Bacteriophages as vehicles of the resistome in cystic fibrosis.

Environmental microbial communities and human microbiota represent a huge
reservoir of mobilizable genes, the 'mobilome', including a pool of genes
encoding antimicrobial resistance, the 'resistome'. Whole-genome sequencing of
bacterial genomes from cystic fibrosis (CF) patients has demonstrated that
bacteriophages contribute significantly to bacterial genome alterations, and
metagenomic analysis of respiratory tract DNA viral communities has revealed the 
presence of genes encoding antimicrobial resistance in bacteriophages of CF
patients. CF airways should now be considered as the site of complex microbiota, 
where bacteriophages are vehicles for the adaptation of bacteria to this specific
environment and for the emergence and selection of multidrug-resistant bacteria
with chimeric repertoires. As phages are already known to be mobilized during
chronic infection of the lungs of patients with CF, it seems particularly
important to improve the understanding of the mechanisms of phage induction to
prevent the spread of virulence and/or antimicrobial resistance determinants
within the CF population as well as in the community. Such a modern point of view
may be a seminal reflection for clinical practice in the future since current
antimicrobial therapy guidelines in the context of CF may lead to the emergence
of genes encoding antimicrobial resistance.