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Sample records for bacterial community acquired

  1. Hydrocephalus in adults with community-acquired bacterial meningitis

    NARCIS (Netherlands)

    E. Soemirien Kasanmoentalib; M.C. Brouwer; A. van der Ende; D. van de Beek

    2010-01-01

    Objective: To evaluate the occurrence, treatment, and outcome of hydrocephalus complicating community-acquired bacterial meningitis in adults. Methods: Case series from a prospective nationwide cohort study from Dutch hospitals from 2006 to 2009. Results: Hydrocephalus was diagnosed in 26 of 577 epi

  2. Procalcitonin for detecting community-acquired bacterial pneumonia

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    Devi Gusmaiyanto

    2015-03-01

    Full Text Available Background Pneumonia is a major cause of morbidity and mortality in children under five years of age. Pneumonia can be of bacterial or viral origin. It is difficult to distinguish between these two agents based on clinical manifestations, as well as radiological and laboratory examinations. Furthermore, bacterial cultures take time to incubate and positive results may only be found in 10-30% of bacterial pneumonia cases. Procalcitonin has been used as a marker to distinguish etiologies, as bacterial infections tend to increase serum procalcitonin levels. Objective To determine the sensitivity, specificity, positive predictive value and negative predictive value of procalcitonin in community-acquired bacterial pneumonia. Method This cross-sectional study was conducted in the Pediatric Health Department of Dr. M. Djamil Hospital, Padang. Subjects were selected by consecutive sampling. Procalcitonin measurements and PCR screening were performed on blood specimens from 32 pneumonia patients and compared. Results Of the 32 subjects, most were boys (56.25%, under 5 years of age (99%, and had poor nutritional status (68.75%. Using a cut-off point of 0.25 ng/mL, procalcitonin level had a sensitivity of 92%, specificity 50%, positive predictive value 88%, and negative predictive value 60% for diagnosing bacterial pneumonia. Using a cut-off point of 0.5 ng/mL, procalcitonin level had a specificity of 46%, specificity 83%, positive predictive value 91%, and negative predictive value 25%. Conclusion A cut-off point of 0.25 ng/mL of procalcitonin level may be more useful to screen for bacterial pneumonia than a cut-off point of 0.5 ng / mL. However, if the 0.25 ng/mL cut-off point is used, careful monitoring will be required for negative results, as up to 40% may actually have bacterial pneumonia. [Paediatr Indones. 2015;55:65-9.].

  3. Procalcitonin for detecting community-acquired bacterial pneumonia

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    Devi Gusmaiyanto

    2016-06-01

    Full Text Available Background Pneumonia is a major cause of morbidity andmortality in children under five years of age. Pneumonia can be ofbacterial or viral origin. It is difficult to distinguish between thesetwo agents based on clinical manifestations, as well as radiologicaland laboratory examinations. Furthermore, bacterial cultures taketime to incubate and positive results may only be found in 10-30%of bacterial pneumonia cases. Procalcitonin has been used as amarker to distinguish etiologies, as bacterial infections tend toincrease serum procalcitonin levels.Objective To determine the sensitivity, specificity, positivepredictive value and negative predictive value of procalcitoninin community-acquired bacterial pneumonia.Method This cross-sectional study was conducted in thePediatric Health Department of Dr. M. Djamil Hospital, Padang.Subjects were selected by consecutive sampling. Procalcitoninmeasurements and PCR screening were performed on bloodspecimens from 32 pneumonia patients and compared.Results Of the 32 subjects, most were boys (56.25%, under 5years of age (99%, and had poor nutritional status (68.75%.Using a cut-off point of 0.25 ng/mL, procalcitonin level hada sensitivity of 92%, specificity 50%, positive predictive value 88%, and negative predictive value 60% for diagnosing bacterial pneumonia. Using a cut-off point of 0.5 ng/mL, procalcitonin level had a specificity of 46%, specificity 83%, positive predictive value 91%, and negative predictive value 25%.Conclusion A cut-off point of 0.25 ng/mL of procalcitonin level may be more useful to screen for bacterial pneumonia than a cutoff point of 0.5 ng / mL. However, if the 0.25 ng/mL cut-off point is used, careful monitoring will be required for negative results, as up to 40% may actually have bacterial pneumonia. [PaediatrIndones. 2015;55:65-9.].

  4. Community acquired urinary tract infection: etiology and bacterial susceptibility

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    Dias Neto José Anastácio

    2003-01-01

    Full Text Available PURPOSE: Urinary tract infections (UTI are one of the most common infectious diseases diagnosed. UTI account for a large proportion of antibacterial drug consumption and have large socio-economic impacts. Since the majority of the treatments begins or is done completely empirically, the knowledge of the organisms, their epidemiological characteristics and their antibacterial susceptibility that may vary with time is mandatory. OBJECTIVE: The aim of this study was to report the prevalence of uropathogens and their antibiotic susceptibility of the community acquired UTI diagnosed in our institution and to provide a national data. METHODS: We analyzed retrospectively the results of urine cultures of 402 patients that had community acquired urinary tract infection in the year of 2003. RESULTS: The mean age of the patients in this study was 45.34 ± 23.56 (SD years. There were 242 (60.2% females and 160 (39.8% males. The most commonly isolated organism was Escherichia coli (58%. Klebsiella sp. (8.4% and Enterococcus sp.(7.9% were reported as the next most common organisms. Of all bacteria isolated from community acquired UTI, only 37% were sensitive to ampicillin, 51% to cefalothin and 52% to trimethoprim/sulfamethoxazole. The highest levels of susceptibility were to imipenem (96%, ceftriaxone (90%, amikacin (90%, gentamicin (88%, levofloxacin (86%, ciprofloxacin (73%, nitrofurantoin (77% and norfloxacin (75%. CONCLUSION: Gram-negative agents are the most common cause of UTI. Fluoroquinolones remains the choice among the orally administered antibiotics, followed by nitrofurantoin, second and third generation cephalosporins. For severe disease that require parenteral antibiotics the choice should be aminoglycosides, third generation cephalosporins, fluoroquinolones or imipenem, which were the most effective.

  5. Surveillance of acute community acquired urinary tract bacterial infections

    Institute of Scientific and Technical Information of China (English)

    Sibanarayan Rath; Rabindra N. Padhy

    2015-01-01

    Objective: To record the antibiotic resistance of community acquired uropathogens over a period of 24 months (May 2011-April 2012). Methods: Urine samples from patients of outpatient department (OPD) were used for isolating urinary tract infection (UTI)-causing bacteria that were cultured on suitable selective media and identified by biochemical tests. Their antibiograms were ascertained by Kirby-Bauer’s disc diffusion method, using 17 antibiotics of 5 different classes. Results: From 2137 urine samples 1332 strains of pathogenic bacteria belonging to 11 species were isolated. Two Gram-positives, Staphylococcus aureus and Enterococcus faecalis and nine Gram-negatives, Acinetobacter baumannii, Citrobacter sp., Escherichia coli, Enterobacter aerogenes, Klebsiella oxytoca, Klebsiella pneumoniae, Proteus mirabilis, Proteus vulgaris and Pseudomonas aeruginosa were isolated. Both S. aureus and E. faecalis were vancomycin resistant, and resistant-strains of all pathogens increased in each 6-month period of study. Particularly, all Gram-negatives were resistant to nitrofurantoin and co-trimoxazole, the most preferred antibiotics of empiric therapy for UTI, but were moderately resistant to gentamicin, ampicillin, amoxyclav, ofloxacin and gatifloxacin. Most Gram-negatives produced extended spectrum β-lactamase. Conclusions: It was concluded that periodic surveillance of pathogens is an essential corollary in effective health management in any country, as empiric therapy is a common/essential practice in effective clinical management.

  6. Procalcitonin for detecting community-acquired bacterial pneumonia

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    Devi Gusmaiyanto; Finny Fitry Yani; Efrida Efrida; Rizanda Machmud

    2016-01-01

    Background Pneumonia is a major cause of morbidity andmortality in children under five years of age. Pneumonia can be ofbacterial or viral origin. It is difficult to distinguish between thesetwo agents based on clinical manifestations, as well as radiologicaland laboratory examinations. Furthermore, bacterial cultures taketime to incubate and positive results may only be found in 10-30%of bacterial pneumonia cases. Procalcitonin has been used as amarker to distinguish etiologies, as bacterial...

  7. Risk factors for community-acquired bacterial meningitis in adults

    NARCIS (Netherlands)

    K.S. Adriani

    2015-01-01

    Bacterial meningitis is an inflammation of the meninges and occurs when bacteria invade the subarachnoid space. The meninges are the protective membranes that surround the brain and the spinal cord. Bacterial meningitis is a life-threatening disease because the proximity of the infection to the brai

  8. Dexamethasone in adults with community-acquired bacterial meningitis

    NARCIS (Netherlands)

    D. van de Beek; J. de Gans

    2006-01-01

    Bacterial meningitis in adults is a severe disease with high fatality and morbidity rates. Experimental studies have shown that the inflammatory response in the subarachnoid space is associated with an unfavourable outcome. In these experiments, corticosteroids, and in particular dexamethasone, were

  9. Arthritis in adults with community-acquired bacterial meningitis: a prospective cohort study

    NARCIS (Netherlands)

    M. Weisfelt; D. van de Beek; L. Spanjaard; J. de Gans

    2006-01-01

    Background: Although the coexistence of bacterial meningitis and arthritis has been noted in several studies, it remains unclear how often both conditions occur simultaneously. Methods: We evaluated the presence of arthritis in a prospective nationwide cohort of 696 episodes of community-acquired ba

  10. Bedside Evaluation of Cerebral Energy Metabolism in Severe Community-Acquired Bacterial Meningitis

    DEFF Research Database (Denmark)

    Rom Poulsen, Frantz; Schulz, Mette; Jacobsen, Anne;

    2015-01-01

    BACKGROUND: Mortality and morbidity have remained high in bacterial meningitis. Impairment of cerebral energy metabolism probably contributes to unfavorable outcome. Intracerebral microdialysis is routinely used to monitor cerebral energy metabolism, and recent experimental studies indicate...... that this technique may separate ischemia and non-ischemic mitochondrial dysfunction. The present study is a retrospective interpretation of biochemical data obtained in a series of patients with severe community-acquired meningitis. METHODS: Cerebral energy metabolism was monitored in 15 patients with severe...... community-acquired meningitis utilizing intracerebral microdialysis and bedside biochemical analysis. According to previous studies, cerebral ischemia was defined as lactate/pyruvate (LP) ratio >30 with intracerebral pyruvate level

  11. Hydrocephalus is a rare outcome in community-acquired bacterial meningitis in adults

    DEFF Research Database (Denmark)

    Bodilsen, Jacob; Schønheyder, Henrik Carl; Nielsen, Henrik I

    2013-01-01

    BACKGROUND: Community-acquired bacterial meningitis (CABM) continues to have a high mortality rate and often results in severe sequelae among survivors. Lately, an increased effort has been focused on describing the neurological complications of meningitis including hydrocephalus. To aid in this ......BACKGROUND: Community-acquired bacterial meningitis (CABM) continues to have a high mortality rate and often results in severe sequelae among survivors. Lately, an increased effort has been focused on describing the neurological complications of meningitis including hydrocephalus. To aid...... in this field of research we set out to ascertain the risk and outcome of hydrocephalus in patients with community-acquired bacterial meningitis (CABM) in North Denmark Region. METHODS: We conducted a retrospective population-based cohort study of CABM cases above 14 years of age. Cases diagnosed during a 13......-year period, 1998 through 2010, were identified in a laboratory register and data were acquired through patient records. Cases not confirmed by culture met other strict inclusion criteria. The diagnosis of hydrocephalus relied upon the radiologists' reports on cranial imaging. Outcome was graded...

  12. Cytokines and Chemokines as Biomarkers of Community-Acquired Bacterial Infection

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    Michal Holub

    2013-01-01

    Full Text Available Routinely used biomarkers of bacterial etiology of infection, such as C-reactive protein and procalcitonin, have limited usefulness for evaluation of infections since their expression is enhanced by a number of different conditions. Therefore, several inflammatory cytokines and chemokines were analyzed with sera from patients hospitalized for moderate bacterial and viral infectious diseases. In total, 57 subjects were enrolled: 21 patients with community-acquired bacterial infections, 26 patients with viral infections, and 10 healthy subjects (control cohorts. The laboratory analyses were performed using Luminex technology, and the following molecules were examined: IL-1Ra, IL-2, IL-4, IL-6, IL-8, TNF-α, INF-γ, MIP-1β, and MCP-1. Bacterial etiology of infection was associated with significantly (P<0.001 elevated serum concentrations of IL-1Ra, IL-2, IL-6, and TNF-α in comparison to levels observed in the sera of patients with viral infections. In the patients with bacterial infections, IL-1Ra and IL-8 demonstrated positive correlation with C-reactive protein, whereas, IL-1Ra, TNF-α, and MCP-1 correlated with procalcitonin. Furthermore, elevated levels of IL-1Ra, IL-6, and TNF-α decreased within 3 days of antibiotic therapy to levels observed in control subjects. The results show IL-1Ra as a potential useful biomarker of community-acquired bacterial infection.

  13. Focal parenchymal lesions in community-acquired bacterial meningitis in adults: a clinico-radiological study

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    Katchanov, Juri [Campus Charite Mitte, Charite, Department of Neurology, Berlin (Germany); University Hospital Charite, Campus Benjamin Franklin, Department of Neurology, Berlin (Germany); Siebert, Eberhard; Klingebiel, Randolf [Campus Charite Mitte, Charite, Department of Neuroradiology, Berlin (Germany); Endres, Matthias [Campus Charite Mitte, Charite, Department of Neurology, Berlin (Germany); Charite-Universitaetsmedizin Berlin, Center for Stroke Research Berlin, Berlin (Germany)

    2009-11-15

    Here, we analyzed the frequency, morphological pattern, and imaging characteristics of focal lesions as a consequence of community-acquired bacterial meningitis. We hypothesized that diffusion-weighted imaging combined with contrast-enhanced imaging, serial scanning, and multimodal vascular studies would provide further insight into the pathological basis of such parenchymal lesions in bacterial meningitis. We reviewed clinical and imaging data (i.e., magnetic resonance tomography, magnetic resonance angiography, computed tomography angiography, digital subtraction angiography) of 68 adult patients admitted to our neurological intensive care unit between March 1998 and February 2009 with the diagnosis of community-acquired bacterial meningitis. We identified seven patients with parenchymal lesions. These lesions could be attributed to four morphological patterns: (1) territorial cerebral ischemia, (2) perforating vessels ischemia, (3) ischemia of presumed cardiac origin, and (4) isolated cortical lesions. Whereas the patterns (1) and (2) were associated with vasculopathy of large- and medium-sized vessels (as shown by cerebral vascular imaging), vessel imaging in (3) and (4) did not show abnormal findings. Our study implies that parenchymal lesions in acute bacterial meningitis are mainly ischemic and due to involvement of large-, medium-, and small-sized arteries of the brain. Diffusion-weighted imaging combined with conventional, CT-, or MR-based cerebral angiography revealed the underlying pathophysiological mechanisms in the majority of patients. Furthermore, we detected two patients with isolated bilateral cortical involvement and normal vessel imaging. These lesions might represent ischemia due to the involvement of small pial and intracortical arteries. (orig.)

  14. Inflammatory response in mixed viral-bacterial community-acquired pneumonia

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    2014-01-01

    Background The role of mixed pneumonia (virus + bacteria) in community-acquired pneumonia (CAP) has been described in recent years. However, it is not known whether the systemic inflammatory profile is different compared to monomicrobial CAP. We wanted to investigate this profile of mixed viral-bacterial infection and to compare it to monomicrobial bacterial or viral CAP. Methods We measured baseline serum procalcitonin (PCT), C reactive protein (CRP), and white blood cell (WBC) count in 171 patients with CAP with definite etiology admitted to a tertiary hospital: 59 (34.5%) bacterial, 66 (39.%) viral and 46 (27%) mixed (viral-bacterial). Results Serum PCT levels were higher in mixed and bacterial CAP compared to viral CAP. CRP levels were higher in mixed CAP compared to the other groups. CRP was independently associated with mixed CAP. CRP levels below 26 mg/dL were indicative of an etiology other than mixed in 83% of cases, but the positive predictive value was 45%. PCT levels over 2.10 ng/mL had a positive predictive value for bacterial-involved CAP versus viral CAP of 78%, but the negative predictive value was 48%. Conclusions Mixed CAP has a different inflammatory pattern compared to bacterial or viral CAP. High CRP levels may be useful for clinicians to suspect mixed CAP. PMID:25073709

  15. Differentiation of bacterial and non-bacterial community-acquired pneumonia by thin-section computed tomography

    International Nuclear Information System (INIS)

    Background and objective: The management of community-acquired pneumonia (CAP) depends, in part, on the identification of the causative agents. The objective of this study was to determine the potential of thin-section computed tomography (CT) in differentiating bacterial and non-bacterial pneumonia. Patients and methods: Thin-section CT studies were prospectively examined in hospitalized CAP patients within 2 days of admission, followed by retrospective assessment by two pulmonary radiologists. Thin-section CT findings on the pneumonias caused by each pathogen were examined, and two types of pneumonias were compared. Using multivariate logistic regression analyses, receiver operating characteristic (ROC) curves were produced. Results: Among 183 CAP episodes (181 patients, 125 men and 56 women, mean age ± S.D.: 61.1 ± 19.7) examined by thin-section CT, the etiologies of 125 were confirmed (94 bacterial pneumonia and 31 non-bacterial pneumonia). Centrilobular nodules were specific for non-bacterial pneumonia and airspace nodules were specific for bacterial pneumonia (specificities of 89% and 94%, respectively) when located in the outer lung areas. When centrilobular nodules were the principal finding, they were specific but lacked sensitivity for non-bacterial pneumonia (specificity 98% and sensitivity 23%). To distinguish the two types of pneumonias, centrilobular nodules, airspace nodules and lobular shadows were found to be important by multivariate analyses. ROC curve analysis discriminated bacterial pneumonia from non-bacterial pneumonia among patients without underlying lung diseases, yielding an optimal point with sensitivity and specificity of 86% and 79%, respectively, but was less effective when all patients were analyzed together (70% and 84%, respectively). Conclusion: Thin-section CT examination was applied for the differentiation of bacterial and non-bacterial pneumonias. Though showing some potential, this examination at the present time would not

  16. CSF lactate for accurate diagnosis of community-acquired bacterial meningitis.

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    Giulieri, S; Chapuis-Taillard, C; Jaton, K; Cometta, A; Chuard, C; Hugli, O; Du Pasquier, R; Bille, J; Meylan, P; Manuel, O; Marchetti, O

    2015-10-01

    CSF lactate measurement is recommended when nosocomial meningitis is suspected, but its value in community-acquired bacterial meningitis is controversial. We evaluated the diagnostic performance of lactate and other CSF parameters in a prospective cohort of adult patients with acute meningitis. Diagnostic accuracy of lactate and other CSF parameters in patients with microbiologically documented episodes was assessed by receiver operating characteristic (ROC) curves. The cut-offs with the best diagnostic performance were determined. Forty-five of 61 patients (74%) had a documented bacterial (n = 18; S. pneumoniae, 11; N. meningitidis, 5; other, 2) or viral (n = 27 enterovirus, 21; VZV, 3; other, 3) etiology. CSF parameters were significantly different in bacterial vs. viral meningitis, respectively (p viral meningitis, with a cutoff set at 3.5 mmol/l providing 100% sensitivity, specificity, PPV, NPV, and efficiency. CSF lactate had the best accuracy for discriminating bacterial from viral meningitis and should be included in the initial diagnostic workup of this condition.

  17. Value of rapid aetiological diagnosis in optimization of antimicrobial treatment in bacterial community acquired pneumonia.

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    Mareković, Ivana; Plecko, Vanda; Boras, Zagorka; Pavlović, Ladislav; Budimir, Ana; Bosnjak, Zrinka; Puretić, Hrvoje; Zele-Starcević, Lidija; Kalenić, Smilja

    2012-06-01

    In 80 adult patients with community acquired pneumonia (CAP) conventional microbiological methods, polymerase chain reaction (PCR) and serum C-reactive protein (CRP) levels were performed and the appropriateness of the empirical antimicrobial treatment was evaluated according to bacterial pathogen detected. The aetiology was determined in 42 (52.5%) patients, with Streptococcus pneumoniae as the most common pathogen. PCR applied to bronchoalveolar lavage (BAL) provided 2 and PCR on sputum samples 1 additional aetiological diagnosis of CAP The mean CRP values in the S. pneumoniae group were not significantly higher than in the group with other aetiological diagnoses (166.89 mg/L vs. 160.11 mg/L, p = 0.457). In 23.8% (10/42) of patients with determined aetiology, the empirical antimicrobial treatment was inappropriate. PCR tests need further investigation, particularly those for the atypical pathogens, as they are predominant in inappropriately treated patients. Our results do not support the use of CRP as a rapid test to guide the antimicrobial treatment in patients with CAP. PMID:22856222

  18. Clinical evaluation of the role of ceftaroline in the management of community acquired bacterial pneumonia

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    Maselli DJ

    2012-02-01

    Full Text Available Diego J Maselli1, Juan F Fernandez1, Christine Y Whong2, Kelly Echevarria1,3, Anoop M Nambiar1,3, Antonio Anzueto1,3, Marcos I Restrepo1,3,41University of Texas Health Science Center, San Antonio, Texas, 2Memorial Hermann – Texas Medical Center, Houston, TX, 3South Texas Veterans Health Care System Audie l Murphy Division, San Antonio, TX, 4Veterans Evidence Research Dissemination and Implementation Center (VERDICT, San Antonio, TX, USAAbstract: Ceftaroline fosamil (ceftaroline was recently approved for the treatment of community-acquired pneumonia (CAP and complicated skin infections. This newly developed cephalosporin possesses a broad spectrum of activity against gram-positive and gram-negative bacteria. Most importantly, ceftaroline demonstrates potent in vitro antimicrobial activity against multi-drug resistant Streptococcus pneumoniae and methicillin-resistant strains of Staphylococcus aureus. In two Phase III, double-blinded, randomized, prospective trials (FOCUS 1 and FOCUS 2, ceftaroline was shown to be non-inferior to ceftriaxone for the treatment of CAP in hospitalized patients. Ceftaroline exhibits low resistance rates and a safety profile similar to that of other cephalosporins. In this review, we will evaluate the pharmacological characteristics, safety, antimicrobial properties, and efficacy of ceftaroline and its applications in the treatment of CAP.Keywords: s. pneumoniae, s. aureus, cephalosporins, pneumonia, ceftaroline, community acquired pneumonia

  19. Clinical evaluation of the role of ceftaroline in the management of community acquired bacterial pneumonia

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    Maselli, Diego J; Fernandez, Juan F; Whong, Christine Y; Echevarria, Kelly; Nambiar, Anoop M; Anzueto, Antonio; Restrepo, Marcos I

    2012-01-01

    Ceftaroline fosamil (ceftaroline) was recently approved for the treatment of community- acquired pneumonia (CAP) and complicated skin infections. This newly developed cephalosporin possesses a broad spectrum of activity against gram-positive and gram-negative bacteria. Most importantly, ceftaroline demonstrates potent in vitro antimicrobial activity against multi-drug resistant Streptococcus pneumoniae and methicillin-resistant strains of Staphylococcus aureus. In two Phase III, double-blinded, randomized, prospective trials (FOCUS 1 and FOCUS 2), ceftaroline was shown to be non-inferior to ceftriaxone for the treatment of CAP in hospitalized patients. Ceftaroline exhibits low resistance rates and a safety profile similar to that of other cephalosporins. In this review, we will evaluate the pharmacological characteristics, safety, antimicrobial properties, and efficacy of ceftaroline and its applications in the treatment of CAP. PMID:22355258

  20. Bacterial Etiology and Antibiotic Resistance Profile of Community-Acquired Urinary Tract Infections in a Cameroonian City

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    Gonsu, Hortense Kamga; Koulla-Shiro, Sinata

    2016-01-01

    Introduction. Community-acquired urinary tract infections (CAUTIs) are usually treated empirically. Geographical variations in etiologic agents and their antibiotic sensitivity patterns are common. Knowledge of antibiotic resistance trends is important for improving evidence-based recommendations for empirical treatment of UTIs. Our aim was to determine the major bacterial etiologies of CAUTIs and their antibiotic resistance patterns in a cosmopolitan area of Cameroon for comparison with prescription practices of local physicians. Methods. We performed a cross-sectional descriptive study at two main hospitals in Yaoundé, collecting a clean-catch mid-stream urine sample from 92 patients having a clinical diagnosis of UTI. The empirical antibiotherapy was noted, and identification of bacterial species was done on CLED agar; antibiotic susceptibility testing was performed using the Kirby-Bauer disc diffusion method. Results. A total of 55 patients had samples positive for a UTI. Ciprofloxacin and amoxicillin/clavulanic acid were the most empirically prescribed antibiotics (30.9% and 23.6%, resp.); bacterial isolates showed high prevalence of resistance to both compounds. Escherichia coli (50.9%) was the most common pathogen, followed by Klebsiella pneumoniae (16.4%). Prevalence of resistance for ciprofloxacin was higher compared to newer quinolones. Conclusions. E. coli and K. pneumoniae were the predominant bacterial etiologies; the prevalence of resistance to commonly prescribed antibiotics was high. PMID:27667998

  1. Bacterial Etiology and Antibiotic Resistance Profile of Community-Acquired Urinary Tract Infections in a Cameroonian City.

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    Nzalie, Rolf Nyah-Tuku; Gonsu, Hortense Kamga; Koulla-Shiro, Sinata

    2016-01-01

    Introduction. Community-acquired urinary tract infections (CAUTIs) are usually treated empirically. Geographical variations in etiologic agents and their antibiotic sensitivity patterns are common. Knowledge of antibiotic resistance trends is important for improving evidence-based recommendations for empirical treatment of UTIs. Our aim was to determine the major bacterial etiologies of CAUTIs and their antibiotic resistance patterns in a cosmopolitan area of Cameroon for comparison with prescription practices of local physicians. Methods. We performed a cross-sectional descriptive study at two main hospitals in Yaoundé, collecting a clean-catch mid-stream urine sample from 92 patients having a clinical diagnosis of UTI. The empirical antibiotherapy was noted, and identification of bacterial species was done on CLED agar; antibiotic susceptibility testing was performed using the Kirby-Bauer disc diffusion method. Results. A total of 55 patients had samples positive for a UTI. Ciprofloxacin and amoxicillin/clavulanic acid were the most empirically prescribed antibiotics (30.9% and 23.6%, resp.); bacterial isolates showed high prevalence of resistance to both compounds. Escherichia coli (50.9%) was the most common pathogen, followed by Klebsiella pneumoniae (16.4%). Prevalence of resistance for ciprofloxacin was higher compared to newer quinolones. Conclusions. E. coli and K. pneumoniae were the predominant bacterial etiologies; the prevalence of resistance to commonly prescribed antibiotics was high. PMID:27667998

  2. [Community-acquired bacterial septic arthritis in adults: diagnosis and treatment].

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    Kohlprath, R; Uçkay, I; Cuerel, C; Al-Mayahi M; Fleury, T Rod; Suva, D; Miozzari, H H

    2015-04-15

    The diagnosis of acute native joint bacterial infection can be difficult, because of its non- specific clinical and biological manifestation. Its management is often an emergency. Following a joint puncture, early joint lavage is performed, either by surgical drainage or by repeated arthrocentesis; and accompanied by systemic antibiotics, of which the ideal duration and route of administration remains unknown. The postoperative care is characterized by joint mobilization to avoid joint stiffening.

  3. Focus on JNJ-Q2, a novel fluoroquinolone, for the management of community-acquired bacterial pneumonia and acute bacterial skin and skin structure infections.

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    Jones, Travis M; Johnson, Steven W; DiMondi, V Paul; Wilson, Dustin T

    2016-01-01

    JNJ-Q2 is a novel, fifth-generation fluoroquinolone that has excellent in vitro and in vivo activity against a variety of Gram-positive and Gram-negative organisms. In vitro studies indicate that JNJ-Q2 has potent activity against pathogens responsible for acute bacterial skin and skin structure infections (ABSSSI) and community-acquired bacterial pneumonia (CABP), such as Staphylococcus aureus and Streptococcus pneumoniae. JNJ-Q2 also has been shown to have a higher barrier to resistance compared to other agents in the class and it remains highly active against drug-resistant organisms, including methicillin-resistant S. aureus, ciprofloxacin-resistant methicillin-resistant S. aureus, and drug-resistant S. pneumoniae. In two Phase II studies, the efficacy of JNJ-Q2 was comparable to linezolid for ABSSSI and moxifloxacin for CABP. Furthermore, JNJ-Q2 was well tolerated, with adverse event rates similar to or less than other fluoroquinolones. With an expanded spectrum of activity and low potential for resistance, JNJ-Q2 shows promise as an effective treatment option for ABSSSI and CABP. Considering its early stage of development, the definitive role of JNJ-Q2 against these infections and its safety profile will be determined in future Phase III studies. PMID:27354817

  4. Focus on JNJ-Q2, a novel fluoroquinolone, for the management of community-acquired bacterial pneumonia and acute bacterial skin and skin structure infections

    Directory of Open Access Journals (Sweden)

    Jones TM

    2016-06-01

    Full Text Available Travis M Jones,1,2 Steven W Johnson,1,3 V Paul DiMondi,1,4 Dustin T Wilson,1,2 1Department of Pharmacy Practice, College of Pharmacy and Health Sciences, Campbell University, Buies Creek, 2Department of Pharmacy, Duke University Hospital, Durham, 3Department of Pharmacy, Forsyth Medical Center, Novant Health, Winston-Salem, 4Department of Pharmacy, Durham VA Medical Center, Durham, NC, USA Abstract: JNJ-Q2 is a novel, fifth-generation fluoroquinolone that has excellent in vitro and in vivo activity against a variety of Gram-positive and Gram-negative organisms. In vitro studies indicate that JNJ-Q2 has potent activity against pathogens responsible for acute bacterial skin and skin structure infections (ABSSSI and community-acquired bacterial pneumonia (CABP, such as Staphylococcus aureus and Streptococcus pneumoniae. JNJ-Q2 also has been shown to have a higher barrier to resistance compared to other agents in the class and it remains highly active against drug-resistant organisms, including methicillin-resistant S. aureus, ciprofloxacin-resistant methicillin-resistant S. aureus, and drug-resistant S. pneumoniae. In two Phase II studies, the efficacy of JNJ-Q2 was comparable to linezolid for ABSSSI and moxifloxacin for CABP. Furthermore, JNJ-Q2 was well tolerated, with adverse event rates similar to or less than other fluoroquinolones. With an expanded spectrum of activity and low potential for resistance, JNJ-Q2 shows promise as an effective treatment option for ABSSSI and CABP. Considering its early stage of development, the definitive role of JNJ-Q2 against these infections and its safety profile will be determined in future Phase III studies. Keywords: JNJ-Q2, fluoroquinolone, ABSSSI, CABP, MRSA

  5. Clinical, Paraclinical, and Antimicrobial Resistance Features of Community-Acquired Acute Bacterial Meningitis at a Large Infectious Diseases Ward in Tehran, Iran.

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    Heydari, Behrooz; Khalili, Hossein; Karimzadeh, Iman; Emadi-Kochak, Hamid

    2016-01-01

    In this study demographic, clinical, paraclinical, microbiological, and therapeutic features of patients with community-acquired acute bacterial meningitis admitted to a referral center for infectious diseases in Iran, have been evaluated. Medical records of adult (> 18 years) individuals with confirmed diagnosis of community-acquired bacterial meningitis during a 4-year period were retrospectively reviewed. All required data were obtained from patients' medical charts. Available findings about antimicrobial susceptibility of isolated bacteria from CSF and/or blood were also collected. Kirby-Bauer disc diffusion method was used to determine their antimicrobial susceptibility profile. Details of medical management including antibiotic regimen, duration, patients' outcome, and possible sequelae of meningitis were recorded. The most commonly isolated microorganism from CSF or blood of patients was Streptococcus pneumonia (33.33%) followed by Neisseria meningitidis (27.78%) and Haemophilus influenza (16.67%). The most common antimicrobial regimen was ceftriaxone plus vancomycin (69.44%) followed by ceftriaxone plus vancomycin plus ampicillin (11.11%). Neurological sequelae of meningitis including cranial nerve palsy, deafness, and hemiparesis were identified in 4 (11.11%), 2 (5.56%), and 1 (2.78%) subjects, respectively. Regarding mortality, only 3 (8.33%) patients died from bacterial meningitis and the remaining 33 individuals discharged from the hospital. In conclusion, findings of the current study demonstrated that the mean incidence of acute bacterial meningitis in a referral infectious diseases ward in Iran was 9 episodes per year. The majority cases of community-acquired acute bacterial meningitis admitted to our center had negative CSF culture and classic triad of meningitis was absent in them. PMID:27610176

  6. The clinical utility of induced sputum for the diagnosis of bacterial community-acquired pneumonia in HIV-infected patients: a prospective cross-sectional study

    Directory of Open Access Journals (Sweden)

    Rosemeri Maurici da Silva

    2006-04-01

    Full Text Available BACKGROUND: Bacterial pneumonias have been overcoming pneumocytosis in frequency. Controversy still remains about how to manage immunocompromised patients and those with lung diseases. Sputum analysis is a noninvasive and simple method, and when interpreted according to specific criteria it may help with diagnosis. We conducted a study to evaluate sensitivity, specificity, positive and negative predicted values, and the accuracy of induced sputum (IS for bacterial community-acquired pneumonia diagnosis in HIV-positive patients. MATERIAL AND METHODS: This cross sectional study evaluated a diagnostic procedure in a reference hospital for HIV patients in Florianópolis, SC, Brazil. From January 1, 2001 to September 30, 2002, 547 HIV-positive patients were analyzed and 54 inpatients with pulmonary infection were selected. Bronchoalveolar lavage (BAL and transbronchial lung biopsy (TBLB were considered the gold standards. Gram stains and quantitative cultures of IS and BAL were obtained. The cut-offs for quantitative cultures were 10(6 CFU/mL for IS and 10(4 CFU/mL for BAL. RESULTS: The mean age was 35.7 years, 79.6% were males and 85.2% were caucasians. The mean lymphocyte count was 124.8/mm³. Bacterial pneumonia was diagnosed in 20 patients. The most prevalent bacteria was Streptococcus pneumoniae. Considering IS for the diagnosis of bacterial pneumonia, sensitivity was 60%, specificity 40%, the positive predictive value was 80%, negative predictive value 20% and accuracy 56%. CONCLUSION: IS with quantitative culture can be helpful for the diagnosis of bacterial pneumonia in HIV-positive patients.

  7. Etiology and antibiotic susceptibility of bacterial pathogens responsible for community-acquired urinary tract infections in Poland.

    Science.gov (United States)

    Stefaniuk, E; Suchocka, U; Bosacka, K; Hryniewicz, W

    2016-08-01

    Urinary tract infections (UTIs) are some of the most common infections in both community and hospital settings infections. With their high rate of incidence, recurrence, complications, diverse etiologic agents, as well as growing antibiotic resistance, UTIs have proven to be a serious challenge for medical professionals. The aim of this study was to obtain data on the susceptibility patterns of pathogens responsible for UTIs in Poland to currently used antibiotics. A total of 396 bacterial isolates were collected between March and May 2013 from 41 centers in all regions of Poland. The majority of isolates were from adult patients (96.2 %); 144 (37.8 %) patients were diagnosed with uncomplicated UTI, while the remaining 237 (62.2 %) had a complicated infection. The most prevalent pathogen was Escherichia coli (71.4 %), followed by Klebsiella spp. (10.8 %) and the Proteae group (7.6 %). Escherichia coli was responsible for 80.6 % of cases of uncomplicated and 65.8 % of complicated infections. Only 65.8 % of E. coli isolates were susceptible to ciprofloxacin (uncomplicated 75.9 %, complicated 58.3 %), 64.0 % to nitrofurantoin (67.2 %, 62.8 %), 65.1 % to trimethoprim/sulfamethoxazole (68.1 %, 62.8 %), and 66.4 % to fosfomycin (77.6 %, 62.2 %). Among E. coli isolates from all UTIs, only 43.4 % were susceptible to ampicillin, with 47.4 % from uncomplicated compared with 40.4 % from complicated infections; 88.2 % to amoxicillin/clavulanic acid (91.4 % vs. 85.9 % complicated); 90.1 % to cefuroxime (93.1 %, 87.8 %); and 94.1 % to cefotaxime (98.2 %, 91.0 %). Thirty-five strains (10.4 %) were capable of producing extended-spectrum β-lactamases (ESBLs). This study demonstrates an increase in multidrug-resistant strains, especially among the leading pathogens associated with UTIs, including E. coli, Klebsiella spp., and Proteus spp. PMID:27189078

  8. Detection of respiratory viral and bacterial pathogens causing pediatric community-acquired pneumonia in Beijing using real-time PCR

    Institute of Scientific and Technical Information of China (English)

    Tie-Gang Zhang; Ai-Hua Li; Min Lyu; Meng Chen; Fang Huang; Jiang Wu

    2015-01-01

    Objective: The aim of this study was to determine the etiology and prevalence of pediatric CAP in Beijing using a real-time polymerase chain reaction (PCR) technique. Methods: Between February 15, 2011 and January 18, 2012, 371 pediatric patients with CAP were enrolled at Beijing Children's Hospital. Sixteen respiratory viruses and two bacteria were detected from tracheal aspirate specimens using commercially available multiplex real-time reverse transcription PCR (RT-PCR) kits. Results: A single viral pathogen was detected in 35.3%of enrolled patients, multiple viruses in 11.6%, and virus/bacteria co-infection in 17.8%. In contrast, only 6.5%of patients had a single bacterial pathogen and 2.2%were infected with multiple bacteria. The etiological agent was unknown for 26.7% of patients. The most common viruses were respiratory syncytial virus (RSV) (43.9%), rhinovirus (14.8%), parainfluenza virus (9.4%), and adenovirus (8.6%). In patients under three years of age, RSV (44.6%), rhinovirus (12.8%), and Streptococcus pneumoniae (9.9%) were the most frequent pathogens. In children aged 3e7 years, S. pneumoniae (38.9%), RSV (30.6%), Haemophilus influenzae (19.4%), and adenovirus (19.4%) were most prevalent. Finally in children over seven years, RSV (47.3%), S. pneumoniae (41.9%), and rhinovirus (21.5%) infections were most frequent. Conclusions: Viral pathogens, specifically RSV, were responsible for the majority of CAP in pediatric patients. However, both S. pneumoniae and H. influenzae contributed as major causes of disease. Commercially available multiplexing real-time PCR allowed for rapid detection of the etiological agent. Copyright © 2015, Chinese Medical Association Production. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

  9. Pneumonia acquired in the Community

    Directory of Open Access Journals (Sweden)

    María Caridad Fragoso Marchante

    2007-06-01

    Full Text Available A bibliographical revision of the main aspects in the diagnosis and treatment of the patients suffering from pneumonia acquired in the community is carried out. Microorganisms responsible for this type of pneumonia are mention in this paper as well as the available diagnostic methods for germs isolation. Different guidelines for diagnosis and treatment of this disease published by several medical societies and scientific institutions are analyzed by means of a review of the stratification index of the patients used in each of them. Aspects related to the duration of the treatment and the possible causes associated with the unfavorable evolution are stated.

  10. Pseudomona pseudomallei community acquired pneumonia

    International Nuclear Information System (INIS)

    This is the first published case report en Colombia about pseudomona pseudomallei community acquired pneumonia. This uncommon pathogen is from the epidemiological standpoint a very important one and medical community should be aware to look after it in those patients where no other etiological pathogen is recovered. A brief summary about epidemiology is showed, emphasizing those regions where it can be found. Likewise, comments about the differential diagnosis are important since it should be considered in those patients where tuberculosis is suspected. This is particularly representative for countries with high tuberculosis rates. Furthermore, a microbiological review is shown, emphasizing on isolation techniques, descriptions about therapeutics and other regarding treatment issues according international standards. Finally; a description about the clinical picture, laboratory findings, treatment and evolution of the case reported are shown for discussion

  11. The value of signs and symptoms in differentiating between bacterial, viral and mixed aetiology in patients with community-acquired pneumonia

    NARCIS (Netherlands)

    Huijskens, Elisabeth G. W.; Koopmans, Marion; Palmen, Fernand M. H.; van Erkel, Adriana J. M.; Mulder, Paul G. H.; Rossen, John W. A.

    2014-01-01

    Current diagnostics for community-acquired pneumonia (CAP) include testing for a wide range of pathogens, which is costly and not always informative. We compared clinical and laboratory parameters of patients with CAP caused by different groups of pathogens to evaluate the potential for targeted dia

  12. Escherichia coli and Community-acquired Gastroenteritis, Melbourne, Australia

    OpenAIRE

    Robins-Browne, Roy M.; Bordun, Anne-Marie; Tauschek, Marija; Bennett-Wood, Vicki R.; Russell, Jacinta; Oppedisano, Frances; Lister, Nicole A.; Bettelheim, Karl A.; Fairley, Christopher K.; Sinclair, Martha I; Hellard, Margaret E

    2004-01-01

    As part of a study to determine the effects of water filtration on the incidence of community-acquired gastroenteritis in Melbourne, Australia, we examined fecal samples from patients with gastroenteritis and asymptomatic persons for diarrheagenic strains of Escherichia coli. Atypical strains of enteropathogenic E. coli (EPEC) were the most frequently identified pathogens of all bacterial, viral, and parasitic agents in patients with gastroenteritis. Moreover, atypical EPEC were more common i...

  13. Community-Acquired Pneumonia in Children: A Multidisciplinary Consensus Review

    OpenAIRE

    Low, Donald E.; Kellner, James D; Allen, Upton; Boucher, Francois D; Kovesi, Thomas; Riesman, John; Davidson, Ross; Joanne M Langley

    2003-01-01

    Community-acquired pneumonia (CAP) is common among children and may have viral, bacterial or, occasionally, other causes. The etiology is complex, with age-related trends, and differs from that in adult CAP, necessitating different management guidelines. There is an absence of current guidelines for the management of pediatric CAP (PCAP) that take into account changing etiologies, antimicrobial-resistance issues and the use of newly licensed antimicrobials. The present review does not provide...

  14. Bacterial Communities: Interactions to Scale

    Science.gov (United States)

    Stubbendieck, Reed M.; Vargas-Bautista, Carol; Straight, Paul D.

    2016-01-01

    In the environment, bacteria live in complex multispecies communities. These communities span in scale from small, multicellular aggregates to billions or trillions of cells within the gastrointestinal tract of animals. The dynamics of bacterial communities are determined by pairwise interactions that occur between different species in the community. Though interactions occur between a few cells at a time, the outcomes of these interchanges have ramifications that ripple through many orders of magnitude, and ultimately affect the macroscopic world including the health of host organisms. In this review we cover how bacterial competition influences the structures of bacterial communities. We also emphasize methods and insights garnered from culture-dependent pairwise interaction studies, metagenomic analyses, and modeling experiments. Finally, we argue that the integration of multiple approaches will be instrumental to future understanding of the underlying dynamics of bacterial communities. PMID:27551280

  15. Bacterial Communities: Interactions to Scale

    Directory of Open Access Journals (Sweden)

    Reed M. Stubbendieck

    2016-08-01

    Full Text Available In the environment, bacteria live in complex multispecies communities. These communities span in scale from small, multicellular aggregates to billions or trillions of cells within the gastrointestinal tract of animals. The dynamics of bacterial communities are determined by pairwise interactions that occur between different species in the community. Though interactions occur between a few cells at a time, the outcomes of these interchanges have ramifications that ripple through many orders of magnitude, and ultimately affect the macroscopic world including the health of host organisms. In this review we cover how bacterial competition influences the structures of bacterial communities. We also emphasize methods and insights garnered from culture-dependent pairwise interaction studies, metagenomic analyses, and modeling experiments. Finally, we argue that the integration of multiple approaches will be instrumental to future understanding of the underlying dynamics of bacterial communities.

  16. Immunomodulation in community-acquired pneumonia

    NARCIS (Netherlands)

    Remmelts, H.H.F.

    2013-01-01

    Community-acquired pneumonia (CAP) is a common disease with considerable morbidity and mortality, despite effective antibiotic treatment. In this thesis, we showed that the major causative microorganisms in CAP trigger distinct inflammatory response profiles in the host. While an inflammatory respon

  17. [Indication of neuro-imaging for the initial management and the follow-up of acute community-acquired bacterial meningitis].

    Science.gov (United States)

    Béquet, D; de Broucker, T

    2009-01-01

    Lumbar puncture is the best way to prove bacterial meningitis. It should be performed without any delay if the diagnosis is suspected. Herniation is a rare complication of LP. CT is normal in most cases of purulent meningitis, including those complicated by a subsequent herniation; normal CT results does not mean that performing a LP is safe. Three main clinical features can help determine which patient is at risk of herniation and should have a CT before LP. This risk has to be determined rapidly in the emergency ward while assessing anamnestic data, localization signs or symptoms, and level of consciousness. Cranial imaging (mainly MRI) is useful in the course of bacterial meningitis. Patients who do not respond well to treatment or with atypical presentation, persistence of fever, or new neurological signs should undergo brain imaging; MRI and CT may identify subdural effusions, brain abscesses, empyemas, hydrocephaly, or brain parenchymal changes (cerebritis, infarction, hemorrhage). CT and MRI are useful to screen for an ENT cause of bacterial meningitis, and mandatory in case of pneumococcal meningitis. Numerous MRI sequences are useful to identify bacterial meningitis complications: SE T1 without and with gadolinium injection, SE T2, FLAIR, gradient-echo T2, diffusion weighted imaging, MR angiography. PMID:19398288

  18. Etiology and antibacterial susceptibility pattern of community-acquired bacterial ocular infections in a tertiary eye care hospital in south India

    Directory of Open Access Journals (Sweden)

    Bharathi M

    2010-01-01

    Full Text Available Aims: To identify the etiology, incidence and prevalence of ocular bacterial infections, and to assess the in vitro susceptibility of these ocular bacterial isolates to commonly used antibiotics. Materials and Methods: Retrospective analysis of consecutive samples submitted for microbiological evaluation from patients who were clinically diagnosed with ocular infections and were treated at a tertiary eye care referral center in South India between January 2002 and December 2007. Results: A total of 4417 ocular samples was submitted for microbiological evaluation, of which 2599 (58.8% had bacterial growth, 456 (10.3% had fungal growth, 15 (0.34% had acanthamoebic growth, 14 (0.32% had mixed microbial growth and the remaining 1333 (30.2% had negative growth. The rate of culture-positivity was found to be 88% (P < 0.001 in eyelids′ infection, 70% in conjunctival, 69% in lacrimal apparatus, 67.4% in corneal, 51.6% in intraocular tissues, 42.9% in orbital and 39.2% in scleral infections. The most common bacterial species isolated were Staphylococcus aureus (26.69% followed by Streptococcus pneumoniae (22.14%. Sta. aureus was more prevalent more in eyelid infections (51.22%; P = 0.001 coagulase-negative staphylococci in endophthalmitis (53.1%; P = 0.001, Str. pneumoniae in lacrimal apparatus and corneal infections (64.19%; P = 0.001, Corynebacterium species in blepharitis and conjunctivitis (71%; P = 0.001, Pseudomonas aeruginosa in keratitis and dacryocystitis (66.5%; P = 0.001, Haemophilus species in dacryocystitis and conjunctivitis (66.7%; P = 0.001, Moraxella lacunata in blepharitis (54.17%; P = 0.001 and Moraxella catarrhalis in dacryocystitis (63.83%; P = 0.001. The largest number of gram-positive isolates was susceptible to moxifloxacin (98.7% and vancomycin (97.9%, and gram-negative isolates to amikacin (93.5% and gatifloxacin (92.7%. Conclusions: Gram-positive cocci were the most frequent bacteria isolated from ocular infections and were

  19. Management of Community -Acquired Acute Bacterial Meningitis in Children%社区获得性急性细菌性脑膜炎患儿的管理

    Institute of Scientific and Technical Information of China (English)

    郭虎; 郑帼

    2011-01-01

    Bacterial meningitis(BM) is a common pediatric infectious disease of the nervous system,which often affect the psychomotor development of children, the correct diagnosis and treatment had always been a challenge. The United States, Europe, Canada, France, England had issued guidelines for the management of BM in 2004 - 2010, which were important reference value for guiding clinicians dealing with BM.%细菌性脑膜炎(BM)是小儿常见的神经系统感染性疾病之一,常影响小儿精神运动发育,其正确的诊断和治疗一直是个挑战;美国、欧洲、加拿大、法国、英国先后于2004 - 2010年发布了BM治疗指南,对于指导临床医师处理BM有重要的参考价值.

  20. [Epidemiology of community-acquired pneumonia in children. Current data].

    Science.gov (United States)

    Marguet, C; Bocquel, N; Mallet, E

    1998-01-01

    Viruses, particularly syncitial respiratory virus, are the main aetiology of community-acquired lower respiratory tract infections in infants, while bacterial agents are more frequently responsible in children older than 3 years. Antimicrobial therapy must take into account the development of reduced susceptibility of penicillin to strains of Streptoccocus pneumoniae and Haemophilus influenzae with beta-lactamase, and high frequency of Mycoplasma pneumoniae and Chlamydia pneumoniae infections. Although the mortality rate has remained low in France, the morbidity appeared to increase in recent years. PMID:10223154

  1. 三亚地区儿童社区获得性肺炎病原菌分布及耐药性分析%Pathogenic bacteria distribution of pediatric community acquired pneumonia and bacterial resistance in Sanya

    Institute of Scientific and Technical Information of China (English)

    麦珍; 阮细玲

    2014-01-01

    目的:了解三亚地区儿童社区获得性肺炎病原菌分布情况及耐药特点,为临床合理使用抗菌药物提供依据。方法回顾分析三亚地区2011年1月至2013年12月确诊的儿童社区获得性肺炎住院患儿阳性痰培养标本485例。结果485株病原菌中,革兰阴性菌占65.36%,革兰阳性菌占29.28%,真菌占5.36%。排名前五位的细菌是肺炎克雷伯菌、金黄色葡萄球菌、鲍曼不动杆菌、大肠埃希菌、肺炎链球菌。革兰阴性菌对阿米卡星、哌拉西林/他唑巴坦、左氧氟沙星、碳青霉烯类抗菌药物的耐药率均小于20.0%。未发现对万古霉素和利奈唑胺耐药的阳性球菌。结论三亚地区儿童社区获得性肺炎病原菌以革兰阴性菌为主,耐药现象与文献报道存在一定差异,因此临床医生应参照本地区流行病学特点合理使用抗菌药物,以控制细菌耐药率的上升。%Objective To analyze the pathogenic bacteria distribution of pediatric community acquired pneumo‐nia and bacteria resistance in Sanya ,so as to provide a basis for rational use of antibiotics .Methods A total of 485 patients confirmed with community acquired pneumonia were enrolled in this study .The sputum culture results and drug susceptibility test were analyzed .Results In all 485 bacterial isolates ,gram negative bacterium strains accoun‐ted for 65 .36% ,gram positive bacterium strains accounted for 29 .28% ,and fungi were accounted for 5 .36% .Kleb‐siella pneumoniae ,Staphylococcus aureus ,Acinetobacter baumanii ,Escherichia coli and Streptococcus pneumoniae were the most common isolates .Less than 20% gram negative bacterium strains were resistant to amikacin ,piperacil‐lin /tazobactam ,levofloxacin and carbapenem .No vancomycin and linezolid resistant gram positive bacterium strains were found .Conclusion Gram negative bacterium strains were the most common pathogenic bacteria of pediatric community

  2. [National consensus for management of community acquired pneumonia in adults].

    Science.gov (United States)

    Saldías P, Fernando; Pérez C, Carlos

    2005-01-01

    Community acquired pneumonia (CAP) is an acute respiratory infection that affects pulmonary parenchyma, and is caused by community acquired microorganisms. In Chile, pneumonia represents the main cause of death due to infectious diseases and is the third specific cause of mortality in adults. In 1999, an experts committee in representation of "Sociedad Chilena de Enfermedades Respiratorias", presented the first National Guidelines for the Treatment of Adult Community Acquired Pneumonia, mainly based in foreign experience and documents, and adapted it to our National Health System Organization. During the last decade, impressive epidemiological and technological changes have occurred, making the update of guidelines for treatment of NAC by several international scientific societies, necessary. These changes include: new respiratory pathogens that are being identified in CAP and affect adult patients (Mycoplasma pneumoniae, Chlamydia pneumoniae, Legionella pneumophila); the increasing senescent adult population that carries multiple co-morbidities; the emergence of antimicrobial resistance among respiratory pathogens associated to massive antibiotic prescription; the development by the pharmaceutical industry of new drugs that are effective for pneumonia treatment (macrolides, ketolides and respiratory fluorquinolones); and the development of new diagnostic techniques for detection of antigens, antibodies, and bacterial DNA by molecular biology, useful in respiratory infections. Based on these antecedents, an Advisory Committee of "Sociedad Chilena de Enfermedades Respiratorias" and "Sociedad Chilena de Infectología" has reviewed the national and international evidence about CAP management in adults in order to update clinical recommendations for our country.

  3. Aetiology of community-acquired neonatal sepsis in low- and middle-income countries

    Directory of Open Access Journals (Sweden)

    Donald Waters

    2011-12-01

    Full Text Available 99% of the approximate 1 million annual neonatal deaths from life-threatening invasive bacterial infections occur in developing countries, at least 50% of which are from home births or community settings. Data concerning aetiology of sepsis in these settings are necessary to inform targeted therapy and devise management guidelines. This review describes and analyses the bacterial aetiology of community-acquired neonatal sepsis in developing countries.

  4. Prevalence and bacterial susceptibility of hospital acquired urinary tract infection

    Directory of Open Access Journals (Sweden)

    Dias Neto José Anastácio

    2003-01-01

    Full Text Available PURPOSE: Urinary tract infection is the most common nosocomially acquired infection. It is important to know the etiology and antibiotic susceptibility infectious agents to guide the initial empirical treatment. OBJECTIVE: To determine the prevalence of bacterial strains and their antibiotic susceptibility in nosocomially acquired urinary tract infection in a university hospital between January and June 2003. METHODS: We analyzed the data of 188 patients with positive urine culture (= 10(5 colony-forming units/mL following a period of 48 hours after admission. RESULTS: Half of patients were male. Mean age was 50.26 ± 22.7 (SD, range 3 months to 88 years. Gram-negative bacteria were the agent in approximately 80% of cases. The most common pathogens were E. coli (26%, Klebsiella sp. (15%, P. aeruginosa (15% and Enterococcus sp. (11%. The overall bacteria susceptibility showed that the pathogens were more sensible to imipenem (83%, second or third generation cephalosporin and aminoglycosides; and were highly resistant to ampicillin (27% and cefalothin (30%. It is important to note the low susceptibility to ciprofloxacin (42% and norfloxacin (43%. CONCLUSION: This study suggests that if one can not wait the results of urine culture, the best choices to begin empiric treatment are imipenem, second or third generation cephalosporin and aminoglycosides. Cefalothin and ampicillin are quite ineffective to treat these infections.

  5. Surfactant protein D (SP-D) serum levels in patients with community-acquired pneumonia

    DEFF Research Database (Denmark)

    Leth-Larsen, Rikke; Nordenbaek, Claudia; Tornoe, Ida;

    2003-01-01

    blood samples from 61 patients hospitalized for community-acquired pneumonia of suspected bacterial origin. On the day of admission to the hospital the serum SP-D concentration was significantly lower than that in healthy subjects. On day 5, the SP-D concentration had increased on average three times...

  6. Aetiology and resistance patterns of community-acquired pneumonia in León, Nicaragua

    NARCIS (Netherlands)

    Matute, A J; Brouwer, W P; Hak, E; Delgado, E; Alonso, E; Hoepelman, I M

    2006-01-01

    We conducted a prevalence study to gain greater insight into the aetiology, bacterial resistance and risk factors for community-acquired pneumonia (CAP) in the region of León, Nicaragua. During the period from July 2002 to January 2005, all consecutive patients with signs and symptoms suggestive of

  7. Significance of anaerobes and oral bacteria in community-acquired pneumonia.

    Directory of Open Access Journals (Sweden)

    Kei Yamasaki

    Full Text Available BACKGROUND: Molecular biological modalities with better detection rates have been applied to identify the bacteria causing infectious diseases. Approximately 10-48% of bacterial pathogens causing community-acquired pneumonia are not identified using conventional cultivation methods. This study evaluated the bacteriological causes of community-acquired pneumonia using a cultivation-independent clone library analysis of the 16S ribosomal RNA gene of bronchoalveolar lavage specimens, and compared the results with those of conventional cultivation methods. METHODS: Patients with community-acquired pneumonia were enrolled based on their clinical and radiological findings. Bronchoalveolar lavage specimens were collected from pulmonary pathological lesions using bronchoscopy and evaluated by both a culture-independent molecular method and conventional cultivation methods. For the culture-independent molecular method, approximately 600 base pairs of 16S ribosomal RNA genes were amplified using polymerase chain reaction with universal primers, followed by the construction of clone libraries. The nucleotide sequences of 96 clones randomly chosen for each specimen were determined, and bacterial homology was searched. Conventional cultivation methods, including anaerobic cultures, were also performed using the same specimens. RESULTS: In addition to known common pathogens of community-acquired pneumonia [Streptococcus pneumoniae (18.8%, Haemophilus influenzae (18.8%, Mycoplasma pneumoniae (17.2%], molecular analysis of specimens from 64 patients with community-acquired pneumonia showed relatively higher rates of anaerobes (15.6% and oral bacteria (15.6% than previous reports. CONCLUSION: Our findings suggest that anaerobes and oral bacteria are more frequently detected in patients with community-acquired pneumonia than previously believed. It is possible that these bacteria may play more important roles in community-acquired pneumonia.

  8. [Differential diagnosis of pulmonary tuberculosis and community-acquired pneumonia].

    Science.gov (United States)

    Deĭkina, O N; Mishin, V Iu; Demikhova, O V

    2007-01-01

    The purpose of this investigation was to enhance the efficiency of differential diagnosis of pneumonia and pulmonary tuberculosis. A hundred and fifty-nine adult patients were examined. These included 78 patients with pulmonary tuberculosis and 81 with community-acquired p neumonia. The clinical features of infiltrative pulmonary tuberculosis (n = 48) and mild community-acquired pneumonia (n = 51) were compared. The course of caseous pneumonia (n = 30) was compared with that of moderate and severe community-acquired pneumonia (n = 30). Significant differences in the manifestations of the intoxication and bronchopulmonary syndrome were not found in patients with community-acquired pneumonia and infiltrative pulmonary tuberculosis. Physical studies showed that in patients with community-acquired pneumonia, moist rale (54.9%) and crepitation (11.8%) were prevalent, but in those with infiltrative tuberculosis rale was absent in 60.4% of cases and the pattern of respiration was unchanged in 79.2%. Chest X-ray studies indicated that in patients with community-acquired pneumonia, lower lobar inflammatory changes were predominant in 62.8% of cases whereas in those with infiltrative pulmonary tuberculosis the process was mainly bilateral (43.8%) with the presence of destructive changes (83.3%) and bronchogenic dissemination (66.7%). In patients with caseous pneumonia, the intoxication syndrome was more significant than in those with severe community-acquired pneumonia. Chest X-ray studies demonstrated that in patients with caseous pneumonia, specific changes were bilateral with the involvement of 2 lobes or more, with destruction and bronchogenic dissemination while in those with community-acquired pneumonia, the pulmonary processes were predominantly bilateral (76.6%) at the lower lobar site (36.7%).

  9. [Differential diagnosis of pulmonary tuberculosis and community-acquired pneumonia].

    Science.gov (United States)

    Deĭkina, O N; Mishin, V Iu; Demikhova, O V

    2007-01-01

    The purpose of this investigation was to enhance the efficiency of differential diagnosis of pneumonia and pulmonary tuberculosis. A hundred and fifty-nine adult patients were examined. These included 78 patients with pulmonary tuberculosis and 81 with community-acquired p neumonia. The clinical features of infiltrative pulmonary tuberculosis (n = 48) and mild community-acquired pneumonia (n = 51) were compared. The course of caseous pneumonia (n = 30) was compared with that of moderate and severe community-acquired pneumonia (n = 30). Significant differences in the manifestations of the intoxication and bronchopulmonary syndrome were not found in patients with community-acquired pneumonia and infiltrative pulmonary tuberculosis. Physical studies showed that in patients with community-acquired pneumonia, moist rale (54.9%) and crepitation (11.8%) were prevalent, but in those with infiltrative tuberculosis rale was absent in 60.4% of cases and the pattern of respiration was unchanged in 79.2%. Chest X-ray studies indicated that in patients with community-acquired pneumonia, lower lobar inflammatory changes were predominant in 62.8% of cases whereas in those with infiltrative pulmonary tuberculosis the process was mainly bilateral (43.8%) with the presence of destructive changes (83.3%) and bronchogenic dissemination (66.7%). In patients with caseous pneumonia, the intoxication syndrome was more significant than in those with severe community-acquired pneumonia. Chest X-ray studies demonstrated that in patients with caseous pneumonia, specific changes were bilateral with the involvement of 2 lobes or more, with destruction and bronchogenic dissemination while in those with community-acquired pneumonia, the pulmonary processes were predominantly bilateral (76.6%) at the lower lobar site (36.7%). PMID:17338353

  10. [Features of morbidity community-acquired pneumonia among young recruits].

    Science.gov (United States)

    Serdukov, D U; Gordienko, A V; Kozlov, M S; Mikhailov, A A; Davydov, P A

    2015-10-01

    Were examined 3338 military personnel of the combined training center. 183 of them diagnosed community-acquired pneumonia, in 3155 focal and infiltrative changes in lung tissue were not identified. The analisys of prevalence been made among young recruits of the acute respiratory illness before arriving in part and at the assembly point, foci of chronic infection, smoking, low body weight. 511 military personnel arrived at the training center in the disease state with symptoms of acute respiratory illness. Examined the relationship these risk factor to the development of community-acquired pneumonia in this category of servicemen. PMID:26827502

  11. Atypical pathogens in community acquired pneumonia of Egyptian children

    Institute of Scientific and Technical Information of China (English)

    Deraz TE; El Sahriggy SA; Shaheen MA; Motawea AA; Gomaa HE; Fawzy SH; Mohamed AA

    2009-01-01

    Objective:Diagnosis of atypical pathogens as an aetiology for community-acquired pneumonia (CAP)in chil-dren is a challenge world wide.The aim of this study was to detect the frequency of atypical pathogens as a cause of community-acquired pneumonia (CAP)in Egyptian children.Methods:From 50 children (with age ranged from 2 months to 1 2 years)hospitalized for community-acquired pneumonia;respiratory sputum samples were collected by induction or spontaneously.All samples were subjected to conventional cultures and Polymer-ase Chain Reaction(PCR)technique DNA extraction for identification of Mycoplasma,Chlamydia pneumoniae and Legionella pneumophila.Results:A definite pathogen was identified in 78% of the studied children;30%typical bacteria,8% candida albicans and atypical bacteria in 40% of the pneumonic children.Chlamydia pneumoniae was isolated from 26% of the children while Mycoplasma pneumoniae was isolated from 1 4%, whereas Legionella pneumophilla was not isolated at all.Conclusion:Atypical pathogens are evident as a po-tential aetiology for community-acquired pneumonia in (1 3.3%)of young and (80%)of older Egyptian chil-dren.

  12. Antibiotic Treatment Strategies for Community-Acquired Pneumonia in Adults

    NARCIS (Netherlands)

    Postma, Douwe F.; Van Werkhoven, Cornelis H.; Van Elden, Leontine J R; Thijsen, Steven F T; Hoepelman, Andy I M; Kluytmans, Jan A J W; Boersma, Wim G.; Compaijen, Clara J.; Van Der Wall, Eva; Prins, Jan M.; Oosterheert, Jan J.; Bonten, Marc J M

    2015-01-01

    BACKGROUND The choice of empirical antibiotic treatment for patients with clinically suspected community-acquired pneumonia (CAP) who are admitted to non-intensive care unit (ICU) hospital wards is complicated by the limited availability of evidence. We compared strategies of empirical treatment (al

  13. Diabetes and risk of community-acquired Staphylococcus aureus bacteremia

    DEFF Research Database (Denmark)

    Smit, Jesper; Søgaard, Mette; Schønheyder, Henrik Carl;

    2016-01-01

    OBJECTIVE: Patients with diabetes may experience higher risk of Staphylococcus aureus bacteremia (SAB) than patients without diabetes due to decreased immunity or coexisting morbidities. We investigated the risk of community-acquired (CA) SAB in persons with and without diabetes. DESIGN: Using...

  14. 75 FR 73107 - Draft Guidance for Industry on Hospital-Acquired Bacterial Pneumonia and Ventilator-Associated...

    Science.gov (United States)

    2010-11-29

    ... Pneumonia and Ventilator-Associated Bacterial Pneumonia: Developing Drugs for Treatment; Availability AGENCY... Pneumonia and Ventilator-Associated Bacterial Pneumonia: Developing Drugs for Treatment.'' The purpose of... antimicrobial drugs for the treatment of hospital- acquired bacterial pneumonia (HABP) and...

  15. Antibiotic resistance pattern of community acquired uropathogens at a tertiary care hospital in Jaipur, Rajasthan

    Directory of Open Access Journals (Sweden)

    Smita Sood

    2012-01-01

    Full Text Available Background: Urinary tract infections (UTIs are amongst the most common infections described in outpatients setting. Objectives : A study was conducted to evaluate the uropathogenic bacterial flora and its antimicrobial susceptibility profile among patients presenting to the out-patient clinics of a tertiary care hospital at Jaipur, Rajasthan. Materials and Methods : 2012 consecutive urine specimens from symptomatic UTI cases attending to the outpatient clinics were processed in the Microbiology lab. Bacterial isolates obtained were identified using biochemical reactions. Antimicrobial susceptibility testing was performed by the Kirby-Bauer disc diffusion method. Extended spectrum beta lactamase (ESBL production was determined by the double disk approximation test and the Clinical and Laboratory Standards Institute (formerly NCCLS confirmatory method. Results: Pathogens were isolated from 346 (17.16% of the 2012 patients who submitted a urine sample. Escherichia coli was the most frequently isolated community acquired uropathogen accounting for 61.84% of the total isolates. ESBL production was observed in 23.83% of E. coli strains and 8.69% of Klebsiella strains. With the exception of Nitrofurantoin, resistance to agents commonly used as empiric oral treatments for UTI was quite high. Conclusion : The study revealed E. coli as the predominant bacterial pathogen for the community acquired UTIs in Jaipur, Rajasthan. An increasing trend in the production ESBLs among UTI pathogens in the community was noted. Nitrofurantoin should be used as empirical therapy for primary, uncomplicated UTIs.

  16. Jellyfish modulate bacterial dynamic and community structure.

    Directory of Open Access Journals (Sweden)

    Tinkara Tinta

    Full Text Available Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into

  17. Тhe features of severe community acquired pneumonia

    Directory of Open Access Journals (Sweden)

    Avramenko I.V.

    2015-06-01

    Full Text Available Based on data from a prospective analysis for the year of observation, the article presents information about the features of severe community acquired pneumonia in patients who were hospitalized at the department of pulmonology (or therapy, as well as department of the intensive care from three teaching hospitals in Dnepropetrovsk, namely "Dnipropetrovsk City Hospital №6», "Dnipropetrovsk City Hospital №2», "Dnipropetrovsk City Hospital №16», which are the clinical ones of "Dnepropetrovsk Medical Academy of the Ministry of Health Ukraine". Dependence of the severity of the condition shown on duration of illness before admission, features of season character of disease. The effect of breathing exercises on the course of the disease. The results can be the basis for a more personal approach to the development of diagnostic and therapeutic programs for patients with severe community-acquired pneumonia.

  18. Early neurovascular uncoupling in the brain during community acquired pneumonia

    OpenAIRE

    Rosengarten, Bernhard; Krekel, Dennis; Kuhnert, Stefan; Schulz, Richard

    2012-01-01

    Introduction Sepsis leads to microcirculatory dysfunction and therefore a disturbed neurovascular coupling in the brain. To investigate if the dysfunction is also present in less severe inflammatory diseases we studied the neurovascular coupling in patients suffering from community acquired pneumonia. Methods Patients were investigated in the acute phase of pneumonia and after recovery. The neurovascular coupling was investigated with a simultaneous electroencephalogram (EEG)-Doppler techniqu...

  19. Clinical features of endemic community-acquired psittacosis

    OpenAIRE

    J.M. Branley; Weston, K M; England, J; Dwyer, D E; Sorrell, T C

    2014-01-01

    Following a large outbreak of community-acquired psittacosis in 2002 in residents of the Blue Mountains, New South Wales, Australia, we reviewed new cases in this area over a 7-year period from 2003 to 2009. Using the 2010 criteria from the Centers for Disease Control National Notifiable Diseases Surveillance System, 85 patients with possible psittacosis were identified, of which 48 were identified as definite or probable infection. Clinical features of these cases are summarized. In addition...

  20. Overview of recent studies of community-acquired pneumonia.

    Science.gov (United States)

    Higgins, K; Singer, M; Valappil, T; Nambiar, S; Lin, D; Cox, E

    2008-12-01

    All recent studies of antibacterial drugs for the indication of community-acquired pneumonia submitted to the US Food and Drug Administration have been designed as noninferiority studies. We provide a summary of results of 7 recent clinical studies of oral antibacterial drugs for treatment of community-acquired pneumonia. In these 7 studies, the majority of patients enrolled had Pneumonia Patient Outcomes Research Team scores of I or II. The percentage of randomized subjects with pathogens identified at baseline ranged from 47% to 76%, and the percentage of subjects with Streptoccocus pneumoniae isolated at baseline ranged from approximately 6% to 20%. The primary end point in these studies was clinical cure, assessed 7-21 days after completion of therapy. Clinical cure rates were >80% in the intent-to-treat populations and >90% in the per-protocol populations. We also briefly summarize the results from several recently submitted clinical studies of intravenously administered antibacterial drugs for treatment of community-acquired pneumonia, in which we found similar results. PMID:18986282

  1. Streptococcus pneumoniae DNA Load in Blood as a Marker of Infection in Patients with Community-Acquired Pneumonia

    NARCIS (Netherlands)

    Peters, R.P.H.; Boer, de R.F.; Schuurman, T.; Gierveld, S.; Kooistra-Smid, M.; Agtmael, van M.A.; Vandenbroucke-Grauls, C.M.J.E.; Persoons, M.C.J.; Savelkoul, P.H.M.

    2009-01-01

    Direct detection of Streptococcus pneumoniae DNA in blood adds to culture results in the etiological diagnosis of patients with community-acquired pneumonia (CAP). Quantification of the amount of DNA, the bacterial DNA load (BDL), provides a measurement of DNAemia that may increase the understanding

  2. Community-acquired pneumonia in older patients: does age influence systemic cytokine levels in community-acquired pneumonia?

    LENUS (Irish Health Repository)

    Kelly, Emer

    2009-03-01

    Community-acquired pneumonia (CAP) is a major cause of death in the elderly. The age-related increase in comorbid illnesses plays a part but the effect of aging on the immune response may be equally important. We aimed to evaluate patients with CAP for evidence of a muted response to infection in elderly patients admitted to hospital compared with a younger patient group.

  3. CIPROFLOXACIN RESISTANCE PATTERN AMONG BACTERIA ISOLATED FROM PATIENTS WITH COMMUNITY-ACQUIRED URINARY TRACT INFECTION

    Science.gov (United States)

    REIS, Ana Carolina Costa; SANTOS, Susana Regia da Silva; de SOUZA, Siane Campos; SALDANHA, Milena Góes; PITANGA, Thassila Nogueira; OLIVEIRA, Ricardo Riccio

    2016-01-01

    SUMMARY Objective: To identify the main bacterial species associated with community-acquired urinary tract infection (UTI) and to assess the pattern of ciprofloxacin susceptibility among bacteria isolated from urine cultures. Methods: We conducted a retrospective study in all the patients with community-acquired UTI seen in Santa Helena Laboratory, Camaçari, Bahia, Brazil during five years (2010-2014). All individuals who had a positive urine culture result were included in this study. Results: A total of 1,641 individuals met the inclusion criteria. Despite the fact that participants were female, we observed a higher rate of resistance to ciprofloxacin in males. The most frequent pathogens identified in urine samples were Escherichia coli, Klebsiella pneumoniae and Staphylococcus saprophyticus. Antimicrobial resistance has been observed mainly for ampicillin, sulfamethoxazole + trimethoprim and ciprofloxacin. Moreover, E. coli has shown the highest rate of ciprofloxacin resistance, reaching 36% of ciprofloxacin resistant strains in 2014. Conclusion: The rate of bacterial resistance to ciprofloxacin observed in the studied population is much higher than expected, prompting the need for rational use of this antibiotic, especially in infections caused by E. coli. Prevention of bacterial resistance can be performed through control measures to limit the spread of resistant microorganisms and a rational use of antimicrobial policy. PMID:27410913

  4. CIPROFLOXACIN RESISTANCE PATTERN AMONG BACTERIA ISOLATED FROM PATIENTS WITH COMMUNITY-ACQUIRED URINARY TRACT INFECTION

    Directory of Open Access Journals (Sweden)

    Ana Carolina Costa REIS

    2016-01-01

    Full Text Available SUMMARY Objective: To identify the main bacterial species associated with community-acquired urinary tract infection (UTI and to assess the pattern of ciprofloxacin susceptibility among bacteria isolated from urine cultures. Methods: We conducted a retrospective study in all the patients with community-acquired UTI seen in Santa Helena Laboratory, Camaçari, Bahia, Brazil during five years (2010-2014. All individuals who had a positive urine culture result were included in this study. Results: A total of 1,641 individuals met the inclusion criteria. Despite the fact that participants were female, we observed a higher rate of resistance to ciprofloxacin in males. The most frequent pathogens identified in urine samples were Escherichia coli, Klebsiella pneumoniae and Staphylococcus saprophyticus. Antimicrobial resistance has been observed mainly for ampicillin, sulfamethoxazole + trimethoprim and ciprofloxacin. Moreover, E. coli has shown the highest rate of ciprofloxacin resistance, reaching 36% of ciprofloxacin resistant strains in 2014. Conclusion: The rate of bacterial resistance to ciprofloxacin observed in the studied population is much higher than expected, prompting the need for rational use of this antibiotic, especially in infections caused by E. coli. Prevention of bacterial resistance can be performed through control measures to limit the spread of resistant microorganisms and a rational use of antimicrobial policy.

  5. Polymicrobial community-acquired pneumonia: An emerging entity.

    Science.gov (United States)

    Cillóniz, Catia; Civljak, Rok; Nicolini, Antonello; Torres, Antoni

    2016-01-01

    Polymicrobial aetiology in community-acquired pneumonia (CAP) is more common than previously recognized. This growing new entity can influence inflammation, host immunity and disease outcomes in CAP patients. However, the true incidence is complicated to determine and probably underestimated due mainly to many cases going undetected, particularly in the outpatient setting, as the diagnostic yield is restricted by the sensitivity of currently available microbiologic tests and the ability to get certain types of clinical specimens. The observed rate of polymicrobial cases may also lead to new antibiotic therapy considerations. In this review, we discuss the pathogenesis, microbial interactions in pneumonia, epidemiology, biomarkers and antibiotic therapy for polymicrobial CAP.

