subdivided by comparison of sequences of diagnostic fragments of 18S rDNA, riboprinting by PCR-RFLP of 18S rDNA, or by mitochondrial DNA RFLP. Drug therapy has been revolutionised with the introduction of the biguanides-chlorhexidine or polyhexamethylene biguanide-with most but not all infections quickly resolving. Failure can still occur occasionally and further research is needed on more effective combination chemotherapy. A number of guanidines have been identified in this paper that could be usefully pursued as part of combination chemotherapy along with the alkylphosphocholines.

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

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    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.

  10. On the evolution and molecular epidemiology of the potyvirus Papaya ringspot virus.

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    Bateson, Marion F; Lines, Rosemarie E; Revill, Peter; Chaleeprom, Worawan; Ha, Cuong V; Gibbs, Adrian J; Dale, James L

    2002-10-01

    The potyvirus Papaya ringspot virus (PRSV) is found throughout the tropics and subtropics. Its P biotype is a devastating pathogen of papaya crops and its W biotype of cucurbits. PRSV-P is thought to arise by mutation from PRSV-W. However, the relative impact of mutation and movement on the structure of PRSV populations is not well characterized. To investigate this, we have determined the coat protein sequences of isolates of both biotypes of PRSV from Vietnam (50), Thailand (13), India (1) and the Philippines (1), and analysed them together with 28 PRSV sequences already published, so that we can better understand the molecular epidemiology and evolution of PRSV. In Thailand, variation was greater among PRSV-W isolates (mean nucleotide divergence 7.6%) than PRSV-P isolates (mean 2.6%), but in Vietnamese populations the P and W biotypes were more but similarly diverse. Phylogenetic analyses of PRSV also involving its closest known relative, Moroccan watermelon mosaic virus, indicate that PRSV may have originated in Asia, particularly in the Indian subcontinent, as PRSV populations there are most diverse and hence have probably been present longest. Our analyses show that mutation, together with local and long-distance movement, contributes to population variation, and also confirms an earlier conclusion that populations of the PRSV-P biotype have evolved on several occasions from PRSV-W populations.

  11. Molecular epidemiology of domestic and sylvatic Trypanosoma cruzi infection in rural northwestern Argentina.

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    Cardinal, Marta V; Lauricella, Marta A; Ceballos, Leonardo A; Lanati, Leonardo; Marcet, Paula L; Levin, Mariano J; Kitron, Uriel; Gürtler, Ricardo E; Schijman, Alejandro G

    2008-11-01

    Genetic diversity of Trypanosoma cruzi populations and parasite transmission dynamics have been well documented throughout the Americas, but few studies have been conducted in the Gran Chaco ecoregion, one of the most highly endemic areas for Chagas disease, caused by T. cruzi. In this study, we assessed the distribution of T. cruzi lineages (identified by PCR strategies) in Triatoma infestans, domestic dogs, cats, humans and sylvatic mammals from two neighbouring rural areas with different histories of transmission and vector control in northern Argentina. Lineage II predominated amongst the 99 isolates characterised and lineage I amongst the six isolates obtained from sylvatic mammals. T. cruzi lineage IIe predominated in domestic habitats; it was found in 87% of 54 isolates from Tr. infestans, in 82% of 33 isolates from dogs, and in the four cats found infected. Domestic and sylvatic cycles overlapped in the study area in the late 1980s, when intense domestic transmission occurred, and still overlap marginally. The introduction of T. cruzi from sylvatic into domestic habitats is likely to occur very rarely in the current epidemiological context. The household distribution of T. cruzi lineages showed that Tr. infestans, dogs and cats from a given house compound shared the same parasite lineage in most cases. Based on molecular evidence, this result lends further support to the importance of dogs and cats as domestic reservoir hosts of T. cruzi. We believe that in Argentina, this is the first time that lineage IIc has been isolated from naturally infected domestic dogs and Tr. infestans.

  12. Clindamycin-resistant methicillin-resistant Staphylococcus aureus: epidemiologic and molecular characteristics and associated clinical factors.

    Science.gov (United States)

    Cadena, Jose; Sreeramoju, Pranavi; Nair, Shalini; Henao-Martinez, Andres; Jorgensen, James; Patterson, Jan E

    2012-09-01

    In this prospective, observational study of 618 consecutive adult patients with skin and soft tissue infections (SSTI) caused by methicillin-resistant Staphylococcus aureus (MRSA), the clinical characteristics, molecular epidemiology, and outcome of patients with clindamycin-resistant MRSA (n = 64) and clindamycin-susceptible MRSA (n = 554) were compared (including factors predictive of clindamycin-resistant MRSA SSTI). Patients with clindamycin-resistant MRSA were more likely to have had antibiotic exposure within 3 months (37.5% versus 17%, P < 0.01), surgery (25% versus 8%, P < 0.01), MRSA infection/colonization within 12 months (23% versus 7%, P < 0.01), or intravascular catheters (5% versus 0.5%, P = 0.02). On multivariate analysis, previous surgery (adjusted odds ratio [AOR] 2.97; 95% confidence interval [CI] 1.5-6.0), history of MRSA (AOR 3.4; 95% CI 1.7-7.1), and exposure to clindamycin (AOR 8.5; 95% CI 2.3-32) and to macrolides (AOR 7.2, 95% CI 1.6-31.8) were independently associated with presence of clindamycin-resistant MRSA. Clinical resolution was similar between groups (77% versus 68%; P = 0.26). Clindamycin-resistant MRSA was less often USA-300 (82% versus 98%, P = 0.004). Clindamycin resistance did not affect MRSA-SSTI clinical outcomes.

  13. 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.

  14. KRAS Mutations in Lung Adenocarcinoma: Molecular and Epidemiological Characteristics, Methods for Detection, and Therapeutic Strategy Perspectives.

    Science.gov (United States)

    Guibert, N; Ilie, M; Long, E; Hofman, V; Bouhlel, L; Brest, P; Mograbi, B; Marquette, C H; Didier, A; Mazieres, J; Hofman, P

    2015-01-01

    KRAS mutations are detected in over one third of lung adenocarcinomas, most frequently in Caucasian and smoker patients. The impact of KRAS mutations on lung adenocarcinoma prognosis is currently subject to debate, as is their impact on the response to chemotherapy and EGFR tyrosine kinase inhibitors. The different methods for KRAS status assessment, based on histological and cytological samples or biological fluids, offer varying sensitivities. Since no treatments are available in clinical routine for KRAS-mutated lung cancer patients, one of the current major challenges in thoracic oncology is developing new dedicated strategic therapies. Different molecules can be developed that act on a post-transcriptional KRAS protein level, blocking its cytoplasmic membrane recruitment. The efficacy of these molecules' targeting of the different signaling pathways activated by the KRAS mutation (such as the MEK and BRAF pathways) is related to the particular KRAS mutation subtype. New therapeutic strategies are currently focused on certain genes linked with KRAS inducing a synthetic lethal interaction. The purpose of this work is to provide an overview of i) the recent epidemiological and molecular findings concerning KRASmutated lung adenocarcinoma, ii) the prognostic impact of KRAS mutations, in particular during response to treatment, iii) the available methods for detecting this mutation, and iv) the current molecules under development for new therapeutic strategies and the clinical trials targeting this genomic alteration.

  15. Molecular epidemiology of human calicivirus gastroenteritis outbreaks in Hungary, 1998 to 2000.

    Science.gov (United States)

    Reuter, Gábor; Farkas, Tibor; Berke, Tamás; Jiang, Xi; Matson, David O; Szücs, György

    2002-11-01

    Between November 1998 and November 2000, 196 stool specimens from 21 outbreaks of acute nonbacterial gastroenteritis occurring in 11 of the 19 counties of Hungary were collected and tested for human caliciviruses. Human caliciviruses were detected and characterized by a type-common enzyme-linked immunosorbent assay (EIA) and reverse transcription-polymerase chain reaction (RT-PCR) followed by cloning and sequencing. Twenty (95%) and 14 (67%) outbreaks were positive by EIA and RT-PCR, respectively, and 12 RT-PCR-positive outbreaks were also confirmed by sequencing. Comparative sequence analysis revealed 13 Norwalk-like virus sequences in the 12 outbreaks, including 11 Norwalk-like virus genogroup II (seven in Hawaii-like, two Lordsdale-like, one Melksham-like, and one Hillingdon-like) and two Norwalk-like virus genogroup I (related to Southampton-like and Desert Shield-like clusters) viruses. Multiple Norwalk-like virus clusters, with a predominance of Hawaii-like viruses, played an important role in nonbacterial gastroenteritis outbreaks during the study period. This is the first country-wide molecular epidemiological investigation of human calicivirus-associated, gastroenteritis outbreaks in Hungary and Central-Eastern Europe.

  16. Molecular epidemiological study of cutaneous leishmaniasis in the focus of bushehr city, southwestern iran.

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    Mohammad Reza Yaghoobi-Ershadi

    2013-12-01

    Full Text Available Cutaneous leishmaniasis (CL represents the most frequent vector borne parasitoses in Iran. The objective of this study was to determine the epidemiological features of CL including human infection and the reservoir host in the city of Bushehr, Bushehr Province, Iran during 2010-2011.Studies on human infection was carried out on 2962 school children aged 7-14 years old from 60 primary schools and among 400 households with a total population of 1568 in four infected districts of the city in December 2010. Serosity materials from patients on glass slides were collected for molecular identification of causative agent. Rodents were caught by Sherman traps and examined for identification of the parasite.Prevalence of scars and ulcers among the inhabitants were 5.86% and 0.12% respectively. Molecular study indicated the presence of two coexisting species: Leishmania major and L. tropica among patients. The scar rate was 1.24% but no ulcers were seen among the students. Nineteen rodents were caught and identified as Tatera indica (47.4% and Rattus norvegicus (52.6%. Specimens from 7 T. indica and 9 R. norvegicus were examined by two techniques, microscopic examination and nested-PCR. Out of 7 T. indica, 14.3% were infected with L. major and 42.9% with L. turanica by nested-PCR. Out of 9 R. norvegicus 22.2% were infected with L. turanica and 11.1% with L. gerbilli.Based on this survey L. major and L. tropica are the causative agents of the disease among patients and T. indica plays a predominant role in the dissemination of L. major in the city.

  17. Phenotypic Characters and Molecular Epidemiology of Campylobacter Jejuni in East China.

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    Zeng, Dexin; Zhang, Xiaoping; Xue, Feng; Wang, Yanhong; Jiang, Luyan; Jiang, Yuan

    2016-01-01

    In this study, we investigated the distribution, phenotypic and molecular typing characters of Campylobacter jejuni in domestic fowl, and livestock populations in East China, to provide some reference for researches on its molecular epidemiology. A total of 1250 samples were collected from different animal sources, and C. jejuni strains were then isolated and tested for antibiotic sensitivity. Antibiotics-resistance gene and pathogenic genes were detected by polymerase chain reaction. Phylogenic analysis on the C. jejuni strains was performed by multilocus sequence typing (MLST) method. The results showed that 108 out of the 1250 samples (mean 8.64%) were C. jejuni positive. These 108 C. jejuni strains were highly sensitive to antibiotics such as chloramphenicol, amoxicillin, amikacin, cefotaxime, and azithromycin, whereas they were highly resistant to antibiotics such as cefoperazone, cotrimoxazole, cefamandole, sulfamethoxazole, and cefradine. Pathogenicity related gene identification indicated that the mean carrying rate of adhesion related gene cadF and racR, flagellin gene flaA, toxin regulating gene cdtA, cdtB, cdtC, wlaN and virB11, heat shock proteins and transferring proteins related genes dnaJ and ceuE, CiaB and pldA were 92.45%, 38.69%, 73.58%, 71.70%, 52.83%, 96.23%, 12.26%, 1.89%, 0.94%, 65.09%, 39.62% and 9.43%, respectively. A total of 58.82% of these strains contained more than 6 pathogenicity-related genes. MLST typed 58 ST types from the 108 isolated C. jejuni strains, including 24 new types, and ST-21 was the major type, accounting for 39.3% of the total strains.

  18. Molecular epidemiology and pathology of spirorchiid infection in green sea turtles (Chelonia mydas).

    Science.gov (United States)

    Chapman, Phoebe A; Owen, Helen; Flint, Mark; Soares Magalhães, Ricardo J; Traub, Rebecca J; Cribb, Thomas H; Kyaw-Tanner, Myat T; Mills, Paul C

    2017-04-01

    Spirorchiid blood fluke infections affect endangered turtle populations globally, and are reported as a common cause of mortality in Queensland green sea turtles. Both the flukes and their ova are pathogenic and can contribute to the stranding or death of their host. Of particular interest are ova-associated brain lesions, which have been associated with host neurological deficits. Accurate estimations of disease frequency and the relative effect of infection relating to different spirorchiid species are made difficult by challenges in morphological identification of adults of some genera, and a lack of species-level identifying features for ova. A new specifically designed molecular assay was used to detect and identify cryptic spirorchiids and their ova in Queensland green sea turtle tissues collected from 2011 to 2014 in order to investigate epidemiology, tissue tropisms and pathology. Eight spirorchiid genotypes were detected in 14 distinct tissues, including multiple tissues for each. We found no evidence of a characteristic pathway of the eggs to the exterior; instead the results suggest that a high proportion of eggs become lost in dead-end tissues. The most common lesions observed were granulomas affecting most organs with varying severity, followed by arteritis and thrombi in the great vessels. The number of spirorchiid types detected increased with the presence and severity of granulomatous lesions. However, compared with other organs the brain showed relatively low levels of spirorchiid diversity. An inverse relationship between host age and spirorchiid diversity was evident for the liver and kidneys, but no such relationship was evident for other organs. Molecular data in this study, the first of its kind, provides the first species-level examination of spirorchiid ova and associated pathology, and paves the way for the future development of targeted ante-mortem diagnosis of spirorchiidiasis.

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

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    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. Molecular epidemiology and pathology of spirorchiid infection in green sea turtles (Chelonia mydas

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    Phoebe A. Chapman

    2017-04-01

    Full Text Available Spirorchiid blood fluke infections affect endangered turtle populations globally, and are reported as a common cause of mortality in Queensland green sea turtles. Both the flukes and their ova are pathogenic and can contribute to the stranding or death of their host. Of particular interest are ova-associated brain lesions, which have been associated with host neurological deficits. Accurate estimations of disease frequency and the relative effect of infection relating to different spirorchiid species are made difficult by challenges in morphological identification of adults of some genera, and a lack of species-level identifying features for ova. A new specifically designed molecular assay was used to detect and identify cryptic spirorchiids and their ova in Queensland green sea turtle tissues collected from 2011 to 2014 in order to investigate epidemiology, tissue tropisms and pathology. Eight spirorchiid genotypes were detected in 14 distinct tissues, including multiple tissues for each. We found no evidence of a characteristic pathway of the eggs to the exterior; instead the results suggest that a high proportion of eggs become lost in dead-end tissues. The most common lesions observed were granulomas affecting most organs with varying severity, followed by arteritis and thrombi in the great vessels. The number of spirorchiid types detected increased with the presence and severity of granulomatous lesions. However, compared with other organs the brain showed relatively low levels of spirorchiid diversity. An inverse relationship between host age and spirorchiid diversity was evident for the liver and kidneys, but no such relationship was evident for other organs. Molecular data in this study, the first of its kind, provides the first species-level examination of spirorchiid ova and associated pathology, and paves the way for the future development of targeted ante-mortem diagnosis of spirorchiidiasis.

  1. Genomics, evolution, and molecular epidemiology of the Streptococcus bovis/Streptococcus equinus complex (SBSEC).

    Science.gov (United States)

    Jans, Christoph; Meile, Leo; Lacroix, Christophe; Stevens, Marc J A

    2015-07-01

    The Streptococcus bovis/Streptococcus equinus complex (SBSEC) is a group of human and animal derived streptococci that are commensals (rumen and gastrointestinal tract), opportunistic pathogens or food fermentation associates. The classification of SBSEC has undergone massive changes and currently comprises 7 (sub)species grouped into four branches based on sequences identities: the Streptococcus gallolyticus, the Streptococcus equinus, the Streptococcus infantarius and the Streptococcus alactolyticus branch. In animals, SBSEC are causative agents for ruminal acidosis, potentially laminitis and infective endocarditis (IE). In humans, a strong association was established between bacteraemia, IE and colorectal cancer. Especially the SBSEC-species S. gallolyticus subsp. gallolyticus is an emerging pathogen for IE and prosthetic joint infections. S. gallolyticus subsp. pasteurianus and the S. infantarius branch are further associated with biliary and urinary tract infections. Knowledge on pathogenic mechanisms is so far limited to colonization factors such as pili and biofilm formation. Certain strain variants of S. gallolyticus subsp. macedonicus and S. infantarius subsp. infantarius are associated with traditional dairy and plant-based food fermentations and display traits suggesting safety. However, due to their close relationship to virulent strains, their use in food fermentation has to be critically assessed. Additionally, implementing accurate and up-to-date taxonomy is critical to enable appropriate treatment of patients and risk assessment of species and strains via recently developed multilocus sequence typing schemes to enable comparative global epidemiology. Comparative genomics revealed that SBSEC strains harbour genomics islands (GI) that seem acquired from other streptococci by horizontal gene transfer. In case of virulent strains these GI frequently encode putative virulence factors, in strains from food fermentation the GI encode functions that are

  2. New Insights into the Molecular Epidemiology and Population Genetics of Schistosoma mansoni in Ugandan Pre-school Children and Mothers

    Science.gov (United States)

    Betson, Martha; Sousa-Figueiredo, Jose C.; Kabatereine, Narcis B.; Stothard, J. Russell

    2013-01-01

    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. PMID:24349589

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

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    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.

  4. Molecular epidemiology of HIV-1 in Rio Grande, RS, Brazil Epidemiologia molecular do HIV-1 em Rio Grande, RS, Brasil

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    Ana Maria Barral de Martínez

    2002-10-01

    Full Text Available We conducted a molecular epidemiological study to investigate HIV-1 strains in Rio Grande, southern Brazil, searching for an association with transmission mode and risk behavior. Patients (185 identified at an AIDS treatment reference Hospital, from 1994 to 1997, were included; from which 107 blood samples were obtained. Nested PCR was realized once for each sample; for amplified samples (69 HIV subtypes were classified using the heteroduplex mobility assay. Subtypes identified were B (75%, C (22% and F (3%. All infections with C were diagnosed after 1994. Comparing patients with B and C, no differences were detected regarding demographic, clinical and laboratory characteristics; survival analysis did not reveal differences in HIV to AIDS evolution. A higher proportion of injecting drug users, IDU (not significant, pUm estudo de epidemiologia molecular foi conduzido para investigar subtipos de HIV-1 circulando em Rio Grande, RS, buscando uma associação com modos de transmissão e comportamentos de risco. Pacientes (185 identificados de 1994 a 1997, em um Hospital de referência para o tratamento da AIDS foram incluidos; amostras de sangue foram obtidas de 107. A reação em cadeia da polimerase (PCR foi realizada uma única vez; nas amostras que amplificaram, (69 o subtipo foi classificado pelo ensaio de mobilidade do heteroduplex (HMA. Os subtipos de HIV identificados foram B (75%, C (22% e F (3%. As infecções com C foram diagnosticadas após 1994. Pacientes infectados com B e C não mostraram diferenças (características demográficas, clínicas e laboratoriais; a análise de sobrevida não mostrou diferenças na evolução HIV-AIDS. Maior proporção de usuários de drogas injetáveis (UDI (não significativa, p<0,07, foi identificada entre infectados com C. Este resultado sugere C ter sido introduzido nesta área através dos UDI, sendo transmitido pelos seus parceiros sexuais, a pessoas com outras práticas de risco.

  5. 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.

