Friday, November 30, 2012
Reducing bias in bacterial community analysis of lower respiratory infections.
Reducing bias in bacterial community analysis of lower respiratory infections.
Nov 2012
Rogers GB, Cuthbertson L, Hoffman LR, Wing PA, Pope C, Hooftman DA, Lilley AK, Oliver A, Carroll MP, Bruce KD, van der Gast CJ.
Source
Molecular Microbiology Research Laboratory, Institute of Pharmaceutical Science, King's College London, London, UK.
Abstract
High-throughput pyrosequencing and quantitative PCR (Q-PCR) analysis offer greatly improved accuracy and depth of characterisation of lower respiratory infections. However, such approaches suffer from an inability to distinguish between DNA derived from viable and non-viable bacteria. This discrimination represents an important step in characterising microbial communities, particularly in contexts with poor clearance of material or high antimicrobial stress, as non-viable bacteria and extracellular DNA can contribute significantly to analyses. Pre-treatment of samples with propidium monoazide (PMA) is an effective approach to non-viable cell exclusion (NVCE). However, the impact of NVCE on microbial community characteristics (abundance, diversity, composition and structure) is not known. Here, adult cystic fibrosis (CF) sputum samples were used as a paradigm. The effects of PMA treatment on CF sputum bacterial community characteristics, as analysed by pyrosequencing and enumeration by species-specific (Pseudomonas aeruginosa) and total bacterial Q-PCR, were assessed. At the local community level, abundances of both total bacteria and of P. aeruginosa were significantly lower in PMA-treated sample portions. Meta-analysis indicated no overall significant differences in diversity; however, PMA treatment resulted in a significant alteration in local community membership in all cases. In contrast, at the metacommunity level, PMA treatment resulted in an increase in community evenness, driven by an increase in diversity, predominately representing rare community members. Importantly, PMA treatment facilitated the detection of both recognised and emerging CF pathogens, significantly influencing 'core' and 'satellite' taxa group membership. Our findings suggest failure to implement NVCE may result in skewed bacterial community analyses.
Labels: bacterial community analyses, cystic fibrosis, DNA, lower respiratory infections, NVCE, PCR, Pseudomonas aeruginosa
# posted by Pat O'Connor @ 8:34 AM
Wednesday, November 14, 2012
Adaptation of Pseudomonas aeruginosa to the cystic fibrosis airway: an evolutionary perspective.
Adaptation of Pseudomonas aeruginosa to the cystic fibrosis airway: an evolutionary perspective.
Nov 2012
Source
1] Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark. [2].
Abstract
The airways of patients with cystic fibrosis (CF) are nearly always infected with many different microorganisms. This environment offers warm, humid and nutrient-rich conditions, but is also stressful owing to frequent antibiotic therapy and the host immune response. Pseudomonas aeruginosa is commonly isolated from the airways of patients with CF, where it most often establishes chronic infections that usually persist for the rest of the lives of the patients. This bacterium is a major cause of mortality and morbidity and has therefore been studied intensely. Here, we discuss how P. aeruginosa evolves from a state of early, recurrent intermittent colonization of the airways of patients with CF to a chronic infection state, and how this process offers opportunities to study bacterial evolution in natural environments. We believe that such studies are valuable not only for our understanding of bacterial evolution but also for the future development of new therapeutic strategies to treat severe chronic infections.
Labels: airway, antibiotic therapy, bacterial evolution, chronic infections, cystic fibrosis, immune response, Pseudomonas aeruginosa
# posted by Pat O'Connor @ 8:11 AM
Sunday, October 21, 2012
Vitamin-D deficiency is associated with chronic bacterial colonisation and disease severity in bronchiectasis.
Vitamin-D deficiency is associated with chronic bacterial colonisation and disease severity in bronchiectasis.
Oct 2012
Source
The University of Edinburgh/MRC Centre for Research Inflammation, The Queen's Medical Research Institute, Edinburgh, UK.
Abstract
INTRODUCTION:
Vitamin-D deficiency has been linked to an increased risk of respiratory infections. The objective of this study was to determine the frequency and clinical importance of vitamin-D deficiency in patients with bronchiectasis.
METHODS:
25-hydroxyvitamin-D was measured by immunoassay in 402 stable patients with bronchiectasis. Patients were classified as vitamin-D deficient -serum 25-hydroxyvitamin-D less then 25 nmol/l, - insufficient - 25 nmol/l-74 nmol/l- or sufficient (≥75 nmol/l). Disease severity was assessed, including exacerbation frequency, measurement of airway inflammatory markers, sputum bacteriology and lung function over 3 years follow-up.