  6. Community-Acquired urinary tract infection by pseudomonas oryzihabitans

    Directory of Open Access Journals (Sweden)

    Sunita M Bhatawadekar

    2013-01-01

    Full Text Available Pseudomonas oryzihabitans and Chrysomonas luteola has been placed in CDC group Ve2 and Ve1 respectively. These bacteria appear to be emerging pathogens. P. oryzihabitans was isolated from cases of bacteremia, CNS infections, wound infections, peritonitis, sinusitis, catheter associated infections in AIDS patient, and pneumonia. Most of the reports of P. oryzihabitans infection were of nosocomial origin in individuals with some predisposing factors. We report here a case of community acquired UTI by P. oryzihabitans in an immune-competent patient with stricture of urethra.

  7. Hospital-acquired and Community-acquired Uropathogens; Modelling of Infection

    Directory of Open Access Journals (Sweden)

    Aija ?ilevi?a

    2005-12-01

    Full Text Available Urinary tract infections are among the most common human infections. They may be community-acquired or nosocomial, and caused by a variety of microorganisms. In the present study, we analysed more than 4000 urine samples collected from in-patients and outpatients, and registered the differences in the etiological spectrum of agents. The most widespread uropathogens are gram-negative rods, from them E. coli, Klebsiella spp. and the non-fermentive genus Pseudomonas. Women are more intensively affected by E. coli. From gram-positive cocci, the leading agents are coagulase negative Staphylococci, followed by S. aureus. No differences were registered between the genders. Polyresistance among gram-negative uropathogens is high.

  8. Bacterial Community Development in Experimental Gingivitis

    OpenAIRE

    Kistler, James O; Veronica Booth; Bradshaw, David J.; Wade, William G.

    2013-01-01

    Current knowledge of the microbial composition of dental plaque in early gingivitis is based largely on microscopy and cultural methods, which do not provide a comprehensive description of oral microbial communities. This study used 454-pyrosequencing of the V1-V3 region of 16S rRNA genes (approximately 500 bp), and bacterial culture, to characterize the composition of plaque during the transition from periodontal health to gingivitis. A total of 20 healthy volunteers abstained from oral hygi...

  9. [ANEMIC SYNDROME IN PATIENTS WITH COMMUNITY-ACQUIRED PNEUMONIA].

    Science.gov (United States)

    Budnevsky, A V; Esaulenko, I E; Ovsyannikov, E S; Labzhaniya, N B; Voronina, E V; Chernov, A V

    2016-01-01

    Community-acquired pneumonia remains a most widespread acute infectious disease of socio-economic significance all over the world. Up to 30% of the patients present with anemia responsible for the unfavourable prognosis and elevated mortality. Not infrequently, anemia is not diagnosed during the hospital stay und therefore remains uncorrected. Severe anemia results in enhanced hypercapnia and slowed maturation of red blood cells in the bone marrow which facilitates the development of ischemic syndrome. Hepcidin, a mediator of inflammation and iron-regulatory hormone, plays an important role in the clinical course of community-acquired pneumonia. Hepsidin production increases during inflammation; it suppresses erythtropoiesis and depletes the iron depot leading to so-called anemia of inflammation. Hypoxia and anemia activate erythtropoiesis, and the released erythropoietin inhibits hepsidin production. During pneumonia resolution, hepsidin promotes recovery from anemia by activating iron absorption. The curreni literature contains few data on the use of hepcidin as a diagnostic marker of anemia. The necessity oftreating anemia in patients with pneumonia under hospital conditions is a matter of discussion. Direct involvement of hepcidin in iron metabolism creates a prerequisite for the treatment of anemia. Medicamental suppression of its activity by stimulating erythtropoiesis can facilitate normalization of iron metabolism and restoration of hemoglobin level.

  10. Clinical features of endemic community-acquired psittacosis

    Directory of Open Access Journals (Sweden)

    J.M. Branley

    2014-01-01

    Full Text Available Following a large outbreak of community-acquired psittacosis in 2002 in residents of the Blue Mountains, New South Wales, Australia, we reviewed new cases in this area over a 7-year period from 2003 to 2009. Using the 2010 criteria from the Centers for Disease Control National Notifiable Diseases Surveillance System, 85 patients with possible psittacosis were identified, of which 48 were identified as definite or probable infection. Clinical features of these cases are summarized. In addition to Chlamydia-specific serology, specimens, where available, underwent nucleic acid testing for chlamydial DNA using real-time PCR. Chlamydophila psittaci DNA was detected in samples from 23 patients. Four of 18 specimens were culture positive. This is the first description of endemic psittacosis, and is characterized in this location by community-acquired psittacosis resulting from inadvertent exposure to birds. The disease is likely to be under-diagnosed, and may often be mistaken for gastroenteritis or meningitis given the frequency of non-respiratory symptoms, particularly without a history of contact with birds. Clinical characteristics of endemic and outbreak-associated cases were similar. The nature of exposure, risk factors and reasons for the occurrence of outbreaks of psittacosis require further investigation.

  11. [CAPNETZ. The competence network for community-acquired pneumonia (CAP)].

    Science.gov (United States)

    Suttorp, Norbert; Welte, Tobias; Marre, Reinhard; Stenger, Steffen; Pletz, Mathias; Rupp, Jan; Schütte, Hartwig; Rohde, Gernot

    2016-04-01

    CAPNETZ is a medical competence network for community-acquired pneumonia (CAP), which was funded by the German Ministry for Education and Research. It has accomplished seminal work on pneumonia over the last 15 years. A unique infrastructure was established which has so far allowed us to recruit and analyze more than 11,000 patients. The CAPNETZ cohort is the largest cohort worldwide and the results obtained relate to all relevant aspects of CAP management (epidemiology, risk stratification via biomarkers or clinical scores, pathogen spectrum, pathogen resistance, antibiotic management, prevention and health care research). Results were published in more than 150 journals and informed the preparation and update of the national S3-guideline. CAPNETZ was also the foundation for further networks like the Pneumonia Research Network on Genetic Resistance and Susceptibility for the Evolution of Severe Sepsis) (PROGRESS), the Systems Medicine of Community Acquired Pneumonia Network (CAPSyS) and SFB-TR84 (Sonderforschungsbereich - Transregio 84). The main recipients (Charité Berlin, University Clinic Ulm and the Hannover Medical School) founded the CAPNETZ foundation and transferred all data and materials rights to this foundation. Moreover, the ministry granted the CAPNETZ foundation the status of being eligible to apply for research proposals and receive research funds. Since 2013 the CAPNETZ foundation has been an associated member of the German Center for Lung Research (DZL). Thus, a solid foundation has been set up for CAPNETZ to continue its success story. PMID:26984399

  12. Community-acquired methicillin-resistant Staphylococcus aureus pyomyositis with myelitis: A rare occurrence with diverse presentation

    Directory of Open Access Journals (Sweden)

    Kulkarni Girish

    2009-12-01

    Full Text Available Staphylococcus aureus is the most common bacterial pathogen implicated in pyomyositis. There are increasing reports of community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA infections. The present case report brings out the diverse clinical manifestations of MRSA infection in the form of paraspinal pyomyositis, myelitis, spinal osteomyelitis, and pneumonia. Molecular typing of the organism confirmed the diagnosis. Patient was successfully treated with vancomycin and surgical drainage. Consideration of the possibility of methicillin-resistance and appropriate antibiotic selection is vital in the treatment of serious community-acquired staphylococcal infections.

  13. Patterning bacterial communities on epithelial cells.

    Directory of Open Access Journals (Sweden)

    Mohammed Dwidar

    Full Text Available Micropatterning of bacteria using aqueous two phase system (ATPS enables the localized culture and formation of physically separated bacterial communities on human epithelial cell sheets. This method was used to compare the effects of Escherichia coli strain MG1655 and an isogenic invasive counterpart that expresses the invasin (inv gene from Yersinia pseudotuberculosis on the underlying epithelial cell layer. Large portions of the cell layer beneath the invasive strain were killed or detached while the non-invasive E. coli had no apparent effect on the epithelial cell layer over a 24 h observation period. In addition, simultaneous testing of the localized effects of three different bacterial species; E. coli MG1655, Shigella boydii KACC 10792 and Pseudomonas sp DSM 50906 on an epithelial cell layer is also demonstrated. The paper further shows the ability to use a bacterial predator, Bdellovibriobacteriovorus HD 100, to selectively remove the E. coli, S. boydii and P. sp communities from this bacteria-patterned epithelial cell layer. Importantly, predation and removal of the P. Sp was critical for maintaining viability of the underlying epithelial cells. Although this paper focuses on a few specific cell types, the technique should be broadly applicable to understand a variety of bacteria-epithelial cell interactions.

  14. Failure of levofloxacin treatment in community-acquired pneumococcal pneumonia

    Directory of Open Access Journals (Sweden)

    Grossi Paolo

    2005-11-01

    Full Text Available Abstract Background Streptococcus pneumoniae is the leading cause of community-acquired pneumonia (CAP. High global incidence of macrolide and penicillin resistance has been reported, whereas fluoroquinolone resistance is uncommon. Current guidelines for suspected CAP in patients with co-morbidity factors and recent antibiotic therapy recommend initial empiric therapy using one fluoroquinolone or one macrolide associated to other drugs (amoxicillin, amoxicillin/clavulanate, broad-spectrum cephalosporins. Resistance to fluoroquinolones is determined by efflux mechanisms and/or mutations in the parC and parE genes coding for topoisomerase IV and/or gyrA and gyrB genes coding for DNA gyrase. No clinical cases due to fluoroquinolone-resistant S. pneumoniae strains have been yet reported from Italy. Case presentation A 72-year-old patient with long history of chronic obstructive pulmonary disease and multiple fluoroquinolone treatments for recurrent lower respiratory tract infections developed fever, increased sputum production, and dyspnea. He was treated with oral levofloxacin (500 mg bid. Three days later, because of acute respiratory insufficiency, the patient was hospitalized. Levofloxacin treatment was supplemented with piperacillin/tazobactam. Microbiological tests detected a S. pneumoniae strain intermediate to penicillin (MIC, 1 mg/L and resistant to macrolides (MIC >256 mg/L and fluoroquinolones (MIC >32 mg/L. Point mutations were detected in gyrA (Ser81-Phe, parE (Ile460-Val, and parC gene (Ser79-Phe; Lys137-Asn. Complete clinical response followed treatment with piperacillin/tazobactam. Conclusion This is the first Italian case of community-acquired pneumonia due to a fluoroquinolone-resistant S. pneumoniae isolate where treatment failure of levofloxacin was documented. Molecular analysis showed a group of mutations that have not yet been reported from Italy and has been detected only twice in Europe. Treatment with piperacillin

  15. Bacterial community reconstruction using compressed sensing.

    Science.gov (United States)

    Amir, Amnon; Zuk, Or

    2011-11-01

    Bacteria are the unseen majority on our planet, with millions of species and comprising most of the living protoplasm. We propose a novel approach for reconstruction of the composition of an unknown mixture of bacteria using a single Sanger-sequencing reaction of the mixture. Our method is based on compressive sensing theory, which deals with reconstruction of a sparse signal using a small number of measurements. Utilizing the fact that in many cases each bacterial community is comprised of a small subset of all known bacterial species, we show the feasibility of this approach for determining the composition of a bacterial mixture. Using simulations, we show that sequencing a few hundred base-pairs of the 16S rRNA gene sequence may provide enough information for reconstruction of mixtures containing tens of species, out of tens of thousands, even in the presence of realistic measurement noise. Finally, we show initial promising results when applying our method for the reconstruction of a toy experimental mixture with five species. Our approach may have a potential for a simple and efficient way for identifying bacterial species compositions in biological samples. All supplementary data and the MATLAB code are available at www.broadinstitute.org/?orzuk/publications/BCS/.

  16. Bacterial Community Diversity Harboured by Interacting Species.

    Directory of Open Access Journals (Sweden)

    Mikaël Bili

    Full Text Available All animals are infected by microbial partners that can be passengers or residents and influence many biological traits of their hosts. Even if important factors that structure the composition and abundance of microbial communities within and among host individuals have been recently described, such as diet, developmental stage or phylogeny, few studies have conducted cross-taxonomic comparisons, especially on host species related by trophic relationships. Here, we describe and compare the microbial communities associated with the cabbage root fly Delia radicum and its three major parasitoids: the two staphylinid beetles Aleochara bilineata and A. bipustulata and the hymenopteran parasitoid Trybliographa rapae. For each species, two populations from Western France were sampled and microbial communities were described through culture independent methods (454 pyrosequencing. Each sample harbored at least 59 to 261 different bacterial phylotypes but was strongly dominated by one or two. Microbial communities differed markedly in terms of composition and abundance, being mainly influenced by phylogenetic proximity but also geography to a minor extent. Surprisingly, despite their strong trophic interaction, parasitoids shared a very low proportion of microbial partners with their insect host. Three vertically transmitted symbionts from the genus Wolbachia, Rickettsia, and Spiroplasma were found in this study. Among them, Wolbachia and Spiroplasma were found in both the cabbage fly and at least one of its parasitoids, which could result from horizontal transfers through trophic interactions. Phylogenetic analysis showed that this hypothesis may explain some but not all cases. More work is needed to understand the dynamics of symbiotic associations within trophic network and the effect of these bacterial communities on the fitness of their hosts.

  17. Emerging Community-Acquired Methicillin-Resistant Staphylococcus Aureus Pneumonia

    Directory of Open Access Journals (Sweden)

    Dragana Orlovic

    2009-04-01

    Full Text Available Background: Methicillin-resistant Staphylococcus aureus (MRSA has been an important nosocomial pathogen worldwide for more than four decades. Community-acquired MRSA infections, generally occurring in previously healthy persons without recognizable risk factors for health care setting-related MRSA, are emerging as serious clinical and public health concerns. The most frequent of these community-based infections include skin and soft tissue infections and necrotizing pneumonias. A majority of causative community-acquired MRSA (CA-MRSA isolates are associated with genes that encode the virulence factor, Panton-Valentine leukocidin (PVL toxin. Aims & Objectives: To describe six cases of CA-MRSA pneumonia recently admitted to our community hospital in Florida, and discuss the epidemiology, clinical features, and management of these expanding infections. Methods/Study Design: The medical records of six patients with radiographically-confirmed pneumonia and positive sputum cultures for MRSA at the time of hospitalization at the Lawnwood Regional Medical Center and Heart Institute, Fort Pierce, Florida, from December 2006 through January 2007, were retrospectively reviewed. All patients were seen by one of the authors (DO, an infectious diseases consultant. Lawnwood Regional Medical Center is a 341-bed, acute care institution and regional referral center for four counties of Treasure Coast, FL. The hospital institution review board gave permission for this study. Results/Findings: Six patients (5 men, 1 woman with CA-MRSA pneumonia were identified. The mean patient age was 57 years (range, 32-79 years. Three patients had no history of previous hospital admission, while two patients had been last hospitalized two years prior to the study admission. Three elderly patients had known co-morbidities predisposing to pneumonia including carcinoma of the lung (2 patients, and cirrhosis, diabetes mellitus, chronic renal failure, COPD, and cardiomyopathy (1

  18. Linezolid has unique immunomodulatory effects in post-influenza community acquired MRSA pneumonia.

    Directory of Open Access Journals (Sweden)

    Urvashi Bhan

    Full Text Available Post influenza pneumonia is a leading cause of mortality and morbidity, with mortality rates approaching 60% when bacterial infections are secondary to multi-drug resistant (MDR pathogens. Staphylococcus aureus, in particular community acquired MRSA (cMRSA, has emerged as a leading cause of post influenza pneumonia.Linezolid (LZD prevents acute lung injury in murine model of post influenza bacterial pneumonia.Mice were infected with HINI strain of influenza and then challenged with cMRSA at day 7, treated with antibiotics (LZD or Vanco or vehicle 6 hours post bacterial challenge and lungs and bronchoalveolar lavage fluid (BAL harvested at 24 hours for bacterial clearance, inflammatory cell influx, cytokine/chemokine analysis and assessment of lung injury.Mice treated with LZD or Vanco had lower bacterial burden in the lung and no systemic dissemination, as compared to the control (no antibiotic group at 24 hours post bacterial challenge. As compared to animals receiving Vanco, LZD group had significantly lower numbers of neutrophils in the BAL (9×10(3 vs. 2.3×10(4, p < 0.01, which was associated with reduced levels of chemotactic chemokines and inflammatory cytokines KC, MIP-2, IFN-γ, TNF-α and IL-1β in the BAL. Interestingly, LZD treatment also protected mice from lung injury, as assessed by albumin concentration in the BAL post treatment with H1N1 and cMRSA when compared to vanco treatment. Moreover, treatment with LZD was associated with significantly lower levels of PVL toxin in lungs.Linezolid has unique immunomodulatory effects on host inflammatory response and lung injury in a murine model of post-viral cMRSA pneumonia.

  19. High-throughput nucleotide sequence analysis of diverse bacterial communities in leachates of decomposing pig carcasses

    OpenAIRE

    Seung Hak Yang; Joung Soo Lim; Modabber Ahmed Khan; Bong Soo Kim; Dong Yoon Choi; Eun Young Lee; Hee Kwon Ahn

    2015-01-01

    The leachate generated by the decomposition of animal carcass has been implicated as an environmental contaminant surrounding the burial site. High-throughput nucleotide sequencing was conducted to investigate the bacterial communities in leachates from the decomposition of pig carcasses. We acquired 51,230 reads from six different samples (1, 2, 3, 4, 6 and 14 week-old carcasses) and found that sequences representing the phylum Firmicutes predominated. The diversity of bacterial 16S rRNA gen...

  20. Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome.

    Science.gov (United States)

    Monaco, Cynthia L; Gootenberg, David B; Zhao, Guoyan; Handley, Scott A; Ghebremichael, Musie S; Lim, Efrem S; Lankowski, Alex; Baldridge, Megan T; Wilen, Craig B; Flagg, Meaghan; Norman, Jason M; Keller, Brian C; Luévano, Jesús Mario; Wang, David; Boum, Yap; Martin, Jeffrey N; Hunt, Peter W; Bangsberg, David R; Siedner, Mark J; Kwon, Douglas S; Virgin, Herbert W

    2016-03-01

    Human immunodeficiency virus (HIV) infection is associated with increased intestinal translocation of microbial products and enteropathy as well as alterations in gut bacterial communities. However, whether the enteric virome contributes to this infection and resulting immunodeficiency remains unknown. We characterized the enteric virome and bacterial microbiome in a cohort of Ugandan patients, including HIV-uninfected or HIV-infected subjects and those either treated with anti-retroviral therapy (ART) or untreated. Low peripheral CD4 T cell counts were associated with an expansion of enteric adenovirus sequences and this increase was independent of ART treatment. Additionally, the enteric bacterial microbiome of patients with lower CD4 T counts exhibited reduced phylogenetic diversity and richness with specific bacteria showing differential abundance, including increases in Enterobacteriaceae, which have been associated with inflammation. Thus, immunodeficiency in progressive HIV infection is associated with alterations in the enteric virome and bacterial microbiome, which may contribute to AIDS-associated enteropathy and disease progression. PMID:26962942

  1. Detection and serotyping of pneumococci in community acquired pneumonia patients without culture using blood and urine samples

    OpenAIRE

    Elberse, K. (Karin); Mens, S.; Cremers, A.J.; Meijvis, S.C.A.; Vlaminckx, B.; de Jonge, M. I.; Meis, J. F. G. M.; Blauwendraat, C.; Pol, I. van de; Schouls, L. M.

    2015-01-01

    Background Treatment of community acquired pneumonia (CAP) patients with antibiotics before laboratory-confirmed diagnosis leads to loss of knowledge on the causative bacterial pathogen. Therefore, an increasing number of pneumococcal infections is identified using non-culture based techniques. However, methods for serotyping directly on the clinical specimen remain scarce. Here we present three approaches for detection and serotyping of pneumococci using samples from patients with CAP. Metho...

  2. Antimicrobial susceptibility patterns of ESBL Escherichia coli isolated from community and hospital-acquired urinary tract infections

    OpenAIRE

    Najwa Al Mously; Ohoud Al Arfaj; Lenah Al Fadhil; Shazia Mukaddam

    2016-01-01

    Context: Increasing resistance of extended-spectrum β-lactamases (ESBL) producing bacteria is an important challenge for clinicians. Aims: Monitor the antibiotic susceptibility pattern of community and hospital acquired urinary tract infections (UTIs) caused by ESBL Escherichia coli. Settings and Design: This is a retrospective observational study that was conducted at a tertiary hospital in Riyadh. Materials and Methods: Results of urine culture with E. coli and their bacterial anti...

  3. An unprecedented outbreak investigation for nosocomial and community-acquired legionellosis in Hong Kong

    Institute of Scientific and Technical Information of China (English)

    CHENG Vincent Chi-chung; HO Pak-leung; TSANG Thomas Ho-fai; YUEN Kwok-yung; WONG Samson Sai-yin; CHEN Jonathan Hon-kwan; CHAN Jasper Fuk-woo; TO Kelvin Kai-wang; POON Rosana Wing-shan; WONG Sally Cheuk-ying; CHAN Kwok-hung; TAI Josepha Wai-ming

    2012-01-01

    Background The environmental sources associated with community-acquired or nosocomial legionellosis were not always detectable in the mainland of China and Hong Kong,China.The objective of this study was to illustrate the control measures implemented for nosocomial and community outbreaks of legionellosis,and to understand the environmental distribution of legionella in the water system in Hong Kong,China.Methods We investigated the environmental sources of two cases of legionellosis acquired in the hospital and the community by extensive outbreak investigation and sampling of the potable water system using culture and genetic testing at the respective premises.Results The diagnosis of nosocomial legionellosis was suspected in a patient presenting with nosocomial pneumonia not responsive to multiple beta-lactam antibiotics with subsequent confirmation by Legionella pneumophila serogroup 1 antigenuria.High counts of Legionella pneumophila were detected in the potable water supply of the 70-year-old hospital building.Another patient on continuous ambulatory peritoneal dialysis presenting with acute community-acquired pneumonia and severe diarrhoea was positive for Legionella pneumophila serogroup 1 by polymerase chain reaction (PCR) testing on both sputum and nasopharyngeal aspirate despite negative antigenuria.Paradoxically the source of the second case was traced to the water system of a newly commissioned office building complex.No further cases were detected after shock hyperchlorination with or without superheating of the water systems.Subsequent legionella counts were drastically reduced.Point-of-care infection control by off-boiled or sterile water for mouth care and installation of water filter for showers in the hospital wards for immunocompromised patients was instituted.Territory wide investigation of the community potable water supply showed that 22.1% of the household water supply was positive at a mean legionella count of 108.56 CFU/ml (range 0.10 to

  4. Bacterial community development in experimental gingivitis.

    Science.gov (United States)

    Kistler, James O; Booth, Veronica; Bradshaw, David J; Wade, William G

    2013-01-01

    Current knowledge of the microbial composition of dental plaque in early gingivitis is based largely on microscopy and cultural methods, which do not provide a comprehensive description of oral microbial communities. This study used 454-pyrosequencing of the V1-V3 region of 16S rRNA genes (approximately 500 bp), and bacterial culture, to characterize the composition of plaque during the transition from periodontal health to gingivitis. A total of 20 healthy volunteers abstained from oral hygiene for two weeks, allowing plaque to accumulate and gingivitis to develop. Plaque samples were analyzed at baseline, and after one and two weeks. In addition, plaque samples from 20 chronic periodontitis patients were analyzed for cross-sectional comparison to the experimental gingivitis cohort. All of the healthy volunteers developed gingivitis after two weeks. Pyrosequencing yielded a final total of 344,267 sequences after filtering, with a mean length of 354 bases, that were clustered into an average of 299 species-level Operational Taxonomic Units (OTUs) per sample. Principal coordinates analysis (PCoA) plots revealed significant shifts in the bacterial community structure of plaque as gingivitis was induced, and community diversity increased significantly after two weeks. Changes in the relative abundance of OTUs during the transition from health to gingivitis were correlated to bleeding on probing (BoP) scores and resulted in the identification of new health- and gingivitis-associated taxa. Comparison of the healthy volunteers to the periodontitis patients also confirmed the association of a number of putative periodontal pathogens with chronic periodontitis. Taxa associated with gingivitis included Fusobacterium nucleatum subsp. polymorphum, Lachnospiraceae [G-2] sp. HOT100, Lautropia sp. HOTA94, and Prevotella oulorum, whilst Rothia dentocariosa was associated with periodontal health. Further study of these taxa is warranted and may lead to new therapeutic approaches

  5. Bacterial community development in experimental gingivitis.

    Science.gov (United States)

    Kistler, James O; Booth, Veronica; Bradshaw, David J; Wade, William G

    2013-01-01

    Current knowledge of the microbial composition of dental plaque in early gingivitis is based largely on microscopy and cultural methods, which do not provide a comprehensive description of oral microbial communities. This study used 454-pyrosequencing of the V1-V3 region of 16S rRNA genes (approximately 500 bp), and bacterial culture, to characterize the composition of plaque during the transition from periodontal health to gingivitis. A total of 20 healthy volunteers abstained from oral hygiene for two weeks, allowing plaque to accumulate and gingivitis to develop. Plaque samples were analyzed at baseline, and after one and two weeks. In addition, plaque samples from 20 chronic periodontitis patients were analyzed for cross-sectional comparison to the experimental gingivitis cohort. All of the healthy volunteers developed gingivitis after two weeks. Pyrosequencing yielded a final total of 344,267 sequences after filtering, with a mean length of 354 bases, that were clustered into an average of 299 species-level Operational Taxonomic Units (OTUs) per sample. Principal coordinates analysis (PCoA) plots revealed significant shifts in the bacterial community structure of plaque as gingivitis was induced, and community diversity increased significantly after two weeks. Changes in the relative abundance of OTUs during the transition from health to gingivitis were correlated to bleeding on probing (BoP) scores and resulted in the identification of new health- and gingivitis-associated taxa. Comparison of the healthy volunteers to the periodontitis patients also confirmed the association of a number of putative periodontal pathogens with chronic periodontitis. Taxa associated with gingivitis included Fusobacterium nucleatum subsp. polymorphum, Lachnospiraceae [G-2] sp. HOT100, Lautropia sp. HOTA94, and Prevotella oulorum, whilst Rothia dentocariosa was associated with periodontal health. Further study of these taxa is warranted and may lead to new therapeutic approaches

  6. Bacterial community development in experimental gingivitis.

    Directory of Open Access Journals (Sweden)

    James O Kistler

    Full Text Available Current knowledge of the microbial composition of dental plaque in early gingivitis is based largely on microscopy and cultural methods, which do not provide a comprehensive description of oral microbial communities. This study used 454-pyrosequencing of the V1-V3 region of 16S rRNA genes (approximately 500 bp, and bacterial culture, to characterize the composition of plaque during the transition from periodontal health to gingivitis. A total of 20 healthy volunteers abstained from oral hygiene for two weeks, allowing plaque to accumulate and gingivitis to develop. Plaque samples were analyzed at baseline, and after one and two weeks. In addition, plaque samples from 20 chronic periodontitis patients were analyzed for cross-sectional comparison to the experimental gingivitis cohort. All of the healthy volunteers developed gingivitis after two weeks. Pyrosequencing yielded a final total of 344,267 sequences after filtering, with a mean length of 354 bases, that were clustered into an average of 299 species-level Operational Taxonomic Units (OTUs per sample. Principal coordinates analysis (PCoA plots revealed significant shifts in the bacterial community structure of plaque as gingivitis was induced, and community diversity increased significantly after two weeks. Changes in the relative abundance of OTUs during the transition from health to gingivitis were correlated to bleeding on probing (BoP scores and resulted in the identification of new health- and gingivitis-associated taxa. Comparison of the healthy volunteers to the periodontitis patients also confirmed the association of a number of putative periodontal pathogens with chronic periodontitis. Taxa associated with gingivitis included Fusobacterium nucleatum subsp. polymorphum, Lachnospiraceae [G-2] sp. HOT100, Lautropia sp. HOTA94, and Prevotella oulorum, whilst Rothia dentocariosa was associated with periodontal health. Further study of these taxa is warranted and may lead to new

  7. Comparative antimicrobial susceptibility of aerobic and facultative bacteria from community-acquired bacteremia to ertapenem in Taiwan

    Directory of Open Access Journals (Sweden)

    Fung Chang-Phone

    2007-07-01

    Full Text Available Abstract Background Ertapenem is a once-a-day carbapenem and has excellent activity against many gram-positive and gram-negative aerobic, facultative, and anaerobic bacteria. The susceptibility of isolates of community-acquired bacteremia to ertapenem has not been reported yet. The present study assesses the in vitro activity of ertapenem against aerobic and facultative bacterial pathogens isolated from patients with community-acquired bacteremia by determining and comparing the MICs of cefepime, cefoxitin, ceftazidime, ceftriaxone, ertapenem, piperacillin, piperacillin-tazobactam, ciprofloxacin, amikacin and gentamicin. The prevalence of extended broad spectrum β-lactamases (ESBL producing strains of community-acquired bacteremia and their susceptibility to these antibiotics are investigated. Methods Aerobic and facultative bacteria isolated from blood obtained from hospitalized patients with community-acquired bacteremia within 48 hours of admission between August 1, 2004 and September 30, 2004 in Chang Gung Memorial Hospital at Keelung, Taiwan, were identified using standard procedures. Antimicrobial susceptibility was evaluated by Etest according to the standard guidelines provided by the manufacturer and document M100-S16 Performance Standards of the Clinical Laboratory of Standard Institute. Antimicrobial agents including cefepime, cefoxitin, ceftazidime, ceftriaxone, ertapenem, piperacillin, piperacillin-tazobactam, ciprofloxacin, amikacin and gentamicin were used against the bacterial isolates to test their MICs as determined by Etest. For Staphylococcus aureus isolates, MICs of oxacillin were also tested by Etest to differentiate oxacillin-sensitive and oxacillin-resistant S. aureus. Results Ertapenem was highly active in vitro against many aerobic and facultative bacterial pathogens commonly recovered from patients with community-acquired bacteremia (128/159, 80.5 %. Ertapenem had more potent activity than ceftriaxone, piperacillin

  8. Higher incidence of perineal community acquired MRSA infections among toddlers

    Directory of Open Access Journals (Sweden)

    Blumenthal Robert M

    2011-10-01

    Full Text Available Abstract Background A six-fold increase in pediatric MRSA infections, prompted us to examine the clinical profile of children with MRSA infections seen at Mercy Children's Hospital, Toledo, Ohio and to characterize the responsible strains. Methods Records were reviewed of pediatric patients who cultured positive for MRSA from June 1 to December 31, 2007. Strain typing by pulsed field gel electrophoresis (PFT and DiversiLab, SCCmec typing, and PCR-based lukSF-PV gene (encodes Panton-Valentine leukocidin, arginine catabolic mobile element (ACME and cap5 gene detection was performed. Results Chart review of 63 patients with MRSA infections revealed that 58(92% were community acquired MRSA (CAMRSA. All CAMRSA were skin and soft tissue infections (SSTI. Twenty five (43% patients were aged mec type IVa and lukSF-PV gene positive. Nearly all contained ACME and about 80% were cap5 positive. Of the 58 USA300 strains by PFT, 55(95% were also identified as USA300 via the automated repetitive sequence-based PCR method from DiversiLab. Conclusions CAMRSA SSTI of the perineum was significantly more common among toddlers and that of the extremities in older children. The infecting strains were all USA300 PFT. Further studies are needed to identify the unique virulence and colonization characteristics of USA300 strains in these infections.

  9. Cefditoren in upper and lower community-acquired respiratory tract infections

    Directory of Open Access Journals (Sweden)

    Francisco Soriano

    2011-02-01

    Full Text Available Francisco Soriano1, María-José Giménez1,2, Lorenzo Aguilar1,21PRISM-AG, Madrid, Spain; 2Microbiology Department, School of Medicine, University Complutense, Madrid, SpainAbstract: This article reviews and updates published data on cefditoren in the evolving scenario of resistance among the most prevalent isolates from respiratory tract infections in the community (Streptococcus pyogenes, Haemophilus influenzae, and Streptococcus pneumoniae. By relating the in vitro activity of cefditoren (in national and multinational surveillance and against isolates with emerging resistant genotypes/phenotypes to its pharmacokinetics, the cefditoren pharmacodynamic activity predicting efficacy (in humans, animal models, and in vitro simulations is analyzed prior to reviewing clinical studies (tonsillopharyngitis, sinusitis, acute exacerbations of chronic bronchitis, and community-acquired pneumonia and the relationship between bacterial eradication and clinical efficacy. The high in vitro activity of cefditoren against the most prevalent respiratory isolates in the community, together with its pharmacokinetics (enabling a twice daily regimen leading to adequate pharmacodynamic indexes covering all S. pyogenes, H. influenzae, and at least 95% S. pneumoniae isolates, makes cefditoren an antibiotic that will play a significant role in the treatment of respiratory tract infections in the community. In the clinical setting, studies carried out with cefditoren showed that treatments with the 400 mg twice daily regimen were associated with high rates of bacteriological response, even against penicillin-nonsusceptible S. pneumoniae, with good correlation between bacteriological efficacy/response and clinical outcome.Keywords: cefditoren, Streptococcus pyogenes, Haemophilus influenzae, Streptococcus pneumoniae, community-acquired respiratory tract infections

  10. Soil bacterial community responses to global changes

    DEFF Research Database (Denmark)

    Bergmark, Lasse

    the bacterial soil population. The thesis addresses the effects of different global change manipulations on the soil microbial community composition (climate change in Manuscript 1-4 and unconventional urban fertilizers in Manuscript 5-6). A special emphasis was put on combining molecular techniques like 454......’ of climate change manipulations on soil microorganisms and nutrient availability in a Danish heathland, where the samples were taken shortly after a prolonged pre-summer drought. The major findings in the study are that warming increased measures of fungi and bacteria and drought might shift/change...... overall importance for ecosystem function in soil is poorly understood. Global change factors may affect the diversity and functioning of soil prokaryotes and thereby ecosystem functioning. To gain a better understanding of the effects of global changes it is of fundamental importance to classify...

  11. Conservation of acquired morphology and community structure in aged biofilms after facing environmental stress.

    Science.gov (United States)

    Saur, T; Escudié, R; Santa-Catalina, G; Bernet, N; Milferstedt, K

    2016-01-01

    The influence of growth history on biofilm morphology and microbial community structure is poorly studied despite its important role for biofilm development. Here, biofilms were exposed to a change in hydrodynamic conditions at different growth stages and we observed how biofilm age affected the change in morphology and bacterial community structure. Biofilms were developed in two bubble column reactors, one operated under constant shear stress and one under variable shear stress. Biofilms were transferred from one reactor to the other at different stages in their development by withdrawing and inserting the support medium from one reactor to the other. The developments of morphology and microbial community structure were followed by image analysis and molecular tools. When transferred early in biofilm development, biofilms adapted to the new hydrodynamic conditions and adopted features of the biofilm already developed in the receiving reactor. Biofilms transferred at a late state of biofilm development continued their initial trajectories of morphology and community development even in a new environment. These biofilms did not immediately adapt to their new environment and kept features acquired during their early growth phase, a property we called memory effect.

  12. Age, sun and substrate: triggers of bacterial communities in lichens.

    Science.gov (United States)

    Cardinale, Massimiliano; Steinová, Jana; Rabensteiner, Johannes; Berg, Gabriele; Grube, Martin

    2012-02-01

    Bacterial communities colonize the surfaces of lichens in a biofilm-like manner. The overall structure of the bacterial communities harboured by the lichens shows similarities, in particular the dominance of not yet cultured Alphaproteobacteria. Parameters causing variation in abundance, composition and spatial organization of the lichen-associated bacterial communities are so far poorly understood. As a first step, we used a microscopic approach to test the significance of both lichen-intrinsic and extrinsic environmental factors on the bacterial communities associated with 11 lichen samples, belonging to six species. Some of these species have thalli with a distinct age gradient. A statistically significant effect can be attributed to the age of the thallus parts, which is an intrinsic factor: growing parts of the lichens host bacterial communities that significantly differ from those of the ageing portions of the thalli. The substrate type (rock, tree, understory) and (at a lower extent) the exposition to the sun also affected the bacterial communities. Interestingly, the abundance of bacterial cells in the lichens was also influenced by the same structure-triggering factors. No effect on the composition with main bacterial groups was attributed to different lichen species, differentiated thallus parts or thallus growth type. Our results are important for the experimental designs in lichen-bacterial ecology. PMID:23757225

  13. Association between Obstructive Sleep Apnea and Community-Acquired Pneumonia.

    Directory of Open Access Journals (Sweden)

    Eusebi Chiner

    Full Text Available We hypothesized that obstructive sleep apnea (OSA can predispose individuals to lower airway infections and community-acquired pneumonia (CAP due to upper airway microaspiration. This study evaluated the association between OSA and CAP.We performed a case-control study that included 82 patients with CAP and 41 patients with other infections (control group. The controls were matched according to age, sex and body mass index (BMI. A respiratory polygraph (RP was performed upon admission for patients in both groups. The severity of pneumonia was assessed according to the Pneumonia Severity Index (PSI. The associations between CAP and the Epworth Sleepiness Scale (ESS, OSA, OSA severity and other sleep-related variables were evaluated using logistic regression models. The associations between OSA, OSA severity with CAP severity were evaluated with linear regression models and non-parametric tests.No significant differences were found between CAP and control patients regarding anthropometric variables, toxic habits and risk factors for CAP. Patients with OSA, defined as individuals with an Apnea-Hypopnea Index (AHI ≥10, showed an increased risk of CAP (OR = 2·86, 95%CI 1·29-6·44, p = 0·01. Patients with severe OSA (AHI≥30 also had a higher risk of CAP (OR = 3·18, 95%CI 1·11-11·56, p = 0·047. In addition, OSA severity, defined according to the AHI quartile, was also significantly associated with CAP (p = 0·007. Furthermore, OSA was significantly associated with CAP severity (p = 0·0002, and OSA severity was also associated with CAP severity (p = 0·0006.OSA and OSA severity are associated with CAP when compared to patients admitted to the hospital for non-respiratory infections. In addition, OSA and OSA severity are associated with CAP severity. These results support the potential role of OSA in the pathogenesis of CAP and could have clinical implications. This link between OSA and infection risk should be explored to investigate the

  14. Determinants for hospitalization in " low-risk" community acquired pneumonia

    Directory of Open Access Journals (Sweden)

    Aliyu Muktar H

    2003-06-01

    Full Text Available Abstract Background A variable decision in managing community acquired pneumonia (CAP is the initial site of care; in-patient versus outpatient. These variations persist despite comprehensive practice guidelines. Patients with a Pneumonia Severity Index (PSI score lower than seventy have low risk for complications and outpatient antibiotic management is recommended in this group. These patients are generally below the age of fifty years, non-nursing home residents, HIV negative and have no major cardiac, hepatic, renal or malignant diseases. Methods A retrospective analysis of 296 low-risk CAP patients evaluated within a year one period at St. Agnes Hospital, Baltimore, Maryland was undertaken. All patients were assigned a PSI score. 208 (70% were evaluated and discharged from the emergency department (E.D. to complete outpatient antibiotic therapy, while 88 (30% were hospitalized. Patients were sub-stratified into classes I-V according to PSI. A comparison of demographic, clinical, social and financial parameters was made between the E.D. discharged and hospitalized groups. Results Statistically significant differences in favor of the hospitalized group were noted for female gender (CI: 1.46-5.89, p= 0.0018, African Americans (CI: 0.31-0.73, p= 0.004, insurance coverage (CI: 0.19-0.63, p= 0.0034, temperature (CI: 0.04-0.09, p= 0.0001 and pulse rate (CI: 0.03-0.14, p= 0.0001. No statistically significant differences were observed between the two groups for altered mental status, hypotension, tachypnea, laboratory/radiological parameters and social indicators (p>0.05. The average length of stay for in-patients was 3.5 days at about eight time's higher cost than outpatient management. There was no difference in mortality or treatment failures between the two groups. The documentation rate and justifications for hospitalizing low risk CAP patients by admitting physicians was less than optimal. Conclusions High fever, tachycardia, female gender

  15. Association between Obstructive Sleep Apnea and Community-Acquired Pneumonia

    Science.gov (United States)

    Chiner, Eusebi; Llombart, Mónica; Valls, Joan; Pastor, Esther; Sancho-Chust, José N.; Andreu, Ada Luz; Sánchez-de-la-Torre, Manuel; Barbé, Ferran

    2016-01-01

    Background We hypothesized that obstructive sleep apnea (OSA) can predispose individuals to lower airway infections and community-acquired pneumonia (CAP) due to upper airway microaspiration. This study evaluated the association between OSA and CAP. Methods We performed a case-control study that included 82 patients with CAP and 41 patients with other infections (control group). The controls were matched according to age, sex and body mass index (BMI). A respiratory polygraph (RP) was performed upon admission for patients in both groups. The severity of pneumonia was assessed according to the Pneumonia Severity Index (PSI). The associations between CAP and the Epworth Sleepiness Scale (ESS), OSA, OSA severity and other sleep-related variables were evaluated using logistic regression models. The associations between OSA, OSA severity with CAP severity were evaluated with linear regression models and non-parametric tests. Findings No significant differences were found between CAP and control patients regarding anthropometric variables, toxic habits and risk factors for CAP. Patients with OSA, defined as individuals with an Apnea-Hypopnea Index (AHI) ≥10, showed an increased risk of CAP (OR = 2·86, 95%CI 1·29–6·44, p = 0·01). Patients with severe OSA (AHI≥30) also had a higher risk of CAP (OR = 3·18, 95%CI 1·11–11·56, p = 0·047). In addition, OSA severity, defined according to the AHI quartile, was also significantly associated with CAP (p = 0·007). Furthermore, OSA was significantly associated with CAP severity (p = 0·0002), and OSA severity was also associated with CAP severity (p = 0·0006). Conclusions OSA and OSA severity are associated with CAP when compared to patients admitted to the hospital for non-respiratory infections. In addition, OSA and OSA severity are associated with CAP severity. These results support the potential role of OSA in the pathogenesis of CAP and could have clinical implications. This link between OSA and infection risk

  16. Bartonella spp. and Coxiella burnetii Associated with Community-Acquired, Culture-Negative Endocarditis, Brazil.

    Science.gov (United States)

    Siciliano, Rinaldo Focaccia; Castelli, Jussara Bianchi; Mansur, Alfredo Jose; Pereira dos Santos, Fabiana; Colombo, Silvia; do Nascimento, Elvira Mendes; Paddock, Christopher D; Brasil, Roosecelis Araújo; Velho, Paulo Eduardo Neves Ferreira; Drummond, Marina Rovani; Grinberg, Max; Strabelli, Tania Mara Varejao

    2015-08-01

    We evaluated culture-negative, community-acquired endocarditis by using indirect immunofluorescent assays and molecular analyses for Bartonella spp. and Coxiella burnetii and found a prevalence of 19.6% and 7.8%, respectively. Our findings reinforce the need to study these organisms in patients with culture-negative, community-acquired endocarditis, especially B. henselae in cat owners.

  17. An Outbreak of Community-Acquired Foodborne Illness Caused by Methicillin-Resistant Staphylococcus aureus

    OpenAIRE

    Jones, Timothy F.; Kellum, Molly E.; Porter, Susan S.; Bell, Michael; Schaffner, William

    2002-01-01

    Infections with methicillin-resistant Staphylococcus aureus (MRSA) are increasingly community acquired. We investigated an outbreak in which a food handler, food specimen, and three ill patrons were culture positive for the same toxin-producing strain of MRSA. This is the first report of an outbreak of gastrointestinal illness caused by community-acquired MRSA.

  18. The role of procalcitonin in adult patients with community-acquired pneumonia--a systematic review

    DEFF Research Database (Denmark)

    Berg, Peter; Lindhardt, Bjarne Ørskov

    2012-01-01

    Promising results in relation to severity assessment and treatment of patients with community-acquired pneumonia (CAP) have recently been presented from the study of procalcitonin (PCT) levels in these patients.......Promising results in relation to severity assessment and treatment of patients with community-acquired pneumonia (CAP) have recently been presented from the study of procalcitonin (PCT) levels in these patients....

  19. 2009-2013年我国16省市社区获得性细菌性腹泻病原菌分布及临床耐药分析%Distribution of the community-acquired bacterial diarrheal pathogens and drug resistance in 16 provinces or cities in China during 2009-2013

    Institute of Scientific and Technical Information of China (English)

    崔恩博; 曲芬; 毛远丽; 陈素明; 张成龙; 王勇; 贾天野; 鲍春梅; 张鞠玲; 王欢; 庞君丽

    2014-01-01

    Objective To analyze the characteristics of the community-acquired bacterial diarrheal pathogen spectrum and drug resistance in China during 5 years. Methods The strains isolated from the stool samples of patients with community-acquired bacterial diarrhea were collected from 16 provinces or cities in China during 2009-2013. The bacteria were incubated with Salmo-nella, Shigella agar, gentamicin agar and MacConkey agar plate and identification of pathogens suspected to be the cause of diarrhea was performed by VITEKⅡinstrument and biochemical reaction trace coding tube. Then, Salmonella, Shigella, Vibrio and diarrhea-genic Escherichia coli were serotyped by serum agglutination test. K-B method was used for antimicrobial susceptibility testing of bacterial pathogens. Results A total of 10 881 strains of diarrheal pathogens, including 7 genus, 22 species and 90 serotypes were isolated from diarrheal patients from 16 provinces or cities in China during 5 years. There were 7632 (70.14%) strains of Shigella, 1351 (12.42%) strains of Vibrio, 981 (9.02%) strains of Salmonella , 341 (3.13%) strains of diarrheagenic Escherichia coli, 302 (2.78%) strains of Aeromonas, 269 (2.47%) strains of Plesiomonas, and 5 (0.05%) strains of Yersinia enterocolitica. The major serotypes of Shigella were F2a, F4a and F1a belonging to group B and the major serotypes of Salmonella were Salmonella enteritidis and Salmonella typhimurium. Drug sensitivity monitoring showed that Shigella had better sensitivity to cefotaxime, cefepime, cefmetazole, imipenem and fosfomycin, with the sensitivity rates of 89.7%, 92.3%, 96.7%, 100%and 97.7%; the sensitive rates of Salmonella to cefotaxime, cefepime, aztreonam, imipenem and fosfomycin were 94.0%, 97.9%, 94.4%, 100% and 96.4%; the sensitive rates of Aeromonas to cefepime, levofloxacin, imipenem and fosfomycin were 80.9%, 80.0%, 92.6% and 84.0%; diarrheagenic Escherichia coli had poor sensitivity to antibiotics generally; Vibrio had good sensitivity to

  20. Stability of multispecies bacterial communities: signaling networks may stabilize microbiomes.

    Directory of Open Access Journals (Sweden)

    Ádám Kerényi

    Full Text Available Multispecies bacterial communities can be remarkably stable and resilient even though they consist of cells and species that compete for environmental resources. In silico models suggest that common signals released into the environment may help selected bacterial species cluster at common locations and that sharing of public goods (i.e. molecules produced and released for mutual benefit can stabilize this coexistence. In contrast, unilateral eavesdropping on signals produced by a potentially invading species may protect a community by keeping invaders away from limited resources. Shared bacterial signals, such as those found in quorum sensing systems, may thus play a key role in fine tuning competition and cooperation within multi-bacterial communities. We suggest that in addition to metabolic complementarity, signaling dynamics may be important in further understanding complex bacterial communities such as the human, animal as well as plant microbiomes.

  1. Viral infection in community-acquired pneumonia: a systematic review and meta-analysis

    Directory of Open Access Journals (Sweden)

    Michael Burk

    2016-06-01

    Full Text Available The advent of PCR has improved the identification of viruses in patients with community-acquired pneumonia (CAP. Several studies have used PCR to establish the importance of viruses in the aetiology of CAP. We performed a systematic review and meta-analysis of the studies that reported the proportion of viral infection detected via PCR in patients with CAP. We excluded studies with paediatric populations. The primary outcome was the proportion of patients with viral infection. The secondary outcome was short-term mortality. Our review included 31 studies. Most obtained PCR via nasopharyngeal or oropharyngeal swab. The pooled proportion of patients with viral infection was 24.5% (95% CI 21.5–27.5%. In studies that obtained lower respiratory samples in >50% of patients, the proportion was 44.2% (95% CI 35.1–53.3%. The odds of death were higher in patients with dual bacterial and viral infection (OR 2.1, 95% CI 1.32–3.31. Viral infection is present in a high proportion of patients with CAP. The true proportion of viral infection is probably underestimated because of negative test results from nasopharyngeal or oropharyngeal swab PCR. There is increased mortality in patients with dual bacterial and viral infection.

  2. Diversity of Bacterial Communities of Fitness Center Surfaces in a U.S. Metropolitan Area

    Directory of Open Access Journals (Sweden)

    Nabanita Mukherjee

    2014-12-01

    Full Text Available Public fitness centers and exercise facilities have been implicated as possible sources for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial community residing on the surfaces in these indoor environments is still unknown. In this study, we investigated the overall bacterial ecology of selected fitness centers in a metropolitan area (Memphis, TN, USA utilizing culture-independent pyrosequencing of the 16S rRNA genes. Samples were collected from the skin-contact surfaces (e.g., exercise instruments, floor mats, handrails, etc. within fitness centers. Taxonomical composition revealed the abundance of Firmicutes phyla, followed by Proteobacter and Actinobacteria, with a total of 17 bacterial families and 25 bacterial genera. Most of these bacterial genera are of human and environmental origin (including, air, dust, soil, and water. Additionally, we found the presence of some pathogenic or potential pathogenic bacterial genera including Salmonella, Staphylococcus, Klebsiella, and Micrococcus. Staphylococcus was found to be the most prevalent genus. Presence of viable forms of these pathogens elevates risk of exposure of any susceptible individuals. Several factors (including personal hygiene, surface cleaning and disinfection schedules of the facilities may be the reasons for the rich bacterial diversity found in this study. The current finding underscores the need to increase public awareness on the importance of personal hygiene and sanitation for public gym users.

  3. Spatial structuring of bacterial communities within individual Ginkgo biloba trees.

    Science.gov (United States)

    Leff, Jonathan W; Del Tredici, Peter; Friedman, William E; Fierer, Noah

    2015-07-01

    Plant-associated microorganisms affect the health of their hosts in diverse ways, yet the distribution of these organisms within individual plants remains poorly understood. To address this knowledge gap, we assessed the spatial variability in bacterial community diversity and composition found on and in aboveground tissues of individual Ginkgo biloba trees. We sampled bacterial communities from > 100 locations per tree, including leaf, branch and trunk samples and used high-throughput sequencing of the 16S rRNA gene to determine the diversity and composition of these communities. Bacterial community structure differed strongly between bark and leaf samples, with bark samples harbouring much greater bacterial diversity and a community composition distinct from leaves. Within sample types, we observed clear spatial patterns in bacterial diversity and community composition that corresponded to the samples' proximity to the exterior of the tree. The composition of the bacterial communities found on trees is highly variable, but this variability is predictable and dependent on sampling location. Moreover, this work highlights the importance of carefully considering plant spatial structure when characterizing the microbial communities associated with plants and their impacts on plant hosts.

  4. High-throughput nucleotide sequence analysis of diverse bacterial communities in leachates of decomposing pig carcasses

    Directory of Open Access Journals (Sweden)

    Seung Hak Yang

    2015-09-01

    Full Text Available The leachate generated by the decomposition of animal carcass has been implicated as an environmental contaminant surrounding the burial site. High-throughput nucleotide sequencing was conducted to investigate the bacterial communities in leachates from the decomposition of pig carcasses. We acquired 51,230 reads from six different samples (1, 2, 3, 4, 6 and 14 week-old carcasses and found that sequences representing the phylum Firmicutes predominated. The diversity of bacterial 16S rRNA gene sequences in the leachate was the highest at 6 weeks, in contrast to those at 2 and 14 weeks. The relative abundance of Firmicutes was reduced, while the proportion of Bacteroidetes and Proteobacteria increased from 3–6 weeks. The representation of phyla was restored after 14 weeks. However, the community structures between the samples taken at 1–2 and 14 weeks differed at the bacterial classification level. The trend in pH was similar to the changes seen in bacterial communities, indicating that the pH of the leachate could be related to the shift in the microbial community. The results indicate that the composition of bacterial communities in leachates of decomposing pig carcasses shifted continuously during the study period and might be influenced by the burial site.

  5. Microbial Etiology of Community-Acquired Pneumonia Among Infants and Children Admitted to the Pediatric Hospital, Ain Shams University

    Science.gov (United States)

    El Seify, Magda Yehia; Fouda, Eman Mahmoud; Ibrahim, Hanan Mohamed; Fathy, Maha Muhammad; Husseiny Ahmed, Asmaa Al; Khater, Walaa Shawky; El Deen, Noha Nagi Mohammed Salah; Abouzeid, Heba Galal Mohamed; Hegazy, Nancy Riyad Ahmed; Elbanna, Heba Salah Sayed

    2016-01-01

    Background While recognizing the etiology of community-acquired pneumonia is necessary for formulating local antimicrobial guidelines, limited data is published about this etiology in Egyptian pediatric patients. Objectives To determine the frequency of bacterial and viral pathogens causing community-acquired pneumonia (CAP) among immunocompetent Egyptian infants and preschool children. Methods Ninety infants and preschool-age children admitted to our hospital with CAP were prospectively included in the study. Etiological agents were identified using conventional bacteriological identification methods and IgM antibodies detection against common atypical respiratory bacteria and viruses. Results An etiology was identified in 59 patients (65.5%). Bacterial pathogens were detected in 43 (47.8%) of the cases while viral pathogens were detected in 23 (25.5%). Coinfection with more than one etiologic agent was evident in seven patients (7.8%). The most common typical bacterial cause of pneumonia was Staphylococcus aureus (n = 12, 13.3%), followed by Streptococcus pneumoniae and Klebsiella pneumoniae (n = 7, 7.8%, each). The commonest atypical bacterium was Mycoplasma pneumoniae (n = 10, 11.1%), whereas the commonest viral etiology was influenza viruses (n = 11, 12.2%). Conclusion Although we could not determine the causative agent in some studied cases, this study provides preliminary data regarding the spectrum and frequency of microorganisms causing CAP in Egyptian infants and preschool children.

  6. Drug resistance in community-acquired respiratory tract infections: role for an emerging antibacterial

    Directory of Open Access Journals (Sweden)

    Lorenzo Aguilar

    2010-06-01

    Full Text Available Lorenzo Aguilar1, María-José Giménez1, José Barberán21Microbiology Department, School of Medicine, University Complutense, Madrid; 2Infectious Diseases Department, Hospital Central de la Defensa Gomez Ulla, Madrid, SpainAbstract: The nasopharynx is the ecological niche where evolution towards resistance occurs in respiratory tract isolates. Dynamics of different bacterial populations in antibiotic-free multibacterial niches are the baseline that antibiotic treatments can alter by shifting the competitive balance in favor of resistant populations. For this reason, antibiotic resistance is increasingly being considered to be an ecological problem. Traditionally, resistance has implied the need for development of new antibiotics for which basic efficacy and safety data are required prior to licensing. Antibiotic development is mainly focused on demonstrating clinical efficacy and setting susceptibility breakpoints for efficacy prediction. However, additional information on pharmacodynamic data predicting absence of selection of resistance and of resistant subpopulations, and specific surveillance on resistance to core antibiotics (to detect emerging resistances and its link with antibiotic consumption in the community are valuable data in defining the role of a new antibiotic, not only from the perspective of its therapeutic potential but also from the ecologic perspective (countering resistances to core antibiotics in the community. The documented information on cefditoren gleaned from published studies in recent years is an example of the role for an emerging oral antibacterial facing current antibiotic resistance in community-acquired respiratory tract infections.Keywords: respiratory tract infection, antibiotic resistance, cefditoren, community

  7. Differential regulation of horizontally acquired and core genome genes by the bacterial modulator H-NS.

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    Rosa C Baños

    2009-06-01

    Full Text Available Horizontal acquisition of DNA by bacteria dramatically increases genetic diversity and hence successful bacterial colonization of several niches, including the human host. A relevant issue is how this newly acquired DNA interacts and integrates in the regulatory networks of the bacterial cell. The global modulator H-NS targets both core genome and HGT genes and silences gene expression in response to external stimuli such as osmolarity and temperature. Here we provide evidence that H-NS discriminates and differentially modulates core and HGT DNA. As an example of this, plasmid R27-encoded H-NS protein has evolved to selectively silence HGT genes and does not interfere with core genome regulation. In turn, differential regulation of both gene lineages by resident chromosomal H-NS requires a helper protein: the Hha protein. Tight silencing of HGT DNA is accomplished by H-NS-Hha complexes. In contrast, core genes are modulated by H-NS homoligomers. Remarkably, the presence of Hha-like proteins is restricted to the Enterobacteriaceae. In addition, conjugative plasmids encoding H-NS variants have hitherto been isolated only from members of the family. Thus, the H-NS system in enteric bacteria presents unique evolutionary features. The capacity to selectively discriminate between core and HGT DNA may help to maintain horizontally transmitted DNA in silent form and may give these bacteria a competitive advantage in adapting to new environments, including host colonization.

  8. Dynamics of seawater bacterial communities in a shellfish hatchery.

    Science.gov (United States)

    Powell, S M; Chapman, C C; Bermudes, M; Tamplin, M L

    2013-08-01

    Bacterial disease is a significant issue for larviculture of several species of shellfish, including oysters. One source of bacteria is the seawater used throughout the hatchery. In this study carried out at a commercial oyster hatchery in Tasmania, Australia, the diversity of the bacterial community and its relationship with larval production outcomes were studied over a 2-year period using terminal restriction fragment length polymorphism and tag-encoded pyrosequencing. The bacterial communities were very diverse, dominated by the Alphaproteobacteria, Gammaproteobacteria, Flavobacteria and Cyanobacteria. The communities were highly variable on scales of days, weeks and seasons. The difference between the intake seawater and treated clean seawater used in the hatchery was smaller than the observed temporal differences in the seawater throughout the year. No clear correlation was observed between production outcomes and the overall bacterial community structure. However, one group of Cyanobacterial sequences was more abundant when mass mortality events occurred than when healthy spat were produced although they were always present.

  9. CHANGING TRENDS OF ANTIBIOGRAM PROFILE IN PATIENTS WITH COMMUNITY ACQUIRED CHRONIC OTITIS MEDIA IN A TERTIARY CARE HOSPITAL

    Directory of Open Access Journals (Sweden)

    Bipasa

    2014-09-01

    Full Text Available : INTRODUCTION: Chronic otitis media (COM is one among the commonest otological diseases encountered in otorhinolaryngological practice and attending ENT OPD especially among the lower socio-economic strata of society. AIMS: This study was carried out to know about the aerobic bacterial flora causing COM and in-vitro antibiotic susceptibility pattern in order to scientifically guide patient management instead of relying on empirical therapy alone. MATERIALS AND METHODS: This study included 100 patients of community acquired COM attending ENT OPD of a tertiary care level hospital. After proper sample collection by sterile aural swabs, they were immediately sent to the microbiology laboratory for processing by aerobic culture, isolation and identification following standard recommended methods and antibiotic susceptibility tests were done by Kirby-Bauer disc diffusion methods as per Clinical and Laboratory Standards Institute (CLSI guidelines. RESULTS: Out of 100 cases of COM, microbiological culture yielded 101 bacterial isolates from 90 patients and 4 fungal isolates (3 isolates of Candida albicans and 1 isolate of Aspergillusfumigatus from 4 patients. Polymicrobial infections were seen in 11.11% patients. In this study Staphylococcus aureus (31.68% was the commonest isolate followed by Pseudomonas aeruginosa (23.76%. Other common bacterial isolates were E.coli, Klebsiellapneumoniae, coagulase negative Staphylococcus (CONS, Proteus mirabilis in descending order. Piperacillin-tazobactum was the most sensitive drug (85.45% among the gram-negative bacteria followed by meropenem (81.81%, amikacin (76.36% and levofloxacin (74.54%. Gram positive bacteria showed 100% sensitivity to vancomycin and 93.47% sensitivity to linezolid. For Methicillin resistant Staphylococcus aureus (MRSA isolates ciprofloxacin, cotrimoxazole, tetracycline, linezolid and vancomycin were found to have good activity. CONCLUSION: This study suggests that the common etiological

  10. Molecular Characterization of Epiphytic Bacterial Communities on Charophycean Green Algae

    OpenAIRE

    Fisher, Madeline M.; Wilcox, Lee W.; Linda E Graham

    1998-01-01

    Epiphytic bacterial communities within the sheath material of three filamentous green algae, Desmidium grevillii, Hyalotheca dissiliens, and Spondylosium pulchrum (class Charophyceae, order Zygnematales), collected from a Sphagnum bog were characterized by PCR amplification, cloning, and sequencing of 16S ribosomal DNA. A total of 20 partial sequences and nine different sequence types were obtained, and one sequence type was recovered from the bacterial communities on all three algae. By phyl...

  11. Functional recovery of biofilm bacterial communities after copper exposure

    Energy Technology Data Exchange (ETDEWEB)

    Boivin, Marie-Elene Y. [National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven (Netherlands) and Vrije Universiteit, Department of Animal Ecology, De Boelelaan 1085, 1081 HV Amsterdam (Netherlands)]. E-mail: marie-elene.boivin@rivm.nl; Massieux, Boris [Netherlands Institutes of Ecology, Centre for Limnology, Rijkstraatweg 6, 3631 AC Nieuwersluis (Netherlands); Breure, Anton M. [National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven (Netherlands); Greve, Gerdit D. [National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven (Netherlands); Vrije Universiteit, Department of Animal Ecology, De Boelelaan 1085, 1081 HV Amsterdam (Netherlands); Rutgers, Michiel [National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven (Netherlands); Admiraal, Wim [University of Amsterdam, Department of Aquatic Ecology and Ecotoxicology, Kruislaan 320, 1098 SM Amsterdam (Netherlands)

    2006-03-15

    Potential of bacterial communities in biofilms to recover after copper exposure was investigated. Biofilms grown outdoor in shallow water on glass dishes were exposed in the laboratory to 0.6, 2.1, 6.8 {mu}mol/l copper amended surface water and a reference and subsequently to un-amended surface water. Transitions of bacterial communities were characterised with denaturing gradient gel electrophoresis (DGGE) and community-level physiological profiles (CLPP). Exposure to 6.8 {mu}mol/l copper provoked distinct changes in DGGE profiles of bacterial consortia, which did not reverse upon copper depuration. Exposure to 2.1 and 6.8 {mu}mol/l copper was found to induce marked changes in CLPP of bacterial communities that proved to be reversible during copper depuration. Furthermore, copper exposure induced the development of copper-tolerance, which was partially lost during depuration. It is concluded that bacterial communities exposed to copper contaminated water for a period of 26 days are capable to restore their metabolic attributes after introduction of unpolluted water in aquaria for 28 days. - Genetically different bacterial communities can have similar functions and tolerance to copper.

  12. Determinants of bacterial communities in Canadian agroforestry systems.

    Science.gov (United States)

    Banerjee, Samiran; Baah-Acheamfour, Mark; Carlyle, Cameron N; Bissett, Andrew; Richardson, Alan E; Siddique, Tariq; Bork, Edward W; Chang, Scott X

    2016-06-01

    Land-use change is one of the most important factors influencing soil microbial communities, which play a pivotal role in most biogeochemical and ecological processes. Using agroforestry systems as a model, this study examined the effects of land uses and edaphic properties on bacterial communities in three agroforestry types covering a 270 km soil-climate gradient in Alberta, Canada. Our results demonstrate that land-use patterns exert stronger effects on soil bacterial communities than soil zones in these agroforestry systems. Plots with trees in agroforestry systems promoted greater bacterial abundance and to some extent species richness, which was associated with more nutrient-rich soil resources. While Acidobacteria, Actinobacteria and Alphaproteobacteria were the dominant bacterial phyla and subphyla across land uses, Arthrobacter, Acidobacteria_Gp16, Burkholderia, Rhodanobacter and Rhizobium were the keystone taxa in these agroforestry systems. Soil pH and carbon contents emerged as the major determinants of bacterial community characteristics. We found non-random co-occurrence and modular patterns of soil bacterial communities, and these patterns were controlled by edaphic factors and not their taxonomy. Overall, this study highlights the drivers and co-occurrence patterns of soil microbial communities in agroforestry systems.

  13. Efficacy of Corticosteroids in Community-acquired Pneumonia A Randomized Double-Blinded Clinical Trial

    NARCIS (Netherlands)

    Snijders, Dominic; Daniels, Johannes M. A.; de Graaff, Casper S.; van der Werf, Tjip S.; Boersma, Wim G.

    2010-01-01

    Rationale: Some studies have shown a beneficial effect of corticosteroids in patients with community-acquired pneumonia (CAP), possibly by diminishing local and systemic antiinflammatory host response. Objectives: To assess the efficacy of adjunctive prednisolone treatment in patients hospitalized w

  14. Acquired Brain Injury Club at a Community College: Opportunities for Support, Involvement, and Leadership

    Science.gov (United States)

    Chinn, Nancy Resendes

    2009-01-01

    College students with acquired brain injuries face unique challenges. The likelihood of individuals with acquired brain injury experiencing isolation, lack of social support, and diminished self-esteem, along with cognitive impairments, is well documented in the literature. This article presents an overview of a community college's club for…

  15. Hydrocarbon pollutants shape bacterial community assembly of harbor sediments

    KAUST Repository

    Barbato, Marta

    2016-02-02

    Petroleum pollution results in co-contamination by different classes of molecules, entailing the occurrence of marine sediments difficult to remediate, as in the case of the Ancona harbor (Mediterranean Sea, Italy). Autochthonous bioaugmentation (ABA), by exploiting the indigenous microbes of the environment to be treated, could represent a successful bioremediation strategy. In this perspective we aimed to i) identify the main drivers of the bacterial communities\\' richness in the sediments, ii) establish enrichment cultures with different hydrocarbon pollutants evaluating their effects on the bacterial communities\\' composition, and iii) obtain a collection of hydrocarbon degrading bacteria potentially exploitable in ABA. The correlation between the selection of different specialized bacterial populations and the type of pollutants was demonstrated by culture-independent analyses, and by establishing a collection of bacteria with different hydrocarbon degradation traits. Our observations indicate that pollution dictates the diversity of sediment bacterial communities and shapes the ABA potential in harbor sediments.

  16. Hydrocarbon pollutants shape bacterial community assembly of harbor sediments.

    Science.gov (United States)

    Barbato, Marta; Mapelli, Francesca; Magagnini, Mirko; Chouaia, Bessem; Armeni, Monica; Marasco, Ramona; Crotti, Elena; Daffonchio, Daniele; Borin, Sara

    2016-03-15

    Petroleum pollution results in co-contamination by different classes of molecules, entailing the occurrence of marine sediments difficult to remediate, as in the case of the Ancona harbor (Mediterranean Sea, Italy). Autochthonous bioaugmentation (ABA), by exploiting the indigenous microbes of the environment to be treated, could represent a successful bioremediation strategy. In this perspective we aimed to i) identify the main drivers of the bacterial communities' richness in the sediments, ii) establish enrichment cultures with different hydrocarbon pollutants evaluating their effects on the bacterial communities' composition, and iii) obtain a collection of hydrocarbon degrading bacteria potentially exploitable in ABA. The correlation between the selection of different specialized bacterial populations and the type of pollutants was demonstrated by culture-independent analyses, and by establishing a collection of bacteria with different hydrocarbon degradation traits. Our observations indicate that pollution dictates the diversity of sediment bacterial communities and shapes the ABA potential in harbor sediments. PMID:26849913

  17. Do honeybees shape the bacterial community composition in floral nectar?

    Directory of Open Access Journals (Sweden)

    Yana Aizenberg-Gershtein

    Full Text Available Floral nectar is considered the most important reward animal-pollinated plants offer to attract pollinators. Here we explore whether honeybees, which act as pollinators, affect the composition of bacterial communities in the nectar. Nectar and honeybees were sampled from two plant species: Amygdalus communis and Citrus paradisi. To prevent the contact of nectar with pollinators, C. paradisi flowers were covered with net bags before blooming (covered flowers. Comparative analysis of bacterial communities in the nectar and on the honeybees was performed by the 454-pyrosequencing technique. No significant differences were found among bacterial communities in honeybees captured on the two different plant species. This resemblance may be due to the presence of dominant bacterial OTUs, closely related to the Arsenophonus genus. The bacterial communities of the nectar from the covered and uncovered C. paradisi flowers differed significantly; the bacterial communities on the honeybees differed significantly from those in the covered flowers' nectar, but not from those in the uncovered flowers' nectar. We conclude that the honeybees may introduce bacteria into the nectar and/or may be contaminated by bacteria introduced into the nectar by other sources such as other pollinators and nectar thieves.

  18. Metamorphosis of a butterfly-associated bacterial community.

    Directory of Open Access Journals (Sweden)

    Tobin J Hammer

    Full Text Available Butterflies are charismatic insects that have long been a focus of biological research. They are also habitats for microorganisms, yet these microbial symbionts are little-studied, despite their likely importance to butterfly ecology and evolution. In particular, the diversity and composition of the microbial communities inhabiting adult butterflies remain uncharacterized, and it is unknown how the larval (caterpillar and adult microbiota compare. To address these knowledge gaps, we used Illumina sequencing of 16S rRNA genes from internal bacterial communities associated with multiple life stages of the neotropical butterfly Heliconius erato. We found that the leaf-chewing larvae and nectar- and pollen-feeding adults of H. erato contain markedly distinct bacterial communities, a pattern presumably rooted in their distinct diets. Larvae and adult butterflies host relatively small and similar numbers of bacterial phylotypes, but few are common to both stages. The larval microbiota clearly simplifies and reorganizes during metamorphosis; thus, structural changes in a butterfly's bacterial community parallel those in its own morphology. We furthermore identify specific bacterial taxa that may mediate larval and adult feeding biology in Heliconius and other butterflies. Although male and female Heliconius adults differ in reproductive physiology and degree of pollen feeding, bacterial communities associated with H. erato are not sexually dimorphic. Lastly, we show that captive and wild individuals host different microbiota, a finding that may have important implications for the relevance of experimental studies using captive butterflies.

  19. Discharge diagnoses versus medical record review in the identification of community-acquired sepsis

    OpenAIRE

    Henry E. Wang; Addis, Dylan R; Donnelly, John P.; Shapiro, Nathan I.; Griffin, Russell L.; Safford, Monika M.; Baddley, John W.

    2015-01-01

    Introduction We evaluated the accuracy of hospital discharge diagnoses in the identification of community-acquired sepsis and severe sepsis. Methods We reviewed 379 serious infection hospitalizations from 2003 to 2012 from the national population-based reasons for geographic and racial differences in stroke (REGARDS) cohort. Through manual review of medical records, we defined criterion-standard community-acquired sepsis events as the presence of a serious infection on hospital presentation w...

  20. Clinical effects and bronchoalveolar transfer of levofloxacin in patients with community-acquired pneumonia

    Institute of Scientific and Technical Information of China (English)

    林耀广; 苏薇; 徐作军; 白彦

    2001-01-01

    @@To evaluate the clinical effects and bronchoalveolar transfer of levofloxacin (LVFX) in patients with community-acquired pneumonia. Twenty-eight outpatients with community-acquired pneumonia (CAP) were observed in an open-label, noncomparative study. The concentrations of levofloxacin in serum and bronchoalveolar lavage fluid (BALF) were measured  by  high-performance  liquid  chromatography (HPLC) with fluorescence detection in 10 patients and 15 non-levofloxacin users.

  1. Supraglacial bacterial community structures vary across the Greenland ice sheet

    DEFF Research Database (Denmark)

    Cameron, Karen A.; Stibal, Marek; Zarsky, Jakub D.;

    2016-01-01

    The composition and spatial variability of microbial communities that reside within the extensive (>200 000 km(2)) biologically active area encompassing the Greenland ice sheet (GrIS) is hypothesized to be variable. We examined bacterial communities from cryoconite debris and surface ice across t...

  2. Duration of Antimicrobial Therapy in Community Acquired Pneumonia: Less Is More

    Directory of Open Access Journals (Sweden)

    Marilia Rita Pinzone

    2014-01-01

    Full Text Available Community acquired pneumonia (CAP represents the most common cause of infection-related morbidity and mortality worldwide. Appropriate treatment of CAP is challenging and sometimes limited by the availability to obtain rapid and timely identification of the etiologic agent in order to initiate or deescalate the correct antimicrobial therapy. As a consequence, prescribers frequently select empiric antimicrobial therapy using clinical judgment, local patterns of antimicrobial resistance, and, sometimes, individual patient expectations. These issues may contribute to prolonged courses of inappropriate therapy. In this review, we discuss the evidence and recommendations from international guidelines for the management of CAP and the clinical trials that specifically addressed duration of antimicrobial therapy for CAP in adults. In randomized controlled trials comparing the clinical efficacy of a short-course antimicrobial regimen versus an extended-course regimen, no differences in terms of clinical success, bacterial eradication, adverse events, and mortality were observed. The use of biomarkers, such as procalcitonin, to guide the initiation and duration of antimicrobial therapy may reduce total antibiotic exposure and treatment duration, healthcare costs, and the risk of developing antimicrobial resistance. In clinical practice, antimicrobial stewardship interventions may improve the management of CAP and may help in reducing treatment duration. Sometimes “less is more” in CAP.

  3. Impact of disinfection on drinking water biofilm bacterial community.

    Science.gov (United States)

    Mi, Zilong; Dai, Yu; Xie, Shuguang; Chen, Chao; Zhang, Xiaojian

    2015-11-01

    Disinfectants are commonly applied to control the growth of microorganisms in drinking water distribution systems. However, the effect of disinfection on drinking water microbial community remains poorly understood. The present study investigated the impacts of different disinfectants (chlorine and chloramine) and dosages on biofilm bacterial community in bench-scale pipe section reactors. Illumina MiSeq sequencing illustrated that disinfection strategy could affect both bacterial diversity and community structure of drinking water biofilm. Proteobacteria tended to predominate in chloraminated drinking water biofilms, while Firmicutes in chlorinated and unchlorinated biofilms. The major proteobacterial groups were influenced by both disinfectant type and dosage. In addition, chloramination had a more profound impact on bacterial community than chlorination.

  4. Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments

    Directory of Open Access Journals (Sweden)

    Lidianne L. Rocha

    2016-01-01

    Full Text Available We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1 to habitats covered by Avicennia schaueriana (S2 and Rhizophora mangle (S3. Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole.

  5. Endophytic bacterial community of a Mediterranean marine angiosperm (Posidonia oceanica

    Directory of Open Access Journals (Sweden)

    Neus eGarcias-Bonet

    2012-09-01

    Full Text Available Bacterial endophytes are crucial for the survival of many terrestrial plants, but little is known about the presence and importance of bacterial endophytes of marine plants. We conducted a survey of the endophytic bacterial community of the long-living Mediterranean marine angiosperm Posidonia oceanica in surface-sterilized tissues (roots, rhizomes and leaves by DGGE. A total of 26 Posidonia oceanica meadows around the Balearic Islands were sampled, and the band patterns obtained for each meadow were compared for the three sampled tissues. Endophytic bacterial sequences were detected in most of the samples analyzed. A total of 34 OTUs (Operational Taxonomic Units were detected. The main OTUs of endophytic bacteria present in P. oceanica tissues belonged primarily to Proteobacteria (α, γ and δ subclasses and Bacteroidetes. The OTUs found in roots significantly differed from those of rhizomes and leaves. Moreover, some OTUs were found to be associated to each type of tissue. Bipartite network analysis revealed differences in the bacterial endophyte communities present on different islands. The results of this study provide a pioneering step toward the characterization of the endophytic bacterial community associated with tissues of a marine angiosperm and reveal the presence of bacterial endophytes that differed among locations and tissue types.

  6. Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments.