  6. Pseudomonas aeruginosa in a neonatal intensive care unit: molecular epidemiology and infection control measures

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    Triassi Maria

    2009-05-01

    Full Text Available Abstract Background Pseudomonas aeruginosa, a non-fermentative, gram-negative rod, is responsible for a wide variety of clinical syndromes in NICU patients, including sepsis, pneumonia, meningitis, diarrhea, conjunctivitis and skin infections. An increased number of infections and colonisations by P. aeruginosa has been observed in the neonatal intensive care unit (NICU of our university hospital between 2005 and 2007. Methods Hand disinfection compliance before and after an educational programme on hand hygiene was evaluated. Identification of microrganisms was performed using conventional methods. Antibiotic susceptibility was evaluated by MIC microdilution. Genotyping was performed by PFGE analysis. Results The molecular epidemiology of Pseudomonas aeruginosa in the NICU of the Federico II University hospital (Naples, Italy and the infection control measures adopted to stop the spreading of P. aeruginosa in the ward were described. From July 2005 to June 2007, P. aeruginosa was isolated from 135 neonates and caused severe infections in 11 of them. Macrorestriction analysis of clinical isolates from 90 neonates identified 20 distinct genotypes, one major PFGE type (A being isolated from 48 patients and responsible for 4 infections in 4 of them, four other distinct recurrent genotypes being isolated in 6 to 4 patients. Seven environmental strains were isolated from the hand of a nurse and from three sinks on two occasions, two of these showing PFGE profiles A and G identical to two clinical isolates responsible for infection. The successful control of the outbreak was achieved through implementation of active surveillance of healthcare-associated infections in the ward together with environmental microbiological sampling and an intense educational programme on hand disinfection among the staff members. Conclusion P. aeruginosa infections in the NICU were caused by the cross-transmission of an epidemic clone in 4 neonates, and by the selection

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

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    Nuntra Suwantarat

    2016-05-01

    Full Text Available Abstract 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” combined with specific Southeast Asian country names (Thailand, Singapore, Malaysia, Vietnam, Indonesia, Philippines, Laos, Cambodia, Myanmar, Brunei. Results There were a total of 175 publications from the following countries: Thailand (77, Singapore (35, Malaysia (32, Vietnam (23, Indonesia (6, Philippines (1, Laos (1, and Brunei (1. We did not find any publications on MDRGN from Myanmar and Cambodia. We did not include publications related to Shigella spp., Salmonella spp., and Vibrio spp. and non-human related studies in our review. English language articles and abstracts were included for analysis. After the abstracts were reviewed, data on MDRGN in Southeast Asia from 54 publications were further reviewed and included in this study. Conclusions MDRGNs are a major contributor of antimicrobial-resistant bacteria in Southeast Asia. The high prevalence of ESBLs has been a major problem since 2005 and is possibly related to the development of carbapenem resistant organisms in this region due to the overuse of carbapenem therapy. Carbapenem–resistant Acinetobacter baumannii is the most common pathogen associated with nosocomial infections in this region followed by carbapenem-resistant Pseudomonas aeruginosa. Although Southeast Asia is not an endemic area for carbapenem-resistant Enterobacteriaceae (CRE, recently, the rate of CRE detection has been increasing. Limited infection control measures, lack of antimicrobial control, such as the presence of

  8. Molecular epidemiology and surveillance of circulating rotavirus and adenovirus in Congolese children with gastroenteritis.

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    Mayindou, Gontran; Ngokana, Berge; Sidibé, Anissa; Moundélé, Victoire; Koukouikila-Koussounda, Felix; Christevy Vouvoungui, Jeannhey; Kwedi Nolna, Sylvie; Velavan, Thirumalaisamy P; Ntoumi, Francine

    2016-04-01

    Infectious Diarrhea caused by rotavirus and adenovirus, is a leading cause of death in children in sub-Sahara Africa but there is limited published data on the diverse rotavirus genotypes and adenovirus serotypes circulating in the Republic of Congo. In this study, we investigated the prevalence of severe diarrhea caused by rotavirus A (RVA) and Adenovirus serotype 40 and 41 in Congolese children hospitalized with severe gastroenteritis. Stool samples were collected from 655 Congolese children less than 60 months of age hospitalized with acute gastroenteritis between June 2012 and June 2013. Rotavirus and adenovirus antigens were tested using commercially available ELISA kits and the RVA G- and P- genotypes were identified by seminested multiplex RT-PCR. Three hundred and four (46.4%) children were tested positive for RVA. Adenovirus infection was found in 5.5% of the 564 tested children. Rotavirus infection was frequently observed in children between 6-12 months (55.9%). The dry season months recorded increased RVA infection while no seasonality of adenovirus infection was demonstrated. The most common RVA genotypes were G1 (57.5%), G2 (6.4%), G1G2 mixture (15.5%), P[8] (58%), P[6] (13.2%), and P[8]P[6] mixture (26%). Additionally, the genotype G12P[6] was significantly associated with increased vomiting. This first study on Congolese children demonstrates a high prevalence and clinical significance of existing rotavirus genotypes. Adenovirus prevalence is similar to that of other Central African countries. This baseline epidemiology and molecular characterization study will contribute significantly to the RVA surveillance after vaccine implementation in the country.

  9. [Evaluation of discriminatory power of molecular epidemiology techniques in Mycobacterium tuberculosis Venezuelan isolates].

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    Méndez, Marìa Victoria; León, Cristy; Escalona, Arnelly; Abadia, Edgar; Da Mata, Omaira; de Waard, Jacobus; Takiff, Howard Eugene

    2016-03-01

    The techniques of spoligotyping and mycobacterial interspersed repetitive unit and variable-number tandem repeat typing with 24 loci (MIRU-VNTR-24), have been used to study the molecular epidemiology of tuberculosis. The aim of this study was: to evaluate the discriminative power of MIRU-VNTR 24 loci alone and in association with spoligotyping in clinical isolates of M tuberculosis in Venezuela; the allelic diversity of the 24 loci; and the discriminative power for the combination of 24 and 15 loci, 12 traditional loci (12t), those with higher allelic diversity and a new combination named 12inv. We analyzed one set of 104 strains of different lineages and a second set of 431 strains belonging to the Latin-America and Mediterranean lineage (LAM) that is predominant in Venezuela. The determination of allelic diversity showed that 4052, 2163b, 424 y 2996 are highly discriminative. Clustering rates of MIRU-VNTR 24 loci, spoligotyping and MIRU-VNTR combined with spoligotyping for 104 isolates were 18.27%, 71.15% and 14.4%, respectively, whereas with the 431 LAM strains the values were 43.2 %, 95.8% and 37.4%. MIRU-VNTR combinations of 15, 12inv and 4 loci were more discriminatory than 12t. Clustering rates for MIRU-VNTR 15 and 12inv loci coupled with spoligotyping in the 104 isolated was 21% and 23%, while for LAM strains was 52% and 46% respectively. The number of different genetics patterns for 15 and 12inv loci were similar. In conclusion, we propose the use of a small number of informative loci MIRU-VNTR coupled to spoligotyping to investigate the transmission of tuberculosis in Venezuela.

  10. Molecular epidemiology of avian leukosis virus subgroup J in layer flocks in China.

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    Gao, Yulong; Yun, Bingling; Qin, Liting; Pan, Wei; Qu, Yue; Liu, Zaisi; Wang, Yongqiang; Qi, Xiaole; Gao, Honglei; Wang, Xiaomei

    2012-03-01

    Avian leukosis virus subgroup J (ALV-J) was first isolated from meat-type chickens in 1988. No field cases of ALV-J infection or tumors in layer chickens were observed worldwide until 2004. However, layer flocks in China have experienced outbreaks of this virus in recent years. The molecular epidemiology of ALV-J strains isolated from layer flocks was investigated. The env genes of 77.8% (21/27) of the ALV-J layer isolates with a high degree of genetic variation were significantly different from the env genes of the prototype strain of ALV-J (HPRS-103) and American and Chinese strains from meat-type chickens (designated ALV-J broiler isolates). A total of 205 nucleotides were deleted from the 3' untranslated region of 89.5% (17/19) of the ALV-J layer isolates. Approximately 94.7% (16/17) of the layer isolates contained a complete E element of 146 to 149 residues. The U3 sequences of 84.2% (16/19) of the ALV-J layer isolates displayed less than 92.5% sequence homology to those of the ALV-J broiler isolates, although the transcriptional regulatory elements that are typical of avian retroviruses were highly conserved. Several unique nucleotide substitutions in the env gene, the U3 region, and the E element of most of the ALV-J layer isolates were detected. These results suggested that the env gene, E element, and U3 region in the ALV-J layer isolates have evolved rapidly and were significantly different from those of the ALV-J broiler isolates. These findings will contribute to a better understanding of the pathogenic mechanism of layer tumor diseases induced by ALV-J.

  11. Molecular epidemiology and genetic diversity of hepatitis B virus in Mar del Plata city, Argentina.

    Science.gov (United States)

    Barbini, Luciana; Elizalde, Mercedes; Torres, Carolina; Campos, Rodolfo

    2013-10-01

    The aim of this work was to describe the current molecular epidemiology and genetic diversity of HBV in Mar del Plata, an important Argentinean touristic city. The phylogenetic analysis of 29 HBV DNA positive serum samples showed that F1b was the predominant subgenotype (sgt, 62.1%), followed by sgt A2 (13.8%) and sgt F4, gt D and gt G (6.9% each). Among anti-HBc IgM positive samples, 75.0% were sgt F1b, followed by sgt F4 (12.5%), sgt A2 (6.25%) and sgt D (6.25%). Three recombinant full length genomes were found: two G/F1b (some of the first gt G detected in Argentina) and one F4/D2. The circulation of clinical important mutations in the city was described. Mutations at the HBsAg were detected in 34.5% of the analyzed samples, associated with laboratory diagnosis and antiviral treatment failures, immune escape and hepatocellular carcinoma. Most of the samples presented wild type BCP/PC sequences. Coalescence analysis for the most prevalent sgt F1b estimated that the diversification mainly occured during mid '90s and the tMRCA was estimated in 1987. Finally, the high presence of the autochthonous sgt F1b, associated with the anti-HBc IgM positive infection and its present-day diversification process, shows the strong impact of internal human migratory movements into the current population of Mar del Plata.

  12. 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.

  13. MOLECULAR-EPIDEMIOLOGICAL INVESTIGATION OF THE OUTBREAK OF ASEPTIC MENINGITIS IN NOVOSIBIRSK REGION

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    A. V. Demina

    2016-01-01

    Full Text Available The aim of this study was to investigate the outbreak of aseptic meningitis in theNovosibirskregion in 2008–2009. We studied genetic diversity and molecular-epidemiological characteristics of human enteroviruses that caused aseptic meningitis. Materials and metods. In the present study we investigated samples of cerebrospinal fluid from 199 patients with a diagnosis “aseptic meningitis”, based on the clinical characteristics of the disease (headache, stiff neck, fever, nausea, vomiting, and confirmed by laboratory tests of spinal fluid (lymphocyte cell count > 10 cells/ml.All samples were tested by PCR for RNA of Enterovirus and Flavivirus and DNA Myc. tuberculosis, Borrelia spp., Neisseria spp. In the samples there were not found RNA Flavivirus, DNA Myc. tuberculosis, Borrelia spp., Neisseria spp., but in 73 samples (37% was identified RNA enterovirus (EV. Determination of nucleotide sequences of 5’UTR and VP1-region of EV revealed that they belong to the following genotypes: the highest percentage was presented by genotype ECHO 30 (62%; another genotypes were Cox A2 (8%, Cox A4 (5%, Cox A14 (3%, Cox A16 (5%, Cox B5 (8%, ECHO 6 (3%, ECHO 9 (3% and ECHO 25 (3%. In 2008 most of the EV that caused the symptoms of aseptic meningitis belonged to genotype ECHO 30 (76%. In 2009 the clinical specimens containing genotype ECHO 30 were not found, but the largest percentage of EV belonged to genotypes Cox A2 (33% and Cox A4 (22%. Thus, in 2008 we recorded outbreak of aseptic meningitis, the major etiological factor was enterovirus ECHO 30. And the rise of the incidence of aseptic meningitis in 2009 is related to the circulation of new genotypes of EV. The investigated strains were deposited in an international database GenBank under accession numbers KP258231-KP258235, HM559584.

  14. 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.

  15. Molecular epidemiology of carbapenem non-susceptible Acinetobacter nosocomialis in a medical center in Taiwan.

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    Yang, Ya-Sung; Lee, Yi-Tzu; Wang, Yung-Chih; Chiu, Chun-Hsiang; Kuo, Shu-Chen; Sun, Jun-Ren; Yin, Ti; Chen, Te-Li; Lin, Jung-Chung; Fung, Chang-Phone; Chang, Feng-Yee

    2015-04-01

    The mechanism by which carbapenem non-susceptible Acinetobacter nosocomialis (CNSAN) is disseminated is rarely described in the literature. In this study, we delineated the molecular epidemiology of CNSAN isolated from patients in a medical center in Taiwan. Fifty-four non-duplicate bloodstream isolates of CNSAN were collected at the Taipei Veterans General Hospital between 2001 and 2007. Pulsed-field gel electrophoresis (PFGE) was performed to determine their clonal relationship. Carbapenem-resistance genes and associated genetic structures were detected by polymerase chain reaction (PCR) mapping. Southern hybridization was performed to determine the plasmid location of carbapenem-resistance genes. Transmissibility of these genes to Acinetobacterbaumannii was demonstrated by conjugation tests. The overall carbapenem non-susceptibility rate among A. nosocomialis isolates during the study period was 21.6% (54/250). PFGE revealed three major pulsotypes: H (n=23), I (n=10), and K (n=8). The most common carbapenem-resistance gene was blaOXA-58 (43/54, 79.6%), containing an upstream insertion sequence IS1006 and a truncated ISAba3 (IS1006-ΔISAba3-like-blaOXA-58). All isolates belonging to the pulsotypes H, I, and K carried plasmid located IS1006-ΔISAba3-like-blaOXA-58. A common plasmid carrying ISAba1-blaOXA-82 was found in six isolates, which belonged to five pulsotypes. A type 1 integron that carried blaIMP-1 was detected in different plasmids of seven isolates, which belonged to five pulsotypes. Plasmids carrying these carbapenem-resistant determinants were transmissible from A. nosocomialis to A. baumannii via conjugation. In this medical center, CNSAN mainly emerged through clonal dissemination; propagation of plasmids and integrons carrying carbapenem-resistant determinants played a minor role. This study showed that plasmids carrying carbapenem-resistant determinants are transmissible from A. nosocomialis to A. baumannii.

  16. Acinetobacter seifertii Isolated from China: Genomic Sequence and Molecular Epidemiology Analyses.

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    Yang, Yunxing; Wang, Jianfeng; Fu, Ying; Ruan, Zhi; Yu, Yunsong

    2016-03-01

    Clinical infections caused by Acinetobacter spp. have increasing public health concerns because of their global occurrence and ability to acquire multidrug resistance. Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) complex encompasses A. calcoaceticus, A. baumannii, A. pittii (formerly genomic species 3), and A nosocomial (formerly genomic species 13TU), which are predominantly responsible for clinical pathogenesis in the Acinetobacter genus. In our previous study, a putative novel species isolated from 385 non-A. baumannii spp. strains based on the rpoB gene phylogenetic tree was reported. Here, the putative novel species was identified as A. seifertii based on the whole-genome phylogenetic tree. A. seifertii was recognized as a novel member of the ACB complex and close to A. baumannii and A. nosocomials. Furthermore, we studied the characteristics of 10 A. seifertii isolates, which were distributed widely in 6 provinces in China and mainly caused infections in the elderly or children. To define the taxonomic status and characteristics, the biochemical reactions, antimicrobial susceptibility testing, pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and whole-genome sequence analysis were performed. The phenotypic characteristics failed to distinguish A. serfertii from other species in the ACB complex. Most of the A. seifertii isolates were susceptible to antibiotics commonly used for nosocomial Acinetobacter spp. infections, but one isolate (strain A362) was resistant to ampicillin/sulbactam, ceftazidime and amikacin. The different patterns of MLST and PFGE suggested that the 10 isolates were not identical and lacked clonal relatedness. Our study reported for the first time the molecular epidemiological and genomic features of widely disseminated A. seifertii in China. These observations could enrich the knowledge of infections caused by non-A. baumannii and may provide a scientific basis for future clinical treatment.

  17. Molecular epidemiology and genetic diversity of hepatitis B virus in Ethiopia.

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    Hundie, Gadissa Bedada; Raj, V Stalin; Michael, Daniel Gebre; Pas, Suzan D; Osterhaus, Albert D M E; Koopmans, Marion P; Smits, Saskia L; Haagmans, Bart L

    2016-06-01

    Although hepatitis B virus (HBV) infection is hyperendemic in Ethiopia and constitutes a major public health problem, little is known about its genetic diversity, genotypes, and circulation. The aim of this study was to determine the molecular epidemiology and genetic diversity of HBV in Ethiopia, using 391 serum samples collected from HBsAg-positive blood donors living in five different geographic regions. The HBV S/pol gene was amplified, sequenced, and HBV genotypes, subgenotypes, serotypes, and major hydrophilic region (MHR) variants were determined. Phylogenetic analysis of 371 samples (95%) revealed the distribution of genotypes A (78%) and D (22%) in Ethiopia. Further phylogenetic analysis identified one subgenotype (A1) within genotype A, and 4 subgenotypes within genotype D (D1; 1.3%, D2; 55%, D4; 2.5%, and D6; 8.8%). Importantly, 24 isolates (30%) of genotype D formed a novel phylogenetic cluster, distinct from any known D subgenotypes, and two A/D recombinants. Analysis of predicted amino-acid sequences within the HBsAg revealed four serotypes: adw2 (79%), ayw1 (3.1%), ayw2 (7.8%), and ayw3 (11.6%). Subsequent examination of sequences showed that 51 HBV isolates (14%) had mutations in the MHR and 8 isolates (2.2%) in the reverse transcriptase known to confer antiviral resistance. This study provides the first description of HBV genetic diversity in Ethiopia with a predominance of subgenotypes A1 and D2, and also identified HBV isolates that could represent a novel subgenotype. Furthermore, a significant prevalence of HBsAg variants in Ethiopian population is revealed.

  18. 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.

  19. Molecular epidemiology and virulence factors of pyogenic liver abscess causing Klebsiella pneumoniae in China.

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    Luo, Y; Wang, Y; Ye, L; Yang, J

    2014-11-01

    The molecular epidemiology and prevalence of virulence factors of isolates from patients with Klebsiella pneumoniae liver abscess (KLA) in mainland China are unknown. Klebsiella pneumoniae isolates were obtained from drainage samples aseptically collected from patients with pyogenic liver abscess (PLA). The genetic similarity of KLA isolates was analyzed by pulsed-field gel electrophoresis. The hypermucoviscosity (HV) phenotype was identified by a positive string test. The K1 and K2 genotypes, the pLVPK-derived genetic loci, aerobactin gene, kfu and alls were detected by PCR amplification. The sequence types (STs) were identified by multilocus sequence typing. Among the 51 non-repetitive KLA isolates, 49 PFGE types have been identified. In total, 19 (37.2%) and 14 (27.4%) of the 51 KLA isolates belonged to clonal complex (CC) 23 and CC65, respectively, while the other 18 isolates (35.3%) were defined as other STs. CC23 consisted of only K1 strains, while CC65 included only K2 strains. All non-K1/K2 strains were classified as STs other than CC23 and CC65. Approximately 70.6% (36/51) of KLA isolates exhibited an HV phenotype. Both K1 and K2 isolates presented significantly higher prevalence of the pLVPK-derived loci than non-K1/K2 isolates. The K1 isolates had a significantly higher prevalence of the kfu and allS genes than K2 and non-K1/K2 isolates, while the K2 isolates exhibited higher repA prevalence than K1 and non-K1/K2 isolates. The majority of KLA isolates belonged to CC23K1 and CC65K2, while other STs with non-K1/K2 capsular types have also been identified. The virulent factors exhibited diverse distribution among the different clones of KLA isolates.

  20. 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.

  1. 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.

  2. [Molecular Epidemiological Analysis of HIV-1 pol Gene Sequences Isolated in Istanbul, Turkey].

    Science.gov (United States)

    Sayan, Murat; Kumbasar Karaosmanoğlu, Hayat; Mete, Birgül; Gündüz, Alper; Aydın, Ozlem; Yemişen, Mücahit; Uzun, Nuriye; Tabak, Fehmi

    2013-01-01

    epidemiologic studies are important tools for tracking the transmission and spread patterns, and for the control of the HIV infections, HIV molecular studies should be expanded in HIV-1 infected Turkish patients. Furthermore, the determined subtypes and CRFs of HIV-1 in Turkey may be expected to contribute to global HIV surveillance systems.

  3. 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

  4. Molecular and Histopathological Changes Associated with Keratoconus

    Science.gov (United States)

    Khaled, Mariam Lotfy; Helwa, Inas; Drewry, Michelle; Seremwe, Mutsa; Estes, Amy

    2017-01-01

    Keratoconus (KC) is a corneal thinning disorder that leads to loss of visual acuity through ectasia, opacity, and irregular astigmatism. It is one of the leading indicators for corneal transplantation in the Western countries. KC usually starts at puberty and progresses until the third or fourth decade; however its progression differs among patients. In the keratoconic cornea, all layers except the endothelium have been shown to have histopathological structural changes. Despite numerous studies in the last several decades, the mechanisms of KC development and progression remain unclear. Both genetic and environmental factors may contribute to the pathogenesis of KC. Many previous articles have reviewed the genetic aspects of KC, but in this review we summarize the histopathological features of different layers of cornea and discuss the differentially expressed proteins in the KC-affected cornea. This summary will help emphasize the major molecular defects in KC and identify additional research areas related to KC, potentially opening up possibilities for novel methods of KC prevention and therapeutic intervention. PMID:28251158

  5. 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.

  6. Biomarkers for Uranium Risk Assessment for the Development of the CURE (Concerted Uranium Research in Europe) Molecular Epidemiological Protocol.

