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The constant increase of antibiotic-resistant strains of bacteria is caused by extensive uses of antibiotics  in medicine and animal breeding. It was suggested that the gut microbiota serves as a reservoir for antibiotics  resistance genes that can be carried from symbiotic bacteria to pathogenic ones, in particular, as a result of transduction.  In the current study, we have searched for antibiotics resistance genes that are located inside prophages in human  gut microbiota using PHASTER prophage predicting tool and CARD antibiotics resistance database. After analysing  metagenomic assemblies of eight samples of antibiotic treated patients, lsaE, mdfA and cpxR/cpxA genes were  identified inside prophages. The abovementioned genes confer resistance to antimicrobial peptides, pleuromutilin,  lincomycins, streptogramins and multidrug resistance. Three (0.46%) of 659 putative prophages predicted  in metagenomic assemblies contained antibiotics resistance genes in their sequences.

Bioinformatics analysis of antimicrobial resistance genes and prophages colocalized in human gut metagenomes