A glimpse of antimicrobial resistance gene diversity in kefir and yoghurt

Abstract

Antimicrobial resistance (AMR) is a global threat gaining more and more practical significance every year. The protection of bacteria against antimicrobials based on antimicrobial resistance genes (ARGs) developed in evolution. One of the essential clinical questions is the origin of ARGs of pathogen bacteria. Since the bacteria can share genetic components by horizontal gene transfer (HGT), all even non-pathogen bacteria may provide ARG to any pathogens when they became close physically. The bacteria of the human gut may make contact with bacteria entered into the body by food. The fermented food contains bacteria in high amount by its nature. Here we studied the diversity of ARG content by a unified metagenomic approach in various kefir and yoghurt products, in grain and isolated bacterial strains. We found numerous ARGs of commonly used fermenting bacteria with diversity characteristics in kefir and yoghurt samples. Even with the strictest filter restrictions we identified ARGs undermining the efficacy of aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, diaminopyrimidine, elfamycin, fluoroquinolone, fosfomycin, glycylcycline, lincosamides, macrolide, monobactam, nitrofuran, nitroimidazole, penam, penem, peptide, phenicol, rifamycin, tetracycline and triclosan. In the case of gene lmrD, we detected genetic environment providing mobility of this ARG. Our findings support that theory during the fermentation process the food ARG content can grow by the bacteria multiplication. Results presented suggest that starting culture strains of fermented food should be monitored and selected to decrease the ARG amount intake by nutrition.