    Science.gov (United States)

    Rocha, Lidianne L; Colares, Geórgia B; Nogueira, Vanessa L R; Paes, Fernanda A; Melo, Vânia M M

    2016-01-01

    We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1) to habitats covered by Avicennia schaueriana (S2) and Rhizophora mangle (S3). Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole. PMID:26989418

  7. Bacterial Community Mapping of the Mouse Gastrointestinal Tract

    OpenAIRE

    Gu, Shenghua; Chen, Dandan; Zhang, Jin-Na; Lv, Xiaoman; WANG Kun; Duan, Li-Ping; Nie, Yong; Wu, Xiao-Lei

    2013-01-01

    Keeping mammalian gastrointestinal (GI) tract communities in balance is crucial for host health maintenance. However, our understanding of microbial communities in the GI tract is still very limited. In this study, samples taken from the GI tracts of C57BL/6 mice were subjected to 16S rRNA gene sequence-based analysis to examine the characteristic bacterial communities along the mouse GI tract, including those present in the stomach, duodenum, jejunum, ileum, cecum, colon and feces. Further a...

  8. Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome.

    Science.gov (United States)

    de Souza, Rafael Soares Correa; Okura, Vagner Katsumi; Armanhi, Jaderson Silveira Leite; Jorrín, Beatriz; Lozano, Núria; da Silva, Márcio José; González-Guerrero, Manuel; de Araújo, Laura Migliorini; Verza, Natália Cristina; Bagheri, Homayoun Chaichian; Imperial, Juan; Arruda, Paulo

    2016-01-01

    Plant microbiome and its manipulation herald a new era for plant biotechnology with the potential to benefit sustainable crop production. However, studies evaluating the diversity, structure and impact of the microbiota in economic important crops are still rare. Here we describe a comprehensive inventory of the structure and assemblage of the bacterial and fungal communities associated with sugarcane. Our analysis identified 23,811 bacterial OTUs and an unexpected 11,727 fungal OTUs inhabiting the endophytic and exophytic compartments of roots, shoots, and leaves. These communities originate primarily from native soil around plants and colonize plant organs in distinct patterns. The sample type is the primary driver of fungal community assemblage, and the organ compartment plays a major role in bacterial community assemblage. We identified core bacterial and fungal communities composed of less than 20% of the total microbial richness but accounting for over 90% of the total microbial relative abundance. The roots showed 89 core bacterial families, 19 of which accounted for 44% of the total relative abundance. Stalks are dominated by groups of yeasts that represent over 12% of total relative abundance. The core microbiome described here comprise groups whose biological role underlies important traits in plant growth and fermentative processes. PMID:27358031

  9. Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome

    Science.gov (United States)

    de Souza, Rafael Soares Correa; Okura, Vagner Katsumi; Armanhi, Jaderson Silveira Leite; Jorrín, Beatriz; Lozano, Núria; da Silva, Márcio José; González-Guerrero, Manuel; de Araújo, Laura Migliorini; Verza, Natália Cristina; Bagheri, Homayoun Chaichian; Imperial, Juan; Arruda, Paulo

    2016-01-01

    Plant microbiome and its manipulation herald a new era for plant biotechnology with the potential to benefit sustainable crop production. However, studies evaluating the diversity, structure and impact of the microbiota in economic important crops are still rare. Here we describe a comprehensive inventory of the structure and assemblage of the bacterial and fungal communities associated with sugarcane. Our analysis identified 23,811 bacterial OTUs and an unexpected 11,727 fungal OTUs inhabiting the endophytic and exophytic compartments of roots, shoots, and leaves. These communities originate primarily from native soil around plants and colonize plant organs in distinct patterns. The sample type is the primary driver of fungal community assemblage, and the organ compartment plays a major role in bacterial community assemblage. We identified core bacterial and fungal communities composed of less than 20% of the total microbial richness but accounting for over 90% of the total microbial relative abundance. The roots showed 89 core bacterial families, 19 of which accounted for 44% of the total relative abundance. Stalks are dominated by groups of yeasts that represent over 12% of total relative abundance. The core microbiome described here comprise groups whose biological role underlies important traits in plant growth and fermentative processes. PMID:27358031

  10. Community-Acquired Methicillin-Resistant "Staphylococcus aureus": Considerations for School Nurses

    Science.gov (United States)

    Alex, Aniltta; Letizia, MariJo

    2007-01-01

    Methicillin-resistant "Staphylococcus aureus" (MRSA) is a disease-causing organism that has been present in hospital settings since the 1960s. However, a genetically distinct strain of MRSA, called community-acquired methicillin-resistant "Staphylococcus aureus" (CA-MRSA), has emerged in recent years in community settings among healthy…

  11. Changes in soil bacterial community structure with increasing disturbance frequency.

    Science.gov (United States)

    Kim, Mincheol; Heo, Eunjung; Kang, Hojeong; Adams, Jonathan

    2013-07-01

    Little is known of the responsiveness of soil bacterial community structure to disturbance. In this study, we subjected a soil microcosm to physical disturbance, sterilizing 90 % of the soil volume each time, at a range of frequencies. We analysed the bacterial community structure using 454 pyrosequencing of the 16S rRNA gene. Bacterial diversity was found to decline with the increasing disturbance frequencies. Total bacterial abundance was, however, higher at intermediate and high disturbance frequencies, compared to low and no-disturbance treatments. Changing disturbance frequency also led to changes in community composition, with changes in overall species composition and some groups becoming abundant at the expense of others. Some phylogenetic groups were found to be relatively more disturbance-sensitive or tolerant than others. With increasing disturbance frequency, phylogenetic species variability (an index of community composition) itself became more variable from one sample to another, suggesting a greater role of chance in community composition. Compared to the tightly clustered community of the original undisturbed soil, in all the aged disturbed soils the lists of most abundant operational taxonomic units (OTUs) in each replicate were very different, suggesting a possible role of stochasticity in resource colonization and exploitation in the aged and disturbed soils. For example, colonization may be affected by whichever localized concentrations of bacterial populations happen to survive the last disturbance and be reincorporated in abundance into each pot. Overall, it appears that the soil bacterial community is very sensitive to physical disturbance, losing diversity, and that certain groups have identifiable 'high disturbance' vs. 'low disturbance' niches.

  12. Streptoccocus pyogenes: a forgotten cause of severe community-acquired pneumonia.

    Science.gov (United States)

    Birch, C; Gowardman, J

    2000-02-01

    We report a case of severe community-acquired pneumonia caused by Streptococcus pyogenes (Lancefield Group A streptoccocus) that was complicated by a streptococcal toxic shock syndrome. Although this micro-organism is an uncommon cause of community-acquired pneumonia, previously well individuals may be infected and the clinical course may be fulminant. A household contact was the likely point of infection. Invasive group A streptococcal disease continues to remain an important cause of morbidity and mortality in the community and therefore will continue to be encountered by intensive care physicians. Treatment of Group A streptococcal infection remains penicillin; however, clindamycin should be added in severe infection. PMID:10701045

  13. SPHINGOMONAS PAUCIMOBILIS INFECTIONS IN CHILDREN: NOSOCOMIAL VERSUS COMMUNITY ACQUIRED INFECTIONS

    Directory of Open Access Journals (Sweden)

    Nuri Bayram

    2013-06-01

    Full Text Available Sphingomonas paucimobilis is a causative agent of infection in immunocompromised patients, and healthcare-associated infections. Although the infections associated with S.paucimobilis occurs rarely, it has been encountered with increasing frequency in clinical settings. In the current study we noted the risk factors and clinical features of the children with S.paucimobilis infections, and the antimicrobial susceptibilities of the isolated strains among the patients. This study was conducted in Dr. Behçet Uz Children’s Hospital, Turkey, during the period of January 2005 and December 2012. The medical records of pediatric patients with positive cultures for S.paucimobilis were reviewed. Sphingomonas paucimobilis isolates were recovered from 24 pediatric patients. The median age was 4 years (ranging from 3 days infant to 15 years and 58,3% were male. Eight (33,3% of the patients were under 1 months of age. Among the patients; 13 (54,2% infections were community related however 11(45.8% infections were nosocomial infection. The median duration of hospital stay was 7 days (ranging from 4 to 22 days. The most effective antibiotics were fluoroquinolones, carbapenems, and trimethoprim/sulfamethoxazole. This is the first largest study in children to evaluate the clinical features of S. paucimobilis infections. Sphingomonas paucimobilis may cause infections in both previously healthy and immunocompromised children. Although variable antimicrobial regimens were achieved to the patients, there was no attributable fatality due to S.paucimobilis infections due to the low virulence of the bacteria.

  14. Experimental sulfate amendment alters peatland bacterial community structure.

    Science.gov (United States)

    Strickman, R J S; Fulthorpe, R R; Coleman Wasik, J K; Engstrom, D R; Mitchell, C P J

    2016-10-01

    As part of a long-term, peatland-scale sulfate addition experiment, the impact of varying sulfate deposition on bacterial community responses was assessed using 16S tag encoded pyrosequencing. In three separate areas of the peatland, sulfate manipulations included an eight year quadrupling of atmospheric sulfate deposition (experimental), a 3-year recovery to background deposition following 5years of elevated deposition (recovery), and a control area. Peat concentrations of methylmercury (MeHg), a bioaccumulative neurotoxin, were measured, the production of which is attributable to a growing list of microorganisms, including many sulfate-reducing Deltaproteobacteria. The total bacterial and Deltaproteobacterial community structures in the experimental treatment differed significantly from those in the control and recovery treatments that were either indistinguishable or very similar to one another. Notably, the relatively rapid return (within three years) of bacterial community structure in the recovery treatment to a state similar to the control, demonstrates significant resilience of the peatland bacterial community to changes in atmospheric sulfate deposition. Changes in MeHg accumulation between sulfate treatments correlated with changes in the Deltaproteobacterial community, suggesting that sulfate may affect MeHg production through changes in the community structure of this group. PMID:27267720

  15. Older Adults: A Proposal for the Management of Community-acquired Pneumonia

    Directory of Open Access Journals (Sweden)

    Miguel Ángel Serra Valdés

    2016-04-01

    Full Text Available Background: community-acquired pneumonia is the leading cause of hospitalization among older adults. It has a high fatality rate. At present, there are several risk and prognosis scores and different clinical practice guidelines available. Objective: to develop a proposal for the management of community-acquired pneumonia in older adults, applicable in both primary care, and the hospital setting. Methods: a search on community-acquired pneumonia, especially in older adults or the elderly, was conducted using index terms and existing guidelines from different countries, companies and regional consensus included in Clinical Evidence, The Cochrane Library, PubMed, Google Scholar, MEDLINE, LIS, Scielo, Medscape, LILACS, Latindex, HINARI, MEDIGRAPHIC-NEWS and others. The publications providing high-quality evidence in accordance with the criteria of the Grading of Recommendations, Assessment, Development and Evaluations approach were selected. Results: a proposal for practical management of community-acquired pneumonia at any level of care in our health system was developed considering the list of medications currently available in the country. Epidemiology, risk factors, risk stratification, treatment, and fatality rate were considered. Conclusions: community-acquired pneumonia is a current problem and future challenge. This proposal can be used by professionals treating this condition at any level of care. Its application could improve care and quality of life and reduce the fatality rate and costs.

  16. Supraglacial bacterial community structures vary across the Greenland ice sheet.

    Science.gov (United States)

    Cameron, Karen A; Stibal, Marek; Zarsky, Jakub D; Gözdereliler, Erkin; Schostag, Morten; Jacobsen, Carsten S

    2016-02-01

    The composition and spatial variability of microbial communities that reside within the extensive (>200 000 km(2)) biologically active area encompassing the Greenland ice sheet (GrIS) is hypothesized to be variable. We examined bacterial communities from cryoconite debris and surface ice across the GrIS, using sequence analysis and quantitative PCR of 16S rRNA genes from co-extracted DNA and RNA. Communities were found to differ across the ice sheet, with 82.8% of the total calculated variation attributed to spatial distribution on a scale of tens of kilometers separation. Amplicons related to Sphingobacteriaceae, Pseudanabaenaceae and WPS-2 accounted for the greatest portion of calculated dissimilarities. The bacterial communities of ice and cryoconite were moderately similar (global R = 0.360, P = 0.002) and the sampled surface type (ice versus cryoconite) did not contribute heavily towards community dissimilarities (2.3% of total variability calculated). The majority of dissimilarities found between cryoconite 16S rRNA gene amplicons from DNA and RNA was calculated to be the result of changes in three taxa, Pseudanabaenaceae, Sphingobacteriaceae and WPS-2, which together contributed towards 80.8 ± 12.6% of dissimilarities between samples. Bacterial communities across the GrIS are spatially variable active communities that are likely influenced by localized biological inputs and physicochemical conditions.

  17. The bacterial community of entomophilic nematodes and host beetles.

    Science.gov (United States)

    Koneru, Sneha L; Salinas, Heilly; Flores, Gilberto E; Hong, Ray L

    2016-05-01

    Insects form the most species-rich lineage of Eukaryotes and each is a potential host for organisms from multiple phyla, including fungi, protozoa, mites, bacteria and nematodes. In particular, beetles are known to be associated with distinct bacterial communities and entomophilic nematodes. While entomopathogenic nematodes require symbiotic bacteria to kill and reproduce inside their insect hosts, the microbial ecology that facilitates other types of nematode-insect associations is largely unknown. To illuminate detailed patterns of the tritrophic beetle-nematode-bacteria relationship, we surveyed the nematode infestation profiles of scarab beetles in the greater Los Angeles area over a five-year period and found distinct nematode infestation patterns for certain beetle hosts. Over a single season, we characterized the bacterial communities of beetles and their associated nematodes using high-throughput sequencing of the 16S rRNA gene. We found significant differences in bacterial community composition among the five prevalent beetle host species, independent of geographical origin. Anaerobes Synergistaceae and sulphate-reducing Desulfovibrionaceae were most abundant in Amblonoxia beetles, while Enterobacteriaceae and Lachnospiraceae were common in Cyclocephala beetles. Unlike entomopathogenic nematodes that carry bacterial symbionts, insect-associated nematodes do not alter the beetles' native bacterial communities, nor do their microbiomes differ according to nematode or beetle host species. The conservation of Diplogastrid nematodes associations with Melolonthinae beetles and sulphate-reducing bacteria suggests a possible link between beetle-bacterial communities and their associated nematodes. Our results establish a starting point towards understanding the dynamic interactions between soil macroinvertebrates and their microbiota in a highly accessible urban environment. PMID:26992100

  18. Distribution of Archaeal and Bacterial communities in a subtropical reservoir

    Directory of Open Access Journals (Sweden)

    Laís Américo Soares

    2015-12-01

    Full Text Available Abstract Aim: Microbial communities play a central role in environmental process such as organic matter mineralization and the nutrient cycling process in aquatic ecosystems. Despite their ecological importance, variability of the structure of archaeal and bacterial communities in freshwater remains understudied. Methods In the present study we investigated the richness and density of archaea and bacteria in the water column and sediments of the Itupararanga Reservoir. We also evaluated the relationship between the communities and the biotic and abiotic characteristics. Samples were taken at five depths in the water column next to the dam and three depths next to the reservoir entrance. Results PCR-DGGE evaluation of the archaeal and bacterial communities showed that both were present in the water column, even in oxygenated conditions. Conclusions The density of the bacteria (qPCR was greater than that of the archaea, a result of the higher metabolic plasticity of bacteria compared with archaea.

  19. Successional Trajectories of Rhizosphere Bacterial Communities over Consecutive Seasons

    OpenAIRE

    Shi, Shengjing; Nuccio, Erin; Herman, Donald J.; Rijkers, Ruud; Estera, Katerina; Li, Jiabao; da Rocha, Ulisses Nunes; He, Zhili; Pett-Ridge, Jennifer; Eoin L. Brodie; Zhou, Jizhong; Firestone, Mary

    2015-01-01

    ABSTRACT It is well known that rhizosphere microbiomes differ from those of surrounding soil, and yet we know little about how these root-associated microbial communities change through the growing season and between seasons. We analyzed the response of soil bacteria to roots of the common annual grass Avena fatua over two growing seasons using high-throughput sequencing of 16S rRNA genes. Over the two periods of growth, the rhizosphere bacterial communities followed consistent successional p...

  20. Panamanian frog species host unique skin bacterial communities

    Directory of Open Access Journals (Sweden)

    Lisa K. Belden

    2015-10-01

    Full Text Available Vertebrates, including amphibians, host diverse symbiotic microbes that contribute to host disease resistance. Globally, and especially in montane tropical systems, many amphibian species are threatened by a chytrid fungus, Batrachochytrium dendrobatidis (Bd, that causes a lethal skin disease. Bd therefore may be a strong selective agent on the diversity and function of the microbial communities inhabiting amphibian skin. In Panamá, amphibian population declines and the spread of Bd have been tracked. In 2012, we completed a field survey in Panamá to examine frog skin microbiota in the context of Bd infection. We focused on three frog species and collected two skin swabs per frog from a total of 136 frogs across four sites that varied from west to east in the time since Bd arrival. One swab was used to assess bacterial community structure using 16S rRNA amplicon sequencing and to determine Bd infection status, and one was used to assess metabolite diversity, as the bacterial production of anti-fungal metabolites is an important disease resistance function. The skin microbiota of the three Panamanian frog species differed in OTU (operational taxonomic unit, ~bacterial species community composition and metabolite profiles, although the pattern was less strong for the metabolites. Comparisons between frog skin bacterial communities from Panamá and the US suggest broad similarities at the phylum level, but key differences at lower taxonomic levels. In our field survey in Panamá, across all four sites, only 35 individuals (~26% were Bd infected. There was no clustering of OTUs or metabolite profiles based on Bd infection status and no clear pattern of west-east changes in OTUs or metabolite profiles across the four sites. Overall, our field survey data suggest that different bacterial communities might be producing broadly similar sets of metabolites across frog hosts and sites. Community structure and function may not be as tightly coupled in

  1. Penicillin as empirical therapy for patients hospitalised with community acquired pneumonia at a Danish hospital

    DEFF Research Database (Denmark)

    Kirk, O; Glenthøj, Jonathan Peter; Dragsted, Ulrik Bak;

    2001-01-01

    INTRODUCTION: We report on the outcome of a study of patients hospitalised with community acquired pneumonia (HCAP) at a Danish university hospital. METHODOLOGY: In a retrospective study of 243 consecutive patients with radiographically verified HCAP, data on clinical and laboratory findings.......3%, respectively, p = 0.94, and the readmission rate 20.3%, 24.0%, and 14.8%, respectively; p = 0.63. CONCLUSION: Patients treated for community-acquired pneumonia at a Danish university hospital had clinical outcomes fully at height with findings from other countries, and half of the patients were successfully...

  2. Gender and Age-Dependent Etiology of Community-Acquired Urinary Tract Infections

    Directory of Open Access Journals (Sweden)

    Enrico Magliano

    2012-01-01

    Full Text Available Urinary tract infections (UTIs are among the most frequent community-acquired infections worldwide. Escherichia coli is the most common UTI pathogen although underlying host factors such as patients’ age and gender may influence prevalence of causative agents. In this study, 61 273 consecutive urine samples received over a 22-month period from outpatients clinics of an urban area of north Italy underwent microbiological culture with subsequent bacterial identification and antimicrobial susceptibility testing of positive samples. A total of 13 820 uropathogens were isolated and their prevalence analyzed according to patient’s gender and age group. Overall Escherichia coli accounted for 67.6% of all isolates, followed by Klebsiella pneumoniae (8.8%, Enterococcus faecalis (6.3%, Proteus mirabilis (5.2%, and Pseudomonas aeruginosa (2.5%. Data stratification according to both age and gender showed E. coli isolation rates to be lower in both males aged ≥60 years (52.2%, E. faecalis and P. aeruginosa being more prevalent in this group (11.6% and 7.8%, resp., as well as in those aged ≤14 years (51.3% in whom P. mirabilis prevalence was found to be as high as 21.2%. Streptococcus agalactiae overall prevalence was found to be 2.3% although it was shown to occur most frequently in women aged between 15 and 59 years (4.1%. Susceptibility of E. coli to oral antimicrobial agents was demonstrated to be as follows: fosfomycin (72.9%, trimethoprim/sulfamethoxazole (72.9%, ciprofloxacin (76.8%, ampicillin (48.0%, and amoxicillin/clavulanate (77.5%. In conclusion, both patients’ age and gender are significant factors in determining UTIs etiology; they can increase accuracy in defining the causative uropathogen as well as providing useful guidance to empiric treatment.

  3. Functional recovery of biofilm bacterial communities after copper exposure.

    NARCIS (Netherlands)

    Boivin, Marie-Elène Y; Massieux, Boris; Breure, Anton M; Greve, Gerdit D; Rutgers, Michiel; Admiraal, Wim

    2006-01-01

    Potential of bacterial communities in biofilms to recover after copper exposure was investigated. Biofilms grown outdoor in shallow water on glass dishes were exposed in the laboratory to 0.6, 2.1, 6.8 micromol/l copper amended surface water and a reference and subsequently to un-amended surface wat

  4. Bacterial community profiles in low microbial abundance sponges

    KAUST Repository

    Giles, Emily

    2012-09-04

    It has long been recognized that sponges differ in the abundance of associated microorganisms, and they are therefore termed either \\'low microbial abundance\\' (LMA) or \\'high microbial abundance\\' (HMA) sponges. Many previous studies concentrated on the dense microbial communities in HMA sponges, whereas little is known about microorganisms in LMA sponges. Here, two LMA sponges from the Red Sea, two from the Caribbean and one from the South Pacific were investigated. With up to only five bacterial phyla per sponge, all LMA sponges showed lower phylum-level diversity than typical HMA sponges. Interestingly, each LMA sponge was dominated by a large clade within either Cyanobacteria or different classes of Proteobacteria. The overall similarity of bacterial communities among LMA sponges determined by operational taxonomic unit and UniFrac analysis was low. Also the number of sponge-specific clusters, which indicate bacteria specifically associated with sponges and which are numerous in HMA sponges, was low. A biogeographical or host-dependent distribution pattern was not observed. In conclusion, bacterial community profiles of LMA sponges are clearly different from profiles of HMA sponges and, remarkably, each LMA sponge seems to harbour its own unique bacterial community. © 2012 Federation of European Microbiological Societies.

  5. Microbial activity and bacterial community structure during degradation of microcystins

    DEFF Research Database (Denmark)

    Christoffersen, K.; Lyck, Susanne; Winding, A.

    2002-01-01

    experiment to evaluate the effects of organic lysates on bacterial proliferation in the absence of microcystin. An exponential decline of the dissolved toxins was observed in all cases with toxins present, and the degradation rates ranged between 0.5 and 1.0 d(-1). No lag phases were observed but slow...... including microcystins, and this resulted in a net accumulation of bacterial cells. The heterotrophic nanoflagellates responded quickly to the bacterial growth and probably consumed a considerable amount of the bacteria. The microbial activities returned to initial values within 5 to 6 d as the toxins....... It was hypothesised that the bacterial community from a lake with frequent occurrence of toxic cyanobacteria can degrade microcystin along with other organic compounds. The initial dissolved microcystin concentrations ranged between 10 and 136 mug 1(-1) (microcystin-LR equivalents) in the laboratory experiment, using...

  6. Community-acquired Clostridium difficile infection: an increasing public health threat

    Directory of Open Access Journals (Sweden)

    Gupta A

    2014-03-01

    Full Text Available Arjun Gupta, Sahil Khanna Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA Abstract: There has been a startling shift in the epidemiology of Clostridium difficile infection over the last decade worldwide, and it is now increasingly recognized as a cause of diarrhea in the community. Classically considered a hospital-acquired infection, it has now emerged in populations previously considered to be low-risk and lacking the traditional risk factors for C. difficile infection, such as increased age, hospitalization, and antibiotic exposure. Recent studies have demonstrated great genetic diversity for C. difficile, pointing toward diverse sources and a fluid genome. Environmental sources like food, water, and animals may play an important role in these infections, apart from the role symptomatic patients and asymptomatic carriers play in spore dispersal. Prospective strain typing using highly discriminatory techniques is a possible way to explore the suspected diverse sources of C. difficile infection in the community. Patients with community-acquired C. difficile infection do not necessarily have a good outcome and clinicians should be aware of factors that predict worse outcomes in order to prevent them. This article summarizes the emerging epidemiology, risk factors, and outcomes for community-acquired C. difficile infection. Keywords: community acquired infection, Clostridium difficile, epidemiology, risk factors, outcome

  7. Severe Community-Acquired Pneumonia Caused by Human Adenovirus in Immunocompetent Adults: A Multicenter Case Series.

    Directory of Open Access Journals (Sweden)

    Dingyu Tan

    Full Text Available Severe community-acquired pneumonia (CAP caused by human adenovirus (HAdV, especially HAdV type 55 (HAdV-55 in immunocompetent adults has raised increasing concerns. Clinical knowledge of severe CAP and acute respiratory distress syndrome induced by HAdV-55 is still limited, though the pathogen has been fully characterized by whole-genome sequencing.We conducted a multicentre retrospective review of all consecutive patients with severe CAP caused by HAdV in immunocompetent adults admitted to the Emergency Department Intensive Care Unit of two hospitals in Northern China between February 2012 and April 2014. Clinical, laboratory, radiological characteristics, treatments and outcomes of these patients were collected and analyzed.A total of 15 consecutive severe CAP patients with laboratory-confirmed adenovirus infections were included. The median age was 30 years and all cases were identified during the winter and spring seasons. HAdV-55 was the most frequently (11/15 detected HAdV type. Persistent high fever, cough and rapid progression of dyspnea were typically reported in these patients. Significantly increased pneumonia severity index (PSI, respiratory rate, and lower PaO2/FiO2, hypersensitive CRP were reported in non-survivors compared to survivors (P = 0.013, 0.022, 0.019 and 0.026, respectively. The rapid development of bilateral consolidations within 10 days after illness onset were the most common radiographic finding, usually accompanied by adjacent ground glass opacities and pleural effusions. Total mortality was 26.7% in this study. Corticosteroids were prescribed to 14 patients in this report, but the utilization rate between survivors and non-survivors was not significant.HAdV and the HAdV-55 sub-type play an important role among viral pneumonia pathogens in hospitalized immunocompetent adults in Northern China. HAdV should be tested in severe CAP patients with negative bacterial cultures and a lack of response to antibiotic

  8. Bacterial community diversity in municipal waste landfill sites.

    Science.gov (United States)

    Song, Liyan; Wang, Yangqing; Tang, Wei; Lei, Yu

    2015-09-01

    Little is known about the bacterial diversity of landfills and how environmental factors impact the diversity. In this study, PCR-based 454 pyrosequencing was used to investigate the bacterial communities of ten landfill leachate samples from five landfill sites in China. A total of 137 K useable sequences from the V3-V6 regions of the 16S rRNA gene were retrieved from 205 K reads. These sequences revealed the presence of a large number of operational taxonomic units (OTUs) in the landfills (709-1599 OTUs per sample). The most predominant bacterial representatives in the landfills investigated, regardless of geographic area, included Gammaproteobacteria, Firmicutes, and Bacteroidetes. The phyla Fusobacteria and Tenericutes were also found for the first time to be predominant in the landfills. The phylum Fusobacteria predominated (51.5 and 48.8%) in two semi-arid landfills, and the phylum Tenericutes dominated (30.6%) at one humid, subtropical landfill. Further, a large number of Pseudomonas was detected in most samples, comprising the dominant group and accounting for 40.9 to 92.4% of the total abundance. Principal component analysis (PCA) and cluster analysis based on OTU abundance showed that the abundant taxa separated the bacterial community. Canonical correlation analysis (CCA) suggested that precipitation and landfilling age significantly impact on the bacterial community structure. The bacterial community function (e.g., cellulolytic bacteria, sulfate-reducing bacteria (SRB), sulfate-oxidizing bacteria, and xenobiotic organic compound (XOC)-degrading bacteria) was also diverse, but the pattern is unclear.

  9. Bacterial communities of two ubiquitous Great Barrier Reef corals reveals both site- and species-specificity of common bacterial associates.

    Directory of Open Access Journals (Sweden)

    E Charlotte E Kvennefors

    Full Text Available BACKGROUND: Coral-associated bacteria are increasingly considered to be important in coral health, and altered bacterial community structures have been linked to both coral disease and bleaching. Despite this, assessments of bacterial communities on corals rarely apply sufficient replication to adequately describe the natural variability. Replicated data such as these are crucial in determining potential roles of bacteria on coral. METHODOLOGY/PRINCIPAL FINDINGS: Denaturing Gradient Gel Electrophoresis (DGGE of the V3 region of the 16S ribosomal DNA was used in a highly replicated approach to analyse bacterial communities on both healthy and diseased corals. Although site-specific variations in the bacterial communities of healthy corals were present, host species-specific bacterial associates within a distinct cluster of gamma-proteobacteria could be identified, which are potentially linked to coral health. Corals affected by "White Syndrome" (WS underwent pronounced changes in their bacterial communities in comparison to healthy colonies. However, the community structure and bacterial ribotypes identified in diseased corals did not support the previously suggested theory of a bacterial pathogen as the causative agent of the syndrome. CONCLUSIONS/SIGNIFICANCE: This is the first study to employ large numbers of replicated samples to assess the bacterial communities of healthy and diseased corals, and the first culture-independent assessment of bacterial communities on WS affected Acroporid corals on the GBR. Results indicate that a minimum of 6 replicate samples are required in order to draw inferences on species, spatial or health-related changes in community composition, as a set of clearly distinct bacterial community profiles exist in healthy corals. Coral bacterial communities may be both site and species specific. Furthermore, a cluster of gamma-proteobacterial ribotypes may represent a group of specific common coral and marine

  10. Comparative Molecular Analysis of Community- or Hospital-Acquired Methicillin-Resistant Staphylococcus aureus

    OpenAIRE

    Fey, P. D.; Saïd-Salim, B.; Rupp, M. E.; Hinrichs, S H; Boxrud, D. J.; Davis, C C; Kreiswirth, B N; Schlievert, P M

    2003-01-01

    Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) is a growing public health concern that has been associated with pediatric fatalities. It is hypothesized that the evolution of CA-MRSA is a recent event due to the acquisition of mec DNA by previously methicillin-susceptible strains that circulated in the community. This study investigated the genetic relatedness between CA-MRSA, hospital-associated MRSA (HA-MRSA), and nonmenstrual toxic shock syndrome (nmTSS) isolates....

  11. Community structure of actively growing bacterial populations in plant pathogen suppressive soil

    NARCIS (Netherlands)

    Hjort, K.; Lembke, A.; Speksnijder, A.G.C.L.; Smalla, K.; Jansson, J.K.

    2007-01-01

    The bacterial community in soil was screened by using various molecular approaches for bacterial populations that were activated upon addition of different supplements. Plasmodiophora brassicae spores, chitin, sodium acetate, and cabbage plants were added to activate specific bacterial populations a

  12. Comparison of bacterial communities in sands and water at beaches with bacterial water quality violations.

    Directory of Open Access Journals (Sweden)

    Elizabeth Halliday

    Full Text Available Recreational water quality, as measured by culturable fecal indicator bacteria (FIB, may be influenced by persistent populations of these bacteria in local sands or wrack, in addition to varied fecal inputs from human and/or animal sources. In this study, pyrosequencing was used to generate short sequence tags of the 16S hypervariable region ribosomal DNA from shallow water samples and from sand samples collected at the high tide line and at the intertidal water line at sites with and without FIB exceedance events. These data were used to examine the sand and water bacterial communities to assess the similarity between samples, and to determine the impact of water quality exceedance events on the community composition. Sequences belonging to a group of bacteria previously identified as alternative fecal indicators were also analyzed in relationship to water quality violation events. We found that sand and water samples hosted distinctly different overall bacterial communities, and there was greater similarity in the community composition between coastal water samples from two distant sites. The dissimilarity between high tide and intertidal sand bacterial communities, although more similar to each other than to water, corresponded to greater tidal range between the samples. Within the group of alternative fecal indicators greater similarity was observed within sand and water from the same site, likely reflecting the anthropogenic contribution at each beach. This study supports the growing evidence that community-based molecular tools can be leveraged to identify the sources and potential impact of fecal pollution in the environment, and furthermore suggests that a more diverse bacterial community in beach sand and water may reflect a less contaminated site and better water quality.

  13. Effects of sulfadiazine on soil bacterial communities

    DEFF Research Database (Denmark)

    Hangler, Martin

    and transport of SDZ at the interphase between dewatered SDZ-amended sewage sludge and soil. SDZ was not mineralized within sludge aggregates and travelled more than 10 mm into the surrounding soil. The strongest PICT response was observed in soils fertilized with organic fertilizers or inorganic NPK fertilizer...... to increasing SDZ-concentrations. Surprisingly, induced community tolerance was not detected either by [3H]-leucine incorporation or by quantification of two genes conferring resistance to sulfonamides. In contrast did SDZ-amendments lead to detection of PICT in soil samples from a long-term field experiment...... designed to test effects on soil quality of a range of different fertilizers in agriculture. In manuscript II extracted bacteria from soil samples representing a broad range of natural soil pH values were tested for their toxicity response to SDZ when amended at different assay pH. Toxicity clearly...

  14. The risk of acquiring bacterial meningitis following surgery in Denmark, 1996-2009

    DEFF Research Database (Denmark)

    Howitz, M F; Homøe, P

    2014-01-01

    SUMMARY: This paper estimates the risk of bacterial meningitis following surgery between 1996 and 2009 in Denmark. We conducted two retrospective nationwide cohort studies; first by linking notified bacterial meningitis cases to the National Patient Registry to see how many had undergone a surgical...... procedure; second, we scrutinized notified bacterial meningitis cases to see if the clinician suspected a surgical procedure to be the aetiology. We found that ear, nose and throat surgery had an 11-fold, and neurosurgery a sevenfold, increased risk compared to the reference group in the first 10 days...... following surgery. Streptococcus pneumoniae was the pathogen most often involved. Operation procedures involving penetration of dura mater was associated with increased risk for post-operative bacterial meningitis. In absolute numbers we found few bacterial meningitis cases after surgery; however, patients...

  15. Bacterial communities in the fruit bodies of ground basidiomycetes

    Science.gov (United States)

    Zagryadskaya, Yu. A.; Lysak, L. V.; Chernov, I. Yu.

    2015-06-01

    Fruit bodies of basidiomycetes at different stages of decomposition serve as specific habitats in forest biocenoses for bacteria and differ significantly with respect to the total bacterial population and abundance of particular bacterial genera. A significant increase in the total bacterial population estimated by the direct microscopic method with acridine orange staining and in the population of saprotrophic bacteria (inoculation of glucose peptone yeast agar) in fruit bodies of basidiomycetes Armillaria mellea and Coprinus comatus was recorded at the final stage of their decomposition in comparison with the initial stage. Gramnegative bacteria predominated in the tissues of fruit bodies at all the stages of decomposition and were represented at the final stage by the Aeromonas, Vibrio, and Pseudomonas genera (for fruit bodies of A. mellea) the Pseudomonas genus (for fruit bodies of C. comatus). The potential influence of bacterial communities in the fruit bodies of soil basidiomycetes on the formation of bacterial communities in the upper soil horizons in forest biocenoses is discussed. The loci connected with the development and decomposition of fruit bodies of basidiomycetes on the soil surface are promising for targeted search of Gram-negative bacteria, the important objects of biotechnology.

  16. Elderly patients with community-acquired pneumonia are not treated according to current guidelines

    DEFF Research Database (Denmark)

    Lindhardt Damsgaard, Tove; Klausen, Henrik Hedegaard; Christiansen, Christina;

    2013-01-01

    Community-acquired pneumonia (CAP) is a major cause of morbidity and mortality in elderly patients, and the most important cause of death in the developed world. Optimised treatment and care will benefit patients as well as the health economy. This study investigated in-hospital compliance...

  17. Prognostic factors for early clinical failure in patients with severe community-acquired pneumonia

    NARCIS (Netherlands)

    Hoogewerf, M; Oosterheert, J J; Hak, E; Hoepelman, I M; Bonten, M J M

    2006-01-01

    For patients with community-acquired pneumonia (CAP), clinical response during the first days of treatment is predictive of clinical outcome. As risk assessments can improve the efficiency of pneumonia management, a prospective cohort study to assess clinical, biochemical and microbiological predict

  18. Oxidative metabolism of neutrophils in patients with community-acquired pneumonia

    Directory of Open Access Journals (Sweden)

    Demidchik Lyudmila Andreevna

    2016-04-01

    Full Text Available At the present time, available views show our limited knowledge of the peculiarities of the functional status of neutrophils and their metabolism in patients with community-acquired pneumonia (CAP. The studying of changes of metabolic status of neutrophils can broaden our views about pneumonia pathogenesis and define datum points of therapeutic effect.

  19. Use of Glucocorticoids and Risk of Community-Acquired Staphylococcus aureus Bacteremia

    DEFF Research Database (Denmark)

    Smit, Jesper; Kaasch, Achim J; Søgaard, Mette;

    2016-01-01

    OBJECTIVE: To investigate whether the use of systemic glucocorticoids is a risk factor for community-acquired Staphylococcus aureus bacteremia (CA-SAB). PATIENTS AND METHODS: We used population-based medical registries in Northern Denmark to conduct a case-control study including all adults...

  20. Gender differences in the outcome of community-acquired Staphylococcus aureus bacteraemia

    DEFF Research Database (Denmark)

    Smit, Jesper; López-Cortés, L E; Kaasch, A J;

    2016-01-01

    Female gender has been suggested to be associated with poor outcome in patients with Staphylococcus aureus bacteraemia (SAB), but existing data remain sparse and conflicting. We investigated clinical outcomes in female and male patients with community-acquired (CA-) SAB. Population-based medical...

  1. Study on epidemic characteristics and etiology of community acquired pneumonia in Guangzhou from 2009 to 2012

    Institute of Scientific and Technical Information of China (English)

    刘慧

    2014-01-01

    Objective To investigate the epidemic characteristics and pathogenic spectrum of community acquired pneumonia(CAP)in Guangzhou from 2009 to 2012.Method 14 major comprehensive hospitals were selected from 11 districts as sentinel hospitals for CAP cases surveillance,including 18 982 223 in total during the 4years.The

  2. Enterovirus D68-associated community-acquired pneumonia in children living in Milan, Italy

    NARCIS (Netherlands)

    Esposito, Susanna; Zampiero, Alberto; Ruggiero, Luca; Madini, Barbara; Niesters, Hubert; Principi, Nicola

    2015-01-01

    Background: An increasing number of children infected by enterovirus D68 (EV-D68) and affected by severe respiratory illness, muscle weakness and paralysis were described in the USA and Canada in 2014 Objectives: To investigate the potential involvement of EV-D68 in determining community-acquired pn

  3. The bacterial communities of Drosophila suzukii collected from undamaged cherries

    Directory of Open Access Journals (Sweden)

    James Angus Chandler

    2014-07-01

    Full Text Available Drosophila suzukii is an introduced pest insect that feeds on undamaged, attached fruit. This diet is distinct from the fallen, discomposing fruits utilized by most other species of Drosophila. Since the bacterial microbiota of Drosophila, and of many other animals, is affected by diet, we hypothesized that the bacteria associated with D. suzukii are distinct from that of other Drosophila. Using 16S rDNA PCR and Illumina sequencing, we characterized the bacterial communities of larval and adult D. suzukii collected from undamaged, attached cherries in California, USA. We find that the bacterial communities associated with these samples of D. suzukii contain a high frequency of Tatumella. Gluconobacter and Acetobacter, two taxa with known associations with Drosophila, were also found, although at lower frequency than Tatumella in four of the five samples examined. Sampling D. suzukii from different locations and/or while feeding on different fruits is needed to determine the generality of the results determined by these samples. Nevertheless this is, to our knowledge, the first study characterizing the bacterial communities of this ecologically unique and economically important species of Drosophila.

  4. Infection by Mycoplasma pneumoniae and its importance as an etiological agent in childhood community-acquired pneumonias

    Directory of Open Access Journals (Sweden)

    Letícia Alves Vervloet

    2007-10-01

    Full Text Available This manuscript reviewed the literature on infection by Mycoplasma pneumoniae with emphasis on etiological aspects of childhood community-acquired pneumonias. Bibliographical research was carried out from Pubmed Medline, MDConsult, HighWire, LILACS, and direct research over the past 10 years with the following keywords: Mycoplasma pneumoniae, pneumonia, and childhood. Fifty-four articles were selected. Mycoplasma pneumoniae has a high incidence in childhood. Clinical presentation includes respiratory and extrarespiratory symptoms. Mycoplasma pneumoniae lung infection can be confused with viral or bacterial pneumonia and is unresponsive to beta-lactams. In addition, co-infections have been reported. Mycoplasma pneumoniae infection occurs in all age groups, being less frequent and more severe in children under the age of five. Its incidence as a causal agent is high. Mycoplasma pneumoniae infections constitute 20%-40% of all community-acquired pneumonias; the severity is highly variable, and this condition may lead to severe sequelae. Mycoplasma pneumoniae frequency is underestimated in clinical practice because of the lack of specific features and a diagnosis that needs serology or PCR. Effective management of M. pneumoniae infections can usually be achieved with macrolides. In Brazil, epidemiological studies are needed in order to assess the incidence of this bacterium.

  5. Community-Acquired Pneumonia: a Comparison between elderly and nonelderly patients

    Directory of Open Access Journals (Sweden)

    S. Jafari

    2006-08-01

    Full Text Available Background: Community-acquired pneumonia could be a life-threatening condition especially in elderly patients. The factors influencing the outcome in elderly patients are thought to be different from those in young adults. We compared the clinical and paraclinical profiles in elderly and nonelderly patients with community-acquired pneumonias. Methods: In this cross-sectional study, seventy nine patients who were hospitalized with community acquired pneumonia over a period of one year were included. Patients' medical records were reviewed; and data related to comorbid conditions, signs and symptoms, laboratory and radiographic findings were gathered using a checklist. Results: The clinical features, laboratory parameters and complications from pneumonia were almost similar in 41 elderly (group I, age ≥65years and 38 young (group II, age<65years subjects. Delirium was seen more in elderly group (p=0.05. The average body temperature and pulse rate were significantly higher in nonelderly group. Sixty one percent of elderly patients and 21% of young patients have Po2 less than 60 (p=0.02. Smoking (29.1%, neurological disturbances (19%, congestive heart failure (15.2%, chronic obstructive pulmonary disease and diabetes mellitus (13.9% were associated comorbidities in both groups. In non elderly group, immune compromise and IV drug use were more common as underlying comorbid conditions. Two of three mortalities were due to elder patients. Conclusion: Community acquired pneumonia could have more serious clinical and abnormal laboratory features in the elderly than younger patients. Mortality rate may be higher in older patients. Comorbid conditions are frequently seen in both elderly and nonelderly patients with community acquired pneumonia, but IV drug use and immune compromise are more frequent in nonelderly patients.

  6. Molecular survey of bacterial communities associated with bacterial chondronecrosis with osteomyelitis (BCO) in broilers.

    Science.gov (United States)

    Jiang, Tieshan; Mandal, Rabindra K; Wideman, Robert F; Khatiwara, Anita; Pevzner, Igal; Min Kwon, Young

    2015-01-01

    Bacterial chondronecrosis with osteomyelitis (BCO) is recognized as an important cause of lameness in commercial broiler chickens (meat-type chickens). Relatively little is known about the microbial communities associated with BCO. This study was conducted to increase our understanding of the microbial factors associated with BCO using a culture-independent approach. Using Illumina sequencing of the hyper-variable region V6 in the 16S rRNA gene, we characterized the bacterial communities in 97 femoral or tibial heads from normal and lame broilers carefully selected to represent diverse variations in age, line, lesion type, floor type, clinical status and bone type. Our in-depth survey based on 14 million assembled sequence reads revealed that complex bacterial communities exist in all samples, including macroscopically normal bones from clinically healthy birds. Overall, Proteobacteria (mean 90.9%) comprised the most common phylum, followed by Firmicutes (6.1%) and Actinobacteria (2.6%), accounting for more than 99% of all reads. Statistical analyses demonstrated that there are differences in bacterial communities in different types of bones (femur vs. tibia), lesion types (macroscopically normal femora or tibiae vs. those with pathognomonic BCO lesions), and among individual birds. This analysis also showed that BCO samples overrepresented genera Staphylococcus, whose species have been frequently isolated in BCO samples in previous studies. Rarefaction analysis demonstrated the general tendency that increased severities of BCO lesions were associated with reduced species diversity in both femoral and tibial samples when compared to macroscopically normal samples. These observations suggest that certain bacterial subgroups are preferentially selected in association with the development of BCO lesions. Understanding the microbial species associated with BCO will identify opportunities for understanding and modulating the pathogenesis of this form of lameness in

  7. Molecular survey of bacterial communities associated with bacterial chondronecrosis with osteomyelitis (BCO in broilers.

    Directory of Open Access Journals (Sweden)

    Tieshan Jiang

    Full Text Available Bacterial chondronecrosis with osteomyelitis (BCO is recognized as an important cause of lameness in commercial broiler chickens (meat-type chickens. Relatively little is known about the microbial communities associated with BCO. This study was conducted to increase our understanding of the microbial factors associated with BCO using a culture-independent approach. Using Illumina sequencing of the hyper-variable region V6 in the 16S rRNA gene, we characterized the bacterial communities in 97 femoral or tibial heads from normal and lame broilers carefully selected to represent diverse variations in age, line, lesion type, floor type, clinical status and bone type. Our in-depth survey based on 14 million assembled sequence reads revealed that complex bacterial communities exist in all samples, including macroscopically normal bones from clinically healthy birds. Overall, Proteobacteria (mean 90.9% comprised the most common phylum, followed by Firmicutes (6.1% and Actinobacteria (2.6%, accounting for more than 99% of all reads. Statistical analyses demonstrated that there are differences in bacterial communities in different types of bones (femur vs. tibia, lesion types (macroscopically normal femora or tibiae vs. those with pathognomonic BCO lesions, and among individual birds. This analysis also showed that BCO samples overrepresented genera Staphylococcus, whose species have been frequently isolated in BCO samples in previous studies. Rarefaction analysis demonstrated the general tendency that increased severities of BCO lesions were associated with reduced species diversity in both femoral and tibial samples when compared to macroscopically normal samples. These observations suggest that certain bacterial subgroups are preferentially selected in association with the development of BCO lesions. Understanding the microbial species associated with BCO will identify opportunities for understanding and modulating the pathogenesis of this form of

  8. Emergence of community-acquired Clostridium difficile infection: the experience of a French hospital and review of the literature

    Directory of Open Access Journals (Sweden)

    Maja Ogielska

    2015-08-01

    Conclusions: CDI can cause community-acquired diarrhoea, and CA-CDI may be more severe than HCA-CDI. Prospective studies of CDI involving people from the general community without risk factors are required to confirm this observation.

  9. MULTILOCI SEQUESTERANT STRAINS OF STREPTOCOCCUS PNEUMONIAE ISOLATED FROM ELDERLY PATIENTS WITH COMMUNITY ACQUIRED PNEUMONIA

    Directory of Open Access Journals (Sweden)

    A. V. Martynova

    2014-01-01

    Full Text Available Comuunity-acquired pneumonias in aged patients is the significant epidemiology problem for the public health of almost all the countries. Even more important the problem of microbiological monitoring and epidemiology surveillance for the S. pneumoniae strains as one of the ubiquitous pathogens causing as the community-acquired pneumonias as well the other infections of respiratory tract, what defines their different epidemiological meaning.Multilocus sequence typing is the perspective method of molecular epidemiological surveillance allowing to define the epidemiologically dangerous clones of the ubiquitous microorganisms as Streptococcus pneumomiae. The aim of our research was to conduct the multilocus sequence typing of pneumococci strains isolated in patients with community acquired pneumonias, bronchitis in aged patients.Materials and methods. There were taken 14 strains of S. pneumoniae, isolated in patients with community-acquired pneumonias (seven of them were multiresistant, eight strains were isolated from patients with the chronical onstructive lung diseases and four strains from carriers. Multilocus sequence typing was conduected according to method to M.C. Enright and B.G. Spratt (1998.Results. The strains, isolated in all populations were the related isolates of the species S. pneumoniae, the most of them had the unique genotype defining the sequence type for every strain. There were 6 strains of Taiwan 19F-14 genotype from 14 strains isolated in aged patients with community-acquired pneumonia. Among strains isolated from carriers there were prevailing the strai of R6 genotype.Conclusion. Multilocus sequence typing allows to identify the new genotypes and to prognose the appearing of epidemiologically dangerous strains with new peculiarities.

  10. Mechanism of uranium (VI) removal by two anaerobic bacterial communities

    International Nuclear Information System (INIS)

    The mechanism of uranium (VI) removal by two anaerobic bacterial consortia, recovered from an uncontaminated site (consortium A) and other from an uranium mine (consortium U), was investigated. The highest efficiency of U (VI) removal by both consortia (97%) occurred at room temperature and at pH 7.2. Furthermore, it was found that U (VI) removal by consortium A occurred by enzymatic reduction and bioaccumulation, while the enzymatic process was the only mechanism involved in metal removal by consortium U. FTIR analysis suggested that after U (VI) reduction, U (IV) could be bound to carboxyl, phosphate and amide groups of bacterial cells. Phylogenetic analysis of 16S rRNA showed that community A was mainly composed by bacteria closely related to Sporotalea genus and Rhodocyclaceae family, while community U was mainly composed by bacteria related to Clostridium genus and Rhodocyclaceae family.

  11. Mechanism of uranium (VI) removal by two anaerobic bacterial communities

    Energy Technology Data Exchange (ETDEWEB)

    Martins, Monica [Centro de Ciencias do Mar, Universidade do Algarve, FCT-DQF (edificio 8), Campus de Gambelas, 8005-139 Faro (Portugal); Faleiro, Maria Leonor [IBB - Centro de Biomedicina Molecular e Estrutural, Universidade do Algarve, FCT, Campus de Gambelas, 8005-139 Faro (Portugal); Costa, Ana M. Rosa da [Centro de Investigacao em Quimica do Algarve, Universidade do Algarve, FCT, DQF, Campus de Gambelas, 8005-139 Faro (Portugal); Chaves, Sandra; Tenreiro, Rogerio [Universidade de Lisboa, Faculdade de Ciencias, Centro de Biodiversidade, Genomica Integrativa e Funcional (BioFIG), Campus de FCUL, Campo Grande, 1749-016 Lisboa (Portugal); Matos, Antonio Pedro [Servico de Anatomia Patologica, Hospital Curry Cabral, Lisboa (Portugal); Costa, Maria Clara, E-mail: mcorada@ualg.pt [Centro de Ciencias do Mar, Universidade do Algarve, FCT-DQF (edificio 8), Campus de Gambelas, 8005-139 Faro (Portugal)

    2010-12-15

    The mechanism of uranium (VI) removal by two anaerobic bacterial consortia, recovered from an uncontaminated site (consortium A) and other from an uranium mine (consortium U), was investigated. The highest efficiency of U (VI) removal by both consortia (97%) occurred at room temperature and at pH 7.2. Furthermore, it was found that U (VI) removal by consortium A occurred by enzymatic reduction and bioaccumulation, while the enzymatic process was the only mechanism involved in metal removal by consortium U. FTIR analysis suggested that after U (VI) reduction, U (IV) could be bound to carboxyl, phosphate and amide groups of bacterial cells. Phylogenetic analysis of 16S rRNA showed that community A was mainly composed by bacteria closely related to Sporotalea genus and Rhodocyclaceae family, while community U was mainly composed by bacteria related to Clostridium genus and Rhodocyclaceae family.

  12. Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators

    Energy Technology Data Exchange (ETDEWEB)

    Wu, C.H.; Sercu, B.; Van De Werhorst, L.C.; Wong, J.; DeSantis, T.Z.; Brodie, E.L.; Hazen, T.C.; Holden, P.A.; Andersen, G.L.

    2010-03-01

    Microbial communities in aquatic environments are spatially and temporally dynamic due to environmental fluctuations and varied external input sources. A large percentage of the urban watersheds in the United States are affected by fecal pollution, including human pathogens, thus warranting comprehensive monitoring. Using a high-density microarray (PhyloChip), we examined water column bacterial community DNA extracted from two connecting urban watersheds, elucidating variable and stable bacterial subpopulations over a 3-day period and community composition profiles that were distinct to fecal and non-fecal sources. Two approaches were used for indication of fecal influence. The first approach utilized similarity of 503 operational taxonomic units (OTUs) common to all fecal samples analyzed in this study with the watershed samples as an index of fecal pollution. A majority of the 503 OTUs were found in the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. The second approach incorporated relative richness of 4 bacterial classes (Bacilli, Bacteroidetes, Clostridia and a-proteobacteria) found to have the highest variance in fecal and non-fecal samples. The ratio of these 4 classes (BBC:A) from the watershed samples demonstrated a trend where bacterial communities from gut and sewage sources had higher ratios than from sources not impacted by fecal material. This trend was also observed in the 124 bacterial communities from previously published and unpublished sequencing or PhyloChip- analyzed studies. This study provided a detailed characterization of bacterial community variability during dry weather across a 3-day period in two urban watersheds. The comparative analysis of watershed community composition resulted in alternative community-based indicators that could be useful for assessing ecosystem health.

  13. Environmental and anthropogenic controls over bacterial communities in wetland soils

    OpenAIRE

    Hartman, Wyatt H.; Curtis J Richardson; Vilgalys, Rytas; Bruland, Gregory L.

    2008-01-01

    Soil bacteria regulate wetland biogeochemical processes, yet little is known about controls over their distribution and abundance. Bacteria in North Carolina swamps and bogs differ greatly from Florida Everglades fens, where communities studied were unexpectedly similar along a nutrient enrichment gradient. Bacterial composition and diversity corresponded strongly with soil pH, land use, and restoration status, but less to nutrient concentrations, and not with wetland type or soil carbon. Sur...

  14. Bacterial community survey of sediments at Naracoorte Caves, Australia

    OpenAIRE

    Ball Andrew S.; Kirby Greg; Bourne Steven; Cao Xiangsheng; Mazaheri Nezhad Fard Ramin; Adetutu Eric M.; Shahsavari Esamaeil; Thorpe Krystal

    2012-01-01

    Bacterial diversity in sediments at UNESCO World Heritage listed Naracoorte Caves was surveyed as part of an investigation carried out in a larger study on assessing microbial communities in caves. Cave selection was based on tourist accessibility; Stick Tomato and Alexandra Cave (> 15000 annual visits) and Strawhaven Cave was used as control (no tourist access). Microbial analysis showed that Bacillus was the most commonly detected microbial genus by culture dependent and independent survey ...

  15. Bacterial communities established in bauxite residues with different restoration histories

    OpenAIRE

    Schmalenberger, Achim; O'Sullivan, Orla; Gahan, Jacinta; Cotter, Paul D.; Courtney, Ronan

    2013-01-01

    peer-reviewed Bauxite residue is the alkaline byproduct generated when alumina is extracted from bauxite ores and is commonly deposited in impoundments. These sites represent hostile environments with increased salinity and alkalinity and little prospect of revegetation when left untreated. This study reports the establishment of bacterial communities in bauxite residues with and without restoration amendments (compost and gypsum addition, revegetation) in samples taken in 2009 and 2011 fr...

  16. Bacterial Community Composition in Lake Tanganyika: Vertical and Horizontal Heterogeneity

    OpenAIRE

    De Wever, Aaike; Muylaert, Koenraad; Van der Gucht, Katleen; Pirlot, Samuel; Cocquyt, Christine; Descy, Jean-Pierre; Plisnier, Pierre-Denis; Vyverman, Wim

    2005-01-01

    Vertical and latitudinal differences in bacterial community composition (BCC) in Lake Tanganyika were studied during the dry season of 2002 by means of denaturing gradient gel electrophoresis analysis of PCR-amplified 16S RNA fragments. Dominant bands were sequenced and identified as members of the Cyanobacteria, Actinobacteria, Nitrospirae, green nonsulfur bacteria, and Firmicutes divisions and the Gamma- and Deltaproteobacteria subdivisions. The BCC in the lake displayed both vertical and l...

  17. Bacterial community mapping of the mouse gastrointestinal tract.

    Directory of Open Access Journals (Sweden)

    Shenghua Gu

    Full Text Available Keeping mammalian gastrointestinal (GI tract communities in balance is crucial for host health maintenance. However, our understanding of microbial communities in the GI tract is still very limited. In this study, samples taken from the GI tracts of C57BL/6 mice were subjected to 16S rRNA gene sequence-based analysis to examine the characteristic bacterial communities along the mouse GI tract, including those present in the stomach, duodenum, jejunum, ileum, cecum, colon and feces. Further analyses of the 283,234 valid sequences obtained from pyrosequencing revealed that the gastric, duodenal, large intestinal and fecal samples had higher phylogenetic diversity than the jejunum and ileum samples did. The microbial communities found in the small intestine and stomach were different from those seen in the large intestine and fecal samples. A greater proportion of Lactobacillaceae were found in the stomach and small intestine, while a larger proportion of anaerobes such as Bacteroidaceae, Prevotellaceae, Rikenellaceae, Lachnospiraceae, and Ruminococcaceae were found in the large intestine and feces. In addition, inter-mouse variations of microbiota were observed between the large intestinal and fecal samples, which were much smaller than those between the gastric and small intestinal samples. As far as we can ascertain, ours is the first study to systematically characterize bacterial communities from the GI tracts of C57BL/6 mice.

  18. Analysis of factors that contribute to treatment failure in patients with community-acquired pneumonia.

    Science.gov (United States)

    Genné, D; Sommer, R; Kaiser, L; Saaïdia, A; Pasche, A; Unger, P F; Lew, D

    2006-03-01

    To determine the causes of treatment failure and to evaluate the prognostic factors in patients hospitalized for community-acquired pneumonia, a prospective, observational study of 228 adult patients hospitalized for a community-acquired pneumonia in the University Hospital of Geneva and the La Chaux-de-Fonds Community Hospital, Switzerland, was conducted. The percentage of patients who failed to improve (as defined by guidelines of the Infectious Disease Society of America) and the causes of treatment failure were assessed, and patients who failed to improve under antimicrobial therapy were compared with those who did improve. In the 54 (24%) patients who failed to improve, a mean increase in length of hospitalization of 4 days was observed. Most causes of treatment failure could be attributed to host factors (61%) rather than to the pathogen (16%) or to an inappropriate antibiotic regimen (3%). After adjusting for potentially confounding variables, concomitant neoplasia (OR 3.25; 95%CI 1.11-9.56), neurological disease (OR 2.34; 95%CI 1.07-5.13), and aspiration pneumonia (OR 2.97; 95%CI 29-6.86]) were associated with failure to improve, whereas monocytosis improved prognosis (OR 0.40; 95%CI 0.20-0.80). Almost one out of four patients hospitalized for community-acquired pneumonia failed to respond to empirical antibiotic treatment. Aspiration pneumonia, concomitant neoplasia, and neurological disease were factors positively associated with failure to improve, whereas monocytosis was linked to a better prognosis. PMID:16528540

  19. Prescription of antibiotics in community-acquired pneumonia in children: are we following the recommendations?

    Science.gov (United States)

    da Fonseca Lima, Eduardo Jorge; Lima, Débora Ellen Pessoa; Serra, George Henrique Cordeiro; Abreu e Lima, Maria Anaide Zacche S; de Mello, Maria Júlia Gonçalves

    2016-01-01

    Objective To assess the adequacy of antibiotic prescription in children hospitalized for pneumonia in a reference pediatric hospital in Brazil. Methods This was a cross-sectional study involving children aged between 1 month and 5 years who were hospitalized between October 2010 and September 2013. The classification of community-acquired pneumonia (CAP) was based on the clinical and radiological criteria of the World Health Organization (WHO). The analysis of antibiotic adequacy was performed according to the main guidelines on CAP treatment, which include the WHO guidelines, Brazilian Society of Pediatrics guidelines, and international guidelines (Pediatrics Infectious Diseases Society, the Infectious Disease Society of America, British Thoracic Society, and Consenso de la Sociedad latinoamericana de Infectología). A multivariate analysis was performed including variables that have statistical significance of P≤0.25 in the bivariate analysis. Results The majority of the 452 hospitalized children were classified as having severe or very severe CAP (85.18%), and inadequate empiric antimicrobial therapy was started in 26.10% (118/452) of them. Ampicillin was the most used empiric antibiotic therapy (62.17%) for pneumonia, followed by a combination of ampicillin and associated with gentamicin. The initially proposed regimen was modified in 29.6% of the patients, and the most frequent change was the replacement of ampicillin by oxacillin combined with chloramphenicol. The median hospitalization time was 8.5 days, and the lethality rate was 1.55%. There was no statistical difference in adequacy in relation to the severity of pneumonia or degree of malnutrition. In the bivariate analysis, inadequacy of antibiotic therapy regimen was higher in patients undergoing oxygen therapy (P<0.05), which was given to 219 patients (48.45%). Pleural effusion was observed in 118 patients (26.11%) and was associated with higher prescription inadequacy, and it was the only factor

  20. Distinct soil bacterial communities revealed under a diversely managed agroecosystem.

    Directory of Open Access Journals (Sweden)

    Raymon S Shange

    Full Text Available Land-use change and management practices are normally enacted to manipulate environments to improve conditions that relate to production, remediation, and accommodation. However, their effect on the soil microbial community and their subsequent influence on soil function is still difficult to quantify. Recent applications of molecular techniques to soil biology, especially the use of 16S rRNA, are helping to bridge this gap. In this study, the influence of three land-use systems within a demonstration farm were evaluated with a view to further understand how these practices may impact observed soil bacterial communities. Replicate soil samples collected from the three land-use systems (grazed pine forest, cultivated crop, and grazed pasture on a single soil type. High throughput 16S rRNA gene pyrosequencing was used to generate sequence datasets. The different land use systems showed distinction in the structure of their bacterial communities with respect to the differences detected in cluster analysis as well as diversity indices. Specific taxa, particularly Actinobacteria, Acidobacteria, and classes of Proteobacteria, showed significant shifts across the land-use strata. Families belonging to these taxa broke with notions of copio- and oligotrphy at the class level, as many of the less abundant groups of families of Actinobacteria showed a propensity for soil environments with reduced carbon/nutrient availability. Orders Actinomycetales and Solirubrobacterales showed their highest abundance in the heavily disturbed cultivated system despite the lowest soil organic carbon (SOC values across the site. Selected soil properties ([SOC], total nitrogen [TN], soil texture, phosphodiesterase [PD], alkaline phosphatase [APA], acid phosphatase [ACP] activity, and pH also differed significantly across land-use regimes, with SOM, PD, and pH showing variation consistent with shifts in community structure and composition. These results suggest that use of

  1. Nosocomial and Community-Acquired Staphylococcus Aureus Bacterimias from 1980 to 1993: Impact of Intravascular Devices and Methicillin Resistance

    NARCIS (Netherlands)

    J.P. Steinberg; C.C. Clarke; B.O. Hackman

    1996-01-01

    textabstractThe rate of nosocomial bacteremia due to Staphylococcus aureus has increased over the past decade, but trends in community-acquired S. aureus bacteremia are less certain. This hospital-based observational study compares nosocomial and community-acquired S. aureus bacteremias during 1980-

  2. Advancing New Antibacterial Drug Development for Treatment of Hospital-Acquired and Ventilator-Associated Bacterial Pneumonia.

    Science.gov (United States)

    Toerner, Joseph G; Rubin, Daniel

    2016-08-15

    The Clinical Trials Transformation Initiative (CTTI), a public-private partnership comprised of representatives from academia, the pharmaceutical industry, and the federal government including the US Food and Drug Administration, formed a group working toward a common goal of intensified research to facilitate the development of new antibacterial drug therapies for treatment of hospital-acquired and ventilator-associated bacterial pneumonia (HABP/VABP). The summary of the CTTI HABP/VABP project in this supplement of Clinical Infectious Diseases is a first step in this direction. PMID:27481951

  3. Use of proton pump inhibitors and the risk of community-acquired pneumonia

    DEFF Research Database (Denmark)

    Gulmez, Sinem Ezgi; Holm, Anette; Frederiksen, Henrik;

    2007-01-01

    BACKGROUND: Recently, the use of proton pump inhibitors (PPIs) has been associated with an increased risk of pneumonia. We aimed to confirm this association and to identify the risk factors. METHODS: We conducted a population-based case-control study using data from the County of Funen, Denmark....... Cases (n=7642) were defined as all patients with a first-discharge diagnosis of community-acquired pneumonia from a hospital during 2000 through 2004. We also selected 34 176 control subjects, who were frequency matched to the cases by age and sex. Data on the use of PPIs and other drugs......, on microbiological samples, on x-ray examination findings, and on comorbid conditions were extracted from local registries. Confounders were controlled by logistic regression. RESULTS: The adjusted odds ratio (OR) associating current use of PPIs with community-acquired pneumonia was 1.5 (95% confidence interval [CI...

  4. Endosymbiont dominated bacterial communities in a dwarf spider.

    Directory of Open Access Journals (Sweden)

    Bram Vanthournout

    Full Text Available The microbial community of spiders is little known, with previous studies focussing primarily on the medical importance of spiders as vectors of pathogenic bacteria and on the screening of known cytoplasmic endosymbiont bacteria. These screening studies have been performed by means of specific primers that only amplify a selective set of endosymbionts, hampering the detection of unreported species in spiders. In order to have a more complete overview of the bacterial species that can be present in spiders, we applied a combination of a cloning assay, DGGE profiling and high-throughput sequencing on multiple individuals of the dwarf spider Oedothorax gibbosus. This revealed a co-infection of at least three known (Wolbachia, Rickettsia and Cardinium and the detection of a previously unreported endosymbiont bacterium (Rhabdochlamydia in spiders. 16S rRNA gene sequences of Rhabdochlamydia matched closely with those of Candidatus R. porcellionis, which is currently only reported as a pathogen from a woodlouse and with Candidatus R. crassificans reported from a cockroach. Remarkably, this bacterium appears to present in very high proportions in one of the two populations only, with all investigated females being infected. We also recovered Acinetobacter in high abundance in one individual. In total, more than 99% of approximately 4.5M high-throughput sequencing reads were restricted to these five bacterial species. In contrast to previously reported screening studies of terrestrial arthropods, our results suggest that the bacterial communities in this spider species are dominated by, or even restricted to endosymbiont bacteria. Given the high prevalence of endosymbiont species in spiders, this bacterial community pattern could be widespread in the Araneae order.

  5. Deodorants and antiperspirants affect the axillary bacterial community.

    Science.gov (United States)

    Callewaert, Chris; Hutapea, Prawira; Van de Wiele, Tom; Boon, Nico

    2014-10-01

    The use of underarm cosmetics is common practice in the Western society to obtain better body odor and/or to prevent excessive sweating. A survey indicated that 95 % of the young adult Belgians generally use an underarm deodorant or antiperspirant. The effect of deodorants and antiperspirants on the axillary bacterial community was examined on nine healthy subjects, who were restrained from using deodorant/antiperspirant for 1 month. Denaturing gradient gel electrophoresis was used to investigate the individual microbial dynamics. The microbial profiles were unique for every person. A stable bacterial community was seen when underarm cosmetics were applied on a daily basis and when no underarm cosmetics were applied. A distinct community difference was seen when the habits were changed from daily use to no use of deodorant/antiperspirant and vice versa. The richness was higher when deodorants and antiperspirants were applied. Especially when antiperspirants were applied, the microbiome showed an increase in diversity. Antiperspirant usage led toward an increase of Actinobacteria, which is an unfavorable situation with respect to body odor development. These initial results show that axillary cosmetics modify the microbial community and can stimulate odor-producing bacteria. PMID:25077920

  6. Glyphosate effects on soil rhizosphere-associated bacterial communities.

    Science.gov (United States)

    Newman, Molli M; Hoilett, Nigel; Lorenz, Nicola; Dick, Richard P; Liles, Mark R; Ramsier, Cliff; Kloepper, Joseph W

    2016-02-01

    Glyphosate is one of the most widely used herbicides in agriculture with predictions that 1.35 million metric tons will be used annually by 2017. With the advent of glyphosate tolerant (GT) cropping more than 10 years ago, there is now concern for non-target effects on soil microbial communities that has potential to negatively affect soil functions, plant health, and crop productivity. Although extensive research has been done on short-term response to glyphosate, relatively little information is available on long-term effects. Therefore, the overall objective was to investigate shifts in the rhizosphere bacterial community following long-term glyphosate application on GT corn and soybean in the greenhouse. In this study, rhizosphere soil was sampled from rhizoboxes following 4 growth periods, and bacterial community composition was compared between glyphosate treated and untreated rhizospheres using next-generation barcoded sequencing. In the presence or absence of glyphosate, corn and soybean rhizospheres were dominated by members of the phyla Proteobacteria, Acidobacteria, and Actinobacteria. Proteobacteria (particularly gammaproteobacteria) increased in relative abundance for both crops following glyphosate exposure, and the relative abundance of Acidobacteria decreased in response to glyphosate exposure. Given that some members of the Acidobacteria are involved in biogeochemical processes, a decrease in their abundance could lead to significant changes in nutrient status of the rhizosphere. Our results also highlight the need for applying culture-independent approaches in studying the effects of pesticides on the soil and rhizosphere microbial community.

  7. Management of severe community-acquired pneumonia in Brazil: a secondary analysis of an international survey

    OpenAIRE

    Rabello, Lígia; Conceição, Catarina; Ebecken, Katia; Lisboa, Thiago; Bozza, Fernando Augusto; Soares, Márcio; Póvoa, Pedro; Salluh, Jorge Ibrain Figueira

    2015-01-01

    Objective This study aimed to evaluate Brazilian physicians’ perceptions regarding the diagnosis, severity assessment, treatment and risk stratification of severe community-acquired pneumonia patients and to compare those perceptions to current guidelines. Methods We conducted a cross-sectional international anonymous survey among a convenience sample of critical care, pulmonary, emergency and internal medicine physicians from Brazil between October and December 2008. The electronic survey ev...

  8. Time to Intubation Is Associated with Outcome in Patients with Community-Acquired Pneumonia

    OpenAIRE

    Hraiech, Sami; Alingrin, Julie; Dizier, Stéphanie; Brunet, Julie; Forel, Jean-Marie; La Scola, Bernard; Roch, Antoine; Papazian, Laurent; Pauly, Vanessa

    2013-01-01

    Introduction It has been suggested that delayed intensive care unit (ICU) transfer is associated with increased mortality for patients with community-acquired pneumonia (CAP). However, ICU admission policies and patient epidemiology vary widely across the world depending on local hospital practices and organizational constraints. We hypothesized that the time from the onset of CAP symptoms to invasive mechanical ventilation could be a relevant prognostic factor. Methods One hundred patients w...

  9. Multiplex PCR for Rapid Detection of Staphylococcus aureus Isolates Suspected to Represent Community-Acquired Strains▿

    OpenAIRE

    Strommenger, B.; Braulke, C.; Pasemann, B.; Schmidt, C.; Witte, W.

    2007-01-01

    The continuous spread of community-acquired methicillin-resistant Staphylococcus aureus (caMRSA) and the introduction of these highly virulent isolates into hospitals represent increasing threats. The timely recognition of caMRSA strains is crucial for infection control purposes. Thus, we developed a PCR-based assay for the easy and rapid determination of those caMRSA clones that currently are the most prevalent in Germany and Central Europe. This assay was able to correctly identify the majo...

  10. Population-Based Surveillance for Hypermucoviscosity Klebsiella pneumoniae Causing Community-Acquired Bacteremia in Calgary, Alberta

    OpenAIRE

    Gisele Peirano; Johann DD Pitout; Laupland, Kevin B; Bonnie Meatherall; Gregson, Daniel B.

    2013-01-01

    The characteristics of hypermucoviscosity isolates among Klebsiella pneumoniae causing community-acquired bacteremia were investigated. The hypermucoviscous phenotype was present in 8.2% of K pneumoniae isolates, and was associated with rmpA and the K2 serotype; liver abscesses were the most common clinical presentation. The present analysis represents the first population-based surveillance study of hypermucoviscosity among K pneumoniae causing bacteremia.

  11. Postpartum Mastitis and Community-acquired Methicillin-resistant Staphylococcus aureus

    OpenAIRE

    Reddy, Pavani; Qi, Chao; Zembower, Teresa; Noskin, Gary A.; Bolon, Maureen

    2007-01-01

    This single-center, case-control study documents a relative increase in methicillin resistance among 48 cases of Staphylococcus aureus–associated postpartum mastitis during 1998–2005. Of 21 cases with methicillin resistance, 17 (81%) occurred in 2005. Twenty (95%) isolates contained the Staphylococcus cassette chromosome mec type IV gene; this suggests that the increase is due to community-acquired methicillin-resistant Staphylococcus aureus.

  12. Biomarkers in community-acquired pneumonia: A state-of-the-art review

    Directory of Open Access Journals (Sweden)

    Renato Seligman

    2012-11-01

    Full Text Available Community-acquired pneumonia (CAP exhibits mortality rates, between 20% and 50% in severe cases. Biomarkers are useful tools for searching for antibiotic therapy modifications and for CAP diagnosis, prognosis and follow-up treatment. This non-systematic state-of-the-art review presents the biological and clinical features of biomarkers in CAP patients, including procalcitonin, C-reactive protein, copeptin, pro-ANP (atrial natriuretic peptide, adrenomedullin, cortisol and D-dimers.

  13. Impact of admission blood glucose level on outcomes in community-acquired pneumonia in older adults

    Directory of Open Access Journals (Sweden)

    Bhattacharya RK

    2013-05-01

    Full Text Available Rajib K Bhattacharya, Jonathan D Mahnken, Sally K RiglerUniversity of Kansas School of Medicine, Kansas City, KS, USABackground: Community-acquired pneumonia (CAP is a common cause of morbidity and mortality in older adults. Although diabetes mellitus is a risk factor for pneumonia, the clinical impact of blood glucose level at the time of admission is not clear. Our goal was to examine the association between admission hyperglycemia and subsequent mortality, length of stay, and readmission outcomes in older adults with CAP.Methods: A retrospective observational study was conducted using hospital data for community-acquired pneumonia admissions in 857 persons from January 1, 2008 to December 31, 2010. We examined the effects of admission glucose level on mortality, length of stay, and 30 day readmission, adjusted for demographic factors and comorbidity.Results: The mean age of the sample was 64 years, and 51% of the subjects were female. Inpatient mortality occurred in 4.6% and the median length of stay was 5 days (interquartile range 3–9 days. Readmission within 30 days occurred in 17%. We found little impact of first glucose measures on in-hospital mortality (P = 0.94, length of stay (P = 0.95, and 30-day readmission (P = 0.56. Subjects 65 years and older trended towards higher in-hospital mortality. Older age, cancer, heart failure, and cirrhosis were associated with adverse outcomes.Conclusion: Glucose level upon admission for community-acquired pneumonia was not associated with adverse outcomes within 30 days in older adults.Keywords: community-acquired pneumonia, hyperglycemia, readmission rates, hospital mortality

  14. Impact of admission blood glucose level on outcomes in community-acquired pneumonia in older adults

    OpenAIRE

    Bhattacharya RK; Mahnken JD; Rigler SK

    2013-01-01

    Rajib K Bhattacharya, Jonathan D Mahnken, Sally K RiglerUniversity of Kansas School of Medicine, Kansas City, KS, USABackground: Community-acquired pneumonia (CAP) is a common cause of morbidity and mortality in older adults. Although diabetes mellitus is a risk factor for pneumonia, the clinical impact of blood glucose level at the time of admission is not clear. Our goal was to examine the association between admission hyperglycemia and subsequent mortality, length of stay, and readmission ...

