Taxonomic variability over functional stability in the microbiome of Cystic Fibrosis patients chronically infected by Pseudomonas aeruginosa

Abstract

Although the cystic fibrosis (CF) lung microbiome has been characterized in several studies, little is still known about the functions harboured by those bacteria, and how they change with disease status and antibiotic treatment. The aim of this study was to investigate the taxonomic and functional temporal dynamics of airways microbiome in a cohort of CF patients. Multiple sputum samples were collected over 15 months from 22 patients with chronic P. aeruginosa infection, for a total of 79 samples. DNA extracted from samples was subjected to shotgun metagenomic sequencing allowing either strain-level taxonomic profiling and assessment of the functional metagenomic repertoire. High inter-patient taxonomic heterogeneity was found with short-term compositional changes during exacerbations and following antibiotic treatment. Each patient exhibited distinct sputum microbial communities at the taxonomic level, and strain-specific colonization of traditional CF pathogens, including P. aeruginosa, and emerging pathogens. Sputum microbiome was found to be extraordinarily resilient following antibiotic treatment, with rapid recovery of taxa and metagenome-associated gene functions. In particular, a large core set of genes, including antibiotic resistance genes, were shared across patients despite observed differences in clinical status or antibiotic treatment, and constantly detected in the lung microbiome of all subjects independently from known antibiotic exposure, suggesting an overall microbiome-associated functions stability despite taxonomic fluctuations of the communities.IMPORTANCEWhile the dynamics of CF sputum microbial composition were highly patient-specific, the overall sputum metagenome composition was stable, showing a high resilience along time and antibiotic exposure. The high degree of redundancy in the CF lung microbiome could testifies ecological aspects connected to the disease that were never considered so far, as the large core-set of genes shared between patients despite observed differences in clinical status or antibiotic treatment. Investigations on the actual functionality (e.g. by metatranscriptomics) of the identified core-set of genes could provide clues on genetic function of the microbiome to be targeted in future therapeutic treatments.

Strain-resolved Dynamics of the Lung Microbiome in Patients with Cystic Fibrosis

“…Importantly, distinguishing these variants would not have been possible without the longitudinal repeated samplings, showing that tracking patients over time provides valuable added information. To our knowledge, only two other shotgun metagenomics studies with multiple reference points per CF patient have been published so far [20,37]. Neither, however, explores longitudinal genomic variation on a sub-strain level within a patient.…”

“…Extensive longitudinal sampling, however, was performed in few prior studies [20,51]. Ours is thus the first study to use longitudinal metagenomics data for describing the dynamics of multiple strain variants of a species in the same CF patient.…”

“…Metagenomics allows to survey bacterial, viral, and fungal populations at once, giving a more complete picture of microbial relative abundances in the CF lung microbiome [17,19]. Consequently, a larger portion of microbiome inhabitants can be classified at the species level [17], and prominent CF pathogens have been classified at the strain level [17,18,20]. Moreover, multiple subpopulations of specific pathogens have been detected in CF through metagenome sequencing [17,18].…”

Is there a role for antibiotics in the treatment of chronic rhinosinusitis?

“…99 Longitudinal studies of the microbiota of patients with CF suggest that the bacterial organisms in the lower airway tract of patients with CF tend to be relatively constant over time, other than during temporary changes associated with acute infections or treatment. [100][101][102] Given the strong correlation between upper and lower airway microbial populations, it could be inferred from these observations that the CF CRS bacterial population is also resistant to change. 103 There is little consensus on the optimal use of antibiotics in CF-related CRS.…”

Prevotella melaninogenica, a Sentinel Species of Antibiotic Resistance in Cystic Fibrosis Respiratory Niche?

“…However, these bacteria remain the unknowns of the lung, both in terms of diversity, resistance or impact on the pathophysiology of CF disease [8]. One of the most prevalent and abundant anaerobic genera described in CF lung is Prevotella, and particularly the species Prevotella melaninogenica [4,5,9]. Contradictory hypotheses on the potential role of Prevotella genus have been previously developed [8].…”