Pyrosequencing reveals transient cystic fibrosis lung microbiome changes with intravenous antibiotics

Smith, Daniel; Badrick, Alison C.; Zakrzewski, Martha; Krause, Lutz; Bell, Scott C.; Anderson, Gregory J.; Reid, David W.

doi:10.1183/09031936.00203013

Cited by 71 publications

(77 citation statements)

References 37 publications

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“…Antibiotics only modestly or transiently alter microbial community structure in the lungs of CF patients despite improvements in health status (68)(69)(70). These observations led us to question whether the salubrious effects of antibiotics were associated less with their microbicidal activity and more with how they affect bacterial phenotypes in the lung, as evidenced by their gene transcription profiles.…”

Section: Discussionmentioning

confidence: 97%

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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Section: Discussionmentioning

confidence: 97%

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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“…Importantly, components of the microbiome (such as the Streptococcus anginosus group) have been associated with disease pathogenesis [14], while other organisms are thought to protect the microbiota by the production of antibiotic degrading enzymes [15, 16]. The administration of systemic antibiotics has been shown to have dramatic, albeit transient, effects on the microbial community composition [17]. However, information as to whether the microbiome influences outcomes or therapeutic response remains limited.…”

Section: Introductionmentioning

confidence: 99%

The effects of inhaled aztreonam on the cystic fibrosis lung microbiome

et al. 2017

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BackgroundAztreonam lysine for inhalation (AZLI) is an inhaled antibiotic used to treat chronic Pseudomonas aeruginosa infection in CF. AZLI improves lung function and quality of life, and reduces exacerbations-improvements attributed to its antipseudomonal activity. Given the extremely high aztreonam concentrations achieved in the lower airways by nebulization, we speculate this may extend its spectrum of activity to other organisms. As such, we sought to determine if AZLI affects the CF lung microbiome and whether community constituents can be used to predict treatment responsiveness.MethodsPatients were included if they had chronic P. aeruginosa infection and repeated sputum samples collected before and after AZLI. Sputum DNA was extracted, and the V3-hypervariable region of the 16S ribosomal RNA (rRNA) gene amplified and sequenced.ResultsTwenty-four patients naïve to AZLI contributed 162 samples. The cohort had a median age of 37.1 years, and a median FEV1 of 44% predicted. Fourteen patients were a priori defined as responders for achieving ≥3% FEV1 improvement following initiation. No significant changes in alpha diversity were noted following AZLI. Furthermore, beta diversity demonstrated clustering with respect to patients, but had no association with AZLI use. However, we did observe a decline in the relative abundance of several individual operational taxonomic units (OTUs) following AZLI initiation suggesting that specific sub-populations of organisms may be impacted. Patients with higher abundance of Staphylococcus and anaerobic organisms including Prevotella and Fusobacterium were less likely to respond to therapy.ConclusionsResults from our study suggest potential alternate/additional mechanisms by which AZLI functions. Moreover, our study suggests that the CF microbiota may be used as a biomarker to predict patient responsiveness to therapy suggesting the microbiome may be harnessed for the personalization of therapies.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-017-0265-7) contains supplementary material, which is available to authorized users.

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“…Notable findings have included the decrease in diversity in the CF airway microbiota associated with advancing age and disease severity [2–4], changes in the microbiota that are associated with the onset of pulmonary exacerbation [5–7], and the response of microbiota to antibiotic treatment [2,8–10]. Because antibiotic use can have a significant short-term impact on culture-independent measures of bacterial community structure [2,8–10], accurate accounting of antibiotic use at the time of sample collection is necessary for meaningful interpretation of CF airway microbiome data. Reliable ascertainment of subjects’ dates of antibiotic use is also necessary to define clinically relevant disease states, including baseline health (B), onset of exacerbation (prior to antibiotic administration) (E), antibiotic treatment (T), and recovery (defined number of days after antibiotic completion) (R) [2].…”

Section: Introductionmentioning

confidence: 99%

Episodic oral antibiotic use in CF: Discordance between the electronic medical record and self-report

Caverly

Kalikin

et al. 2016

Journal of Cystic Fibrosis

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Background Accurate accounting of antibiotic use is necessary for studies comparing the CF airway microbiota across clinically relevant disease states. While poor adherence to chronic therapies is well described for individuals with CF, use patterns of episodic oral antibiotics are less clear. Methods Eleven individuals with CF completed daily questionnaires regarding antibiotic use for a mean of 458 days. Self-report of episodic oral antibiotic use was compared to antibiotic prescription data in the electronic medical record (EMR). Results Self-reported use of episodic oral antibiotics differed from EMR data an average of 8.3% of days per subject. The majority of these discrepancies were due to self-reported use of oral antibiotics outside of the EMR-documented dates of antibiotic prescription. Conclusions Discrepancies exist between self-reported use of episodic oral antibiotics and EMR data that have implications for studies of the CF airway microbiota.

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Pyrosequencing reveals transient cystic fibrosis lung microbiome changes with intravenous antibiotics

Cited by 71 publications

References 37 publications

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

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

The effects of inhaled aztreonam on the cystic fibrosis lung microbiome

Episodic oral antibiotic use in CF: Discordance between the electronic medical record and self-report

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