Decade-long bacterial community dynamics in cystic fibrosis airways

Abstract

The structure and dynamics of bacterial communities in the airways of persons with cystic fibrosis (CF) remain largely unknown. We characterized the bacterial communities in 126 sputum samples representing serial collections spanning 8-9 y from six age-matched male CF patients. Sputum DNA was analyzed by bar-coded pyrosequencing of the V3-V5 hypervariable region of the 16S rRNA gene, defining 662 operational taxonomic units (OTUs) from >633,000 sequences. Bacterial community diversity decreased significantly over time in patients with typically progressive lung disease but remained relatively stable in patients with a mild lung disease phenotype. Antibiotic use, rather than patient age or lung function, was the primary driver of decreasing diversity. Interpatient variability in community structure exceeded intrapatient variability in serial samples. Antibiotic treatment was associated with pronounced shifts in community structure, but communities showed both short-and longterm resilience after antibiotic perturbation. There was a positive correlation between OTU occurrence and relative abundance, with a small number of persistent OTUs accounting for the greatest abundance. Significant changes in community structure, diversity, or total bacterial density at the time of pulmonary exacerbation were not observed. Despite decreasing community diversity in patients with progressive disease, total bacterial density remained relatively stable over time. These findings show the critical relationship between airway bacterial community structure, disease stage, and clinical state at the time of sample collection. These features are the key parameters with which to assess the complex ecology of the CF airway. microbial ecology | microbiome | antibiotics

The Limitations of In Vitro Experimentation in Understanding Biofilms and Chronic Infection

“…Other studies place diversity higher, with an average of 5.4 bacterial species per chronic wound [36]. Such degrees of species diversity are also observed in the CF lung, resulting from the diverse microenvironments that arise [97][98][99][100]. Conversely, Kirketerp-Moller and colleagues (2008) [5] struggled to identify multiple species during a venous leg ulcer study, highlighting the diversity and complexity of different types of chronic infection.…”

Antibiotic Management of Lung Infections in Cystic Fibrosis. I. The Microbiome, Methicillin-Resistant Staphylococcus aureus, Gram-Negative Bacteria, and Multiple Infections

“…The Human Microbiome Project, a National Institutes of Health-sponsored initiative launched in 2007, applying culture-independent methods to assess bacterial ecology, has significantly broadened this view. Numerous studies now provide compelling evidence that the airways of persons with CF may be inhabited by diverse bacterial communities composed of dozens of species (14)(15)(16)(17)(18)(19)(20)(21)(22)(23). In addition to "typical" CF pathogens, "nonpathogenic oral bacteria," including many obligate and facultative anaerobic species, are often present in densities that well exceed those of the traditional opportunists associated with CF (4).…”

Le microbiome pulmonaire en 2015

“…À ce jour, la majorité des données de séquençage à haut-débit concernant le bactériote et le bactériome qui a été publiée porte sur la mucoviscidose. Ainsi, d'après les résultats de Zhao et al [15], le microbiote pulmonaire des patients évolue avec l'âge. La diversité de la communauté bactérienne est en effet diminuée chez les patients plus âgés chez lesquels la famille Pseudomonadaceae prédo-mine [15].…”

“…Ainsi, d'après les résultats de Zhao et al [15], le microbiote pulmonaire des patients évolue avec l'âge. La diversité de la communauté bactérienne est en effet diminuée chez les patients plus âgés chez lesquels la famille Pseudomonadaceae prédo-mine [15]. L'infection chronique par P. aeruginosa, qui est considéré comme le pathogène le plus fréquemment rencontré chez les patients atteints de mucoviscidose, est associée à la diminution de la fonction pulmonaire [7,26].…”

“…À côté de P. aeruginosa, d'autres espèces ou genres (Streptococcus, Prevotella, Veillonella, Rothia, Actinomyces, Gemella, Granulicatella, Fusobacterium, Neisseria, Atopobium, etc.) ont été identifiés comme étant importants dans la constitution du microbiote pulmonaire au cours de la mucoviscidose [9,11,[13][14][15][16][17][18][19][20]. L'ensemble de ces études tend à montrer qu'il existe une corrélation significative entre la diversité du microbiome pulmonaire et l'âge, le statut clinique et l'état de la fonction pulmonaire des patients [11, 15-17, 20, 26].…”