Bioinformatics Analysis of Antimicrobial Resistance Genes and Prophages Colocalized in Human Gut Metagenomes

Abstract

The constant increase of bacterial antibiotic-resistant strains is directly linked to a common use of antibiotics in medicine and animal breeding. It is suggested that the gut microbiota serves as a reservoir for antibiotic resistance genes that can be transferred from symbiotic bacteria to pathogenic ones, particularly due to phage transduction. In this study, using the PHASTER prophage predicting tool and CARD antibiotics resistance database we have searched for antibiotic resistance genes that are located within prophages in human gut microbiota. After analysing metagenomic assemblies of eight samples of antibiotic treated patients, lsaE, mdfA, and cpxR/cpxA genes were identified inside prophages. These genes confer resistance to antimicrobial peptides, pleuromutilin, lincomycins, streptogramins and also multidrug resistance. Three (0.46%) of 659 putative prophages predicted in the metagenomic assemblies contained antibiotics resistance genes in their sequences.