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

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.Uvelichenie doli lekarstvenno-ustoĭchivykh shtammov bakteriĭ neposredstvenno sviazano s shirokim primeneniem antibiotikov v meditsine i zhivotnovodstve. Predpolagaetsia, chto mikroflora kishechnika sluzhit rezervuarom genov antibiotikorezistentnosti, kotorye mogut peredavat'sia ot simbioticheskikh bakteriĭ k patogennym mikroorganizmam, v tom chisle v rezul'tate fagovoĭ transduktsii. S ispol'zovaniem programmy predskazaniia profagov PHASTER i bazy dannykh genov antibiotikorezistentnosti CARD proveden poisk genov antibiotikorezistentnosti, nakhodiashchikhsia v sostave profagov, v mikrobnom soobshchestve kishechnika cheloveka. V rezul'tate analiza metagenomnykh sborok vos'mi obraztsov v sostave posledovatel'nosteĭ profagov byli obnaruzheny geny lsaE, mdfA i cpxR/cpxA, prisutstvie kotorykh obespechivaet ustoĭchivost' bakteriĭ k antimikrobnym peptidam, plevromutilinu, linkomitsinam, streptograminam gruppy A, a takzhe mnozhestvennuiu lekarstvennuiu ustoĭchivost'. Iz 659 predpolozhitel'nykh profagov, predskazannykh v metagenomnykh sborkakh, tri (0,46%) imeli v svoem sostave geny antibiotikorezistentnosti.