Comprehensive Comparative Genomic revels: Bacteroides fragilis is a reservoir of antibiotic resistance genes in the gut microbiota

Abstract

Bacteroides fragilis are commensal bacteria of the gut microbiota of mammals and may cause severe infection in a susceptible host. Treatment can be cumbersome if multidrug resistant strains are present in the affected tissue. The principal aim of this study was to provide new insights into the genomic properties of B. fragilis through different approaches in comparative genomics. Results revealed that the pan-genome is opened, and an intense exchange of genetic material reinforces this inference. The Don complex, responsible for extraintestinal adaptation, is present in all strains, suggesting a crucial role for B. fragilis adaptation. CRISPR-Cas system is at 76% of the samples, but it apparently has low accuracy against prophage. Multidrug resistance genes are in 80% of strains. Conjugative transposons and integrative and conjugative elements (ICE) are the main spreaders of genes for antimicrobial resistance. We also reported evidence for horizontal gene transfer (HGT) of antimicrobial resistance genes among the B. fragilis strains and Bacteriodales. At least 398 genes are under positive selection, including genes for antimicrobial resistance and transport of toxins and nutrients.