Comprehensive Comparative Genomic revels:Bacteroides fragilisis 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.

PathogenicBacteroides fragilisstrains can emerge from gut-resident commensals

“…We next evaluated the rate of gene gain and loss in relation to core gene evolution, finding a significant correlation between core genome phylogeny branch length and gene gain and loss events (Student’s t-test, p=3.4e-70) ( Figure 1C ). This indicates that B. fragilis exhibits considerable genetic diversity and proficiently assimilates new genes, a characteristic often observed in bacteria within diverse communities 28 . The extensive accessory genome of B. fragilis highlights its genomic plasticity, which is crucial for the acquisition of new genetic determinants that support the transition from a commensal lifestyle to survival in extra-intestinal niches 29 .…”