    Science.gov (United States)

    Guéguen, Yann; Roy, Laurence; Hornhardt, Sabine; Badie, Christophe; Hall, Janet; Baatout, Sarah; Pernot, Eileen; Tomasek, Ladislav; Laurent, Olivier; Ebrahimian, Teni; Ibanez, Chrystelle; Grison, Stephane; Kabacik, Sylwia; Laurier, Dominique; Gomolka, Maria

    2017-01-01

    Despite substantial experimental and epidemiological research, there is limited knowledge of the uranium-induce health effects after chronic low-dose exposures in humans. Biological markers can objectively characterize pathological processes or environmental responses to uranium and confounding agents. The integration of such biological markers into a molecular epidemiological study would be a useful approach to improve and refine estimations of uranium-induced health risks. To initiate such a study, Concerted Uranium Research in Europe (CURE) was established, and involves biologists, epidemiologists and dosimetrists. The aims of the biological work package of CURE were: 1. To identify biomarkers and biological specimens relevant to uranium exposure; 2. To define standard operating procedures (SOPs); and 3. To set up a common protocol (logistic, questionnaire, ethical aspects) to perform a large-scale molecular epidemiologic study in uranium-exposed cohorts. An intensive literature review was performed and led to the identification of biomarkers related to: 1. retention organs (lungs, kidneys and bone); 2. other systems/organs with suspected effects (cardiovascular system, central nervous system and lympho-hematopoietic system); 3. target molecules (DNA damage, genomic instability); and 4. high-throughput methods for the identification of new biomarkers. To obtain high-quality biological materials, SOPs were established for the sampling and storage of different biospecimens. A questionnaire was developed to assess potential confounding factors. The proposed strategy can be adapted to other internal exposures and should improve the characterization of the biological and health effects that are relevant for risk assessment.

  7. Confirming Mycobacterium tuberculosis transmission from a cadaver to an embalmer using molecular epidemiology.

    Science.gov (United States)

    Anderson, Janelle A; Meissner, Jeanne Sullivan; Ahuja, Shama Desai; Shashkina, Elena; O'Flaherty, Tholief; Proops, Douglas C

    2015-05-01

    Genotyping results and epidemiologic investigation were used to confirm tuberculosis transmission from a cadaver to an embalmer. This investigation highlights the utility of genotyping in identifying unsuspected epidemiologic links and unusual transmission settings. In addition, the investigation provides additional evidence for the occupational risk of tuberculosis among funeral service workers and indicates a need for education about tuberculosis risk and the importance of adhering to appropriate infection control measures among funeral service workers.

  8. 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...... was found for all age groups (range, 13-36%). The decrease was present for both sexes, but most prominent in girls. The incidence of complicated acute appendicitis decreased by 10%. CONCLUSION: The incidence of acute appendicitis is declining. The incidence of uncomplicated appendicitis appears...

  9. 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

  10. Challenges and opportunities in international molecular cancer prevention research: An ASPO Molecular Epidemiology and the Environment and International Cancer Prevention Interest Groups Report.

    Science.gov (United States)

    Epplein, Meira; Bostick, Roberd M; Mu, Lina; Ogino, Shuji; Braithwaite, Dejana; Kanetsky, Peter A

    2014-11-01

    The International Agency for Research on Cancer estimates that over half of the new cancer cases and almost two-thirds of the cancer deaths in 2012 occurred in low and middle income countries. To discuss the challenges and opportunities to reducing the burden of cancer worldwide, the Molecular Epidemiology and the Environment and the International Issues in Cancer Special Interest Groups joined forces to hold a session during the 38th Annual Meeting of the American Society of Preventive Oncology (March 2014, Arlington, Virginia). The session highlighted three topics of particular interest to molecular cancer prevention researchers working internationally, specifically: 1) biomarkers in cancer research; 2) environmental exposures and cancer; and 3) molecular pathological epidemiology. A major factor for successful collaboration illuminated during the discussion was the need for strong, committed, and reliable international partners. A key element of establishing such relationships is to thoroughly involve individual international collaborators in the development of the research question; engaged international collaborators are particularly motivated to champion and shepherd the project through all necessary steps, including issues relating to institutional review boards, political sensitivity, laboratory-based assays, and tumor subtyping. Also essential is allotting time for the building, maintaining, and investing in such relationships so that successful international collaborations may take root and bloom. While there are many challenges inherent to international molecular cancer research, the opportunities for furthering the science and prevention of cancer worldwide are great, particularly at this time of increasing cancer incidence and prevalence in low and middle income countries.

  11. 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

  12. West Nile virus epidemiology and factors triggering change in its distribution in Europe.

    Science.gov (United States)

    Pradier, S; Lecollinet, S; Leblond, A

    2012-12-01

    West Nile virus (WNV) has historically been considered among the least virulent members of the Japanese serogroup complex (family Flaviviridae, genus Flavivirus). The WNV natural cycle involves birds as the main amplifying hosts and several species of mosquito as vectors. Many outbreaks occurred during the past decade, causing severe human encephalitis in the Old World, and the virus has become established in many European countries. Emergence of WNV is difficult to predict and even more difficult to prevent. In this review, the latest information on the epidemiology, transmission dynamics and clinical aspects of WNV is presented, with particular focus on specific factors likely to trigger changes in the distribution of the disease in Europe, such as climate changes and their consequences on the potential vectors of WNV or bird migration routes. The control of some anthropogenic and environmental factors could help prevent extension and re-emergence of WNV epidemics.

  13. 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

    OpenAIRE

    Ma Eugenia Jiménez-Corona; Lourdes García-García; Alfredo Ponce de León; Miriam Bobadilla-del Valle; Martha Torres; Sergio Canizales-Quintero; Carmen Palacios-Merino; Susana Molina-Hernández; Rosa Areli Martínez-Gamboa; Luis Juárez-Sandino; Bulmaro Cano-Arellano; Leticia Ferreyra-Reyes; Luis Pablo Cruz-Hervert; Renata Báez-Saldaña; Elizabeth Ferreira-Guerrero

    2009-01-01

    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 e...

  14. 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.

  15. 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.

  16. 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

  17. 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

  18. Hemoglobinopathy: molecular epidemiological characteristics and health effects on Hakka people in the Meizhou region, southern China.

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    Min Lin

    Full Text Available BACKGROUND: Hemoglobinopathies are the most common inherited diseases in southern China. However, there have been only a few epidemiological studies of hemoglobinopathies in Guangdong province. MATERIALS AND METHODS: Peripheral blood samples were collected from 15299 "healthy" unrelated subjects of dominantly ethnic Hakka in the Meizhou region, on which hemoglobin electrophoresis and routine blood tests were performed. Suspected cases with hemoglobin variants and hereditary persistence of fetal hemoglobin (HPFH were further characterized by PCR, DNA sequencing, reverse dot blot (RDB or multiplex ligation-dependent probe amplification (MLPA. In addition, 1743 samples were randomly selected from the 15299 subjects for thalassemia screening, and suspected thalassemia carriers were identified by PCR and RDB. RESULTS: The gene frequency of hemoglobin variants was 0.477% (73/15299. The five main subgroups of the ten hemoglobin variants were Hb E, Hb G-Chinese, Hb Q-Tahiland, Hb New York and Hb J-Bangkok. 277 cases (15.89%, 277/1743 of suspected thalassemia carriers with microcytosis (MCV<82 fl were found by thalassemia screening, and were tested by a RDB gene chip to reveal a total of 196 mutant chromosomes: including 124 α-thalassemia mutant chromosomes and 72 β-thalassemia mutant chromosomes. These results give a heterozygote frequency of 11.24% for common α and β thalassemia in the Hakka population in the Meizhou region. 3 cases of HPFH/δβ-thalassemia were found, including 2 cases of Vietnamese HPFH (FPFH-7 and a rare Belgian( Gγ((Aγδβ⁰-thalassemia identified in Chinese. CONCLUSIONS: Our results provide a detailed prevalence and molecular characterization of hemoglobinopathies in Hakka people of the Meizhou region. The estimated numbers of pregnancies each year in the Meizhou region, in which the fetus would be at risk for β thalassemia major or intermedia, Bart's hydrops fetalis, and Hb H disease, are 25 (95% CI, 15 to 38, 40 (95% CI

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

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    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.

  20. HIV-1 molecular epidemiology among newly diagnosed HIV-1 individuals in Hebei, a low HIV prevalence province in China

    Science.gov (United States)

    Lu, Xinli; Kang, Xianjiang; Liu, Yongjian; Cui, Ze; Guo, Wei; Zhao, Cuiying; Li, Yan; Chen, Suliang; Li, Jingyun; Zhang, Yuqi; Zhao, Hongru

    2017-01-01

    New human immunodeficiency virus type 1 (HIV-1) diagnoses are increasing rapidly in Hebei. The aim of this study presents the most extensive HIV-1 molecular epidemiology investigation in Hebei province in China thus far. We have carried out the most extensive systematic cross-sectional study based on newly diagnosed HIV-1 positive individuals in 2013, and characterized the molecular epidemiology of HIV-1 based on full length gag-partial pol gene sequences in the whole of Hebei. Nine HIV-1 genotypes based on full length gag-partial pol gene sequence were identified among 610 newly diagnosed naïve individuals. The four main genotypes were circulating recombinant form (CRF)01_AE (53.4%), CRF07_BC (23.4%), subtype B (15.9%), and unique recombinant forms URFs (4.9%). Within 1 year, three new genotypes (subtype A1, CRF55_01B, CRF65_cpx), unknown before in Hebei, were first found among men who have sex with men (MSM). All nine genotypes were identified in the sexually contracted HIV-1 population. Among 30 URFs, six recombinant patterns were revealed, including CRF01_AE/BC (40.0%), CRF01_AE/B (23.3%), B/C (16.7%), CRF01_AE/C (13.3%), CRF01_AE/B/A2 (3.3%) and CRF01_AE/BC/A2 (3.3%), plus two potential CRFs. This study elucidated the complicated characteristics of HIV-1 molecular epidemiology in a low HIV-1 prevalence northern province of China and revealed the high level of HIV-1 genetic diversity. All nine HIV-1 genotypes circulating in Hebei have spread out of their initial risk groups into the general population through sexual contact, especially through MSM. This highlights the urgency of HIV prevention and control in China. PMID:28178737

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

    Directory of Open Access Journals (Sweden)

    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.

  2. Implicación del semental caprino en la agalaxia contagiosa : epidemiología descriptiva y molecular

    OpenAIRE

    Gómez Martín, Ángel

    2015-01-01

    La agalaxia contagiosa caprina (AC) es una de las enfermedades con mayores repercusiones socioeconómicas del sector de los pequeños rumiantes. Los avances en el conocimiento de la epidemiología molecular y analítica de la enfermedad, así como los aspectos más relevantes que habrán de ser estudiados en un futuro, fueron abordados en una revisión por invitación en la revista The Veterinary Journal (Estudio 1). No obstante, esta Tesis Doctoral se ha centrado en estudiar las implicaciones epidemi...

  3. Implicación del semental caprino en la agalaxia contagiosa : epidemiología descriptiva y molecular

    OpenAIRE

    Gómez Martín, Ángel

    2015-01-01

    La agalaxia contagiosa caprina (AC) es una de las enfermedades con mayores repercusiones socioeconómicas del sector de los pequeños rumiantes. Los avances en el conocimiento de la epidemiología molecular y analítica de la enfermedad, así como los aspectos más relevantes que habrán de ser estudiados en un futuro, fueron abordados en una revisión por invitación en la revista The Veterinary Journal (Estudio 1). No obstante, esta Tesis Doctoral se ha centrado en estudiar las implicaciones epidem...

  4. Investigación sobre epidemiología convencional y molecular de tuberculosis en Orizaba, Veracruz, 1995-2008

    OpenAIRE

    Ma Eugenia Jiménez-Corona; Lourdes García-García; Alfredo Ponce de León; Miriam Bobadilla-del Valle; Martha Torres; Sergio Canizales-Quintero; Carmen Palacios-Merino; Susana Molina-Hernández; Rosa Areli Martínez-Gamboa; Luis Juárez-Sandino; Bulmaro Cano-Arellano; Leticia Ferreyra-Reyes; Luis Pablo Cruz-Hervert; Renata Báez-Saldaña; Elizabeth Ferreira-Guerrero

    2009-01-01

    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 e...

  5. Predicting the effect of climate change on African trypanosomiasis: integrating epidemiology with parasite and vector biology.

    Science.gov (United States)

    Moore, Sean; Shrestha, Sourya; Tomlinson, Kyle W; Vuong, Holly

    2012-05-07

    Climate warming over the next century is expected to have a large impact on the interactions between pathogens and their animal and human hosts. Vector-borne diseases are particularly sensitive to warming because temperature changes can alter vector development rates, shift their geographical distribution and alter transmission dynamics. For this reason, African trypanosomiasis (sleeping sickness), a vector-borne disease of humans and animals, was recently identified as one of the 12 infectious diseases likely to spread owing to climate change. We combine a variety of direct effects of temperature on vector ecology, vector biology and vector-parasite interactions via a disease transmission model and extrapolate the potential compounding effects of projected warming on the epidemiology of African trypanosomiasis. The model predicts that epidemics can occur when mean temperatures are between 20.7°C and 26.1°C. Our model does not predict a large-range expansion, but rather a large shift of up to 60 per cent in the geographical extent of the range. The model also predicts that 46-77 million additional people may be at risk of exposure by 2090. Future research could expand our analysis to include other environmental factors that influence tsetse populations and disease transmission such as humidity, as well as changes to human, livestock and wildlife distributions. The modelling approach presented here provides a framework for using the climate-sensitive aspects of vector and pathogen biology to predict changes in disease prevalence and risk owing to climate change.

  6. Analysis of the epidemiological dynamics during the 1982-1983 epidemic of foot-and-mouth disease in Denmark based on molecular high-resolution strain identification

    DEFF Research Database (Denmark)

    Christensen, Laurids Siig; Normann, Preben; Thykier-Nielsen, Søren

    2005-01-01

    An epidemic of foot-and-mouth disease (FMD) causing a total of 23 cases in 1982-1983, primarily on the island of Funen, Denmark, was subjected to molecular epidemiological investigations. In an attempt to exploit the quasi-species nature of foot-and-mouth disease virus strains for molecular high...

  7. 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.

  8. 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

  9. 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

  10. Modelling the effect of changes in vaccine effectiveness and transmission contact rates on pertussis epidemiology.

    Science.gov (United States)

    Pesco, P; Bergero, P; Fabricius, G; Hozbor, D

    2014-06-01

    The incidence of the highly infectious respiratory disease named pertussis or whooping cough has been increasing for the past two decades in different countries, as in much of the highly vaccinated world. A decrease in vaccine effectiveness over time, especially when acellular vaccines were used for primary doses and boosters, and pathogen adaptation to the immunity conferred by vaccines have been proposed as possible causes of the resurgence. The contributions of these factors are not expected to be the same in different communities, and this could lead to different epidemiological trends. In fact, differences in the magnitude and dynamics of pertussis outbreaks as well as in the distribution of notified cases by age have been reported in various regions. Using an age-structured mathematical model designed by us, we evaluated how the changes in some of the parameters that could be related to the above proposed causes of disease resurgence - vaccine effectiveness and effective transmission rates - may impact on pertussis transmission. When a linear decrease in vaccine effectiveness (VE) was assayed, a sustained increase in pertussis incidence was detected mainly in infants and children. On the other hand, when changes in effective transmission rates (βij) were made, a dynamic effect evidenced by the presence of large peaks followed by deep valleys was detected. In this case, greater incidence in adolescents than in children was observed. These different trends in the disease dynamics due to modifications in VE or βij were verified in 18 possible scenarios that represent different epidemiological situations. Interestingly we found that both incidence trends produced by the model and their age distribution resemble the profiles obtained from data reported in several regions. The implications of these correlations are discussed.

  11. 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.

  12. 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

  13. Epidemiology, clinical manifestations, and molecular typing of salmonella typhi isolated from patients with typhoid fever in Lebanon.

    Science.gov (United States)

    Kanj, Souha S; Kanafani, Zeina A; Shehab, Marwa; Sidani, Nisreen; Baban, Tania; Baltajian, Kedak; Dakdouki, Ghenwa K; Zaatari, Mohamad; Araj, George F; Wakim, Rima Hanna; Dbaibo, Ghassan; Matar, Ghassan M

    2015-06-01

    The objective of this study was to examine the epidemiology and the clinical manifestations of typhoid fever as well as the susceptibility and strain relatedness of Salmonella typhi isolates in Lebanon from 2006 to 2007. A total of 120 patients with typhoid fever were initially identified from various areas of the country based on positive culture results for S. typhi from blood, urine, stools, bone marrow and/or positive serology. Clinical, microbiological and molecular analysis was performed on cases with complete data available. These results indicated that drinking water was an unlikely mode of transmission of the infection. Despite increasing reports of antimicrobial resistance among S. typhi isolates, the vast majority of these isolates were susceptible to various antibiotic agents, including ampicillin, cephalosporins, quinolones, and trimethoprim/sulfamethoxazole. Molecular analysis of the isolates revealed a predominance of one single genotype with no variation in distribution across the geographical regions.

  14. Discovery of colorectal cancer PIK3CA mutation as potential predictive biomarker: power and promise of molecular pathological epidemiology.

    Science.gov (United States)

    Ogino, S; Lochhead, P; Giovannucci, E; Meyerhardt, J A; Fuchs, C S; Chan, A T

    2014-06-05

    Regular use of aspirin reduces incidence and mortality of various cancers, including colorectal cancer. Anticancer effect of aspirin represents one of the 'Provocative Questions' in cancer research. Experimental and clinical studies support a carcinogenic role for PTGS2 (cyclooxygenase-2), which is an important enzymatic mediator of inflammation, and a target of aspirin. Recent 'molecular pathological epidemiology' (MPE) research has shown that aspirin use is associated with better prognosis and clinical outcome in PIK3CA-mutated colorectal carcinoma, suggesting somatic PIK3CA mutation as a molecular biomarker that predicts response to aspirin therapy. The PI3K (phosphatidylinositol-4,5-bisphosphonate 3-kinase) enzyme has a pivotal role in the PI3K-AKT signaling pathway. Activating PIK3CA oncogene mutations are observed in various malignancies including breast cancer, ovarian cancer, brain tumor, hepatocellular carcinoma, lung cancer and colon cancer. The prevalence of PIK3CA mutations increases continuously from rectal to cecal cancers, supporting the 'colorectal continuum' paradigm, and an important interplay of gut microbiota and host immune/inflammatory reaction. MPE represents an interdisciplinary integrative science, conceptually defined as 'epidemiology of molecular heterogeneity of disease'. As exposome and interactome vary from person to person and influence disease process, each disease process is unique (the unique disease principle). Therefore, MPE concept and paradigm can extend to non-neoplastic diseases including diabetes mellitus, cardiovascular diseases, metabolic diseases, and so on. MPE research opportunities are currently limited by paucity of tumor molecular data in the existing large-scale population-based studies. However, genomic, epigenomic and molecular pathology testings (for example, analyses for microsatellite instability, MLH1 promoter CpG island methylation, and KRAS and BRAF mutations in colorectal tumors) are becoming routine

  15. Multilocus sequence typing as a tool for studying the molecular epidemiology and population structure of Brachyspira hyodysenteriae.

    Science.gov (United States)

    La, Tom; Phillips, Nyree D; Harland, Belinda L; Wanchanthuek, Phatthanaphong; Bellgard, Matthew I; Hampson, David J

    2009-09-18

    The purpose of this study was to develop and apply a multilocus sequence typing (MLST) scheme to study the molecular epidemiology of Brachyspira hyodysenteriae, the aetiological agent of swine dysentery. Sequences of seven conserved genomic loci were examined in 111 B. hyodysenteriae strains. Fifty-eight of these previously had been analysed by multilocus enzyme electrophoresis (MLEE), and for some the results of pulsed field gel electrophoresis (PFGE), restriction endonuclease analysis (REA) and/or serotyping also were available. The discriminatory power of these methods was compared. The strains were divided into 67 sequence types (STs) and 46 amino acid types (AATs) by MLST. The Index of Association value was significantly different from zero, indication that the population was clonal. Eleven clonal complexes (Cc) comprising between 2 and 10 STs were recognised. A population snapshot based on AATs placed 77.5% of the isolates from 30 of the AATs into one major cluster. The founder type AAT9 included 13 strains from nine STs that were isolated in Australia, Sweden, Germany and Belgium, including one from a mallard. The MLST results were generally comparable to those produced by MLEE. The MLST system had a similar discriminatory power to PFGE, but was more discriminatory than REA, MLEE or serotyping. MLST data provided evidence for likely transmission of strains between farms, but also for the occurrence of temporal "micro-evolution" of strains on individual farms. Overall, the MLST system proved to be a useful new tool for investigating the molecular epidemiology and diversity of B. hyodysenteriae.

  16. Differential findings regarding molecular epidemiology of tuberculosis between two consecutive periods in the context of steady increase of immigration.

