Genomic Variation among Contemporary Pseudomonas aeruginosa Isolates from Chronically Infected Cystic Fibrosis Patients

Chung, Jade C. S.; Becq, Jennifer; Fraser, Louise; Schulz-Trieglaff, Ole; Bond, Nicholas J.; Foweraker, Juliet; Bruce, Kenneth D.; Smith, Geoffrey; Welch, Martin

doi:10.1128/jb.01050-12

Cited by 82 publications

(88 citation statements)

References 49 publications

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“…Thus the P. aeruginosa WinCF responses may reflect the true physiology of this microbe and others like it in the CF lung and is in stark contrast to the physiology of the Attack Community during exacerbation events. However, P. aeruginosa exhibits large strain differentiation in the CF lungs (Chung et al, 2012;Klockgether et al, 2013), making conceptualizing the organism in the context of CF challenging. Also, while observed as a member of the Climax Community in the patient in this study, it cannot be inferred that P. aeruginosa has a limited role in all exacerbations.…”

Section: Sources Of the Fermentative Responsementioning

confidence: 99%

A Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation

et al. 2014

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There is a poor understanding of how the physiology of polymicrobial communities in cystic fibrosis (CF) lungs contributes to pulmonary exacerbations and lung function decline. In this study, a microbial culture system based on the principles of the Winogradsky column (WinCF system) was developed to study the physiology of CF microbes. The system used glass capillary tubes filled with artificial sputum medium to mimic a clogged airway bronchiole. Chemical indicators were added to observe microbial physiology within the tubes. Characterization of sputum samples from seven patients showed variation in pH, respiration, biofilm formation and gas production, indicating that the physiology of CF microbial communities varied among patients. Incubation of homogenized tissues from an explant CF lung mirrored responses of a Pseudomonas aeruginosa pure culture, supporting evidence that end-stage lungs are dominated by this pathogen. Longitudinal sputum samples taken through two exacerbation events in a single patient showed that a two-unit drop in pH and a 30% increase in gas production occurred in the tubes prior to exacerbation, which was reversed with antibiotic treatment. Microbial community profiles obtained through amplification and sequencing of the 16S rRNA gene showed that fermentative anaerobes became more abundant during exacerbation and were then reduced during treatment where P. aeruginosa became the dominant bacterium. Results from the WinCF experiments support the model where two functionally different CF microbial communities exist, the persistent Climax Community and the acute Attack Community. Fermentative anaerobes are hypothesized to be the core members of the Attack Community and production of acidic and gaseous products from fermentation may drive developing exacerbations. Treatment targeting the Attack Community may better resolve exacerbations and resulting lung damage.

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Section: Sources Of the Fermentative Responsementioning

confidence: 99%

A Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation

et al. 2014

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“…The most Drug sequence influences evolution of resistance commonly mutated gene was fusA1, which encodes elongation factor G and was mutated in 11 different replicate lineages adapted to tobramycin. fusA1 has been observed to be mutated in clinical isolates of P. aeruginosa [39][40][41], as well as in adaptive evolution studies to aminoglycosides in P. aeruginosa [34] and E. coli [12,16,18]. Mutations in fusA1 may also contribute to altered intracellular (p)ppGpp levels, which may modulate virulence in P. aeruginosa [41].…”

Section: Genomic Mutations Of Adapted Lineagesmentioning

confidence: 99%

“…fusA1 has been observed to be mutated in clinical isolates of P. aeruginosa [39][40][41], as well as in adaptive evolution studies to aminoglycosides in P. aeruginosa [34] and E. coli [12,16,18]. Mutations in fusA1 may also contribute to altered intracellular (p)ppGpp levels, which may modulate virulence in P. aeruginosa [41]. Mutations in gyrA and gyrB were observed during ciprofloxacin evolution, but none were observed in parC and parE (the other genes of the quinolone resistance-determining region [29]).…”

Section: Genomic Mutations Of Adapted Lineagesmentioning

confidence: 99%

History of Antibiotic Adaptation Influences Microbial Evolutionary Dynamics During Subsequent Treatment

Yen

Papin

2016

Preprint

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Antibiotic regimens often include the sequential changing of drugs to limit the development and evolution of resistance of bacterial pathogens. It remains unclear how history of adaptation to one antibiotic can influence the resistance profiles when bacteria subsequently adapt to a different antibiotic. Here, we experimentally evolved Pseudomonas aeruginosa to six 2-drug sequences. We observed drug order-specific effects, whereby adaptation to the first drug can limit the rate of subsequent adaptation to the second drug, adaptation to the second drug can restore susceptibility to the first drug, or final resistance levels depend on the order of the 2-drug sequence. These findings demonstrate how resistance not only depends on the current drug regimen but also the history of past regimens. These orderspecific effects may allow for rational forecasting of the evolutionary dynamics of bacteria given knowledge of past adaptations and provide support for the need to consider the history of past drug exposure when designing strategies to mitigate resistance and combat bacterial infections. Author summaryBacteria readily adapt to their environments and can develop ways to survive and grow in the presence of antibiotics. While many studies have investigated how bacteria evolve to become resistant to single drugs, it is unclear how adaptation to other drugs and environments in the past affect the way bacteria adapt to new drugs and environments. In this study, we allowed bacteria in a laboratory setting to adapt to three different antibiotics. We first exposed wild-type susceptible bacteria to high concentrations of the three antibiotics individually and then exposed these populations to each of the other drugs. By tracking the levels of resistance to all three drugs in all of the treatments, we identified cases in which past adaptation to one treatment influenced subsequent evolutionary dynamics with regard to both phenotypes (levels of resistance) and genotypes (genes that became mutated). Additionally, by allowing bacterial isolates originating from human patients to adapt to the three drugs, we recapitulated a subset of the adaptation history-dependent evolutionary dynamics. Overall, this study sheds light on how adaptation history in PLOS Biology | https://doi.org/10.1371/journal