  15. Severe community-acquired pneumonia caused by Mycoplasma pneumoniae in young female patient

    Directory of Open Access Journals (Sweden)

    Milancic Nena

    2015-09-01

    Full Text Available Mycoplasma pneumonia is common agent causing community acquired pneumonia in younger population. However, the course of illness is usually benign and is rarely associated with pulmonary complications. We report a 27 years old female patient with unilateral pneumonia followed by pleural effusion and adhesions on the same side. This potential source of infection should be considered in young patients where resolution of symptoms from pneumonia is delayed.

  16. Independent radiographic prognostic factors in patients with hospital-treated community-acquired pneumonia

    International Nuclear Information System (INIS)

    Purpose: To evaluate the independent prognostic impact of the chest radiograph for mortality from community-acquired pneumonia requiring hospitalization. Methods: Chest radiographs of 67 patients with hospital-treated community-acquired pneumonia were analyzed with regard to the prognostic implications of radiographic patterns, extent and density of infiltrates, and its evolution during treatment. Results: Non-survivors had a significantly higher extent of infiltrates (p=0.008), density of infiltrates (p=0.05), and radiographic spread during follow-up within 48-72 hours (p=0.0001). In multivariate analysis, persistent or progressive infiltrates were associated with a 47fold increase, and persistent or progressive density of infiltrates with an 18fold increase in risk of mortality. The presence of both parameters could correctly predict 96% of survivors and 90% of non-survivors. Conclusions: The chest radiograph is an independent predictor of the severity of pneumonia. Both persistent or progressive infiltrates and persistent or progressive density of infiltrates are independently associated with mortality from community-acquired pneumonia. (orig.)

  17. Clinical data analysis of 19 cases of community-acquired adenovirus pneumonia in immunocompetent adults.

    Science.gov (United States)

    Yu, Hong-Xia; Zhao, Mao-Mao; Pu, Zeng-Hui; Wang, Yun-Qiang; Liu, Yan

    2015-01-01

    The aim of this study was to investigate the characteristics of clinical manifestations, laboratory tests and imaging changes of community-acquired adenovirus pneumonia in immunocompetent adults. A retrospective study was performed on 19 adult community-acquired adenovirus pneumonia cases in Yantai, whereby the clinical data were collected and analyzed. Of 19 cases, 14 (73.68%) had fever and 17 (89.47%) had cough symptoms. Moreover, 14 cases (73.68%) had normal white blood cell counts, while 11 cases (57.89%) exhibited a reduction in lymphocyte proportion. Among the 19 cases, 17 cases exhibited lesions in a single lung, while 2 cases involved bilateral lungs. The lesions predominantly exhibited ground glass-like changes. The clinical manifestations of adult community-acquired adenovirus pneumonia patients with normal immune functions were mild, with such presenting symptoms as fever, cough, and sputum; most patients did not exhibit high levels of white blood cells or low lymphocyte counts, and the imaging features (ground glass-like effusion) were indicative of single-lung involvement.

  18. Chest radiographic characteristics of community-acquired Legionella pneumonia in the elderly

    Institute of Scientific and Technical Information of China (English)

    Zhang Zhigang; Liu Xinmin; Chen Luzeng; Qiu Jianxing

    2014-01-01

    Background Legionella is an important community-acquired pneumonia pathogen.Although the elderly are especially susceptible to Legionella,few studies have looked at comparative radiographic features of Legionella pneumonia in this population.The aim of this study was to explore the chest radiographic characteristics of community-acquired Legionella pneumonia in the elderly.Methods Serial chest radiographs obtained in 34 patients hospitalized with serologically proven Legionella pneumonia were retrospectively reviewed.Chest x-ray features of an aged group of ≥65 years were assessed and compared with a non-aged group of <65 years old with regard to initial patterns and distributions of pulmonary abnormalities,accompanying signs,and progression.Results The most common initial presentation was a patchy alveolar infiltrate involving a single lobe,most often the lower lobe.There was no middle or lingular lobe involvement in the aged group patients,but bilateral pleural effusion was significantly more common in this group.In the aged group patients,radiographic progression following adequate therapy,despite a clinical response,was more often noted and the radiographs were less likely to have returned to the premorbid state at discharge,but the differences were not significant between the two groups.Conclusion The discrepancy between imaging findings and clinical symptoms seems more prominent in community-acquired Legionella pneumonia in the elderly.

  19. Quantitative Analysis of Lung Ultrasonography for the Detection of Community-Acquired Pneumonia: A Pilot Study

    Directory of Open Access Journals (Sweden)

    Francesco Corradi

    2015-01-01

    Full Text Available Background and Objective. Chest X-ray is recommended for routine use in patients with suspected pneumonia, but its use in emergency settings is limited. In this study, the diagnostic performance of a new method for quantitative analysis of lung ultrasonography was compared with bedside chest X-ray and visual lung ultrasonography for detection of community-acquired pneumonia, using thoracic computed tomography as a gold standard. Methods. Thirty-two spontaneously breathing patients with suspected community-acquired pneumonia, undergoing computed tomography examination, were consecutively enrolled. Each hemithorax was evaluated for the presence or absence of abnormalities by chest X-ray and quantitative or visual ultrasonography. Results. Quantitative ultrasonography showed higher sensitivity (93%, specificity (95%, and diagnostic accuracy (94% than chest X-ray (64%, 80%, and 69%, resp., visual ultrasonography (68%, 95%, and 77%, resp., or their combination (77%, 75%, and 77%, resp.. Conclusions. Quantitative lung ultrasonography was considerably more accurate than either chest X-ray or visual ultrasonography in the diagnosis of community-acquired pneumonia and it may represent a useful first-line approach for confirmation of clinical diagnosis in emergency settings.

  20. Methicillin-resistant and methicillin-susceptible community-acquired Staphylococcus aureus infection among children

    Directory of Open Access Journals (Sweden)

    Renata Tavares Gomes

    2013-10-01

    Full Text Available Methicillin-resistant Staphylococcus aureus has emerged as a pathogen associated with community-acquired infections worldwide. We report the spectrum of community-acquired S. aureus infections and compare the patients infected with methicillin-susceptible or methicillin-resistant strains among patients aged <20 years. Overall, 90 cases of community acquired S. aureus were detected in an 11-year period. Clinical and microbiological data were registered. Fifty-nine (66% patients were male and the median age was two years. The majority (87% of the patients were hospitalized and chronic underlying illnesses were detected in 27 (30% cases. Overall, 34 (37.8% patients had skin/soft tissue infections and 56 (62.2% patients had deep-seated infection. Four (5.1% patients were transferred to the intensive care unit and two (2.6% died. Complications were detected in 17 (18.9% cases, such as pleural effusion (41.2%, osteomyelitis (23.5%, and sepsis (17.6%. Six (6.7% methicillin-resistant strains were detected. Patients infected with methicillin-susceptible or methicillin-resistant strains had similar baseline characteristics and treatment outcomes. Approximately 93% of the cases received systemic antibiotics, out of which 59 (65.5% used oxacillin or cefalotin. Both methicillin-susceptible and methicillin-resistant S. aureus strains resulted in morbidity and death among children in this setting where methicillin-resistant strains are infrequent.

  1. Bacterial Communities Associated with Different Anthurium andraeanum L. Plant Tissues

    Science.gov (United States)

    Sarria-Guzmán, Yohanna; Chávez-Romero, Yosef; Gómez-Acata, Selene; Montes-Molina, Joaquín Adolfo; Morales-Salazar, Eleacin; Dendooven, Luc; Navarro-Noya, Yendi E.

    2016-01-01

    Plant-associated microbes have specific beneficial functions and are considered key drivers for plant health. The bacterial community structure of healthy Anthurium andraeanum L. plants was studied by 16S rRNA gene pyrosequencing associated with different plant parts and the rhizosphere. A limited number of bacterial taxa, i.e., Sinorhizobium, Fimbriimonadales, and Gammaproteobacteria HTCC2089 were enriched in the A. andraeanum rhizosphere. Endophytes were more diverse in the roots than in the shoots, whereas all shoot endophytes were found in the roots. Streptomyces, Flavobacterium succinicans, and Asteroleplasma were only found in the roots, Variovorax paradoxus only in the stem, and Fimbriimonas 97%-OTUs only in the spathe, i.e., considered specialists, while Brevibacillus, Lachnospiraceae, Pseudomonas, and Pseudomonas pseudoalcaligenes were generalist and colonized all plant parts. The anaerobic diazotrophic bacteria Lachnospiraceae, Clostridium sp., and Clostridium bifermentans colonized the shoot system. Phylotypes belonging to Pseudomonas were detected in the rhizosphere and in the substrate (an equiproportional mixture of soil, cow manure, and peat), and dominated the endosphere. Pseudomonas included nine 97%-OTUs with different patterns of distribution and phylogenetic affiliations with different species. P. pseudoalcaligenes and P. putida dominated the shoots, but were also found in the roots and rhizosphere. P. fluorescens was present in all plant parts, while P. resinovorans, P. denitrificans, P. aeruginosa, and P. stutzeri were only detected in the substrate and rhizosphere. The composition of plant-associated bacterial communities is generally considered to be suitable as an indicator of plant health. PMID:27524305

  2. Bacterial community structure in aquifers corresponds to stratigraphy

    Science.gov (United States)

    Beyer, Andrea; Möller, Silke; Neumann, Stefan; Burow, Katja; Gutmann, Falko; Lindner, Julia; Müsse, Steffen; Kothe, Erika; Büchel, Georg

    2014-05-01

    So far, groundwater microbiology with respect to different host rocks has not been well described in the literature. However, factors influencing the communities would be of interest to provide a tool for mapping groundwater paths. The Thuringian Basin (Germany) studied here, contains formations of the Permian (Zechstein) and also Triassic period of Buntsandstein, Muschelkalk and Keuper, all of which can be found to crop out at the surface in different regions. We analyzed the bacterial community of nine natural springs and sixteen groundwater wells of the respective rock formations as well as core material from the Zechstein salts. For that we sampled in a mine 3 differnet salt rock samples (carnallitite, halite and sylvinitite). To validate the different approaches, similar rock formations were compared and a consistent microbial community for Buntsandstein could be verified. Similary, for Zechstein, the presence of halophiles was seen with cultivation, isolation directly from the rock material and also in groundwater with DNA-dependent approaches. A higher overlap between sandstone- and limestone-derived communities was visible as if compared to the salt formations. Principal component analysis confirmed formation specific patterns for Muschelkalk, Buntsandstein and Zechstein for the bacterial taxa present, with some overlaps. Bacilli and Gammaproteobacteria were the major groups, with the genera Pseudomonas, Marinomonas, Bacillus, Marinobacter and Pseudoalteromonas representing the communities. The bacteria are well adapted to their respective environment with survival strategies including a wide range of salinity which makes them suitable as tracers for fluid movement below the ground. The results indicate the usefulness and robustness of the approach taken here to investigate aquifer community structures in dependence of the stratigraphy of the groundwater reservoir.

  3. The changing face of community-acquired methicillin-resistant Staphylococcus aureus.

    Science.gov (United States)

    Kale, P; Dhawan, B

    2016-01-01

    Methicillin-resistant Staphylococcus aureus (MRSA) is an important cause of infection, both in hospitalised patients with significant healthcare exposure and in patients without healthcare risk factors. Community-acquired methicillin-resistant S. aureus (CA-MRSA) are known for their rapid community transmission and propensity to cause aggressive skin and soft tissue infections and community-acquired pneumonia. The distinction between the healthcare-associated (HA)-MRSA and CA-MRSA is gradually fading owing to the acquisition of multiple virulence factors and genetic elements. The movement of CA-MRSA strains into the nosocomial setting limits the utility of using clinical risk factors alone to designate community or HA status. Identification of unique genetic characteristics and genotyping are valuable tools for MRSA epidemiological studies. Although the optimum pharmacotherapy for CA-MRSA infections has not been determined, many CA-MRSA strains remain broadly susceptible to several non-β-lactam antibacterial agents. This review aimed at illuminating the characteristic features of CA-MRSA, virulence factors, changing clinical settings and molecular epidemiology, insurgence into the hospital settings and therapy with drug resistance. PMID:27514947

  4. The changing face of community-acquired methicillin-resistant Staphylococcus aureus

    Directory of Open Access Journals (Sweden)

    P Kale

    2016-01-01

    Full Text Available Methicillin-resistant Staphylococcus aureus (MRSA is an important cause of infection, both in hospitalised patients with significant healthcare exposure and in patients without healthcare risk factors. Community-acquired methicillin-resistant S. aureus (CA-MRSA are known for their rapid community transmission and propensity to cause aggressive skin and soft tissue infections and community-acquired pneumonia. The distinction between the healthcare-associated (HA-MRSA and CA-MRSA is gradually fading owing to the acquisition of multiple virulence factors and genetic elements. The movement of CA-MRSA strains into the nosocomial setting limits the utility of using clinical risk factors alone to designate community or HA status. Identification of unique genetic characteristics and genotyping are valuable tools for MRSA epidemiological studies. Although the optimum pharmacotherapy for CA-MRSA infections has not been determined, many CA-MRSA strains remain broadly susceptible to several non-β-lactam antibacterial agents. This review aimed at illuminating the characteristic features of CA-MRSA, virulence factors, changing clinical settings and molecular epidemiology, insurgence into the hospital settings and therapy with drug resistance.

  5. Bacterial Communities Vary between Sinuses in Chronic Rhinosinusitis Patients.

    Science.gov (United States)

    Joss, Tom V; Burke, Catherine M; Hudson, Bernard J; Darling, Aaron E; Forer, Martin; Alber, Dagmar G; Charles, Ian G; Stow, Nicholas W

    2015-01-01

    Chronic rhinosinusitis (CRS) is a common and potentially debilitating disease characterized by inflammation of the sinus mucosa for longer than 12 weeks. Bacterial colonization of the sinuses and its role in the pathogenesis of this disease is an ongoing area of research. Recent advances in culture-independent molecular techniques for bacterial identification have the potential to provide a more accurate and complete assessment of the sinus microbiome, however there is little concordance in results between studies, possibly due to differences in the sampling location and techniques. This study aimed to determine whether the microbial communities from one sinus could be considered representative of all sinuses, and examine differences between two commonly used methods for sample collection, swabs, and tissue biopsies. High-throughput DNA sequencing of the bacterial 16S rRNA gene was applied to both swab and tissue samples from multiple sinuses of 19 patients undergoing surgery for treatment of CRS. Results from swabs and tissue biopsies showed a high degree of similarity, indicating that swabbing is sufficient to recover the microbial community from the sinuses. Microbial communities from different sinuses within individual patients differed to varying degrees, demonstrating that it is possible for distinct microbiomes to exist simultaneously in different sinuses of the same patient. The sequencing results correlated well with culture-based pathogen identification conducted in parallel, although the culturing missed many species detected by sequencing. This finding has implications for future research into the sinus microbiome, which should take this heterogeneity into account by sampling patients from more than one sinus. PMID:26834708

  6. Antimicrobial activity of prulifloxacin in comparison with other fluoroquinolones against community-acquired urinary and respiratory pathogens isolated in Greece.

    Science.gov (United States)

    Karageorgopoulos, D E; Maraki, S; Vatopoulos, A C; Samonis, G; Schito, G C; Falagas, M E

    2013-11-01

    Prulifloxacin, the prodrug of ulifloxacin, is a broad-spectrum fluoroquinolone rather recently introduced in certain European countries. We compared the antimicrobial potency of ulifloxacin with that of other fluoroquinolones against common urinary and respiratory bacterial pathogens. The microbial isolates were prospectively collected between January 2007 and May 2008 from patients with community-acquired infections in Greece. Minimum inhibitory concentrations (MICs) were determined for ciprofloxacin, levofloxacin, moxifloxacin (for respiratory isolates only), and ulifloxacin using the E-test method. The binary logarithms of the MICs [log2(MICs)] were compared by using the Wilcoxon signed-ranks test. A total of 409 isolates were studied. Ulifloxacin had the lowest geometric mean MIC for the 161 Escherichia coli, 59 Proteus mirabilis, and 22 Staphylococcus saprophyticus urinary isolates, the second lowest geometric mean MIC for the 38 Streptococcus pyogenes respiratory isolates (after moxifloxacin), and the third lowest geometric mean MIC for the 114 Haemophilus influenzae and the 15 Moraxella catarrhalis respiratory isolates (after ciprofloxacin and moxifloxacin). Compared with levofloxacin, ulifloxacin had lower log2(MICs) against E. coli (p < 0.001), P. mirabilis (p < 0.001), S. saprophyticus (p < 0.001), and S. pyogenes (p < 0.001). Compared with ciprofloxacin, ulifloxacin had lower log2(MICs) against P. mirabilis (p < 0.001), S. saprophyticus (p = 0.008), and S. pyogenes (p < 0.001), but higher log2(MICs) against H. influenzae (p < 0.001) and M. catarrhalis (p = 0.001). In comparison with other clinically relevant fluoroquinolones, ulifloxacin had the most potent antimicrobial activity against the community-acquired urinary isolates studied and very good activity against the respiratory isolates. PMID:23686506

  7. Viral impacts on bacterial communities in Arctic cryoconite

    DEFF Research Database (Denmark)

    Bellas, Christopher M.; Anesio, Alexandre M.; Telling, Jon;

    2013-01-01

    The surfaces of glaciers are extreme ecosystems dominated by microbial communities. Viruses are found in abundance here, with a high frequency of bacteria displaying visible virus infection. In this study, viral and bacterial production was measured in Arctic cryoconite holes to address the control......, virus production was found to be high, up to 8.98 x 10(7) virus like particles g(-1) dry wt. h(-1) were produced, which is comparable to virus production in sediments around the globe. The virus burst size was assessed by transmission electron microscopy and found to be amongst the lowest recorded...

  8. Bacterial communities of two parthenogenetic aphid species cocolonizing two host plants across the Hawaiian Islands.

    Science.gov (United States)

    Jones, Ryan T; Bressan, Alberto; Greenwell, April M; Fierer, Noah

    2011-12-01

    Aphids (Hemiptera: Aphididae) have been the focus of several studies with respect to their interactions with inherited symbionts, but bacterial communities of most aphid species are still poorly characterized. In this research, we used bar-coded pyrosequencing to characterize bacterial communities in aphids. Specifically, we examined the diversity of bacteria in two obligately parthenogenetic aphid species (the melon aphid, Aphis gossypii, and the cardamom aphid, Pentalonia caladii) cocolonizing two plant species (taro, Colocasia esculenta, and ginger, Alpinia purpurata) across four Hawaiian Islands (Hawaii, Kauai, Maui, and Oahu). Results from this study revealed that heritable symbionts dominated the bacterial communities for both aphid species. The bacterial communities differed significantly between the two species, and A. gossypii harbored a more diverse bacterial community than P. caladii. The bacterial communities also differed across aphid populations sampled from the different islands; however, communities did not differ between aphids collected from the two host plants. PMID:21965398

  9. Associations between Ectomycorrhizal Fungi and Bacterial Needle Endophytes in Pinus radiata: Implications for Biotic Selection of Microbial Communities

    Science.gov (United States)

    Rúa, Megan A.; Wilson, Emily C.; Steele, Sarah; Munters, Arielle R.; Hoeksema, Jason D.; Frank, Anna C.

    2016-01-01

    Studies of the ecological and evolutionary relationships between plants and their associated microbes have long been focused on single microbes, or single microbial guilds, but in reality, plants associate with a diverse array of microbes from a varied set of guilds. As such, multitrophic interactions among plant-associated microbes from multiple guilds represent an area of developing research, and can reveal how complex microbial communities are structured around plants. Interactions between coniferous plants and their associated microbes provide a good model system for such studies, as conifers host a suite of microorganisms including mutualistic ectomycorrhizal (ECM) fungi and foliar bacterial endophytes. To investigate the potential role ECM fungi play in structuring foliar bacterial endophyte communities, we sampled three isolated, native populations of Monterey pine (Pinus radiata), and used constrained analysis of principal coordinates to relate the community matrices of the ECM fungi and bacterial endophytes. Our results suggest that ECM fungi may be important factors for explaining variation in bacterial endophyte communities but this effect is influenced by population and environmental characteristics, emphasizing the potential importance of other factors — biotic or abiotic — in determining the composition of bacterial communities. We also classified ECM fungi into categories based on known fungal traits associated with substrate exploration and nutrient mobilization strategies since variation in these traits allows the fungi to acquire nutrients across a wide range of abiotic conditions and may influence the outcome of multi-species interactions. Across populations and environmental factors, none of the traits associated with fungal foraging strategy types significantly structured bacterial assemblages, suggesting these ECM fungal traits are not important for understanding endophyte-ECM interactions. Overall, our results suggest that both biotic

  10. Associations between ectomycorrhizal fungi and bacterial needle endophytes in Pinus radiata: implications for biotic selection of microbial communities

    Directory of Open Access Journals (Sweden)

    Megan Arlene Rúa

    2016-03-01

    Full Text Available Studies of the ecological and evolutionary relationships between plants and their associated microbes have long been focused on single microbes, or single microbial guilds, but in reality, plants associate with a diverse array of microbes from a varied set of guilds. As such, multitrophic interactions among plant-associated microbes from multiple guilds represent an area of developing research, and can reveal how complex microbial communities are structured around plants. Interactions between coniferous plants and their associated microbes provide a good model system for such studies, as conifers host a suite of microorganisms including mutualistic ectomycorrhizal (ECM fungi and foliar bacterial endophytes. To investigate the potential role ECM fungi play in structuring foliar bacterial endophyte communities, we sampled three isolated, native populations of Monterey pine (Pinus radiata, and used constrained analysis of principal coordinates to relate the community matrices of the ECM fungi and bacterial endophytes. Our results suggest that ECM fungi may be important factors for explaining variation in bacterial endophyte communities but this effect is influenced by population and environmental characteristics, emphasizing the potential importance of other factors — biotic or abiotic — in determining the composition of bacterial communities. We also classified ECM fungi into categories based on known fungal traits associated with substrate exploration and nutrient mobilization strategies since variation in these traits allows the fungi to acquire nutrients across a wide range of abiotic conditions and may influence the outcome of multi-species interactions. Across populations and environmental factors, none of the traits associated with fungal foraging strategy types significantly structured bacterial assemblages, suggesting these ECM fungal traits are not important for understanding endophyte-ECM interactions. Overall, our results suggest

  11. Associations between Ectomycorrhizal Fungi and Bacterial Needle Endophytes in Pinus radiata: Implications for Biotic Selection of Microbial Communities.

    Science.gov (United States)

    Rúa, Megan A; Wilson, Emily C; Steele, Sarah; Munters, Arielle R; Hoeksema, Jason D; Frank, Anna C

    2016-01-01

    Studies of the ecological and evolutionary relationships between plants and their associated microbes have long been focused on single microbes, or single microbial guilds, but in reality, plants associate with a diverse array of microbes from a varied set of guilds. As such, multitrophic interactions among plant-associated microbes from multiple guilds represent an area of developing research, and can reveal how complex microbial communities are structured around plants. Interactions between coniferous plants and their associated microbes provide a good model system for such studies, as conifers host a suite of microorganisms including mutualistic ectomycorrhizal (ECM) fungi and foliar bacterial endophytes. To investigate the potential role ECM fungi play in structuring foliar bacterial endophyte communities, we sampled three isolated, native populations of Monterey pine (Pinus radiata), and used constrained analysis of principal coordinates to relate the community matrices of the ECM fungi and bacterial endophytes. Our results suggest that ECM fungi may be important factors for explaining variation in bacterial endophyte communities but this effect is influenced by population and environmental characteristics, emphasizing the potential importance of other factors - biotic or abiotic - in determining the composition of bacterial communities. We also classified ECM fungi into categories based on known fungal traits associated with substrate exploration and nutrient mobilization strategies since variation in these traits allows the fungi to acquire nutrients across a wide range of abiotic conditions and may influence the outcome of multi-species interactions. Across populations and environmental factors, none of the traits associated with fungal foraging strategy types significantly structured bacterial assemblages, suggesting these ECM fungal traits are not important for understanding endophyte-ECM interactions. Overall, our results suggest that both biotic species

  12. Plant community and soil chemistry responses to long-term nitrogen inputs drive changes in alpine bacterial communities.

    Science.gov (United States)

    Yuan, Xia; Knelman, Joseph E; Gasarch, Eve; Wang, Deli; Nemergut, Diana R; Seastedt, Timothy R

    2016-06-01

    Bacterial community composition and diversity was studied in alpine tundra soils across a plant species and moisture gradient in 20 y-old experimental plots with four nutrient addition regimes (control, nitrogen (N), phosphorus (P) or both nutrients). Different bacterial communities inhabited different alpine meadows, reflecting differences in moisture, nutrients and plant species. Bacterial community alpha-diversity metrics were strongly correlated with plant richness and the production of forbs. After meadow type, N addition proved the strongest determinant of bacterial community structure. Structural Equation Modeling demonstrated that tundra bacterial community responses to N addition occur via changes in plant community composition and soil pH resulting from N inputs, thus disentangling the influence of direct (resource availability) vs. indirect (changes in plant community structure and soil pH) N effects that have remained unexplored in past work examining bacterial responses to long-term N inputs in these vulnerable environments. Across meadow types, the relative influence of these indirect N effects on bacterial community structure varied. In explicitly evaluating the relative importance of direct and indirect effects of long-term N addition on bacterial communities, this study provides new mechanistic understandings of the interaction between plant and microbial community responses to N inputs amidst environmental change.

  13. [Prolonged cultivation of an anaerobic bacterial community producing hydrogen].

    Science.gov (United States)

    Belokopytov, B F; Ryzhmanova, Ia V; Laurinavichius, K S; Shcherbakova, V A

    2012-01-01

    This paper studies various methods of long-term maintenance of the process of hydrogen evolution during the growth of an aerobic bacterial community on a starch-containing environment. When cultured in separable trip fermentation mode for 72 days, from 0.10 to 0.23 H2/l of medium/day was formed. The regime of regular reseeding lasted more than 100 days, forming an average of 0.81 1 H2/l of medium/day. The advantages and disadvantages of different methods of microbial hydrogen production during a dark starch fermentation process are presented. From the obtained H2 forming microbial communities, we isolated an anaerobic spore-forming bacterium (strain BF). Phylogenetic analysis of the 16S RNA gene sequence of the new strain showed that according to its genotype it belongs to the Clostridium butyricum species.

  14. Characterization of Olkiluoto bacterial and archaeal communities by 454 pyrosequencing

    Energy Technology Data Exchange (ETDEWEB)

    Bomberg, M.; Nyyssoenen, M.; Itaevaara, M. [VTT Technical Research Centre of Finland, Espoo (Finland)

    2012-06-15

    Recent advancement in sequencing technologies, 'Next Generation Sequencing', such as FLX 454 pyrosequencing has made it possible to obtain large amounts of sequence data where previously only few sequences could be obtained. This technique is especially useful for the study of community composition of uncultured microbial populations in environmental samples. In this project, the FLX 454 pyrosequencing technique was used to obtain up to 20 000 16S rRNA sequences or 10 000 mRNA sequences from each sample for identification of the microbial species composition as well as for comparison of the microbial communities between different samples. This project focused on the characterization of active microbial communities in the groundwater at the final disposal site of high radioactive wastes in Olkiluoto by FLX 454 pyrosequencing of the bacterial and archaeal ribosomal RNA as well as of the mRNA transcripts of the dsrB gene and mcrA gene of sulphate reducing bacteria and methanogenic archaea, respectively. Specific emphasis was put on studying the relationship of active and latent sulphate reducers and methanogens by qPCR due to their important roles in deep geobiochemical processes connected to copper corrosion. Seven packered boreholes were sampled anaerobically in Olkiluoto during 2009-2010. Groundwater was pumped from specific depths and the microbial cells werecollected by filtration on a membrane. Active microbial communities were studied based on RNA extracted from the membranes and translated to copy DNA, followed by sequencing by 454 Tag pyrosequencing. A total of 27 different bacterial and 17 archaeal taxonomic groups were detected.

  15. Bacteriological and clinical profile of Community acquired pneumonia in hospitalized patients

    Directory of Open Access Journals (Sweden)

    Shah Bashir

    2010-01-01

    Full Text Available The aim of our study was to obtain comprehensive insight into the bacteriological and clinical profile of community-acquired pneumonia requiring hospitalization. The patient population consisted of 100 patients admitted with the diagnosis of community-acquired pneumonia (CAP, as defined by British Thoracic society, from December 1998 to Dec 2000, at the Sher- i-Kashmir institute of Medical Sciences Soura, Srinagar, India. Gram negative organisms were the commonest cause (19/29, followed by gram positive (10/29. In 71 cases no etiological cause was obtained. Pseudomonas aeruginosa was the commonest pathogen (10/29, followed by Staphylococcus aureus (7/29, Escherichia coli (6/29, Klebsiella spp. (3/29, Streptococcus pyogenes (1/29, Streptococcus pneumoniae (1/29 and Acinetobacter spp. (1/29. Sputum was the most common etiological source of organism isolation (26 followed by blood (6, pleural fluid (3, and pus culture (1. Maximum number of patients presented with cough (99%, fever (95%, tachycardia (92%, pleuritic chest pain (75%, sputum production (65% and leucocytosis (43%. The commonest predisposing factors were smoking (65%, COPD (57%, structural lung disease (21%, diabetes mellitus (13%, and decreased level of consciousness following seizure (eight per cent and chronic alcoholism (one per cent. Fourteen patients, of whom, nine were males and five females, died. Staphylococcus aureus was the causative organism in four, Pseudomonas in two, Klebsiella in one, and no organism was isolated in seven cases. The factors predicting mortality at admission were - age over 62 years, history of COPD or smoking, hypotension, altered sensorium, respiratory failure, leucocytosis, and s0 taphylococcus pneumonia and undetermined etiology. The overall rate of identification of microbial etiology of community-acquired pneumonia was 29%, which is very low, and if serological tests for legionella, mycoplasma and viruses are performed the diagnostic yield would

  16. Populations of Stored Product Mite Tyrophagus putrescentiae Differ in Their Bacterial Communities

    Science.gov (United States)

    Erban, Tomas; Klimov, Pavel B.; Smrz, Jaroslav; Phillips, Thomas W.; Nesvorna, Marta; Kopecky, Jan; Hubert, Jan

    2016-01-01

    Background: Tyrophagus putrescentiae colonizes different human-related habitats and feeds on various post-harvest foods. The microbiota acquired by these mites can influence the nutritional plasticity in different populations. We compared the bacterial communities of five populations of T. putrescentiae and one mixed population of T. putrescentiae and T. fanetzhangorum collected from different habitats. Material: The bacterial communities of the six mite populations from different habitats and diets were compared by Sanger sequencing of cloned 16S rRNA obtained from amplification with universal eubacterial primers and using bacterial taxon-specific primers on the samples of adults/juveniles or eggs. Microscopic techniques were used to localize bacteria in food boli and mite bodies. The morphological determination of the mite populations was confirmed by analyses of CO1 and ITS fragment genes. Results: The following symbiotic bacteria were found in compared mite populations: Wolbachia (two populations), Cardinium (five populations), Bartonella-like (five populations), Blattabacterium-like symbiont (three populations), and Solitalea-like (six populations). From 35 identified OTUs97, only Solitalea was identified in all populations. The next most frequent and abundant sequences were Bacillus, Moraxella, Staphylococcus, Kocuria, and Microbacterium. We suggest that some bacterial species may occasionally be ingested with food. The bacteriocytes were observed in some individuals in all mite populations. Bacteria were not visualized in food boli by staining, but bacteria were found by histological means in ovaria of Wolbachia-infested populations. Conclusion: The presence of Blattabacterium-like, Cardinium, Wolbachia, and Solitalea-like in the eggs of T. putrescentiae indicates mother to offspring (vertical) transmission. Results of this study indicate that diet and habitats influence not only the ingested bacteria but also the symbiotic bacteria of T. putrescentiae. PMID

  17. Analysis of intestinal bacterial community diversity of adult Dastarcus helophoroides.

    Science.gov (United States)

    Zhang, Z Q; He, C; Li, M L

    2014-01-01

    Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE), and a culture-dependent technique were used to study the diversity of the intestinal bacterial community in adult Dastarcus helophoroides (Fairmaire) (Coleoptera: Bothrideridae). Universal bacterial primers targeting 200 bp regions of the 16S rDNA gene were used in the PCR-DGGE assay, and 14 bright bands were obtained. The intestinal bacteria detected by PCR-DGGE were classified to Enterococcus (Lactobacillales: Enterococcaceae), Bacillus (Bacillales: Bacillaceae), Cellvibrio (Pseudomonadales: Pseudomonadaceae), Caulobacter (Caulobacterales: Caulobacteraceae), and uncultured bacteria, whereas those isolated by the culture-dependent technique belonged to Staphylococcus (Bacillales: Staphylococcaceae), Pectobacterium Enterobacteriales: Enterobacteriaceae), and Enterobacter (Enterobacteriales: Enterobacteriaceae). These intestinal bacteria represented the groups Lactobacillales (Enterococcus), Pseudomonadales (Cellvibrio), Caulobacterales (Caulobacter), Bacilli (Bacillus and Staphylococcus), and Gammaproteobacteria (Pectobacterium and Enterobacter). Our results demonstrated that PCR-DGGE analysis and the culture-dependent technique were useful in determining the intestinal bacteria of D. helophoroides and the two methods should be integrated to characterize the microbial community and diversity. PMID:25373236

  18. The structure and functions of bacterial communities in an agrocenosis

    Science.gov (United States)

    Dobrovol'skaya, T. G.; Khusnetdinova, K. A.; Manucharova, N. A.; Balabko, P. N.

    2016-01-01

    The most significant factor responsible for the specific taxonomic composition of the bacterial communities in the agrocenosis studied was found to be a part or organ of plants (leaves, flowers, roots, fruits). A stage of plant ontogeny also determines changes of taxa. In the course of the plant growth, eccrisotrophic bacteria are replaced by hydrolytic ones that belong to the group of cellulose-decomposing bacteria. Representatives of the proteobacteria genera that are difficult to identify by phenotypic methods were determined using molecular-biological methods. They were revealed only on oat leaves in the moist period. As the vetch-oat mixture was fertilized with BIOUD-1 (foliar application) in the phyllosphere of both oats and vetch, on all the plant organs, representatives of the Rhodococcus genus as dominants were isolated. This fact was related to the capability of bacteria to decompose the complex aromatic compounds that are ingredients of the fertilizers applied. Another positive effect for plants of the bacterial communities forming in agrocenoses is the presence of bacteria that are antagonists of phytopathogenic bacteria. Thus, in agrocenoses, some interrelationships promoting the growth and reproduction of plants are formed in crop plants and bacteria.

  19. Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities.

    Directory of Open Access Journals (Sweden)

    Sebastian Germerodt

    2016-06-01

    Full Text Available Bacterial communities are taxonomically highly diverse, yet the mechanisms that maintain this diversity remain poorly understood. We hypothesized that an obligate and mutual exchange of metabolites, as is very common among bacterial cells, could stabilize different genotypes within microbial communities. To test this, we developed a cellular automaton to model interactions among six empirically characterized genotypes that differ in their ability and propensity to produce amino acids. By systematically varying intrinsic (i.e. benefit-to-cost ratio and extrinsic parameters (i.e. metabolite diffusion level, environmental amino acid availability, we show that obligate cross-feeding of essential metabolites is selected for under a broad range of conditions. In spatially structured environments, positive assortment among cross-feeders resulted in the formation of cooperative clusters, which limited exploitation by non-producing auxotrophs, yet allowed them to persist at the clusters' periphery. Strikingly, cross-feeding helped to maintain genotypic diversity within populations, while amino acid supplementation to the environment decoupled obligate interactions and favored auxotrophic cells that saved amino acid production costs over metabolically autonomous prototrophs. Together, our results suggest that spatially structured environments and limited nutrient availabilities should facilitate the evolution of metabolic interactions, which can help to maintain genotypic diversity within natural microbial populations.

  20. SENSITIVITY TO ANTIBACTERIAL DRUGS IN AGENTS OF COMMUNITY-ACQUIRED INFECTIONS

    Directory of Open Access Journals (Sweden)

    Osolodchenko T.,

    2015-04-01

    Full Text Available Introduction The widespread and uncontrolled use of antibiotics leads to selection of resistant strains and rise to atypical forms of most infectious agents. Constantly progressive resistance of microorganisms is currently the most important negative phenomenon of antibiotic therapy. The aim of the work was to optimize antibiotic therapy in community-acquired infections. The objective of study was to determine the range and degree of resistance in clinical isolates of microorganisms of different taxonomic groups, obtained from patients in outpatient care. Material and methods 213 clinical isolates of microorganisms obtained from patients in outpatient care were studied: 34,7 % strains were obtained from patients with inflammatory processes in upper respiratory tract, 11,7 % – with ear inflammation, 36,6 % – with inflammatory diseases of urinary and genital tracts, 11,3 % – with of skin and soft tissues inflammation, 4,2 % – eye inflammation and 1,4 % – with postoperative infectious complications. The collection of clinical material was performed accordingly before the start of antibacterial therapy. Microorganisms’ isolation and identification were carried out with the help of microbiological methods according to the regulatory documents. The study of resistance of bacterial strains to the antibacterial drugs was performed with the help of disc diffusion method on the Muller-Hinton nutritional medium and of fungal strains – on Saburo medium with the use of standard commercial discs. Results and discussion The array and level of resistance to antibacterial drugs in clinical isolates of microorganisms of different taxonomic groups obtained from patients in outpatient care was established. The research has established that 43,3 % Staphylococcus spp. isolates possessed polyantibiotic resistance and 3,8 % – extensive resistance, only sensitivity to aminoglycosides and glycopeptides was preserved. The majority of beta

  1. Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure.

    Science.gov (United States)

    de Steenhuijsen Piters, Wouter A A; Bogaert, Debby

    2016-01-01

    The upper respiratory tract is colonized by a diverse array of commensal bacteria that harbor potential pathogens, such as Streptococcus pneumoniae. As long as the local microbial ecosystem-also called "microbiome"-is in balance, these potentially pathogenic bacterial residents cause no harm to the host. However, similar to macrobiological ecosystems, when the bacterial community structure gets perturbed, potential pathogens can overtake the niche and cause mild to severe infections. Recent studies using next-generation sequencing show that S. pneumoniae, as well as other potential pathogens, might be kept at bay by certain commensal bacteria, including Corynebacterium and Dolosigranulum spp. Bomar and colleagues are the first to explore a specific biological mechanism contributing to the antagonistic interaction between Corynebacterium accolens and S. pneumoniae in vitro [L. Bomar, S. D. Brugger, B. H. Yost, S. S. Davies, K. P. Lemon, mBio 7(1):e01725-15, 2016, doi:10.1128/mBio.01725-15]. The authors comprehensively show that C. accolens is capable of hydrolyzing host triacylglycerols into free fatty acids, which display antipneumococcal properties, suggesting that these bacteria might contribute to the containment of pneumococcus. This work exemplifies how molecular epidemiological findings can lay the foundation for mechanistic studies to elucidate the host-microbe and microbial interspecies interactions underlying the bacterial community structure. Next, translation of these results to an in vivo setting seems necessary to unveil the magnitude and importance of the observed effect in its natural, polymicrobial setting. PMID:26838716

  2. Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure

    Directory of Open Access Journals (Sweden)

    Wouter A. A. de Steenhuijsen Piters

    2016-03-01

    Full Text Available The upper respiratory tract is colonized by a diverse array of commensal bacteria that harbor potential pathogens, such as Streptococcus pneumoniae. As long as the local microbial ecosystem—also called “microbiome”—is in balance, these potentially pathogenic bacterial residents cause no harm to the host. However, similar to macrobiological ecosystems, when the bacterial community structure gets perturbed, potential pathogens can overtake the niche and cause mild to severe infections. Recent studies using next-generation sequencing show that S. pneumoniae, as well as other potential pathogens, might be kept at bay by certain commensal bacteria, including Corynebacterium and Dolosigranulum spp. Bomar and colleagues are the first to explore a specific biological mechanism contributing to the antagonistic interaction between Corynebacterium accolens and S. pneumoniae in vitro [L. Bomar, S. D. Brugger, B. H. Yost, S. S. Davies, K. P. Lemon, mBio 7(1:e01725-15, 2016, doi:10.1128/mBio.01725-15]. The authors comprehensively show that C. accolens is capable of hydrolyzing host triacylglycerols into free fatty acids, which display antipneumococcal properties, suggesting that these bacteria might contribute to the containment of pneumococcus. This work exemplifies how molecular epidemiological findings can lay the foundation for mechanistic studies to elucidate the host-microbe and microbial interspecies interactions underlying the bacterial community structure. Next, translation of these results to an in vivo setting seems necessary to unveil the magnitude and importance of the observed effect in its natural, polymicrobial setting.

  3. A rare case of community acquired Burkholderia cepacia infection presenting as pyopneumothorax in an immunocompetent individual

    Institute of Scientific and Technical Information of China (English)

    Suman S Karanth; Hariharan Regunath; Kiran Chawla; Mukhyaprana Prabhu

    2012-01-01

    Burkholderia cepacia (B. cepacia) infection is rarely reported in an immunocompetent host. It is a well known occurence in patients with cystic fibrosis and chronic granulomatous disease where it increases both morbidity and mortality. It has also been included in the list of organisms causing nosocomial infections in an immunocompetent host, most of them transmitted from the immunocompromised patient in which this organism harbors. We report a rare case of isolation of B. cepacia from the bronchoalveolar lavage fluid of an immunocompetent agriculturist who presented with productive cough and fever associated with a pyopneumothorax. This is the first case of community acquired infection reported in an immunocompetent person in India.

  4. Community-acquired Klebsiella pneumoniae liver abscess: an emerging infection in Ireland and Europe.

    LENUS (Irish Health Repository)

    Moore, R

    2013-02-05

    INTRODUCTION: Klebsiella pneumoniae has emerged as a predominant cause of community-acquired mono-microbial pyogenic liver abscess. This was first described in Taiwan and has been widely reported in Asia. This infectious entity has been described in Europe, with single case reports predominating. METHODS: We present three cases in one year from our institution in Ireland and review the European literature to date. RESULTS\\/CONCLUSION: Klebsiella pneumoniae invasive liver abscess syndrome is now emerging in Europe and notably is not restricted to individuals of Asian descent.

  5. A rare case of community acquired Burkholderia cepacia infection presenting as pyopneumothorax in an immunocompetent individual

    Directory of Open Access Journals (Sweden)

    Suman S Karanth

    2012-02-01

    Full Text Available Burkholderia cepacia (B. cepacia infection is rarely reported in an immunocompetent host. It is a well known occurence in patients with cystic fibrosis and chronic granulomatous disease where it increases both morbidity and mortality. It has also been included in the list of organisms causing nosocomial infections in an immunocompetent host, most of them transmitted from the immunocompromised patient in which this organism harbors. We report a rare case of isolation of B. cepacia from the bronchoalveolar lavage fluid of an immunocompetent agriculturist who presented with productive cough and fever associated with a pyopneumothorax. This is the first case of community acquired infection reported in an immunocompetent person in India.

  6. Ultrasound Monitoring and Age Sonographic Characteristics of Community-Acquired Pneumonia in Children

    OpenAIRE

    Т.I. Dianova; D.V. Safonov

    2015-01-01

    The aim of the investigation was to study ultrasound semiotics of community-acquired pneumonias in children of different age, and its dynamics in the course of treatment. Materials and Methods. Pneumonia semiotics study and dynamic monitoring of the disease have been carried out on the basis of chest ultrasound of 154 children divided into 4 age groups: 14 infants (9.1%) from birth to 3 months; 60 children (39.0%) from 3 months to 3 years of age; 49 children (31.8%) from 4 to 7 years of a...

  7. Associations between bacterial communities of house dust and infant gut

    Energy Technology Data Exchange (ETDEWEB)

    Konya, T.; Koster, B. [Division of Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto (Canada); Maughan, H. [Department of Cell and Systems Biology, University of Toronto (Canada); Escobar, M. [Division of Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto (Canada); Azad, M.B. [Department of Pediatrics, University of Alberta (Canada); Guttman, D.S. [Department of Cell and Systems Biology, University of Toronto (Canada); Sears, M.R. [Department of Medicine, McMaster University (Canada); Becker, A.B. [University of Manitoba (Canada); Brook, J.R. [Division of Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto (Canada); Environment Canada (Canada); Takaro, T.K. [Faculty of Health Science, Simon Fraser University (Canada); Kozyrskyj, A.L. [Department of Pediatrics, University of Alberta (Canada); Scott, J.A., E-mail: james.scott@utoronto.ca [Division of Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto (Canada)

    2014-05-01

    The human gut is host to a diverse and abundant community of bacteria that influence health and disease susceptibility. This community develops in infancy, and its composition is strongly influenced by environmental factors, notably perinatal anthropogenic exposures such as delivery mode (Cesarean vs. vaginal) and feeding method (breast vs. formula); however, the built environment as a possible source of exposure has not been considered. Here we report on a preliminary investigation of the associations between bacteria in house dust and the nascent fecal microbiota from 20 subjects from the Canadian Healthy Infant Longitudinal Development (CHILD) Study using high-throughput sequence analysis of portions of the 16S rRNA gene. Despite significant differences between the dust and fecal microbiota revealed by Nonmetric Multidimensional Scaling (NMDS) analysis, permutation analysis confirmed that 14 bacterial OTUs representing the classes Actinobacteria (3), Bacilli (3), Clostridia (6) and Gammaproteobacteria (2) co-occurred at a significantly higher frequency in matched dust–stool pairs than in randomly permuted pairs, indicating an association between these dust and stool communities. These associations could indicate a role for the indoor environment in shaping the nascent gut microbiota, but future studies will be needed to confirm that our findings do not solely reflect a reverse pathway. Although pet ownership was strongly associated with the presence of certain genera in the dust for dogs (Agrococcus, Carnobacterium, Exiguobacterium, Herbaspirillum, Leifsonia and Neisseria) and cats (Escherichia), no clear patterns were observed in the NMDS-resolved stool community profiles as a function of pet ownership.

  8. Associations between bacterial communities of house dust and infant gut

    International Nuclear Information System (INIS)

    The human gut is host to a diverse and abundant community of bacteria that influence health and disease susceptibility. This community develops in infancy, and its composition is strongly influenced by environmental factors, notably perinatal anthropogenic exposures such as delivery mode (Cesarean vs. vaginal) and feeding method (breast vs. formula); however, the built environment as a possible source of exposure has not been considered. Here we report on a preliminary investigation of the associations between bacteria in house dust and the nascent fecal microbiota from 20 subjects from the Canadian Healthy Infant Longitudinal Development (CHILD) Study using high-throughput sequence analysis of portions of the 16S rRNA gene. Despite significant differences between the dust and fecal microbiota revealed by Nonmetric Multidimensional Scaling (NMDS) analysis, permutation analysis confirmed that 14 bacterial OTUs representing the classes Actinobacteria (3), Bacilli (3), Clostridia (6) and Gammaproteobacteria (2) co-occurred at a significantly higher frequency in matched dust–stool pairs than in randomly permuted pairs, indicating an association between these dust and stool communities. These associations could indicate a role for the indoor environment in shaping the nascent gut microbiota, but future studies will be needed to confirm that our findings do not solely reflect a reverse pathway. Although pet ownership was strongly associated with the presence of certain genera in the dust for dogs (Agrococcus, Carnobacterium, Exiguobacterium, Herbaspirillum, Leifsonia and Neisseria) and cats (Escherichia), no clear patterns were observed in the NMDS-resolved stool community profiles as a function of pet ownership

  9. Bacterial and protist community changes during a phytoplankton bloom

    KAUST Repository

    Pearman, John K.

    2015-10-01

    The present study aims to characterize the change in the composition and structure of the bacterial and microzooplankton planktonic communities in relation to the phytoplankton community composition during a bloom. High-throughput amplicon sequencing of regions of the 16S and 18S rRNA gene was undertaken on samples collected during a 20 day (d) mesocosm experiment incorporating two different nutrient addition treatments [Nitrate and Phosphate (NPc) and Nitrate, Phosphate and Silicate (NPSc)] as well as a control. This approach allowed us to discriminate the changes in species composition across a broad range of phylogenetic groups using a common taxonomic level. Diatoms dominated the bloom in the NPSc treatment while dinoflagellates were the dominant phytoplankton in the control and NPc treatment. Network correlations highlighted significant interactions between OTUs within each treatment including changes in the composition of Paraphysomonas OTUs when the dominant Chaetoceros OTU switched. The microzooplankton community composition responded to changes in the phytoplankton composition while the prokaryotic community responded more to changes in ammonia concentration.

  10. Associations between bacterial communities of house dust and infant gut.

    Science.gov (United States)

    Konya, T; Koster, B; Maughan, H; Escobar, M; Azad, M B; Guttman, D S; Sears, M R; Becker, A B; Brook, J R; Takaro, T K; Kozyrskyj, A L; Scott, J A

    2014-05-01

    The human gut is host to a diverse and abundant community of bacteria that influence health and disease susceptibility. This community develops in infancy, and its composition is strongly influenced by environmental factors, notably perinatal anthropogenic exposures such as delivery mode (Cesarean vs. vaginal) and feeding method (breast vs. formula); however, the built environment as a possible source of exposure has not been considered. Here we report on a preliminary investigation of the associations between bacteria in house dust and the nascent fecal microbiota from 20 subjects from the Canadian Healthy Infant Longitudinal Development (CHILD) Study using high-throughput sequence analysis of portions of the 16S rRNA gene. Despite significant differences between the dust and fecal microbiota revealed by Nonmetric Multidimensional Scaling (NMDS) analysis, permutation analysis confirmed that 14 bacterial OTUs representing the classes Actinobacteria (3), Bacilli (3), Clostridia (6) and Gammaproteobacteria (2) co-occurred at a significantly higher frequency in matched dust-stool pairs than in randomly permuted pairs, indicating an association between these dust and stool communities. These associations could indicate a role for the indoor environment in shaping the nascent gut microbiota, but future studies will be needed to confirm that our findings do not solely reflect a reverse pathway. Although pet ownership was strongly associated with the presence of certain genera in the dust for dogs (Agrococcus, Carnobacterium, Exiguobacterium, Herbaspirillum, Leifsonia and Neisseria) and cats (Escherichia), no clear patterns were observed in the NMDS-resolved stool community profiles as a function of pet ownership.

  11. Microbial communities of urban stormwater sediments: the phylogenetic structure of bacterial communities varies with porosity.

    Science.gov (United States)

    Badin, Anne-Laure; Mustafa, Tarfa; Bertrand, Cédric; Monier, Armelle; Delolme, Cécile; Geremia, Roberto A; Bedell, Jean-Philippe

    2012-08-01

    This study focuses on the distribution of bacterial and fungal communities within the microstructure of a multi-contaminated sedimentary layer resulting from urban stormwater infiltration. Fractionation was performed on the basis of differential porosity and aggregate grain size, resulting in five fractions: leachable fitting macroporosity, 1000 μm. Amounts of both bacterial and fungal biomasses are greater in the < 10 μm and leachable fractions. The aggregates contain numerous bacteria but very low amounts of fungal biomass. Single-strand conformational polymorphism molecular profiles highlighted the differences between bacterial and fungal communities of the leachable fraction and those of the aggregates. Random Sanger sequencing of ssu clones revealed that these differences were mainly because of the presence of Epsilonproteobacteria and Firmicutes in the leachable fractions, while the aggregates contained more Cyanobacteria. The Cyanobacteria phylotypes in the aggregates were dominated by the sequences related to Microcoleus vaginatus while the leachable fractions presented the sequences of chloroplastic origin. Therefore, more than 50% of the phylotypes observed were related to Proteobacteria while 40% were related to Cyanobacteria and Bacteroidetes. Preferential distribution of clades in almost all the phyla or classes detected was observed. This study provides insight into the identities of dominant members of the bacterial communities of urban sediments. Microcoleus vaginatus appeared to predominate in pioneer soils. PMID:22404135

  12. Investigation of bacterial community composition and abundance in a lowland arable catchment

    OpenAIRE

    Albaggar, Ali

    2014-01-01

    This study aimed to characterise the bacterial community composition and abundance in the River Wensum in Norfolk using epifluorescence microscopy (EFM), automated ribosomal intergenic analysis (ARISA) and 454 pyrosequencing. It also aimed to determine the effects of spatial and temporal variations and environmental factors on bacterial community composition and abundance in this intensively farmed lowland catchment. The three techniques provided the same trends in bacterial community composi...

  13. Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest.

    Science.gov (United States)

    Kembel, Steven W; O'Connor, Timothy K; Arnold, Holly K; Hubbell, Stephen P; Wright, S Joseph; Green, Jessica L

    2014-09-23

    The phyllosphere--the aerial surfaces of plants, including leaves--is a ubiquitous global habitat that harbors diverse bacterial communities. Phyllosphere bacterial communities have the potential to influence plant biogeography and ecosystem function through their influence on the fitness and function of their hosts, but the host attributes that drive community assembly in the phyllosphere are poorly understood. In this study we used high-throughput sequencing to quantify bacterial community structure on the leaves of 57 tree species in a neotropical forest in Panama. We tested for relationships between bacterial communities on tree leaves and the functional traits, taxonomy, and phylogeny of their plant hosts. Bacterial communities on tropical tree leaves were diverse; leaves from individual trees were host to more than 400 bacterial taxa. Bacterial communities in the phyllosphere were dominated by a core microbiome of taxa including Actinobacteria, Alpha-, Beta-, and Gammaproteobacteria, and Sphingobacteria. Host attributes including plant taxonomic identity, phylogeny, growth and mortality rates, wood density, leaf mass per area, and leaf nitrogen and phosphorous concentrations were correlated with bacterial community structure on leaves. The relative abundances of several bacterial taxa were correlated with suites of host plant traits related to major axes of plant trait variation, including the leaf economics spectrum and the wood density-growth/mortality tradeoff. These correlations between phyllosphere bacterial diversity and host growth, mortality, and function suggest that incorporating information on plant-microbe associations will improve our ability to understand plant functional biogeography and the drivers of variation in plant and ecosystem function.

  14. Emergence of Raoultella ornithinolytica on O'ahu: a case of community-acquired R. ornithinolytica urinary tract infection.

    Science.gov (United States)

    Nakasone, Elizabeth S; Kaneshiro, Ricky; Min, Kathleen; Tokeshi, Jinichi

    2015-05-01

    Human infection with Raoultella ornithinolytica is rare, with only ten cases having been reported previously. This case report describes a local patient diagnosed with community-acquired R. ornithinolytica urinary tract infection in 2014.

  15. Analysis of the effectiveness of physical rehabilitation according spirographic indicators in community-acquired pneumonia during convalescence

    Directory of Open Access Journals (Sweden)

    Kalmykova Y.S.

    2014-05-01

    Full Text Available Purpose : to make a program of physical rehabilitation for convalescents after community-acquired pneumonia, promotes normalization of respiratory function. The objectives of the study was to evaluate the dynamics spirographic indicators during convalescence community-acquired pneumonia. Material: the study involved 28 women aged 19 to 24 years with a diagnosis of community-acquired pneumonia after convalescent. Results: the positive influence of physiotherapy based dance aerobics; morning hygienic gymnastics; therapeutic massage and physical therapy on indicators of lung volumes, ventilation and bronchial patency according spirographic research. Conclusion: in community-acquired pneumonia during the convalescence period recommended physical rehabilitation, which includes curative gymnastics based on dance aerobics, morning hygienic gymnastics, massage therapy, physiotherapy. It improves the functionality of the cardiorespiratory system, nonspecific immunity and overall physical performance level.

  16. Biogeographic Congruency among Bacterial Communities from Terrestrial Sulfidic Springs

    Directory of Open Access Journals (Sweden)

    Brendan eHeadd

    2014-09-01

    Full Text Available Terrestrial sulfidic springs support diverse microbial communities by serving as stable conduits for geochemically diverse and nutrient-rich subsurface waters. Microorganisms that colonize terrestrial springs likely originate from groundwater, but may also be sourced from the surface. As such, the biogeographic distribution of microbial communities inhabiting sulfidic springs should be controlled by a combination of spring geochemistry and surface and subsurface transport mechanisms, and not necessarily geographic proximity to other springs. We examined the bacterial diversity of seven springs to test the hypothesis that occurrence of taxonomically similar microbes, important to the sulfur cycle, at each spring is controlled by geochemistry. Complementary Sanger sequencing and 454 pyrosequencing of 16S rRNA genes retrieved five proteobacterial classes, and Bacteroidetes, Chlorobi, Chloroflexi, and Firmicutes phyla from all springs, which suggested the potential for a core sulfidic spring microbiome. Among the putative sulfide-oxidizing groups (Epsilonproteobacteria and Gammaproteobacteria, up to 83% of the sequences from geochemically similar springs clustered together. Abundant populations of Hydrogenimonas-like or Sulfurovum-like spp. (Epsilonproteobacteria occurred with abundant Thiothrix and Thiofaba spp. (Gammaproteobacteria, but Arcobacter-like and Sulfurimonas spp. (Epsilonproteobacteria occurred with less abundant gammaproteobacterial populations. These distribution patterns confirmed that geochemistry rather than biogeography regulates bacterial dominance at each spring. Potential biogeographic controls were related to paleogeologic sedimentation patterns that could control long-term microbial transport mechanisms that link surface and subsurface environments. Knowing the composition of a core sulfidic spring microbial community could provide a way to monitor diversity changes if a system is threatened by anthropogenic processes or

  17. Acute haematogenous community-acquired methicillin-resistant Staphylococcus aureus osteomyelitis in an adult: Case report and review of literature

    OpenAIRE

    Dhanoa Amreeta; Singh Vivek; Mansor Azura; Yusof Mohd; Lim King-Ting; Thong Kwai-Lin

    2012-01-01

    Abstract Background Methicillin-resistant Staphylococcus aureus (MRSA) has of late emerged as a cause of community-acquired infections among immunocompetent adults without risk factors. Skin and soft tissue infections represent the majority of community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) clinical presentations, whilst invasive and life-threatening illness like necrotizing pneumonia, necrotizing fasciitis, pyomyositis, osteomyelitis and sepsis syndrome are less comm...

  18. Epidemiology of community-acquired pneumonia and implications for vaccination of children living in developing and newly industrialized countries: A systematic literature review

    Science.gov (United States)

    DeAntonio, Rodrigo; Yarzabal, Juan-Pablo; Cruz, James Philip; Schmidt, Johannes E.; Kleijnen, Jos

    2016-01-01

    ABSTRACT This systematic review evaluated the epidemiology of community-acquired pneumonia in children <6 y of age within 90 developing and newly industrialized countries. Literature searches (1990–2011), based on MEDLINE, EMBASE, Cochrane, CAB Global Health, WHO, UNICEF, country-specific websites, conferences, health-technology-assessment agencies, and the reference lists of included studies, yielded 8,734 records; 62 of 340 studies were included in this review. The highest incidence rate among included studies was 0.51 episodes/child-year, for children <5 y of age in Bangladesh. The highest prevalence was in Chinese children <6 months of age (37.88%). The main bacterial pathogens were Streptococcus pneumoniae, Haemophilus influenzae and Mycoplasma pneumoniae and the main viral pathogens were respiratory syncytial virus, adenovirus and rhinovirus. Community-acquired pneumonia remains associated with high rates of morbidity and mortality. Improved and efficient surveillance and documentation of the epidemiology and burden of community-acquired pneumonia across various geographical regions is warranted. PMID:27269963

  19. Incidence of community-acquired pneumonia in the population of four municipalities in eastern Finland.

    Science.gov (United States)

    Jokinen, C; Heiskanen, L; Juvonen, H; Kallinen, S; Karkola, K; Korppi, M; Kurki, S; Rönnberg, P R; Seppä, A; Soimakallio, S

    1993-05-01

    Between September 1, 1981, and August 31, 1982, all patients with suspected or confirmed pneumonia among the 46,979 inhabitants of four municipalities in the province of Kuopio, Finland, were reported to a pneumonia register by their attending physicians. In addition, two study pathologists reported all cases of pneumonia found at autopsy, and two permanent registers were checked for retrospective identification of patients. Chest radiographs were obtained from 97% of all patients. The final diagnosis was based on radiologic or autopsy criteria. A total 546 patients (323 males and 223 females) had community-acquired pneumonia; of these, 37% were less than 15 years of age, and 31% were 60 years of age or older. Nineteen percent of the patients had defined chronic conditions, and 42% were admitted to hospital. The case fatality rate was 4%. The overall incidence of community-acquired pneumonia per 1,000 inhabitants per year was 11.6 (13.9 in males, 9.4 in females). The age-specific incidence per 1,000 inhabitants per year was as follows: age or = 75 years, 34.2. PMID:8317455

  20. Initial community and environment determine the response of bacterial communities to dispersant and oil contamination.

    Science.gov (United States)

    Ortmann, Alice C; Lu, YueHan

    2015-01-15

    Bioremediation of seawater by natural bacterial communities is one potential response to coastal oil spills, but the success of the approach may vary, depending on geographical location, oil composition and the timing of spill. The short term response of coastal bacteria to dispersant, oil and dispersed oil was characterized using 16S rRNA gene tags in two mesocosm experiments conducted two months apart. Despite differences in the amount of oil-derived alkanes across the treatments and experiments, increases in the contributions of hydrocarbon degrading taxa and decreases in common estuarine bacteria were observed in response to dispersant and/or oil. Between the two experiments, the direction and rates of changes in particulate alkane concentrations differed, as did the magnitude of the bacterial response to oil and/or dispersant. Together, our data underscore large variability in bacterial responses to hydrocarbon pollutants, implying that bioremediation success varies with starting biological and environmental conditions. PMID:25487088

  1. [Critical evaluation and predictive value of clinical presentation in out-patients with acute community-acquired pneumonia].

    Science.gov (United States)

    Mayaud, C; Fartoukh, M; Prigent, H; Parrot, A; Cadranel, J

    2006-01-01

    Diagnostic probability of community-acquired pneumonia (CAP) depends on data related to age and clinical and radiological findings. The critical evaluation of data in the literature leads to the following conclusions: 1) the prevalence of CAP in a given population with acute respiratory disease is 5% in outpatients and 10% in an emergency care unit. This could be as low as 2% in young people and even higher than 40% in hospitalized elderly patients; 2) the collection of clinical data is linked to the way the patient is examined and to the expertise of the clinician. The absolute lack of "vital signs" has a good negative predictive value in CAP; presence of unilateral crackles has a good positive predictive value; 3) there is a wide range of X-ray abnormalities: localized alveolar opacities; interstitial opacities, limited of diffused. The greatest radiological difficulties are encountered in old people with disorders including chronic respiratory or cardiac opacities and as a consequence of the high prevalence of bronchopneumonia episodes at this age; 4) among patients with lower respiratory tract (LRT) infections, the blood levels of leukocytes, CRP and procalcitonine are higher in CAP patients, mainly when their disease has a bacterial origin. Since you have not a threshold value reliably demonstrated in large populations with LRT infections or acute respiratory disease, presence or absence of these parameters could only be taken as a slight hint for a CAP diagnosis. PMID:17084571

  2. Prevalence and clinical features of respiratory syncytial virus in children hospitalized for community-acquired pneumonia in northern Brazil

    Directory of Open Access Journals (Sweden)

    Lamarão Letícia

    2012-05-01

    Full Text Available Abstract Background Childhood pneumonia and bronchiolitis is a leading cause of illness and death in young children worldwide with Respiratory Syncytial Virus (RSV as the main viral cause. RSV has been associated with annual respiratory disease outbreaks and bacterial co-infection has also been reported. This study is the first RSV epidemiological study in young children hospitalized with community-acquired pneumonia (CAP in Belém city, Pará (Northern Brazil. Methods With the objective of determining the prevalence of RSV infection and evaluating the patients’ clinical and epidemiological features, we conducted a prospective study across eight hospitals from November 2006 to October 2007. In this study, 1,050 nasopharyngeal aspirate samples were obtained from hospitalized children up to the age of three years with CAP, and tested for RSV antigen by direct immunofluorescence assay and by Reverse Transcription Polymerase Chain Reaction (RT-PCR for RSV Group identification. Results RSV infection was detected in 243 (23.1% children. The mean age of the RSV-positive group was lower than the RSV-negative group (12.1 months vs 15.5 months, pppppp Conclusion The present study highlights the relevance of RSV infection in hospitalized cases of CAP in our region; our findings warrant the conduct of further investigations which can help design strategies for controlling the disease.

  3. Cumulative clinical experience from over a decade of use of levofloxacin in community-acquired pneumonia: critical appraisal and role in therapy

    Directory of Open Access Journals (Sweden)

    Noreddin AM

    2011-10-01

    Full Text Available Ayman M Noreddin1, Walid F Elkhatib2, Kenji M Cunnion3, George G Zhanel41Department of Pharmacy Practice, Hampton University, Hampton, VA, USA; 2Department of Microbiology and Immunology, Ain-Shams University, Cairo, Egypt; 3Department of Pediatrics, East Virginia Medical School, Norfolk, VA, USA; 4Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada Abstract: Levofloxacin is the synthetic L-isomer of the racemic fluoroquinolone, ofloxacin. It interferes with critical processes in the bacterial cell such as DNA replication, transcription, repair, and recombination by inhibiting bacterial topoisomerases. Levofloxacin has broad spectrum activity against several causative bacterial pathogens of community-acquired pneumonia (CAP. Oral levofloxacin is rapidly absorbed and is bioequivalent to the intravenous formulation such that patients can be conveniently transitioned between these formulations when moving from the inpatient to the outpatient setting. Furthermore, levofloxacin demonstrates excellent safety, and has good tissue penetration maintaining adequate concentrations at the site of infection. The efficacy and tolerability of levofloxacin 500 mg once daily for 10 days in patients with CAP are well established. Furthermore, a high-dose (750 mg and short-course (5 days of once-daily levofloxacin has been approved for use in the US in the treatment of CAP, acute bacterial sinusitis, acute pyelonephritis, and complicated urinary tract infections. The high-dose, short-course levofloxacin regimen maximizes its concentration-dependent antibacterial activity, decreases the potential for drug resistance, and has better patient compliance.Keywords: levofloxacin, community-acquired pneumonia, pharmacodynamics, resistance, pharmacokinetics, clinical use

  4. Bacterial community in Haemaphysalis ticks of domesticated animals from the Orang Asli communities in Malaysia.

    Science.gov (United States)

    Khoo, Jing-Jing; Chen, Fezshin; Kho, Kai Ling; Ahmad Shanizza, Azzy Iyzati; Lim, Fang-Shiang; Tan, Kim-Kee; Chang, Li-Yen; AbuBakar, Sazaly

    2016-07-01

    Ticks are vectors in the transmission of many important infectious diseases in human and animals. Ticks can be readily found in the semi-forested areas such as the settlements of the indigenous people in Malaysia, the Orang Asli. There is still minimal information available on the bacterial agents associated with ticks found in Malaysia. We performed a survey of the bacterial communities associated with ticks collected from domestic animals found in two Orang Asli villages in Malaysia. We collected 62 ticks, microscopically and molecularly identified as related to Haemaphysalis wellingtoni, Haemaphysalis hystricis and Haemaphysalis bispinosa. Bacterial 16s rRNA hypervariable region (V6) amplicon libraries prepared from the tick samples were sequenced on the Ion Torrent PGM platform. We detected a total of 392 possible bacterial genera after pooling and sequencing 20 samples, indicating a diverse bacterial community profile. Dominant taxa include the potential tick endosymbiont, Coxiella. Other dominant taxa include the tick-associated pathogen, Rickettsia, and environmental bacteria such as Bacillus, Mycobacterium, Sphingomonas and Pseudomonas. Other known tick-associated bacteria were also detected, including Anaplasma, Ehrlichia, Rickettsiella and Wolbachia, albeit at very low abundance. Specific PCR was performed on selected samples to identify Rickettsia and Coxiella. Sequence of Rickettsia felis, which causes spotted fever in human and cats, was identified in one sample. Coxiella endosymbionts were detected in three samples. This study provides the baseline knowledge of the microbiome of ticks in Malaysia, focusing on tick-associated bacteria affecting the Orang Asli communities. The role of the herein found Coxiella and Rickettsia in tick physiology or disease transmission merits further investigation. PMID:27132518

  5. Changes in northern Gulf of Mexico sediment bacterial and archaeal communities exposed to hypoxia

    Science.gov (United States)

    Biogeochemical changes in marine sediments during coastal water hypoxia are well described, but less is known about underlying changes in microbial communities. Bacterial and archaeal communities in Louisiana continental shelf (LCS) hypoxic zone sediments were characterized by py...

  6. Determination Of Uncultured Endo phytic Bacterial Community From Rice Root

    International Nuclear Information System (INIS)

    Culture-independent approaches were developed for rapid analysis of microbial community diversity in various environments. Direct analysis based on 16S rDNA as the phylogenetic markers is the most ordinary, conventional and suitable methods for bacterial diversity analysis. The objective of this study is to investigate the microbial diversity from the rice root tissues using culture-independent approach by 16S rDNA library construction. The 16S rDNAs were directly extracted from a total genomic DNA by polymerase chain reaction (PCR) amplification using with the bacteria-specific primer set. The 16S rDNAs were subsequently analysed by cloning and restriction digestion. The amplified ribosomal DNA restriction analysis (ARDRA) clustered the 16S rDNAs into eight majority patterns. These predominant patterns were analysed by DNA sequencing. A better understanding at microbial diversity level is critical to potentiate the endophyte as plant growth promoters. (author)

  7. Dynamics of bacterial community in the gut of Cornu aspersum

    Directory of Open Access Journals (Sweden)

    ZDRAVKA KOLEVA

    2015-12-01

    Full Text Available The dynamics of the bacterial community in the intestinal tract of Cornu aspersum was investigated during different states of its life cycle. Two approaches were applied – culture and non-culture. The non-culture approach was performed by ARDRA of 16S rDNA using two of the six tested endonucleases. Data were analyzed by hierarchical cluster analysis. The restriction of 16S rDNA samples from the snail of different physiological states with endonucleases HinfI and Csp6I resulted in generation of different profiles depending on the snail states. By the culture approach we found that the total number of cultivable bacteria, representatives of Enterobacteriaceae, lactic acid bacteria, amylolitic and cellulolytic bacteria were the most abundant in active state of the snails. Cellulolytic bacteria were not detected in juveniles of C. aspersum. Escherichia coli, Clostridium perfringens as well as bacteria from the genus Salmonella, Shigella and Pseudomonas were not detected. Bacteria of the genus Aeromonas were found in juveniles of C. aspersum, after that their number decrease and were not found in hibernating snails. On the base of the two applied approaches this study shows that the bacterial flora in the intestinal tract of C. aspersum is affected by the seasonal and environmental variations and undergoes quantitative and qualitative changes during the different states of the life cycle. The snails harbor in their gut intestinal bacteria, which possess biochemical potentiality to degrade the plant components.

  8. Altamira cave Paleolithic paintings harbor partly unknown bacterial communities.

    Science.gov (United States)

    Schabereiter-Gurtner, Claudia; Saiz-Jimenez, Cesareo; Piñar, Guadalupe; Lubitz, Werner; Rölleke, Sabine

    2002-05-21

    Since it has been reported that microorganisms can affect painting pigments, Paleolithic painting microbiology deserves attention. The present study is the first report on the bacterial colonization of the valuable Paleolithic paintings in the famous Altamira cave (Spain). One sample taken from a painting area in the Polychromes Hall was analyzed culture-independently. This was the first time microbiologists were allowed to take sample material directly from Altamira paintings. Identification methods included PCR amplification of 16S rRNA genes (16S rDNA) and community fingerprinting by denaturing gradient gel electrophoresis (DGGE). The applied approach gave insight into a great bacterial taxonomic diversity, and allowed the detection of unexpected and unknown bacteria with potential effects on the conservation of the painting. Regarding the number of 29 visible DGGE bands in the community fingerprint, the numbers of analyzed clones described about 72% of the phylogenetic diversity present in the sample. Thirty-eight percent of the sequences analyzed were phylogenetically most closely related to cultivated bacteria, while the majority (62%) were most closely related to environmental 16S rDNA clones. Bacteria identified in Altamira were related with sequence similarities between 84.8 and 99.4% to members of the cosmopolitan Proteobacteria (52.3%), to members of the Acidobacterium division (23.8%), Cytophaga/Flexibacter/Bacteroides phylum (9.5%), green non-sulfur bacteria (4.8%), Planctomycetales (4.8%) and Actinobacteria (4.8%). The high number of clones most closely related to environmental 16S rDNA clones showed the broad spectrum of unknown and yet to be cultivated bacteria in Altamira cave. PMID:12052543

  9. Metabolic Requirements of Escherichia coli in Intracellular Bacterial Communities during Urinary Tract Infection Pathogenesis

    Science.gov (United States)

    Conover, Matt S.; Hadjifrangiskou, Maria; Palermo, Joseph J.; Hibbing, Michael E.; Dodson, Karen W.

    2016-01-01

    ABSTRACT Uropathogenic Escherichia coli (UPEC) is the primary etiological agent of over 85% of community-acquired urinary tract infections (UTIs). Mouse models of infection have shown that UPEC can invade bladder epithelial cells in a type 1 pilus-dependent mechanism, avoid a TLR4-mediated exocytic process, and escape into the host cell cytoplasm. The internalized UPEC can clonally replicate into biofilm-like intracellular bacterial communities (IBCs) of thousands of bacteria while avoiding many host clearance mechanisms. Importantly, IBCs have been documented in urine from women and children suffering acute UTI. To understand this protected bacterial niche, we elucidated the transcriptional profile of bacteria within IBCs using microarrays. We delineated the upregulation within the IBC of genes involved in iron acquisition, metabolism, and transport. Interestingly, lacZ was highly upregulated, suggesting that bacteria were sensing and/or utilizing a galactoside for metabolism in the IBC. A ΔlacZ strain displayed significantly smaller IBCs than the wild-type strain and was attenuated during competitive infection with a wild-type strain. Similarly, a galK mutant resulted in smaller IBCs and attenuated infection. Further, analysis of the highly upregulated gene yeaR revealed that this gene contributes to oxidative stress resistance and type 1 pilus production. These results suggest that bacteria within the IBC are under oxidative stress and, consistent with previous reports, utilize nonglucose carbon metabolites. Better understanding of the bacterial mechanisms used for IBC development and establishment of infection may give insights into development of novel anti-virulence strategies. PMID:27073089

  10. Metabolic Requirements of Escherichia coli in Intracellular Bacterial Communities during Urinary Tract Infection Pathogenesis

    Directory of Open Access Journals (Sweden)

    Matt S. Conover

    2016-04-01

    Full Text Available Uropathogenic Escherichia coli (UPEC is the primary etiological agent of over 85% of community-acquired urinary tract infections (UTIs. Mouse models of infection have shown that UPEC can invade bladder epithelial cells in a type 1 pilus-dependent mechanism, avoid a TLR4-mediated exocytic process, and escape into the host cell cytoplasm. The internalized UPEC can clonally replicate into biofilm-like intracellular bacterial communities (IBCs of thousands of bacteria while avoiding many host clearance mechanisms. Importantly, IBCs have been documented in urine from women and children suffering acute UTI. To understand this protected bacterial niche, we elucidated the transcriptional profile of bacteria within IBCs using microarrays. We delineated the upregulation within the IBC of genes involved in iron acquisition, metabolism, and transport. Interestingly, lacZ was highly upregulated, suggesting that bacteria were sensing and/or utilizing a galactoside for metabolism in the IBC. A ΔlacZ strain displayed significantly smaller IBCs than the wild-type strain and was attenuated during competitive infection with a wild-type strain. Similarly, a galK mutant resulted in smaller IBCs and attenuated infection. Further, analysis of the highly upregulated gene yeaR revealed that this gene contributes to oxidative stress resistance and type 1 pilus production. These results suggest that bacteria within the IBC are under oxidative stress and, consistent with previous reports, utilize nonglucose carbon metabolites. Better understanding of the bacterial mechanisms used for IBC development and establishment of infection may give insights into development of novel anti-virulence strategies.