    Science.gov (United States)

    Iñigo, J; García de Viedma, D; Arce, A; Palenque, E; Herranz, M; Rodríguez, E; Ruiz-Serrano, M J; Bouza, E; Chaves, F

    2013-03-01

    The demographic characteristics of the population of Madrid, with a steady increase in immigrants, from 4.7% in 1998 to 17.4% in 2007, provide an opportunity to study in depth the transmission of TB. Our aim was to compare two 3-year longitudinal molecular studies of TB to define transmission patterns and predictors of clustering. Two prospective population-based molecular and epidemiological studies (2002-2004 and 2005-2007) of TB patients were conducted in nine urban districts in Madrid using the same methodology. During the period 2002-2007, 2248 cases of TB were reported, and the incidence decreased from 23.5 per 100,000 in 2002 to 20.8 in 2007 (p epidemiology study provides clues to interpret the decrease in the incidence of TB in a context of steady increase of immigration. In our region, the decrease in the incidence of TB can be explained predominantly as a result of a decline in recent transmission.

  17. Chapter 2. Fasciola, lymnaeids and human fascioliasis, with a global overview on disease transmission, epidemiology, evolutionary genetics, molecular epidemiology and control.

    Science.gov (United States)

    Mas-Coma, Santiago; Valero, María Adela; Bargues, María Dolores

    2009-01-01

    almost total genetic isolation. Recent sequencing results suggest that present assumptions on fasciolid-lymnaeid specificity might be wrong. The crucial role of lymnaeids in fascioliasis transmission, epidemiology and control was the reason for launching a worldwide lymnaeid molecular characterization initiative. This initiative has already furnished useful results on several continents. A standardized methodology for fasciolids and lymnaeids is proposed herein in order that future work is undertaken on a comparable basis. A complete understanding of molecular epidemiology is expected to help greatly in designing global actions and local interventions for control of fascioliasis.

  18. 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

    The prevalence of hepatitis C virus (HCV) genotype 4 has increased throughout Europe. This is an epidemiological study of patients infected chronically with HCV genotype 4 in Denmark. The HCV strains analyzed originated from patient samples collected between 1999 and 2007 as part of the national...... Danish hepatitis B and C network, DANHEP. Sequence analyses were based on the envelope 1 region of HCV. Results from a total of 72 patients indicated a high degree of genetic heterogeneity. Fifty-six patients (78%) were infected with one of the three dominating subtypes: 4d, 4a, or 4r. The remaining 16...... 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...

  19. 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 ...

  20. 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

  1. Molecular epidemiology of Acinetobacter baumannii and Acinetobacter nosocomialis in Germany over a 5-year period (2005-2009).

    Science.gov (United States)

    Schleicher, X; Higgins, P G; Wisplinghoff, H; Körber-Irrgang, B; Kresken, M; Seifert, H

    2013-08-01

    To investigate the species distribution within the Acinetobacter calcoaceticus-Acinetobacter baumannii complex and the molecular epidemiology of A. baumannii and Acinetobacter nosocomialis, 376 Acinetobacter isolates were collected prospectively from hospitalized patients at 15 medical centres in Germany during three surveillance studies conducted over a 5-year period. Species identification was performed by molecular methods. Imipenem minimum inhibitory concentrations (MIC) were determined by broth microdilution. The prevalence of the most common carbapenemase-encoding genes was investigated by oxacillinase (OXA) -multiplex polymerase chain reaction (PCR). The molecular epidemiology was investigated by repetitive sequence-based PCR (rep-PCR; DiversiLab™). Acinetobacter pittii was the most prevalent Acinetobacter species (n = 193), followed by A. baumannii (n = 140), A. calcoaceticus (n = 10) and A. nosocomialis (n = 8). The majority of A. baumannii was represented by sporadic isolates (n = 70, 50%) that showed unique rep-PCR patterns, 25 isolates (18%) clustered with one or two other isolates, and only 45 isolates (32%) belonged to one of the previously described international clonal lineages. The most prevalent clonal lineage was international clone (IC) 2 (n = 34) and IC 1 (n = 6). According to CLSI, 25 A. baumannii isolates were non-susceptible to imipenem (MIC ≥ 8 mg/L), all of which produced an OXA-58-like or OXA-23-like carbapenemase. The rate of imipenem susceptibility among A. baumannii isolates decreased from 96% in 2005 to 76% in 2009. All other Acinetobacter isolates were susceptible to imipenem. The population structure of carbapenem-susceptible A. baumannii in Germany is highly diverse. Imipenem non-susceptibility was strongly associated with the clonal lineages IC 2 and IC 1. These data underscore the high clonality of carbapenem-resistant A. baumannii isolates.

  2. 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.

  3. 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.

    Directory of Open Access Journals (Sweden)

    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.

  4. 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

  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. 在眼病调查基础上如何开展分子流行病学研究%How to develop molecular epidemiology in conventional epidemiology survey on eye diseases in China

    Institute of Scientific and Technical Information of China (English)

    管怀进

    2012-01-01

    Molecular epidemiology is a new branch of eye epidemiology that combines theories and methods in both epidemiology and molecular biology.The definition of molecular epidemiology is to use biological and,in particular,genetic markers (nucleic acid,protein ) as measures for detecting the propensity of a disease developing,or as an indicator of a disease or an exposure in the studies of disease distribution.Molecular epidemiology has the same objectives as conventional ophthalmic epidemiology in a defined population.The main designs used in ophthalmic molecular epidemiology include descriptive study,case control study,and nested case control study.Currently,molecular experimental techniques mainly include single nucleotide polymorphism,ELISA,protein and mRNA array,microRNA and the study of epigenetic markers.Gene susceptibility biomarker is one of the most commonly used molecular markers.The findings of ophthalmic molecular epidemiology studies can be used to design personalized therapy.Undoubtedly,ophthalmic molecular epidemiology will evolve and develop in the new era for the prevention and control of complex eye diseases such as age-related macular degeneration,cataract,glaucoma and diabetic retinopathy.%分子流行病学是疾病研究中将流行病学和分子生物学相结合的一个流行病学新分支,它主要是在基因、蛋白质水平上寻找生物学标志与疾病发生发展的关系,从而评估疾病的发生倾向、判定疾病的分布与暴露.眼病分子流行病学研究可以在传统流行病学调查的人群中,选择描述性眼病调查、病例对照研究、巢式病例对照研究、队列研究等设计,应用单核苷酸多态性、基因拷贝数多态性、生物芯片(微阵列)、microRNA、表观遗传学、DNA测序等分子生物学技术,测定体液及眼组织内的核酸、蛋白质、脂质及其代谢产物,从而探讨年龄相关性白内障、年龄相关性黄斑变性、青光眼和糖尿病视网膜病变

  7. 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.

  8. Molecular Epidemiology and Evolution of Influenza Viruses Circulating within European Swine between 2009 and 2013

    DEFF Research Database (Denmark)

    J. Watson, Simon; Langat, Pinky; M. Reid, Scott;

    2015-01-01

    . Contrasting epidemiological dynamics were observed for two of these genotypes, H1huN2 and H3N2, with the former showing multiple long-lived geographically isolated lineages, while the latter had short-lived geographically diffuse lineages. At least 32 human-swine transmission events have resulted in A(H1N1...... in swine differ at the global level. IMPORTANCE The influenza A(H1N1)pdm09 virus contains a reassortant genome with segments derived from separate virus lineages that evolved in different regions of the world. In particular, its neuraminidase and matrix segments were derived from the Eurasian avian virus...

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

    Directory of Open Access Journals (Sweden)

    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.

  10. Current trends of Mycobacterium tuberculosis molecular epidemiology in Saudi Arabia and associated demographical factors.

    Science.gov (United States)

    Al-Hajoj, Sahal; Varghese, Bright; Al-Habobe, Farah; Shoukri, Mohammed M; Mulder, Arnout; van Soolingen, Dick

    2013-06-01

    Data are scarce on demographical factors related to the population structure of Mycobacterium tuberculosis in Saudi Arabia. A study was conducted on 902 clinical isolates to explore current trends in the phylogeography and associated demographical factors of tuberculosis by using spoligotyping and 24 loci based MIRU-VNTR typing. Young male patients (aged 16-29 and 30-44) were predominant in this cohort. The phylogenetic diversity among M. tuberculosis isolates was found high, as almost all known genetic lineages were identified. Delhi/CAS (26.4%), EAI (13.7%) and Haarlem (11.3%) were the most common lineages observed, particularly among the low age groups (16-29 and 30-44 years), whereas elderly patients (>60 years) showed a predominance in the lineages S, Ghana, TUR and Uganda-I. A statistically significant association was observed between gender of the patients and lineages of EAI (p value 0.026) and LAM (p value 0.005). Overall, molecular strain cluster rate was 34.4% with an elevated rate among patients aged below 15 years (43.1%), while cases among the elderly (>60 years) showed the lowest degree of clustering (12.5%). The largest level of clustering was noticed among cases caused by strains of the lineages Haarlem (59.8%), Beijing (55.8%) and LAM (42.8%). The current population structure of M. tuberculosis in Saudi Arabia is highly diverse with significant associations to demography, transmission dynamics and origin of the patients. The difference in genotype distributions among low and high aged patients reflects the ongoing change in the strain population structure in the country.

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. Investigation of mechanism and molecular epidemiology of linezolid-resistant Enterococcus faecalis in China.

    Science.gov (United States)

    Wang, Lipeng; He, Yunyan; Xia, Yun; Wang, Huijuan; Liang, Shumei

    2014-08-01

    Enterococcus is a major cause of important nosocomial infections. Linezolid, the first member of an entirely new class of antibiotics (oxazolidinones), is effective against serious infections caused by Enterococcus. However, resistance to linezolid has been discovered throughout the world rapidly. From 2011 to 2013, nine linezolid-resistant E. faecalis isolates were collected and the possible mechanisms of linezolid resistance, including mutations in domain V of 23S rRNA genes and in ribosomal proteins L3 and L4, and the multiresistance gene cfr, were investigated. Furthermore, an epidemiological survey of the nine linezolid-resistant E. faecalis isolates was performed by pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST) and DiversiLab. The three methods were compared to evaluate their merits and demerits, respectively. We failed to find the resistance mechanisms that have been revealed in recent years by PCR and sequencing analysis in the linezolid-resistant E. faecalis. Epidemiological investigation suggested that a small-scale outbreak of linezolid-resistant E. faecalis emerged in neurosurgery ICU from March to May of 2013. DiversiLab was a reliable typing tool and a suitable alternative to PFGE because it was as discriminatory as PFGE and better than MLST.

  16. Molecular Epidemiology of Pasteurella multocida Circulating in India by Multilocus Sequence Typing.

    Science.gov (United States)

    Sarangi, L N; Thomas, P; Gupta, S K; Kumar, S; Viswas, K N; Singh, V P

    2016-04-01

    Multilocus sequence typing (MLST), a sequence-based typing method for bacterial pathogens, is currently the best method for long-term epidemiological study and to understand the population structure of the bacteria. This investigation was carried out to study the diversity of Pasteurella multocida isolates circulating in India. Ten different sequence types (ST) identified in this study are ST 122 from cattle, goat, mithun and pig; ST 50 from pig; ST 9 from cattle and sheep; ST 229 from cattle and goat; ST 71 and ST 277 from cattle; and ST 129, ST 280, ST 281 and ST 282 from avian species. Of these, ST 277, ST 280, ST 281 and ST 282 were identified for the first time. The analysis of results provides novel epidemiological information on the circulation of multiple STs across India. The majority of STs or their variants identified in this study have already been reported from different parts of the globe. This suggests that probably transboundary spread of strains across countries and continents has occurred across evolutionary time and is still happening. The isolation of ST 122 from small ruminants and pigs suggests that these species may be included in the preventive vaccination policy for effective control of haemorrhagic septicaemia in India.

  17. Changing epidemiology of gastroesophageal reflux disease in the Asian-Pacific region: an overview.

    Science.gov (United States)

    Goh, K L

    2004-09-01

    Gastroesophageal reflux disease (GERD) is a common disease in the West, which now appears to be also increasing in prevalence in the Asian Pacific region. The reasons for this changing epidemiology are two-fold: an increased awareness among doctors and patients, and/or a true increase in the prevalence of the disease. Prevalence rates of reflux esophagitis (RE) of up to 16% and prevalence of GERD symptoms of up to 9% have been reported in the Asian population. However, the frequency of strictures and Barrett's esophagus remain very low. Non-erosive reflux disease (NERD) appears to be the most common form of GERD among Asian patients accounting for 50-70% of cases with GERD. Among Asian patients differences can also be discerned among different ethnic groups. For example, in Malaysia where a multiracial society exists, RE is significantly more common among Indians compared to Chinese and Malays whereas NERD is more frequently seen in the Indian and Malays compared to the Chinese. The reasons for these differences are not known but may indicate both genetic factors and environmental factors peculiar to the particular racial group. GERD has also been increasing in the region demonstrating a time-lag phenomenon compared to the West. Differing predisposition to GERD among different ethnic groups would mean that such an increase would be more prominent among certain racial groups.

  18. 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.

  19. 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

  20. Impact of gastrointestinal parasitic nematodes of sheep, and the role of advanced molecular tools for exploring epidemiology and drug resistance - an Australian perspective.

    Science.gov (United States)

    Roeber, Florian; Jex, Aaron R; Gasser, Robin B

    2013-05-27

    Parasitic nematodes (roundworms) of small ruminants and other livestock have major economic impacts worldwide. Despite the impact of the diseases caused by these nematodes and the discovery of new therapeutic agents (anthelmintics), there has been relatively limited progress in the development of practical molecular tools to study the epidemiology of these nematodes. Specific diagnosis underpins parasite control, and the detection and monitoring of anthelmintic resistance in livestock parasites, presently a major concern around the world. The purpose of the present article is to provide a concise account of the biology and knowledge of the epidemiology of the gastrointestinal nematodes (order Strongylida), from an Australian perspective, and to emphasize the importance of utilizing advanced molecular tools for the specific diagnosis of nematode infections for refined investigations of parasite epidemiology and drug resistance detection in combination with conventional methods. It also gives a perspective on the possibility of harnessing genetic, genomic and bioinformatic technologies to better understand parasites and control parasitic diseases.

  1. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  3. 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.

  4. Molecular epidemiology of J-subgroup avian leukosis virus isolated from meat-type chickens in South China between 2013 and 2014.

    Science.gov (United States)

    Avian leukosis virus subgroup J (ALV-J) caused high mortality rate associated with tumor formation and decreased fertility, which resulted in major economic losses in poultry industry worldwide. To assess the status of ALV-J infection in meat-type chickens in south China, molecular epidemiology of A...

  5. [Eco-epidemiology: towards epidemiology of complexity].

    Science.gov (United States)

    Bizouarn, Philippe

    2016-05-01

    In order to solve public health problems posed by the epidemiology of risk factors centered on the individual and neglecting the causal processes linking the risk factors with the health outcomes, Mervyn Susser proposed a multilevel epidemiology called eco-epidemiology, addressing the interdependence of individuals and their connection with molecular, individual, societal, environmental levels of organization participating in the causal disease processes. The aim of this epidemiology is to integrate more than a level of organization in design, analysis and interpretation of health problems. After presenting the main criticisms of risk-factor epidemiology focused on the individual, we will try to show how eco-epidemiology and its development could help to understand the need for a broader and integrative epidemiology, in which studies designed to identify risk factors would be balanced by studies designed to answer other questions equally vital to public health.

  6. The Use of Molecular Techniques for the Diagnosis and Epidemiologic Study of Sexually Transmitted Infections.

    Science.gov (United States)

    Black; Morse

    2000-02-01

    Molecular diagnostic tests are more sensitive and, in many cases, more specific than conventional laboratory methods for the detection of sexually transmitted infections. Here, we review recently developed molecular methods for the diagnosis and subtyping of the most common sexually transmitted infections: infections caused by Chlamydia trachomatis, Neisseria gonorrhoeae, human papillomavirus, Trichomonas vaginalis, and the agents of genital ulcer disease (Haemophilus ducreyi, herpes simplex virus, Treponema pallidum, and Calymmatobacterium granulomatis). We also provide an overview of the laboratory diagnostic tests and clinical specimens to use when infection with these agents is suspected.

  7. 77 FR 2072 - Proposed Collection; Comment Request; Prevalence, Incidence, Epidemiology and Molecular Variants...

    Science.gov (United States)

    2012-01-13

    ... HUMAN SERVICES National Institutes of Health Proposed Collection; Comment Request; Prevalence, Incidence... algorithm (RITA). This research effort will allow for an evaluation of trends in the trafficking of non-B... molecular variants in the USA and other funded international REDS-III sites in South Africa and China,...

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

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    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..

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

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    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.

  10. 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.

  11. Molecular Epidemiology of Influenza A/H3N2 Viruses Circulating in Mexico from 2003 to 2012

    Science.gov (United States)

    Escalera-Zamudio, Marina; Nelson, Martha I.; Cobián Güemes, Ana Georgina; López-Martínez, Irma; Cruz-Ortiz, Natividad; Iguala-Vidales, Miguel; García, Elvia Rodríguez; Barrera-Badillo, Gisela; Díaz-Quiñonez, Jose Alberto; López, Susana; Arias, Carlos F.; Isa, Pavel

    2014-01-01

    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. PMID:25075517

  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. Epidemiological usefulness of changes in hemolytic activity of Vibrio cholerae biotype El Tor during the seventh pandemic.

    OpenAIRE

    Barrett, T J; Blake, P A

    1981-01-01

    Hemolytic Vibrio cholerae biotype El Tor strains were isolated in the United States in 1973 and 1978 after they had supposedly disappeared worldwide during the 1960s and 1970s. We decided to examine the change in prevalence of hemolytic El Tor strains since the beginning of the seventh pandemic and evaluate the usefulness of hemolytic activity as an epidemiological marker. A total of 48 isolates of V. cholerae biotype El Tor isolated in the Eastern Hemisphere between 1960 and 1979, along with...

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

    Directory of Open Access Journals (Sweden)

    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.

  15. 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.

  16. Molecular epidemiology of human cases of tuberculosis by Mycobacterium bovis in Mexico.

    Science.gov (United States)

    Milián-Suazo, Feliciano; Pérez-Guerrero, Laura; Arriaga-Díaz, Camila; Escartín-Chávez, Minerva

    2010-10-01

    The purpose of this study was to evaluate the role of Mycobacterium bovis in human cases of tuberculosis (TB) in an endemic area of the disease in cattle. Sputum, urine and other tissue samples were obtained from: (1) TB-symptomatic patients, (2) dairy farm workers and (3) abattoir workers. Samples of macroscopic lesions suspicious of TB were also obtained from cattle at slaughter in the same geographic area. A total of 562 human samples were collected: 255 from symptomatic patients, 218 from farm workers and 93 from abattoir workers. Samples were analysed by the bacillus acido-alcohol resitant (BAAR) and polymerase chain reaction (PCR) tests and cultured in Stonebrink and Löwenstein-Jensen. Spoligotyping was performed in all isolates obtained by culture and the DNA obtained by PCR. From the total number of human cases, 34 (6%) showed M. bovis spoligotype; eight spoligotypes from cattle showed an identical pattern to three spoligotypes from humans; a different set of spoligotypes from cattle (n = 8) had only one spacer difference to a set of spoligotypes from humans (n = 2). These results provide further evidence that infected cattle represent a risk to public health and support previous reports about the role of M. bovis in Mexican patients. There is no doubt that genotyping M. bovis isolates collected from cattle may have a substantial impact on our understanding of the epidemiology of TB.

  17. Molecular epidemiology of human and animal tuberculosis in Ibadan, Southwestern Nigeria.

    Science.gov (United States)

    Jenkins, A O; Cadmus, S I B; Venter, E H; Pourcel, C; Hauk, Y; Vergnaud, G; Godfroid, J

    2011-07-05

    From 2005 to 2007, Mycobacterium tuberculosis complex (MTC) strains were isolated from cattle, goats and pigs samples collected at the Bodija abattoir and from human samples from tuberculosis patients and livestock traders at the Akinyele cattle market in Ibadan, Southwestern Nigeria. Seventy four isolates obtained from humans (24) and livestock (50) were identified as MTC strains. Thirty two isolates were spoligotyped. Nineteen of these 32 isolates were identified as M. tuberculosis whilst 13 were identified as Mycobacterium bovis. M. bovis was isolated from two humans, whereas M. tuberculosis was isolated from a bovine, a pig and a goat. All the M. bovis isolates identified in this study belonged to the Africa 1 clonal complex. Multiple locus VNTR [variable number of tandem repeats] analysis (MLVA) was carried out on the 74 isolates. Three major clusters were defined. Group A consisted of 24 M. tuberculosis isolates (MLVA genotypes 1-18). One strain was isolated from a bovine and one from a pig. Group B consisted of 49 M. bovis strains (MLVA genotypes 19-48), mainly of cattle origin but also included four goat, nine pig and two human isolates. Group C consisted of a single M. tuberculosis isolate (MLVA genotype 49) obtained from a goat. Spoligotyping and MLVA confirmed it as clustering with the East Africa Indian clade found in humans in Sudan and the Republic of Djibouti. The isolation of three M. tuberculosis strains from livestock raises the question of their epidemiological importance as a source of infection for humans.