RESULTS:
Fifty percent of bronchiectasis patients were vitamin-D deficient, Forty three percent insufficient and onlyseven percent sufficient. This compared to only twelve percent of age and sex matched controls with vitamin-D deficiency. Vitamin-D deficient patients were more frequently chronically colonised with bacteria, twenty one point four percent of vitamin-D deficient subjects were colonised with Pseudomonas aeruginosa compared to ten point four percent of insufficient patients and Three point six percent of sufficient patients.. Vitamin-D deficient patients had lower FEV one percent predicted , and more frequent pulmonary exacerbations. Vitamin-D deficient patients had higher sputum levels of inflammatory markers and demonstrated a more rapid decline in lung function over 3 years follow-up. Defects in neutrophil function and assessment of airway LL-37 levels did not provide a mechanistic explanation for these findings. Vitamin-D deficient patients had, however, higher levels of Vitamin-D Binding Protein in sputum sol.
CONCLUSIONS:
Vitamin-D deficiency is common in bronchiectasis and correlates with markers of disease severity. The mechanism of this association is unclear.
Labels: airway inflammatory markers, bacterial colonisation, bronchiectasis, disease severity, lung function, Pseudomonas aeruginosa, sputum bacteriology, Vitamin-D deficiency
# posted by Pat O'Connor @ 8:56 AM
Monday, August 27, 2012
Update on bacterial nosocomial infections.
Update on bacterial nosocomial infections.
Aug 2012
Source
Department of Medical Laboratory Sciences & Pathology, College of Public Health & Medical Sciences, Jimma University, Jimma, Ethiopia.
Abstract
With increasing use of antimicrobial agents and advance in lifesaving medical practices which expose the patients for invasive procedures, are associated with the ever increasing of nosocomial infections. Despite an effort in hospital infection control measures, health care associated infections are associated with significant morbidity and mortality adding additional health care expenditure which may leads to an economic crisis. The problem is further complicated with the emergence of difficult to treat multidrug resistant (MDR) microorganism in the hospital environment. Virtually every pathogen has the potential to cause infection in hospitalized patients but only limited number of both gram positive and gram negative bacteria are responsible for the majority of nosocomial infection. Among them Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa and Enterococci takes the leading. Many intrinsic and extrinsic factors predispose hospitalized patients for these pathogens. Following simple hospital hygienic practices and strictly following standard medical procedures greatly reduces infection to a significant level although not all nosocomial infections are avoidable. The clinical spectrum caused by nosocomial pathogens depend on body site of infection, the involving pathogen and the patient's underlying condition. Structural and non structural virulence factors associated with the bacteria are responsible for the observed clinical manifestation. Bacteria isolation and characterization from appropriate clinical materials with antimicrobial susceptibility testing is the standard of laboratory diagnosis.
Labels: antimicrobial, drug resistance, Enterococci, escherichia coli, gram negative, gram positive, hospital infection, nosocomial infections, pathogens, Pseudomonas aeruginosa, Staphylococcus aureus
# posted by Pat O'Connor @ 9:59 AM
Sunday, April 29, 2007
Pseudomonas aeruginosa kills six babies in Canada
Six babies die of sink bacteria in Canada
April 28, 2007
Montreal's Ste-Justine Hospital has confirmed that six premature babies who died three years ago in it were infected from bacteria found in a poorly maintained plumbing system, according to Canadian media reports Saturday.
The reports said that about 50 babies had contracted pseudomonas aeruginosa. Four of them, all born prematurely, died. The deaths of two other babies may also have been caused by the bacteria.
The bacterium typically targets the respiratory system, causing pneumonia and septicemia. The premature babies in the neo-natal ward are particularly vulnerable because of their already compromised immune systems.
After the first baby died in 2004, the hospital disinfected the crowded ward and searched for the source of the bacterium but over the next 18 months, five more babies died.
April 28, 2007
Montreal's Ste-Justine Hospital has confirmed that six premature babies who died three years ago in it were infected from bacteria found in a poorly maintained plumbing system, according to Canadian media reports Saturday.
The reports said that about 50 babies had contracted pseudomonas aeruginosa. Four of them, all born prematurely, died. The deaths of two other babies may also have been caused by the bacteria.
The bacterium typically targets the respiratory system, causing pneumonia and septicemia. The premature babies in the neo-natal ward are particularly vulnerable because of their already compromised immune systems.
After the first baby died in 2004, the hospital disinfected the crowded ward and searched for the source of the bacterium but over the next 18 months, five more babies died.
The hospital closed the ward in December 2005 and discovered that the bacterium was breeding in the ward's sinks, which were not draining properly, the reports showed.
The hospital replaced its aging plumbing system and built a new neo-natal ward to open next year.
Ste-Justine said the situation is now under control and there have been no deaths in the last two years.
Quebec Health Minister Philippe Couillard, under fire for this scandal, insisted Friday the public was never at risk.