  11. Influences of plant type on bacterial and archaeal communities in constructed wetland treating polluted river water.

    Science.gov (United States)

    Long, Yan; Yi, Hao; Chen, Sili; Zhang, Zhengke; Cui, Kai; Bing, Yongxin; Zhuo, Qiongfang; Li, Bingxin; Xie, Shuguang; Guo, Qingwei

    2016-10-01

    Both bacteria and archaeal communities can play important roles in biogeochemical processes in constructed wetland (CW) system. However, the influence of plant type on microbial community in surface water CW remains unclear. The present study investigated bacterial and archaeal communities in five surface water CW systems with different plant species. The abundance, richness, and diversity of both bacterial and archaeal communities considerably differed in these five CW systems. Compared with the other three CW systems, the CW systems planted with Vetiveria zizanioides or Juncus effusus L. showed much higher bacterial abundance but lower archaeal abundance. Bacteria outnumbered archaea in each CW system. Moreover, the CW systems planted with V. zizanioides or J. effusus L. had relatively lower archaeal but higher bacterial richness and diversity. In each CW system, bacterial community displayed much higher richness and diversity than archaeal community. In addition, a remarkable difference of both bacterial and archaeal community structures was observed in the five studied CW systems. Proteobacteria was the most abundant bacterial group (accounting for 33-60 %). Thaumarchaeota organisms (57 %) predominated in archaeal communities in CW systems planted with V. zizanioides or J. effusus L., while Woesearchaeota (23 or 24 %) and Euryarchaeota (23 or 15 %) were the major archaeal groups in CW systems planted with Cyperus papyrus or Canna indica L. Archaeal community in CW planted with Typha orientalis Presl was mainly composed of unclassified archaea. Therefore, plant type exerted a considerable influence on microbial community in surface water CW system. PMID:27392623

  12. Local and regional factors influencing bacterial community assembly.

    Science.gov (United States)

    Lindström, Eva S; Langenheder, Silke

    2012-02-01

    The classical view states that microbial biogeography is not affected by dispersal barriers or historical events, but only influenced by the local contemporary habitat conditions (species sorting). This has been challenged during recent years by studies suggesting that also regional factors such as mass effect, dispersal limitation and neutral assembly are important for the composition of local bacterial communities. Here we summarize results from biogeography studies in different environments, i.e. in marine, freshwater and soil as well in human hosts. Species sorting appears to be the most important mechanism. However, this result might be biased since this is the mechanism that is easiest to measure, detect and interpret. Hence, the importance of regional factors may have been underestimated. Moreover, our survey indicates that different assembly mechanisms might be important for different parts of the total community, differing, for example, between generalists and specialists, and between taxa of different dispersal ability and motility. We conclude that there is a clear need for experimental studies, first, to clearly separate regional and local factors in order to study their relative importance, and second, to test whether there are differences in assembly mechanisms depending on different taxonomic or functional groups.

  13. Epiphytic bacterial community composition on two common submerged macrophytes in brackish water and freshwater

    OpenAIRE

    Blindow Irmgard; Blume Maja; Hempel Melanie; Gross Elisabeth M

    2008-01-01

    Abstract Background Plants and their heterotrophic bacterial biofilm communities possibly strongly interact, especially in aquatic systems. We aimed to ascertain whether different macrophytes or their habitats determine bacterial community composition. We compared the composition of epiphytic bacteria on two common aquatic macrophytes, the macroalga Chara aspera Willd. and the angiosperm Myriophyllum spicatum L., in two habitats, freshwater (Lake Constance) and brackish water (Schaproder Bodd...

  14. Bacterial communities in Arctic first-year drift ice during the winter/spring transition.

    Science.gov (United States)

    Eronen-Rasimus, Eeva; Piiparinen, Jonna; Karkman, Antti; Lyra, Christina; Gerland, Sebastian; Kaartokallio, Hermanni

    2016-08-01

    Horizontal and vertical variability of first-year drift-ice bacterial communities was investigated along a North-South transect in the Fram Strait during the winter/spring transition. Two different developmental stages were captured along the transect based on the prevailing environmental conditions and the differences in bacterial community composition. The differences in the bacterial communities were likely driven by the changes in sea-ice algal biomass (2.6-5.6 fold differences in chl-a concentrations). Copiotrophic genera common in late spring/summer sea ice, such as Polaribacter, Octadecabacter and Glaciecola, dominated the bacterial communities, supporting the conclusion that the increase in the sea-ice algal biomass was possibly reflected in the sea-ice bacterial communities. Of the dominating bacterial genera, Polaribacter seemed to benefit the most from the increase in algal biomass, since they covered approximately 39% of the total community at the southernmost stations with higher (>6 μg l(-1) ) chl-a concentrations and only 9% at the northernmost station with lower chl-a concentrations (ice bacterial communities also varied between the ice horizons at all three stations and thus we recommend that for future studies multiple ice horizons be sampled to cover the variability in sea-ice bacterial communities in spring. PMID:27264318

  15. Community-Acquired Pneumonia and Empyema Caused by Citrobacter koseri in an Immunocompetent Patient

    Directory of Open Access Journals (Sweden)

    Miguel Angel Ariza-Prota

    2015-01-01

    Full Text Available Citrobacter species, belonging to the family Enterobacteriaceae, are environmental organisms commonly found in soil, water, and the intestinal tracts of animals and humans. Citrobacter koseri is known to be an uncommon but serious cause of both sporadic and epidemic septicemia and meningitis in neonates and young infants. Most cases reported have occurred in immunocompromised hosts. The infections caused by Citrobacter are difficult to treat with usual broad spectrum antibiotics owing to rapid generation of mutants and have been associated with high death rates in the past. We believe this is the first case described in the literature of a community-acquired pneumonia and empyema caused by Citrobacter koseri in an immunocompetent adult patient.

  16. Norovirus Genotypes in Hospital Settings - Differences between Nosocomial and Community-Acquired Infections

    DEFF Research Database (Denmark)

    Franck, Kristina Træholt; Nielsen, Rikke Thoft; Holzknecht, Barbara Juliane;

    2015-01-01

    BACKGROUND:  Norovirus is a major cause of gastroenteritis and hospital outbreaks, leading to substantial morbidity and direct healthcare expenses as well as indirect societal costs. The aim of the study was to estimate the proportion of nosocomial norovirus infections among inpatients tested...... positive for norovirus in Denmark, 2002-2010, and to study the distribution of norovirus genotypes among inpatients with nosocomial and community-acquired norovirus infections, respectively. METHODS:  Admission and stool sampling dates from 3656 NoV infected patients were used to estimate the proportion...... of nosocomial infections. The associations between nosocomial infection and patient age, gender, and norovirus genotype GII.4 were examined. RESULTS:  Of the 3656 inpatients, 63% were classified as having nosocomial infections. Among these 9 capsid and 8 polymerase norovirus genotypes were detected whereas...

  17. Lung scintigraphy in differential diagnosis of peripheral lung cancer and community-acquired pneumonia

    Science.gov (United States)

    Krivonogov, Nikolay G.; Efimova, Nataliya Y.; Zavadovsky, Konstantin W.; Lishmanov, Yuri B.

    2016-08-01

    Ventilation/perfusion lung scintigraphy was performed in 39 patients with verified diagnosis of community-acquired pneumonia (CAP) and in 14 patients with peripheral lung cancer. Ventilation/perfusion ratio, apical-basal gradients of ventilation (U/L(V)) and lung perfusion (U/L(P)), and alveolar capillary permeability of radionuclide aerosol were determined based on scintigraphy data. The study demonstrated that main signs of CAP were increases in ventilation/perfusion ratio, perfusion and ventilation gradient on a side of the diseased lung, and two-side increase in alveolar capillary permeability rate for radionuclide aerosol. Unlike this, scintigraphic signs of peripheral lung cancer comprise an increase in ventilation/perfusion ratio over 1.0 on a side of the diseased lung with its simultaneous decrease on a contralateral side, normal values of perfusion and ventilation gradients of both lungs, and delayed alveolar capillary clearance in the diseased lung compared with the intact lung.

  18. A review of the role of Haemophilus influenzae in community-acquired pneumonia

    Directory of Open Access Journals (Sweden)

    Mary PE Slack

    2015-06-01

    Full Text Available In an era when Haemophilus influenzae type b (Hib conjugate vaccine is widely used, the incidence of Hib as a cause of community-acquired pneumonia (CAP has dramatically declined. Non-typeable H. influenzae (NTHi strains and, occasionally, other encapsulated serotypes of H. influenzae are now the cause of the majority of invasive H. influenzae infections, including bacteraemic CAP. NTHi have long been recognised as an important cause of lower respiratory tract infection, including pneumonia, in adults, especially those with underlying diseases. The role of NTHi as a cause of non-bacteraemic CAP in children is less clear. In this review the evidence for the role of NTHi and capsulated strains of H. influenzae will be examined.

  19. How well do discharge diagnoses identify hospitalised patients with community-acquired infections? - a validation study

    DEFF Research Database (Denmark)

    Henriksen, Daniel Pilsgaard; Nielsen, Stig Lønberg; Laursen, Christian Borbjerg;

    2014-01-01

    BACKGROUND: Credible measures of disease incidence, trends and mortality can be obtained through surveillance using manual chart review, but this is both time-consuming and expensive. ICD-10 discharge diagnoses are used as surrogate markers of infection, but knowledge on the validity of infections...... admitted to a medical ED in a one-year period (September 2010-August 2011), to establish if they were hospitalised with community-acquired infection. Using the manual review as gold standard, we calculated the sensitivity, specificity, predictive values, and likelihood ratios of discharge diagnoses......-10 diagnoses was 79.9% (95%CI: 78.1-81.3%), specificity 83.9% (95%CI: 82.6-85.1%), positive likelihood ratio 4.95 (95%CI: 4.58-5.36) and negative likelihood ratio 0.24 (95%CI: 0.22-0.26). The two most common sites of infection, the lower respiratory tract and urinary tract, had positive likelihood...

  20. Diagnostic and prognostic accuracy of clinical and laboratory parameters in community-acquired pneumonia

    Directory of Open Access Journals (Sweden)

    Nusbaumer Charly

    2007-03-01

    Full Text Available Abstract Background Community-acquired pneumonia (CAP is the most frequent infection-related cause of death. The reference standard to diagnose CAP is a new infiltrate on chest radiograph in the presence of recently acquired respiratory signs and symptoms. This study aims to evaluate the diagnostic and prognostic accuracy of clinical signs and symptoms and laboratory biomarkers for CAP. Methods 545 patients with suspected lower respiratory tract infection, admitted to the emergency department of a university hospital were included in a pre-planned post-hoc analysis of two controlled intervention trials. Baseline assessment included history, clinical examination, radiography and measurements of procalcitonin (PCT, highly sensitive C-reactive protein (hsCRP and leukocyte count. Results Of the 545 patients, 373 had CAP, 132 other respiratory tract infections, and 40 other final diagnoses. The AUC of a clinical model including standard clinical signs and symptoms (i.e. fever, cough, sputum production, abnormal chest auscultation and dyspnea to diagnose CAP was 0.79 [95% CI, 0.75–0.83]. This AUC was significantly improved by including PCT and hsCRP (0.92 [0.89–0.94]; p Conclusion PCT, and to a lesser degree hsCRP, improve the accuracy of currently recommended approaches for the diagnosis of CAP, thereby complementing clinical signs and symptoms. PCT is useful in the severity assessment of CAP.

  1. [Two Cases of Rapidly Progressive Community-acquired Pneumonia Due to Pseudomonas aeruginosa].

    Science.gov (United States)

    Takakura, Akira; Katono, Ken; Harada, Shinya; Igawa, Satoshi; Katagiri, Masato; Yanase, Nobuo; Masuda, Noriyuki

    2015-01-01

    Pseudomonas aeruginosa is a significant causative bacterium in hospital-acquired pneumonia and nursing and healthcare-associated pneumonia, but it seems to be rare in community-acquired pneumonia (CAP). We report two cases of severe CAP due to P. aeruginosa. Case 1: A 52-year-old man was referred to our hospital for chest and back pain. He was being treated for diabetes mellitus and had a long history of smoking. Chest images showed consolidation in the right upper lobe. Soon after hospitalization, he developed sepsis shock and died seven hours later. Case 2: A 73-year-old man with a history of heavy smoking was referred to our hospital for right chest pain. Chest images showed right upper lobe pneumonia. Although wide-spectrum antimicrobial agents were administrated, he died ten hours after admission. In both cases, there was a rapid progression to death, despite administration of a broad spectrum of antibiotics and treatment for sepsis. In cases of CAP involving the right upper lobe, the possibility of bacteremia and rapid progress should be considered. PMID:26548298

  2. Community-acquired methicillin-resistant Staphylococcus aureus in Central Australia.

    Science.gov (United States)

    Stevens, Claire L; Ralph, Anna; McLeod, James E T; McDonald, Malcolm I

    2006-01-01

    To date, there has been scant information about the burden of methicillin-resistant Staphylococcus aureus infections in Central Australia. Our aims were to determine the proportion of Staphylococcus aureus infections due to methicillin-resistant strains in Central Australia, to characterise resistance to non-beta lactam antibiotics and to correlate findings with available demographic information. We retrospectively reviewed S. aureus isolates identified by the Microbiology Laboratory of the Pathology Department, Alice Springs Hospital between September 2005 and February 2006. Multi-resistance was defined as resistance to three or more non-beta lactam antibiotics. We identified the recovery site and extended antibiotic resistance profile of each isolate. Demographic data included place of residence, discharge diagnosis and ethnicity. There were 524 S. aureus isolates: 417 (79.6%) methicillin-sensitive S. aureus, 104 (19.7%) non-multi-resistant MRSA (nmrMRSA) and 3 (0.7%) multi-resistant MRSA (mrMRSA). MRSA accounted for 7/22 (32%) invasive infections and 91/474 (19.2%) cases of staphylococcal skin infections. Aboriginal people comprised 89 per cent (93/104) of patients with nmrMRSA; 57 per cent lived in remote communities, 21 per cent in suburban Alice Springs, and 18 per cent in Alice Springs Town Camps. Six per cent (6/104) of nmrMRSA were hospital-acquired. Of the nmrMRSA isolates, 57 per cent (59/104) were resistant to erythromycin and 7 per cent (7/104) to fusidic acid. All MRSA isolates were susceptible to co-trimoxazole. In conclusion, Central Australia has high rates of community-acquired nmrMRSA and low rates of multi-resistant MRSA. Erythromycin resistance in S. aureus is also common. These findings should prompt the review of antimicrobial prescribing guidelines for the region, especially for treatment of skin and soft tissue infections.

  3. Bacterial Communities in Malagasy Soils with Differing Levels of Disturbance Affecting Botanical Diversity

    OpenAIRE

    Blasiak, Leah C.; Schmidt, Alex W.; Andriamiarinoro, Honoré; Mulaw, Temesgen; Rasolomampianina, Rado; Wendy L Applequist; Birkinshaw, Chris; Rejo-Fienena, Félicitée; Lowry, Porter P.; Schmidt, Thomas M; Hill, Russell T.

    2014-01-01

    Madagascar is well-known for the exceptional biodiversity of its macro-flora and fauna, but the biodiversity of Malagasy microbial communities remains relatively unexplored. Understanding patterns of bacterial diversity in soil and their correlations with above-ground botanical diversity could influence conservation planning as well as sampling strategies to maximize access to bacterially derived natural products. We present the first detailed description of Malagasy soil bacterial communitie...

  4. Modulation of Post-Antibiotic Bacterial Community Reassembly and Host Response by Candida albicans

    OpenAIRE

    Erb Downward, John R.; Falkowski, Nicole R.; Mason, Katie L.; Ryan Muraglia; Huffnagle, Gary B.

    2013-01-01

    The introduction of Candida albicans into cefoperazone-treated mice results in changes in bacterial community reassembly. Our objective was to use high-throughput sequencing to characterize at much greater depth the specific changes in the bacterial microbiome. The colonization of C. albicans significantly altered bacterial community reassembly that was evident at multiple taxonomic levels of resolution. There were marked changes in the levels of Bacteriodetes and Lactobacillaceae. Lachnospir...

  5. Association between Hypoalbuminaemia and Mortality in Patients with Community-Acquired Bacteraemia Is Primarily Related to Acute Disorders

    Science.gov (United States)

    Magnussen, Bjarne; Oren Gradel, Kim; Gorm Jensen, Thøger; Kolmos, Hans Jørn; Pedersen, Court; Just Vinholt, Pernille; Touborg Lassen, Annmarie

    2016-01-01

    We sought to investigate whether hypoalbuminaemia was mainly caused by acute or chronic factors in patients with community-acquired bacteraemia. In this population-based study, we considered 1844 adult cases of community-acquired bacteraemia that occurred in Funen, Denmark between 2000 and 2008. We used a stepwise prognostic predisposition-insult-response-organ dysfunction (PIRO) logistic regression model by initially including age and comorbidity, then added bacterial species, and finally sepsis severity. The models were furthermore analysed using receiver operating characteristic (ROC) curves. Outcomes comprised mortality incidence on days 0–30 and 31–365 after the bacteraemia episode. Each step was performed with and without baseline albumin level measured on the date of bacteraemia. In 422 patients, their latest albumin measurement taken 8–30 days before the date of bacteraemia was also used in the analysis together with the baseline albumin level. For each decrease of 1g/L in plasma albumin level, the odds ratios (95% confidence intervals) of mortality in the period of 0–30 days after bacteraemia were 0.86 (0.84–0.88) in both predisposition (P) and predisposition-insult (PI) models and 0.87 (0.85–0.89) in the full PIRO-model. The AUC values were 0.78 and 0.66 for mortality in the period of 0–30 days in the model comprising only predisposition factors with and without albumin levels added as a factor, respectively. The AUC values in the full PIRO-model were 0.81 and 0.73 with and without consideration of albumin levels, respectively. A higher proportion of patients died within 30 days if there was a decrease in the albumin level between days 8 and 30 before bacteraemia and the actual bacteraemia date. A single plasma albumin measurement on the bacteraemia date was a better prognostic predictor of short-term mortality than the sepsis severity score. PMID:27611431

  6. Differences in Bacterial Community Structure on Hydrilla verticillata and Vallisneria americana in a Freshwater Spring

    OpenAIRE

    Gordon-Bradley, Nadine; Lymperopoulou, Despoina S.; Williams, Henry Neal

    2014-01-01

    The phylogenetic composition of the epiphytic bacterial community of an invasive aquatic plant (Hydrilla verticillata) and a native species (Vallisneria americana [eelgrass]) of the Wakulla Spring (Florida) was investigated, along with the water column bacterial composition, using clone libraries of the 16S rRNA genes. The bacterial clones from three clone libraries were classified into 182 operational taxonomic units (OTUs), most of which were affiliated with bacterial divisions commonly fou...

  7. [Prophylaxis of Community-Acquired Pneumonia Outbreaks with Pneumococcal Polysaccharide Vaccine. Prospects Analysis for Russian Military Community].

    Science.gov (United States)

    Guchev, I A; Klochkov, O I; Sinopalnikov, A I

    2016-01-01

    Pneumococcal pneumonia and other diseases caused by pneumococci still remain the main factors of high morbidity and mortality rates throughout the world. Pneumococci as the leading pathogens of community-acquired pneumonia (CAP), acute otitis media and sinusitis also cause a number of other serious systemic disorders including invasive infections with high mortality in spite of the antimicrobial resistance status and adequate antimicrobials choice. Pneumococcal infections are responsible for 5-35% or more of community-acquired pneumonias. The burden of pneumonia (up to 100-200 per thousand) is recorded among military recruits in training centers. Since the specific environment of the soldiers could be carrected, their health protection requires medical surveillance. For these reasons, polysaccharide and more immunogenic conjugated pneumococcal vaccines were developed. There is now an urgent need to understand whether such vaccines are effective in military conscripts. Controversy about the effectiveness and value of the polysaccharide (PPV-23) vaccine as a CAP morbidity restriction measure still persists. There were implemented plenty of metaanalyses of pneumococcal vaccines in adults. Some of them showed that the vaccine was effective against bacteremic pneumococcal pneumonia in 'low risk' healthy adults and elders. There have been a number of poor quality observational studies in Russia where 'all pneumonia cases' were considered as an endpoint. It remains controversial whether these observational studies provide adequate evidence to justify the use of the polysaccharide vaccine in the groups of healthy young men for whom it is being advocated. In our analysis we found weak evidence supporting pneumococcal vaccination with PPV-23 for this group. Nevertheless, favorable tendency was found to immunize. It is the reason for a trail to find pharmacoepidemiological support for vaccination by novel conjugated vaccines with better immunogenicity. PMID:27337866

  8. Amazonian dark Earth and plant species from the Amazon region contribute to shape rhizosphere bacterial communities.

    Science.gov (United States)

    Barbosa Lima, Amanda; Cannavan, Fabiana Souza; Navarrete, Acacio Aparecido; Teixeira, Wenceslau Geraldes; Kuramae, Eiko Eurya; Tsai, Siu Mui

    2015-05-01

    Amazonian Dark Earths (ADE) or Terra Preta de Índio formed in the past by pre-Columbian populations are highly sustained fertile soils supported by microbial communities that differ from those extant in adjacent soils. These soils are found in the Amazon region and are considered as a model soil when compared to the surrounding and background soils. The aim of this study was to assess the effects of ADE and its surrounding soil on the rhizosphere bacterial communities of two leguminous plant species that frequently occur in the Amazon region in forest sites (Mimosa debilis) and open areas (Senna alata). Bacterial community structure was evaluated using terminal restriction fragment length polymorphism (T-RFLP) and bacterial community composition by V4 16S rRNA gene region pyrosequencing. T-RFLP analysis showed effect of soil types and plant species on rhizosphere bacterial community structure. Differential abundance of bacterial phyla, such as Acidobacteria, Actinobacteria, Verrucomicrobia, and Firmicutes, revealed that soil type contributes to shape the bacterial communities. Furthermore, bacterial phyla such as Firmicutes and Nitrospira were mostly influenced by plant species. Plant roots influenced several soil chemical properties, especially when plants were grown in ADE. These results showed that differences observed in rhizosphere bacterial community structure and composition can be influenced by plant species and soil fertility due to variation in soil attributes. PMID:25103911

  9. Detection of intracellular bacterial communities in human urinary tract infection.

    Directory of Open Access Journals (Sweden)

    David A Rosen

    2007-12-01

    Full Text Available BACKGROUND: Urinary tract infections (UTIs are one of the most common bacterial infections and are predominantly caused by uropathogenic Escherichia coli (UPEC. While UTIs are typically considered extracellular infections, it has been recently demonstrated that UPEC bind to, invade, and replicate within the murine bladder urothelium to form intracellular bacterial communities (IBCs. These IBCs dissociate and bacteria flux out of bladder facet cells, some with filamentous morphology, and ultimately establish quiescent intracellular reservoirs that can seed recurrent infection. This IBC pathogenic cycle has not yet been investigated in humans. In this study we sought to determine whether evidence of an IBC pathway could be found in urine specimens from women with acute UTI. METHODS AND FINDINGS: We collected midstream, clean-catch urine specimens from 80 young healthy women with acute uncomplicated cystitis and 20 asymptomatic women with a history of UTI. Investigators were blinded to culture results and clinical history. Samples were analyzed by light microscopy, immunofluorescence, and electron microscopy for evidence of exfoliated IBCs and filamentous bacteria. Evidence of IBCs was found in 14 of 80 (18% urines from women with UTI. Filamentous bacteria were found in 33 of 80 (41% urines from women with UTI. None of the 20 urines from the asymptomatic comparative group showed evidence of IBCs or filaments. Filamentous bacteria were present in all 14 of the urines with IBCs compared to 19 (29% of 66 samples with no evidence of IBCs (p < 0.001. Of 65 urines from patients with E. coli infections, 14 (22% had evidence of IBCs and 29 (45% had filamentous bacteria, while none of the gram-positive infections had IBCs or filamentous bacteria. CONCLUSIONS: The presence of exfoliated IBCs and filamentous bacteria in the urines of women with acute cystitis suggests that the IBC pathogenic pathway characterized in the murine model may occur in humans. The

  10. Gut bacterial communities across tadpole ecomorphs in two diverse tropical anuran faunas

    Science.gov (United States)

    Vences, Miguel; Lyra, Mariana L.; Kueneman, Jordan G.; Bletz, Molly C.; Archer, Holly M.; Canitz, Julia; Handreck, Svenja; Randrianiaina, Roger-Daniel; Struck, Ulrich; Bhuju, Sabin; Jarek, Michael; Geffers, Robert; McKenzie, Valerie J.; Tebbe, Christoph C.; Haddad, Célio F. B.; Glos, Julian

    2016-04-01

    Animal-associated microbial communities can play major roles in the physiology, development, ecology, and evolution of their hosts, but the study of their diversity has yet focused on a limited number of host species. In this study, we used high-throughput sequencing of partial sequences of the bacterial 16S rRNA gene to assess the diversity of the gut-inhabiting bacterial communities of 212 specimens of tropical anuran amphibians from Brazil and Madagascar. The core gut-associated bacterial communities among tadpoles from two different continents strongly overlapped, with eight highly represented operational taxonomic units (OTUs) in common. In contrast, the core communities of adults and tadpoles from Brazil were less similar with only one shared OTU. This suggests a community turnover at metamorphosis. Bacterial diversity was higher in tadpoles compared to adults. Distinct differences in composition and diversity occurred among gut bacterial communities of conspecific tadpoles from different water bodies and after experimental fasting for 8 days, demonstrating the influence of both environmental factors and food on the community structure. Communities from syntopic tadpoles clustered by host species both in Madagascar and Brazil, and the Malagasy tadpoles also had species-specific isotope signatures. We recommend future studies to analyze the turnover of anuran gut bacterial communities at metamorphosis, compare the tadpole core communities with those of other aquatic organisms, and assess the possible function of the gut microbiota as a reservoir for protective bacteria on the amphibian skin.

  11. Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice

    Energy Technology Data Exchange (ETDEWEB)

    Howe, Adina; Ringus, Daina L.; Williams, Ryan J.; Choo, Zi-Ning; Greenwald, Stephanie M.; Owens, Sarah M.; Coleman, Maureen L.; Meyer, Folker; Chang, Eugene B.

    2015-10-16

    To improve our understanding of the stability of mammalian intestinal communities, we characterized the responses of both bacterial and viral communities in murine fecal samples to dietary changes between high- and low-fat (LF) diets. Targeted DNA extraction methods for bacteria, virus-like particles and induced prophages were used to generate bacterial and viral metagenomes as well as 16S ribosomal RNA amplicons. Gut microbiome communities from two cohorts of C57BL/6 mice were characterized in a 6-week diet perturbation study in response to high fiber, LF and high-refined sugar, milkfat (MF) diets. The resulting metagenomes from induced bacterial prophages and extracellular viruses showed significant overlap, supporting a largely temperate viral lifestyle within these gut microbiomes. The resistance of baseline communities to dietary disturbances was evaluated, and we observed contrasting responses of baseline LF and MF bacterial and viral communities. In contrast to baseline LF viral communities and bacterial communities in both diet treatments, baseline MF viral communities were sensitive to dietary disturbances as reflected in their non-recovery during the washout period. The contrasting responses of bacterial and viral communities suggest that these communities can respond to perturbations independently of each other and highlight the potentially unique role of viruses in gut health.

  12. Archaeal and Bacterial Communities Associated with the Surface Mucus of Caribbean Corals Differ in Their Degree of Host Specificity and Community Turnover Over Reefs

    NARCIS (Netherlands)

    Frade, P.R.; Roll, K.; Bergauer, K.; Herndl, G.

    2016-01-01

    Comparative studies on the distribution of archaeal versus bacterial communities associatedwith the surface mucus layer of corals have rarely taken place. It has thereforeremained enigmatic whether mucus-associated archaeal and bacterial communities exhibita similar specificity towards coral hosts a

  13. Outcomes in elderly Danish citizens admitted with community-acquired pneumonia. Regional differences, in a public healthcare system

    DEFF Research Database (Denmark)

    Hedegaard Klausen, Henrik; Petersen, J; Lindhardt, T;

    2012-01-01

    OBJECTIVES: To evaluate regional differences in and risk factors for admission, length of stay, mortality, and readmission for community-acquired pneumonia in elderly Danish patients. METHODS: National registry study on elderly Danish citizens with an acute admission in 2009 owing to community......-acquired pneumonia. We studied differences among hospitals in length of stay, in-hospital mortality, mortality within 30 days of discharge, and readmission within 30 days after discharge using Cox regression models with adjustments for age, sex, ventilatory support, and co-morbidity by Charlson's index score....... RESULTS: A total of 11,332 elderly citizens were admitted with community-acquired pneumonia. Mortality during admission and 30-days from discharge were 11.6% and 16.2%, respectively. Readmission rates within 30 days of discharge were 12.3%. There were significantly differences between hospitals in length...

  14. Bacterial Communities in Rhizosphere of Maize Studied by T-RFLP

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    Ondreičková Katarína

    2014-12-01

    Full Text Available The terminal restriction fragment length polymorphism munities from different collecting places was evaluated was used to determine the bacterial diversity in rhizo- by principal component analysis. Results showed that sphere of maize (Zea mays L. collected from four sites the most different bacterial community originated from of experimental field plot in two dates of the vegetation marginal part of the experimental field plot collected in season (July and September. The 16S rRNA gene was September was caused probably by combination of the amplified from metagenomic DNA using universal eubac- marginal effect and drought before sampling date in Sep- terial primers and PCR products were digested separately tember. Other rhizosphere samples showed from moderate with three restriction enzymes. Significant differences in to small differences in the structure of the bacterial com- the number of terminal restriction fragments among rhi- munity. Nevertheless, significant differences among all zosphere samples and between sampling dates were not collected bacterial communities were not observed. detected (P < 0.05. Variation within the bacterial communities from different collecting places was evaluated by principal component analysis. Results showed that the most different bacterial community originated from marginal part of the experimental field plot collected in September was caused probably by combination of the marginal effect and drought before sampling date in September. Other rhizosphere samples showed from moderate to small differences in the structure of the bacterial community. Nevertheless, significant differences among all collected bacterial communities were not observed.

  15. Bacterial community analysis of Tatsoi cultivated by hydroponics.

    Science.gov (United States)

    Koo, Ok K; Kim, Hun; Kim, Hyun J; Baker, Christopher A; Ricke, Steven C

    2016-07-01

    Tatsoi (Brassica narinosa) is a popular Asian salad green that is mostly consumed as a source of fresh produce. The purpose of this study was to assess the microbial diversity of Tatsoi cultivated in a hydroponic system and of its ecosystem. Tatsoi leaves, nutrient solution, and perlite/earth samples from a trickle feed system (TFS) and an ebb-and-flow system (EFS) were collected and their microbial communities were analyzed by pyrosequencing analysis. The results showed that most bacteria in the leaves from the TFS contained genus Sporosarcina (99.6%), while Rhizobium (60.4%) was dominant in the leaves from the EFS. Genus Paucibacter (18.21%) and Pelomonas (12.37%) were the most abundant microbiota in the nutrient solution samples of the TFS. In the EFS, the nutrient solution samples contained mostly genus Rhodococcus and Acinetobacter. Potential microbial transfer between the leaves and the ecosystem was observed in the EFS, while samples in the TFS were found to share only one species between the leaves, nutrient solution, and earth. Together, these results show that the bacterial populations in Tatsoi and in its ecosystem are highly diverse based on the cultivation system. PMID:27070460

  16. Bacterial community analysis of Tatsoi cultivated by hydroponics.

    Science.gov (United States)

    Koo, Ok K; Kim, Hun; Kim, Hyun J; Baker, Christopher A; Ricke, Steven C

    2016-07-01

    Tatsoi (Brassica narinosa) is a popular Asian salad green that is mostly consumed as a source of fresh produce. The purpose of this study was to assess the microbial diversity of Tatsoi cultivated in a hydroponic system and of its ecosystem. Tatsoi leaves, nutrient solution, and perlite/earth samples from a trickle feed system (TFS) and an ebb-and-flow system (EFS) were collected and their microbial communities were analyzed by pyrosequencing analysis. The results showed that most bacteria in the leaves from the TFS contained genus Sporosarcina (99.6%), while Rhizobium (60.4%) was dominant in the leaves from the EFS. Genus Paucibacter (18.21%) and Pelomonas (12.37%) were the most abundant microbiota in the nutrient solution samples of the TFS. In the EFS, the nutrient solution samples contained mostly genus Rhodococcus and Acinetobacter. Potential microbial transfer between the leaves and the ecosystem was observed in the EFS, while samples in the TFS were found to share only one species between the leaves, nutrient solution, and earth. Together, these results show that the bacterial populations in Tatsoi and in its ecosystem are highly diverse based on the cultivation system.

  17. Molecular Characterization of Streptococcus agalactiae Causing Community- and Hospital-Acquired Infections in Shanghai, China.

    Science.gov (United States)

    Jiang, Haoqin; Chen, Mingliang; Li, Tianming; Liu, Hong; Gong, Ye; Li, Min

    2016-01-01

    Streptococcus agalactiae, a colonizing agent in pregnant women and the main cause of neonatal sepsis and meningitis, has been increasingly associated with invasive disease in nonpregnant adults. We collected a total of 87 non-repetitive S. agalactiae isolates causing community-acquired (CA) and hospital-acquired (HA) infections in nonpregnant adults from a teaching hospital in Shanghai between 2009 and 2013. We identified and characterized their antibiotic resistance, sequence type (ST), serotype, virulence, and biofilm formation. The most frequent STs were ST19 (29.9%), ST23 (16.1%), ST12 (13.8%), and ST1 (12.6%). ST19 had significantly different distributions between CA- and HA-group B Streptococci (GBS) isolates. The most frequent serotypes were III (32.2%), Ia (26.4%), V (14.9%), Ib (13.8%), and II (5.7%). Serotype III/ST19 was significantly associated with levofloxacin resistance in all isoates. The HA-GBS multidrug resistant rate was much higher than that of CA-GBS. Virulence genes pavA, cfb were found in all isolates. Strong correlations exist between serotype Ib (CA and HA) and surface protein genes spb1 and bac, serotype III (HA) and surface protein gene cps and GBS pilus cluster. The serotype, epidemic clone, PFGE-based genotype, and virulence gene are closely related between CA-GBS and HA-GBS, and certain serotypes and clone types were significantly associated with antibiotic resistance. However, CA-GBS and HA-GBS still had significant differences in their distribution of clone types, antibiotic resistance, and specific virulence genes, which may provide a basis for infection control. PMID:27625635

  18. Epidemiology, microbiology and mortality associated with community-acquired bacteremia in northeast Thailand: a multicenter surveillance study.

    Directory of Open Access Journals (Sweden)

    Manas Kanoksil

    Full Text Available BACKGROUND: National statistics in developing countries are likely to underestimate deaths due to bacterial infections. Here, we calculated mortality associated with community-acquired bacteremia (CAB in a developing country using routinely available databases. METHODS/PRINCIPAL FINDINGS: Information was obtained from the microbiology and hospital database of 10 provincial hospitals in northeast Thailand, and compared with the national death registry from the Ministry of Interior, Thailand for the period between 2004 and 2010. CAB was defined in patients who had pathogenic organisms isolated from blood taken within 2 days of hospital admission without a prior inpatient episode in the preceding 30 days. A total of 15,251 CAB patients identified, of which 5,722 (37.5% died within 30 days of admission. The incidence rate of CAB between 2004 and 2010 increased from 16.7 to 38.1 per 100,000 people per year, and the mortality rate associated with CAB increased from 6.9 to 13.7 per 100,000 people per year. In 2010, the mortality rate associated with CAB was lower than that from respiratory tract infection, but higher than HIV disease or tuberculosis. The most common causes of CAB were Escherichia coli (23.1%, Burkholderia pseudomallei (19.3%, and Staphylococcus aureus (8.2%. There was an increase in the proportion of Extended-Spectrum Beta-Lactamases (ESBL producing E. coli and Klebsiella pneumoniae over time. CONCLUSIONS: This study has demonstrated that national statistics on causes of death in developing countries could be improved by integrating information from readily available databases. CAB is neglected as an important cause of death, and specific prevention and intervention is urgently required to reduce its incidence and mortality.

  19. High creatinine clearance in critically ill patients with community-acquired acute infectious meningitis

    Directory of Open Access Journals (Sweden)

    Lautrette Alexandre

    2012-09-01

    Full Text Available Abstract Background A high dose of anti-infective agents is recommended when treating infectious meningitis. High creatinine clearance (CrCl may affect the pharmacokinetic / pharmacodynamic relationships of anti-infective drugs eliminated by the kidneys. We recorded the incidence of high CrCl in intensive care unit (ICU patients admitted with meningitis and assessed the diagnostic accuracy of two common methods used to identify high CrCl. Methods Observational study performed in consecutive patients admitted with community-acquired acute infectious meningitis (defined by >7 white blood cells/mm3 in cerebral spinal fluid between January 2006 and December 2009 to one medical ICU. During the first 7 days following ICU admission, CrCl was measured from 24-hr urine samples (24-hr-UV/P creatinine and estimated according to Cockcroft-Gault formula and the simplified Modification of Diet in Renal Disease (MDRD equation. High CrCl was defined as CrCl >140 ml/min/1.73 m2 by 24-hr-UV/P creatinine. Diagnostic accuracy was performed with ROC curves analysis. Results Thirty two patients were included. High CrCl was present in 8 patients (25% on ICU admission and in 15 patients (47% during the first 7 ICU days for a median duration of 3 (1-4 days. For the Cockcroft-Gault formula, the best threshold to predict high CrCl was 101 ml/min/1.73 m2 (sensitivity: 0.96, specificity: 0.75, AUC = 0.90 ± 0.03 with a negative likelihood ratio of 0.06. For the simplified MDRD equation, the best threshold to predict high CrCl was 108 ml/min/1.73 m2 (sensitivity: 0.91, specificity: 0.80, AUC = 0.88 ± 0.03 with a negative likelihood ratio of 0.11. There was no difference between the estimated methods in the diagnostic accuracy of identifying high CrCl (p = 0.30. Conclusions High CrCl is frequently observed in ICU patients admitted with community-acquired acute infectious meningitis. The estimated methods of CrCl could be used as a screening tool to

  20. Impact and indication of early systemic corticosteroids for very severe community-acquired pneumonia

    Directory of Open Access Journals (Sweden)

    Ugajin M

    2013-08-01

    Full Text Available Motoi Ugajin, Kenichi Yamaki, Natsuko Hirasawa, Takanori Kobayashi, Takeo YagiDepartment of Respiratory Medicine, Ichinomiya-Nishi Hospital, Ichinomiya City, Aichi Prefecture, JapanBackground: The efficacy of systemic corticosteroids in community-acquired pneumonia (CAP has not yet been confirmed. We prospectively investigated the clinical features of patients treated with early adjunctive systemic corticosteroids and its clinical impact in very severe CAP.Methods: One hundred and one consecutive CAP patients having a pneumonia severity index of >130 points were enrolled from August 2010 through February 2013. Early adjunctive systemic corticosteroids were defined as administration of systemic corticosteroids equivalent to prednisone of ≥20 mg/day added to initial antibiotics. The multivariate analysis was performed to evaluate the independent factors associated with mortality.Results: Thirty-two patients (31.7% died within 28 days of admission. Early adjunctive systemic corticosteroids were administered in 30 patients (29.7%, who more frequently had alteration of mental status, serious respiratory failure, or underlying lung diseases and received fluoroquinolones as initial antibiotics. In most patients treated with early adjunctive systemic corticosteroids, the dosage was less than 60 mg/day of an equivalent to prednisone by bolus intravenous infusion for a period shorter than 8 days. The occurrence of adverse events did not differ between the groups. Factors independently associated with mortality were blood urea nitrogen (hazard ratio [HR] 1.02, 95% confidence interval [CI] 1.00–1.04, serum albumin (HR 0.44, 95% CI 0.22–0.86, a requirement for intensive care (HR 4.93, 95% CI 1.75–13.87, and the therapy with early adjunctive systemic corticosteroids (HR 0.29, 95% CI 0.11–0.81.Conclusion: Early adjunctive systemic corticosteroids may have an effect to reduce the mortality in very severe CAP, although a larger-scale study is necessary

  1. Urothelial cultures support intracellular bacterial community formation by uropathogenic Escherichia coli.

    Science.gov (United States)

    Berry, Ruth E; Klumpp, David J; Schaeffer, Anthony J

    2009-07-01

    Uropathogenic Escherichia coli (UPEC) causes most community-acquired and nosocomial urinary tract infections (UTI). In a mouse model of UTI, UPEC invades superficial bladder cells and proliferates rapidly, forming biofilm-like structures called intracellular bacterial communities (IBCs). Using a gentamicin protection assay and fluorescence microscopy, we developed an in vitro model for studying UPEC proliferation within immortalized human urothelial cells. By pharmacologic manipulation of urothelial cells with the cholesterol-sequestering drug filipin, numbers of intracellular UPEC CFU increased 8 h and 24 h postinfection relative to untreated cultures. Enhanced UPEC intracellular proliferation required that the urothelial cells, but not the bacteria, be filipin treated prior to infection. However, neither UPEC frequency of invasion nor early intracellular trafficking events to a Lamp1-positive compartment were modulated by filipin. Upon inspection by fluorescence microscopy, cultures with enhanced UPEC intracellular proliferation exhibited large, dense bacterial aggregates within cells that resembled IBCs but were contained with Lamp1-positive vacuoles. While an isogenic fimH mutant was capable of forming these IBC-like structures, the mutant formed significantly fewer than wild-type UPEC. Similar to IBCs, expression of E. coli iron acquisition systems was upregulated by intracellular UPEC. Expression of other putative virulence factors, including hlyA, cnf1, fliC, kpsD, and the biofilm adhesin yfaL also increased, while expression of fimA decreased and that of flu did not change. These results indicate that UPEC differentially regulates virulence factors in the intracellular environment. Thus, immortalized urothelial cultures that recapitulate IBC formation in vitro represent a novel system for the molecular and biochemical characterization of the UPEC intracellular life cycle.

  2. Moonmilk deposits originate from specific bacterial communities in Altamira Cave (Spain).

    Science.gov (United States)

    Portillo, Maria C; Gonzalez, Juan M

    2011-01-01

    The influence of bacterial communities on the formation of carbonate deposits such as moonmilk was investigated in Altamira Cave (Spain). The study focuses on the relationship between the bacterial communities at moonmilk deposits and those forming white colonizations, which develop sporadically throughout the cave. Using molecular fingerprinting of the metabolically active bacterial communities detected through RNA analyses, the development of white colonizations and moonmilk deposits showed similar bacterial profiles. White colonizations were able to raise the pH as a result of their metabolism (reaching in situ pH values above 8.5), which was proportional to the nutrient supply. Bacterial activity was analyzed by nanorespirometry showing higher metabolic activity from bacterial colonizations than uncolonized areas. Once carbonate deposits were formed, bacterial activity decreased drastically (down to 5.7% of the white colonization activity). This study reports on a specific type of bacterial community leading to moonmilk deposit formation in a cave environment as a result of bacterial metabolism. The consequence of this process is a macroscopic phenomenon of visible carbonate depositions and accumulation in cave environments. PMID:20717660

  3. Etiologic profile and antimicrobial susceptibility of community-acquired urinary tract infection in two Cameroonian towns

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    Akoachere Jane-Francis Tatah

    2012-05-01

    Full Text Available Abstract Background Urinary tract infection (UTI represents one of the most common diseases encountered in community medical practice. In resource poor settings, treatment is usually empiric due to the high cost and long duration required for reporting diagnosis by culture and antibiotic susceptibility testing. With the growing problem of drug resistance knowledge of antibiotic susceptibility pattern is pertinent for successful eradication of invading pathogens. Our study, the first of its kind in Cameroon, analyzed the distribution and antibiotic susceptibility of bacteria causing community-acquired urinary tract infection (CAUTI in two towns (Bamenda and Buea with a large number of young and middle aged persons, to provide data that could guide empiric treatment. Findings We cultured 235 urine specimens and analyzed the antibiotic susceptibility of isolates by the disc diffusion technique. Uropathogens were recovered from 137 (58.3%, with prevalence rates in Buea and Bamenda being 65.9% and 54% respectively. Predominant pathogens were Escherichia coli (31.4%, Klebsiella oxytoca (25.5% and Staphylococcus spp (24.1%. Geographic variation in uropathogen distribution and antibiotic susceptibility was observed, and a significant difference in pathogen distribution with respect to gender. The 20–39 years age group had the highest prevalence of infection. All pathogens isolated were detected in this group. Isolates exhibited low susceptibility to antibiotics tested. Bamenda isolates generally exhibited lower susceptibility compared to those from Buea. Conclusion Regional variation in etiology of CAUTI and antibiotic susceptibility observed in our study emphasizes the need to establish local and national antimicrobial resistance monitoring systems in Cameroon to provide information for the development of CAUTI treatment guidelines.

  4. Acute myocardial infarction versus other cardiovascular events in community-acquired pneumonia

    Directory of Open Access Journals (Sweden)

    Stefano Aliberti

    2015-09-01

    Full Text Available The aim of the present study was to define the prevalence, characteristics, risk factors and impact on clinical outcomes of acute myocardial infarction (AMI versus other cardiovascular events (CVEs in patients with community-acquired pneumonia (CAP. This was an international, multicentre, observational, prospective study of CAP patients hospitalised in eight hospitals in Italy and Switzerland. Three groups were identified: those without CVEs, those with AMI and those with other CVEs. Among 905 patients, 21 (2.3% patients experienced at least one AMI, while 107 (11.7% patients experienced at least one other CVE. Patients with CAP and either AMI or other CVEs showed a higher severity of the disease than patients with CAP alone. Female sex, liver disease and the presence of severe sepsis were independent predictors for the occurrence of AMI, while female sex, age >65 years, neurological disease and the presence of pleural effusion predicted other CVEs. In-hospital mortality was significantly higher among those who experienced AMI in comparison to those experiencing other CVEs (43% versus 21%, p=0.039. The presence of AMI showed an adjusted odds ratio for in-hospital mortality of 3.57 (p=0.012 and for other CVEs of 2.63 (p=0.002. These findings on AMI versus other CVEs as complications of CAP may be important when planning interventional studies on cardioprotective medications.

  5. Optimal imaging strategy for community-acquired Staphylococcus aureus musculoskeletal infections in children

    International Nuclear Information System (INIS)

    Invasive musculoskeletal infections from community-acquired methicillin-resistant and methicillin-susceptible Staphylococcus aureus (CA-SA) are increasingly encountered in children. Imaging is frequently requested in these children for diagnosis and planning of therapeutic interventions. To appraise the diagnostic efficacy of imaging practices performed for CA-SA osteomyelitis and its complications. A retrospective review was conducted of the clinical charts and imaging studies of CA-SA osteomyelitis cases since 2001 at a large children's hospital. Of 199 children diagnosed with CA-SA osteomyelitis, 160 underwent MRI examination and 35 underwent bone scintigraphy. The sensitivity of MRI and bone scintigraphy for CA-SA osteomyelitis was 98% and 53%, respectively. In all discordant cases, MRI was correct compared to bone scintigraphy. Extraosseous complications of CA-SA osteomyelitis detected only by MRI included subperiosteal abscesses (n = 77), pyomyositis (n = 43), septic arthritis (n = 31), and deep venous thrombosis (n = 12). MRI is the preferred imaging modality for the investigation of pediatric CA-SA musculoskeletal infection because it offers superior sensitivity for osteomyelitis compared to bone scintigraphy and detects extraosseous complications that occur in a substantial proportion of patients. (orig.)

  6. Assessment of Treatment of Community Acquired Severe Pneumonia by Two Different Antibiotics

    Science.gov (United States)

    Bilal, Jalal Ali; Eldouch, Widad; Abdin, Ali

    2016-01-01

    Introduction Pneumonia is common presentation in the emergency room and is still a cause of morbidity and mortality. The rationale of this study was to test the trend of paediatricians to achieve rapid response facing severe pneumonia, the lack of agreed on plan for the management of community acquired pneumonia (CAP) and the few experiences regarding injectable form of β-lactam antimicrobial. Materials and Methods This is a prospective case control study, purposive randomized sampling, three patients were excluded since their information was incomplete, 132 patients were randomly divided into groups, one group named control group (penicillin according to the guidelines of WHO 2013), 33 patients; second group treated by β-lactam inhibitors (Augmentin IV) 50 patients; and third group treated by 3rd generation cephalosporin (ceftriaxone) 49 patients. The study was conducted at the main tertiary care and paediatrics teaching hospital in Khartoum capital of Sudan. The study was completed within the duration from 2010 to 2011. Results Both group showed more or less similar results regarding response, as well as the failure rate however, the Augmentin and ceftriaxone groups showed a little bit better survival than the control group. Conclusion Antibiotics decrease the mortality rate among the pneumonia patients provided that it is given early in the disease. PMID:27437318

  7. Multiplex PCR for rapid detection of Staphylococcus aureus isolates suspected to represent community-acquired strains.

    Science.gov (United States)

    Strommenger, B; Braulke, C; Pasemann, B; Schmidt, C; Witte, W

    2008-02-01

    The continuous spread of community-acquired methicillin-resistant Staphylococcus aureus (caMRSA) and the introduction of these highly virulent isolates into hospitals represent increasing threats. The timely recognition of caMRSA strains is crucial for infection control purposes. Thus, we developed a PCR-based assay for the easy and rapid determination of those caMRSA clones that currently are the most prevalent in Germany and Central Europe. This assay was able to correctly identify the majority of the isolates as caMRSA of sequence type 80 (ST80), clonal complex 1 (USA400), and ST8 (USA300). In combination with spa typing-BURP (based upon repeat pattern) analysis and resistance typing, it provides a means for the extensive characterization of suspicious isolates. Thus, this assay represents a reliable tool for monitoring the emergence and spread of different caMRSA clones. The resulting information, in combination with careful interpretation of the epidemiological records, might help to prevent the further spread of those highly virulent caMRSA clones. PMID:18032620

  8. Utility of Plasma Osteopontin Levels in Management of Community-Acquired Pneumonia

    Science.gov (United States)

    Chang, Jer-Hwa; Hung, Wen-Yueh; Bai, Kuan-Jen; Yang, Shun-Fa; Chien, Ming-Hsien

    2016-01-01

    Osteopontin (OPN) is an essential cytokine involved in immune cell recruitment and an important regulator of inflammation. The purpose of this study was to examine differences in OPN plasma levels between before and after antibiotic treatment in hospitalized adult patients with community-acquired pneumonia (CAP). OPN levels were measured in 93 patients with CAP and 54 healthy controls using a commercial enzyme-linked immunosorbent assay (ELISA). The CURB-65, Pneumonia Severity Index (PSI), and Acute Physiology and Chronic Health Evaluation II (APACHE II) scores were used to determine the CAP severity in patients upon initial hospitalization. A decline in the number of white blood cells (WBCs) and neutrophils, and decreases in the levels of OPN and C-reactive protein (CRP) were observed after antibiotic treatment. Only the plasma level of OPN, but not CRP, was correlated with the severity of CAP based on the PSI (r = 0.514, p < 0.001), CURB-65 (r = 0.396, p < 0.001), and APACHE II scores (r = 0.473, p < 0.001). The OPN level also showed a significant correlation with the length of hospital stay (r = 0.210, p = 0.044). In conclusion, plasma level of OPN may act as diagnostic adjuvant biomarkers for CAP and further play a role in clinical assessment of the severity of CAP, which could potentially guide the development of treatment strategies. PMID:27647996

  9. Usefulness of Plasma YKL-40 in Management of Community-Acquired Pneumonia Severity in Patients

    Directory of Open Access Journals (Sweden)

    Hsiang-Ling Wang

    2013-11-01

    Full Text Available Plasma YKL-40 level has been reported as playing a significant role in community-acquired pneumonia (CAP. However, the correlation between plasma level of YKL-40 and the severity of CAP has not been reported. This study identifies the relationship between plasma level changes of the YKL-40 gene in adult patients hospitalized with CAP. The ELISA was used to measure the plasma YKL-40 level from 61 adult CAP patients before and after antibiotic treatment and from 60 healthy controls. The plasma YKL-40 levels were significantly increased in patients with CAP compared to normal controls. Moreover, the plasma concentration of YKL-40 correlated with the severity of CAP based on the pneumonia severity index (PSI score (r = 0.630, p < 0.001, the CURB-65 (confusion, uremia, respiratory rate, BP, age 65 years score (r = 0.640, p < 0.001, the Acute Physiology And Chronic Health Evaluation II (APACHE II score (r = 0.539, p < 0.001 and length of hospital stay (r = 0.321, p = 0.011, respectively. In conclusion, plasma YKL-40 may play a role in the diagnosis and clinical assessment of CAP severity, which could potentially guide the development of treatment strategies.

  10. Using data-driven rules to predict mortality in severe community acquired pneumonia.

    Directory of Open Access Journals (Sweden)

    Chuang Wu

    Full Text Available Prediction of patient-centered outcomes in hospitals is useful for performance benchmarking, resource allocation, and guidance regarding active treatment and withdrawal of care. Yet, their use by clinicians is limited by the complexity of available tools and amount of data required. We propose to use Disjunctive Normal Forms as a novel approach to predict hospital and 90-day mortality from instance-based patient data, comprising demographic, genetic, and physiologic information in a large cohort of patients admitted with severe community acquired pneumonia. We develop two algorithms to efficiently learn Disjunctive Normal Forms, which yield easy-to-interpret rules that explicitly map data to the outcome of interest. Disjunctive Normal Forms achieve higher prediction performance quality compared to a set of state-of-the-art machine learning models, and unveils insights unavailable with standard methods. Disjunctive Normal Forms constitute an intuitive set of prediction rules that could be easily implemented to predict outcomes and guide criteria-based clinical decision making and clinical trial execution, and thus of greater practical usefulness than currently available prediction tools. The Java implementation of the tool JavaDNF will be publicly available.

  11. Clinical predictors for Legionella in patients presenting with community-acquired pneumonia to the emergency department

    Directory of Open Access Journals (Sweden)

    Frei Reno

    2009-01-01

    Full Text Available Abstract Background Legionella species cause severe forms of pneumonia with high mortality and complication rates. Accurate clinical predictors to assess the likelihood of Legionella community-acquired pneumonia (CAP in patients presenting to the emergency department are lacking. Methods We retrospectively compared clinical and laboratory data of 82 consecutive patients with Legionella CAP with 368 consecutive patients with non-Legionella CAP included in two studies at the same institution. Results In multivariate logistic regression analysis we identified six parameters, namely high body temperature (OR 1.67, p Legionella CAP. Using optimal cut off values of these six parameters, we calculated a diagnostic score for Legionella CAP. The median score was significantly higher in Legionella CAP as compared to patients without Legionella (4 (IQR 3–4 vs 2 (IQR 1–2, p Legionella pneumonia. Conversely, of the 73 patients (16% with ≥4 points, 66% of patients had Legionella CAP. Conclusion Six clinical and laboratory parameters embedded in a simple diagnostic score accurately identified patients with Legionella CAP. If validated in future studies, this score might aid in the management of suspected Legionella CAP.

  12. Optimal imaging strategy for community-acquired Staphylococcus aureus musculoskeletal infections in children

    Energy Technology Data Exchange (ETDEWEB)

    Browne, Lorna P.; Cassady, Christopher I.; Krishnamurthy, Rajesh; Guillerman, R.P. [Texas Children' s Hospital, Edward B. Singleton Department of Diagnostic Imaging, Houston, TX (United States); Mason, Edward O.; Kaplan, Sheldon L. [Texas Children' s Hospital, Department of Pediatrics, Baylor College of Medicine, Infectious Disease Service, Houston, TX (United States)

    2008-08-15

    Invasive musculoskeletal infections from community-acquired methicillin-resistant and methicillin-susceptible Staphylococcus aureus (CA-SA) are increasingly encountered in children. Imaging is frequently requested in these children for diagnosis and planning of therapeutic interventions. To appraise the diagnostic efficacy of imaging practices performed for CA-SA osteomyelitis and its complications. A retrospective review was conducted of the clinical charts and imaging studies of CA-SA osteomyelitis cases since 2001 at a large children's hospital. Of 199 children diagnosed with CA-SA osteomyelitis, 160 underwent MRI examination and 35 underwent bone scintigraphy. The sensitivity of MRI and bone scintigraphy for CA-SA osteomyelitis was 98% and 53%, respectively. In all discordant cases, MRI was correct compared to bone scintigraphy. Extraosseous complications of CA-SA osteomyelitis detected only by MRI included subperiosteal abscesses (n = 77), pyomyositis (n = 43), septic arthritis (n = 31), and deep venous thrombosis (n = 12). MRI is the preferred imaging modality for the investigation of pediatric CA-SA musculoskeletal infection because it offers superior sensitivity for osteomyelitis compared to bone scintigraphy and detects extraosseous complications that occur in a substantial proportion of patients. (orig.)

  13. Etiology of community-acquired pneumonia in hospitalized patients in Jordan

    International Nuclear Information System (INIS)

    To ascertain the causative organisms of community acquired pneumonia (Cap) in Jordanian patients requiring hospital admission. A prospective study of both adults and children admitted to Princess Basma and Princess Rahma Teaching Hospitals in Irbid, Jordan with a diagnosis of CAP over a 6-month period from April to October 2002. A total of 35 adult patients were admitted with a mean age of 47 years, and 63 children with a mean age of 3 years. A pathogen was isolated from 25 (71%) adults, and from 17 (27%) children, and sputum cultures gave the best diagnostic yield. In adults Streptococcus pneumoniae was the most common isolate (26%), followed by Chlamydia pneumoniae (23%), Haemophilus influenzae (17%), Mycoplasma pneumoniae (9%), and Legionella pneumophila and Klebsiella pneumoniae (6%) each. Seven of the 9 gram negative isolates were from patients with some co morbid illness. While in children, Chlamydia pneumoniae was the most common (14%), followed by Mycoplasma pneumoniae (6%), and Streptococcus pneumoniae, Haemophilus influenzae, and Pseudomonas aeruginosa (3%) each. Streptococcus pneumoniae and atypical microorganisms are the most common cause of CAP in previously healthy adults; while in those with associated co morbid illness, gram negative organisms are the likely cause. In children, the overall detection rate of causative organisms was low with atypical microorganisms being the most common. (author)

  14. Characterization of Bacterial Communities in Deep-Sea Hydrothermal Vents from Three Oceanic Regions.

    Science.gov (United States)

    He, Tianliang; Zhang, Xiaobo

    2016-04-01

    Deep-sea hydrothermal vents are considered to be one of the most spectacular ecosystems on Earth. Microorganisms form the basis of the food chain in vents controlling the vent communities. However, the diversity of bacterial communities in deep-sea hydrothermal vents from different oceans remains largely unknown. In this study, the pyrosequencing of 16S rRNA gene was used to characterize the bacterial communities of the venting sulfide, seawater, and tubeworm trophosome from East Pacific Rise, South Atlantic Ridge, and Southwest Indian Ridge, respectively. A total of 23,767 operational taxonomic units (OTUs) were assigned into 42 different phyla. Although Proteobacteria, Actinobacteria, and Bacteroidetes were the predominant phyla in all vents, differences of bacterial diversity were observed among different vents from three oceanic regions. The sulfides of East Pacific Rise possessed the most diverse bacterial communities. The bacterial diversities of venting seawater were much lower than those of vent sulfides. The symbiotic bacteria of tubeworm Ridgeia piscesae were included in the bacterial community of vent sulfides, suggesting their significant ecological functions as the primary producers in the deep-sea hydrothermal vent ecosystems. Therefore, our study presented a comprehensive view of bacterial communities in deep-sea hydrothermal vents from different oceans. PMID:26626941

  15. Characterization of Bacterial Communities in Deep-Sea Hydrothermal Vents from Three Oceanic Regions.

    Science.gov (United States)

    He, Tianliang; Zhang, Xiaobo

    2016-04-01

    Deep-sea hydrothermal vents are considered to be one of the most spectacular ecosystems on Earth. Microorganisms form the basis of the food chain in vents controlling the vent communities. However, the diversity of bacterial communities in deep-sea hydrothermal vents from different oceans remains largely unknown. In this study, the pyrosequencing of 16S rRNA gene was used to characterize the bacterial communities of the venting sulfide, seawater, and tubeworm trophosome from East Pacific Rise, South Atlantic Ridge, and Southwest Indian Ridge, respectively. A total of 23,767 operational taxonomic units (OTUs) were assigned into 42 different phyla. Although Proteobacteria, Actinobacteria, and Bacteroidetes were the predominant phyla in all vents, differences of bacterial diversity were observed among different vents from three oceanic regions. The sulfides of East Pacific Rise possessed the most diverse bacterial communities. The bacterial diversities of venting seawater were much lower than those of vent sulfides. The symbiotic bacteria of tubeworm Ridgeia piscesae were included in the bacterial community of vent sulfides, suggesting their significant ecological functions as the primary producers in the deep-sea hydrothermal vent ecosystems. Therefore, our study presented a comprehensive view of bacterial communities in deep-sea hydrothermal vents from different oceans.

  16. The Community-Acquired Pneumonia immunization Trial in Adults (CAPiTA) : What is the future of pneumococcal conjugate vaccination in elderly?

    NARCIS (Netherlands)

    Van Werkhoven, Cornelis H.; Bonten, Marc Jm

    2015-01-01

    Pneumococcal community-acquired pneumonia (PCAP) and invasive pneumococcal disease (IPD) are important causes of morbidity and mortality in elderly. In the Community-Acquired Pneumonia immunization Trial in Adults (CAPiTA), a randomized double-blind placebo-controlled trial of 84,496 community-dwell

  17. Seasonal variation of bacterial communities in shellfish harvesting waters: preliminary study before applying phage therapy.

    Science.gov (United States)

    Pereira, C; Santos, L; Silva, A P; Silva, Y J; Cunha, A; Romalde, J L; Nunes, M L; Almeida, A

    2015-01-15

    The recurrent emergence of infections outbreaks associated with shellfish consumption is an important health problem, which results in substantial economic losses to the seafood industry. Even after depuration, shellfish is still involved in outbreaks caused by pathogenic bacteria, which increases the demand for new efficient strategies to control the shellfish infection transmission. Phage therapy during the shellfish depuration is a promising approach, but its success depends on a detailed understanding of the dynamics of bacterial communities in the harvesting waters. This study intends to evaluate the seasonal dynamics of the overall bacterial communities, disease-causing bacterial populations and bacterial sanitary quality indicators in two authorized harvesting-zones at Ria de Aveiro. During the hot season, the total bacterial community presented high complexity and new prevalent populations of the main shellfish pathogenic bacteria emerged. These results indicate that the spring/summer season is a critical period during which phage therapy should be applied. PMID:25484114

  18. Diversity surveys of soil bacterial community by cultivation-based methods and molecular fingerprinting techniques

    Institute of Scientific and Technical Information of China (English)

    LUO Hai-feng; QI Hong-yan; ZHANG Hong-xun

    2004-01-01

    By combining the cultivation methods with molecular fingerprinting techniques, the diversity surveys of soil bacterial community in 13 areas of China were carried out. The cultivable heterotrophic diversity was investigated by colony morphology on solid LB medium. Genetic diversity was measured as bands on denaturing gradient gel electrophoresis(DGGE) by the extraction and purification of the total soil DNA, and amplification of bacterial 16S rDNA fragments by polymerase chain reaction ( PCR). The Shannon-Wiener indices of diversity (H), richness (S)and evenness( EH ) were employed to estimate the diversity of soil bacterial community. The results showed that there was an obvious diversification existed in soil from the different areas. However, the genetic diversity estimated by PCR-DGGE can provide more comprehensive information on bacterial community than the cultivation-based methods. Therefore, it is suggested to combine the traditional methods with genetic fingerprinting techniques to survey and estimate soil bacterial diversity.

  19. Diversity and abundance of the bacterial community of the red Macroalga Porphyra umbilicalis: did bacterial farmers produce macroalgae?

    Directory of Open Access Journals (Sweden)

    Lilibeth N Miranda

    Full Text Available Macroalgae harbor microbial communities whose bacterial biodiversity remains largely uncharacterized. The goals of this study were 1 to examine the composition of the bacterial community associated with Porphyra umbilicalis Kützing from Schoodic Point, ME, 2 determine whether there are seasonal trends in species diversity but a core group of bacteria that are always present, and 3 to determine how the microbial community associated with a laboratory strain (P.um.1 established in the presence of antibiotics has changed. P. umbilicalis blades (n = 5, fall 2010; n = 5, winter 2011; n = 2, clonal P.um.1 were analyzed by pyrosequencing over two variable regions of the 16 S rDNA (V5-V6 and V8; 147,880 total reads. The bacterial taxa present were classified at an 80% confidence threshold into eight phyla (Bacteroidetes, Proteobacteria, Planctomycetes, Chloroflexi, Actinobacteria, Deinococcus-Thermus, Firmicutes, and the candidate division TM7. The Bacteroidetes comprised the majority of bacterial sequences on both field and lab blades, but the Proteobacteria (Alphaproteobacteria, Gammaproteobacteria were also abundant. Sphingobacteria (Bacteroidetes and Flavobacteria (Bacteroidetes had inverse abundances on natural versus P.um.1 blades. Bacterial communities were richer and more diverse on blades sampled in fall compared to winter. Significant differences were observed between microbial communities among all three groups of blades examined. Only two OTUs were found on all 12 blades, and only one of these, belonging to the Saprospiraceae (Bacteroidetes, was abundant. Lewinella (as 66 OTUs was found on all field blades and was the most abundant genus. Bacteria from the Bacteroidetes, Proteobacteria and Planctomycetes that are known to digest the galactan sulfates of red algal cell walls were well-represented. Some of these taxa likely provide essential morphogenetic and beneficial nutritive factors to P. umbilicalis and may have had

  20. Temporal dynamics of sediment bacterial communities in monospecific stands of Juncus maritimus and Spartina maritima.

    Science.gov (United States)

    Cleary, D F R; Polónia, A R M; Sousa, A I; Lillebø, A I; Queiroga, H; Gomes, N C M

    2016-09-01

    In the present study, we used 16S rRNA barcoded pyrosequencing to investigate to what extent monospecific stands of different salt marsh plant species (Juncus maritimus and Spartina maritima), sampling site and temporal variation affect sediment bacterial communities. We also used a bioinformatics tool, PICRUSt, to predict metagenome gene functional content. Our results showed that bacterial community composition from monospecific stands of both plant species varied temporally, but both host plant species maintained compositionally distinct communities of bacteria. Juncus sediment was characterised by higher abundances of Alphaproteobacteria, Myxococcales, Rhodospirillales, NB1-j and Ignavibacteriales, while Spartina sediment was characterised by higher abundances of Anaerolineae, Synechococcophycidae, Desulfobacterales, SHA-20 and Rhodobacterales. The differences in composition and higher taxon abundance between the sediment bacterial communities of stands of both plant species may be expected to affect overall metabolic diversity. In line with this expectation, there were also differences in the predicted enrichment of selected metabolic pathways. In particular, bacterial communities of Juncus sediment were predicted to be enriched for pathways related to the degradation of various (xenobiotic) compounds. Bacterial communities of Spartina sediment in turn were predicted to be enriched for pathways related to the biosynthesis of various bioactive compounds. Our study highlights the differences in composition and predicted functions of sediment-associated bacterial communities from two different salt marsh plant species. Loss of salt marsh habitat may thus be expected to both adversely affect microbial diversity and ecosystem functioning and have consequences for environmental processes such as nutrient cycling and pollutant remediation. PMID:27061465

  1. Incidence and risk factors for community-acquired acute gastroenteritis in north-west Germany in 2004

    NARCIS (Netherlands)

    Karsten, C; Baumgarte, S; Friedrich, A W; von Eiff, C; Becker, K; Wosniok, W; Ammon, A; Bockemühl, J; Karch, H; Huppertz, H-I

    2009-01-01

    In developed countries, acute gastroenteritis (AGE) is a major source of morbidity. However, only a few studies have estimated its incidence and the associated medical burden. This population-based study determined the incidence of community-acquired AGE patients seeking medical care and the relativ

  2. Expressive Art for the Social and Community Integration of Adolescents with Acquired Brain Injuries: A Systematic Review

    Science.gov (United States)

    Goyal, Anita; Keightley, Michelle L.

    2008-01-01

    Adolescents with acquired brain injuries suffer from social and community withdrawal that result in isolation from their peer groups. The review highlights the evidence of effectiveness of expressive art interventions in the form of theatre for populations with difficulties in physical, emotional, cognitive, or social functioning. A systematic…

  3. Do We Know When, What and For How Long to Treat? Antibiotic Therapy for Pediatric Community-acquired Pneumonia

    NARCIS (Netherlands)

    Esposito, Susanna; Cohen, Robert; Domingo, Javier Diez; Pecurariu, Oana Falup; Greenberg, David; Heininger, Ulrich; Knuf, Markus; Lutsar, Irja; Principi, Nicola; Rodrigues, Fernanda; Sharland, Mike; Spoulou, Vana; Syrogiannopoulos, George A.; Usonis, Vytautas; Vergison, Anne; Schaad, Urs B.

    2012-01-01

    Community-acquired pneumonia (CAP) is a common cause of morbidity among children in developed countries and accounts for an incidence of 10-40 cases per 1000 children in the first 5 years of life. Given the clinical, social and economic importance of CAP, there is general agreement that prompt and a

  4. Outbreaks of Infection Caused by Community-Acquired Methicillin-Resistant Staphylococcus aureus in a Canadian Correctional Facility

    Directory of Open Access Journals (Sweden)

    Cheryl L Main

    2005-01-01

    Full Text Available BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA has been identified in prison settings in the United States. The present study investigated two clusters of skin and soft tissue infection caused by community-acquired (CA MRSA in a correctional facility in southern Ontario.

  5. Are pathogenic leptospira species agents of community-acquired pneumonia? case reports of leptospirosis presenting as pneumonia

    NARCIS (Netherlands)

    M.H. Gasem; H. Farida (Helmia); A. Ahmed (Ahmed); J.A. Severin (Julitte A.); A. Suryanto (Agus); B. Isbandrio; H.A. Verbrugh (Henri); R.A. Hartskeerl (Rudy); P.J. Van Den Broek (Peterhans J.)

    2016-01-01

    textabstractWe report four Indonesian cases meeting the clinical and radiological criteria for community-acquired pneumonia and other findings suggestive of leptospirosis. Quantitative PCR (qPCR) analyses of serum and urine samples and serology confirmed the diagnosis of leptospirosis in each. Resul

  6. Individualized treatment strategies in community-acquired pneumonia : from initial inflammatory response to long-term prognosis

    NARCIS (Netherlands)

    Bruns, A.H.W.

    2010-01-01

    Community-acquired pneumonia (CAP) is one of the most important causes of hospital admissions and together with influenza the third leading cause of death worldwide. Moreover, treatment of CAP largely contributes to the global burden of antibiotic resistance. In present thesis, we explored options f

  7. Epidemiological study of community-and hospital-acquired intraabdominal infections

    Institute of Scientific and Technical Information of China (English)

    Shu Zhang; Wenxiang Huang

    2015-01-01

    Purpose: To investigate and analyze the clinical and etiological characteristics of community-acquired intraabdominal infections (CIAIs) and hospital-acquired or nosocomial intraabdominal infections (NIAls) in a comprehensive hospital, to understand the characteristics, pathogen composition, and drug resistance of CIAIs as well as NIAIs, and to provide a reference for clinical treatment.Methods: We collected the clinical data of patients with intraabdominal infections admitted to our hospital from June 2013 to June 2014.In vitro drug sensitivity tests were conducted to separate pathogens, and the data were analyzed using the WHONET 5.4 software and SPSS 13.0 software.Results: A total of 221 patients were enrolled in the study, including 144 with CIAIs (55 mild-moderate and 89 severe) and 77 with NIAIs.We isolated 322 pathogenic strains, including 234 strains of gramnegative bacteria, 82 strains of gram-positive bacteria, and 6 strains of fungi.Based on clinical features, NIAIs and severe CIAIs presented significantly higher values in age, length of hospital stay, mortality, and the incidence of severe intra-abdominal infection than mild-moderate CIAIs (p < 0.05).There was no significant difference in the prognosis between NIAIs and severe CIAIs.Primary diseases leading to CIAIs and NIAIs mostly were hepatobiliary diseases and gastrointestinal diseases respectively.Bacteria isolated from various types of IAIs mainly were Enterobacteriaceae;mild-moderate CIAIs mostly were mono-infection of gram-negative bacteria;NIAIs mostly were mixed infections of gram-negative and gram-positive bacteria;and severe CIAIs were from either type of infection.The rate of Extended Spectrum β-Lactamase-producing Escherichia coli and Klebsiella pneumoniae was much higher in NIAIs than in CIAls (p < 0.05).The antimicrobial drug sensitivity of gram-negative bacteria isolated from NIAIs was significantly lower than that of CIAIs.Conclusion: CIAIs and NIAls have their own unique clinical

  8. Characterization of copper-resistant bacteria and bacterial communities from copper-polluted agricultural soils of central Chile

    Directory of Open Access Journals (Sweden)

    Altimira Fabiola

    2012-09-01

    Full Text Available Abstract Background Copper mining has led to Cu pollution in agricultural soils. In this report, the effects of Cu pollution on bacterial communities of agricultural soils from Valparaiso region, central Chile, were studied. Denaturing gradient gel electrophoresis (DGGE of the 16S rRNA genes was used for the characterization of bacterial communities from Cu-polluted and non-polluted soils. Cu-resistant bacterial strains were isolated from Cu-polluted soils and characterized. Results DGGE showed a similar high number of bands and banding pattern of the bacterial communities from Cu-polluted and non-polluted soils. The presence of copA genes encoding the multi-copper oxidase that confers Cu-resistance in bacteria was detected by PCR in metagenomic DNA from the three Cu-polluted soils, but not in the non-polluted soil. The number of Cu-tolerant heterotrophic cultivable bacteria was significantly higher in Cu-polluted soils than in the non-polluted soil. Ninety two Cu-resistant bacterial strains were isolated from three Cu-polluted agricultural soils. Five isolated strains showed high resistance to copper (MIC ranged from 3.1 to 4.7 mM and also resistance to other heavy metals. 16S rRNA gene sequence analyses indicate that these isolates belong to the genera Sphingomonas, Stenotrophomonas and Arthrobacter. The Sphingomonas sp. strains O12, A32 and A55 and Stenotrophomonas sp. C21 possess plasmids containing the Cu-resistance copA genes. Arthrobacter sp. O4 possesses the copA gene, but plasmids were not detected in this strain. The amino acid sequences of CopA from Sphingomonas isolates (O12, A32 and A55, Stenotrophomonas strain (C21 and Arthrobacter strain (O4 are closely related to CopA from Sphingomonas, Stenotrophomonas and Arthrobacter strains, respectively. Conclusions This study suggests that bacterial communities of agricultural soils from central Chile exposed to long-term Cu-pollution have been adapted by acquiring Cu genetic determinants

  9. Temporally invariable bacterial community structure in the Arabian Sea oxygen minimum zone.

    Digital Repository Service at National Institute of Oceanography (India)

    Jain, A.; Bandekar, M.; Gomes, J.; Shenoy, D.M.; Meena, R.M.; Naik, H.; Khandeparkar, R.; Ramaiah, N.

    The Northeastern Arabian Sea (NEAS) is a recognized region of intense denitrification, with a 200 to 1200 m anoxic water column. We studied the abundance of bacteria, viral particles and the bacterial community (BC), in addition to various chemical...