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“…A recent study has suggested that a mixture of strains influenced traits such as drug response in ways that were difficult to predict from the study of single strains (9). Clinical isolates of P. aeruginosa, even from the same respiratory sample, can have striking differences in phenotypes, including colony morphology, quorum-sensing regulation, and motility (9)(10)(11)(12)(13), and recent data highlight that there is gene expression diversity even among phenotypically similar strains (9). Given the significant limitations of the aforementioned laboratory approaches, novel methods for directly interrogating population-level microbial gene expression in the CF lung are needed to provide accurate information about the growth and virulence of P. aeruginosa in the CF airway.…”

mentioning

confidence: 99%

Use of a Multiplex Transcript Method for Analysis of Pseudomonas aeruginosa Gene Expression Profiles in the Cystic Fibrosis Lung

et al. 2016

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The discovery of therapies that modulate Pseudomonas aeruginosa virulence or that can eradicate chronic P. aeruginosa lung infections associated with cystic fibrosis (CF) will be advanced by an improved understanding of P. aeruginosa behavior in vivo. We demonstrate the use of multiplexed Nanostring technology to monitor relative abundances of P. aeruginosa transcripts across clinical isolates, in serial samples, and for the purposes of comparing microbial physiology in vitro and in vivo. The expression of 75 transcripts encoded by genes implicated in CF lung disease was measured in a variety of P. aeruginosa strains as well as RNA serial sputum samples from four P. aeruginosa-colonized subjects with CF collected over 6 months. We present data on reproducibility, the results from different methods of normalization, and demonstrate high concordance between transcript relative abundance data obtained by Nanostring or transcriptome sequencing (RNA-Seq) analysis. Furthermore, we address considerations regarding sequence variation between strains during probe design. Analysis of P. aeruginosa grown in vitro identified transcripts that correlated with the different phenotypes commonly observed in CF clinical isolates. P. aeruginosa transcript profiles in RNA from CF sputum indicated alginate production in vivo, and transcripts involved in quorum-sensing regulation were less abundant in sputum than strains grown in the laboratory. P. aeruginosa gene expression patterns from sputum clustered closely together relative to patterns for laboratory-grown cultures; in contrast, laboratory-grown P. aeruginosa showed much greater transcriptional variation with only loose clustering of strains with different phenotypes. The clustering within and between subjects was surprising in light of differences in inhaled antibiotic and respiratory symptoms, suggesting that the pathways represented by these 75 transcripts are stable in chronic CF P. aeruginosa lung infections. Several factors complicate the comparison of in vitro studies on Pseudomonas aeruginosa with infections in the cystic fibrosis (CF) lung. First, many different P. aeruginosa strains cause CF lung infections; thus, reliance on commonly used laboratory strains might limit our understanding of P. aeruginosa in CF (1-3). Second, laboratory or cell culture studies rarely incorporate coinfecting species and lack components of the lung environment, such as immune response factors, that shape P. aeruginosa phenotypes (4, 5). We know little about how these environmental stimuli influence P. aeruginosa (6-8). To complicate matters further, a single CF sputum sample contains mixtures of P. aeruginosa genotypes and phenotypes. A recent study has suggested that a mixture of strains influenced traits such as drug response in ways that were difficult to predict from the study of single strains (9). Clinical isolates of P. aeruginosa, even from the same respiratory sample, can have striking differences in phenotypes, including colony morphology, quorum-sensing regulation, and motili...

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Genomic Variation among Contemporary Pseudomonas aeruginosa Isolates from Chronically Infected Cystic Fibrosis Patients

Abstract: ABSTRACTThe airways of individuals with cystic fibrosis (CF) often become chronically infected with unique strains of the opportunistic pathogenPseudomonas aeruginosa. Several lines of evidence suggest that the infectingP. aeruginosa Show more

Cited by 82 publications

References 49 publications

A Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation

A Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation

History of Antibiotic Adaptation Influences Microbial Evolutionary Dynamics During Subsequent Treatment

Use of a Multiplex Transcript Method for Analysis of Pseudomonas aeruginosa Gene Expression Profiles in the Cystic Fibrosis Lung

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