  18. Molecular epidemiology of carbapenem-resistant Acinetobacter baumannii in South America.

    Science.gov (United States)

    Rodríguez, Carlos Hernán; Balderrama Yarhui, Norah; Nastro, Marcela; Nuñez Quezada, Tamara; Castro Cañarte, Glenda; Magne Ventura, Raquel; Ugarte Cuba, Tayita; Valenzuela, Natalia; Roach, Freddy; Mota, María Inés; Burger, Noelia; Velázquez Aguayo, Gladys; Ortellado-Canese, Juana; Bruni, Geni; Pandolfo, Cecilia; Bastyas, Nadya; Famiglietti, Angela

    2016-10-01

    One hundred and twenty-six epidemiologically sequential, unrelated, carbapenem-resistant Acinetobacter baumannii isolates from nine hospitals in six countries of South America were collected between July 2013 and June 2014. Genes coding for Ambler class D and B carbapenemases were sought by PCR. All isolates were typed using the 3-locus sequence typing and blaOXA-51-like sequence-based typing techniques. The blaOXA-23 gene was recovered in all the participating hospitals and in all the isolates of seven of nine medical centres. The blaOXA-72 gene was only recovered in the two medical centres from Guayaquil city, Ecuador. Trilocus sequence typing revealed the presence of sequence groups SG2, SG4 and SG5. blaOXA-51-like sequence-based typing revealed the presence of blaOXA-132, blaOXA-65, blaOXA-69 and blaOXA-64. Our results showed that the population of carbapenem-resistant A. baumannii in South America was principally associated with ST79, ST25 and ST15 (92 %) and harboured the blaOXA-23 gene mainly. CC2 was not detected.

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

    Science.gov (United States)

    Nakamura, Sayuri; Ochiai, Kenji; Ochi, Akihiro; Yabushita, Hiroki; Abe, Asumi; Kishi, Sayaka; Sunden, Yuji; Umemura, Takashi

    2014-01-01

    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. 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.

  1. Impact of Bisphenol A on the Cardiovascular System — Epidemiological and Experimental Evidence and Molecular Mechanisms

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    Xiaoqian Gao

    2014-08-01

    Full Text Available Bisphenol A (BPA is a ubiquitous plasticizing agent used in the manufacturing of polycarbonate plastics and epoxy resins. There is well-documented and broad human exposure to BPA. The potential risk that BPA poses to the human health has attracted much attention from regulatory agencies and the general public, and has been extensively studied. An emerging and rapidly growing area in the study of BPA’s toxicity is its impact on the cardiovascular (CV system. Recent epidemiological studies have shown that higher urinary BPA concentration in humans is associated with various types of CV diseases, including angina, hypertension, heart attack and coronary and peripheral arterial disease. Experimental studies have demonstrated that acute BPA exposure promotes the development of arrhythmias in female rodent hearts. Chronic exposure to BPA has been shown to result in cardiac remodeling, atherosclerosis, and altered blood pressure in rodents. The underlying mechanisms may involve alteration of cardiac Ca2+ handling, ion channel inhibition/activation, oxidative stress, and genome/transcriptome modifications. In this review, we discuss these recent findings that point to the potential CV toxicity of BPA, and highlight the knowledge gaps in this growing research area.

  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. Epidemiología molecular de las tuberculosis bovina y humana en una zona endémica de Querétaro, México Molecular epidemiology of cattle and human tuberculosis in Mexico

    Directory of Open Access Journals (Sweden)

    Laura Pérez-Guerrero

    2008-08-01

    Full Text Available OBJETIVO: Determinar el papel de la tuberculosis bovina en la tuberculosis humana. MATERIAL Y MÉTODOS: Se analizaron 255 muestras de pacientes sintomáticos, sembradas en medios de Stonebrink y Löwenstein-Jensen y analizadas por PCRMPB70 anidada y luego por spoligotyping. RESULTADOS: De las 255 muestras, 74 fueron positivas a la PCR y 20 al aislamiento: de las primeras, 58 (78% mostraron espoligotipo de M. tuberculosis y 5 (6.7% de M. bovis; de las segundas, 8 (47% revelaron espoligotipo de M. tuberculosis y 8 (47% de M. bovis. De las 94 muestras positivas al aislamiento o PCR, 66 (70% correspondieron a M. tuberculosis y 13 (13.8% a M. bovis. Los patrones moleculares de cuatro muestras de M. bovis de seres humanos fueron idénticos a los de las cepas de M. bovis de ganado. CONCLUSIONES: Se demuestra que M. bovis juega un papel importante en la epidemiología de la tuberculosis humana y representa un riesgo para la salud pública.OBJECTIVE: The purpose of the study was to determine the role of bovine TB in cases of human TB. MATERIAL AND METHODS: Two-hundred and fifty-five samples from symptomatic patients were included in the study. All samples were cultured in Stonebrink and Lowënstein-Jensen media and analyzed using a nested PCRMPB70. The molecular analysis was performed by spoligotyping. RESULTS: From 255 samples, 74 were PCR-positive and 20 were culture-positive. From 94 samples positive to PCR or to isolation, 66 (70% showed a spoligotype compatible with M. tuberculosis, and 13 (13.8% with M. bovis. Four fingerprints of M. bovis from humans were identical to the fingerprints of M. bovis from cattle in the same region. CONCLUSIONS: Our study shows that M. bovis plays an important role in the epidemiology of TB in humans and that TB in cattle represents a risk to public health.

  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. Molecular typing and epidemiological survey of prevalence of Clostridium perfringens types by multiplex PCR.

    OpenAIRE

    1997-01-01

    Clostridium perfringens has been classified into five toxigenic types (A through E) on the basis of its capability to produce major lethal toxins (alpha, beta, epsilon, and iota toxins). Seroneutralization with mice or guinea pigs has been used to type each toxin, but this conventional method has some disadvantages. Therefore, we used a molecular biological technique to type the bacterium in the present study. A multiplex PCR was developed for this purpose. This method has several advantages ...

  6. 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

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

    Institute of Scientific and Technical Information of China (English)

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

    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 ofS.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,accessorygeneregulator(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.

  8. [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.

  9. 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.

  10. Molecular epidemiology of Campylobacter jejuni infection in Israel-a nationwide study.

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    Weinberger, M; Moran-Gilad, J; Rokney, A; Davidov, Y; Agmon, V; Peretz, C; Valinsky, L

    2016-12-01

    The incidence of Campylobacter infection in Israel, particularly among children Campylobacter jejuni in Israel over a decade (2003-2012) using multilocus sequence typing (MLST) combined with demographic metadata. Representative clinical isolates (438) from a large national repository together with selected veterinary isolates (74) were subject to MLST. The distribution of age groups, ethnicity and clinical source across various genotypes was evaluated using Poisson modelling. The 512 studied isolates were assigned 126 distinct sequence types (STs) (18.8% novel STs) grouped into 21 clonal complexes (CCs). Most human, poultry and bovine STs clustered together in the leading CCs. Three dominant STs (ST21, ST6608, ST4766) were detected only since 2006. Patients infected with the leading CCs were similarly distributed along densely populated areas. The frequency of blood isolates was higher in patients infected with CC353 (relative rate (RR)=2.0, 95% CI 1.03-3.9, adjusted p value (adj.p) 0.047) and CC42 (RR=4.4, 95% CI 1.7-11.6, adj.p 0.018) and lower with CC257 (RR=0.3, 95% CI 0.1-0.9, adj. p 0.047). The distribution of age groups and ethnicity also varied across the leading CCs. In conclusion, C. jejuni isolates in a national sample appeared highly diverse with a high proportion of new STs. Phylogenic analysis was compatible with poultry and cattle as possible food sources of clinical infection. Demographic characteristics of the infected patients coupled with strain invasiveness across different genotypes revealed a complex epidemiology of C. jejuni transmission in Israel.

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

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    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.

  12. Molecular epidemiology and strain-specific characteristics of Streptococcus agalactiae at the herd and cow level.

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    Mahmmod, Y S; Klaas, I C; Katholm, J; Lutton, M; Zadoks, R N

    2015-10-01

    Host-adaptation of Streptococcus agalactiae subpopulations has been described whereby strains that are commonly associated with asymptomatic carriage or disease in people differ phenotypically and genotypically from those causing mastitis in dairy cattle. Based on multilocus sequence typing (MLST), the most common strains in dairy herds in Denmark belong to sequence types (ST) that are also frequently found in people. The aim of this study was to describe epidemiological and diagnostic characteristics of such strains in relation to bovine mastitis. Among 1,199 cattle from 6 herds, cow-level prevalence of S. agalactiae was estimated to be 27.4% based on PCR and 7.8% based on bacteriological culture. Quarter-level prevalence was estimated at 2.8% based on bacteriological culture. Per herd, between 2 and 26 isolates were characterized by pulsed-field gel electrophoresis (PFGE) and MLST. Within each herd, a single PFGE type and ST predominated, consistent with a contagious mode of transmission or point source infection within herds. Evidence of within-herd evolution of S. agalactiae was detected with both typing methods, although ST belonged to a single clonal complex (CC) per herd. Detection of CC23 (3 herds) was associated with significantly lower approximate count (colony-forming units) at the quarter level and significantly lower cycle threshold value at the cow level than detection of CC1 (2 herds) or CC19 (1 herd), indicating a lower bacterial load in CC23 infections. Median values for the number of infected quarters and somatic cell count (SCC) were numerically but not significantly lower for cows infected with CC23 than for cows with CC1 or CC19. For all CC, an SCC threshold of 200,000 cells/mL was an unreliable indicator of infection status, and prescreening of animals based on SCC as part of S. agalactiae detection and eradication campaigns should be discouraged.

  13. Phenotypes, genotypes, serotypes and molecular epidemiology of erythromycin-resistant Streptococcus agalactiae in Italy.

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    De Francesco, M A; Caracciolo, S; Gargiulo, F; Manca, N

    2012-08-01

    The purpose of this investigation was to analyse Streptococcus agalactiae (group B Streptococcus, GBS) isolates collected in Italy from vaginal and urine samples in respect to their clonality, distribution of virulence factors and antimicrobial resistance determinants. Three hundred and eighty-eight GBS were recovered from clinical samples. They were analysed for antibiotic resistance profiling. Erythromycin-resistant strains were further characterised by multilocus sequence typing (MLST), serotyping and the detection of alp genes of the alpha-like protein (Alp) family. GBS isolates represented 40 different sequence types (STs), grouped in five clonal complexes (CCs) and belonged to seven serotypes. Most serotype V strains (81%) possessed alp2-3; serotype Ia carried mainly epsilon, while the serotype III mainly rib. All isolates were susceptible to penicillin, whereas resistance to erythromycin was detected in 15% of isolates. Most erythromycin-resistant GBS strains were of serotype V (56.8%) and belonged to the CC-1 group (50%). Macrolide resistance phenotypes were the cMLS(B) (46.5%) and the M phenotypes (46.5%) due to the presence of ermB and mefA/E genes, respectively. These results provide data which establish a baseline for monitoring erythromycin resistance in this region and also provide an insight into the correlation among clonal types, serotypes, surface protein and resistance genes. The increased prevalence of strains that displayed the M phenotype strengthens the importance of the epidemiological surveillance of macrolide resistance in GBS, which may also represent an important reservoir of resistance genes for other species.

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

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    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

  15. 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

  16. Human T-cell lymphotropic virus type 1 subtype C molecular variants among indigenous australians: new insights into the molecular epidemiology of HTLV-1 in Australo-Melanesia.

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    Olivier Cassar

    Full Text Available BACKGROUND: HTLV-1 infection is endemic among people of Melanesian descent in Papua New Guinea, the Solomon Islands and Vanuatu. Molecular studies reveal that these Melanesian strains belong to the highly divergent HTLV-1c subtype. In Australia, HTLV-1 is also endemic among the Indigenous people of central Australia; however, the molecular epidemiology of HTLV-1 infection in this population remains poorly documented. FINDINGS: Studying a series of 23 HTLV-1 strains from Indigenous residents of central Australia, we analyzed coding (gag, pol, env, tax and non-coding (LTR genomic proviral regions. Four complete HTLV-1 proviral sequences were also characterized. Phylogenetic analyses implemented with both Neighbor-Joining and Maximum Likelihood methods revealed that all proviral strains belong to the HTLV-1c subtype with a high genetic diversity, which varied with the geographic origin of the infected individuals. Two distinct Australians clades were found, the first including strains derived from most patients whose origins are in the North, and the second comprising a majority of those from the South of central Australia. Time divergence estimation suggests that the speciation of these two Australian clades probably occurred 9,120 years ago (38,000-4,500. CONCLUSIONS: The HTLV-1c subtype is endemic to central Australia where the Indigenous population is infected with diverse subtype c variants. At least two Australian clades exist, which cluster according to the geographic origin of the human hosts. These molecular variants are probably of very ancient origin. Further studies could provide new insights into the evolution and modes of dissemination of these retrovirus variants and the associated ancient migration events through which early human settlement of Australia and Melanesia was achieved.

  17. 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.

  18. 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.

  19. 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.

  20. Molecular epidemiology of Plasmodium species prevalent in Yemen based on 18 s rRNA

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    A Azazy Ahmed

    2010-11-01

    Full Text Available Abstract Background Malaria is an endemic disease in Yemen and is responsible for 4.9 deaths per 100,000 population per year and 43,000 disability adjusted life years lost. Although malaria in Yemen is caused mainly by Plasmodium falciparum and Plasmodium vivax, there are no sequence data available on the two species. This study was conducted to investigate the distribution of the Plasmodium species based on the molecular detection and to study the molecular phylogeny of these parasites. Methods Blood samples from 511 febrile patients were collected and a partial region of the 18 s ribosomal RNA (18 s rRNA gene was amplified using nested PCR. From the 86 positive blood samples, 13 Plasmodium falciparum and 4 Plasmodium vivax were selected and underwent cloning and, subsequently, sequencing and the sequences were subjected to phylogenetic analysis using the neighbor-joining and maximum parsimony methods. Results Malaria was detected by PCR in 86 samples (16.8%. The majority of the single infections were caused by P. falciparum (80.3%, followed by P. vivax (5.8%. Mixed infection rates of P. falciparum + P. vivax and P. falciparum + P. malariae were 11.6% and 2.3%, respectively. All P. falciparum isolates were grouped with the strain 3D7, while P. vivax isolates were grouped with the strain Salvador1. Phylogenetic trees based on 18 s rRNA placed the P. falciparum isolates into three sub-clusters and P. vivax into one cluster. Sequence alignment analysis showed 5-14.8% SNP in the partial sequences of the 18 s rRNA of P. falciparum. Conclusions Although P. falciparum is predominant, P. vivax, P. malariae and mixed infections are more prevalent than has been revealed by microscopy. This overlooked distribution should be considered by malaria control strategy makers. The genetic polymorphisms warrant further investigation.

  1. Molecular Characterization of Pasteurella multocida: Its Implication with Epidemiology and The Development of Local Isolate Vaccines

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    Supar

    2007-12-01

    Full Text Available Pasteurella multocida strains are the causative agents of pasteurellosis attacking wide range domestic and wild animals. The important pasteurellosis in animals in Indonesia are Haemorrhagic septicaemic (HS or Septicaemia epizootica (SE in large and small ruminants, fowl cholera in poultry and water powls. HS associated with P. multocida in large ruminants was controlled by killed whole cell vaccines produced by the use of P. multocida Katha strain, whereas fowl cholera was controlled by antimicrobial drugs. At present, there are only a limited molecular biology techniques have been applied to investigate P. multocida isolates from different geographic locations in Indonesia. Genomic DNA of P. multocida from HS cases from various provinces which were treated with restriction endonuclease ApaI and analysed by means of pulsed-field gel electrophoreses (PFGE demonstrated the presence of high degree distinctive DNA pattern compared to that of the vaccine (Katha strain from Burma and other reference strains. Similar different patterns were found in genomic DNA of local P. multocida isolates from cholera disease of chicken and ducks. P. multocida isolates from some provinces showed different DNA patterns to each other. These DNA pattern differences were probably associated with the alteration of their pathogenicity, antigenicity and immunogenicity, but it has not been confirmed yet. Vaccines prepared from P. multocida isolate originated from local HS cases and local cholera demonstrated better protection in experimental animals against heterologous and homologous challenges, in terms of higher and consistency antibody responses compared to that of Katha strain or imported P. multocida poultry strains. This supports the potential aspects of molecular characterization of local P. multocida isolates kept at the BCC Unit. These isolates may play an important role in developing local master seeds to produce pasteurellosis local vaccines which would be more

  2. 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.

  3. 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

  4. HTLV-3/4 and simian foamy retroviruses in humans: discovery, epidemiology, cross-species transmission and molecular virology.

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    Gessain, Antoine; Rua, Réjane; Betsem, Edouard; Turpin, Jocelyn; Mahieux, Renaud

    2013-01-05

    Non-human primates are considered to be likely sources of viruses that can infect humans and thus pose a significant threat to human population. This is well illustrated by some retroviruses, as the simian immunodeficiency viruses and the simian T lymphotropic viruses, which have the ability to cross-species, adapt to a new host and sometimes spread. This leads to a pandemic situation for HIV-1 or an endemic one for HTLV-1. Here, we present the available data on the discovery, epidemiology, cross-species transmission and molecular virology of the recently discovered HTLV-3 and HTLV-4 deltaretroviruses, as well as the simian foamy retroviruses present in different human populations at risk, especially in central African hunters. We discuss also the natural history in humans of these retroviruses of zoonotic origin (magnitude and geographical distribution, possible inter-human transmission). In Central Africa, the increase of the bushmeat trade during the last decades has opened new possibilities for retroviral emergence in humans, especially in immuno-compromised persons.

  5. Molecular epidemiology of HIV-associated tuberculosis in Dar es Salaam, Tanzania: strain predominance, clustering, and polyclonal disease.

    Science.gov (United States)

    Adams, Lisa V; Kreiswirth, Barry N; Arbeit, Robert D; Soini, Hanna; Mtei, Lillian; Matee, Mecky; Bakari, Muhammad; Lahey, Timothy; Wieland-Alter, Wendy; Shashkina, Elena; Kurepina, Natalia; Driscoll, Jeffrey R; Pallangyo, Kisali; Horsburgh, C Robert; von Reyn, C Fordham

    2012-08-01

    Molecular typing of Mycobacterium tuberculosis can be used to elucidate the epidemiology of tuberculosis, including the rates of clustering, the frequency of polyclonal disease, and the distribution of genotypic families. We performed IS6110 typing and spoligotyping on M. tuberculosis strains isolated from HIV-infected subjects at baseline or during follow-up in the DarDar Trial in Tanzania and on selected community isolates. Clustering occurred in 203 (74%) of 275 subjects: 124 (80%) of 155 HIV-infected subjects with baseline isolates, 56 (69%) of 81 HIV-infected subjects with endpoint isolates, and 23 (59%) of 39 community controls. Overall, 113 (41%) subjects had an isolate representing the East Indian "GD" family. The rate of clustering was similar among vaccine and placebo recipients and among subjects with or without cellular immune responses to mycobacterial antigens. Polyclonal disease was detected in 6 (43%) of 14 patients with multiple specimens typed. Most cases of HIV-associated tuberculosis among subjects from this study in Dar es Salaam resulted from recently acquired infection. Polyclonal infection was detected and isolates representing the East Indian GD strain family were the most common.

  6. Transmission of tuberculosis in Havana, Cuba: a molecular epidemiological study by IS6110 restriction fragment length polymorphism typing

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    Diaz R

    2001-01-01

    Full Text Available The combination of molecular and conventional epidemiological methods has improved the knowledge about the transmission of tuberculosis in urban populations. To examine transmission of tuberculosis in Havana, Cuba, with DNA fingerprinting, we studied 51 out of 92 Mycobacterium tuberculosis strains isolated from tuberculosis patients who resided in Havana and whose infection was culture-confirmed in the period from September 1997 to March 1998. Isolates from 28 patients (55% had unique IS6110 restriction fragment length polymorphism (RFLP patterns, while isolates from 23 others (45% had identical patterns and belonged to 7 clusters. Three clusters consisting of six, five and two cases were each related to small outbreaks that occurred in a closed setting. Three other clustered cases were linked to a large outbreak that occurred in another institution. Younger patients were more correlated to clustering than older ones. The finding that 45% of the isolates had clustered RFLP patterns suggests that recent transmission is a key factor in the tuberculosis cases in Havana. The IS6110 RFLP typing made it possible to define the occurrence of outbreaks in two closed institutions.

  7. 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.

  8. Global molecular epidemiology and genetic diversity of Fusarium, a significant emerging group of human opportunists from 1958 to 2015.

    Science.gov (United States)

    Al-Hatmi, Abdullah Ms; Hagen, Ferry; Menken, Steph Bj; Meis, Jacques F; de Hoog, G Sybren

    2016-12-07

    Fusarium is a rapidly emerging, multidrug-resistant genus of fungal opportunists that was first identified in 1958 and is presently recognized in numerous cases of fusariosis each year. The authors examined trends in global Fusarium distribution, clinical presentation and prevalence since 1958 with the assumption that their distributions in each region had remained unaltered. The phylogeny and epidemiology of 127 geographically diverse isolates, representing 26 Fusarium species, were evaluated using partial sequences of the RPB2 and TEF1 genes, and compared with AFLP fingerprinting data. The molecular data of the Fusarium species were compared with archived data, which enabled the interpretation of hundreds of cases published in the literature. Our findings indicate that fusariosis is globally distributed with a focus in (sub)tropical areas. Considerable species diversity has been observed; genotypic features did not reveal any clustering with either the clinical data or environmental origins. This study suggests that infections with Fusarium species might be truly opportunistic. The three most common species are F. falciforme and F. keratoplasticum (members of F. solani species complex), followed by F. oxysporum (F. oxysporum species complex).