Sainte-Justine is Quebec's only health care establishment exclusively dedicated to children, adolescents and mothers.
NewsLabels: premature baby, Pseudomonas aeruginosa
# posted by Pat O'Connor @ 7:13 PM
Thursday, April 26, 2007
Prediction of specific pathogens in patients with sepsis
Prediction of specific pathogens in patients with sepsis: evaluation of TREAT, a computerized decision support system.
J Antimicrob Chemother. 2007 Apr
Paul M, Nielsen AD, Goldberg E, Andreassen S, Tacconelli E, Almanasreh N, Frank U, Cauda R,
Leibovici L.
Department of Medicine E, Rabin Medical Center, Beilinson Campus, Petah-Tiqva 49100, Israel.
Background
Prediction of bacterial infections and their pathogens allows for early, directed investigation and treatment. We assessed the ability of TREAT, a computerized decision support system, to predict specific pathogens. Methods TREAT uses data available within the first few hours of infection presentation in a causal probabilistic network to predict sites of infection and specific pathogens. We included 3529 patients (920 with microbiologically documented infections) participating in the observational and interventional trials of the TREAT system in Israel, Germany and Italy.
Discriminatory performance of TREAT to predict individual pathogens was expressed by the AUC with 95% confidence intervals. Calibration was assessed using the Hosmer-Lemeshow goodness-of-fit statistic. Results The AUCs for Gram-negative bacteria, including Pseudomonas aeruginosa, Acinetobacter baumannii, Klebsiella spp. and Escherichia coli, ranged between 0.70 and 0.80 (all significant). Adequate calibration was demonstrated for any Gram-negative infection and individual bacteria, except for E. coli.
Discrimination and calibration were acceptable for Enterococcus spp. (AUC 0.71, 0.65-0.78), but not for Staphylococcus aureus (AUC 0.63, 0.55-0.71). The few infections caused by Candida spp. and Clostridium difficile were well predicted (AUCs 0.74, 0.54-0.95; and 0.94, 0.88-1.00, respectively). The coverage with TREAT's recommendation exceeded that observed with physicians' treatment for all pathogens, except Candida spp.
Conclusions TREAT predicted individual pathogens causing infection well. Prediction of S. aureus was inferior to that observed with other pathogens. TREAT can be used to triage patients by the risk for specific pathogens. The system's predictions enable it to prescribe appropriate antibiotic treatment prior to pathogen identification.
PMID: 17449883 [PubMed - as supplied by publisher]
J Antimicrob Chemother. 2007 Apr
Paul M, Nielsen AD, Goldberg E, Andreassen S, Tacconelli E, Almanasreh N, Frank U, Cauda R,
Leibovici L.
Department of Medicine E, Rabin Medical Center, Beilinson Campus, Petah-Tiqva 49100, Israel.
Background
Prediction of bacterial infections and their pathogens allows for early, directed investigation and treatment. We assessed the ability of TREAT, a computerized decision support system, to predict specific pathogens. Methods TREAT uses data available within the first few hours of infection presentation in a causal probabilistic network to predict sites of infection and specific pathogens. We included 3529 patients (920 with microbiologically documented infections) participating in the observational and interventional trials of the TREAT system in Israel, Germany and Italy.
Discriminatory performance of TREAT to predict individual pathogens was expressed by the AUC with 95% confidence intervals. Calibration was assessed using the Hosmer-Lemeshow goodness-of-fit statistic. Results The AUCs for Gram-negative bacteria, including Pseudomonas aeruginosa, Acinetobacter baumannii, Klebsiella spp. and Escherichia coli, ranged between 0.70 and 0.80 (all significant). Adequate calibration was demonstrated for any Gram-negative infection and individual bacteria, except for E. coli.
Discrimination and calibration were acceptable for Enterococcus spp. (AUC 0.71, 0.65-0.78), but not for Staphylococcus aureus (AUC 0.63, 0.55-0.71). The few infections caused by Candida spp. and Clostridium difficile were well predicted (AUCs 0.74, 0.54-0.95; and 0.94, 0.88-1.00, respectively). The coverage with TREAT's recommendation exceeded that observed with physicians' treatment for all pathogens, except Candida spp.
Conclusions TREAT predicted individual pathogens causing infection well. Prediction of S. aureus was inferior to that observed with other pathogens. TREAT can be used to triage patients by the risk for specific pathogens. The system's predictions enable it to prescribe appropriate antibiotic treatment prior to pathogen identification.
PMID: 17449883 [PubMed - as supplied by publisher]
Labels: Acinetobacter baumannii, escherichia coli, Klebsiella spp, Pseudomonas aeruginosa, sepsis, Staphylococcus aureus, TREAT
# posted by Pat O'Connor @ 1:22 PM
