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 main determinants of AMR are the antimicrobial resistance genes (ARGs). Since bacteria can share genetic components via horizontal gene transfer, even non-pathogenic bacteria may provide ARG to any pathogens which they become physically close to (e.g. in the human gut). In addition, fermented food naturally contains bacteria in high amounts. In this study, we examined the diversity of ARG content in various kefir and yoghurt samples (products, grains, bacterial strains) using a unified metagenomic approach. We found numerous ARGs of commonly used fermenting bacteria. Even with the strictest filter restrictions, we identified ARGs undermining the efficacy of aminocoumarins, aminoglycosides, carbapenems, cephalosporins, cephamycins, diaminopyrimidines, elfamycins, fluoroquinolones, fosfomycins, glycylcyclines, lincosamides, macrolides, monobactams, nitrofurans, nitroimidazoles, penams, penems, peptides, phenicols, rifamycins, tetracyclines and triclosan. In the case of gene lmrD, we detected genetic environment providing mobility of this ARG. Our findings support the theory that during the fermentation process, the ARG content of foods can grow due to bacterial multiplication. The results presented suggest that the starting culture strains of fermented foods should be monitored and selected in order to decrease the intake of ARGs via foods.

A survey on antimicrobial resistance genes of frequently used bacteria in kefir and yoghurt

“…We found numerous and diverse ARGs in commonly used bacterial strains of kefir and yoghurt products. Thus, the results of our study support the findings of several other recent studies which have also identified ARGs in probiotics 5,6,[33][34][35] . We also found that many of them have the potential to be mobile.…”

“…The transfer of antimicrobial resistance genes (ARGs) is enhanced by being linked with mobile genetic elements (MGEs), particularly plasmids 3,4 . In this study, as a continuation of our work 5,6 , we explored the possible development of AMR due to HGT during the fermentation of food produce derived from animal sources, namely kefir and yoghurt products. The multiplication of bacteria during the fermentation process is widely known and understood.…”

Mobile Antimicrobial Resistance Genes in Probiotics

“…In the Bifidobacterium genus, ARGs were associated with four species ( B. animalis , B. bifidum , B. breve and B. longum ). None of the B. animalis , B. bifidum , B. breve and B. longum related B. adolescentis rpoB mutants conferring resistance to rifampicin and tet(W/N/W) are specific for the identified species but both genes have previously been described in them [ 6 , 52 , 53 , 54 , 55 ]. B. bifidum ileS conferring resistance to mupirocin reported in B. bifidum supposedly cannot be exclusively linked to this species of the genus, but it had been identified in it before [ 56 ].…”

Role of probiotics and vitamins in maintaining a healthy gut microbiome: recent advances

“…Thus, the challenge is to monitor and select the starting culture strains of fermented foods in order to decrease the intake of ARGs via foods. (24)…”