  10. Denaturing gradient gel electrophoresis profiling of bacterial communities composition in Arabian Sea

    Digital Repository Service at National Institute of Oceanography (India)

    Singh, S.K.; Ramaiah, N.

    Denaturing gradient gel electrophoresis (DGGE) was used to elucidate spatial and temporal variations in bacterial community composition (BCC) from four locations along the central west coast of India. DNA extracts from 36 water samples collected...

  11. Comparison of bacterial communities of conventional and A-stage activated sludge systems

    NARCIS (Netherlands)

    Gonzalez-Martinez, A.; Rodriguez-Sanchez, A.; Lotti, T.; Garcia-Ruiz, M.J.; Gonzalez-Lopez, J.; Van Loosdrecht, M.C.M.

    2016-01-01

    The bacterial community structure of 10 different wastewater treatment systems and their influents has been investigated through pyrosequencing, yielding a total of 283486 reads. These bioreactors had different technological configurations: conventional activated sludge (CAS) systems and very highly

  12. Impact of oil contamination and biostimulation on the diversity of indigenous bacterial communities in soil microcosms

    NARCIS (Netherlands)

    Evans, FF; Rosado, AS; Sebastian, GV; Casella, R; Machado, PLOA; Holmstrom, C; Kjelleberg, S; van Elsas, JD; Seldin, L

    2004-01-01

    The aim of this study was to analyse the effect of oil contamination and biostimulation (soil pH raise, and nitrogen, phosphate and sulphur addition) on the diversity of a bacterial community of an acidic Cambisol under Atlantic Forest. The experiment was based on the enumeration of bacterial popula

  13. Comparative pyrosequencing analysis of bacterial community change in biofilm formed on seawater reverse osmosis membrane.

    Science.gov (United States)

    Kim, In S; Lee, Jinwook; Kima, Sung-Jo; Yu, Hye-Weon; Jang, Am

    2014-01-01

    The change in bacterial community structure induced by bacterial competition and succession was investigated during seawater reverse osmosis (SWRO) in order to elucidate a possible link between the bacterial consortium on SWRO membranes and biofouling. To date, there has been no definitive characterization of the microbial diversity in SWRO in terms of distinguishing time-dependent changes in the richness or abundance of bacterial species. For bacterial succession within biofilms on the membrane surface, SWRO using a cross-flow filtration membrane test unit was operated for 5 and 100h, respectively. As results of the pyrosequencing analysis, bacterial communities differed considerably among seawater and the 5 and 100 h samples. From a total of 33,876 pyrosequences (using a 95% sequence similarity), there were less than 1% of shared species, confirming the influence of the operational time factor and lack of similarity of these communities. During SWRO operation, the abundance of Pseudomonas stutzeri BBSPN3 (GU594474) belonging to gamma-Proteobacteria suggest that biofouling of SWRO membrane might be driven by the dominant influence of a specific species. In addition, among the bacterial competition of five bacterial species (Pseudomonas aeruginosa, Bacillus sp., Rhodobacter sp., Flavobacterium sp., and Mycobacterium sp.) competing for bacterial colonization on the SWRO membrane surfaces, it was exhibited that Bacillus sp. was the most dominant. The dominant influences ofPseudomonas sp. and Bacillus sp. on biofouling during actual SWRO is decisive depending on higher removal efficiency of the seawater pretreatment. PMID:24600849

  14. Comparative pyrosequencing analysis of bacterial community change in biofilm formed on seawater reverse osmosis membrane.

    Science.gov (United States)

    Kim, In S; Lee, Jinwook; Kima, Sung-Jo; Yu, Hye-Weon; Jang, Am

    2014-01-01

    The change in bacterial community structure induced by bacterial competition and succession was investigated during seawater reverse osmosis (SWRO) in order to elucidate a possible link between the bacterial consortium on SWRO membranes and biofouling. To date, there has been no definitive characterization of the microbial diversity in SWRO in terms of distinguishing time-dependent changes in the richness or abundance of bacterial species. For bacterial succession within biofilms on the membrane surface, SWRO using a cross-flow filtration membrane test unit was operated for 5 and 100h, respectively. As results of the pyrosequencing analysis, bacterial communities differed considerably among seawater and the 5 and 100 h samples. From a total of 33,876 pyrosequences (using a 95% sequence similarity), there were less than 1% of shared species, confirming the influence of the operational time factor and lack of similarity of these communities. During SWRO operation, the abundance of Pseudomonas stutzeri BBSPN3 (GU594474) belonging to gamma-Proteobacteria suggest that biofouling of SWRO membrane might be driven by the dominant influence of a specific species. In addition, among the bacterial competition of five bacterial species (Pseudomonas aeruginosa, Bacillus sp., Rhodobacter sp., Flavobacterium sp., and Mycobacterium sp.) competing for bacterial colonization on the SWRO membrane surfaces, it was exhibited that Bacillus sp. was the most dominant. The dominant influences ofPseudomonas sp. and Bacillus sp. on biofouling during actual SWRO is decisive depending on higher removal efficiency of the seawater pretreatment.

  15. Clinical efficacy and safety of moxifloxacin versus levofloxacin plus metronidazole for community-acquired pneumonia with aspiration factors

    Institute of Scientific and Technical Information of China (English)

    Sun Tieying; Sun Li; Wang Rongmei; Ren Xiaoping; Sui Dong-jiang; Pu Chun; Ren Yajuan

    2014-01-01

    Background Community-acquired pneumonia (CAP) is a common infectious disease throughout the world and the incidence continues to grow as the population ages.Aspiration is an important pathogenic mechanism for pneumonia in the elderly and the management of patients with community-acquired pneumonia with aspiration factors is a major medical problem.Our study aimed to assess whether moxifloxacin in comparison to levofloxacin plus metronidazole are effective and safe in the treatment of community-acquired pneumonia with aspiration factors.Methods In this prospective,multicenter,open-label,randomized controlled trial,77 patients with mild-to-moderate community-acquired pneumonia with aspiration factors were enrolled and randomly assigned to receive moxifloxacin or levofloxacin plus metronidazole.The primary efficacy variables were clinical outcomes in evaluable patients at a follow-up visit 7 to 14 days after the end of therapy.Results Seven days after the end of therapy a clinical cure was achieved for 76.7% (23 of 37) of efficacy-evaluable patients in the moxifloxacin group and 51.7% (15 of 40) of patients in the levofloxacin plus metronidazole group.There was a significant difference between the two groups (x2=4.002,P <0.05).Bacteriological success rates were similar in the moxifloxacin group (93.3%) and levofloxacin plus metronidazole group (96.4%),there was no significant difference between the two groups (P >0.05).The overall adverse event rate was 10.8% (4/37) in the moxifloxacin group versus 17.5% (7/40) in the levofloxacin plus metronidazole group,there was no significant difference between the two groups (P>0.05).No serious adverse events were observed.Conclusions Moxifloxacin is effective and safe for treatment of community-acquired pneumonia with aspiration factors.And the regimen of moxifloxacin monotherapy is more convenient compared with levofloxacin plus metronidazole.

  16. Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests

    Science.gov (United States)

    Kaiser, Kristin; Wemheuer, Bernd; Korolkow, Vera; Wemheuer, Franziska; Nacke, Heiko; Schöning, Ingo; Schrumpf, Marion; Daniel, Rolf

    2016-01-01

    Soil bacteria provide a large range of ecosystem services such as nutrient cycling. Despite their important role in soil systems, compositional and functional responses of bacterial communities to different land use and management regimes are not fully understood. Here, we assessed soil bacterial communities in 150 forest and 150 grassland soils derived from three German regions by pyrotag sequencing of 16S rRNA genes. Land use type (forest and grassland) and soil edaphic properties strongly affected bacterial community structure and function, whereas management regime had a minor effect. In addition, a separation of soil bacterial communities by sampling region was encountered. Soil pH was the best predictor for bacterial community structure, diversity and function. The application of multinomial log-linear models revealed distinct responses of abundant bacterial groups towards pH. Predicted functional profiles revealed that differences in land use not only select for distinct bacterial populations but also for specific functional traits. The combination of 16S rRNA data and corresponding functional profiles provided comprehensive insights into compositional and functional adaptations to changing environmental conditions associated with differences in land use and management. PMID:27650273

  17. Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests

    Science.gov (United States)

    Kaiser, Kristin; Wemheuer, Bernd; Korolkow, Vera; Wemheuer, Franziska; Nacke, Heiko; Schöning, Ingo; Schrumpf, Marion; Daniel, Rolf

    2016-09-01

    Soil bacteria provide a large range of ecosystem services such as nutrient cycling. Despite their important role in soil systems, compositional and functional responses of bacterial communities to different land use and management regimes are not fully understood. Here, we assessed soil bacterial communities in 150 forest and 150 grassland soils derived from three German regions by pyrotag sequencing of 16S rRNA genes. Land use type (forest and grassland) and soil edaphic properties strongly affected bacterial community structure and function, whereas management regime had a minor effect. In addition, a separation of soil bacterial communities by sampling region was encountered. Soil pH was the best predictor for bacterial community structure, diversity and function. The application of multinomial log-linear models revealed distinct responses of abundant bacterial groups towards pH. Predicted functional profiles revealed that differences in land use not only select for distinct bacterial populations but also for specific functional traits. The combination of 16S rRNA data and corresponding functional profiles provided comprehensive insights into compositional and functional adaptations to changing environmental conditions associated with differences in land use and management.

  18. Distinct soil bacterial communities along a small-scale elevational gradient in alpine tundra

    Directory of Open Access Journals (Sweden)

    Congcong eShen

    2015-06-01

    Full Text Available The elevational diversity pattern for microorganisms has received great attention recently but is still understudied, and phylogenetic relatedness is rarely studied for microbial elevational distributions. Using a bar-coded pyrosequencing technique, we examined the biodiversity patterns for soil bacterial communities of tundra ecosystem along 2000–2500 m elevations on Changbai Mountain in China. Bacterial taxonomic richness displayed a linear decreasing trend with increasing elevation. Phylogenetic diversity and mean nearest taxon distance (MNTD exhibited a unimodal pattern with elevation. Bacterial communities were more phylogenetically clustered than expected by chance at all elevations based on the standardized effect size of MNTD metric. The bacterial communities differed dramatically among elevations, and the community composition was significantly correlated with soil total carbon, total nitrogen, C:N ratio, and dissolved organic carbon. Multiple ordinary least squares regression analysis showed that the observed biodiversity patterns strongly correlated with soil total carbon and C:N ratio. Taken together, this is the first time that a significant bacterial diversity pattern has been observed across a small-scale elevational gradient. Our results indicated that soil carbon and nitrogen contents were the critical environmental factors affecting bacterial elevational distribution in Changbai Mountain tundra. This suggested that ecological niche-based environmental filtering processes related to soil carbon and nitrogen contents could play a dominant role in structuring bacterial communities along the elevational gradient.

  19. Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests.

    Science.gov (United States)

    Kaiser, Kristin; Wemheuer, Bernd; Korolkow, Vera; Wemheuer, Franziska; Nacke, Heiko; Schöning, Ingo; Schrumpf, Marion; Daniel, Rolf

    2016-09-21

    Soil bacteria provide a large range of ecosystem services such as nutrient cycling. Despite their important role in soil systems, compositional and functional responses of bacterial communities to different land use and management regimes are not fully understood. Here, we assessed soil bacterial communities in 150 forest and 150 grassland soils derived from three German regions by pyrotag sequencing of 16S rRNA genes. Land use type (forest and grassland) and soil edaphic properties strongly affected bacterial community structure and function, whereas management regime had a minor effect. In addition, a separation of soil bacterial communities by sampling region was encountered. Soil pH was the best predictor for bacterial community structure, diversity and function. The application of multinomial log-linear models revealed distinct responses of abundant bacterial groups towards pH. Predicted functional profiles revealed that differences in land use not only select for distinct bacterial populations but also for specific functional traits. The combination of 16S rRNA data and corresponding functional profiles provided comprehensive insights into compositional and functional adaptations to changing environmental conditions associated with differences in land use and management.

  20. Mucus Sugar Content Shapes the Bacterial Community Structure in Thermally Stressed Acropora muricata

    OpenAIRE

    Lee, Sonny T. M.; Davy, Simon K.; Tang, Sen-Lin; Kench, Paul S.

    2016-01-01

    It has been proposed that the chemical composition of a coral’s mucus can influence the associated bacterial community. However, information on this topic is rare, and non-existent for corals that are under thermal stress. This study therefore compared the carbohydrate composition of mucus in the coral Acropora muricata when subjected to increasing thermal stress from 26 to 31°C, and determined whether this composition correlated with any changes in the bacterial community. Results showed tha...

  1. Phylogenetic characterization of the heterotrophic bacterial communities inhabiting a marine recirculating aquaculture system

    OpenAIRE

    Michaud, L; Lo Giudice, A; Troussellier, Marc; Smedile, F; Bruni, V.; Blancheton, J. P.

    2009-01-01

    Aims: The aim of the present work was to characterize the heterotrophic bacterial community of a marine recirculating aquaculture system (RAS). Methods and Results: An experimental RAS was sampled for the rearing water (RW) and inside the biofilter. Samples were analysed for bacterial abundances, community structure and composition by using a combination of culture-dependent and -independent techniques. The most represented species detected among biofilter clones was Pseudomonas stutzeri, whi...

  2. Genetic difference but functional similarity among fish gut bacterial communities through molecular and biochemical fingerprints

    OpenAIRE

    Mouchet, M.A.; Bouvier, C.; Bouvier, T.; Troussellier, Marc; Escalas, A.; Mouillot, D.

    2012-01-01

    Considering the major involvement of gut microflora in the digestive function of various macro-organisms, bacterial communities inhabiting fish guts may be the main actors of organic matter degradation by fish. Nevertheless, the extent and the sources of variability in the degradation potential of gut bacterial communities are largely overlooked. Using Biolog Ecoplate (TM) and denaturing gradient gel electrophoresis (DGGE), we explored functional (i.e. the ability to degrade organic matter) a...

  3. Rumen bacterial communities can be acclimated faster to high concentrate diets than currently implemented feedlot programs

    OpenAIRE

    Anderson, C L; Schneider, C.J.; Erickson, G.E.; MacDonald, J C; Fernando, S. C.

    2016-01-01

    Abstract Aims Recent studies have demonstrated RAMP ®, a complete starter feed, to have beneficial effects for animal performance. However, how RAMP may elicit such responses is unknown. To understand if RAMP adaptation results in changes in the rumen bacterial community that can potentially affect animal performance, we investigated the dynamics of rumen bacterial community composition in corn‐adapted and RAMP‐adapted cattle. Methods and Results During gradual acclimation of the rumen bacter...

  4. Variations in Bacterial Community in a Temperate Lake Associated with an Agricultural Watershed.

    Science.gov (United States)

    Song, Liyan; Li, Lei

    2016-08-01

    Terrestrially derived carbon and nutrients are washed into lakes, providing nutritional drivers for both microbial heterotrophy and phototrophy. Changes in the quantity and diversity of carbon and nutrients exported from watersheds in response to alterations in long-term land use have led to a need for evaluation of the linkage between watershed-exported carbon and nutrients and bacterial community structure in watershed associated lakes. To learn more about these interactions, we investigated Muskrat Lake in Michigan, which has a well-defined moderately sized watershed dominated by agriculture. We measured the water chemistry, characterized the dissolved organic carbon, and determined the structure of the bacterial communities at the inlet and center of this lake (five depths per site) over the summer and fall of 2008. The lake had temporal and rain event-based fluctuations in water chemistry, as well as temporal and rain event-dependent shifts in bacterial communities as measured by terminal restriction fragment length polymorphism. Agricultural watershed inputs were observed in the lake during and after rain events. Terminal restriction fragment length polymorphism and 454 pyrosequencing of the bacterial communities indicated that there were differences over time and that the dominant phylotypes shifted between summer and late fall. Some populations (e.g., Polynucleobacter and Mycobacterium) increased during fall, while others (e.g., Gemmatimonas) diminished. Redundancy and partitioning analyses showed that water chemistry is highly correlated with variations in the bacterial community of the lake, which explained 34 % of the variations in the bacterial community. Dissolved organic carbon had the greatest effects on variations in the Muskrat Lake bacterial community (2 %). The results of this study provide information that will enable a better understanding of the interaction between the bacterial community of lakes and changes in chemical properties as a

  5. Gut bacterial community structure of two Australian tropical fruit fly species (Diptera: Tephritidae)

    OpenAIRE

    Narit Thaochan; Richard A.I. Drew; Anuchit Chinajariyawong; Anurag Sunpapao; Chaninun Pornsuriya

    2015-01-01

    The community structure of the alimentary tract bacteria of two Australian fruit fly species, Bactrocera cacuminata (Hering) and Bactrocera tryoni (Froggatt), was studied using a molecular cloning method based on the 16S rRNA gene. Differences in the bacterial community structure were shown between the crops and midguts of the two species and sexes of each species. Proteobacteria was the dominant bacterial phylum in the flies, especially bacteria in the order Gammaproteobacteria w...

  6. Analysis of the Clinical Characteristics and Antibiotics Resistance of Community-acquired Methicillin-resistant Staphylococcus aureus

    Institute of Scientific and Technical Information of China (English)

    章税锋; 徐志江; 王林峰

    2004-01-01

    The purpose of this investigation is to study the clinical characteristics of infections by community-acquired methicillin-resistant Staphylococcus aureus (MRSA) and the condition of antibiotics resistance of the clinical isolates in order to guide for the rational use of antibiotics. With the clinical isolates from cases of hospital-acquired MRSA at the same period as contro|s, the clinical characteristics of infections by community-acquired MRSA in Hangzhou area and the pattern of non-β-lactamase antibiotics resistance were determined in this study. It was found that the average age of patients with community-acquired MRSA infections was 30.89 + 13.3, in comparison with those of the hospital-acquired patients of 56.0 + 11.8, appearing to be younger than those of the latter, and the former showing no any basic illness. Both of the former and the latter were sensitive to vancomycin ( 100% vs 100% ), and they had the same degrees of sensitivity to rifampicin, fosfomycin, and STM/TMP (86.8%vs88.1%, P>0.05; 81.6% vs 82.9%, P>0.05; and 52.6% vs 61.9%, P>0.05, respectively). The former was more sensitive to netimycin, chndamycin, erythromycin and minocycline than those of the latter (73.7% vs50.5%, P<0.01; 60.5% vs45.7%, P<0.05; 28.9% vs 11.4%, P<0.01; and81.6% vs58.6%, P<0.01 respectively). Meanwhile, the incidence of multi-resistant strain of isolates in the former was significantly lowerthan that of the latter (31.6% vs 81.0%, P < 0.01). In conclusion, it appears that the strains of clinical isolates isolated from patients with the community-acquired MRSA infections show different clinical characteristics and antimicrobial susceptibility in comparison with those of the hospital-acquired cases of infection, and this necessitates an alteration in the chemotherapy of infections suspected to be caused by community-acquired MRSA.

  7. Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria.

    Directory of Open Access Journals (Sweden)

    Sujatha Srinivasan

    Full Text Available BACKGROUND: Bacterial vaginosis (BV is a common condition that is associated with numerous adverse health outcomes and is characterized by poorly understood changes in the vaginal microbiota. We sought to describe the composition and diversity of the vaginal bacterial biota in women with BV using deep sequencing of the 16S rRNA gene coupled with species-level taxonomic identification. We investigated the associations between the presence of individual bacterial species and clinical diagnostic characteristics of BV. METHODOLOGY/PRINCIPAL FINDINGS: Broad-range 16S rRNA gene PCR and pyrosequencing were performed on vaginal swabs from 220 women with and without BV. BV was assessed by Amsel's clinical criteria and confirmed by Gram stain. Taxonomic classification was performed using phylogenetic placement tools that assigned 99% of query sequence reads to the species level. Women with BV had heterogeneous vaginal bacterial communities that were usually not dominated by a single taxon. In the absence of BV, vaginal bacterial communities were dominated by either Lactobacillus crispatus or Lactobacillus iners. Leptotrichia amnionii and Eggerthella sp. were the only two BV-associated bacteria (BVABs significantly associated with each of the four Amsel's criteria. Co-occurrence analysis revealed the presence of several sub-groups of BVABs suggesting metabolic co-dependencies. Greater abundance of several BVABs was observed in Black women without BV. CONCLUSIONS/SIGNIFICANCE: The human vaginal bacterial biota is heterogeneous and marked by greater species richness and diversity in women with BV; no species is universally present. Different bacterial species have different associations with the four clinical criteria, which may account for discrepancies often observed between Amsel and Nugent (Gram stain diagnostic criteria. Several BVABs exhibited race-dependent prevalence when analyzed in separate groups by BV status which may contribute to increased

  8. INFECTION WITH HHV-6 OF MILITARY MEN AFFECTED BY COMMUNITY-ACQUIRED PNEUMONIA

    Directory of Open Access Journals (Sweden)

    Brusnik SV

    2016-09-01

    Full Text Available Human herpesvirus, 6 type (HHV-6 was isolated at the end of the 20th century from the blood leukocytes of patients with lymphoproliferative diseases. Serological studies conducted in different countries, indicate ubiquitylation of the HHV-6 and the existence of two antigenic variants - HHV-6A and HHV-6B. Their high tropism is determined in vitro to lymphocytic, nervous and dendritic cells of the CNS. Virus replicates in many cell, primary and passaged cultures of different origins. The reproduction cycle of HHV-6 continues on average 4-5 days forming syncytiums and intracytoplasmic and intranuclear inclusions. Significant destruction and lysis almost 90 % of infected cells is reported after 5-10 day of monitoring. The utility of experimentation investigating the role of HHV-6 in the development of acute and chronic diseases in respiratory tract is caused by the fact that many patients, particularly those with chronic diseases, have complaints to chronic fatigue, decreased performance and low-grade temperature more than 3-6 months. Several studies demonstrate the presence of HHV-6 in saliva, salivary and bronchiolar glands, in swabs from pharyngonasal cavity and gorge. Tropism of HHV-6 to oropharyngeal epithelium with the possibility of finding the virus in the saliva and swabs from pharyngonasal cavity and gorge was found at the end of 20th century. This fact gave the basis for work determining the level of infection by this pathogen in patients with infectious and inflammatory pathology of the respiratory tract. Materials and methods. Serological studies were conducted with 38 soldiers affected by community-acquired pneumonia. Most of the surveyed patients were ranged in age from 20 to 45 years old, middle age (32,5±1,5 years. Patients were in stationary treatment in the Kharkov military hospital. The criteria for inclusion in the study on the infection of HHV-6 were soldiers affected by community-acquired pneumonia with atypical course of

  9. Effect of Metal-Rich Sewage Sludge Application on the Bacterial Communities of Grasslands

    OpenAIRE

    Barkay, Tamar; Tripp, Susan C.; Betty H. Olson

    1985-01-01

    The effect of long-term application of heavy metal-laden sewage sludge on the total heterotrophic aerobic and the cadmium-resistant soil bacterial communities was studied. Gram-positive bacteria were completely absent from resistant communities. These findings suggest that this group is highly susceptible to Cd. Shannon's diversity indices estimated for total communities did not reveal negative effects on the communities that developed in the presence of sludge. However, Cd-resistant communit...

  10. Etiology of childhood community acquired pneumonia and its implications for vaccination

    Directory of Open Access Journals (Sweden)

    Nascimento-Carvalho Cristiana M.C.

    2001-01-01

    Full Text Available Pneumonia is an important cause of morbidity and mortality among children throughout the world. Vaccines are available for some organisms, but they are underutilized and/or still in development. To evaluate the potential impact of vaccines, we review studies in which the etiology of childhood community-acquired pneumonia was recorded. In North America and Europe (9 studies, the etiology of pneumonia was established in 62% of studied children (range 43%-88% by use of noninvasive specific methods for microbiologic diagnosis. The most often identified agents were S. pneumoniae (22%, respiratory syncytial virus (RSV (20%, Haemophilus influenzae (7%, and Mycoplasma pneumoniae (15%. In Africa and South America (8 studies, bacteria were recovered from 56% (range 32%-68% of severely ill children studied by lung aspirate. The most often isolated bacteria were Streptococcus pneumoniae (33% and Haemophilus influenzae (21%. A high percentage of H. influenzae strains were not serotype b. Throughout the world, children requiring hospitalization were most likely to have infection caused by pneumococcus H. influenzae or RSV. Out patients also had Mycoplasma pneumoniae. Countries in Africa and Asia recorded 2 to 10 times more children with pneumonia (7 to 40/100 annually than in the USA. Widespread use of pneumococcal and H. influenzae type b conjugate vaccines could reduce the frequency of childhood pneumonia by one-third. Further reduction will require development of non-type b H. influenzae, RSV and M. pneumoniae vaccines. This could result in a > 50% reduction of pneumonia in children. This goal should be sought and achieved as soon as possible.

  11. Optimizing antibiotic therapy of group IV community-acquired pneumonia patients

    Directory of Open Access Journals (Sweden)

    Dziublyk Ya.O.

    2014-06-01

    Full Text Available The aim of the study was to evaluate the clinical and economical effectiveness of differentiated antibacterial therapy of group IV patients with community-acquired pneumonia (CAP. Materials and methods. 42 patients, admitted to the hospital with severe CAP without risk factors for P. aeruginosa infection were randomized in three groups in 1:1:1 ratio. All patients received sequential antibacterial therapy with i.v. amoxicillin/clavulanate or ceftriaxone, or ertapenem in combination with azithromycin switched to oral amoxicillin/clavulanate, cefuroxime axetil in combination with oral azithromycin or levofloxacin, respectively, after initial improvement in 3–4 days. A comparative effectiveness analysis was performed based on clinical, laboratory and economic data. Results. Treatment outcomes in all subgroups of patients were similar: in 1st subgroup the cure rate was (28,6  12,1 %, improvement – in (49,4  13,2 % of patients; in 2nd and 3rd subgroups the cure/improvement rates were (35,7  12,8 and (42,9 13,2 %, respectively (р  0,05. Conclusion. Antibacterial therapy, always empiric and differentiated depending on severity of disease, con¬comitant conditions and previous use of antibiotics within 3 months of the onset of the disease, is a milestone of treatmet of CAP patients. A sequential antibiotic therapy with either aminopenicillin (amoxicillin/clavulanate of 3rd generation cephalosporin (ceftriaxone/cefuroxime axetil in combination with macrolide (azithromycin or carbapenem (ertapenem, followed by levofloxacin is recommended in hospitalized clinical group IV CAP patients without risk factors for P. aeruginosa infection. In current group of patients pharmacoeconomic analysis confirmed the expediency of administration a sequential antibiotic therapy with parenteral amoxicillin/clavulanat or ceftriaxone in combination with azithromycin, followed by oral amoxicillin/clavulanat or cefuroxime axetil in combination with

  12. Etiology and antimicrobial resistance of community-acquired pneumonia in adult patients in China

    Institute of Scientific and Technical Information of China (English)

    TAO Li-li; DENG Wei-wu; HU Bi-jie; HE Li-xian; WEI Li; XIE Hong-mei; WANG Bao-qing; LI Hua-ying; CHEN Xue-hua; ZHOU Chun-mei

    2012-01-01

    Background Appropriate antimicrobial therapy of community-acquired pneumonia (CAP) is mainly based on the distribution of etiology and antimicrobial resistance of major pathogens.We performed a prospective observational study of adult with CAP in 36 hospitals in China.Methods Etiological pathogens were isolated in each of the centers,and all of the isolated pathogens were sent to Zhongshan Hospital for antimicrobial susceptibility tests using agar dilution.Results A total of 593 patients were enrolled in this study,and 242 strains of bacteria were isolated from 225 patients.Streptococcus pneumoniae (79/242,32.6%) was the most frequently isolated pathogen,followed by Haemophilus influenzae (55/242,22.7%) and Klebsiella pneumoniae (25/242,10.3%).Totally 527 patients underwent serological tests for atypical pathogens; Mycoplasma pneumoniae and Chlamydia pneumoniae infections were identified in 205 (38.9%)and 60 (11.4%) patients respectively.Legionella pneumophila infections were identified in 4.0% (13/324) of patients.The non-susceptibility rate of isolated Streptococcus pneumoniae to erythromycin and penicillin was 63.2% and 19.1%respectively.Six patients died from the disease,the 30-day mortality rate was 1.1% (6/533).Conclusions The top three bacteria responsible for CAP in Chinese adults were Streptococcus pneumonia,Haemophitus influenza and Klebsiella pneumonia.There was also a high prevalence of atypical pathogens and mixed pathogens.The resistance rates of the major isolated pathogens were relatively low except for the high prevalence of macrolide resistance in Streptococcus pneumoniae.

  13. Community-acquired pneumonia: economics of inpatient medical care vis-à-vis clinical severity,

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    Vojislav Cupurdija

    2015-02-01

    Full Text Available Objective: To assess the direct and indirect costs of diagnosing and treating community-acquired pneumonia (CAP, correlating those costs with CAP severity at diagnosis and identifying the major cost drivers. Methods: This was a prospective cost analysis study using bottom-up costing. Clinical severity and mortality risk were assessed with the pneumonia severity index (PSI and the mental Confusion-Urea-Respiratory rate-Blood pressure-age ≥ 65 years (CURB-65 scale, respectively. The sample comprised 95 inpatients hospitalized for newly diagnosed CAP. The analysis was run from a societal perspective with a time horizon of one year. Results: Expressed as mean ± standard deviation, in Euros, the direct and indirect medical costs per CAP patient were 696 ± 531 and 410 ± 283, respectively, the total per-patient cost therefore being 1,106 ± 657. The combined budget impact of our patient cohort, in Euros, was 105,087 (66,109 and 38,979 in direct and indirect costs, respectively. The major cost drivers, in descending order, were the opportunity cost (lost productivity; diagnosis and treatment of comorbidities; and administration of medications, oxygen, and blood derivatives. The CURB-65 and PSI scores both correlated with the indirect costs of CAP treatment. The PSI score correlated positively with the overall frequency of use of health care services. Neither score showed any clear relationship with the direct costs of CAP treatment. Conclusions: Clinical severity at admission appears to be unrelated to the costs of CAP treatment. This is mostly attributable to unwarranted hospital admission (or unnecessarily long hospital stays in cases of mild pneumonia, as well as to over-prescription of antibiotics. Authorities should strive to improve adherence to guidelines and promote cost-effective prescribing practices among physicians in southeastern Europe.

  14. Reading and interpretation of chest X-ray in adults with community-acquired pneumonia

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    Diana Carolina Moncada

    2011-12-01

    Full Text Available INTRODUCTION: Traditional reading of chest X-rays usually has a low prognostic value and poor agreement. OBJECTIVE: This study aimed to determine the interobserver and intraobserver agreement using two reading formats in patients with community-acquired pneumonia, and to explore their association with etiology and clinical outcomes. METHODS: A pulmonologist and a radiologist, who were blind to clinical data, interpreted 211 radiographs using a traditional analysis format (type and location of pulmonary infiltrates and pleural findings, and a quantitative analysis (pulmonary damage categorized from 0 to 10. For both, the interobserver and intraobserver agreement was estimated (Kappa statistic and intraclass correlation coefficient. The latter was assessed in a subsample of 25 radiographs three months after the initial reading. Finally, the observers made a joint reading to explore its prognostic usefulness via multivariate analysis. RESULTS: Seventy-four chest radiographs were discarded due to poor quality. With the traditional reading, the mean interobserver agreement was moderate (0.43. It was considered good when the presence of pleural effusion, and the location of the infiltrates in the right upper lobe and both lower lobes, were evaluated; moderate for multilobar pneumonia; and poor for the type of infiltrates. The mean intraobserver agreement for each reviewer was 0.71 and 0.5 respectively. The quantitative reading had an agreement between good and excellent (interobserver 0.72, intraobserver 0.85 and 0.61. Radiological findings were neither associated to a specific pathogen nor to mortality. CONCLUSION: In patients with pneumonia, the interpretation of the chest X-ray, especially the smallest of details, depends solely on the reader.

  15. DIAGNOSTIC BEHAVIOR OF COMMUNITY-ACQUIRED PNEUMONIA: SURVEY CONDUCTED IN SOME REGIONS OF CHINA

    Institute of Scientific and Technical Information of China (English)

    TANG Wei; DENG Wei-wu

    2006-01-01

    Objective To analyze the spectrum of microbiological agents causing community-acquired pneumonia (CAP) in recent years. We also investigated the procedure of diagnosis as well as the empirical treatment for this disease in OPD (outpatient department) of pulmonary disease. Methods A total of 7097 patients from 150 hospitals in 24 provinces in China were enrolled in the study from Nov. 2002 to Mar. 2003. Every patient was diagnosed, treated and registered at the same time. Diagnostic behavior for doctors include chest radiograph and/or CT examination of the lung, as well as collecting sputum samples at the time of diagnosis for bacteria culture to identify the pathogen. Appointed staff fulfilled the questionnaires and information sheets in each center. After that,data were computerized and analyzed. Results There were 7404 valid information sheets and 7097 questionnaires taken into count. The majority CAP patients were from cities ( 77.3% ), most of those who had medical insurance. Most CAP patients had productive cough (81.1% ), and 76.7% and 18.2% CAP patients received chest film and CT examination respectively for diagnosis. Only 24% patients received sputum sample tested and with 36% got positive results. Streptococcus pneumoniae remained the main pathogen of CAP (43. 2% ). Most doctors used to prescribe β-lactam antibiotics as the first line of empirical therapy of CAP (51.1%) with oral taken as the main method for drug using (66.3% ). Conclusion This survey provides a key point of empirical therapy in China.The procedure for diagnosing as well as the empirical treatment of CAP in OPD of pulmonary disease in China still to be improved, especially in accessing the pathogen. Guidelines developed to recognize and evaluate CAP should base on epidemiological information of the pathogen prevalence, then could offer a rational approach to the initial management of the CAP patients.

  16. The Seropositivity Rate of Atypical Agents in Patients with Community-Acquired Pneumonia

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    Ruhan Karakoc Gunes

    2007-08-01

    Full Text Available The aim of this study was to investigate the IgM antibody positivities of atypical pneumonia agents in patients with community-acquired pneumonia (CAP, and to compare the results with controls. The serum samples which were collected from 87 adult patients and 21 healthy controls have been investigated by a commercial ELISA (Pneumobact ELISA IgM, Vircell, Spain in which four different atypical pneumonia agents were fixed onto a slide. In the patients group, IgM positivity rates for the agents were as follows, respectively; 2.3% for Legionella pneumophila, 56.3% Chlamydia pneumoniae, 33.3% for Mycoplasma pneumoniae, 9.2% for Coxiella burnetii. The rates of IgM positivities in the control group varied 7% for all of the agents except M. Pneumoniae and C. Pneumoniae and 2 of these controls were positive for L. Pneumophila IgM, one was positive for C. Burnetii IgM. According to the statistical evaluation, there were significant differences for IgM seropositivities to Mycoplasma pneumoniae and Chlamydia Pneumoniae,between the patient and the control groups (p0.05. We showed that the seropositivity rate of atypical agents in patients with CAP was significantly higher when compared to healthy control group. This result suggests us, atypical agents might be responsible in CAP patients in a great amount. Furthermore, our study also suggests that clinical and radiological findings are not useful for discriminating atypical from typical pneumonia. [TAF Prev Med Bull 2007; 6(4.000: 279-284

  17. Pneumonia acquired in the Community Neumonía adquirida en la comunidad

    Directory of Open Access Journals (Sweden)

    Dianelis Sierra Martínez

    Full Text Available A bibliographical revision of the main aspects in the diagnosis and treatment of the patients suffering from pneumonia acquired in the community is carried out. Microorganisms responsible for this type of pneumonia are mention in this paper as well as the available diagnostic methods for germs isolation. Different guidelines for diagnosis and treatment of this disease published by several medical societies and scientific institutions are analyzed by means of a review of the stratification index of the patients used in each of them. Aspects related to the duration of the treatment and the possible causes associated with the unfavorable evolution are stated.
    Se realizó una revisión bibliográfica de los aspectos fundamentales en el diagnóstico y tratamiento de los pacientes con neumonía adquirida en la comunidad. Se hace referencia a los microorganismos responsables de las neumonías, así como a los métodos diagnósticos disponibles para el aislamiento de los gérmenes. Se analizan las diferentes Guías de Diagnóstico y Tratamiento de la enfermedad, emitidas por varias sociedades e instituciones científicas, mediante una revisión de los índices para la estratificación de los pacientes, utilizados por cada una de ellas. Además, se abordan aspectos relacionados con la duración del tratamiento y las posibles causas relacionadas con su evolución desfavorable.

  18. A Greenhouse Assay on the Effect of Applied Urea Amount on the Rhizospheric Soil Bacterial Communities.

    Science.gov (United States)

    Shang, Shuanghua; Yi, Yanli

    2015-12-01

    The rhizospheric bacteria play key role in plant nutrition and growth promotion. The effects of increased nitrogen inputs on plant rhizospheric soils also have impacted on whole soil microbial communities. In this study, we analyzed the effects of applied nitrogen (urea) on rhizospheric bacterial composition and diversity in a greenhouse assay using the high-throughput sequencing technique. To explore the environmental factors driving the abundance, diversity and composition of soil bacterial communities, the relationship between soil variables and the bacterial communities were also analyzed using the mantel test as well as the redundancy analysis. The results revealed significant bacterial diversity changes at different amounts of applied urea, especially between the control treatment and the N fertilized treatments. Mantel tests showed that the bacterial communities were significantly correlated with the soil nitrate nitrogen, available nitrogen, soil pH, ammonium nitrogen and total organic carbon. The present study deepened the understanding about the rhizospheric soil microbial communities under different amounts of applied urea in greenhouse conditions, and our work revealed the environmental factors affecting the abundance, diversity and composition of rhizospheric bacterial communities.

  19. Bacterial community composition of a wastewater treatment system reliant on N{sub 2} fixation

    Energy Technology Data Exchange (ETDEWEB)

    Reid, N.M.; Bowers, T.H.; Lloyd-Jones, G. [Scion, Rotorua (New Zealand)

    2008-05-15

    The temporal stability and change of the dominant phylogenetic groups of the domain bacteria were studied in a model plant-based industrial wastewater treatment system showing high levels of organic carbon removal supported by high levels of N{sub 2} fixation. Community profiles were obtained through terminal restriction fragment length polymorphism analysis and cloning of 16S rRNA amplicons followed by sequencing. Bacterial community profiles showed that ten common terminal restriction fragments made up approximately 50% of the measured bacterial community. As much as 42% of the measured bacterial community could be monitored by using quantitative PCR and primers that targeted three dominant operational taxonomic units. Despite changes in wastewater composition and dissolved oxygen levels, the bacterial community composition appeared stable and was dominated by {alpha}-Proteobacteria and {beta}-Proteobacteria, with a lesser amount of the highly diverse bacterial phylum Bacteroidetes. A short period of considerable change in the bacterial community composition did not appear to affect treatment performance indicating functional redundancy in this treatment system. (orig.)

  20. Bacterial community structure and diversity in a black soil as affected by long-term fertilization

    Institute of Scientific and Technical Information of China (English)

    WEI Dan; YANG Qian; ZHANG Jun-Zheng; WANG Shuang; CHEN Xue-Li; ZHANG Xi-Lin; LI Wei-Qun

    2008-01-01

    Black soil (Mollisol) is one of the main soil types in northeastern China.Biolog and polymerase chain reactiondenaturing gradient gel electrophoresis (PCR-DGGE) methods were used to examine the influence of various fertilizer combinations on the structure and function of the bacterial community in a black soil collected from Harbin,Heilongjiang Province.Biolog results showed that substrate richness and catabolic diversity of the soil bacterial community were the greatest in the chemical fertilizer and chemical fertilizer+manure treatments.The metabolic ability of the bacterial community in the manure treatment was similar to the control.DGGE fingerprinting indicated similarity in the distribution of most 16S rDNA bands among all treatments,suggesting that microorganisms with those bands were stable and not influenced by fertilization.However,chemical fertilizer increased the diversity of soil bacterial community.Principal component analysis of Biolog and DGGE data revealed that the structure and function of the bacterial community were similar in the control and manure treatments,suggesting that the application of manure increased the soil microbial population,but had no effect on the bacterial community structure.Catabolic function was similar in the chemical fertilizer and chemical fertilizer+manure treatments,but the composition structure of the soil microbes differed between them.The use of chemical fertilizers could result in a decline in the catabolic activity of fast-growing or eutrophic bacteria.

  1. Deterministic assembly processes govern bacterial community structure in the Fynbos, South Africa.

    Science.gov (United States)

    Moroenyane, I; Chimphango, S B M; Wang, J; Kim, H-K; Adams, Jonathan Miles

    2016-08-01

    The Mediterranean Fynbos vegetation of South Africa is well known for its high levels of diversity, endemism, and the existence of very distinct plant communities on different soil types. Studies have documented the broad taxonomic classification and diversity patterns of soil microbial diversity, but none has focused on the community assembly processes. We hypothesised that bacterial phylogenetic community structure in the Fynbos is highly governed by deterministic processes. We sampled soils in four Fynbos vegetation types and examined bacterial communities using Illumina HiSeq platform with the 16S rRNA gene marker. UniFrac analysis showed that the community clustered strongly by vegetation type, suggesting a history of evolutionary specialisation in relation to habitats or plant communities. The standardised beta mean nearest taxon distance (ses. β NTD) index showed no association with vegetation type. However, the overall phylogenetic signal indicates that distantly related OTUs do tend to co-occur. Both NTI (nearest taxon index) and ses. β NTD deviated significantly from null models, indicating that deterministic processes were important in the assembly of bacterial communities. Furthermore, ses. β NTD was significantly higher than that of null expectations, indicating that co-occurrence of related bacterial lineages (over-dispersion in phylogenetic beta diversity) is determined by the differences in environmental conditions among the sites, even though the co-occurrence pattern did not correlate with any measured environmental parameter, except for a weak correlation with soil texture. We suggest that in the Fynbos, there are frequent shifts of niches by bacterial lineages, which then become constrained and evolutionary conserved in their new environments. Overall, this study sheds light on the relative roles of both deterministic and neutral processes in governing bacterial communities in the Fynbos. It seems that deterministic processes play a major

  2. Deterministic assembly processes govern bacterial community structure in the Fynbos, South Africa.

    Science.gov (United States)

    Moroenyane, I; Chimphango, S B M; Wang, J; Kim, H-K; Adams, Jonathan Miles

    2016-08-01

    The Mediterranean Fynbos vegetation of South Africa is well known for its high levels of diversity, endemism, and the existence of very distinct plant communities on different soil types. Studies have documented the broad taxonomic classification and diversity patterns of soil microbial diversity, but none has focused on the community assembly processes. We hypothesised that bacterial phylogenetic community structure in the Fynbos is highly governed by deterministic processes. We sampled soils in four Fynbos vegetation types and examined bacterial communities using Illumina HiSeq platform with the 16S rRNA gene marker. UniFrac analysis showed that the community clustered strongly by vegetation type, suggesting a history of evolutionary specialisation in relation to habitats or plant communities. The standardised beta mean nearest taxon distance (ses. β NTD) index showed no association with vegetation type. However, the overall phylogenetic signal indicates that distantly related OTUs do tend to co-occur. Both NTI (nearest taxon index) and ses. β NTD deviated significantly from null models, indicating that deterministic processes were important in the assembly of bacterial communities. Furthermore, ses. β NTD was significantly higher than that of null expectations, indicating that co-occurrence of related bacterial lineages (over-dispersion in phylogenetic beta diversity) is determined by the differences in environmental conditions among the sites, even though the co-occurrence pattern did not correlate with any measured environmental parameter, except for a weak correlation with soil texture. We suggest that in the Fynbos, there are frequent shifts of niches by bacterial lineages, which then become constrained and evolutionary conserved in their new environments. Overall, this study sheds light on the relative roles of both deterministic and neutral processes in governing bacterial communities in the Fynbos. It seems that deterministic processes play a major

  3. Acute Renal Failure in Association with Community-Acquired Clostridium difficile Infection and McKittrick-Wheelock Syndrome

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    Robert M. Learney

    2011-08-01

    Full Text Available We report the case of a 65-year-old Caucasian woman who experienced two separate episodes of acute renal failure within an 18-month period, both requiring emergency admission and complicated treatment. Each episode was precipitated by hypovolaemia from intestinal fluid losses, but from two rare and independent pathologies. Her first admission was attributed to community-acquired Clostridium difficile-associated diarrhoea (CDAD and was treated in the intensive therapy unit. She returned 18 months later with volume depletion and electrolyte disturbances, but on this occasion a giant hypersecretory villous adenoma of the rectum (McKittrick-Wheelock syndrome was diagnosed following initial abnormal findings on digital rectal examination by a junior physician. Unlike hospital-acquired C. difficile, community-acquired infection is not common, although increasing numbers are being reported. Whilst community-acquired CDAD can be severe, it rarely causes acute renal failure. This case report highlights the pathological mechanisms whereby C. difficile toxin and hypersecretory villous adenoma of the rectum can predispose to acute renal failure, as well as the values of thorough clinical examination in the emergency room, and early communication with intensivist colleagues in dire situations.

  4. The impact of shrimp farming effluent on bacterial communities in mangrove waters, Ceará, Brazil.

    Science.gov (United States)

    Sousa, O V; Macrae, A; Menezes, F G R; Gomes, N C M; Vieira, R H S F; Mendonça-Hagler, L C S

    2006-12-01

    The effects of shrimp farm effluents on bacterial communities in mangroves have been infrequently reported. Classic and molecular biology methods were used to survey bacterial communities from four mangroves systems. Water temperature, salinity, pH, total heterotrophic bacteria and maximum probable numbers of Vibrio spp. were investigated. Genetic profiles of bacterial communities were also characterized by polymerase chain reaction (PCR) amplification of eubacterial and Vibrio 16S rDNA using denaturing gradient gel electrophoresis (DGGE). Highest heterotrophic counts were registered in the mangrove not directly polluted by shrimp farming. The Enterobacteriaceae and Chryseomonas luteola dominated the heterotrophic isolates. Vibrio spp. pathogenic to humans and shrimps were identified. Eubacterial genetic profiles suggest a shared community structure independent of mangrove system. Vibrio genetic profiles were mangrove specific. Neither microbial counts nor genetic profiling revealed a significant decrease in species richness associated with shrimp farm effluent. The complex nature of mangrove ecosystems and their microbial communities is discussed.

  5. Inter- and Intraspecific Variations of Bacterial Communities Associated with Marine Sponges from San Juan Island, Washington

    KAUST Repository

    Lee, O. O.

    2009-04-10

    This study attempted to assess whether conspecific or congeneric sponges around San Juan Island, Washington, harbor specific bacterial communities. We used a combination of culture-independent DNA fingerprinting techniques (terminal restriction fragment length polymorphism and denaturing gradient gel electrophoresis [DGGE]) and culture-dependent approaches. The results indicated that the bacterial communities in the water column consisted of more diverse bacterial ribotypes than and were drastically different from those associated with the sponges. High levels of similarity in sponge-associated bacterial communities were found only in Myxilla incrustans and Haliclona rufescens, while the bacterial communities in Halichondria panicea varied substantially among sites. Certain terminal restriction fragments or DGGE bands were consistently obtained for different individuals of M. incrustans and H. rufescens collected from different sites, suggesting that there are stable or even specific associations of certain bacteria in these two sponges. However, no specific bacterial associations were found for H. panicea or for any one sponge genus. Sequencing of nine DGGE bands resulted in recovery of seven sequences that best matched the sequences of uncultured Proteobacteria. Three of these sequences fell into the sponge-specific sequence clusters previously suggested. An uncultured alphaproteobacterium and a culturable Bacillus sp. were found exclusively in all M. incrustans sponges, while an uncultured gammaproteobacterium was unique to H. rufescens. In contrast, the cultivation approach indicated that sponges contained a large proportion of Firmicutes, especially Bacillus, and revealed large variations in the culturable bacterial communities associated with congeneric and conspecific sponges. This study revealed sponge species-specific but not genus- or site-specific associations between sponges and bacterial communities and emphasized the importance of using a combination

  6. Nitrogen deposition alters soil chemical properties and bacterial communities in the Inner Mongolia grassland

    Institute of Scientific and Technical Information of China (English)

    Ximei Zhang; Xingguo Han

    2012-01-01

    Nitrogen deposition has dramatically altered biodiversity and ecosystem functioning on the earth; however,its effects on soil bacterial community and the underlying mechanisms of these effects have not been thoroughly examined.Changes in ecosystems caused by nitrogen deposition have traditionally been attributed to increased nitrogen content.In fact,nitrogen deposition not only leads to increased soil total N content,but also changes in the NH4+-N content,NO3--N content and pH,as well as changes in the heterogeneity of the four indexes.The soil indexes for these four factors,their heterogeneity and even the plant community might be routes through which nitrogen deposition alters the bacterial community.Here,we describe a 6-year nitrogen addition experiment conducted in a typical steppe ecosystem to investigate the ecological mechanism by which nitrogen deposition alters bacterial abundance,diversity and composition.We found that various characteristics of the bacterial community were explained by different environmental factors.Nitrogen deposition decreased bacterial abundance that is positively related to soil pH value.In addition,nitrogen addition decreased bacterial diversity,which is negatively related to soil total N content and positively related to soil NO3--N heterogeneity.Finally,nitrogen.addition altered bacterial composition that is significantly related to soil NH4+-N content.Although nitrogen deposition significantly altered plant biomass,diversity and composition,these characteristics of plant community did not have a significant impact on processes of nitrogen deposition that led to alterations in bacterial abundance,diversity and composition.Therefore,more sensitive molecular technologies should be adopted to detect the subtle shifts of microbial community structure induced by the changes of plant community upon nitrogen deposition.

  7. Airborne bacterial communities in residences: similarities and differences with fungi.

    Directory of Open Access Journals (Sweden)

    Rachel I Adams

    Full Text Available Genetic analysis of indoor air has uncovered a rich microbial presence, but rarely have both the bacterial and fungal components been examined in the same samples. Here we present a study that examined the bacterial component of passively settled microbes from both indoor and outdoor air over a discrete time period and for which the fungal component has already been reported. Dust was allowed to passively settle in five common locations around a home - living room, bedroom, bathroom, kitchen, and balcony - at different dwellings within a university-housing complex for a one-month period at two time points, once in summer and again in winter. We amplified the bacterial 16S rRNA gene in these samples and analyzed them with high-throughput sequencing. Like fungal OTU-richness, bacterial OTU-richness was higher outdoors then indoors and was invariant across different indoor room types. While fungal composition was structured largely by season and residential unit, bacterial composition varied by residential unit and room type. Bacteria from putative outdoor sources, such as Sphingomonas and Deinococcus, comprised a large percentage of the balcony samples, while human-associated taxa comprised a large percentage of the indoor samples. Abundant outdoor bacterial taxa were also observed indoors, but the reverse was not true; this is unlike fungi, in which the taxa abundant indoors were also well-represented outdoors. Moreover, there was a partial association of bacterial composition and geographic distance, such that samples separated by even a few hundred meters tended have greater compositional differences than samples closer together in space, a pattern also observed for fungi. These data show that while the outdoor source for indoor bacteria and fungi varies in both space and time, humans provide a strong and homogenizing effect on indoor bacterial bioaerosols, a pattern not observed in fungi.

  8. Soil bacterial communities respond to mowing and nutrient addition in a steppe ecosystem.

    Science.gov (United States)

    Zhang, Ximei; Chen, Quansheng; Han, Xingguo

    2013-01-01

    In many grassland ecosystems, nitrogen (N) and phosphorus (P) are added to improve plant productivity, and the aboveground plant biomass is mowed and stored as hay for the bullamacow. Nutrient addition and mowing affect the biodiversity and ecosystem functioning, and most of the previous studies have primarily focused on their effects on macro-organisms, neglecting the responses of soil microbial communities. In this study, we examined the changes in three community attributes (abundance, richness, and composition) of the entire bacterial kingdom and 16 dominant bacterial phyla/classes in response to mowing, N addition, P addition, and their combinations, by conducting a 5-year experiment in a steppe ecosystem in Inner Mongolia, China. Overall, N addition had a greater effect than mowing and P addition on most of these bacterial groups, as indicated by changes in the abundance, richness and composition in response to these treatments. N addition affected these soil bacterial groups primarily through reducing soil pH and increasing available N content. Meanwhile, the 16 bacterial phyla/classes responded differentially to these experimental treatments, with Acidobacteria, Acidimicrobidae, Deltaproteobacteria, and Gammaproteobacteria being the most sensitive. The changes in the abundance, richness, and composition of various bacterial groups could imply some potential shift in their ecosystem functions. Furthermore, the important role of decreased soil pH caused by N addition in affecting soil bacterial communities suggests the importance of restoring acidified soil to maintain soil bacterial diversity. PMID:24391915

  9. Bacterial communities in Malagasy soils with differing levels of disturbance affecting botanical diversity.

    Science.gov (United States)

    Blasiak, Leah C; Schmidt, Alex W; Andriamiarinoro, Honoré; Mulaw, Temesgen; Rasolomampianina, Rado; Applequist, Wendy L; Birkinshaw, Chris; Rejo-Fienena, Félicitée; Lowry, Porter P; Schmidt, Thomas M; Hill, Russell T

    2014-01-01

    Madagascar is well-known for the exceptional biodiversity of its macro-flora and fauna, but the biodiversity of Malagasy microbial communities remains relatively unexplored. Understanding patterns of bacterial diversity in soil and their correlations with above-ground botanical diversity could influence conservation planning as well as sampling strategies to maximize access to bacterially derived natural products. We present the first detailed description of Malagasy soil bacterial communities from a targeted 16S rRNA gene survey of greater than 290,000 sequences generated using 454 pyrosequencing. Two sampling plots in each of three forest conservation areas were established to represent different levels of disturbance resulting from human impact through agriculture and selective exploitation of trees, as well as from natural impacts of cyclones. In parallel, we performed an in-depth characterization of the total vascular plant morphospecies richness within each plot. The plots representing different levels of disturbance within each forest did not differ significantly in bacterial diversity or richness. Changes in bacterial community composition were largest between forests rather than between different levels of impact within a forest. The largest difference in bacterial community composition with disturbance was observed at the Vohibe forest conservation area, and this difference was correlated with changes in both vascular plant richness and soil pH. These results provide the first survey of Malagasy soil bacterial diversity and establish a baseline of botanical diversity within important conservation areas.

  10. Bacterial community structure and function shift across a northern boreal forest fire chronosequence

    Science.gov (United States)

    Sun, Hui; Santalahti, Minna; Pumpanen, Jukka; Köster, Kajar; Berninger, Frank; Raffaello, Tommaso; Asiegbu, Fred O.; Heinonsalo, Jussi

    2016-01-01

    Soil microbial responses to fire are likely to change over the course of forest recovery. Investigations on long-term changes in bacterial dynamics following fire are rare. We characterized the soil bacterial communities across three different times post fire in a 2 to 152-year fire chronosequence by Illumina MiSeq sequencing, coupled with a functional gene array (GeoChip). The results showed that the bacterial diversity did not differ between the recently and older burned areas, suggesting a concomitant recovery in the bacterial diversity after fire. The differences in bacterial communities over time were mainly driven by the rare operational taxonomic units (OTUs analysis using gene signal intensity revealed that the sites with different fire histories formed separate clusters, suggesting potential differences in maintaining essential biogeochemical soil processes. Soil temperature, pH and water contents were the most important factors in shaping the bacterial community structures and function. This study provides functional insight on the impact of fire disturbance on soil bacterial community. PMID:27573440

  11. Regulation of bacterial communities through antimicrobial activity by the coral holobiont.

    Science.gov (United States)

    Kvennefors, E Charlotte E; Sampayo, Eugenia; Kerr, Caroline; Vieira, Genyess; Roff, George; Barnes, Andrew C

    2012-04-01

    Interactions between corals and associated bacteria and amongst these bacterial groups are likely to play a key role in coral health. However, the complexity of these interactions is poorly understood. We investigated the functional role of specific coral-associated bacteria in maintaining microbial communities on the coral Acropora millepora (Ehrenberg 1834) and the ability of coral mucus to support or inhibit bacterial growth. Culture-independent techniques were used to assess bacterial community structures whilst bacterial culture was employed to assess intra- and inter-specific antimicrobial activities of bacteria. Members of Pseudoalteromonas and ribotypes closely related to Vibrio coralliilyticus displayed potent antimicrobial activity against a range of other cultured isolates and grew readily on detached coral mucus. Although such bacterial ribotypes would be expected to have a competitive advantage, they were rare or absent on intact and healthy coral colonies growing in situ (analysed using denaturing gradient gel electrophoresis and 16S rRNA gene sequencing). The most abundant bacterial ribotypes found on healthy corals were Gammaproteobacteria, previously defined as type A coral associates. Our results indicate that this group of bacteria and specific members of the Alphaproteobacteria described here as 'type B associates' may be important functional groups for coral health. We suggest that bacterial communities on coral are kept in check by a combination of host-derived and microbial interactions and that the type A associates in particular may play a key role in maintaining stability of microbial communities on healthy coral colonies. PMID:21984347

  12. Bacterial communities in Malagasy soils with differing levels of disturbance affecting botanical diversity.

    Science.gov (United States)

    Blasiak, Leah C; Schmidt, Alex W; Andriamiarinoro, Honoré; Mulaw, Temesgen; Rasolomampianina, Rado; Applequist, Wendy L; Birkinshaw, Chris; Rejo-Fienena, Félicitée; Lowry, Porter P; Schmidt, Thomas M; Hill, Russell T

    2014-01-01

    Madagascar is well-known for the exceptional biodiversity of its macro-flora and fauna, but the biodiversity of Malagasy microbial communities remains relatively unexplored. Understanding patterns of bacterial diversity in soil and their correlations with above-ground botanical diversity could influence conservation planning as well as sampling strategies to maximize access to bacterially derived natural products. We present the first detailed description of Malagasy soil bacterial communities from a targeted 16S rRNA gene survey of greater than 290,000 sequences generated using 454 pyrosequencing. Two sampling plots in each of three forest conservation areas were established to represent different levels of disturbance resulting from human impact through agriculture and selective exploitation of trees, as well as from natural impacts of cyclones. In parallel, we performed an in-depth characterization of the total vascular plant morphospecies richness within each plot. The plots representing different levels of disturbance within each forest did not differ significantly in bacterial diversity or richness. Changes in bacterial community composition were largest between forests rather than between different levels of impact within a forest. The largest difference in bacterial community composition with disturbance was observed at the Vohibe forest conservation area, and this difference was correlated with changes in both vascular plant richness and soil pH. These results provide the first survey of Malagasy soil bacterial diversity and establish a baseline of botanical diversity within important conservation areas. PMID:24465484

  13. Bacterial communities in Malagasy soils with differing levels of disturbance affecting botanical diversity.

    Directory of Open Access Journals (Sweden)

    Leah C Blasiak

    Full Text Available Madagascar is well-known for the exceptional biodiversity of its macro-flora and fauna, but the biodiversity of Malagasy microbial communities remains relatively unexplored. Understanding patterns of bacterial diversity in soil and their correlations with above-ground botanical diversity could influence conservation planning as well as sampling strategies to maximize access to bacterially derived natural products. We present the first detailed description of Malagasy soil bacterial communities from a targeted 16S rRNA gene survey of greater than 290,000 sequences generated using 454 pyrosequencing. Two sampling plots in each of three forest conservation areas were established to represent different levels of disturbance resulting from human impact through agriculture and selective exploitation of trees, as well as from natural impacts of cyclones. In parallel, we performed an in-depth characterization of the total vascular plant morphospecies richness within each plot. The plots representing different levels of disturbance within each forest did not differ significantly in bacterial diversity or richness. Changes in bacterial community composition were largest between forests rather than between different levels of impact within a forest. The largest difference in bacterial community composition with disturbance was observed at the Vohibe forest conservation area, and this difference was correlated with changes in both vascular plant richness and soil pH. These results provide the first survey of Malagasy soil bacterial diversity and establish a baseline of botanical diversity within important conservation areas.

  14. Phylogenetic analysis of bacterial community in deep-sea sediment from the western Pacific "warm pool"

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    A depth profile of bacterial community structure in one deep-sea sediment core of the western Pacific "warm pool" (WP) was investigated and compared with that in a sediment sample from the eastern Pacific (EP) by phylogenetic analysis of 16S rDNA fragments.Five bacterial 16S rDNA clone libraries were constructed, and t33 clones with different restriction fragment length polymorphism(RFLP) patterns were sequenced. A phylogenetic analysis of these sequences revealed that the bacterial diversity in a sample from the WP was more abundant than that in the EP sample. The bacterial population in the sediment core of WP was composed of eight major lineages of the domain bacteria. Among them the γ-Proteobacteria was the predominant and most diverse group in each section of WP sediment core, followed by the α-Proteobacteria. The genus Colwellia belonging to γ-Proteobacteria was predominant in this sample.The shift of bacterial communities among different sections of the WP sediment core was δ-, ε-Proteobacteria, and Cytopahga-Flexibacteria-Bacteroides (CFB) group. The ratios between them in the bacterial communities all showed inversely proportional to the depth of sediment. The sequences related to sulphate reducing bacteria (SRB) were detected in every section. The bacterial community structure in this sediment core might be related to the environmental characteristics of the surface seawater of the western Pacific WP.

  15. Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes

    Directory of Open Access Journals (Sweden)

    J. Comte

    2015-07-01

    Full Text Available Permafrost thaw ponds and lakes are widespread across the northern landscape and may play a central role in global biogeochemical cycles, yet knowledge about their microbial ecology is limited. We sampled a set of thaw ponds and lakes as well as shallow rock-basin lakes that are located in distinct valleys along a North–South permafrost degradation gradient. We applied high-throughput sequencing of the 16S rRNA gene to determine co-occurrence patterns among bacterial taxa, and then analyzed these results relative to environmental variables to identify factors controlling bacterial community structure. Network analysis was applied to identify possible ecological linkages among the bacterial taxa and with abiotic and biotic variables. The results showed an overall high level of shared taxa among bacterial communities within each valley, however the bacterial co-occurrence patterns were non-random, with evidence of habitat preferences. There were taxonomic differences in bacterial assemblages among the different valleys that were statistically related to dissolved organic carbon concentration, conductivity and phytoplankton biomass. Co-occurrence networks revealed complex interdependencies within the bacterioplankton communities and showed contrasting linkages to environmental conditions among the main bacterial phyla. The thaw pond networks were composed of a limited number of highly connected taxa. This "small world network" property would render the communities more robust to environmental change but vulnerable to the loss of microbial keystone species.

  16. Bacterial community structure and function shift across a northern boreal forest fire chronosequence.

    Science.gov (United States)

    Sun, Hui; Santalahti, Minna; Pumpanen, Jukka; Köster, Kajar; Berninger, Frank; Raffaello, Tommaso; Asiegbu, Fred O; Heinonsalo, Jussi

    2016-01-01

    Soil microbial responses to fire are likely to change over the course of forest recovery. Investigations on long-term changes in bacterial dynamics following fire are rare. We characterized the soil bacterial communities across three different times post fire in a 2 to 152-year fire chronosequence by Illumina MiSeq sequencing, coupled with a functional gene array (GeoChip). The results showed that the bacterial diversity did not differ between the recently and older burned areas, suggesting a concomitant recovery in the bacterial diversity after fire. The differences in bacterial communities over time were mainly driven by the rare operational taxonomic units (OTUs cycling pathways were present in all sites showing high redundancy in the gene profiles. However, hierarchical cluster analysis using gene signal intensity revealed that the sites with different fire histories formed separate clusters, suggesting potential differences in maintaining essential biogeochemical soil processes. Soil temperature, pH and water contents were the most important factors in shaping the bacterial community structures and function. This study provides functional insight on the impact of fire disturbance on soil bacterial community. PMID:27573440

  17. Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Natacha Bodenhausen

    Full Text Available Diverse communities of bacteria inhabit plant leaves and roots and those bacteria play a crucial role for plant health and growth. Arabidopsis thaliana is an important model to study plant pathogen interactions, but little is known about its associated bacterial community under natural conditions. We used 454 pyrosequencing to characterize the bacterial communities associated with the roots and the leaves of wild A. thaliana collected at 4 sites; we further compared communities on the outside of the plants with communities in the endophytic compartments. We found that the most heavily sequenced bacteria in A. thaliana associated community are related to culturable species. Proteobacteria, Actinobacteria, and Bacteroidetes are the most abundant phyla in both leaf and root samples. At the genus level, sequences of Massilia and Flavobacterium are prevalent in both samples. Organ (leaf vs root and habitat (epiphytes vs endophytes structure the community. In the roots, richness is higher in the epiphytic communities compared to the endophytic compartment (P = 0.024, while the reverse is true for the leaves (P = 0.032. Interestingly, leaf and root endophytic compartments do not differ in richness, diversity and evenness, while they differ in community composition (P = 0.001. The results show that although the communities associated with leaves and roots share many bacterial species, the associated communities differ in structure.

  18. Differentiation of tuberculous pneumonia and community-acquired pneumonia; usefulness of chest radiography and serum CA-125

    International Nuclear Information System (INIS)

    To determine whether tuberculous pneumonia can be distinguished from community-acquired pneumonia on the basis of chest radiographic findings only and the diagnostic utility of differences in serum CA-125 levels. Forty-five patients with a high fever (>38 .deg. C) in whom chest radiography revealed lobar consolidation were retrospectively studied. In 27 cases, the presence of acid-fast bacilli in sputum (n=21), the isolation of Mycobacterium tuberculosis from bronchoscopic biopsy tissue and sputum cultures (n=16), and improvement in the findings of serial radiography and in clinical symptoms during antituberculous therapy (n=1) let to a diagnosis of tuberculous pneumonia. A diagnosis of community-acquired pneumonia (n=18) was based on improvement in the serial radiographic findings obtained during antibacterial therapy (n=16), and the isolation of bacteria from sputum and pleural fluid culture (n=2). On the basis of independently analysed findings, radiologist determined the presence or absence of nodular density, cavitary lesions and loss of lung volume, while two radiologists differentiated between tuberculous pneumonia and community-acquired pneumonia. Initial chest radiographs of tuberculous pneumonia revealed nodular density in 89% of cases, cavitary lesions in 29%, and loss of lung volume nodular density was in 26%, while those of community-acquired pneumonia demonstrated nodular density in only 22%, cavitary lesions in 6%, and loss of lung volume in none was a significant statistical difference in nodular density, cavitary lesions and loss of lung volume (p < 0.005). The average serum CA-125 level in tuberculous pneumonia was 306.5 (range, 21.3-1078) U/ml, whereas the average level in community-acquired pneumonia was 38.0 (range, 11.3-114.8) U/ml (p < 0.005). Initial chest radiography can differentiate between tuberculous and community-acquired pneumonia on the basis of nodular density, cavitary lesions and loss of lung volume and differences in CA-125

  19. Differentiation of tuberculous pneumonia and community-acquired pneumonia; usefulness of chest radiography and serum CA-125

    Energy Technology Data Exchange (ETDEWEB)

    Park, Dong Man; Kim, Jeong Sook; Kim, Young Hwan; Kim, Su Young; Hur, Gham; Choi, Soo Jeon [Inje Univ. College of Medicine, Pusan (Korea, Republic of)

    2000-11-01

    To determine whether tuberculous pneumonia can be distinguished from community-acquired pneumonia on the basis of chest radiographic findings only and the diagnostic utility of differences in serum CA-125 levels. Forty-five patients with a high fever (>38 .deg. C) in whom chest radiography revealed lobar consolidation were retrospectively studied. In 27 cases, the presence of acid-fast bacilli in sputum (n=21), the isolation of Mycobacterium tuberculosis from bronchoscopic biopsy tissue and sputum cultures (n=16), and improvement in the findings of serial radiography and in clinical symptoms during antituberculous therapy (n=1) let to a diagnosis of tuberculous pneumonia. A diagnosis of community-acquired pneumonia (n=18) was based on improvement in the serial radiographic findings obtained during antibacterial therapy (n=16), and the isolation of bacteria from sputum and pleural fluid culture (n=2). On the basis of independently analysed findings, radiologist determined the presence or absence of nodular density, cavitary lesions and loss of lung volume, while two radiologists differentiated between tuberculous pneumonia and community-acquired pneumonia. Initial chest radiographs of tuberculous pneumonia revealed nodular density in 89% of cases, cavitary lesions in 29%, and loss of lung volume nodular density was in 26%, while those of community-acquired pneumonia demonstrated nodular density in only 22%, cavitary lesions in 6%, and loss of lung volume in none was a significant statistical difference in nodular density, cavitary lesions and loss of lung volume (p < 0.005). The average serum CA-125 level in tuberculous pneumonia was 306.5 (range, 21.3-1078) U/ml, whereas the average level in community-acquired pneumonia was 38.0 (range, 11.3-114.8) U/ml (p < 0.005). Initial chest radiography can differentiate between tuberculous and community-acquired pneumonia on the basis of nodular density, cavitary lesions and loss of lung volume and differences in CA-125

  20. Bacterial community in sclerotia of Cenococcum species and soil in sub-alpine forest, central Japan

    Science.gov (United States)

    Nonoyama, Y.; Narisawa, K.; Ohta, H.; Watanabe, M.

    2009-04-01

    Species of Cenococcum, ectomycorrhizal fungi, may be particularly abundant in cold- or nutrient-stressed habitats. The fungus is easily recognized by its jet-black hyphae, and distinct compact masses of fungal mycelium called sclerotia. They are hard, black, comparatively smooth and mostly spherical. Sclerotia are formed in rhizosphere and can provide sufficient inoculums for several years. The purpose of this study is to investigate bacterial community inside sclerotia, with an interest on contribution of sclerotia to microbial diversity in rhizosphere. To investigate bacterial community inside of the fungal sclerotia by 16S rDNA gene clone library, several hundred of sclerotia (ca. 1g) were collected from sub-alpine forest soil in central Japan. Furthermore, three sclerotium grains were applied to investigate internal bacteria community by culture method. The isolated bacterial strains were then proceeded to determine their 16S rDNA partial sequences. The predominant group determined by clone library analysis of 16S ribosomal RNA genes with DNA from the sclerotia was Acidobacteria in both sclerotia and soil. Bacterial community of sclerotia showed higher diversity compared to soil. On the contrary, bacterial flora isolated from single sclerotium differed each other. Additionally, the bacterial community was composed by limited species of related genus.

  1. Bacterial communities associated with the ctenophores Mnemiopsis leidyi and Beroe ovata.

    Science.gov (United States)

    Daniels, Camille; Breitbart, Mya

    2012-10-01

    Residing in a phylum of their own, ctenophores are gelatinous zooplankton that drift through the ocean's water column. Although ctenophores are known to be parasitized by a variety of eukaryotes, no studies have examined their bacterial associates. This study describes the bacterial communities associated with the lobate ctenophore Mnemiopsis leidyi and its natural predator Beroe ovata in Tampa Bay, Florida, USA. Investigations using terminal restriction fragment length polymorphism (T-RFLP) and cloning and sequencing of 16S rRNA genes demonstrated that ctenophore bacterial communities were distinct from the surrounding water. In addition, each ctenophore genus contained a unique microbiota. Ctenophore samples contained fewer bacterial operational taxonomic units (OTUs) by T-RFLP and lower diversity communities by 16S rRNA gene sequencing than the water column. Both ctenophore genera contained sequences related to bacteria previously described in marine invertebrates, and sequences similar to a sea anemone pathogen were abundant in B. ovata. Temporal sampling revealed that the ctenophore-associated bacterial communities varied over time, with no single OTU detected at all time points. This is the first report of distinct and dynamic bacterial communities associated with ctenophores, suggesting that these microbial consortia may play important roles in ctenophore ecology. Future work needs to elucidate the functional roles and mode of acquisition of these bacteria. PMID:22571334

  2. Molecular assessment of bacterial community dynamics and functional endpoints during sediment bioaccumulation test

    NARCIS (Netherlands)

    Diepens, N.J.; Dimitrov, M.R.; Koelmans, A.A.; Smidt, H.

    2015-01-01

    Whole sediment toxicity tests play an important role in environmental risk assessment of organic chemicals. It is not clear, however, to what extent changing microbial community composition and associated functions affect sediment test results. We assessed the development of bacterial communities in

  3. Racial variations in processes of care for patients with community-acquired pneumonia

    Directory of Open Access Journals (Sweden)

    Whittle Jeff

    2004-08-01

    Full Text Available Abstract Background Patients hospitalized with community acquired pneumonia (CAP have a substantial risk of death, but there is evidence that adherence to certain processes of care, including antibiotic administration within 8 hours, can decrease this risk. Although national mortality data shows blacks have a substantially increased odds of death due to pneumonia as compared to whites previous studies of short-term mortality have found decreased mortality for blacks. Therefore we examined pneumonia-related processes of care and short-term mortality in a population of patients hospitalized with CAP. Methods We reviewed the records of all identified Medicare beneficiaries hospitalized for pneumonia between 10/1/1998 and 9/30/1999 at one of 101 Pennsylvania hospitals, and randomly selected 60 patients at each hospital for inclusion. We reviewed the medical records to gather process measures of quality, pneumonia severity and demographics. We used Medicare administrative data to identify 30-day mortality. Because only a small proportion of the study population was black, we included all 240 black patients and randomly selected 720 white patients matched on age and gender. We performed a resampling of the white patients 10 times. Results Males were 43% of the cohort, and the median age was 76 years. After controlling for potential confounders, blacks were less likely to receive antibiotics within 8 hours (odds ratio with 95% confidence interval 0.6, 0.4–0.97, but were as likely as whites to have blood cultures obtained prior to receiving antibiotics (0.7, 0.3–1.5, to have oxygenation assessed within 24 hours of presentation (1.6, 0.9–3.0, and to receive guideline concordant antibiotics (OR 0.9, 0.6–1.7. Black patients had a trend towards decreased 30-day mortality (0.4, 0.2 to 1.0. Conclusion Although blacks were less likely to receive optimal care, our findings are consistent with other studies that suggest better risk-adjusted survival

  4. Impact of guidelines on antibiotics prescription for community-acquired pneumonia

    Directory of Open Access Journals (Sweden)

    Lázaro A. Vélez

    2008-11-01

    Full Text Available PREVIOUS PRESENTATION: This study was presented in part at the 47th Interscience Conference on Antimicrobial Agents and Chemotherapy (ICAAC; September 17, 2007; Chicago, Ill. CONFLICT OF INTEREST STATEMENT: Lázaro Vélez has received research funding from Astra-Zeneca and Roche Colombia, and has been a consultant for Pfizer. Other authors did not declare conflicts of interest. BACKGROUND: Community Acquired Pneumonia (CAP is an important reason to prescribe antibiotics in hospitals. Since etiologic diagnosis is cumbersome, most clinicians use initial broad coverage as suggested by local/international guidelines. This approach may induce overprescription of antibiotics, increasing costs, resistance and adverse effects. Our aim was to quantify the impact that overprescription of antibiotic has on the implementation of IDSA/ATS 2007 guidelines. METHODS: A prospective cohort study conducted at 11 hospitals in Medellín, Colombia, 2005-06. We included 205 adult CAP patients with an identified pathogen. Four categories of appropriateness were established: appropriate, insufficient, excessive and useless. To quantify the magnitude of antibiotic prescription, we compared the Defined Daily Doses (DDD of antibiotics suggested for the empiric treatment by IDSA/ATS 2007 guidelines according to severity (mild, moderate and severe CAP with the DDD of the antibiotics that would be prescribed based on the identified respiratory pathogen. FINDINGS: Empiric coverage recommended by IDSA/ATS resulted appropriate in 24.9%, insufficient in 2.4%, excessive in 57.6% and useless in 15.1%. Total antibiotic consumption for the included patients, according to identified pathogens, would be 2.255 DDD. Predicted antibiotic use based on IDSA/ATS guidelines would increase to 4.440 (97% more. The DDD raise was higher in moderate and severe categories compared to mild CAP (130%, 129.4% and 53.9%, respectively. INTERPRETATION: Implementation of IDSA/ATS 2007 guidelines for the

  5. Changes in soil bacterial communities induced by the invasive plant Pennisetum setaceum in a semiarid environment

    Science.gov (United States)

    Rodriguez-Caballero, Gema; Caravaca, Fuensanta; del Mar Alguacil, María; Fernández-López, Manuel; José Fernández-González, Antonio; García-Orenes, Fuensanta; Roldán, Antonio

    2016-04-01

    Invasive alien species are considered as a global threat being among the main causes of biodiversity loss. Plant invasions have been extensively studied from different disciplines with the purpose of identifying predictor traits of invasiveness and finding solutions. However, less is known about the implication of the rhizosphere microbiota in these processes, even when it is well known the importance of the interaction between plant rhizosphere and microbial communities. The objective of this study was to determine whether native and invasive plants support different bacterial communities in their rhizospheres and whether there are bacterial indicator species that might be contributing to the invasion process of these ecosystems. We carried out a study in five independent locations under Mediterranean semiarid conditions, where the native Hyparrhenia hirta is being displaced by Pennisetum setaceum, an aggressive invasive Poaceae and soil bacterial communities were amplified and 454-pyrosequenced. Changes in the composition and structure of the bacterial communities, owing to the invasive status of the plant, were detected when the richness and alpha-diversity estimators were calculated as well as when we analyzed the PCoA axes scores. The Indicator Species Analysis results showed a higher number of indicators for invaded communities at all studied taxonomic levels. In conclusion, the effect of the invasiveness and its interaction with the soil location has promoted shifts in the rhizosphere bacterial communities which might be facilitating the invader success in these ecosystems.