  9. Molecular epidemiology and a loop-mediated isothermal amplification method for diagnosis of infection with rabies virus in Zambia.

    Science.gov (United States)

    Muleya, Walter; Namangala, Boniface; Mweene, Aaron; Zulu, Luke; Fandamu, Paul; Banda, Douglas; Kimura, Takashi; Sawa, Hirofumi; Ishii, Akihiro

    2012-01-01

    The National Livestock Epidemiology and Information Center (NALEIC) in Zambia reported over 132 cases of canine rabies diagnosed by the direct fluorescent antibody test (DFAT) from 2004 to 2009. In this study, the lineage of rabies virus (RABV) in Zambia was determined by phylogenetic analysis of the nucleoprotein (N) and glycoprotein (G) gene sequences. Total RNA was extracted from 87-DFAT brain specimens out of which only 35 (40%) were positive on nested reverse transcription polymerase chain reaction (RT-PCR) for each gene, and 26 being positive for both genes. Positive specimens for the N (n=33) and G (n=35) genes were used for phylogenetic analysis. Phylogenetic analysis of the N gene showed two phylogenetic clusters in Zambia belonging to the Africa 1b lineage present in eastern and southern Africa. While one cluster exclusively comprised Zambian strains, the other was more heterogeneous regarding the RABV origins and included strains from Tanzania, Mozambique and Zambia. Phylogenetic analysis of the G gene revealed similar RABV strains in different hosts and regions of Zambia. We designed primers for reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay from the consensus sequence of the N gene in an attempt to improve the molecular diagnosis of RABV in Zambia. The specificity and reproducibility of the RT-LAMP assay was confirmed with actual clinical specimens. Therefore, the RT-LAMP assay presented in this study may prove to be useful for routine diagnosis of rabies in Zambia.

  10. Characteristics of the Molecular Epidemiology of CTX-M-Producing Escherichia coli Isolated from a Tertiary Hospital in Daejeon, Korea.

    Science.gov (United States)

    Kim, Semi; Sung, Ji Youn; Cho, Hye Hyun; Kwon, Kye Chul; Koo, Sun Hoe

    2016-09-28

    The aims of this study were to characterize the molecular epidemiological profiles of CTX-M-producing uropathogenic Escherichia coli isolates from a tertiary hospital in Daejeon, Korea, and to investigate the genetic diversity and compare the prevalence of sequence types (STs) in different areas. Extended spectrum β-lactamase-producing E. coli strains isolated from urine were analyzed for CTX-M, integrons, and insertion sequence common regions (ISCRs) by PCR and sequencing. Multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), phylogenetic analysis, and rep-PCR were also used for molecular typing of the isolates. Of 80 CTX-M producers, 31 and 46 expressed CTX-M-15 and CTX-M-14, respectively. MLST analysis indicated that the most prevalent ST was ST131 (n = 34, 42.5%), followed by ST38 (n = 22, 27.5%), ST405 (n = 8, 10.0%), and ST69 (n = 6, 7.5%). Most CTX-M producers harbored class 1 integrons. ST131 strains belonged to phylogenetic group B2 and showed identical rep-PCR patterns, whereas ST69, ST38, and ST405 strains belonged to phylogenetic group D; the ST38 and ST405 strains displayed the same rep-PCR pattern, respectively. ST131 and ST38 isolates showed 21 and 19 distinct types, respectively, by PFGE. In Daejeon, D-ST38 CTX-M-14 producers were relatively more prevalent than in other countries and Korean cities. Our results indicate that CTX-M-producing E. coli isolates belonged mostly to ST131 or ST38 and were more related to hospital-onset than to community-onset infections and that the blaCTX-M gene may vary according to the ST.

  11. 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.

  12. 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

  13. 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.

  14. Open-angle glaucoma : From epidemiology to molecular aspects and anatomical features

    NARCIS (Netherlands)

    H. Springelkamp (Henriët)

    2016-01-01

    markdownabstractOpen-angle glaucoma (OAG) is an important cause of irreversible blindness. In OAG, loss of retinal ganglion cells leads to damage of the optic nerve. This causes visual field loss and eventually blindness. Changes in the optic nerve head (ONH) can be examined with confocal scanning l

  15. 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.

  16. 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

  17. Epidemiology and health-environment relationship: reflections on environmental change, sustainable development and population health

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    Diana M. Montoya

    2009-08-01

    Full Text Available This essay presents a discussion on current environmental problems and their relationship to the health of populations. The limitations of the model of economic and social development are analyzed focusing on the augmentation of the capital and the industrial production and its negative impact on natural resources, the balance of ecosystems and human vulnerability. The methodological basics and the developments in environmental epidemiological approach are exposed analyzing their main potential application. Finally, options for solutions are formulated linking them to the premises of sustainable development and environmental justice. The responsibility of the academic environment is pointed out in the training of human and scientific resources in the field of environmental epidemiology, as well as the role of the community in terms of environmental awareness and active participation from a point of view that becomes critical, responsible and capable of defining proposals to make part of the solution.

  18. Molecular typing and epidemiological survey of prevalence of Clostridium perfringens types by multiplex PCR.

    Science.gov (United States)

    Yoo, H S; Lee, S U; Park, K Y; Park, Y H

    1997-01-01

    Clostridium perfringens has been classified into five toxigenic types (A through E) on the basis of its capability to produce major lethal toxins (alpha, beta, epsilon, and iota toxins). Seroneutralization with mice or guinea pigs has been used to type each toxin, but this conventional method has some disadvantages. Therefore, we used a molecular biological technique to type the bacterium in the present study. A multiplex PCR was developed for this purpose. This method has several advantages in comparison with seroneutralization with mice or guinea pigs. By this method, we also investigated the most prevalent type(s) of the organism in Korean calves, piglets, and chickens showing clinical symptoms such as diarrhea, enterotoxemia, and necrotic enteritis. Only type A was isolated from calves and chickens, while type C (2 of 14 isolates), in addition to type A, was isolated from piglets. These results suggested that seroneutralization could be replaced by our new method and that type A of C. perfringens is the most prevalent type in livestock in Korea.

  19. A novel bacterial disease of the European shore crab, Carcinus maenas molecular pathology and epidemiology.

    Science.gov (United States)

    Eddy, Fiona; Powell, Adam; Gregory, Simon; Nunan, Linda M; Lightner, Donald V; Dyson, Paul J; Rowley, Andrew F; Shields, Robin J

    2007-09-01

    Several rickettsia-like diseases have been reported in arthropods (insects and crustaceans), some of which result in significant losses of economically important species such as shrimp and crabs. This study reports on the molecular pathology of a recently emerged disease of the European shore crab, Carcinus maenas, termed milky disease - named as a result of the unusual milky appearance of the haemolymph (blood). This disease was more prevalent (>26 %) during summer months when the water temperature in a pilot crab farm was approximately 19 degrees C. The putative causative agent of the disease was a Gram-negative bacterium that could not be cultured on a range of agar-based growth media. Diseased crabs showed significant reductions in free blood cell numbers and total serum protein. Such animals also displayed raised levels of glucose and ammonium in blood. Ultrastructural and in situ hybridization studies revealed that the causative agent associated with milky disease multiplied in the fixed phagocytes of the hepatopancreas (digestive gland), ultimately to be released into the haemolymph, where the circulating blood cells showed little response to the presence of these agents. Attempts to induce the infection by short-term temperature stress failed, as did transmission experiments where healthy crabs were fed infected tissues from milky disease affected individuals. Sequence analysis of the 16S rRNA gene from the milky disease bacteria indicated that they are a previously undescribed species of alpha-proteobacteria with little phylogenetic similarity to members of the order Rickettsiales.

  20. Molecular epidemiology of Trypanosoma cruzi and Triatoma dimidiata in costal Ecuador.

    Science.gov (United States)

    Wong, Yim Yan; Sornosa Macias, Karen Jeniffer; Guale Martínez, Doris; Solorzano, Luis F; Ramirez-Sierra, Maria Jesus; Herrera, Claudia; Dumonteil, Eric

    2016-07-01

    Chagas disease is a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi. In Ecuador, Triatoma dimidiata and Rhodnius ecuadoriensis are the main vector species, responsible for over half of the cases of T. cruzi infection in the country. T. dimidiata is believed to have been introduced in Ecuador during colonial times, and its elimination from the country is thus believed to be feasible. We investigated here the molecular ecology of T. dimidiata and T. cruzi in costal Ecuador to further guide control efforts. Analysis of the Internal Transcribed Spacer 2 (ITS-2) of 23 specimens from Progreso, Guayas, unambiguously supported the likely importation of T. dimidiata from Central America to Ecuador. The observation of a very high parasite infection rate (54%) and frequent feeding on humans (3/5) confirmed a continued risk of transmission to humans. All genotyped parasites corresponded to TcI DTU and Trypanosoma rangeli was not detected in T. dimidiata. TcI subgroups corresponded to TcIa (25%), and mixed infections with TcIa and TcId (75%). Further studies should help clarify T. cruzi genetic structure in the country, and the possible impact of the introduction of T. dimidiata on the circulating parasite strains. The elevated risk posed by this species warrants continuing efforts for its control, but its apparent mobility between peridomestic and domestic habitats may favor reinfestation following insecticide spraying.

  1. Molecular epidemiology of Mycobacterium tuberculosis in aboriginal peoples of Taiwan, 2006-2011.

    Science.gov (United States)

    Chen, Yih-Yuan; Chang, Jia-Ru; Huang, Wei-Feng; Kuo, Shu-Chen; Yeh, Jun-Jun; Lee, Jen-Jyh; Jang, Chang-Sheng; Sun, Jun-Ren; Chiueh, Tzong-Shi; Su, Ih-Jen; Dou, Horng-Yunn

    2014-04-01

    Previous research revealed a 6-fold higher incidence of tuberculosis (TB) amongst aborigines compared to Han Chinese in Taiwan. To investigate the reasons for this disparity, we genotyped Mycobacterium tuberculosis (MTB) strains obtained from members of different aboriginal tribes in different geographical regions of Taiwan by using molecular methods. In total, 177 isolates of MTB collected from patients at four hospitals in Taiwan from January 2006 to December 2011 were analysed by spoligotyping, mycobacterial interspersed repetitive unit-variable number tandem-repeat (MIRU-VNTR) typing. The most prevalent strains in the eastern and central regions of Taiwan were Beijing (45.7% in eastern) and Haarlem (39.1% in eastern, 37.1% in central) lineages, whereas in southern regions the most prevalent strains were EAI (47.7%) and Haarlem (20.5%) lineages. The high prevalence of EAI in southern Taiwan aborigines may be closely associated with Austronesian culture. This study provides a first overview of the M. tuberculosis strains circulating in aboriginal populations in Taiwan. The high prevalences of certain MTB lineages within aboriginal sub-populations suggest that transmission of MTB may have been restricted to close contacts.

  2. 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.

  3. Incidence of respiratory viruses in a pediatric population: molecular and epidemiological aspects

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    Anna Di Taranto

    2012-09-01

    Full Text Available Introduction: Respiratory infections are not well defined and the etiology is often unknown. Material and method: four hundred fortynine subjectrs were enrolled in the study; in all patientes there was a suspect of inflammatory diseases of the respiratory tract. At admission, a nasopharyngeal swab was made. A multiplex PCR was performed after extraction and reverse transcription of viral RNA. The amplified fragments were revealed by using an electrophoresis separation. Results: Two hundred and four patients (45.4% were hospitalized for infection of the upper respiratory tract, 141 (31.4% for lower respiratory infection and the remaining (23% for other symptoms. One hundred fiftyseven (35% patients were positive for human influenza A (H1N1 subtype and 184 for other respiratory viruses,of which 59 (32% gave a positive for respiratory syncytial virus, 42 (23% for rhinovirus, 31 (17% for parainfluenza virus, 12 (6.5% for coronavirus, 28 (15% for adenovirus and 6 (3% for influenza B (3% and 6 (3% for metapneumovirus. The M1 gene sequence of influenza A H1N1 strains from 12 patients had a high identity with that of the reference virus. Conclusion: Furthermore H1N1 and RSV were the main causative agents of acute respiratory infection. A molecular approach provides an accurate and rapid aetiological diagnosis of viral respiratory infections. The molecolar features in the M1 gene suggested that the H1N1 influenza strains circulating in Apulia region had a conserved genetic make up.

  4. 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.

  5. 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.

  6. Estudios de epidemiología molecular en población inmigrante en España

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    Fernando González-Candelas

    2014-01-01

    Full Text Available Fundamentos: La epidemiología molecular es una nueva disciplina que permite la integración de la información sobre la variabilidad genética de patógenos infecciosos con su difusión en la población y subgrupos de la misma incluyendo, por ejemplo, las mutaciones de resistencia a antibióticos y antivirales. El objetivo es conocer qué posibles diferencias existe en las características genéticas de los agentes infecciosos que afectan a las poblaciones inmigrante y autóctoctona en España. Métodos: Se revisaron artículos originales publicados entre 1998-2013, con las palabras clave “epidemiología molecular”, “tipado molecular”, “secuenciación”, “inmigrante”, “España”. Resultados: De un total de 267 artículos identificados inicialmente,50 pasaron los diferentes filtros establecidos. De ellos, 36 analizan las infecciones por Mycobacterium tuberculosis y VIH, seguidos de los que analizan infecciones por Staphylococcus aureus (3 y el Virus de la Hepatitis B (3. Conclusiones: Los objetivos principales de estos trabajos fueron eltipado del patógeno y la determinación de la frecuencia de mutaciones de resistencia. Los estudios más frecuentes correspondieron a cohortes retrospectivas, seguidos por los estudios ecológicos y los ensayos clínicos. En general los estudios son descriptivos y su ámbito por el tipo y tamaño de muestra es bastante restringido. En varios se determina que las cepas o variantes del patógeno encontradas en inmigrantes tienen su origen más probable en sus países de origen, si bien otros también ponen de manifiesto la transmisión desde la población autóctona a la inmigrante.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. How dormant is Mycobacterium tuberculosis during latency? A study integrating genomics and molecular epidemiology

    DEFF Research Database (Denmark)

    Yang, Zhenhua; Rosenthal, Mariana; Rosenberg, Noah A;

    2011-01-01

    Mycobacterium tuberculosis may survive for decades in the human body in a state termed latent tuberculosis infection (LTBI). We investigated the occurrence during LTBI of insertion/deletion events in a selected set of mononucleotide simple sequence repeats, DNA sequence changes in four M....... tuberculosis genes, and large sequence variations in 4750 M. tuberculosis open reading frames. We studied 13 paired M. tuberculosis clinical isolates, with each pair representing a reactivation of LTBI more than three decades after primary infection. Absence of sequence variations between paired isolates...

  17. How dormant is Mycobacterium tuberculosis during latency? A study integrating genomics and molecular epidemiology.

    Science.gov (United States)

    Yang, Zhenhua; Rosenthal, Mariana; Rosenberg, Noah A; Talarico, Sarah; Zhang, Lixin; Marrs, Carl; Thomsen, Vibeke Østergaard; Lillebaek, Troels; Andersen, Aase B

    2011-07-01

    Mycobacterium tuberculosis may survive for decades in the human body in a state termed latent tuberculosis infection (LTBI). We investigated the occurrence during LTBI of insertion/deletion events in a selected set of mononucleotide simple sequence repeats, DNA sequence changes in four M. tuberculosis genes, and large sequence variations in 4750 M. tuberculosis open reading frames. We studied 13 paired M. tuberculosis clinical isolates, with each pair representing a reactivation of LTBI more than three decades after primary infection. Absence of sequence variations between paired isolates in nearly all investigated loci suggests a low likelihood of bacterial replication during LTBI.

  18. Transient Changes in Molecular Geometries and How to Model Them

    DEFF Research Database (Denmark)

    Dohn, Asmus Ougaard

    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...... 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...... of purely classical MD simulations to literature Direct Dynamics simulations delineate the boundaries for the force-field approximation: Classical MD provides a solvent shell response sufficient for experimental fits, but fails to model specific solvent shell changes, such as intercalation. The first Direct...

  19. Prospective Multicenter Study of the Epidemiology, Molecular Identification, and Antifungal Susceptibility of Candida parapsilosis, Candida orthopsilosis, and Candida metapsilosis Isolated from Patients with Candidemia ▿

    OpenAIRE

    Cantón, Emilia; Pemán, Javier; Quindós, Guillermo; Eraso, Elena; Miranda-Zapico, Ilargi; Álvarez, María; Merino, Paloma; Campos-Herrero, Isolina; Marco, Francesc; de la Pedrosa, Elia Gomez G.; Yagüe, Genoveva; Guna, Remedios; Rubio, Carmen; Miranda, Consuelo; Pazos, Carmen

    2011-01-01

    A 13-month prospective multicenter study including 44 hospitals was carried out to evaluate the epidemiology of Candida parapsilosis complex candidemia in Spain. Susceptibility to amphotericin B, flucytosine, fluconazole, itraconazole, voriconazole, posaconazole, anidulafungin, caspofungin, and micafungin was tested by the microdilution colorimetric method. A total of 364 C. parapsilosis complex isolates were identified by molecular methods: C. parapsilosis (90.7%), Candida orthopsilosis (8.2...

  20. Molecular epidemiology of contagious bovine pleuropneumonia in Tanzania based on amplified fragment length polymorphism and pulsed-field gel electrophoresis analysis

    DEFF Research Database (Denmark)

    Kusiluka, L.J.M.; Ojeniyi, B.; Friis, N.F.;

    2001-01-01

    The genetic diversity of 60 field strains of Mycoplasma mycoides ssp. mycoides, small colony type (M,. mycoides), comprising 56 isolates from cattle in Tanzania, one from Kenya, two from Botswana and one from Portugal, as well as the type (PG1(T)) and vaccine (T-1-SR49) strains, was ivestigated. ......, this study; has demonstrated that AFLP and PFGE are potential tools for molecular epidemiological studies of M. mycoides SC infections....

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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

  6. 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

  7. Scientific Statement on the Diagnostic Criteria, Epidemiology, Pathophysiology, and Molecular Genetics of Polycystic Ovary Syndrome.

    Science.gov (United States)

    Dumesic, Daniel A; Oberfield, Sharon E; Stener-Victorin, Elisabet; Marshall, John C; Laven, Joop S; Legro, Richard S

    2015-10-01

    Polycystic ovary syndrome (PCOS) is a heterogeneous and complex disorder that has both adverse reproductive and metabolic implications for affected women. However, there is generally poor understanding of its etiology. Varying expert-based diagnostic criteria utilize some combination of oligo-ovulation, hyperandrogenism, and the presence of polycystic ovaries. Criteria that require hyperandrogenism tend to identify a more severe reproductive and metabolic phenotype. The phenotype can vary by race and ethnicity, is difficult to define in the perimenarchal and perimenopausal period, and is exacerbated by obesity. The pathophysiology involves abnormal gonadotropin secretion from a reduced hypothalamic feedback response to circulating sex steroids, altered ovarian morphology and functional changes, and disordered insulin action in a variety of target tissues. PCOS clusters in families and both female and male relatives can show stigmata of the syndrome, including metabolic abnormalities. Genome-wide association studies have identified a number of candidate regions, although their role in contributing to PCOS is still largely unknown.

  8. 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

    and microbiological data of all MRSA patients from the years 2000 to 2008 were collected prospectively. Isolates were characterized by pulsed-field gel electrophoresis (PFGE), sequencing of the repeat region of the Staphylococcus protein A gene (spa typing), staphylococcal cassette chromosome mec (SCCmec) typing......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...

  9. 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

  10. 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...... isolates of diverse origin identified by routine phenotyping as C coli were examined. Molecular tools identified some 12% of field isolates as Campylobacter jejuni, emphasizing the need for improved identification methods in routine laboratories. Cluster analysis of AFLP profiles of 174 confirmed C. coli...

  11. 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.