  6. Potential mechanisms and environmental controls of TiO2 nanoparticle effects on soil bacterial communities.

    Science.gov (United States)

    Ge, Yuan; Priester, John H; Van De Werfhorst, Laurie C; Schimel, Joshua P; Holden, Patricia A

    2013-12-17

    It has been reported that engineered nanoparticles (ENPs) alter soil bacterial communities, but the underlying mechanisms and environmental controls of such effects remain unknown. Besides direct toxicity, ENPs may indirectly affect soil bacteria by changing soil water availability or other properties. Alternatively, soil water or other environmental factors may mediate ENP effects on soil bacterial communities. To test, we incubated nano-TiO2-amended soils across a range of water potentials for 288 days. Following incubation, the soil water characteristics, organic matter, total carbon, total nitrogen, and respiration upon rewetting (an indicator of bioavailable organic carbon) were measured. Bacterial community shifts were characterized by terminal restriction fragment length polymorphism (T-RFLP). The endpoint soil water holding had been reported previously as not changing with this nano-TiO2 amendment; herein, we also found that some selected soil properties were unaffected by the treatments. However, we found that nano-TiO2 altered the bacterial community composition and reduced diversity. Nano-TiO2-induced community dissimilarities increased but tended to approach a plateau when soils became drier. Taken together, nano-TiO2 effects on soil bacteria appear to be a result of direct toxicity rather than indirectly through nano-TiO2 affecting soil water and organic matter pools. However, such directs effects of nano-TiO2 on soil bacterial communities are mediated by soil water. PMID:24256577

  7. Active bacterial community structure along vertical redox gradients in Baltic Sea sediment

    Energy Technology Data Exchange (ETDEWEB)

    Jansson, Janet; Edlund, Anna; Hardeman, Fredrik; Jansson, Janet K.; Sjoling, Sara

    2008-05-15

    Community structures of active bacterial populations were investigated along a vertical redox profile in coastal Baltic Sea sediments by terminal-restriction fragment length polymorphism (T-RFLP) and clone library analysis. According to correspondence analysis of T-RFLP results and sequencing of cloned 16S rRNA genes, the microbial community structures at three redox depths (179 mV, -64 mV and -337 mV) differed significantly. The bacterial communities in the community DNA differed from those in bromodeoxyuridine (BrdU)-labeled DNA, indicating that the growing members of the community that incorporated BrdU were not necessarily the most dominant members. The structures of the actively growing bacterial communities were most strongly correlated to organic carbon followed by total nitrogen and redox potentials. Bacterial identification by sequencing of 16S rRNA genes from clones of BrdU-labeled DNA and DNA from reverse transcription PCR (rt-PCR) showed that bacterial taxa involved in nitrogen and sulfur cycling were metabolically active along the redox profiles. Several sequences had low similarities to previously detected sequences indicating that novel lineages of bacteria are present in Baltic Sea sediments. Also, a high number of different 16S rRNA gene sequences representing different phyla were detected at all sampling depths.

  8. Virulence factors and phylogenetic grouping of Escherichia coli isolates from patients with bacteraemia of urinary tract origin relate to sex and hospital- vs. community-acquired origin

    DEFF Research Database (Denmark)

    Skjøt-Rasmussen, Line; Ejrnæs, Karen; Lundgren, Bettina;

    2012-01-01

    of urinary tract origin according to virulence-associated genes (VAGs), phylogroups, and antimicrobial resistance, and the relation of these factors to hospital- vs. community-acquired origin, sex, and mortality. We found papAH to be associated with community-acquired (CA) rather than hospital-acquired (HA......Worldwide, Escherichia coli is a leading cause of bloodstream infections. Bacteraemia cases in both community- and hospital-acquired infections are often due to E. coli, and it is a major cause of mortality from these infections. These invasive infections are primarily due to extraintestinal...... between the epidemiology and pathogenesis of E. coli bacteraemia of urinary tract origin....

  9. Characterization of the bacterial communities of life stages of free living lone star ticks (Amblyomma americanum.

    Directory of Open Access Journals (Sweden)

    Amanda Jo Williams-Newkirk

    Full Text Available The lone star tick (Amblyomma americanum is an abundant and aggressive biter of humans, domestic animals, and wildlife in the southeastern-central USA and an important vector of several known and suspected zoonotic bacterial pathogens. However, the biological drivers of bacterial community variation in this tick are still poorly defined. Knowing the community context in which tick-borne bacterial pathogens exist and evolve is required to fully understand the ecology and immunobiology of the ticks and to design effective public health and veterinary interventions. We performed a metagenomic survey of the bacterial communities of questing A. americanum and tested 131 individuals (66 nymphs, 24 males, and 41 females from five sites in three states. Pyrosequencing was performed with barcoded eubacterial primers targeting variable 16S rRNA gene regions 5-3. The bacterial communities were dominated by Rickettsia (likely R. amblyommii and an obligate Coxiella symbiont, together accounting for 6.7-100% of sequences per tick. DNAs from Midichloria, Borrelia, Wolbachia, Ehrlichia, Pseudomonas, or unidentified Bacillales, Enterobacteriaceae, or Rhizobiales groups were also detected frequently. Wolbachia and Midichloria significantly co-occurred in Georgia (p<0.00001, but not in other states. The significance of the Midichloria-Wolbachia co-occurrence is unknown. Among ticks collected in Georgia, nymphs differed from adults in both the composition (p = 0.002 and structure (p = 0.002 of their bacterial communities. Adults differed only in their community structure (p = 0.002 with males containing more Rickettsia and females containing more Coxiella. Comparisons among adult ticks collected in New York and North Carolina supported the findings from the Georgia collection despite differences in geography, collection date, and sample handling, implying that the differences detected are consistent attributes. The data also suggest that some members of

  10. Impact of cadmium on the bacterial communities in the gut of Metaphire posthuma

    Energy Technology Data Exchange (ETDEWEB)

    Liang, Shih-Hsiung; Chen, Mu-Hsuan; Chen, Chien-Cheng; Chen, Colin S. [Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan (China); Chen, Jiun-Hong [Department of Life Science, National Taiwan University, Taipei, Taiwan (China); Chen, Ssu Ching, E-mail: osycchna@ksts.seed.net.tw [Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan (China)

    2009-12-30

    The effects of cadmium (Cd) contamination in soil onto the bacterial communities of the guts pooled from ten Metaphire posthuma were addressed during 14 days' incubation. We found that about 50% of Cd (5 mg/kg, dry weight soil) in the contaminated soil was bio-accumulated into the earthworms. DNA was extracted from the guts of M. posthuma and their dwelling soil irrespective of Cd treatment for the analysis of the bacterial communities of guts in M. posthuma and in soil by PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis). A distinctive cluster of bacterial communities of the guts in the earthworm with and without Cd treatment using the analysis of unweighted pair-group method using arithmetic averages (UPGMA) was observed, indicating that the bacterial community of guts could be changed by Cd. However, no differences in the bacterial communities in soil irrespective of Cd treatment were observed, which could be resulted from the bioremediation of Cd by earthworms leading to insignificant effect of Cd on bacterial communities in soil. For the sequencing of some of the dominant bands in the DGGE profile, Bradyrhizobium japonicum, Stenotrophomonas sp. D2, and Labrys, sp. CC-BB4, whose sequences display an identity of more than 97% using blast program against a known sequence in the GeneBank database and Ribosomal database, were identified. Collectively, our results showed that earthworm treatment can decrease the concentrations of Cd in soil, and Cd cause a shift in the bacterial communities in the guts of M. posthuma. The application of M. posthuma for Cd bioremediation would be desired.

  11. Bacterial community composition and structure in an Urban River impacted by different pollutant sources.

    Science.gov (United States)

    Ibekwe, A Mark; Ma, Jincai; Murinda, Shelton E

    2016-10-01

    Microbial communities in terrestrial fresh water are diverse and dynamic in composition due to different environmental factors. The goal of this study was to undertake a comprehensive analysis of bacterial composition along different rivers and creeks and correlate these to land-use practices and pollutant sources. Here we used 454 pyrosequencing to determine the total bacterial community composition, and bacterial communities that are potentially of fecal origin, and of relevance to water quality assessment. The results were analyzed using UniFrac coupled with principal coordinate analysis (PCoA) to compare diversity, abundance, and community composition. Detrended correspondence analysis (DCA) and canonical correspondence analysis (CCA) were used to correlate bacterial composition in streams and creeks to different environmental parameters impacting bacterial communities in the sediment and surface water within the watershed. Bacteria were dominated by the phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria, with Bacteroidetes significantly (P<0.001) higher in all water samples than sediment, where as Acidobacteria and Actinobacteria where significantly higher (P<0.05) in all the sediment samples than surface water. Overall results, using the β diversity measures, coupled with PCoA and DCA showed that bacterial composition in sediment and surface water was significantly different (P<0.001). Also, there were differences in bacterial community composition between agricultural runoff and urban runoff based on parsimony tests using 454 pyrosequencing data. Fecal indicator bacteria in surface water along different creeks and channels were significantly correlated with pH (P<0.01), NO2 (P<0.03), and NH4N (P<0.005); and in the sediment with NO3 (P<0.015). Our results suggest that microbial community compositions were influenced by several environmental factors, and pH, NO2, and NH4 were the major environmental factors driving FIB in surface water

  12. Analysis of bacterial communities and bacterial pathogens in a biogas plant by the combination of ethidium monoazide, PCR and Ion Torrent sequencing.

    Science.gov (United States)

    Luo, Gang; Angelidaki, Irini

    2014-09-01

    The present study investigated the changes of bacterial community composition including bacterial pathogens along a biogas plant, i.e. from the influent, to the biogas reactor and to the post-digester. The effects of post-digestion temperature and time on the changes of bacterial community composition and bacterial pathogens were also studied. Microbial analysis was made by Ion Torrent sequencing of the PCR amplicons from ethidium monoazide treated samples, and ethidium monoazide was used to cleave DNA from dead cells and exclude it from PCR amplification. Both similarity and taxonomic analysis showed that the bacterial community composition in the influent was changed after anaerobic digestion. Firmicutes were dominant in all the samples, while Proteobacteria decreased in the biogas reactor compared with the influent. Variations of bacterial community composition in the biogas reactor with time were also observed. This could be attributed to varying composition of the influent. Batch experiments showed that the methane recovery from the digested residues (obtained from biogas reactor) was mainly related with post-digestion temperature. However, post-digestion time rather than temperature had a significant effect on the changes of bacterial community composition. The changes of bacterial community composition were also reflected in the changes of relative abundance of bacterial pathogens. The richness and relative abundance of bacterial pathogens were reduced after anaerobic digestion in the biogas reactor. It was found in batch experiments that bacterial pathogens showed the highest relative abundance and richness after 30 days' post-digestion. Streptococcus bovis was found in all the samples. Our results showed that special attention should be paid to the post-digestion since the increase in relative abundance of bacterial pathogens after post-digestion might reflect regrowth of bacterial pathogens and limit biosolids disposal vectors.

  13. Community-Acquired Serratia Marcescens Spinal Epidural Abscess in a Patient Without Risk Factors: Case Report and Review

    Directory of Open Access Journals (Sweden)

    Michael D Parkins

    2008-01-01

    Full Text Available Serratia marcescens has rarely been reported as an agent of invasive disease in patients presenting from the community. Furthermore, S marcescens is frequently opportunistic, affecting individuals with serious medical comorbidities including immune suppression and diabetes. A case of a community-acquired S marcescens spontaneous lumbar epidural abscess presenting as cauda equina syndrome is reported in a previously well 36-year-old man with no identifiable risk factors. To the authors’ knowledge, this is the first report of invasive S marcescens causing disease in a patient with no medical comorbidities.

  14. Community-acquired Serratia marcescens spinal epidural abscess in a patient without risk factors: Case report and review.

    Science.gov (United States)

    Parkins, Michael D; Gregson, Daniel B

    2008-05-01

    Serratia marcescens has rarely been reported as an agent of invasive disease in patients presenting from the community. Furthermore, S marcescens is frequently opportunistic, affecting individuals with serious medical comorbidities including immune suppression and diabetes. A case of a community-acquired S marcescens spontaneous lumbar epidural abscess presenting as cauda equina syndrome is reported in a previously well 36-year-old man with no identifiable risk factors. To the authors' knowledge, this is the first report of invasive S marcescens causing disease in a patient with no medical comorbidities.

  15. A prospective evaluation of community acquired gastroenteritis in paediatric practices: impact and disease burden of rotavirus infection

    OpenAIRE

    Fruhwirth, M; Karmaus, W; Moll-Schuler, I; Brosl, S; Mutz, I

    2001-01-01

    AIMS—To examine the disease burden and epidemiology of community acquired rotavirus gastroenteritis in Austrian children treated in a paediatric practice.
METHODS—A prospective, population based, multicentre study in four paediatric practices and two children's hospitals (Innsbruck and Leoben). Children ⩽ 48 months of age presenting with gastroenteritis during a six month period of rotavirus peak between December 1997and May 1998 were included. Prospective testing of stoo...

  16. Community-acquired pneumonia and survival of critically ill acute exacerbation of COPD patients in respiratory intensive care units

    OpenAIRE

    Cheng, Yusheng; Lu, Zhiwei; Tu,Xiongwen; Chen, Liang; Chen, Hu; Yang, Jian; Wang, Jinyan; Zhang, Liqin

    2016-01-01

    Zhiwei Lu,* Yusheng Cheng,* Xiongwen Tu, Liang Chen, Hu Chen, Jian Yang, Jinyan Wang, Liqin Zhang Department of Respiratory Medicine, Yijishan Hospital of Wannan Medical College, Wuhu, People’s Republic of China *These authors contributed equally to this work Purpose: The aim of this study was to appraise the effect of community-acquired pneumonia (CAP) on inhospital mortality in critically ill acute exacerbation of COPD (AECOPD) patients admitted to a respiratory intens...

  17. Five-Year Outbreak of Community- and Hospital-Acquired Mycobacterium porcinum Infections Related to Public Water Supplies ▿ †

    OpenAIRE

    Brown-Elliott, Barbara A.; Wallace, Richard J.; Tichindelean, Carmen; Sarria, Juan C.; McNulty, Steven; Vasireddy, Ravikaran; Bridge, Linda; Mayhall, C. Glenn; Turenne, Christine; Loeffelholz, Michael

    2011-01-01

    Mycobacterium porcinum is a rarely encountered rapidly growing Mycobacterium (RGM). We identified M. porcinum from 24 patients at a Galveston university hospital (University of Texas Medical Branch) over a 5-year period. M. porcinum was considered a pathogen in 11 (46%) of 24 infected patients, including 4 patients with community-acquired disease. Retrospective patient data were collected, and water samples were cultured. Molecular analysis of water isolates, clustered clinical isolates, and ...

  18. Understanding variation in quality of antibiotic use for community-acquired pneumonia: Effect of patient, professional and hospital factors

    OpenAIRE

    Schouten, Jeroen; Hulscher, Marlies; Kullberg, Bart Jan; Cox, Angela; Gyssens, Inge; Van Der Meer, Jos,; Grol, Richard

    2005-01-01

    textabstractObjectives: To develop effective and targeted interventions to improve care for patients with community-acquired pneumonia (CAP), insight is needed into the factors that influence the quality of antibiotic use. Therefore, we measured the performance of nine quality indicators and studied determinants of variation in the quality of antibiotic use. Patients and methods: Data on 498 prospectively included patients with CAP from eight medium-sized Dutch hospitals were extracted from t...

  19. Dynamic bacterial communities on reverse-osmosis membranes in a full-scale desalination plant.

    Science.gov (United States)

    Manes, C-L de O; West, N; Rapenne, S; Lebaron, P

    2011-01-01

    To better understand biofouling of seawater reverse osmosis (SWRO) membranes, bacterial diversity was characterized in the intake water, in subsequently pretreated water and on SWRO membranes from a full-scale desalination plant (FSDP) during a 9 month period. 16S rRNA gene fingerprinting and sequencing revealed that bacterial communities in the water samples and on the SWRO membranes were very different. For the different sampling dates, the bacterial diversity of the active and the total bacterial fractions of the water samples remained relatively stable over the sampling period whereas the bacterial community structure on the four SWRO membrane samples was significantly different. The richness and evenness of the SWRO membrane bacterial communities increased with usage time with an increase in the Shannon diversity index of 2.2 to 3.7. In the oldest SWRO membrane (330 days), no single operational taxonomic unit (OTU) dominated and the majority of the OTUs fell into the Alphaproteobacteria or the Planctomycetes. In striking contrast, a Betaproteobacteria OTU affiliated to the genus Ideonella was dominant and exclusively found in the membrane used for the shortest time (10 days). This suggests that bacteria belonging to this genus could be one of the primary colonizers of the SWRO membrane. Knowledge of the dominant bacterial species on SWRO membranes and their dynamics should help guide culture studies for physiological characterization of biofilm forming species. PMID:21108068

  20. Dynamic bacterial communities on reverse-osmosis membranes in a full-scale desalination plant.

    Science.gov (United States)

    Manes, C-L de O; West, N; Rapenne, S; Lebaron, P

    2011-01-01

    To better understand biofouling of seawater reverse osmosis (SWRO) membranes, bacterial diversity was characterized in the intake water, in subsequently pretreated water and on SWRO membranes from a full-scale desalination plant (FSDP) during a 9 month period. 16S rRNA gene fingerprinting and sequencing revealed that bacterial communities in the water samples and on the SWRO membranes were very different. For the different sampling dates, the bacterial diversity of the active and the total bacterial fractions of the water samples remained relatively stable over the sampling period whereas the bacterial community structure on the four SWRO membrane samples was significantly different. The richness and evenness of the SWRO membrane bacterial communities increased with usage time with an increase in the Shannon diversity index of 2.2 to 3.7. In the oldest SWRO membrane (330 days), no single operational taxonomic unit (OTU) dominated and the majority of the OTUs fell into the Alphaproteobacteria or the Planctomycetes. In striking contrast, a Betaproteobacteria OTU affiliated to the genus Ideonella was dominant and exclusively found in the membrane used for the shortest time (10 days). This suggests that bacteria belonging to this genus could be one of the primary colonizers of the SWRO membrane. Knowledge of the dominant bacterial species on SWRO membranes and their dynamics should help guide culture studies for physiological characterization of biofilm forming species.

  1. Distribution and antimicrobial susceptibility of bacteria from adults with community-acquired pneumonia or complicated skin and soft tissue infections in France: the nationwide French PREMIUM study.

    Science.gov (United States)

    Leprince, C; Desroches, M; Emirian, A; Coutureau, C; Anais, L; Fihman, V; Soussy, C J; Decousser, J W

    2015-10-01

    The empirical therapy of community-acquired pneumonia (CAP) and complicated skin and soft tissue infections (cSSTIs) must be based on updated bacterial distribution and susceptibility data. A nationwide study consecutively collected 1288 isolates from CAP (n=467) and cSSTIs (n=821) from 18 French hospitals between 2012 and 2013. The MIC values of commonly used antimicrobial agents, including ceftaroline, were determined. Bacterial distribution featured Pneumococcus, Haemophilus influenzae, and Staphylococcus aureus for CAPs and S. aureus, β-hemolytic streptococci and Enterobacteriaceae for cSSTIs. Antimicrobial susceptibility testing indicated i) the sustained third-generation cephalosporins and levofloxacin activity against pneumococci and H. influenzae, ii) no methicillin-resistant Staphylococcus aureus emergence among respiratory pathogens, iii) the high in vitro activity of ceftaroline against staphylococci from cSSTIs (98.7% susceptibility), and iv) the worrisome decreasing fluoroquinolone and third-generation cephalosporin susceptibilities among Enterobacteriaceae. This laboratory-based survey depicts a contrasting situation and supports the scoring of patients for the resistant pathogen risk before empirical therapy. PMID:26166208

  2. The intestinal bacterial community in the food waste-reducing larvae of Hermetia illucens.

    Science.gov (United States)

    Jeon, Hyunbum; Park, Soyoung; Choi, Jiyoung; Jeong, Gilsang; Lee, Sang-Beom; Choi, Youngcheol; Lee, Sung-Jae

    2011-05-01

    As it is known that food waste can be reduced by the larvae of Hermetia illucens (Black soldier fly, BSF), the scientific and commercial value of BSF larvae has increased recently. We hypothesised that the ability of catabolic degradation by BSF larvae might be due to intestinal microorganisms. Herein, we analysed the bacterial communities in the gut of BSF larvae by pyrosequencing of extracting intestinal metagenomic DNA from larvae that had been fed three different diets. The 16S rRNA sequencing results produced 9737, 9723 and 5985 PCR products from larval samples fed food waste, cooked rice and calf forage, respectively. A BLAST search using the EzTaxon program showed that the bacterial community in the gut of larvae fed three different diets was mainly composed of the four phyla with dissimilar proportions. Although the composition of the bacterial communities depended on the different nutrient sources, the identified bacterial strains in the gut of BSF larvae represented unique bacterial species that were unlike the intestinal microflora of other insects. Thus, our study analysed the structure of the bacterial communities in the gut of BSF larvae after three different feedings and assessed the application of particular bacteria for the efficient degradation of organic compounds. PMID:21267722

  3. Soil bacterial community responses to warming and grazing in a Tibetan alpine meadow.

    Science.gov (United States)

    Li, Yaoming; Lin, Qiaoyan; Wang, Shiping; Li, Xiangzhen; Liu, Wentso; Luo, Caiyun; Zhang, Zhenhua; Zhu, Xiaoxue; Jiang, Lili; Li, Xine

    2016-01-01

    Warming and grazing significantly affect the structure and function of an alpine meadow ecosystem. Yet, the responses of soil microbes to these disturbances are not well understood. Controlled asymmetrical warming (+1.2/1.7°C during daytime/nighttime) with grazing experiments were conducted to study microbial response to warming, grazing and their interactions. Significant interactive effects of warming and grazing were observed on soil bacterial α-diversity and composition. Warming only caused significant increase in bacterial α-diversity under no-grazing conditions. Grazing induced no substantial differences in bacterial α-diversity and composition irrespective of warming. Warming, regardless of grazing, caused a significant increase in soil bacterial community similarity across space, but grazing only induced significant increases under no-warming conditions. The positive effects of warming on bacterial α-diversity and grazing on community similarity were weakened by grazing and warming, respectively. Soil and plant variables explained well the variations in microbial communities, indicating that changes in soil and plant properties may primarily regulate soil microbial responses to warming in this alpine meadow. The results suggest that bacterial communities may become more similar across space in a future, warmed climate and moderate grazing may potentially offset, at least partially, the effects of global warming on the soil microbial diversity. PMID:26635411

  4. Differences in Bacterial Community Structure on Hydrilla verticillata and Vallisneria americana in a Freshwater Spring

    Science.gov (United States)

    Gordon-Bradley, Nadine; Lymperopoulou, Despoina S.; Williams, Henry Neal

    2014-01-01

    The phylogenetic composition of the epiphytic bacterial community of an invasive aquatic plant (Hydrilla verticillata) and a native species (Vallisneria americana [eelgrass]) of the Wakulla Spring (Florida) was investigated, along with the water column bacterial composition, using clone libraries of the 16S rRNA genes. The bacterial clones from three clone libraries were classified into 182 operational taxonomic units (OTUs), most of which were affiliated with bacterial divisions commonly found in freshwater ecosystems. Based on the identified classes, the bacterial communities on eelgrass and Hydrilla were distinct, such that Planctomycetes, Cyanobacteria, Bacilli and Actinobacteria were found on eelgrass and in the water column but not on Hydrilla. On the other hand, Deltaproteobacteria and Verrucomicrobiae were found on Hydrilla and in the water column but not on eelgrass. Further distinctions observed were that Armatimonadia and Deinococci were found only on Hydrilla while Gemmatimonadetes was found only on eelgrass. Our results indicated differences between the epiphytic bacterial community on the two plants and the water column at the species level, but an even representation of the most abundant phylogenetic taxa (classes) in all three libraries was revealed. Statistical comparison of the retrieved sequences confirmed that the three libraries did not differ significantly at the community level (LIBSHUFF, p <0.05). PMID:24553106

  5. Differences in bacterial community structure on Hydrilla verticillata and Vallisneria americana in a freshwater spring.

    Science.gov (United States)

    Gordon-Bradley, Nadine; Lymperopoulou, Despoina S; Williams, Henry Neal

    2014-01-01

    The phylogenetic composition of the epiphytic bacterial community of an invasive aquatic plant (Hydrilla verticillata) and a native species (Vallisneria americana [eelgrass]) of the Wakulla Spring (Florida) was investigated, along with the water column bacterial composition, using clone libraries of the 16S rRNA genes. The bacterial clones from three clone libraries were classified into 182 operational taxonomic units (OTUs), most of which were affiliated with bacterial divisions commonly found in freshwater ecosystems. Based on the identified classes, the bacterial communities on eelgrass and Hydrilla were distinct, such that Planctomycetes, Cyanobacteria, Bacilli and Actinobacteria were found on eelgrass and in the water column but not on Hydrilla. On the other hand, Deltaproteobacteria and Verrucomicrobiae were found on Hydrilla and in the water column but not on eelgrass. Further distinctions observed were that Armatimonadia and Deinococci were found only on Hydrilla while Gemmatimonadetes was found only on eelgrass. Our results indicated differences between the epiphytic bacterial community on the two plants and the water column at the species level, but an even representation of the most abundant phylogenetic taxa (classes) in all three libraries was revealed. Statistical comparison of the retrieved sequences confirmed that the three libraries did not differ significantly at the community level (LIBSHUFF, p <0.05). PMID:24553106

  6. Distinct Bacterial Communities in Surficial Seafloor Sediments Following the 2010 Deepwater Horizon Blowout.

    Science.gov (United States)

    Yang, Tingting; Speare, Kelly; McKay, Luke; MacGregor, Barbara J; Joye, Samantha B; Teske, Andreas

    2016-01-01

    A major fraction of the petroleum hydrocarbons discharged during the 2010 Macondo oil spill became associated with and sank to the seafloor as marine snow flocs. This sedimentation pulse induced the development of distinct bacterial communities. Between May 2010 and July 2011, full-length 16S rRNA gene clone libraries demonstrated bacterial community succession in oil-polluted sediment samples near the wellhead area. Libraries from early May 2010, before the sedimentation event, served as the baseline control. Freshly deposited oil-derived marine snow was collected on the surface of sediment cores in September 2010, and was characterized by abundantly detected members of the marine Roseobacter cluster within the Alphaproteobacteria. Samples collected in mid-October 2010 closest to the wellhead contained members of the sulfate-reducing, anaerobic bacterial families Desulfobacteraceae and Desulfobulbaceae within the Deltaproteobacteria, suggesting that the oil-derived sedimentation pulse triggered bacterial oxygen consumption and created patchy anaerobic microniches that favored sulfate-reducing bacteria. Phylotypes of the polycyclic aromatic hydrocarbon-degrading genus Cycloclasticus, previously found both in surface oil slicks and the deep hydrocarbon plume, were also found in oil-derived marine snow flocs sedimenting on the seafloor in September 2010, and in surficial sediments collected in October and November 2010, but not in any of the control samples. Due to the relative recalcitrance and stability of polycyclic aromatic compounds, Cycloclasticus represents the most persistent microbial marker of seafloor hydrocarbon deposition that we could identify in this dataset. The bacterial imprint of the DWH oil spill had diminished in late November 2010, when the bacterial communities in oil-impacted sediment samples collected near the Macondo wellhead began to resemble their pre-spill counterparts and spatial controls. Samples collected in summer of 2011 did not show

  7. Antimicrobial susceptibility profile of community acquired and nosocomial isolates ofEscherichiacoli from clinical blood culture specimens at a Nigerian university teaching hospital

    Institute of Scientific and Technical Information of China (English)

    Jombo GTA; Akpan S; Epoke J; Denen Akaa P; Eyong KI; Gyuse AN

    2010-01-01

    Objective:To ascertain the antibiotic susceptibility patterns ofEscherichia coli recovered from blood culture specimens in Calabar, Nigeria.Methods: The study was retrospective in nature and was carried out at University of Calabar Teaching Hospital(UCTH)Calabar. Data generated from blood culture specimens over a five year period (Feb.2004-Feb.2009) was compiled, relevant information such as age, sex, organism recovered and antibiotic susceptibility patterns were obtained from patients records. Samples were collected, transported, stored and processed using standard laboratory procedures. Data obtained was analysed using Epi Info6 statistical software.Results:Escherichia coli was responsible for15.3% (31/203) of the blood infections being the third most common microorganism encountered. The community acquired(CA) isolates of the organism were significantly less resistant (P0.05). Majority(>95.0%) of theNC isolates ofEscherichia coli were resistant to six of the antibiotics tested.Conclusions: Control mechanisms for hospital acquired infections should be stepped up so as to limit the spread of the highly resistant bacterial strains. Also the sale and consumption of antibiotics by the public need to be regulated.

  8. Robustness of the Bacterial Community in the Cabbage White Butterfly Larval Midgut

    OpenAIRE

    Robinson, Courtney J; Schloss, Patrick; Ramos, Yolied; Raffa, Kenneth; Handelsman, Jo

    2009-01-01

    Microbial communities typically vary in composition and structure over space and time. Little is known about the inherent characteristics of communities that govern various drivers of these changes, such as random variation, changes in response to perturbation, or susceptibility to invasion. In this study, we use 16S ribosomal RNA gene sequences to describe variation among bacterial communities in the midguts of cabbage white butterfly (Pieris rapae) larvae and examine the influence of commun...

  9. Nutrient-responsive regulation determines biodiversity in a colicin-mediated bacterial community

    OpenAIRE

    Hol, F.J.H. (Felix); Voges, M.J.; Dekker, C.; Keymer, J.E.

    2014-01-01

    Background Antagonistic interactions mediated by antibiotics are strong drivers of bacterial community dynamics which shape biodiversity. Colicin production by Escherichia coli is such an interaction that governs intraspecific competition and is involved in promoting biodiversity. It is unknown how environmental cues affect regulation of the colicin operon and thus influence antibiotic-mediated community dynamics. Results Here, we investigate the community dynamics of colicin-producing, -sens...

  10. Light structures phototroph, bacterial and fungal communities at the soil surface.

    Directory of Open Access Journals (Sweden)

    Lawrence O Davies

    Full Text Available The upper few millimeters of soil harbour photosynthetic microbial communities that are structurally distinct from those of underlying bulk soil due to the presence of light. Previous studies in arid zones have demonstrated functional importance of these communities in reducing soil erosion, and enhancing carbon and nitrogen fixation. Despite being widely distributed, comparative understanding of the biodiversity of the soil surface and underlying soil is lacking, particularly in temperate zones. We investigated the establishment of soil surface communities on pasture soil in microcosms exposed to light or dark conditions, focusing on changes in phototroph, bacterial and fungal communities at the soil surface (0-3 mm and bulk soil (3-12 mm using ribosomal marker gene analyses. Microbial community structure changed with time and structurally similar phototrophic communities were found at the soil surface and in bulk soil in the light exposed microcosms suggesting that light can influence phototroph community structure even in the underlying bulk soil. 454 pyrosequencing showed a significant selection for diazotrophic cyanobacteria such as Nostoc punctiforme and Anabaena spp., in addition to the green alga Scenedesmus obliquus. The soil surface also harboured distinct heterotrophic bacterial and fungal communities in the presence of light, in particular, the selection for the phylum Firmicutes. However, these light driven changes in bacterial community structure did not extend to the underlying soil suggesting a discrete zone of influence, analogous to the rhizosphere.

  11. Changes in assembly processes in soil bacterial communities following a wildfire disturbance.

    Science.gov (United States)

    Ferrenberg, Scott; O'Neill, Sean P; Knelman, Joseph E; Todd, Bryan; Duggan, Sam; Bradley, Daniel; Robinson, Taylor; Schmidt, Steven K; Townsend, Alan R; Williams, Mark W; Cleveland, Cory C; Melbourne, Brett A; Jiang, Lin; Nemergut, Diana R

    2013-06-01

    Although recent work has shown that both deterministic and stochastic processes are important in structuring microbial communities, the factors that affect the relative contributions of niche and neutral processes are poorly understood. The macrobiological literature indicates that ecological disturbances can influence assembly processes. Thus, we sampled bacterial communities at 4 and 16 weeks following a wildfire and used null deviation analysis to examine the role that time since disturbance has in community assembly. Fire dramatically altered bacterial community structure and diversity as well as soil chemistry for both time-points. Community structure shifted between 4 and 16 weeks for both burned and unburned communities. Community assembly in burned sites 4 weeks after fire was significantly more stochastic than in unburned sites. After 16 weeks, however, burned communities were significantly less stochastic than unburned communities. Thus, we propose a three-phase model featuring shifts in the relative importance of niche and neutral processes as a function of time since disturbance. Because neutral processes are characterized by a decoupling between environmental parameters and community structure, we hypothesize that a better understanding of community assembly may be important in determining where and when detailed studies of community composition are valuable for predicting ecosystem function.

  12. Comparison of intestinal bacterial communities in grass carp, Ctenopharyngodon idellus, from two different habitats

    Science.gov (United States)

    Ni, Jiajia; Yu, Yuhe; Zhang, Tanglin; Gao, Lei

    2012-09-01

    The intestinal bacteria of vertebrates form a close relationship with their host. External and internal conditions of the host, including its habitat, affect the intestinal bacterial community. Similarly, the intestinal bacterial community can, in turn, influence the host, particularly with respect to disease resistance. We compared the intestinal bacterial communities of grass carp that were collected from farm-ponds or a lake. We conducted denaturing gradient gel electrophoresis of amplified 16S rRNA genes, from which 66 different operational taxonomic units were identified. Using both the unweighted pair-group method with arithmetic means clustering and principal component analysis ordination, we found that the intestinal bacterial communities from the two groups of pond fish were clustered together and inset into the clusters of wild fish, except for DF-7, and there was no significant correlation between genetic diversity of grass carp and their intestinal bacterial communities (Mantel one-tailed test, R=0.157, P=0.175). Cetobacterium appeared more frequently in the intestine of grass carp collected from pond. A more thorough understanding of the role played by intestinal microbiota on fish health would be of considerable benefit to the aquaculture industry.

  13. Comparison of intestinal bacterial communities in grass carp,Ctenopharyngodon idellus,from two different habitats

    Institute of Scientific and Technical Information of China (English)

    NI Jiajia; YU Yuhe; ZHANG Tanglin; GAO Lei

    2012-01-01

    The intestinal bacteria of vertebrates form a close relationship with their host.External and internal conditions of the host,including its habitat,affect the intestinal bacterial community.Similarly,the intestinal bacterial community can,in turn,influence the host,particularly with respect to disease resistance.We compared the intestinal bacterial communities of grass carp that were collected from farm-ponds or a lake.We conducted denaturing gradient gel electrophoresis of amplified 16S rRNA genes,from which 66 different operational taxonomic units were identified.Using both the unweighted pair-group method with arithmetic means clustering and principal component analysis ordination,we found that the intestinal bacterial communities from the two groups of pond fish were clustered together and inset into the clusters of wild fish,except for DF-7,and there was no significant correlation between genetic diversity of grass carp and their intestinal bacterial communities(Mantel one-tailed test,R=0.157,P=0.175).Cetobacterium appeared more frequently in the intestine of grass carp collected from pond.A more thorough understanding of the role played by intestinal microbiota on fish health would be of considerable benefit to the aquaculture industry.

  14. Response of bacterial communities to environmental changes in a mesoscale subtropical watershed, Southeast China.

    Science.gov (United States)

    Hu, Anyi; Yang, Xiaoyong; Chen, Nengwang; Hou, Liyuan; Ma, Ying; Yu, Chang-Ping

    2014-02-15

    This study used 16S rRNA gene-based pyrosequencing (16S-pyrotag) to investigate both planktonic and benthic bacterial communities in two main tributaries (North River and West River) of the Jiulong River Watershed (JRW), a mesoscale subtropical watershed that has experienced intensive human perturbation in recent decades. The results of 16S-pyrotag showed that benthic bacterial communities were clearly more diverse and uniform than surface bacterioplankton communities. The results of taxonomic assignments indicated that Betaproteobacteria, Actinobacteria and Firmicutes were significantly more abundant in planktonic than in benthic communities, whereas the relative abundances of Acidobacteria, Delta-, Gammaproteobacteria, Chloroflexi and Nitrospira were higher in sediment than in water samples. In particular, several sewer- and fecal-pollution bacterial indicators were observed in water samples, implying that the water bodies of the JRW were contaminated by fecal pollution. Using the typical freshwater bacteria (TFB) taxonomic framework, 57.6 ± 10%, 27.6 ± 10.9% and 10.4 ± 6.9% of sequences recovered from planktonic communities could be assigned to lineages, clades and tribes of TFB, respectively. The relatively lower abundance of TFB implied that some unknown or unique autochthonous bacterioplankton populations occurred in the JRW. The principal coordinate analysis (PCoA) and one way analysis of similarity (ANOSIM) analysis demonstrated that planktonic bacterial community structures were significantly different between North River and West River, whereas benthic communities from these two tributaries were grouped together. Multivariate statistical analysis revealed that nutrient concentrations and stoichiometry were the key drivers of both α- and β-diversity patterns of bacterioplankton communities. Overall, our results indicate that the diversity, composition and structure of planktonic bacterial communities are sensitive to water chemistry (e.g., nutrient

  15. Manipulating Bacterial Communities by in situ Microbiome Engineering.

    Science.gov (United States)

    Sheth, Ravi U; Cabral, Vitor; Chen, Sway P; Wang, Harris H

    2016-04-01

    Microbial communities inhabit our entire planet and have a crucial role in biogeochemical processes, agriculture, biotechnology, and human health. Here, we argue that 'in situ microbiome engineering' represents a new paradigm of community-scale genetic and microbial engineering. We discuss contemporary applications of this approach to directly add, remove, or modify specific sets of functions and alter community-level properties in terrestrial, aquatic, and host-associated microbial communities. Specifically, we highlight emerging in situ genome engineering approaches as tractable techniques to manipulate microbial communities with high specificity and efficacy. Finally, we describe opportunities for technological innovation and ways to bridge existing knowledge gaps to accelerate the development of in situ approaches for microbiome manipulations. PMID:26916078

  16. Predictors of inhospital mortality and re-hospitalization in older adults with community-acquired pneumonia: a prospective cohort study

    Directory of Open Access Journals (Sweden)

    Marrie Tom

    2010-05-01

    Full Text Available Abstract Background A better understanding of potentially modifiable predictors of in-hospital mortality and re-admission to the hospital following discharge may help to improve management of community-acquired pneumonia in older adults. We aimed to assess the associations of potentially modifiable factors with mortality and re-hospitalization in older adults hospitalized with community-acquired pneumonia. Methods A prospective cohort study was conducted from July 2003 to April 2005 in two Canadian cities. Patients aged 65 years or older hospitalized for community-acquired pneumonia were followed up for up to 30 days from initial hospitalization for mortality and these patients who were discharged alive within 30 days of initial hospitalization were followed up to 90 days of initial hospitalization for re-hospitalization. Separate logistic regression analyses were performed identify the predictors of mortality and re-hospitalization. Results Of 717 enrolled patients hospitalized for community-acquired pneumonia, 49 (6.8% died within 30 days of hospital admission. Among these patients, 526 were discharged alive within 30 days of hospitalization of whom 58 (11.2% were re-hospitalized within 90 days of initial hospitalization. History of hip fracture (odds ratio (OR = 4.00, 95% confidence interval (CI = (1.46, 10.96, P = .007, chronic obstructive pulmonary disease (OR = 2.31, 95% CI = (1.18, 4.50, P = .014, cerebrovascular disease (OR = 2.11, 95% CI = (1.03, 4.31, P = .040 were associated with mortality. Male sex (OR = 2.35, 95% CI = (1.13, 4.85, P = .022 was associated with re-hospitalization while vitamin E supplementation was protective (OR = 0.37 (0.16, 0.90, P = .028. Lower socioeconomic status, prior influenza and pneumococcal vaccinations, appropriate antibiotic prescription upon admission, and lower nutrition risk were not significantly associated with mortality or re-hospitalization. Conclusion Chronic comorbidities appear to be the most

  17. Effects of Hospital-Based Physical Therapy on Hospital Discharge Outcomes among Hospitalized Older Adults with Community-Acquired Pneumonia and Declining Physical Function

    OpenAIRE

    Kim, Sun Jung; Lee, Joo Hun; Han, Boram; Lam, Julia; Bukowy, Elizabeth; Rao, Avinash; Vulcano, Jordan; Andreeva, Anelia; Bertelson, Heather; Shin, Hyun Phil; Yoo, Ji Won

    2015-01-01

    To examine whether hospital-based physical therapy is associated with functional changes and early hospital readmission among hospitalized older adults with community-acquired pneumonia and declining physical function. Study design was a retrospective observation study. Participants were community-dwelling older adults admitted to medicine floor for community-acquired pneumonia (n = 1,058). Their physical function using Katz activities of daily living (ADL) Index declined between hospital adm...

  18. Bacterial communities in full-scale wastewater treatment systems

    OpenAIRE

    Cydzik-Kwiatkowska, Agnieszka; Zielińska, Magdalena

    2016-01-01

    Bacterial metabolism determines the effectiveness of biological treatment of wastewater. Therefore, it is important to define the relations between the species structure and the performance of full-scale installations. Although there is much laboratory data on microbial consortia, our understanding of dependencies between the microbial structure and operational parameters of full-scale wastewater treatment plants (WWTP) is limited. This mini-review presents the types of microbial consortia in...

  19. Identification and ecology of bacterial communities associated with necroses of three cactus species.

    OpenAIRE

    Foster, J. L.; Fogleman, J C

    1993-01-01

    To compare the bacterial communities residing in necrotic tissues of columnar cacti of the Sonoran Desert, isolates from 39 organ pipe, 19 saguaro, and 16 senita cacti were obtained. The isolates were clustered into 28 conspecific groups on the basis of their fatty acid profiles. The distributions of the individual bacterial isolates varied among cactus species. Seven of the 28 species groups were unique to a particular cactus species, whereas 8 species groups were found in all three cacti. T...

  20. Bacterial communities in fish sauce mash using culture-dependent and -independent methods

    OpenAIRE

    Fukui, Youhei; Yoshida, Mitsuhiro; Shozen, Kei-ichi; Funatsu, Yasuhiro; Takano, Takashi; OIKAWA, Hiroshi; Yano, Yutaka; Satomi, Masataka

    2012-01-01

    In fish sauce production, microorganisms are associated with the fermentation process; however, the sequential changes in the bacterial communities have never been examined throughout the period of fermentation. In this study, we determined the bacterial floras in a fish sauce mash over 8 months, using three different culture media and 16S rRNA gene clone library analysis. During the first 4 weeks, viable counts of non-halophilic and halophilic bacteria decreased and were dominated by Staphyl...

  1. Identification of Household Bacterial Community and Analysis of Species Shared with Human Microbiome

    OpenAIRE

    Jeon, Yoon-Seong; Chun, Jongsik; Kim, Bong-Soo

    2013-01-01

    Microbial populations in indoor environments, where we live and eat, are important for public health. Various bacterial species reside in the kitchen, and refrigerators, the major means of food storage within kitchens, can be a direct source of food borne illness. Therefore, the monitoring of microbiota in the refrigerator is important for food safety. We investigated and compared bacterial communities that reside in the vegetable compartment of the refrigerator and on the seat of the toilet,...

  2. Bacterial Communities in Rhizosphere of Maize Studied by T-RFLP

    OpenAIRE

    Ondreičková Katarína; Ficek Andrej; Mihálik Daniel; Gubišová Marcela; Hudcovicová Martina; Drahovská Hana; Kraic Ján

    2014-01-01

    The terminal restriction fragment length polymorphism munities from different collecting places was evaluated was used to determine the bacterial diversity in rhizo- by principal component analysis. Results showed that sphere of maize (Zea mays L.) collected from four sites the most different bacterial community originated from of experimental field plot in two dates of the vegetation marginal part of the experimental field plot collected in season (July and September). The 16S rRNA gene was ...

  3. Molecular Phylogenetic Diversity and Spatial Distribution of Bacterial Communities in Cooling Stage during Swine Manure Composting

    OpenAIRE

    Guo, Yan; Zhang, Jinliang; Yan, Yongfeng; Wu, Jian; Zhu, Nengwu; Deng, Changyan

    2015-01-01

    Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and subsequent sub-cloning and sequencing were used in this study to analyze the molecular phylogenetic diversity and spatial distribution of bacterial communities in different spatial locations during the cooling stage of composted swine manure. Total microbial DNA was extracted, and bacterial near full-length 16S rRNA genes were subsequently amplified, cloned, RFLP-screened, and sequenced. A total of 420 positive ...

  4. Bacterial Diversity and Community Structure in Two Bornean Nepenthes Species with Differences in Nitrogen Acquisition Strategies.

    Science.gov (United States)

    Sickel, Wiebke; Grafe, T Ulmar; Meuche, Ivonne; Steffan-Dewenter, Ingolf; Keller, Alexander

    2016-05-01

    Carnivorous plants of the genus Nepenthes have been studied for over a century, but surprisingly little is known about associations with microorganisms. The two species Nepenthes rafflesiana and Nepenthes hemsleyana differ in their pitcher-mediated nutrient sources, sequestering nitrogen from arthropod prey and arthropods as well as bat faeces, respectively. We expected bacterial communities living in the pitchers to resemble this diet difference. Samples were taken from different parts of the pitchers (leaf, peristome, inside, outside, digestive fluid) of both species. Bacterial communities were determined using culture-independent high-throughput amplicon sequencing. Bacterial richness and community structure were similar in leaves, peristomes, inside and outside walls of both plant species. Regarding digestive fluids, bacterial richness was higher in N. hemsleyana than in N. rafflesiana. Additionally, digestive fluid communities were highly variable in structure, with strain-specific differences in community composition between replicates. Acidophilic taxa were mostly of low abundance, except the genus Acidocella, which strikingly reached extremely high levels in two N. rafflesiana fluids. In N. hemsleyana fluid, some taxa classified as vertebrate gut symbionts as well as saprophytes were enriched compared to N. rafflesiana, with saprophytes constituting potential competitors for nutrients. The high variation in community structure might be caused by a number of biotic and abiotic factors. Nitrogen-fixing bacteria were present in both study species, which might provide essential nutrients to the plant at times of low prey capture and/or rare encounters with bats. PMID:26790863

  5. The role of abiotic environmental conditions and herbivory in shaping bacterial community composition in floral nectar.

    Directory of Open Access Journals (Sweden)

    Michal Samuni-Blank

    Full Text Available Identifying the processes that drive community assembly has long been a central theme in ecology. For microorganisms, a traditional prevailing hypothesis states that "everything is everywhere, but the environment selects". Although the bacterial community in floral nectar may be affected by both atmosphere (air-borne bacteria and animals as dispersal vectors, the environmental and geographic factors that shape microbial communities in floral nectar are unknown. We studied culturable bacterial communities in Asphodelus aestivus floral nectar and in its typical herbivorous bug Capsodes infuscatus, along an aridity gradient. Bacteria were sampled from floral nectar and bugs at four sites, spanning a geographical range of 200 km from Mediterranean to semi-arid conditions, under open and bagged flower treatments. In agreement with the niche assembly hypothesis, the differences in bacterial community compositions were explained by differences in abiotic environmental conditions. These results suggest that microbial model systems are useful for addressing macro-ecological questions. In addition, similar bacterial communities were found in the nectar and on the surface of the bugs that were documented visiting the flowers. These similarities imply that floral nectar bacteria dispersal is shaped not only by air borne bacteria and nectar consumers as previously reported, but also by visiting vectors like the mirid bugs.

  6. Safe-site effects on rhizosphere bacterial communities in a high-altitude alpine environment.

    Science.gov (United States)

    Ciccazzo, Sonia; Esposito, Alfonso; Rolli, Eleonora; Zerbe, Stefan; Daffonchio, Daniele; Brusetti, Lorenzo

    2014-01-01

    The rhizosphere effect on bacterial communities associated with three floristic communities (RW, FI, and M sites) which differed for the developmental stages was studied in a high-altitude alpine ecosystem. RW site was an early developmental stage, FI was an intermediate stage, M was a later more matured stage. The N and C contents in the soils confirmed a different developmental stage with a kind of gradient from the unvegetated bare soil (BS) site through RW, FI up to M site. The floristic communities were composed of 21 pioneer plants belonging to 14 species. Automated ribosomal intergenic spacer analysis showed different bacterial genetic structures per each floristic consortium which differed also from the BS site. When plants of the same species occurred within the same site, almost all their bacterial communities clustered together exhibiting a plant species effect. Unifrac significance value (P < 0.05) on 16S rRNA gene diversity revealed significant differences (P < 0.05) between BS site and the vegetated sites with a weak similarity to the RW site. The intermediate plant colonization stage FI did not differ significantly from the RW and the M vegetated sites. These results pointed out the effect of different floristic communities rhizospheres on their soil bacterial communities.

  7. Safe-Site Effects on Rhizosphere Bacterial Communities in a High-Altitude Alpine Environment

    Directory of Open Access Journals (Sweden)

    Sonia Ciccazzo

    2014-01-01

    Full Text Available The rhizosphere effect on bacterial communities associated with three floristic communities (RW, FI, and M sites which differed for the developmental stages was studied in a high-altitude alpine ecosystem. RW site was an early developmental stage, FI was an intermediate stage, M was a later more matured stage. The N and C contents in the soils confirmed a different developmental stage with a kind of gradient from the unvegetated bare soil (BS site through RW, FI up to M site. The floristic communities were composed of 21 pioneer plants belonging to 14 species. Automated ribosomal intergenic spacer analysis showed different bacterial genetic structures per each floristic consortium which differed also from the BS site. When plants of the same species occurred within the same site, almost all their bacterial communities clustered together exhibiting a plant species effect. Unifrac significance value (P<0.05 on 16S rRNA gene diversity revealed significant differences (P<0.05 between BS site and the vegetated sites with a weak similarity to the RW site. The intermediate plant colonization stage FI did not differ significantly from the RW and the M vegetated sites. These results pointed out the effect of different floristic communities rhizospheres on their soil bacterial communities.

  8. Can the Bacterial Community of a High Arctic Glacier Surface Escape Viral Control?

    Science.gov (United States)

    Rassner, Sara M. E.; Anesio, Alexandre M.; Girdwood, Susan E.; Hell, Katherina; Gokul, Jarishma K.; Whitworth, David E.; Edwards, Arwyn

    2016-01-01

    Glacial ice surfaces represent a seasonally evolving three-dimensional photic zone which accumulates microbial biomass and potentiates positive feedbacks in ice melt. Since viruses are abundant in glacial systems and may exert controls on supraglacial bacterial production, we examined whether changes in resource availability would promote changes in the bacterial community and the dynamics between viruses and bacteria of meltwater from the photic zone of a Svalbard glacier. Our results indicated that, under ambient nutrient conditions, low estimated viral decay rates account for a strong viral control of bacterial productivity, incurring a potent viral shunt of a third of bacterial carbon in the supraglacial microbial loop. Moreover, it appears that virus particles are very stable in supraglacial meltwater, raising the prospect that viruses liberated in melt are viable downstream. However, manipulating resource availability as dissolved organic carbon, nitrogen, and phosphorous in experimental microcosms demonstrates that the photic zone bacterial communities can escape viral control. This is evidenced by a marked decline in virus-to-bacterium ratio (VBR) concomitant with increased bacterial productivity and number. Pyrosequencing shows a few bacterial taxa, principally Janthinobacterium sp., dominate both the source meltwater and microcosm communities. Combined, our results suggest that viruses maintain high VBR to promote contact with low-density hosts, by the manufacture of robust particles, but that this necessitates a trade-off which limits viral production. Consequently, dominant bacterial taxa appear to access resources to evade viral control. We propose that a delicate interplay of bacterial and viral strategies affects biogeochemical cycling upon glaciers and, ultimately, downstream ecosystems. PMID:27446002

  9. Effects of Dispersal and Initial Diversity on the Composition and Functional Performance of Bacterial Communities.

    Science.gov (United States)

    Zha, Yinghua; Berga, Mercè; Comte, Jérôme; Langenheder, Silke

    2016-01-01

    Natural communities are open systems and consequently dispersal can play an important role for the diversity, composition and functioning of communities at the local scale. It is, however, still unclear how effects of dispersal differ depending on the initial diversity of local communities. Here we implemented an experiment where we manipulated the initial diversity of natural freshwater bacterioplankton communities using a dilution-to-extinction approach as well as dispersal from a regional species pool. The aim was further to test whether dispersal effects on bacterial abundance and functional parameters (average community growth rates, respiration rates, substrate utilisation ability) differ in dependence of the initial diversity of the communities. First of all, we found that both initial diversity and dispersal rates had an effect on the recruitment of taxa from a regional source, which was higher in communities with low initial diversity and at higher rates of dispersal. Higher initial diversity and dispersal also promoted higher levels of richness and evenness in local communities and affected, both, separately or interactively, the functional performance of communities. Our study therefore suggests that dispersal can influence the diversity, composition and functioning of bacterial communities and that this effect may be enhanced if the initial diversity of communities is depleted. PMID:27182596

  10. Signs and symptoms indicative of community-acquired pneumonia in infants under six months

    Directory of Open Access Journals (Sweden)

    Maria de Fátima Bazhuni Pombo March

    2005-04-01

    Full Text Available OBJECTIVE: Evaluation of the clinical signs and symptoms predicting bacterial and viral pneumonia, in accordance with the Brazilian National Control Program for Acute Respiratory (ARI. METHODS: Observational prospective study. Seventy-six children from birth to six months of age who had pneumonia were studied in the emergency room. The patients were subdivided into two groups, based on radiological findings (gold-standard: 47 had bacterial pneumonia, and 29 had viral pneumonia. The frequencies, sensitivities, and specificities of the signs and symptoms were evaluated. RESULTS: The sensibilities and sensitivities of general findings in bacterial pneumonia were, respectively: fever 53.2%/40.0%; hypoactivity 68.4%/55.6% and prostration detected by the doctor 72.7%/55.0%. The same findings in viral pneumonias showed, respectively: 37.9%/40.0%, 66.7%/55.6% and 66.7%/55.6%. The sensibilities and sensitivities of respiratory findings in bacterial pneumonia were, respectively: coughing 66.0/38.1%, Respiratory rate = 50 ripm 76.6%/38.1%, altered respiratory auscultation 91.3%/10.5%, and chest indrawing 46.7%/80.0%. The same findings in viral pneumonias were, respectively: 69.0%/38.1%, 86.2%/38.1%, 85.7%/10.5% and 44.8%/80.0%. CONCLUSION: Analysis of signs and symptoms in each group did not distinguish bacterial from viral pneumonia. Our findings reinforce the adequacy of the ARI program in Brazil, which gives an early diagnosis of pneumonia, independent of its etiology.

  11. Temperature adaptation of soil bacterial communities along an Antarctic climate gradient: predicting responses to climate warming

    DEFF Research Database (Denmark)

    Rinnan, Riikka; Rousk, Johannes; Yergeau, Etienne;

    2009-01-01

    the leucine incorporation technique, in order to predict future changes in temperature sensitivity of resident soil bacterial communities. Soil samples were collected along a climate gradient consisting of locations on the Antarctic Peninsula (Anchorage Island, 67 °34'S, 68 °08'W), Signy Island (60 °43'S, 45......Soil microorganisms, the central drivers of terrestrial Antarctic ecosystems, are being confronted with increasing temperatures as parts of the continent experience considerable warming. Here we determined short-term temperature dependencies of Antarctic soil bacterial community growth rates, using...... °38'W) and the Falkland Islands (51 °76'S 59 °03'W). At each location, experimental plots were subjected to warming by open top chambers (OTCs) and paired with control plots on vegetated and fell-field habitats. The bacterial communities were adapted to the mean annual temperature of their environment...

  12. Bacterial Community in Different Populations of Rice Brown Planthopper Nilaparvata lugens (Stål)

    Institute of Scientific and Technical Information of China (English)

    XU Hong-xing; ZHENG Xu-song; YANG Ya-jun; WANG Xin; YE Gong-yin; LU Zhong-xian

    2014-01-01

    The structures of bacterial communities in the brown planthopper (BPH) Nilaparvata lugens (Stål) from different geographic and resistant virulent populations were analyzed by using denatured gradient gel electrophoresis (DGGE). Results showed that the bacterial communities in BPH nymph from the first to the fifth instars varied with nymphal growth and development. The bacterial communities in the first-instar BPH nymph were similar to those in adults. Nine geographic BPH populations were divided into three groups based on the cluster analysis of DGGE fingerprint. The first group was from the Philippines;the second group was from Thailand and Hainan, Yunnan and Zhejiang provinces of China; and the third group was from Vietnam and Guangxi, Hunan and Jiangxi provinces of China. BPH populations adapted to different resistant rice varieties. The BPH populations from Mudgo (with resistant gene Bph1) and ASD7 (with resistant gene bph2) differed with those of the susceptible rice variety TN1.

  13. Variations of Bacterial Community Structure and Composition in Mangrove Sediment at Different Depths in Southeastern Brazil

    Directory of Open Access Journals (Sweden)

    Lucas William Mendes

    2014-12-01

    Full Text Available Tropical mangroves are considered one of the most productive ecosystems of the world, being characterized as nurseries and food sources for fish and other animals. Microorganisms play important roles in these environments, and the study of bacterial communities is of paramount importance for a better comprehension of mangrove dynamics. This study focused on the structure and composition of bacterial communities in mangrove sediments at different depths and points, located in Southeastern Brazil. Terminal Restriction Fragment Length Polymorphism (T-RFLP was used to determine the community structure, and 16S rRNA gene pyrosequencing was used to characterize the community composition. Redundancy analysis of T-RFLP patterns revealed differences in bacterial community structure according to soil attributes and depth. The parameters K and depth presented significant correlation with general community structure. Most sequences were classified into the phylum Proteobacteria (88%, which presented differences according to the depth, where the classes Betaproteobacteria (21% and Deltaproteobacteria (16% were abundant at 10 cm and Epsilonproteobacteria (35% was abundant at 40 cm depth. Clear differences were observed in community composition as shown by the differential distribution of the phyla Firmicutes (1.13% and 3.8%, for 10 cm and 40 cm respectively, Chloroflexi (2.8% and 0.75%, and Acidobacteria (2.75% and 0.57% according to the depth. Bacterial diversity measurements indicated higher diversity in shallow samples. Taken together, our findings indicate that mangrove holds a diverse bacterial community, which is shaped by the variations found in the ecosystem, such as sediment properties and depth.

  14. Effects of different methods of DNA extraction for activated sludge on the subsequent analysis of bacterial community profiles.

    Science.gov (United States)

    Sun, Lianpeng; Ouyang, Xiong; Tang, Yueheng; Yang, Ying; Luo, Ying

    2012-02-01

    The effect of different DNA extraction protocols on activated sludge DNA yield and bacterial community composition was evaluated by temperature gradient gel electrophoresis (TGGE). Nine different procedures to extract DNA were compared-sonication (30s), sonication (40s), sonication (50s), freezing-thawing, bead milling, sodium dodecyl sulfate (SDS)-lysozyme, SDS-proteinase K, SDS-lysozyme-proteinase, and a commercial extraction kit. It was found that the TGGE profiles and the DNA band numbers made significant differences via various extraction methods. The yield and purity of DNA extracted by sonication and other physical methods were not satisfactory, while the DNA purity extracted by SDS and other chemical-biological methods were better. Crude DNA extracts isolated by sonication and other physical methods passed the polymerase chain reaction, despite the absence of purification and acquired affluent DNA bands in TGGE. The affluence of bands in TGGE was not consistent with the yield and purification of DNA, but was correlative with extraction protocols. To analyze the activated sludge bacterial community by TGGE fingerprint, it is necessary to make a synthesis of the TGGE fingerprint profiles of chemical and physical DNA extraction methods to overcome the representative bias.

  15. Impacts of poultry house environment on poultry litter bacterial community composition.

    Directory of Open Access Journals (Sweden)

    Michael D Dumas

    Full Text Available Viral and bacterial pathogens are a significant economic concern to the US broiler industry and the ecological epicenter for poultry pathogens is the mixture of bedding material, chicken excrement and feathers that comprises the litter of a poultry house. This study used high-throughput sequencing to assess the richness and diversity of poultry litter bacterial communities, and to look for connections between these communities and the environmental characteristics of a poultry house including its history of gangrenous dermatitis (GD. Cluster analysis of 16S rRNA gene sequences revealed differences in the distribution of bacterial phylotypes between Wet and Dry litter samples and between houses. Wet litter contained greater diversity with 90% of total bacterial abundance occurring within the top 214 OTU clusters. In contrast, only 50 clusters accounted for 90% of Dry litter bacterial abundance. The sixth largest OTU cluster across all samples classified as an Arcobacter sp., an emerging human pathogen, occurring in only the Wet litter samples of a house with a modern evaporative cooling system. Ironically, the primary pathogenic clostridial and staphylococcal species associated with GD were not found in any house; however, there were thirteen 16S rRNA gene phylotypes of mostly gram-positive phyla that were unique to GD-affected houses and primarily occurred in Wet litter samples. Overall, the poultry house environment appeared to substantially impact the composition of litter bacterial communities and may play a key role in the emergence of food-borne pathogens.

  16. Impacts of poultry house environment on poultry litter bacterial community composition.

    Science.gov (United States)

    Dumas, Michael D; Polson, Shawn W; Ritter, Don; Ravel, Jacques; Gelb, Jack; Morgan, Robin; Wommack, K Eric

    2011-01-01

    Viral and bacterial pathogens are a significant economic concern to the US broiler industry and the ecological epicenter for poultry pathogens is the mixture of bedding material, chicken excrement and feathers that comprises the litter of a poultry house. This study used high-throughput sequencing to assess the richness and diversity of poultry litter bacterial communities, and to look for connections between these communities and the environmental characteristics of a poultry house including its history of gangrenous dermatitis (GD). Cluster analysis of 16S rRNA gene sequences revealed differences in the distribution of bacterial phylotypes between Wet and Dry litter samples and between houses. Wet litter contained greater diversity with 90% of total bacterial abundance occurring within the top 214 OTU clusters. In contrast, only 50 clusters accounted for 90% of Dry litter bacterial abundance. The sixth largest OTU cluster across all samples classified as an Arcobacter sp., an emerging human pathogen, occurring in only the Wet litter samples of a house with a modern evaporative cooling system. Ironically, the primary pathogenic clostridial and staphylococcal species associated with GD were not found in any house; however, there were thirteen 16S rRNA gene phylotypes of mostly gram-positive phyla that were unique to GD-affected houses and primarily occurred in Wet litter samples. Overall, the poultry house environment appeared to substantially impact the composition of litter bacterial communities and may play a key role in the emergence of food-borne pathogens.

  17. Bacterial community in sediment from the Western Pacific "Warm Pool" and its relationship to environment

    Institute of Scientific and Technical Information of China (English)

    ZENG Runying; ZHAO Jing; ZHANG Rui; LIN Nianwei

    2005-01-01

    Total DNAs were extracted from different sections of deep sea sediment core sample collected from the Western Pacific "Warm Pool". The bacterial 16S ribosomal DNA (rDNA) clone libraries were constructed and analyzed by PCR-restriction fragment length polymorphism (RFLP) and DNA sequencing. The bacterial communities in these samples and their relationship to environment were analyzed consequently. The results indicated that among eight main bacterial groups found in these sediments, members of the γ-Proteobacteria were most abundant in each section of sediment core sample and the genus Colwellia belonging to γ-Proteobacteria was dominant in this area. Members of the α-Proteobacteria were found commonly existing in these samples, while members belonging to β-Proteobacteria were seldom detected. The diversity of bacterial communities from different sections of sediment core sample was δ- and ε-Proteo- bacteria and the bacterial group including genera Cytopahga, Flexibacteria and Bacteroides (CFB group). These bacteria all were inversely proportional to the depth of sediment. Phylogenetic analysis showed that there were 18%-30% and 15%-25% of total bacterial communities related to methane and sulfur metabolism respectively in each section of core sample, implicating that the metabolism of sulfur and methane played an important role in the substance and energy cycles of the Western Pacific "Warm Pool".

  18. Stress and the microbiome: linking glucocorticoids to bacterial community dynamics in wild red squirrels.

    Science.gov (United States)

    Stothart, Mason R; Bobbie, Colleen B; Schulte-Hostedde, Albrecht I; Boonstra, Rudy; Palme, Rupert; Mykytczuk, Nadia C S; Newman, Amy E M

    2016-01-01

    Bacterial diversity within animals is emerging as an essential component of health, but it is unknown how stress may influence the microbiome. We quantify a proximate link between the oral microbiome and hypothalamic-pituitary-adrenal (HPA) axis activity using faecal glucocorticoid metabolites (FGM) in wild red squirrels (Tamiasciurus hudsonicus). Not only was bacterial diversity lower at higher levels of FGM, but also between capture periods a change in bacterial relative abundance was related to an increase in FGM. These linkages between the HPA axis and microbiome communities represent a powerful capacity for stress to have multi-dimensional effects on health. PMID:26740566

  19. Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA: molecular background, virulence, and relevance for public health

    Directory of Open Access Journals (Sweden)

    MF Bonesso

    2011-01-01

    Full Text Available Staphylococcus aureus and coagulase-negative Staphylococcus (CoNS are frequently found in nosocomial environments as the main pathogen in several infections. In 1961, reports of nosocomial S. aureus resistant to methicillin, the drug of choice against penicillin-resistant strains, required new alternatives and vancomycin started being used to treat infections caused by methicillin-resistant S. aureus (MRSA. Community-acquired methicillin-resistant S. aureus (CA-MRSA was first reported in 1990 affecting patients without risk factors for infection with MRSA of hospital origin. MRSA of community origin harbor the genes responsible for the synthesis of Panton-Valentine leukocidin (PVL, a toxin associated with skin and soft tissue infections and that carries the staphylococcal cassette chromosome mec (SCCmec type IV. CA-MRSA emergence has caused great impact on the worldwide medical community since the presence of this pathogen in patients without risk factors represents a high risk to public health.

  20. Increasing antimicrobial resistance in Escherichia coli isolates from community-acquired urinary tract infections during 1998-2003 in Manisa, Turkey.

    Science.gov (United States)

    Kurutepe, Semra; Surucuoglu, Suheyla; Sezgin, Cenk; Gazi, Horu; Gulay, Mehmet; Ozbakkaloglu, Beril

    2005-06-01

    Urinary tract infections are among the most common infections with an increasing resistance to antimicrobials. The aim of this study was to determine the change in antimicrobial susceptibility of Escherichia coli isolates from patients with community-acquired urinary tract infection (UTI) for the years 1998 through 2003 and to suggest that the current empirical antibiotic therapy used for these patients is inappropriate. During the study period, 7,335 community urine samples of which 1,203 (16.4%) grew bacterial isolates were analyzed. Among the total of 1,203 isolates, 880 (73.2%) were E. coli. The range of resistance of E. coli to ampicillin was 47.8 to 64.6% and that to trimethoprim-sulfamethoxazole was 37.1 to 44.6% during the study period. The susceptibility pattern of E. coli to nitrofurantoin and cefuroxime did not vary significantly over the 6-year period. There was a significant increase in the susceptibility of E. coli to ciprofloxacin (11.3 - 26.7%), amoxicillin-clavulanate (18.4 - 29.2%) and gentamicin (7.0 - 25.6%) (P < 0.05). Empirical initial treatment with ampicillin and trimethoprim-sulfamethoxazole was thus inadequate in approximately half of UTI cases in our region. PMID:15973007

  1. Humpback whale populations share a core skin bacterial community: towards a health index for marine mammals?

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    Amy Apprill

    Full Text Available Microbes are now well regarded for their important role in mammalian health. The microbiology of skin--a unique interface between the host and environment--is a major research focus in human health and skin disorders, but is less explored in other mammals. Here, we report on a cross-population study of the skin-associated bacterial community of humpback whales (Megaptera novaeangliae, and examine the potential for a core bacterial community and its variability with host (endogenous or geographic/environmental (exogenous specific factors. Skin biopsies or freshly sloughed skin from 56 individuals were sampled from populations in the North Atlantic, North Pacific and South Pacific oceans and bacteria were characterized using 454 pyrosequencing of SSU rRNA genes. Phylogenetic and statistical analyses revealed the ubiquity and abundance of bacteria belonging to the Flavobacteria genus Tenacibaculum and the Gammaproteobacteria genus Psychrobacter across the whale populations. Scanning electron microscopy of skin indicated that microbial cells colonize the skin surface. Despite the ubiquity of Tenacibaculum and Psychrobater spp., the relative composition of the skin-bacterial community differed significantly by geographic area as well as metabolic state of the animals (feeding versus starving during migration and breeding, suggesting that both exogenous and endogenous factors may play a role in influencing the skin-bacteria. Further, characteristics of the skin bacterial community from these free-swimming individuals were assembled and compared to two entangled and three dead individuals, revealing a decrease in the central or core bacterial community members (Tenacibaculum and Psychrobater spp., as well as the emergence of potential pathogens in the latter cases. This is the first discovery of a cross-population, shared skin bacterial community. This research suggests that the skin bacteria may be connected to humpback health and immunity and could

  2. Functional Characterization of Bacterial Communities Responsible for Fermentation of Doenjang: A Traditional Korean Fermented Soybean Paste

    Science.gov (United States)

    Jung, Woo Yong; Jung, Ji Young; Lee, Hyo Jung; Jeon, Che Ok

    2016-01-01

    Doenjang samples were prepared in triplicate and their microbial abundance, bacterial communities, and metabolites throughout fermentation were analyzed to investigate the functional properties of microorganisms in doenjang. Viable bacterial cells were approximately three orders of magnitude higher than fungal cells, suggesting that bacteria are more responsible for doenjang fermentation. Pyrosequencing and proton nuclear magnetic resonance spectroscopy were applied for the analysis of bacterial communities and metabolites, respectively. Bacterial community analysis based on 16S rRNA gene sequences revealed that doenjang samples included Bacillus, Enterococcus, Lactobacillus, Clostridium, Staphylococcus, Corynebacterium, Oceanobacillus, and Tetragenococcus. These genera were found either in doenjang-meju or solar salts, but not in both, suggesting two separate sources of bacteria. Bacillus and Enterococcus were dominant genera during the fermentation, but their abundances were not associated with metabolite changes, suggesting that they may not be major players in doenjang fermentation. Tetragenococcus was dominant in 108 day-doenjang samples, when lactate, acetate, putrescine, and tyramine increased quickly as glucose and fructose decreased, indicating that Tetragenococcus might be primarily responsible for organic acid and biogenic amine production. Lactobacillus was identified as a dominant group from the 179-day samples, associated with the increase of γ-aminobutyric acid (GABA) and the decrease of galactose, indicating a potential role for this genus as a major GABA producer during fermentation. The results of this study clarified the functional properties of major bacterial communities in the doenjang fermentation process, contributing to the production of safe and high-quality doenjang. PMID:27303399

  3. Molecular profiling of rhizosphere bacterial communities associated with Prosopis juliflora and Parthenium hysterophorus.

    Science.gov (United States)

    Jothibasu, K; Chinnadurai, C; Sundaram, Sp; Kumar, K; Balachandar, Dananjeyan

    2012-03-01

    Prosopis juliflora and Parthenium hysterophorus are the two arid, exotic weeds of India that are characterized by distinct, profuse growth even in nutritionally poor soils and environmentally stressed conditions. Owing to the exceptional growth nature of these two plants, they are believed to harbor some novel bacterial communities with wide adaptability in their rhizosphere. Hence, in the present study, the bacterial communities associated with the rhizosphere of Prosopis and Parthenium were characterized by clonal 16S rRNA gene sequence analysis. The culturable microbial counts in the rhizosphere of these two plants were higher than bulk soils, possibly influenced by the root exudates of these two plants. The phylogenetic analysis of V1_V2 domains of the 16S rRNA gene indicated a wider range of bacterial communities present in the rhizosphere of these two plants than in bulk soils and the predominant genera included Acidobacteria, Gammaproteobacteria, and Bacteriodetes in the rhizosphere of Prosopis, and Acidobacteria, Betaproteobacteria, and Nitrospirae in the Parthenium rhizosphere. The diversity of bacterial communities was more pronounced in the Parthenium rhizosphere than in the Prosopis rhizosphere. This culture-independent bacterial analysis offered extensive possibilities of unraveling novel microbes in the rhizospheres of Prosopis and Parthenium with genes for diverse functions, which could be exploited for nutrient transformation and stress tolerance in cultivated crops.

  4. Functional Characterization of Bacterial Communities Responsible for Fermentation of Doenjang: A Traditional Korean Fermented Soybean Paste.

    Science.gov (United States)

    Jung, Woo Yong; Jung, Ji Young; Lee, Hyo Jung; Jeon, Che Ok

    2016-01-01

    Doenjang samples were prepared in triplicate and their microbial abundance, bacterial communities, and metabolites throughout fermentation were analyzed to investigate the functional properties of microorganisms in doenjang. Viable bacterial cells were approximately three orders of magnitude higher than fungal cells, suggesting that bacteria are more responsible for doenjang fermentation. Pyrosequencing and proton nuclear magnetic resonance spectroscopy were applied for the analysis of bacterial communities and metabolites, respectively. Bacterial community analysis based on 16S rRNA gene sequences revealed that doenjang samples included Bacillus, Enterococcus, Lactobacillus, Clostridium, Staphylococcus, Corynebacterium, Oceanobacillus, and Tetragenococcus. These genera were found either in doenjang-meju or solar salts, but not in both, suggesting two separate sources of bacteria. Bacillus and Enterococcus were dominant genera during the fermentation, but their abundances were not associated with metabolite changes, suggesting that they may not be major players in doenjang fermentation. Tetragenococcus was dominant in 108 day-doenjang samples, when lactate, acetate, putrescine, and tyramine increased quickly as glucose and fructose decreased, indicating that Tetragenococcus might be primarily responsible for organic acid and biogenic amine production. Lactobacillus was identified as a dominant group from the 179-day samples, associated with the increase of γ-aminobutyric acid (GABA) and the decrease of galactose, indicating a potential role for this genus as a major GABA producer during fermentation. The results of this study clarified the functional properties of major bacterial communities in the doenjang fermentation process, contributing to the production of safe and high-quality doenjang. PMID:27303399

  5. Mucus sugar content shapes the bacterial community structure in thermally stressed Acropora muricata

    OpenAIRE

    Lee, Sonny T. M.; Davy, Simon K.; Sen-Lin eTang; Kench, Paul S.

    2016-01-01

    It has been proposed that the chemical composition of a coral’s mucus can influence the associated bacterial community. However, information on this topic is rare, and non-existent for corals that are under thermal stress. This study therefore compared the carbohydrate composition of mucus in the coral Acropora muricata when subjected to increasing thermal stress from 26°C to 31°C, and determined whether this composition correlated with any changes in the bacterial community. Results showed t...

  6. Characterization of a Bacterial Community in an Abandoned Semiarid Lead-Zinc Mine Tailing Site▿ †

    OpenAIRE

    Mendez, Monica O.; Neilson, Julia W; Maier, Raina M.

    2008-01-01

    Bacterial diversity in mine tailing microbial communities has not been thoroughly investigated despite the correlations that have been observed between the relative microbial diversity and the success of revegetation efforts at tailing sites. This study employed phylogenetic analyses of 16S rRNA genes to compare the bacterial communities present in highly disturbed, extremely (pH 2.7) and moderately (pH 5.7) acidic lead-zinc mine tailing samples from a semiarid environment with those from a v...

  7. Community acquired Roseomonas infection in a pre-existing Tubercular lung lesion

    Directory of Open Access Journals (Sweden)

    Navinchandra M Kaore

    2014-01-01

    Full Text Available Roseomonas are nonfermenting opportunistic Gram-negative bacilli belonging to the newly established genus of Roseomonas. The clinical experience with the species is limited and is difficult to diagnose because of limited expertise and lack of commercially available identification kits with any of the automated systems. This is a first ever reported case of secondary bacterial infection due to Roseomonas genomospecies 6 in a patient of pulmonary tuberculosis from the Indian subcontinent.

  8. Variable effects of dispersal on productivity of bacterial communities due to changes in functional trait composition.

    Directory of Open Access Journals (Sweden)

    Ina Severin

    Full Text Available Previous studies have shown variable relationships between dispersal rate and ecosystem functioning, but the reasons for and mechanisms behind variable dispersal rate-functioning patterns are currently unknown. In this study we used six bacterial lake water communities in a laboratory experiment in order to investigate how dispersal among communities influences community productivity by evaluating three different mechanisms: 1 changes in taxonomic diversity, 2 changes in phylogenetic diversity or 3 changes in the composition of functional traits. The experiment was conducted in two phases; (A a dialysis bag experiment where the dispersal rate among six communities was manipulated and the subsequent change in bacterial diversity and growth rate was recorded, and (B a regrowth experiment where we manipulated available resources to study how well a taxon grows on certain organic carbon resources, i.e. their functional traits. From experiment (B we could thus estimate changes in functional traits in communities in experiment (A. Bacterial production was affected by dispersal, but not consistently among lakes. Neither change in taxonomic or phylogenetic diversity with dispersal could explain the observed dispersal-productivity relationships. Instead, changes in trait composition with dispersal, especially the communities' ability to use p-coumaric acid, an aromatic compound, could explain the observed dispersal-productivity relationships. Changes in this trait caused by dispersal seemed especially important for bacterial productivity in waters with a high aromaticity of the organic matter pool. We conclude that the effect of dispersal on bacterial communities can affect ecosystem functioning in different ways, through changes in functional key-traits which are important for the local environment.

  9. Pyrosequencing-based assessment of bacterial community structure in mine soils affected by mining subsidence

    Institute of Scientific and Technical Information of China (English)

    Li Yuanyuan a; Chen Longqian a; ⇑; Wen Hongyu b; Zhou Tianjian a; Zhang Ting a

    2014-01-01

    Based on the 454 pyrosequencing approach, this research evaluated the influence of coal mining subsi-dence on soil bacterial diversity and community structure in Chinese mining area. In order to characterize the bacterial community comparatively, this study selected a field experiment site with coal-excavated subsidence soils and an adjacent site with non-disturbed agricultural soils, respectively. The dataset com-prises 24512 sequences that are affiliated to the 7 phylogenetic groups: proteobacteria, actinobacteria, bacteroidetes, gemmatimonadetes, chloroflexi, nitrospirae and unclassified phylum. Proteobacteria is the largest bacterial phylum in all samples, with a marked shift of the proportions of alpha-, beta-, and gammaproteobacteria. The results show that undisturbed soils are relatively more diverse and rich than subsided soils, and differences in abundances of dominant taxonomic groups between the two soil groups are visible. Compared with the control, soil nutrient contents decline achieves significant level in subsided soils. Correlational analysis showed bacterial diversity indices have significantly positive corre-lation with soil organic matter, total N, total P, and available K, but in negative relation with soil salinity. Ground subsidence noticeably affects the diversity and composition of soil microbial community. Degen-eration of soil fertility and soil salinization inhibits the sole-carbon-source metabolic ability of microbial community, leading to the simplification of advantage species and uneven distribution of microbial spe-cies. This work demonstrates the great potential of pyrosequencing technique in revealing microbial diversity and presents background information of microbial communities of mine subsidence land.

  10. A high-throughput sequencing ecotoxicology study of freshwater bacterial communities and their responses to tebuconazole.

    Science.gov (United States)

    Pascault, Noémie; Roux, Simon; Artigas, Joan; Pesce, Stéphane; Leloup, Julie; Tadonleke, Rémy D; Debroas, Didier; Bouchez, Agnès; Humbert, Jean-François

    2014-12-01

    The pollution of lakes and rivers by pesticides is a growing problem worldwide. However, the impacts of these substances on microbial communities are still poorly understood, partly because next-generation sequencing (NGS) has rarely been used in an ecotoxicology context to study bacterial communities despite its interest for accessing rare taxa. Microcosm experiments were carried out to evaluate the effects of tebuconazole (TBZ) on the structure and composition of bacterial communities from two types of freshwater ecosystem (lakes and rivers) with differing histories of pollutant contamination (pristine vs. previously exposed sites). Pyrosequencing revealed that bacterial diversity was higher in the river than in the lakes and in previously exposed sites than in pristine sites. Lakes and river stations shared very few OTUs, and differences at the phylum level were identified between these ecosystems (i.e. the relative importance of Actinobacteria and Gammaproteobacteria). Despite differences between these ecosystems and their contamination history, no significant effect of TBZ on bacterial community structure or composition was observed. Compared to functional parameters that displayed variable responses, we demonstrated that a combination of classical methods and NGS is necessary to investigate the ecotoxicological responses of microbial communities to pollutants.

  11. Diazotrophic potential among bacterial communities associated with wild and cultivated Agave species.

    Science.gov (United States)

    Desgarennes, Damaris; Garrido, Etzel; Torres-Gomez, Miryam J; Peña-Cabriales, Juan J; Partida-Martinez, Laila P

    2014-12-01

    Agaves are major biotic resources in arid and semi-arid ecosystems. Despite their ecological, economical and cultural relevance, many aspects of the microbial communities associated with agaves are still unknown. Here, we investigated the bacterial communities associated with two Agave species by 16S rRNA- Denaturing gradient gel electrophoresis fingerprinting and sequencing. We also evaluated the effects of biotic and abiotic factors in the structure of the bacterial communities. In parallel, we isolated and characterized diazotrophic bacteria associated with agaves, as Agave soils are characterized by their low nitrogen content. Our results demonstrate that in Agave, the structure of prokaryotic assemblages was mostly influenced by the community group, where the soil, episphere, and endosphere were clearly distinct. Proteobacteria (γ and α), Actinobacteria, and Acidobacteria were the dominant phyla. Bacterial communities in the episphere of agaves were mainly influenced by the host species, whereas in the endosphere were affected by the season. Fifteen bacterial taxa were common and abundant in the endosphere of both Agave species during the dry season. Notably, some of the confirmed diazotrophic strains belonged to this group, suggesting a possible beneficial role in planta. PMID:25314594

  12. Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes

    Science.gov (United States)

    Comte, J.; Lovejoy, C.; Crevecoeur, S.; Vincent, W. F.

    2016-01-01

    Permafrost thaw ponds and lakes are widespread across the northern landscape and may play a central role in global biogeochemical cycles, yet knowledge about their microbial ecology is limited. We sampled a set of thaw ponds and lakes as well as shallow rock-basin lakes that are located in distinct valleys along a north-south permafrost degradation gradient. We applied high-throughput sequencing of the 16S rRNA gene to determine co-occurrence patterns among bacterial taxa (operational taxonomic units, OTUs), and then analyzed these results relative to environmental variables to identify variables controlling bacterial community structure. Network analysis was applied to identify possible ecological linkages among the bacterial taxa and with abiotic and biotic variables. The results showed an overall high level of shared taxa among bacterial communities within each valley; however, the bacterial co-occurrence patterns were non-random, with evidence of habitat preferences. There were taxonomic differences in bacterial assemblages among the different valleys that were statistically related to dissolved organic carbon concentration, conductivity and phytoplankton biomass. Co-occurrence networks revealed complex interdependencies within the bacterioplankton communities and showed contrasting linkages to environmental conditions among the main bacterial phyla. The thaw pond networks were composed of a limited number of highly connected taxa. This "small world network" property would render the communities more robust to environmental change but vulnerable to the loss of microbial "keystone species". These highly connected nodes (OTUs) in the network were not merely the numerically dominant taxa, and their loss would alter the organization of microbial consortia and ultimately the food web structure and functioning of these aquatic ecosystems.

  13. Community-acquired methicillin-resistant Staphylococcus aureus: What do we need to know?

    OpenAIRE

    Witte, Wolfgang

    2009-01-01

    Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has become a matter of concern worldwide, in particular in the USA. For the analysis of emergence and spread, clear definitions based on epidemiological origin are needed for discrimination between CA-MRSA, healthcare-associated community MRSA, and healthcare-associated MRSA (HA-MRSA). Although its role in pathogenesis is currently under debate, the capability for Panton-Valentine leukocidin formation is associated wit...

  14. Dynamic of bacterial communities attached to lightened phytodetritus.

    Science.gov (United States)

    Petit, Morgan; Bonin, Patricia; Amiraux, Rémi; Michotey, Valérie; Guasco, Sophie; Armitano, Joshua; Jourlin-Castelli, Cécile; Vaultier, Frédéric; Méjean, Vincent; Rontani, Jean-François

    2015-09-01

    The effects of singlet oxygen ((1)O2) transfer to bacteria attached on phytodetritus were investigated under laboratory-controlled conditions. For this purpose, a nonaxenic culture of Emiliania huxleyi in late stationary phase was studied for bacterial viability. Our results indicated that only 9 ± 3% of attached bacteria were alive compared to 46 ± 23% for free bacteria in the E. huxleyi culture. Apparently, under conditions of low irradiance (36 W m(-2)), during the culture, the cumulative dose received (22,000 kJ m(-2)) was sufficiently important to induce an efficient (1)O2 transfer to attached bacteria during the senescence of E. huxleyi cells. At this stage, attached bacteria appeared to be dominated by pigmented bacteria (Maribacter, Roseobacter, Roseovarius), which should resist to (1)O2 stress probably due to their high contents of carotenoids. After subsequent irradiation of the culture until fully photodegradation of chlorophyll, DGGE analyses showed that the diversity of bacteria attached to E. huxleyi cells is modified by light. Photooxidative alterations of bacteria were confirmed by the increasing amounts of cis-vaccenic photoproducts (bacterial marker) per bacteria observed during irradiation time. Interestingly, preliminary chemotaxis experiments showed that Shewanella oneidensis considered here as a model of motile bacteria was attracted by phytodetritus producing or not (1)O2. This lack of repulsive effects could explain the high mortality rate of bacteria measured on E. huxleyi cells. PMID:25687611

  15. Temporal changes in soil bacterial and archaeal communities with different fertilizers in tea orchards.

    Science.gov (United States)

    Wang, Hua; Yang, Shao-hui; Yang, Jing-ping; Lv, Ya-min; Zhao, Xing; Pang, Ji-liang

    2014-11-01

    It is important to understand the effects of temporal changes in microbial communities in the acidic soils of tea orchards with different fertilizers. A field experiment involving organic fertilizer (OF), chemical fertilizer (CF), and unfertilized control (CK) treatments was arranged to analyze the temporal changes in the bacterial and archaeal communities at bimonthly intervals based on the 16S ribosomal RNA (rRNA) gene using terminal restriction fragment length polymorphism (T-RFLP) profiling. The abundances of total bacteria, total archaea, and selected functional genes (bacterial and archaeal amoA, bacterial narG, nirK, nirS, and nosZ) were determined by quantitative polymerase chain reaction (qPCR). The results indicate that the structures of bacterial and archaeal communities varied significantly with time and fertilization based on changes in the relative abundance of dominant T-RFs. The abundancy of the detected genes changed with time. The total bacteria, total archaea, and archaeal amoA were less abundant in July. The bacterial amoA and denitrifying genes were less abundant in September, except the nirK gene. The OF treatment increased the abundance of the observed genes, while the CF treatment had little influence on them. The soil temperature significantly affected the bacterial and archaeal community structures. The soil moisture was significantly correlated with the abundance of denitrifying genes. Of the soil chemical properties, soil organic carbon was the most important factor and was significantly correlated with the abundance of the detected genes, except the nirK gene. Overall, this study demonstrated the effects of both temporal alteration and organic fertilizer on the structures of microbial communities and the abundance of genes involved in the nitrogen cycle.

  16. Molecular characterization of bacterial communities in the human gastrointestinal tract

    NARCIS (Netherlands)

    Zoetendal, E.G.

    2001-01-01

    The human gastrointestinal (GI) tract is a complex ecosystem in which host and microbial cells live in close contact with each other. The microbial community in the human GI tract has an important nutritional and protective function and mainly consists of anaerobic bacteria. After birth, the germ-fr

  17. Coral-associated bacterial communities on Ningaloo Reef, Western Australia.

    Science.gov (United States)

    Ceh, Janja; Van Keulen, Mike; Bourne, David G

    2011-01-01

    Coral-associated microbial communities from three coral species (Pocillopora damicornis, Acropora tenuis and Favites abdita) were examined every 3 months (January, March, June, October) over a period of 1 year on Ningaloo Reef, Western Australia. Tissue from corals was collected throughout the year and additional sampling of coral mucus and seawater samples was performed in January. Tissue samples were also obtained in October from P. damicornis coral colonies on Rottnest Island off Perth, 1200 km south of Ningaloo Reef, to provide comparisons between coral-microbial associates in different locations. The community structures of the coral-associated microorganisms were analysed using phylogenetic analysis of 16S rRNA gene clone libraries, which demonstrated highly diverse microbial profiles among all the coral species sampled. Principal component analysis revealed that samples grouped according to time and not species, indicating that coral-microbial associations may be a result of environmental drivers such as oceanographic characteristics, benthic community structure and temperature. Tissue samples from P. damicornis at Rottnest Island revealed similarities in bacteria to the samples at Ningaloo Reef. This study highlights that coral-associated microbial communities are highly diverse; however, the complex interactions that determine the stability of these associations are not necessarily dependent on coral host specificity. PMID:21044100

  18. Effects of transient temperature conditions on the divergence of activated sludge bacterial community structure and function.

    Science.gov (United States)

    Nadarajah, Nalina; Allen, D Grant; Fulthorpe, Roberta R

    2007-06-01

    The effect of temperature fluctuations on bacterial community structure and function in lab-scale sequencing batch reactors treating bleached kraft mill effluent was investigated. An increase in temperature from 30 to 45 degrees C caused shifts in both bacterial community structure and function. Triplicate reactors were highly similar for 40 days following startup. After the temperature shift, their community structure and function started to diverge from each other and from the control. A multi-response permutation procedure confirmed that the variability in community structure between transient and control reactors were greater than that among the triplicate transient reactors. The fact that these disturbances manifest themselves in different ways in apparently identical reactors suggests a high degree of variability between replicate systems.

  19. Variable effects of dispersal on productivity of bacterial communities due to changes in functional trait composition

    DEFF Research Database (Denmark)

    Severin, Ina; Östman, Örjan; Lindström, Eva S.

    2013-01-01

    ) a dialysis bag experiment where the dispersal rate among six communities was manipulated and the subsequent change in bacterial diversity and growth rate was recorded, and (B) a regrowth experiment where we manipulated available resources to study how well a taxon grows on certain organic carbon resources, i......Previous studies have shown variable relationships between dispersal rate and ecosystem functioning, but the reasons for and mechanisms behind variable dispersal rate - functioning patterns are currently unknown. In this study we used six bacterial lake water communities in a laboratory experiment...... in order to investigate how dispersal among communities influences community productivity by evaluating three different mechanisms: 1) changes in taxonomic diversity, 2) changes in phylogenetic diversity or 3) changes in the composition of functional traits. The experiment was conducted in two phases; (A...

  20. Long- term manure exposure increases soil bacterial community potential for plasmid uptake

    DEFF Research Database (Denmark)

    Musovic, Sanin; Klümper, Uli; Dechesne, Arnaud;

    2014-01-01

    Microbial communities derived from soils subject to different agronomic treatments were challenged with three broad host range plasmids, RP4, pIPO2tet and pRO101, via solid surface filter matings to assess their permissiveness. Approximately 1 in 10 000 soil bacterial cells could receive and main......Microbial communities derived from soils subject to different agronomic treatments were challenged with three broad host range plasmids, RP4, pIPO2tet and pRO101, via solid surface filter matings to assess their permissiveness. Approximately 1 in 10 000 soil bacterial cells could receive...... and maintain the plasmids. The community permissiveness increased up to 100% in communities derived from manured soil. While the plasmid transfer frequency was significantly influenced by both the type of plasmid and the agronomic treatment, the diversity of the transconjugal pools was purely plasmid dependent...

  1. [Algo-bacterial communities of the Kulunda steppe (Altai region, Russia) soda lakes].

    Science.gov (United States)

    Samylina, O S; Sapozhnikov, F V; Gaĭnanova, O Iu; Riabova, A V; Nikitin, M A; Sorokin, D Iu

    2015-01-01

    The composition and macroscopic structure of the floating oxygenic phototrophic communities from Kulunda steppe soda lakes (Petukhovskoe sodovoe, Tanatara VI, and Gorchiny 3) was described based on the data of the 2011 and 2012 expeditions (Winogradsky Institute of Microbiology). The algo-bacterial community with a green alga Ctenocladus circinnatus as an edificator was the typical one. Filamentous Geitlerinema sp. and Nodosilinea sp. were the dominant cyanobacteria. Apart from C. circinnatus, the algological component of the community contained unicellular green algae Dunaliella viridis and cf. Chlorella minutissima, as well as diatoms (Anomeoneis sphaerophora, Brchysira brebissonii, Brachysira zellensis, Mastogloia pusilla var. subcapitata, Nitzschia amphibia, Nitzschia communis, and Nitzschia sp.1). The latter have not been previously identified in the lakes under study. In all lakes, a considerable increase in salinity was found to result in changes in the composition and macroscopic structure of algo-bacterial communities. PMID:25916153

  2. Treatment of adults with community-acquired respiratory tract infections: results of a multicentric clinical trial with gatifloxacin

    Directory of Open Access Journals (Sweden)

    Medeiros Eduardo Alexandrino Servolo

    2002-01-01

    Full Text Available Respiratory tract infections have an important clinical and economic impact and they are the most common indication for antibiotic use in outpatient practice. This prospective, multicenter non-controlled trial assessed the efficacy and safety of gatifloxacin in the treatment of community-acquired respiratory tract infections. Patients were treated with a daily oral dose of gatifloxacin 400 mg for 7-14 days. The diagnosis of respiratory infection was made based on the clinical condition and/or radiologic findings. A total of 5,044 adult patients with community-acquired respiratory infections was treated with gatifloxacin in different centers in Brazil between March 1, 2001, and October 31, 2001. Among the 5,044 patients treated, 1,501 patients (29.76% had community-acquired pneumonia, 756 (14.99% had acute exacerbation of chronic bronchitis and 2,787 (55.25% had acute sinusitis. Of the total of patients treated, 3,607 (71.51% were considered cured, 1,261 (25% progressed with some clinical improvement, 28 (0.56% presented a relapse, 56 (1.11% failed to treatment and 92 (1.82% were unable to be evaluated. Adverse events were described in 634 (12.57% patients. The most common adverse events were: nausea (2.24%; dyspepsia (1.86%; diarrhea (0.79%; change in taste (0.46%; insomnia and irritability (0.22%; dizziness (0.77%; headache (0.42%; allergic reaction (0.18%; Central Nervous System alterations - insomnia, agitation, anxiety - (0.46%. This study showed that the treatment of respiratory tract infections with gatifloxacin was safe and efficient and had a low incidence of adverse events.

  3. Surveillance of Antibiotic Resistance among Hospital- and Community-Acquired Toxigenic Clostridium difficile Isolates over 5-Year Period in Kuwait

    Science.gov (United States)

    Jamal, Wafaa Y.; Rotimi, Vincent O.

    2016-01-01

    Clostridium difficile infection (CDI) is a leading and an important cause of diarrhea in a healthcare setting especially in industrialized countries. Community-associated CDI appears to add to the burden on healthcare setting problems. The aim of the study was to investigate the antimicrobial resistance of healthcare-associated and community-acquired C. difficile infection over 5 years (2008–2012) in Kuwait. A total of 111 hospital-acquired (HA-CD) and 35 community-acquired Clostridium difficile (CA-CD) clinical isolates from stool of patients with diarrhoea were studied. Antimicrobial susceptibility testing of 15 antimicrobial agents against these pathogens was performed using E test method. There was no evidence of resistance to amoxicillin-clavulanic acid, daptomycin, linezolid, piperacillin-tazobactam, teicoplanin and vancomycin by both HA-CD and CA-CD isolates. Metronidazole had excellent activity against CA-CD but there was a 2.9% resistance rate against HA-CD isolates. Ampicillin, clindamycin, levofloxacin and imipenem resistance rates among the HC-CD vs. CA-CD isolates were 100 vs. 47.4%; 43 vs. 47.4%; 100 vs. 100% and 100 vs. 89%, respectively. An unexpected high rifampicin resistance rate of 15.7% emerged amongst the HA-CD isolates. In conclusion, vancomycin resistance amongst the HA-CD and CA-CD isolates was not encountered in this series but few metronidazole resistant hospital isolates were isolated. High resistance rates of ampicillin, clindamycin, levofloxacin, and imipenem resistance were evident among both CA-CD and HA-CD isolates. Rifampicin resistance is emerging among the HA-CD isolates. PMID:27536994

  4. Seasonal fluctuations of bacterial community diversity in agricultural soil and experimental validation by laboratory disturbance experiments.

    Science.gov (United States)

    Meier, Christoph; Wehrli, Bernhard; van der Meer, Jan Roelof

    2008-08-01

    Natural fluctuations in soil microbial communities are poorly documented because of the inherent difficulty to perform a simultaneous analysis of the relative abundances of multiple populations over a long time period. Yet, it is important to understand the magnitudes of community composition variability as a function of natural influences (e.g., temperature, plant growth, or rainfall) because this forms the reference or baseline against which external disturbances (e.g., anthropogenic emissions) can be judged. Second, definition of baseline fluctuations in complex microbial communities may help to understand at which point the systems become unbalanced and cannot return to their original composition. In this paper, we examined the seasonal fluctuations in the bacterial community of an agricultural soil used for regular plant crop production by using terminal restriction fragment length polymorphism profiling (T-RFLP) of the amplified 16S ribosomal ribonucleic acid (rRNA) gene diversity. Cluster and statistical analysis of T-RFLP data showed that soil bacterial communities fluctuated very little during the seasons (similarity indices between 0.835 and 0.997) with insignificant variations in 16S rRNA gene richness and diversity indices. Despite overall insignificant fluctuations, between 8 and 30% of all terminal restriction fragments changed their relative intensity in a significant manner among consecutive time samples. To determine the magnitude of community variations induced by external factors, soil samples were subjected to either inoculation with a pure bacterial culture, addition of the herbicide mecoprop, or addition of nutrients. All treatments resulted in statistically measurable changes of T-RFLP profiles of the communities. Addition of nutrients or bacteria plus mecoprop resulted in bacteria composition, which did not return to the original profile within 14 days. We propose that at less than 70% similarity in T-RFLP, the bacterial communities risk to

  5. Emergence of Collective Territorial Defense in Bacterial Communities: Horizontal Gene Transfer Can Stabilize Microbiomes

    OpenAIRE

    János Juhász; Attila Kertész-Farkas; Dóra Szabó; Sándor Pongor

    2014-01-01

    Multispecies bacterial communities such as the microbiota of the gastrointestinal tract can be remarkably stable and resilient even though they consist of cells and species that compete for resources and also produce a large number of antimicrobial agents. Computational modeling suggests that horizontal transfer of resistance genes may greatly contribute to the formation of stable and diverse communities capable of protecting themselves with a battery of antimicrobial agents while preserving ...

  6. Bacterial communities and species-specific associations with the mucus of Brazilian coral species

    OpenAIRE

    Camila Carlos; Tatiana T. Torres; Ottoboni, Laura M.M.

    2013-01-01

    We investigated the existence of species-specific associations between Brazilian coral species and bacteria. Pyrosequencing of the V3 region of the 16S rDNA was used to analyze the taxonomic composition of bacterial communities associated with the mucus of four coral species (Madracis decactis, Mussismilia hispida, Palythoa caribaeorum, and Tubastraea coccinea) in two seasons (winter and summer), which were compared with the surrounding water and sediment. The microbial communities found in s...

  7. Changes in Bacterial and Fungal Communities across Compost Recipes, Preparation Methods, and Composting Times

    Science.gov (United States)

    Neher, Deborah A.; Weicht, Thomas R.; Bates, Scott T.; Leff, Jonathan W.; Fierer, Noah

    2013-01-01

    Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and fungal communities in compost produced at a commercial-scale. Bacterial and fungal communities responded to both compost recipe and composting method. Specifically, bacterial communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and fungal communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed by Ascomycota and finally Basidiomycota. Zygomycota were associated more with manure-silage and hay than hardwood composts. Most commercial composters focus on the thermophilic phase as an economic means to insure sanitation of compost from pathogens. However, the community succeeding the thermophilic phase begs further investigation to determine how the microbial dynamics observed here can be best managed

  8. Phenotypic and genotypic adaptation of aerobic heterotrophic sediment bacterial communities to mercury stress.

    OpenAIRE

    Barkay, T; Olson, B. H.

    1986-01-01

    The effects of mercury contamination of lake sediments on the phenotypic and genotypic mercury resistance of the indigenous heterotrophic aerobic bacterial communities were investigated. Strong positive correlations between mercury sediment concentration and the frequency of the gene coding for mercury volatilization (mer) (r = 0.96) or the phenotypic mercury resistance (r = 0.86) of the studied communities suggested that the inheritance via selection or genetic exchange of the mer gene had p...

  9. Bacterial communities associated with the surfaces of fresh fruits and vegetables.

    Directory of Open Access Journals (Sweden)

    Jonathan W Leff

    Full Text Available Fresh fruits and vegetables can harbor large and diverse populations of bacteria. However, most of the work on produce-associated bacteria has focused on a relatively small number of pathogenic bacteria and, as a result, we know far less about the overall diversity and composition of those bacterial communities found on produce and how the structure of these communities varies across produce types. Moreover, we lack a comprehensive view of the potential effects of differing farming practices on the bacterial communities to which consumers are exposed. We addressed these knowledge gaps by assessing bacterial community structure on conventional and organic analogs of eleven store-bought produce types using a culture-independent approach, 16 S rRNA gene pyrosequencing. Our results demonstrated that the fruits and vegetables harbored diverse bacterial communities, and the communities on each produce type were significantly distinct from one another. However, certain produce types (i.e., sprouts, spinach, lettuce, tomatoes, peppers, and strawberries tended to share more similar communities as they all had high relative abundances of taxa belonging to the family Enterobacteriaceae when compared to the other produce types (i.e., apples, peaches, grapes, and mushrooms which were dominated by taxa belonging to the Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria phyla. Although potentially driven by factors other than farming practice, we also observed significant differences in community composition between conventional and organic analogs within produce types. These differences were often attributable to distinctions in the relative abundances of Enterobacteriaceae taxa, which were generally less abundant in organically-grown produce. Taken together, our results suggest that humans are exposed to substantially different bacteria depending on the types of fresh produce they consume with differences between conventionally and organically

  10. Temporal changes in soil bacterial and archaeal communities with different fertilizers in tea orchards* #

    OpenAIRE

    Wang, Hua; Yang, Shao-hui; Yang, Jing-ping; Lv, Ya-min; Zhao, Xing; Pang, Ji-liang

    2014-01-01

    It is important to understand the effects of temporal changes in microbial communities in the acidic soils of tea orchards with different fertilizers. A field experiment involving organic fertilizer (OF), chemical fertilizer (CF), and unfertilized control (CK) treatments was arranged to analyze the temporal changes in the bacterial and archaeal communities at bimonthly intervals based on the 16S ribosomal RNA (rRNA) gene using terminal restriction fragment length polymorphism (T-RFLP) profili...

  11. Cardiac complications in patients with community-acquired pneumonia: a systematic review and meta-analysis of observational studies.

    OpenAIRE

    Corrales-Medina, Vicente F; Suh, Kathryn N.; Gregory Rose; Chirinos, Julio A.; Steve Doucette; D. William Cameron; Dean A Fergusson

    2011-01-01

    Editors' Summary Background Community-acquired pneumonia (CAP), that is, pneumonia infections contracted outside of hospital or health care settings, is a common condition and can be fatal, particularly to older people. For example, every year, an estimated 5–6 million people contract this form of pneumonia in the US, leading to 1.1 million people being admitted to hospitals and causing 60,000 deaths—the most frequent cause of infectious disease-related mortality. In the US for example, more ...

  12. Short- and long-term mortality in patients with community-acquired severe sepsis and septic shock

    DEFF Research Database (Denmark)

    Storgaard, Merete; Hallas, Jesper; Gahrn-Hansen, Bente;

    2013-01-01

    Background: Severe sepsis and septic shock have a high 30-day mortality (10-50%), but the long-term mortality is not well described. The purpose of this study was to describe long-term mortality among patients with community-acquired severe sepsis or septic shock compared to a population...... (multivariate Cox regression controlling for age, sex, and Charlson comorbidity index). Conclusions: Patients with severe sepsis and septic shock who survived the first 30 days had a 2.7 times higher mortality hazard in the first year and a 2.3 times higher mortality hazard in the next 3 y, compared to persons...

  13. Vitamin D deficiency is associated with community-acquired clostridium difficile infection: a case–control study

    OpenAIRE

    Sahay, Tanya; Ananthakrishnan, Ashwin N.

    2014-01-01

    Background Clostridium difficile infection (CDI) is increasingly recognized as an important community acquired pathogen causing disease (CA-CDI). Vitamin D [25(OH)D] has immune modulatory effects and plays an important role in intestinal immunity. The role of vitamin D in CA-CDI has not been examined previously. Methods This was a single referral center case–control study. Cases comprised of all patients with CA-CDI who had a serum 25(OH)D measured within 12 months prior to infection. Control...

  14. Response of bacterial community structure and function to experimental rainwater additions in a coastal eutrophic embayment

    Science.gov (United States)

    Teira, Eva; Hernando-Morales, Víctor; Martínez-García, Sandra; Figueiras, Francisco G.; Arbones, Belén; Álvarez-Salgado, Xosé Antón

    2013-03-01

    Although recognized as a potentially important source of both inorganic and organic nutrients, the impact of rainwater on microbial populations from marine planktonic systems has been poorly assessed. The effect of rainwater additions on bacterioplankton metabolism and community composition was evaluated in microcosm experiments enclosing natural marine plankton populations from the Ría de Vigo (NW Spain). The experiments were conducted during three different seasons (spring, autumn and winter) using rainwater collected at three different locations: marine, urban and rural sites. Bacterial abundance and production significantly increased up to 1.3 and 1.8-fold, respectively, after urban rainwater additions in spring, when ambient nutrient concentration was very low. Overall, the increments in bacterial production were higher than those in bacterial respiration, which implies that a higher proportion of carbon consumed by bacteria would be available to higher trophic levels. The response of the different bacterial groups to distinct rainwater types differed between seasons. The most responsive bacterial groups were Betaproteobacteria which significantly increased their abundance after urban (in spring and winter) and marine (in spring) rainwater additions, and Bacteroidetes which positively responded to all rainwater treatments in spring and to urban rainwater in autumn. Gammaproteobacteria and Roseobacter responded only to urban (in spring) and marine (in winter) rainwater treatment, respectively. The responses to rainwater additions were moderate and transient, and the resulting bacterial community structure was not importantly altered.

  15. Assessment of bacterial community structure in nitrifying biofilm under inorganic carbon-sufficient and -limited conditions.

    Science.gov (United States)

    Bae, Hyokwan; Chung, Yun-Chul; Yang, Heejeong; Lee, Changsoo; Aryapratama, Rio; Yoo, Young J; Lee, Seockheon

    2015-01-01

    In this work, nitrification and changes in the composition of the total bacterial community under inorganic carbon (IC)-limited conditions, in a nitrifying moving bed biofilm reactor, was investigated. A culture-independent analysis of cloning and sequencing based on the 16S rRNA gene was applied to quantify the bacterial diversity and to determine bacterial taxonomic assignment. IC concentrations had significant effects on the stability of ammonia-oxidation as indicated by the reduction of the nitrogen conversion rate with high NH4(+)-N loadings. The predominance of Nitrosomonas europaea was maintained in spite of changes in the IC concentration. In contrast, heterotrophic bacterial species contributed to a high bacterial diversity, and to a dynamic shift in the bacterial community structure, under IC-limited conditions. In this study, individual functions of heterotrophic bacteria were estimated based on taxonomic information. Possible key roles of coexisting heterotrophic bacteria are the assimilation of organic compounds of extracellular polymeric substances produced by nitrifiers, and biofilm formation by providing a filamentous structure and aggregation properties.

  16. Bacterial communities in fish sauce mash using culture-dependent and -independent methods.

    Science.gov (United States)

    Fukui, Youhei; Yoshida, Mitsuhiro; Shozen, Kei-ichi; Funatsu, Yasuhiro; Takano, Takashi; Oikawa, Hiroshi; Yano, Yutaka; Satomi, Masataka

    2012-01-01

    In fish sauce production, microorganisms are associated with the fermentation process; however, the sequential changes in the bacterial communities have never been examined throughout the period of fermentation. In this study, we determined the bacterial floras in a fish sauce mash over 8 months, using three different culture media and 16S rRNA gene clone library analysis. During the first 4 weeks, viable counts of non-halophilic and halophilic bacteria decreased and were dominated by Staphylococcus species. Between 4 and 6 weeks, halophilic and highly halophilic bacterial counts markedly increased from 10(7) to 10(8) cfu/g, and the predominant species changed to Tetragenococcus halophilus. The occurrence of T. halophilus was associated with an increase of lactic acid and a reduction of pH values. In contrast, non-halophilic bacterial counts decreased to 10(6) cfu/g by 6 weeks with Bacillus subtilis as the dominant isolate. Clone library analysis revealed that the dominant bacterial group also changed from Staphylococcus spp. to T. halophilus, and the changes were consistent with those of the floras of halophilic and highly halophilic isolates. This is the first report describing a combination approach of culture and clone library methods for the analysis of bacterial communities in fish sauce mash. PMID:22990487

  17. Dynamics of bacterial communities in soils of rainforest fragments under restoration processes

    Science.gov (United States)

    Vasconcellos, Rafael; Zucchi, Tiago; Taketani, Rodrigo; Andreote, Fernando; Cardoso, Elke

    2014-05-01

    The Brazilian Atlantic Forest ("Mata Atlântica") has been largely studied due to its valuable and unique biodiversity. Unfortunately, this priceless ecosystem has been widely deforested and only 10% of its original area still remains. Many projects have been successfully implemented to restore its fauna and flora but there is a lack of information on how the soil bacterial communities respond to this process. Thus, our aim was to evaluate the influence of soil attributes and seasonality on soil bacterial communities of rainforest fragments under restoration processes. Soil samples from a native site and two ongoing restoration fragments with different ages of implementation (10 and 20 years) were collected and assayed by using culture-independent approaches. Our findings demonstrate that seasonality barely altered the bacterial distribution whereas soil chemical attributes and plant diversity highly influenced the bacterial community structure during the restoration process. Moreover, the strict relationship observed for two bacterial groups, Solibacteriaceae and Verrucomicrobia, one with the youngest (10 years) and the other with the oldest (native) site suggests their use as bioindicators of soil quality and soil recovery of forest fragments under restoration.

  18. Bacterial community characterization in the soils of native and restored rainforest fragments.

    Science.gov (United States)

    Vasconcellos, Rafael L F; Zucchi, Tiago D; Taketani, Rodrigo G; Andreote, Fernando D; Cardoso, Elke J B N

    2014-11-01

    The Brazilian Atlantic Forest ("Mata Atlântica") has been largely studied due to its valuable and unique biodiversity. Unfortunately, this priceless ecosystem has been widely deforested and only 10 % of its original area is still untouched. Some projects have been successfully implemented to restore its fauna and flora but there is a lack of information on how the soil bacterial communities respond to this process. Thus, our aim was to evaluate the influence of soil attributes and seasonality on soil bacterial communities of rainforest fragments under restoration processes. Soil samples from a native site and two ongoing restoration fragments with different times of implementation (10 and 20 years) were collected and assayed by using culture-independent approaches. Our findings demonstrate that seasonality barely altered the bacterial distribution whereas soil chemical attributes and plant species were related to bacterial community structure during the restoration process. Moreover, the strict relationship observed for two bacterial groups, Solibacteriaceae and Verrucomicrobia, increasing from the more recently planted (10 years) to the native site, with the 20 year old restoration site in the middle, which may suggest their use as bioindicators of soil quality and recovery of forest fragments being restored. PMID:25155863

  19. Seasonal changes in nitrogen-cycle gene abundances and in bacterial communities in acidic forest soils.

    Science.gov (United States)

    Jung, Jaejoon; Yeom, Jinki; Han, Jiwon; Kim, Jisun; Park, Woojun

    2012-06-01

    The abundance of genes related to the nitrogen biogeochemical cycle and the microbial community in forest soils (bacteria, archaea, fungi) were quantitatively analyzed via real-time PCR using 11 sets of specific primers amplifying nifH, bacterial amoA, archaeal amoA, narG, nirS, nirK, norB, nosZ, bacterial 16S rRNA gene, archaeal 16S rRNA gene, and the ITS sequence of fungi. Soils were sampled from Bukhan Mountain from September of 2010 to July of 2011 (7 times). Bacteria were the predominant microbial community in all samples. However, the abundance of archaeal amoA was greater than bacterial amoA throughout the year. The abundances of nifH, nirS, nirK, and norB genes changed in a similar pattern, while narG and nosZ appeared in sensitive to the environmental changes. Clone libraries of bacterial 16S rRNA genes were constructed from summer and winter soil samples and these revealed that Acidobacteria was the most predominant phylum in acidic forest soil environments in both samples. Although a specific correlation of environmental factor and gene abundance was not verified by principle component analysis, our data suggested that the combination of biological, physical, and chemical characteristics of forest soils created distinct conditions favoring the nitrogen biogeochemical cycle and that bacterial communities in undisturbed acidic forest soils were quite stable during seasonal change. PMID:22752898

  20. Changes of Bacterial Community Structure in Copper Mine Tailings After Colonization of Reed (Phragmites communis)

    Institute of Scientific and Technical Information of China (English)

    CHEN Yu-Qing; REN Guan-Ju; AN Shu-Qing; SUN Qing-Ye; LIU Chang-Hong; SHUANG Jing-Lei

    2008-01-01

    Soil samples were collected from both bare and vegetated mine tailings to study the changes in bacterial communities and soil chemical properties of copper mine tailings due to reed (Phragmites communis) colonization. The structures of bacterial communities were investigated using culture-independent 16S rRNA gene sequencing method. The bacterial diversity in the bare mine tailing was lower than that of the vegetated mine tailing. The former was dominated by sulfur metabolizing bacteria, whereas the latter was by nitrogen fixing bacteria. The bare mine tailing was acidic (pH = 3.78), whereas the vegetated mine tailing was near neutral (pH = 7.28). The contents of organic matter, total nitrogen, and ammonium acetate-extractable otassium in vegetated mine tailings were significantly higher than those in the bare mine tailings (P < 0.01), whereas available phosphorus and electrical conductivity were significantly lower than those in the bare mine tailings (P < 0.01). The results demonstrated that 16S rRNA gene sequencing could be successfully used to study the bacterial diversity in mine tailings. The colonization of the mine tailings by reed significantly changed the bacterial community and the chemical properties of tailings. The complex interactions between bacteria and plants deserve further investigation.

  1. Pyrosequencing reveals the influence of organic and conventional farming systems on bacterial communities.

    Directory of Open Access Journals (Sweden)

    Ru Li

    Full Text Available It has been debated how different farming systems influence the composition of soil bacterial communities, which are crucial for maintaining soil health. In this research, we applied high-throughput pyrosequencing of V1 to V3 regions of bacterial 16S rRNA genes to gain further insight into how organic and conventional farming systems and crop rotation influence bulk soil bacterial communities. A 2×2 factorial experiment consisted of two agriculture management systems (organic versus conventional and two crop rotations (flax-oat-fababean-wheat versus flax-alfalfa-alfalfa-wheat was conducted at the Glenlea Long-Term Crop Rotation and Management Station, which is Canada's oldest organic-conventional management study field. Results revealed that there is a significant difference in the composition of bacterial genera between organic and conventional management systems but crop rotation was not a discriminator factor. Organic farming was associated with higher relative abundance of Proteobacteria, while Actinobacteria and Chloroflexi were more abundant in conventional farming. The dominant genera including Blastococcus, Microlunatus, Pseudonocardia, Solirubrobacter, Brevundimonas, Pseudomonas, and Stenotrophomonas exhibited significant variation between the organic and conventional farming systems. The relative abundance of bacterial communities at the phylum and class level was correlated to soil pH rather than other edaphic properties. In addition, it was found that Proteobacteria and Actinobacteria were more sensitive to pH variation.

  2. Comparative Study of Bacterial Communities in Nepenthes Pitchers and Their Correlation to Species and Fluid Acidity.

    Science.gov (United States)

    Kanokratana, Pattanop; Mhuanthong, Wuttichai; Laothanachareon, Thanaporn; Tangphatsornruang, Sithichoke; Eurwilaichitr, Lily; Kruetreepradit, Trongtham; Mayes, Shawn; Champreda, Verawat

    2016-08-01

    Pitchers are specialized digestive organs of carnivorous plants which evolved for trapping prey and represent a unique environment harboring hidden diversity of unexplored microbes forming transient hydrolytic microcosms. In this study, the diversity of bacterial communities in the pitcher fluids of seven local Nepenthes found in Thailand was assessed by tagged 16S ribosomal RNA (rRNA) gene amplicon sequencing on an Ion PGM™ platform. A total of 1,101,000 filtered sequences were obtained which were taxonomically classified into 20 phyla, 48 classes, 72 orders, 153 families, and 442 genera while the remainder (1.43 %) could not be assigned to any existing taxa. Proteobacteria represented the predominant members in closed pitchers and more diversified bacterial taxa particularly Bacteriodetes and Actinobacteria, showed increasing abundance in open pitchers containing insect bodies. Principal coordinate analysis revealed that distribution of bacterial taxa was not significantly related to the Nepenthes species but strongly correlated to the pH of the pitcher fluids (pH 1.7-6.7). Acidicella was a highly dominant bacterial genus in acidic pitcher fluids while Dyella and Mycobacterium were also common genera in most pitchers. A unique microbial community structure was found in Nepenthes ampullaria which could reflect their adaptation to digest leaf litter, in addition to insect prey. The work revealed the highly unexplored nature of bacterial microcosms in Nepenthes pitcher fluids and provides insights into their community structure in this unique ecological system. PMID:27287538

  3. Bacterial community composition and extracellular enzyme activity in temperate streambed sediment during drying and rewetting.

    Directory of Open Access Journals (Sweden)

    Elisabeth Pohlon

    Full Text Available Droughts are among the most important disturbance events for stream ecosystems; they not only affect stream hydrology but also the stream biota. Although desiccation of streams is common in Mediterranean regions, phases of dryness in headwaters have been observed more often and for longer periods in extended temperate regions, including Central Europe, reflecting global climate change and enhanced water withdrawal. The effects of desiccation and rewetting on the bacterial community composition and extracellular enzyme activity, a key process in the carbon flow of streams and rivers, were investigated in a typical Central European stream, the Breitenbach (Hesse, Germany. Wet streambed sediment is an important habitat in streams. It was sampled and exposed in the laboratory to different drying scenarios (fast, intermediate, slow for 13 weeks, followed by rewetting of the sediment from the fast drying scenario via a sediment core perfusion technique for 2 weeks. Bacterial community structure was analyzed using CARD-FISH and TGGE, and extracellular enzyme activity was assessed using fluorogenic model substrates. During desiccation the bacterial community composition shifted toward composition in soil, exhibiting increasing proportions of Actinobacteria and Alphaproteobacteria and decreasing proportions of Bacteroidetes and Betaproteobacteria. Simultaneously the activities of extracellular enzymes decreased, most pronounced with aminopeptidases and less pronounced with enzymes involved in the degradation of polymeric carbohydrates. After rewetting, the general ecosystem functioning, with respect to extracellular enzyme activity, recovered after 10 to 14 days. However, the bacterial community composition had not yet achieved its original composition as in unaffected sediments within this time. Thus, whether the bacterial community eventually recovers completely after these events remains unknown. Perhaps this community undergoes permanent changes

  4. Natural Sunlight Shapes Crude Oil-Degrading Bacterial Communities in Northern Gulf of Mexico Surface Waters.

    Science.gov (United States)

    Bacosa, Hernando P; Liu, Zhanfei; Erdner, Deana L

    2015-01-01

    Following the Deepwater Horizon (DWH) spill in 2010, an enormous amount of oil was observed in the deep and surface waters of the northern Gulf of Mexico. Surface waters are characterized by intense sunlight and high temperature during summer. While the oil-degrading bacterial communities in the deep-sea plume have been widely investigated, the effect of natural sunlight on those in oil polluted surface waters remains unexplored to date. In this study, we incubated surface water from the DWH site with amendments of crude oil, Corexit dispersant, or both for 36 days under natural sunlight in the northern Gulf of Mexico. The bacterial community was analyzed over time for total abundance, density of alkane and polycyclic aromatic hydrocarbon degraders, and community composition via pyrosequencing. Our results showed that, for treatments with oil and/or Corexit, sunlight significantly reduced bacterial diversity and evenness and was a key driver of shifts in bacterial community structure. In samples containing oil or dispersant, sunlight greatly reduced abundance of the Cyanobacterium Synechococcus but increased the relative abundances of Alteromonas, Marinobacter, Labrenzia, Sandarakinotalea, Bartonella, and Halomonas. Dark samples with oil were represented by members of Thalassobius, Winogradskyella, Alcanivorax, Formosa, Pseudomonas, Eubacterium, Erythrobacter, Natronocella, and Coxiella. Both oil and Corexit inhibited the Candidatus Pelagibacter with or without sunlight exposure. For the first time, we demonstrated the effects of light in structuring microbial communities in water with oil and/or Corexit. Overall, our findings improve understanding of oil pollution in surface water, and provide unequivocal evidence that sunlight is a key factor in determining bacterial community composition and dynamics in oil polluted marine waters. PMID:26648916

  5. Effects of Plant Biomass, Plant Diversity, and Water Content on Bacterial Communities in Soil Lysimeters: Implications for the Determinants of Bacterial Diversity▿ †

    OpenAIRE

    Zul, Delita; Denzel, Sabine; Kotz, Andrea; Overmann, Jörg

    2007-01-01

    Soils may comprise tens of thousands to millions of bacterial species. It is still unclear whether this high level of diversity is governed by functional redundancy or by a multitude of ecological niches. In order to address this question, we analyzed the reproducibility of bacterial community composition after different experimental manipulations. Soil lysimeters were planted with four different types of plant communities, and the water content was adjusted. Group-specific phylogenetic finge...

  6. Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland

    Science.gov (United States)

    Cassman, Noriko A.; Leite, Marcio F. A.; Pan, Yao; de Hollander, Mattias; van Veen, Johannes A.; Kuramae, Eiko E.

    2016-03-01

    Inorganic fertilization and mowing alter soil factors with subsequent effects–direct and indirect - on above- and below-ground communities. We explored direct and indirect effects of long-term fertilization (N, P, NPK, Liming) and twice yearly mowing on the plant, bacterial and fungal communities and soil factors. We analyzed co-variation using 16S and 18S rRNA genes surveys, and plant frequency and edaphic factors across treatments. The plant and fungal communities were distinct in the NPK and L treatments, while the bacterial communities and soil factors were distinct in the N and L treatments. Plant community diversity and evenness had low diversity in the NPK and high diversity in the liming treatment, while the diversity and evenness of the bacterial and fungal communities did not differ across treatments, except of higher diversity and evenness in the liming treatment for the bacteria. We found significant co-structures between communities based on plant and fungal comparisons but not between plant and bacterial nor bacterial and fungal comparisons. Our results suggested that the plant and fungal communities are more tightly linked than either community with the bacterial community in fertilized soils. We found co-varying plant, bacterial and fungal taxa in different treatments that may indicate ecological interactions.

  7. Convergent development of anodic bacterial communities in microbial fuel cells.

    KAUST Repository

    Yates, Matthew D

    2012-05-10

    Microbial fuel cells (MFCs) are often inoculated from a single wastewater source. The extent that the inoculum affects community development or power production is unknown. The stable anodic microbial communities in MFCs were examined using three inocula: a wastewater treatment plant sample known to produce consistent power densities, a second wastewater treatment plant sample, and an anaerobic bog sediment. The bog-inoculated MFCs initially produced higher power densities than the wastewater-inoculated MFCs, but after 20 cycles all MFCs on average converged to similar voltages (470±20 mV) and maximum power densities (590±170 mW m(-2)). The power output from replicate bog-inoculated MFCs was not significantly different, but one wastewater-inoculated MFC (UAJA3 (UAJA, University Area Joint Authority Wastewater Treatment Plant)) produced substantially less power. Denaturing gradient gel electrophoresis profiling showed a stable exoelectrogenic biofilm community in all samples after 11 cycles. After 16 cycles the predominance of Geobacter spp. in anode communities was identified using 16S rRNA gene clone libraries (58±10%), fluorescent in-situ hybridization (FISH) (63±6%) and pyrosequencing (81±4%). While the clone library analysis for the underperforming UAJA3 had a significantly lower percentage of Geobacter spp. sequences (36%), suggesting that a predominance of this microbe was needed for convergent power densities, the lower percentage of this species was not verified by FISH or pyrosequencing analyses. These results show that the predominance of Geobacter spp. in acetate-fed systems was consistent with good MFC performance and independent of the inoculum source.

  8. Metamorphosis of a Butterfly-Associated Bacterial Community

    OpenAIRE

    Hammer, Tobin J.; Owen McMillan, W; Noah Fierer

    2014-01-01

    Butterflies are charismatic insects that have long been a focus of biological research. They are also habitats for microorganisms, yet these microbial symbionts are little-studied, despite their likely importance to butterfly ecology and evolution. In particular, the diversity and composition of the microbial communities inhabiting adult butterflies remain uncharacterized, and it is unknown how the larval (caterpillar) and adult microbiota compare. To address these knowledge gaps, we used Ill...

  9. Effects of bacterial communities on biofuel-producing microalgae: stimulation, inhibition and harvesting.

    Science.gov (United States)

    Wang, Hui; Hill, Russell T; Zheng, Tianling; Hu, Xiaoke; Wang, Bin

    2016-01-01

    Despite the great interest in microalgae as a potential source of biofuel to substitute for fossil fuels, little information is available on the effects of bacterial symbionts in mass algal cultivation systems. The bacterial communities associated with microalgae are a crucial factor in the process of microalgal biomass and lipid production and may stimulate or inhibit growth of biofuel-producing microalgae. In addition, we discuss here the potential use of bacteria to harvest biofuel-producing microalgae. We propose that aggregation of microalgae by bacteria to achieve >90% reductions in volume followed by centrifugation could be an economic approach for harvesting of biofuel-producing microalgae. Our aims in this review are to promote understanding of the effects of bacterial communities on microalgae and draw attention to the importance of this topic in the microalgal biofuel field.

  10. [Vertical structure of bacterial communities in peats of the Yakhroma River floodplain].

    Science.gov (United States)

    Dobrovol'skaia, T G; Golovchenko, A V; Pozdniakov, A I

    2007-01-01

    The abundance and taxonomic structure of soil bacterial communities have been studied in different geomorphological parts of the Yakhroma floodplain. It has been found that the numbers of bacteria reach a peak in calcareous peat soil under forest near the floodplain terrace, decreasing to a minimum in soddy alluvial soil near the riverbed. All soils are characterized by the presence of different ecological-trophic bacterial groups capable of peat destruction. Seasonal dynamics of the structure of bacterial communities and, in some soil types, its spatial dynamics accounted for by changes in the botanical structure of peat across its profile have been revealed. All peat soils in the floodplain have high contents of organic matter and neutral pH and, therefore, are favorable biotopes for the development of saprotrophic bacteria. This, in turn, largely accounts for high productivity and stability of this agroecosystem as a whole. PMID:18038631

  11. Invertebrate footprints on detritus processing, bacterial community structure, and spatiotemporal redox profiles

    OpenAIRE

    Hunting, E.R.; Whatley, M. H.; Geest, van der, A.H.M.; Mulder, C; Kraak, M.H.S.; Breure, A M; Admiraal, W.

    2012-01-01

    Detritus processing is driven by a complex interplay between macroinvertebrate and microbial activities. Bioturbation/feeding activities of invertebrates in sediments are known to influence decomposition rates. However, direct effects of invertebrates on bacterial communities and detritus processing remain ill-defined, mainly because identifying interactions between invertebrates and sediments is methodologically challenging. We incubated 5 macroinvertebrate species with various bioturbation/...

  12. Physiological and DNA fingerprinting of the bacterial community of Meloidogyne fallax egg masses

    NARCIS (Netherlands)

    Papert, A; Kok, CJ; van Elsas, JD

    2004-01-01

    Bacterial communities associated with the plant-parasitic nematode Meloidogyne fallax egg masses were compared with those present in the rhizoplane. Two agricultural soils with different nematode population dynamics were used in a glasshouse study, with either potato or tomato as host plant for the

  13. Gut bacterial community structure of two Australian tropical fruit fly species (Diptera: Tephritidae

    Directory of Open Access Journals (Sweden)

    Narit Thaochan

    2015-12-01

    Full Text Available The community structure of the alimentary tract bacteria of two Australian fruit fly species, Bactrocera cacuminata (Hering and Bactrocera tryoni (Froggatt, was studied using a molecular cloning method based on the 16S rRNA gene. Differences in the bacterial community structure were shown between the crops and midguts of the two species and sexes of each species. Proteobacteria was the dominant bacterial phylum in the flies, especially bacteria in the order Gammaproteobacteria which was prominent in all clones. The total bacterial community consisted of Proteobacteria (more than 75% of clones, except in the crop of B. cacuminata where more than 50% of clones belonged to Firmicutes. Firmicutes gave the number of the secondary community structure in the fly’s gut. Four orders, Alpha-, Beta-, Delta- and Gammaproteobacteria and the phyla Firmicutes and Actinobacteria were found in both fruit fly species, while the order Epsilonproteobacteria and the phylum Bacteroidetes were found only in B. tryoni. Two phyla, Actinobacteria and Bacteroidetes, were rare and less frequent in the flies. There was a greater diversity of bacteria in the crop of the two fruit fly species than in the midgut. The midgut of B. tryoni females and the midgut of B. cacuminata males had the lowest bacterial diversity.

  14. Diversity and biogeochemical structuring of bacterial communities across the Porangahau ridge accretionary prism, New Zealand

    NARCIS (Netherlands)

    Hamdan, L.J.; Gillevet, P.M.; Pohlman, J.W.; Sikaroodi, M.; Greinart, J.; Coffin, R.B.

    2011-01-01

    Sediments from the Porangahau ridge, located off the northeastern coast of New Zealand, were studied to describe bacterial community structure in conjunction with differing biogeochemical regimes across the ridge. Low diversity was observed in sediments from an eroded basin seaward of the ridge and

  15. Bacterial community structure of a full-scale biofilter treating pig house exhaust air

    DEFF Research Database (Denmark)

    Kristiansen, Anja; Pedersen, Kristina Hadulla; Nielsen, Per Halkjær;

    2011-01-01

    Biological air filters represent a promising tool for treating emissions of ammonia and odor from pig facilities. Quantitative fluorescence in situ hybridization (FISH) and 16S rRNA gene sequencing were used to investigate the bacterial community structure and diversity in a full-scale biofilter...

  16. Responses of the coastal bacterial community to viral infection of the algae

    NARCIS (Netherlands)

    Sheik, A.R.; Brussaard, C.P.D.; Lavik, G.; Lam, P.; Musat, N.; Krupke, A.; Littmann, S.; Strous, M.; Kuypers, M.M.M.

    2014-01-01

    The release of organic material upon algal cell lyses has a key role in structuring bacterial communities and affects the cycling of biolimiting elements in the marine environment. Here we show that already before cell lysis the leakage or excretion of organic matter by infected yet intact algal cel

  17. Bacterial community composition and diversity of five different permafrost-affected soils of Northeast Greenland.

    Science.gov (United States)

    Ganzert, Lars; Bajerski, Felizitas; Wagner, Dirk

    2014-08-01

    Greenland is one of the regions of interest with respect to climate change and global warming in the Northern Hemisphere. Little is known about the structure and diversity of the terrestrial bacterial communities in ice-free areas in northern Greenland. These soils are generally poorly developed and usually carbon- and nitrogen-limited. Our goal was to provide the first insights into the soil bacterial communities from five different sites in Northeast Greenland using culture-independent and culture-dependent methods. The comparison of environmental and biological data showed that the soil bacterial communities are diverse and significantly pH-dependent. The most frequently detected OTUs belonged to the phyla Acidobacteria, Bacteroidetes and (Alpha-, Beta-, Delta-) Proteobacteria. Low pH together with higher nitrogen and carbon concentrations seemed to support the occurrence of (Alpha-, Beta-, Delta-) Proteobacteria (at the expense of Acidobacteria), whereas Bacteroidetes were predominant at higher values of soil pH. Our study indicates that pH is the main factor for shaping bacterial community, but carbon and nitrogen concentrations as well may become important, especially for selecting oligotrophic microorganisms.

  18. Influence of housing characteristics on bacterial and fungal communities in homes of asthmatic children.

    Science.gov (United States)

    Dannemiller, K C; Gent, J F; Leaderer, B P; Peccia, J

    2016-04-01

    Variations in home characteristics, such as moisture and occupancy, affect indoor microbial ecology as well as human exposure to microorganisms. Our objective was to determine how indoor bacterial and fungal community structure and diversity are associated with the broader home environment and its occupants. Next-generation DNA sequencing was used to describe fungal and bacterial communities in house dust sampled from 198 homes of asthmatic children in southern New England. Housing characteristics included number of people/children, level of urbanization, single/multifamily home, reported mold, reported water leaks, air conditioning (AC) use, and presence of pets. Both fungal and bacterial community structures were non-random and demonstrated species segregation (C-score, P children, and pets) characteristics. Occupant density measures were associated with beneficial bacterial taxa, including Lactobacillus johnsonii as measured by qPCR. A more complete knowledge of indoor microbial communities is useful for linking housing characteristics to human health outcomes. Microbial assemblies in house dust result, in part, from the building's physical and occupant characteristics. PMID:25833176

  19. High concentrations of methyl fluoride affect the bacterial community in a thermophilic methanogenic sludge.

    Directory of Open Access Journals (Sweden)

    Liping Hao

    Full Text Available To precisely control the application of methyl fluoride (CH3F for analysis of methanogenic pathways, the influence of 0-10% CH3F on bacterial and archaeal communities in a thermophilic methanogenic sludge was investigated. The results suggested that CH3F acts specifically on acetoclastic methanogenesis. The inhibitory effect stabilized at an initial concentration of 3-5%, with around 90% of the total methanogenic activity being suppressed, and a characteristic of hydrogenotrophic pathway in isotope fractionation was demonstrated under this condition. However, extended exposure (12 days to high concentrations of CH3F (>3% altered the bacterial community structure significantly, resulting in increased diversity and decreased evenness, which can be related to acetate oxidation and CH3F degradation. Bacterial clone library analysis showed that syntrophic acetate oxidizing bacteria Thermacetogenium phaeum were highly enriched under the suppression of 10% CH3F. However, the methanogenic community did not change obviously. Thus, excessive usage of CH3F over the long term can change the composition of the bacterial community. Therefore, data from studies involving the use of CH3F as an acetoclast inhibitor should be interpreted with care. Conversely, CH3F has been suggested as a factor to stimulate the enrichment of syntrophic acetate oxidizing bacteria.

  20. High-Resolution Melt Analysis for Rapid Comparison of Bacterial Community Compositions

    DEFF Research Database (Denmark)

    Hjelmsø, Mathis Hjort; Hansen, Lars Hestbjerg; Bælum, Jacob;

    2014-01-01

    In the study of bacterial community composition, 16S rRNA gene amplicon sequencing is today among the preferred methods of analysis. The cost of nucleotide sequence analysis, including requisite computational and bioinformatic steps, however, takes up a large part of many research budgets. High-r...

  1. Influence of uranium on bacterial communities: a comparison of natural uranium-rich soils with controls.

    Directory of Open Access Journals (Sweden)

    Laure Mondani

    Full Text Available This study investigated the influence of uranium on the indigenous bacterial community structure in natural soils with high uranium content. Radioactive soil samples exhibiting 0.26% - 25.5% U in mass were analyzed and compared with nearby control soils containing trace uranium. EXAFS and XRD analyses of soils revealed the presence of U(VI and uranium-phosphate mineral phases, identified as sabugalite and meta-autunite. A comparative analysis of bacterial community fingerprints using denaturing gradient gel electrophoresis (DGGE revealed the presence of a complex population in both control and uranium-rich samples. However, bacterial communities inhabiting uraniferous soils exhibited specific fingerprints that were remarkably stable over time, in contrast to populations from nearby control samples. Representatives of Acidobacteria, Proteobacteria, and seven others phyla were detected in DGGE bands specific to uraniferous samples. In particular, sequences related to iron-reducing bacteria such as Geobacter and Geothrix were identified concomitantly with iron-oxidizing species such as Gallionella and Sideroxydans. All together, our results demonstrate that uranium exerts a permanent high pressure on soil bacterial communities and suggest the existence of a uranium redox cycle mediated by bacteria in the soil.

  2. HRT and nutrients affect bacterial communities grown on recirculation aquaculture system effluents

    NARCIS (Netherlands)

    Schneider, O.; Chabrillon-Popelka, M.; Smidt, H.; Haenen, O.L.M.; Sereti, V.; Eding, E.H.; Verreth, J.A.J.

    2007-01-01

    In a recirculation aquaculture system the drumfilter effluent can be used as substrate for heterotrophic bacterial production, which can be recycled as feed. Because the bacteria might contain pathogens, which could reduce its suitability as feed, it is important to characterize these communities. B

  3. Community-acquired Methicillin-resistant Staphylococcus Aureus (CA-MRSA):A Public Health Concern in Athletic Settings

    Institute of Scientific and Technical Information of China (English)

    Lindsay K. Drewes

    2008-01-01

    @@ Background Methicillin-resistant Staphylococcus aureus (MRSA) is a type of bacteria, commonly manifesting itself in the form of skin infections, and resistant to beta-lactum antibiotics[2]. These infections were seen in hospital settings starting in the 1960s in patients that had recently been hospitalized or undergone a medical procedure[3]. In the 1980s reports were first published in the literature of MRSA acquired in otherwise healthy individuals from community settingsr[4,5]. An increased occurrence of community-associated Methicillin-resistant Staphylococcus aureus (CA-MRSA) has been on the rise since the late 1990s and manifests itself as a skin infection in populations without other previously known risk factors[6-8].

  4. Time-based distribution of Staphylococcus saprophyticus pulsed field gel-electrophoresis clusters in community-acquired urinary tract infections

    Directory of Open Access Journals (Sweden)

    Viviane Santos de Sousa

    2013-02-01

    Full Text Available The epidemiology of urinary tract infections (UTI by Staphylococcus saprophyticus has not been fully characterised and strain typing methods have not been validated for this agent. To evaluate whether epidemiological relationships exist between clusters of pulsed field gel-electrophoresis (PFGE genotypes of S. saprophyticus from community-acquired UTI, a cross-sectional surveillance study was conducted in the city of Rio de Janeiro, Brazil. In total, 32 (16% female patients attending two walk-in clinics were culture-positive for S. saprophyticus. Five PFGE clusters were defined and evaluated against epidemiological data. The PFGE clusters were grouped in time, suggesting the existence of community point sources of S. saprophyticus. From these point sources, S. saprophyticus strains may spread among individuals.

  5. Time-based distribution of Staphylococcus saprophyticus pulsed field gel-electrophoresis clusters in community-acquired urinary tract infections.

    Science.gov (United States)

    Sousa, Viviane Santos de; Rabello, Renata Fernandes; Dias, Rubens Clayton da Silva; Martins, Ianick Souto; Santos, Luisa Barbosa Gomes da Silva dos; Alves, Elisabeth Mendes; Riley, Lee Woodford; Moreira, Beatriz Meurer

    2013-02-01

    The epidemiology of urinary tract infections (UTI) by Staphylococcus saprophyticus has not been fully characterised and strain typing methods have not been validated for this agent. To evaluate whether epidemiological relationships exist between clusters of pulsed field gel-electrophoresis (PFGE) genotypes of S. saprophyticus from community-acquired UTI, a cross-sectional surveillance study was conducted in the city of Rio de Janeiro, Brazil. In total, 32 (16%) female patients attending two walk-in clinics were culture-positive for S. saprophyticus. Five PFGE clusters were defined and evaluated against epidemiological data. The PFGE clusters were grouped in time, suggesting the existence of community point sources of S. saprophyticus. From these point sources, S. saprophyticus strains may spread among individuals.

  6. Bacterial community diversity and variation in spray water sources and the tomato fruit surface

    Directory of Open Access Journals (Sweden)

    Ottesen Andrea R

    2011-04-01

    Full Text Available Abstract Background Tomato (Solanum lycopersicum consumption has been one of the most common causes of produce-associated salmonellosis in the United States. Contamination may originate from animal waste, insects, soil or water. Current guidelines for fresh tomato production recommend the use of potable water for applications coming in direct contact with the fruit, but due to high demand, water from other sources is frequently used. We sought to describe the overall bacterial diversity on the surface of tomato fruit and the effect of two different water sources (ground and surface water when used for direct crop applications by generating a 454-pyrosequencing 16S rRNA dataset of these different environments. This study represents the first in depth characterization of bacterial communities in the tomato fruit surface and the water sources commonly used in commercial vegetable production. Results The two water sources tested had a significantly different bacterial composition. Proteobacteria was predominant in groundwater samples, whereas in the significantly more diverse surface water, abundant phyla also included Firmicutes, Actinobacteria and Verrucomicrobia. The fruit surface bacterial communities on tomatoes sprayed with both water sources could not be differentiated using various statistical methods. Both fruit surface environments had a high representation of Gammaproteobacteria, and within this class the genera Pantoea and Enterobacter were the most abundant. Conclusions Despite the major differences observed in the bacterial composition of ground and surface water, the season long use of these very different water sources did not have a significant impact on the bacterial composition of the tomato fruit surface. This study has provided the first next-generation sequencing database describing the bacterial communities living in the fruit surface of a tomato crop under two different spray water regimes, and therefore represents an

  7. Community-acquired pneumonia due to pandemic A(H1N12009 influenzavirus and methicillin resistant Staphylococcus aureus co-infection.

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    Ronan J Murray

    Full Text Available BACKGROUND: Bacterial pneumonia is a well described complication of influenza. In recent years, community-onset methicillin-resistant Staphylococcus aureus (cMRSA infection has emerged as a contributor to morbidity and mortality in patients with influenza. Since the emergence and rapid dissemination of pandemic A(H1N12009 influenzavirus in April 2009, initial descriptions of the clinical features of patients hospitalized with pneumonia have contained few details of patients with bacterial co-infection. METHODOLOGY/PRINCIPAL FINDINGS: Patients with community-acquired pneumonia (CAP caused by co-infection with pandemic A(H1N12009 influenzavirus and cMRSA were prospectively identified at two tertiary hospitals in one Australian city during July to September 2009, the period of intense influenza activity in our region. Detailed characterization of the cMRSA isolates was performed. 252 patients with pandemic A(H1N12009 influenzavirus infection were admitted at the two sites during the period of study. Three cases of CAP due to pandemic A(H1N12009/cMRSA co-infection were identified. The clinical features of these patients were typical of those with S. aureus co-infection or sequential infection following influenza. The 3 patients received appropriate empiric therapy for influenza, but inappropriate empiric therapy for cMRSA infection; all 3 survived. In addition, 2 fatal cases of CAP caused by pandemic A(H1N12009/cMRSA co-infection were identified on post-mortem examination. The cMRSA infections were caused by three different cMRSA clones, only one of which contained genes for Panton-Valentine Leukocidin (PVL. CONCLUSIONS/SIGNIFICANCE: Clinicians managing patients with pandemic A(H1N12009 influenzavirus infection should be alert to the possibility of co-infection or sequential infection with virulent, antimicrobial-resistant bacterial pathogens such as cMRSA. PVL toxin is not necessary for the development of cMRSA pneumonia in the setting of pandemic

  8. Influence of socioeconomic status on community-acquired pneumonia outcomes in elderly patients requiring hospitalization: a multicenter observational study

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    Carratalà Jordi

    2010-07-01

    Full Text Available Abstract Background The associations between socioeconomic status and community-acquired pneumonia outcomes in adults have been studied although studies did not always document a relationship. The aim of this multicenter observational study was to determine the association between socioeconomic status and community-acquired pneumonia outcomes in the elderly, in the context of a public health system providing universal free care to the whole population. Methods A total of 651 patients aged ≥65 years hospitalized due to community-acquired pneumonia through the emergency departments of five Spanish public hospitals were recruited and followed up between May 2005 and January 2007. The primary outcomes studied were: length of stay, intensive care unit admission, overall mortality and readmission. Socioeconomic status was measured using both individual and community data: occupation [categorized in six social groups (I, II, III, IVa, IVb and V], educational level (≤ primary level or ≥ secondary level and disposable family income of the municipality or district of residence [>12,500 € (high municipality family income and ≤12,500 € (low municipality family income]. The six social groups were further categorized as upper/middle social class (groups I-IVb and lower class (group V. Bivariate and multivariate analyses were performed. OR and their 95% confidence intervals were calculated. All statistical tests were two tailed and statistical significance was established as p Results 17.7% of patients lived in a municipality or district with a high municipality family income and 63.6% were upper/middle social class (I-IVb. Only 15.7% of patients had a secondary education. The adjusted analysis showed no association between pneumonia outcomes and social class, educational level or municipality family income. However, length of stay increased significantly in patients in whom the factors, living alone and being a smoker or ex-smoker coincided (p

  9. Evaluation of different nucleic acid amplification techniques for the detection of M. pneumoniae, C. pneumoniae and Legionella spp. in respiratory specimens from patients with community-acquired pneumonia

    NARCIS (Netherlands)

    Loens, K; Beck, T; Ursi, D; Overdijk, M; Sillekens, P; Goossens, H; Ieven, M; Niesters, Bert

    2008-01-01

    The number of pathogens involved in community-acquired pneumonia, with varying susceptibilities to antimicrobials, is numerous constituting an enormous challenge for diagnostic microbiology. Differentiation of infections due to Streptococcus pneumoniae and those due to Mycoplasma pneumoniae, Chlamyd

  10. Efficacy and Safety of, and Patient Satisfaction with, Colonoscopic-Administered Fecal Microbiota Transplantation in Relapsing and Refractory Community- and Hospital-Acquired Clostridium difficile Infection

    Directory of Open Access Journals (Sweden)

    Muhammad Ali Khan

    2014-01-01

    Full Text Available OBJECTIVE: To report the efficacy and safety of, and patient satisfaction with, colonoscopic fecal microbiota transplantation (FMT for community- and hospital-acquired Clostridium difficile infection (CDI.

  11. Mesocosms of aquatic bacterial communities from the Cuatro Cienegas Basin (Mexico): a tool to test bacterial community response to environmental stress.

    Science.gov (United States)

    Pajares, Silvia; Bonilla-Rosso, German; Travisano, Michael; Eguiarte, Luis E; Souza, Valeria

    2012-08-01

    Microbial communities are responsible for important ecosystem processes, and their activities are regulated by environmental factors such as temperature and solar ultraviolet radiation. Here we investigate changes in aquatic microbial community structure, diversity, and evenness in response to changes in temperature and UV radiation. For this purpose, 15 mesocosms were seeded with both microbial mat communities and plankton from natural pools within the Cuatro Cienegas Basin (Mexico). Clone libraries (16S rRNA) were obtained from water samples at the beginning and at the end of the experiment (40 days). Phylogenetic analysis indicated substantial changes in aquatic community composition and structure in response to temperature and UV radiation. Extreme treatments with elevation in temperature or UV radiation reduced diversity in relation to the Control treatments, causing a reduction in richness and increase in dominance, with a proliferation of a few resistant operational taxonomic units. Each phylum was affected differentially by the new conditions, which translates in a differential modification of ecosystem functioning. This suggests that the impact of environmental stress, at least at short term, will reshape the aquatic bacterial communities of this unique ecosystem. This work also demonstrates the possibility of designing manageable synthetic microbial community ecosystems where controlled environmental variables can be manipulated. Therefore, microbial model systems offer a complementary approach to field and laboratory studies of global research problems associated with the environment.

  12. Mesocosms of aquatic bacterial communities from the Cuatro Cienegas Basin (Mexico): a tool to test bacterial community response to environmental stress.

    Science.gov (United States)

    Pajares, Silvia; Bonilla-Rosso, German; Travisano, Michael; Eguiarte, Luis E; Souza, Valeria

    2012-08-01

    Microbial communities are responsible for important ecosystem processes, and their activities are regulated by environmental factors such as temperature and solar ultraviolet radiation. Here we investigate changes in aquatic microbial community structure, diversity, and evenness in response to changes in temperature and UV radiation. For this purpose, 15 mesocosms were seeded with both microbial mat communities and plankton from natural pools within the Cuatro Cienegas Basin (Mexico). Clone libraries (16S rRNA) were obtained from water samples at the beginning and at the end of the experiment (40 days). Phylogenetic analysis indicated substantial changes in aquatic community composition and structure in response to temperature and UV radiation. Extreme treatments with elevation in temperature or UV radiation reduced diversity in relation to the Control treatments, causing a reduction in richness and increase in dominance, with a proliferation of a few resistant operational taxonomic units. Each phylum was affected differentially by the new conditions, which translates in a differential modification of ecosystem functioning. This suggests that the impact of environmental stress, at least at short term, will reshape the aquatic bacterial communities of this unique ecosystem. This work also demonstrates the possibility of designing manageable synthetic microbial community ecosystems where controlled environmental variables can be manipulated. Therefore, microbial model systems offer a complementary approach to field and laboratory studies of global research problems associated with the environment. PMID:22460437</