  12. Molecular epidemiology of Brucella genotypes in patients at a major hospital in central Peru.

    Science.gov (United States)

    Nöckler, Karsten; Maves, Ryan; Cepeda, David; Draeger, Angelika; Mayer-Scholl, Anne; Chacaltana, Jesus; Castañeda, María; Espinosa, Benjamin; Castillo, Rosa; Hall, Eric; Al Dahouk, Sascha; Gilman, Robert H; Cabeza, Franco; Smits, Henk L

    2009-10-01

    The multiple-locus variable-number repeat analysis of 90 human Brucella melitensis isolates from a large urban area in central Peru revealed variations at 4 (Bruce07, Bruce09, Bruce18, and Bruce42) out of 16 loci investigated, of which 1 (Bruce42) also is used for species identification. Ten genotypes were identified, separated by the number of Bruce42 repeats into two groups that may have distinct phenotypic characteristics. Whereas genotypes with five or six Bruce42 repeats were cultured mainly from adult patients, genotypes with three Bruce42 repeats were isolated from children and young adolescents as well as from adults. In addition, the isolates with three Bruce42 repeats were obtained more often from patients with splenomegaly (P = 0.02) or hepatomegaly (P = 0.006). An annual variation in the diversity of genotypes was observed, possibly reflecting changes in sources of fresh dairy products, supply routes to city shops and markets, and the movement of infected dairy goat herds.

  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. Immunological and molecular epidemiological characteristics of acute and fulminant viral hepatitis A

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    Husain Syed A

    2011-05-01

    Full Text Available Abstract Background Hepatitis A virus is an infection of liver; it is hyperendemic in vast areas of the world including India. In most cases it causes an acute self limited illness but rarely fulminant. There is growing concern about change in pattern from asymptomatic childhood infection to an increased incidence of symptomatic disease in the adult population. Objective In-depth analysis of immunological, viral quantification and genotype of acute and fulminant hepatitis A virus. Methods Serum samples obtained from 1009 cases of suspected acute viral hepatitis was employed for different biochemical and serological examination. RNA was extracted from blood serum, reverse transcribed into cDNA and amplified using nested PCR for viral quantification, sequencing and genotyping. Immunological cell count from freshly collected whole blood was carried out by fluorescence activated cell sorter. Results Fulminant hepatitis A was mostly detected with other hepatic viruses. CD8+ T cells count increases in fulminant hepatitis to a significantly high level (P = 0.005 compared to normal healthy control. The immunological helper/suppressor (CD4+/CD8+ ratio of fulminant hepatitis was significantly lower compared to acute cases. The serologically positive patients were confirmed by RT-PCR and total of 72 (69.2% were quantified and sequenced. The average quantitative viral load of fulminant cases was significantly higher (P Conclusions Immunological factors in combination with viral load defines the severity of the fulminant hepatitis A. Phylogenetic analysis of acute and fulminant hepatitis A confirmed genotypes IIIA as predominant against IA with no preference of disease severity.

  15. 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.

  16. 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

  17. 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

  18. Impact of immigration on tuberculosis in a low-incidence area of Italy: a molecular epidemiological approach.

    Science.gov (United States)

    Garzelli, C; Lari, N; Cuccu, B; Tortoli, E; Rindi, L

    2010-11-01

    The effects that immigration might have on the epidemiology of tuberculosis (TB) in a low-incidence area of Italy was investigated by determining, in autochthonous and immigrant TB patients, the molecular characteristics of the Mycobacterium tuberculosis complex (MTBC) isolates, which may provide information on their phylogeographical origin. A total of 1080 MTBC strains, collected during a 4- year period in Tuscany from 614 Italian-born and 466 foreign-born patients, were genotyped by spoligotyping and assigned to the different phylogeographical lineages that constitute the MTBC. The autochthonous Euro-American phylogeographical lineage, which includes the spoligotype families T, Haarlem, Latin American–Mediterranean (LAM), S and X, was highly prevalent among Italian-born patients, with a total of 477 cases (77.7%), and foreign-born TB patients, with a total of 270 cases (57.9%); 24 Italian-born (3.9%) and 141 foreign- born (30.3%) TB cases were due to MTBC genotypic families associated with distant geographical areas, i.e. East African–Indian (EAI), Beijing, Central Asian (CAS), and Mycobacterium africanum. Strains of Mycobacterium bovis and strains of undefined genotype, which are all considered together, as it is not possible to assign a specific geographical origin, accounted for 113 (18.4%) Italian cases and 55 (11.8%) foreign-born cases. A total of 79 Italian TB cases (12.9%) have been attributed to transmission from immigrants to the local population. No significant contribution to drug resistance appeared to be associated with imported MTBC strains. It is concluded that, at present, the overall impact of imported TB on public health in the low-incidence study area is relatively modest and of the same order as in other western countries.

  19. Molecular Epidemiology and Clinical Impact of Acinetobacter calcoaceticus-baumannii Complex in a Belgian Burn Wound Center.

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    Daniel De Vos

    Full Text Available 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.

  20. 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

  1. 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.

  2. Antimicrobial Resistance and Molecular Epidemiology of Escherichia coli Causing Bloodstream Infections in Three Hospitals in Shanghai, China.

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    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.

  3. 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.

  4. 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.

  5. Molecular epidemiology of HIV-1 among the HIV infected people of Manipur, Northeastern India: Emergence of unique recombinant forms.

    Science.gov (United States)

    Sharma, Adhikarimayum Lakhikumar; Singh, Thiyam Ramsing; Devi, Khuraijam Ranjana; Singh, Lisam Shanjukumar

    2016-11-21

    According to the Joint National Programme on HIV/AIDS (UNAIDS), the northeastern region of India has the highest HIV prevalence in the country. This study was conducted to determine the current HIV-1 molecular epidemiology of Manipur, a state in northeast India. Blood samples from HIV-1 seropositive subjects were collected between June 2011 and February 2014. The partial regions of HIV-1 genes; pol and tat-vpu-env were independently amplified, sequenced, analyzed, and genotyped. Based on all sequences generated from 110 samples using pol and/or tat-vpu-env gene, the overall HIV-1 genotypes distribution of Manipur was as follows: 65.45% (72/110) subtype C, 32.73% (36/110) unique recombinant forms (URFs), and 1.82% (2/110) subtype B. The distribution of HIV-1 genotypes among the risk groups was: heterosexual: 58.33% (35/60) subtype C, 38.33% (23/60) URFs, and 3.34% (2/60) subtype B; intravenous drug users (IDUs): 85.36% (35/41) subtype C, 9.76% (4/41) URFs, and 4.88% (2/41) subtype B; mother to child (MTC): 50% (3/6) URFs and 50% (3/6) subtype C and blood transfusion: 100% (3/3) subtype C. The findings for the first time revealed the emergence of URFs of HIV-1 in Manipur which is predominant among the sexual and MTC risk groups as compared to IDUs. Taking together, this study illustrated that Manipur is the "recombinant hotspot of HIV" of India. The results will provide the clinical importance for continuous monitoring of HIV-infections in order to design appropriate prevention measures to limit the spread of new HIV infections.

  6. Population genetic analysis of Serpulina pilosicoli and its molecular epidemiology in villages in the eastern Highlands of Papua New Guinea.

    Science.gov (United States)

    Trott, D J; Mikosza, A S; Combs, B G; Oxberry, S L; Hampson, D J

    1998-07-01

    The population genetics of Serpulina pilosicoli and its molecular epidemiology in villages in the Eastern Highlands province of Papua New Guinea were investigated. Multilocus enzyme electrophoresis (MLEE) was used to analyse 164 isolates from humans and animals. These were divided into 33 electrophoretic types (ETs), four of which contained 65% of the isolates. The mean genetic diversity (n = number of ETs) for 145 human isolates was 0.18, and the mean number of alleles at five polymorphic loci was 2.6. The species appeared to be recombinant, as there was a lack of linkage disequilibrium, and 25% of all the possible combinations of alleles was present in the population. PFGE analysis using the enzymes M/ul and Sa/l divided 157 of the isolates into 99 PFGE types, demonstrating the existence of considerable strain diversity in a geographically restricted area. The two techniques were in excellent agreement; however, PFGE was more discriminatory for strain typing than was MLEE. Nine out of 19 (47.4%) culture-positive individuals were colonized by the same PFGE type of S. pilosicoli when retested after 6 weeks. For three individuals, the PFGE profiles of the second isolate differed from the first in only one or two DNA bands, while the other seven individuals were colonized with distinct PFGE types on each occasion. In two cases, strains with the same PFGE pattern were isolated from humans and dogs, suggesting that cross-species transmission of S. pilosicoli may occur naturally and that the infection can be zoonotic.

  7. Molecular epidemiology of HIV-1 subtypes in India: origin and evolutionary history of the predominant subtype C.

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    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

  8. Molecular epidemiological investigation of a diffuse outbreak caused by Salmonella enterica serotype Montevideo isolates in Osaka Prefecture, Japan.

    Science.gov (United States)

    Harada, Tetsuya; Sakata, Junko; Kanki, Masashi; Seto, Kazuko; Taguchi, Masumi; Kumeda, Yuko

    2011-10-01

    In Osaka Prefecture, Japan, three foodborne outbreaks were caused by Salmonella enterica serotype Montevideo in rapid succession between September 2007 and May 2008. Further, Salmonella Montevideo was also isolated from several sporadic diarrhea patients and asymptomatic carriers examined during approximately the identical period. To investigate the relatedness of the isolates, we performed antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE) analysis, and multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) for 29 Salmonella Montevideo isolates obtained in this region between 1991 and 2008. Although antimicrobial susceptibility tests had low discriminatory power, PFGE patterns revealed 17 unique types with outbreaks, one sporadic patient, and three different carriers between 2007 and 2008 had nearly identical PFGE patterns and were classified into the identical MLVA type; further, the isolates with this PFGE and MLVA pattern appeared only at that time between 1991 and 2008. These data strongly suggest that genetically identical Salmonella Montevideo strains may have caused the 2007 and 2008 outbreaks in Osaka Prefecture. Our results demonstrate that PFGE using XbaI and BlnI is useful for discriminating between Salmonella Montevideo isolates, even within a limited area, and reconfirm that continuous epidemiological surveillance for bacterial intestinal infections such as salmonellosis may be useful to not only monitor changes in the genetic diversity of isolates, but to also detect diffuse outbreaks.

  9. [Molecular epidemiology of Mycobacterium tuberculosis and its prospect based on variable number of tandem repeat (VNTR) genotyping--a strategy in Osaka City, Japan].

    Science.gov (United States)

    Wada, Takayuki; Hase, Atsushi

    2010-12-01

    The methodological establishment of variable number of tandem repeat(s) (VNTR) genotyping of Mycobacterium tuberculosis has opened a new era of molecular epidemiology against tuberculosis (TB). The method can provide simple, rapid and accurate identification of clinical isolates from TB patients that makes it possible to compare the isolates among different laboratories. Such advantages of VNTR not only help us certify the identification of isolates in putative outbreaks easily but also promote the reasonable estimation of unidentified transmissions in surveillance studies. Recently, the Japan Anti-Tuberculosis Association (JATA) (12)-VNTR has become a standard genotyping method of M. tuberculosis, and its spread has been expected in Japan. In Osaka City, located in the western part of the country, JATA (12)-VNTR has been applied to molecular epidemiological study of TB. Moreover, the additional 12 VNTR loci have been analyzed for various purposes, such as to enhance the discriminatory power (public health needs) or to further analyze the population genetic structure (research needs). As the nationwide findings of VNTR genotyping of M. tuberculosis are accumulated, this technology will be increasingly useful for detecting transmission of any specific strain in large geographic areas that could not be recognized by conventional epidemiological methods. The needs for the VNTR genotyping of M. tuberculosis and its practical uses are expected to expand drastically in the future.

  10. 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.

  11. 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

  12. A phenomenological relationship between molecular geometry change and conformational energy change

    Science.gov (United States)

    Bodi, Andras; Bjornsson, Ragnar; Arnason, Ingvar

    2010-08-01

    A linear correlation is established between the change in the axial/equatorial conformational energy difference and the change in the molecular geometry transformation during conformational inversion in substituted six-membered ring systems, namely in the 1-substituted cyclohexane/silacyclohexane, cyclohexane/ N-substituted piperidine and 1-substituted silacyclohexane/ P-substituted phosphorinane compound families, and for the analogous gauche/anti conformational isomerism in 1-substituted propanes/1-silapropanes. The nuclear repulsion energy parameterizes the molecular geometry, and changes in the conformational energy between the related compound families are linearly correlated with the changes in the nuclear repulsion energy difference based on DFT (B3LYP, M06-2X), G3B3, and CBS-QB3 calculations. This correlation reproduces the sometimes remarkable contrast between the conformational behavior of analogous compounds, e.g., the lack of a general equatorial preference in silacyclohexanes.

  13. Biomarcadores moleculares em câncer: implicações para a pesquisa epidemiológica e a saúde pública Molecular biomarkers in cancer: implications for epidemiological research and public health

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    Victor Wünsch Filho

    2001-06-01

    Full Text Available O desenvolvimento das áreas de genética e biologia molecular tem sido admirável nas últimas décadas e isso tem repercutido intensamente na epidemiologia. Neste artigo, discute-se a ampliação das fronteiras da pesquisa epidemiológica em câncer com a incorporação das técnicas da genética e da biologia molecular. Examina-se o conhecimento atual dos biomarcadores de exposição e de suscetibilidade, o papel das mutações genéticas na carcinogênese, a aplicação destas nos estudos epidemiológicos e implicações para a prevenção. Perscrutando o meio interno dos indivíduos, a epidemiologia molecular e a genética representam um avanço tanto para a avaliação da exposição, quanto para a detecção de indivíduos suscetíveis, e possuem imenso potencial para ampliar a compreensão dos mecanismos da carcinogênese e dos efeitos de fatores de risco no câncer. Entretanto, por serem necessariamente mais invasivas, essas abordagens remetem a importantes questões no campo da ética. A comunidade científica de saúde pública e a sociedade devem guardar vigilância sobre os usos e aplicações deste novo conhecimento, avaliando seus desdobramentos à luz da bioéticaIdentification of molecular biomarkers is a common result of current cancer epidemiological research. Both genetic and molecular epidemiology have enjoyed impressive developments in recent decades, with important repercussions on traditional epidemiological approaches. In this paper we evaluate the new frontiers of cancer epidemiology, incorporating both genetic and molecular biology approaches. We examine the current knowledge of molecular biomarkers for exposure and susceptibility to cancer, the role of gene mutations in carcinogenesis, and their application to epidemiological studies. By exploring the status of relevant biomarkers, these approaches become effective in evaluating exposure and susceptibility and show enormous potential for elucidating mechanisms of

  14. 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...

  15. 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.

  16. Molecular epidemiology of clinical and carrier strains of methicillin resistant Staphylococcus aureus (MRSA in the hospital settings of north India

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    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

  17. 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

  18. Mechanisms, molecular and sero-epidemiology of antimicrobial resistance in bacterial respiratory pathogens isolated from Japanese children

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    Sunakawa Keisuke

    2007-08-01

    Full Text Available Abstract Background The clinical management of community-acquired respiratory tract infections (RTIs is complicated by the increasing worldwide prevalence of antibacterial resistance, in particular, β-lactam and macrolide resistance, among the most common causative bacterial pathogens. This study aimed to determine the mechanisms and molecular- and sero-epidemiology of antibacterial resistance among the key paediatric respiratory pathogens in Japan. Methods Isolates were collected at 18 centres in Japan during 2002 and 2003 from children with RTIs as part of the PROTEKT surveillance programme. A proportion of Haemophilus influenzae isolates was subjected to sequencing analysis of the ftsI gene; phylogenetic relatedness was assessed using multilocus sequence typing. Streptococcus pneumoniae isolates were screened for macrolide-resistance genotype by polymerase chain reaction and serotyped using the capsular swelling method. Susceptibility of isolates to selected antibacterials was performed using CLSI methodology. Results and Discussion Of the 557 H. influenzae isolates collected, 30 (5.4% were β-lactamase-positive [BL+], 115 (20.6% were BL-nonproducing ampicillin-resistant (BLNAR; MIC ≥ 4 mg/L and 79 (14.2% were BL-nonproducing ampicillin-intermediate (BLNAI; MIC 2 mg/L. Dabernat Group III penicillin binding protein 3 (PBP3 amino acid substitutions in the ftsI gene were closely correlated with BLNAR status but phylogenetic analysis indicated marked clonal diversity. PBP mutations were also found among BL+ and BL-nonproducing ampicillin-sensitive isolates. Of the antibacterials tested, azithromycin and telithromycin were the most active against H. influenzae (100% and 99.3% susceptibility, respectively. A large proportion (75.2% of the 468 S. pneumoniae isolates exhibited macrolide resistance (erythromycin MIC ≥ 1 mg/L; erm(B was the most common macrolide resistance genotype (58.8%, followed by mef(A (37.2%. The most common pneumococcal

  19. 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

  20. Comprehensive Characterization of HIV-1 Molecular Epidemiology and Demographic History in the Brazilian Region Most Heavily Affected by AIDS

    Science.gov (United States)

    Machado Fritsch, Hegger; de Medeiros, Rúbia Marília; Maletich Junqueira, Dennis; Esteves de Matos Almeida, Sabrina; Pinto, Aguinaldo Roberto

    2016-01-01

    ABSTRACT The high incidence of AIDS cases and the dominance of HIV-1 subtype C infections are two features that distinguish the HIV-1 epidemic in the two southernmost Brazilian states (Rio Grande do Sul [RS] and Santa Catarina [SC]) from the epidemic in other parts of the country. Nevertheless, previous studies on HIV molecular epidemiology were conducted mainly in capital cities, and a more comprehensive understanding of factors driving this unique epidemic in Brazil is necessary. Blood samples were collected from individuals in 13 municipalities in the Brazilian southern region. HIV-1 env and pol genes were submitted to phylogenetic analyses for assignment of subtype, and viral population phylodynamics were reconstructed by applying Skygrid and logistic coalescent models in a Bayesian analysis. A high prevalence of subtype C was observed in all sampled locations; however, an increased frequency of recombinant strains was found in RS, with evidence for new circulating forms (CRFs). In the SC state, subtype B and C epidemics were associated with distinct exposure groups. Although logistic models estimated similar growth rates for HIV-1 subtype C (HIV-1C) and HIV-1B, a Skygrid plot reveals that the former epidemic has been expanding for a longer time. Our results highlight a consistent expansion of HIV-1C in south Brazil, and we also discuss how heterosexual and men who have sex with men (MSM) transmission chains might have impacted the current prevalence of HIV-1 subtypes in this region. IMPORTANCE The AIDS epidemic in south Brazil is expanding rapidly, but the circumstances driving this condition are not well known. A high prevalence of HIV-1 subtype C was reported in the capital cities of this region, in contrast to the subtype B dominance in the rest of the country. This study sought to comparatively investigate the HIV-1 subtype B and C epidemics by sampling individuals from several cities in the two states with the highest AIDS incidences in Brazil. Our

  1. 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.

  2. Changing Epidemiology of Hepatocellular Adenoma in the United States: Review of the Literature

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    Charissa Y. Chang

    2013-01-01

    Full Text Available Hepatocellular adenoma (HCA is a benign neoplasm arising from hepatocytes. There is evidence that the inflammatory subtype may be associated with obesity and alcohol use and that men with metabolic syndrome may be at risk for malignant transformation of HCA. We sought to explore the combined experience of US centers as reported in the literature to document the epidemiologic shift in risk factors for HCA formation in the United States, namely, a shift from oral contraceptive pills (OCPs to an emerging role of obesity as a contributing factor. Methods. Publications reporting HCA in the United States were identified through a PubMed search and a review of the literature. We excluded publications prior to 1970, single case reports, and publications for which there was no data available regarding patient characteristics including OCP use and the number of adenomas. Conclusion. Whereas earlier reports of HCA in the United States described cases exclusively in women exposed to OCPs, there is a trend towards an increase in HCAs reported in men, HCAs in the absence of OCP use, and increased reporting of multiple HCAs. This may be a result of newer OCP formulations and increasing prevalence of obesity.

  3. 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.

  4. 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.

  5. Subtype-independent near full-length HIV-1 genome sequencing and assembly to be used in large molecular epidemiological studies and clinical management

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    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.

  6. 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...... Was differentiated into two lineages, Arctic 1 and Arctic 2, with good bootstrap Support. Arctic I is mainly comprised of Canadian isolates with a single fox isolate front Maine in the USA. Arctic 2 was further divided into sub-lineages: 2a/2b. Arctic 2a comprises isolates from the Arctic regions of Yakutia...

  7. The rate of molecular adaptation in a changing environment.

    Science.gov (United States)

    Lourenço, João M; Glémin, Sylvain; Galtier, Nicolas

    2013-06-01

    It is currently unclear whether the amino acid substitutions that occur during protein evolution are primarily driven by adaptation, or reflect the random accumulation of neutral changes. When estimated from genomic data, the proportion of adaptive amino acid substitutions, called α, was found to vary greatly across species, from nearly zero in humans to above 0.5 in Drosophila. These variations have been interpreted as reflecting differences in effective population size, adaptation being supposedly more efficient in large populations. Here, we investigate the influence of effective population size and other biological parameters on the rate of adaptive evolution by simulating the evolution of a coding sequence under Fisher's geometric formalism. We explicitly model recurrent environmental changes and the subsequent adaptive walks, followed by periods of stasis during which purifying selection dominates. We show that, under a variety of conditions, the effective population size has only a moderate influence on α, and an even weaker influence on the per generation rate of selective sweeps, modifying the prevalent view in current literature. The rate of environmental change and, interestingly, the dimensionality of the phenotypic space (organismal complexity) affect the adaptive rate more deeply than does the effective population size. We discuss the reasons why verbal arguments have been misleading on that subject and revisit the empirical evidence. Our results question the relevance of the "α" parameter as an indicator of the efficiency of molecular adaptation.

  8. 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.

  9. Extended-spectrum beta-lactamase-producing Klebsiella spp. in a neonatal intensive care unit: risk factors for the infection and the dynamics of the molecular epidemiology.

    Science.gov (United States)

    Kristóf, K; Szabó, D; Marsh, J W; Cser, V; Janik, L; Rozgonyi, F; Nobilis, A; Nagy, K; Paterson, D L

    2007-08-01

    The extended-spectrum beta-lactamase (ESBL)-producing Klebsiella spp. cause worldwide problems in intensive care units. The aim of this study was to investigate the molecular epidemiology of ESBL-producing Klebsiella pneumoniae and K. oxytoca strains in a neonatal intensive care unit (NICU) in Budapest, Hungary and to determine the risk factors of the infections and the epidemiological features. Infections with Klebsiella spp. were analyzed retrospectively by reviewing the medical records between January 2001 and December 2005. Antibiotic susceptibility tests, isoelectric focusing, pulsed field gel electrophoresis, plasmid analysis, PCR for bla(TEM) and bla(SHV) and DNA sequencing analysis were performed on ESBL-producing Klebsiella isolates. A total of 45 babies were found to be infected with non-ESBL-producing Klebsiella spp. and 39 with ESBL-producing Klebsiella spp. Of the parameters analyzed, including sex, gestational age, twin pregnancy, birth weight, presence of central vascular catheter, mechanical ventilator use, parenteral nutrition, polymicrobial infection, caesarean section, transfusion and mortality, we found no statistically significant difference between the ESBL and the non-ESBL groups, or between the K. pneumoniae and K. oxytoca species. Further characterization of the ESBL-producing K. pneumoniae and K. oxytoca strains isolated between February 2001 and January 2003 revealed three distinct PFGE patterns of SHV-5-producing K. pneumoniae (A, B, E) and two distinct patterns of SHV-12-producing K. oxytoca (C,D) isolates; these had different plasmid profiles. From July to November 2005, a new SHV-5 producing K. oxytoca (F) was isolated. The molecular epidemiology of ESBL-producing organisms in a NICU over time shows substantial shifts in predominant strains. The ESBL production of the infected organisms has an impact on the survival of newborn babies with infections caused by Klebsiella spp.

  10. 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.

  11. 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...

  12. Climate change and the molecular ecology of Arctic marine mammals.

    Science.gov (United States)

    O'Corry-Crowe, Gregory

    2008-03-01

    Key to predicting likely consequences of future climate change for Arctic marine mammals is developing a detailed understanding of how these species use their environment today and how they were affected by past climate-induced environmental change. Genetic analyses are uniquely placed to address these types of questions. Molecular genetic approaches are being used to determine distribution and migration patterns, dispersal and breeding behavior, population structure and abundance over time, and the effects of past and present climate change in Arctic marine mammals. A review of published studies revealed that population subdivision, dispersal, and gene flow in Arctic marine mammals was shaped primarily by evolutionary history, geography, sea ice, and philopatry to predictable, seasonally available resources. A meta-analysis of data from 38 study units across seven species found significant relationships between neutral genetic diversity and population size and climate region, revealing that small, isolated subarctic populations tend to harbor lower diversity than larger Arctic populations. A few small populations had substantially lower diversity than others. By contrast, other small populations retain substantial neutral diversity despite extensive population declines in the 19th and 20th centuries. The evolutionary and contemporary perspectives gained from these studies can be used to model the consequences of different climate projections for individual behavior and population structure and ultimately individual fitness and population viability. Future research should focus on: (1) the use of ancient-DNA techniques to directly reconstruct population histories through the analysis of historical and prehistorical material, (2) the use of genomic technologies to identify, map, and survey genes that directly influence fitness, (3) long-term studies to monitor populations and investigate evolution in contemporary time, (4) further Arctic-wide, multispecies analyses

  13. Predicting the effect of climate change on African trypanosomiasis: integrating epidemiology with parasite and vector biology

    NARCIS (Netherlands)

    Moore, S.; Shrestha, S.; Tomlinson, K.W.; Vuong, H.

    2012-01-01

    Climate warming over the next century is expected to have a large impact on the interactions between pathogens and their animal and human hosts. Vector-borne diseases are particularly sensitive to warming because temperature changes can alter vector development rates, shift their geographical distri

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. Changing epidemiology of group B streptococcal infections among adults in Iceland: 1975-2014.

    Science.gov (United States)

    Björnsdóttir, E S; Martins, E R; Erlendsdóttir, H; Haraldsson, G; Melo-Cristino, J; Kristinsson, K G; Ramirez, M

    2016-04-01

    We studied the bacterial characteristics and incidence of invasive infections caused by group B streptococci (GBS) in adults in Iceland in 1975-2014. A total of 145 isolates were characterized by serotyping, antimicrobial susceptibility, multilocus sequence typing and surface protein gene profiling. Disease incidence increased during the studied period (p <0.001), reaching 2.17 cases/100 000 person-years in 2013-14. Overall, serotype Ia was the most frequently found (23%), but serotypes Ib, II, III and V showed similar prevalence (14%-17%). Although there were notable changes in the proportion of most serotypes during the study period, only the decline of serotype III was statistically supported (p = 0.003) and was reflected in a decrease of clonal complexes CC17 and CC19 that included most serotype III isolates (p <0.04). On the other hand, the increase in frequency of CC1 was caused by two lineages expressing distinct serotypes: ST1/V/alp3 and ST196/IV/eps. Underlying the relative stability of serotype Ia were major changes in the lineages expressing this serotype, with an increase in the relative importance of CC23, including both ST23/Ia/eps and ST24/Ia/bca lineages, and a decrease in CC7. Nine cases of invasive GBS disease were caused by ST7, of possible zoonotic origin. All isolates were susceptible to penicillin. Rates of erythromycin and clindamycin resistance were 8.3% and 9.7%, respectively. An over-representation of resistance solely to clindamycin was associated with the unusual lsaC gene and serotype III ST19/rib lineage (p <0.001).

  19. Differences in epidemiological and molecular characteristics of nasal colonization with Staphylococcus aureus (MSSA-MRSA in children from a university hospital and day care centers.

    Directory of Open Access Journals (Sweden)

    Erika A Rodríguez

    Full Text Available BACKGROUND: Clinical significance of Staphylococcus aureus colonization has been demonstrated in hospital settings; however, studies in the community have shown contrasting results regarding the relevance of colonization in infection by community-associated MRSA (CA-MRSA. In Colombia there are few studies on S. aureus colonization. The aim of this study was to determine the molecular and epidemiological characteristics of nasal colonization by S. aureus (MSSA-MRSA in children from a university hospital and day care centers (DCCs of Medellin, Colombia. METHODS: An observational cross-sectional study was conducted in 400 children (200 in each setting, aged 0 months to 5 years, during 2011. Samples were collected from each nostril and epidemiological information was obtained from the parents. Genotypic analysis included spa typing, PFGE, MLST, SCCmec typing, detection of genes for virulence factors and agr groups. RESULTS: Frequency of S. aureus colonization was 39.8% (n = 159 (hospital 44.5% and DCCs 35.0% and by MRSA, 5.3% (n = 21 (hospital 7.0% and DCCs 3.5%. Most S. aureus colonized children were older than two years (p = 0.005, the majority of them boys (59.1%, shared a bedroom with a large number of people (p = 0.028, with history of β-Lactamase inhibitors usage (p = 0.020. MSSA strains presented the greatest genotypic diversity with 15 clonal complexes (CC. MRSA isolates presented 6 CC, most of them (47.6% belonged to CC8-SCCmec IVc and were genetically related to previously reported infectious MRSA strains. CONCLUSION: Differences in epidemiological and molecular characteristics between populations may be useful for the understanding of S. aureus nasal colonization dynamics and for the design of strategies to prevent S. aureus infection and dissemination. The finding of colonizing MRSA with similar molecular characteristics of those causing infection demonstrates the dissemination capacity of S. aureus and the risk of

  20. Epidemiología molecular de infecciones por micobacterias en pacientes del Hospital Regional 1° de Octubre

    OpenAIRE

    María del Rocío Thompson Bonilla; Gabina Calderón Rosete; Hayde Nallely Moreno Sandoval; José Luis Merino García; Manuel Lara Lozano; Celia Piña Leyva; Guillermina Rosas Sandoval; Sergio Israel Rangel Guerrero; Esmeralda Morán Mendoza; Jorge Rodríguez Gallegos; Juana Salazar Salinas; Ricardo Núñez Ceballos; Juan Antonio González Barrios

    2014-01-01

    En este trabajo se comentan varios aspectos acerca de la tuberculosis y se analizan los resultados de muestras remitidas por el Departamento de Epidemiología al Servicio de Medicina Genómica para integrar diagnósticos de probable infección por Mycobacterium tuberculosis. En el periodo comprendido de diciembre de 2012 a agosto de 2013, se analizaron 89 muestras de las cuales obtuvimos una identificación positiva en 24 de ellas, 22 fueron positivas a M. tuberculosis y 2 a M. abscessus. De acuer...

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. Molecular epidemiology of extended-spectrum beta-lactamases among Escherichia coli isolates collected in a Swedish hospital and its associated health care facilities from 2001 to 2006.

    Science.gov (United States)

    Fang, Hong; Ataker, Ferda; Hedin, Göran; Dornbusch, Kathrine

    2008-02-01

    The genetic characteristics and molecular epidemiology of extended-spectrum beta-lactamases (ESBLs) among Escherichia coli isolates were investigated at a general hospital and its associated health care facilities in Stockholm, Sweden, during the period from 2001 to 2006. Of 87 consecutive nonduplicate ESBL-positive isolates, 80 isolates encoded CTX-M-type ESBLs, 64 of which were group 1 enzymes. TEM-type and OXA-type beta-lactamases were encoded in 63 and 59% of the ESBL isolates, respectively. Pulsed-field gel electrophoresis (PFGE) analysis revealed 40 different pulsotypes, consisting of 11 clones accounting for 66% of all isolates, and 29 unique patterns. Moreover, of the 11 clones, clones 1 and 4 comprised half of the clonally related isolates (28 of 57). Clone 1 was a persistent endemic clone in the area throughout the years, and clone 4 emerged in 2003. However, in recent years, clone 1 isolates were no longer predominant and were gradually replaced by new emerging strains. Concerning beta-lactamase gene profiles in relation to PFGE pulsotypes, clone-related bla profiles were observed in certain clones, while in most cases different bla profiles could be observed in the same clone, and the same bla profile could be present in different clones. The molecular epidemiology of ESBL-positive E. coli in the area shows shifts in predominant strains and increased clonal diversity over time. The study also indicated that both clonal spread of epidemic strains and transfer of transposable genetic elements might contribute to the proliferation of ESBLs.

  7. 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.

  8. Molecular epidemiology and functional assessment of novel allelic variants of SLC26A4 in non-syndromic hearing loss patients with enlarged vestibular aqueduct in China.

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    Yongyi Yuan

    Full Text Available BACKGROUND: Mutations in SLC26A4, which encodes pendrin, are a common cause of deafness. SLC26A4 mutations are responsible for Pendred syndrome and non-syndromic enlarged vestibular aqueduct (EVA. The mutation spectrum of SLC26A4 varies widely among ethnic groups. To investigate the incidence of EVA in Chinese population and to provide appropriate genetic testing and counseling to patients with SLC26A4 variants, we conducted a large-scale molecular epidemiological survey of SLC26A4. METHODS: A total of 2352 unrelated non-syndromic hearing loss patients from 27 different regions of China were included. Hot spot regions of SLC26A4, exons 8, 10 and 19 were sequenced. For patients with one allelic variant in the hot spot regions, the other exons were sequenced one by one until two mutant alleles had been identified. Patients with SLC26A4 variants were then examined by temporal bone computed tomography scan for radiological diagnosis of EVA. Ten SLC26A4 variants were cloned for functional study. Confocal microscopy and radioisotope techniques were used to examine the membrane expression of pendrin and transporter function. RESULTS: Of the 86 types of variants found, 47 have never been reported. The ratio of EVA in the Chinese deaf population was at least 11%, and that in patients of Han ethnicity reached at least 13%. The mutational spectrum and mutation detection rate of SLC26A4 are distinct among both ethnicities and regions of Mainland China. Most of the variants caused retention of pendrin in the intracellular region. All the mutant pendrins showed significantly reduced transport capability. CONCLUSION: An overall description of the molecular epidemiological findings of SLC26A4 in China is provided. The functional assessment procedure can be applied to identification of pathogenicity of variants. These findings are valuable for genetic diagnosis, genetic counseling, prenatal testing and pre-implantation diagnosis in EVA families.

  9. 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.

  10. Molecular Epidemiology of Blastocystis sp. in Various Animal Groups from Two French Zoos and Evaluation of Potential Zoonotic Risk

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    Moriniere, Romain; Gantois, Nausicaa; Benamrouz-Vanneste, Sadia; Delgado-Viscogliosi, Pilar; Guyot, Karine; Li, Luen-Luen; Monchy, Sébastien; Noël, Christophe; Poirier, Philippe; Nourrisson, Céline; Wawrzyniak, Ivan; Delbac, Frédéric; Bosc, Stéphanie; Chabé, Magali; Petit, Thierry; Certad, Gabriela; Viscogliosi, Eric

    2017-01-01

    Blastocystis sp. is a common intestinal parasite infecting humans and a wide range of animals worldwide. It exhibits an extensive genetic diversity and 17 subtypes (STs) have thus far been identified in mammalian and avian hosts. Since several STs are common to humans and animals, it was proposed that a proportion of human infections may result from zoonotic transmission. However, the contribution of each animal source to human infection remains to be clarified. Therefore, the aim of this study was to expand our knowledge of the epidemiology and host specificity of this parasite by performing the largest epidemiological survey ever conducted in animal groups in terms of numbers of species screened. A total of 307 stool samples from 161 mammalian and non-mammalian species in two French zoos were screened by real-time PCR for the presence of Blastocystis sp. Overall, 32.2% of the animal samples and 37.9% of the species tested were shown to be infected with the parasite. A total of 111 animal Blastocystis sp. isolates were subtyped, and 11 of the 17 mammalian and avian STs as well as additional STs previously identified in reptiles and insects were found with a varying prevalence according to animal groups. These data were combined with those obtained from previous surveys to evaluate the potential risk of zoonotic transmission of Blastocystis sp. through the comparison of ST distribution between human and animal hosts. This suggests that non-human primates, artiodactyls and birds may serve as reservoirs for human infection, especially in animal handlers. In contrast, other mammals such as carnivores, and non-mammalian groups including reptiles and insects, do not seem to represent significant sources of Blastocystis sp. infection in humans. In further studies, more intensive sampling and screening of potential new animal hosts will reinforce these statements and expand our understanding of the circulation of Blastocystis sp. in animal and human populations. PMID

  11. 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.

  12. 10 years of prophylaxis with nebulized liposomal amphotericin B and the changing epidemiology of Aspergillus spp. infection in lung transplantation.

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    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.

  13. Molecular diagnostics: the changing culture of medical microbiology.

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    Bullman, Susan; Lucey, Brigid; Sleator, Roy D

    2012-01-01

    Diagnostic molecular biology is arguably the fastest growing area in current laboratory-based medicine. Growth of the so called 'omics' technologies has, over the last decade, led to a gradual migration away from the 'one test, one pathogen' paradigm, toward multiplex approaches to infectious disease diagnosis, which have led to significant improvements in clinical diagnostics and ultimately improved patient care.

  14. Structural changes in polytetrafluoroethylene molecular chains upon sliding against steel

    NARCIS (Netherlands)

    Shen, J.T.; Pei, Y.T.; Hosson, J.Th.M. De

    2014-01-01

    In this work, the influence of dry sliding between a steel counterpart ball and polytetrafluoroethylene (PTFE) plate sample on the transformation of PTFE molecular structure is investigated. With X-ray diffraction, differential scanning calorimetry, Fourier transform infrared (FT-IR) spectroscopy an

  15. Environmental surveillance and molecular epidemiology of waterborne pathogen Legionella pneumophila in health-care facilities of Northeastern Greece: a 4-year survey.

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    Alexandropoulou, Ioanna G; Ntougias, Spyridon; Konstantinidis, Theocharis G; Parasidis, Theodoros A; Panopoulou, Maria; Constantinidis, Theodoros C

    2015-05-01

    A 4-year proactive environmental surveillance of Legionella spp. in the water distribution and cooling systems of five health-care facilities was carried out as part of the strategy for the prevention of hospital-acquired Legionnaires' disease in Northeastern Greece. Legionella spp. were detected in 71 out of 458 collected samples. The majority of strains belonged to Legionella pneumophila serogroups 2-15 (75.0%), while all L. pneumophila serogroup 1 strains (23.6%) were isolated from a single hospital. The highest percentage of positive samples was found in distal sites (19.4%), while no Legionella strains were detected in cooling systems. Each hospital was colonized at least once with L. pneumophila, while remedial actions resulted in significant reduction of Legionella concentration. The molecular epidemiology of environmental L. pneumophila strains was also investigated using random amplified polymorphic DNA (RAPD) and multi-gene sequence-based analysis. Based on RAPD patterns, L. pneumophila serogroups 2-15 and serogroup 1 strains were classified into 24 and 9 operational taxonomic units (OTUs), respectively. Sequencing of housekeeping and diversifying pressure-related genes recommended by European Working Group for Legionella Infections (EWGLI) revealed not only a high intraspecies variability but also the circulation and persistence of one specific genotyping profile in the majority of hospitals. This study highlights the necessity for diachronic surveillance of Legionella in health-care facilities by adopting both cultural and molecular methods.

  16. 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.

  17. Tumor-based case-control studies of infection and cancer: muddling the when and where of molecular epidemiology.

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    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.

  18. Molecular epidemiology of Newcastle disease in Mexico and the potential spillover of viruses from poultry into wild bird species.

    Science.gov (United States)

    Cardenas Garcia, Stivalis; Navarro Lopez, Roberto; Morales, Romeo; Olvera, Miguel A; Marquez, Miguel A; Merino, Ruben; Miller, Patti J; Afonso, Claudio L

    2013-08-01

    Newcastle disease, one of the most important health problems that affects the poultry industry around the world, is caused by virulent strains of Newcastle disease virus. Newcastle disease virus is considered to be endemic in several countries in the Americas, including Mexico. In order to control Newcastle disease outbreaks and spread, intensive vaccination programs, which include vaccines formulated with strains isolated at least 60 years ago, have been established. These vaccines are dissimilar in genotype to the virulent Newcastle disease viruses that had been circulating in Mexico until 2008. Here, 28 isolates obtained between 2008 and 2011 from different regions of Mexico from free-living wild birds, captive wild birds, and poultry were phylogenetically and biologically characterized in order to study the recent epidemiology of Newcastle disease viruses in Mexico. Here we demonstrate that, until recently, virulent viruses from genotype V continued to circulate and evolve in the country. All of the Newcastle disease viruses of low virulence, mostly isolated from nonvaccinated free-living wild birds and captive wild birds, were highly similar to LaSota (genotype II) and PHY-LMV42 (genotype I) vaccine strains. These findings, together with the discovery of two virulent viruses at the Mexican zoo, suggest that Newcastle disease viruses may be escaping from poultry into the environment.

  19. Molecular epidemiology of Mycoplasma hyopneumoniae from outbreaks of enzootic pneumonia in domestic pig and the role of wild boar.

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    Kuhnert, Peter; Overesch, Gudrun

    2014-11-07

    Mycoplasma hyopneumoniae is the major cause of enzootic pneumonia (EP) in domestic pigs, a disease with low mortality but high morbidity, having a great economic impact for producers. In Switzerland EP has been successfully eradicated, however, sporadic outbreaks are observed with no obvious source. Besides the possibility of recurrent outbreaks due to persisting M. hyopneumoniae strains within the pig population, there is suspicion that wild boars might introduce M. hyopneumoniae into swine herds. To elucidate possible links between domestic pig and wild boar, epidemiological investigations of recent EP outbreaks were initiated and lung samples of pig and wild boar were tested for the presence of specific genotypes by multilocus sequence typing (MLST). Despite generally different genotypes in wild boar, outbreak strains could be found in geographically linked wild boar lungs after, but so far not before the outbreak. Recurrent outbreaks in a farm were due to the same strain, indicating unsuccessful sanitation rather than reintroduction by wild boar. In another case outbreaks in six different farms were caused by the same strain never found in wild boar, confirming spread between farms due to hypothesized animal transport. Results indicate the presence of identical lineages of wild boar and domestic pig strains, and possible transmission of M. hyopneumoniae between wild boar and pig. However, the role of wild boar might be rather one as a recipient than a transmitter. More important than contact to wild boar for sporadic outbreaks in Switzerland is apparently persistence of M. hyopneumoniae within a farm as well as transmission between farms.

  20. [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

  1. 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 H