Lactic acid bacteria and bifidobacteria deliberately introduced into the agro-food chain do not significantly increase the antimicrobial resistance gene pool

Vita Rozman; Petra Mohar Lorbeg; Primož Treven; Tomaž Accetto; Majda Golob; Irena Zdovc; Bojana Bogovič Matijašić

doi:10.1080/19490976.2022.2127438

Lactic acid bacteria and bifidobacteria deliberately introduced into the agro-food chain do not significantly increase the antimicrobial resistance gene pool

Gut Microbes. 2022 Jan-Dec;14(1):2127438. doi: 10.1080/19490976.2022.2127438.

Authors

Vita Rozman¹, Petra Mohar Lorbeg¹, Primož Treven¹, Tomaž Accetto², Majda Golob³, Irena Zdovc³, Bojana Bogovič Matijašić¹

Affiliations

¹ University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Institute of Dairy Science and Probiotics, Domžale, Slovenia.
² University of Ljubljana, Biotechnical Faculty, Department of Microbiology, Chair of Microbial Diversity, Microbiomics and Biotechnology, Ljubljana, Slovenia.
³ University of Ljubljana, Veterinary Faculty, Institute of Microbiology and Parasitology, Ljubljana, Slovenia.

Abstract

Lactic acid bacteria (LAB) and bifidobacteria may serve as reservoirs of antimicrobial resistance, but the risk posed by strains intentionally introduced into the agro-food chain has not yet been thoroughly investigated. The aim of our study was to evaluate whether probiotics, starter and protective cultures, and feed additives represent a risk to human health. In addition to commercial strains of LAB and bifidobacteria, isolates from human milk or colostrum, intestinal mucosa or feces, and fermented products were analyzed. Phenotypic susceptibility data of 474 strains showed that antimicrobial resistance was more common in intestinal isolates than in commercial strains. Antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) were characterized in the whole genome sequences of 1114 strains using comparative genomics. Intrinsic ARGs were abundant in enterococci, bifidobacteria, and lactococci but were considered non-risky due to the absence of MGEs. The results revealed that 13.8% of commercial strains contained acquired ARGs, most frequently for tetracycline. We associated 75.5% of the acquired ARGs with known or novel MGEs, and their potential for transmission was assessed by examining metagenomic sequences. We confirmed that ARGs and MGEs were not as abundant or diverse in commercial strains as in human intestinal isolates or isolates from human milk, suggesting that strains intentionally introduced into the agro-food chain do not pose a significant threat. However, attention should be paid especially to individual probiotic strains containing elements that have been shown to have high potential for transferability in the gut microbiota.Abbreviations: ARG, antimicrobial resistance gene; ICE, integrative and conjugative element; IME, integrative and mobilizable element; LAB, lactic acid bacteria; MDR, multidrug resistance; MIC, minimum inhibitory concentration; MGE, mobile genetic element; TRRPP, tetracycline-resistant ribosomal protection protein; WGS, whole genome sequences.

Keywords: Lactic acid bacteria; antimicrobial resistance; bifidobacteria; metagenomes; mobile genetic element; probiotic; resistance gene; starter culture; whole genome sequences.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Anti-Bacterial Agents / pharmacology
Bifidobacterium / genetics
Drug Resistance, Bacterial / genetics
Food Chain
Gastrointestinal Microbiome*
Gene Pool
Humans
Lactobacillales* / genetics
Tetracyclines

Substances

Anti-Bacterial Agents
Tetracyclines

Grants and funding

This research was supported by the Slovenian Research Agency (Ljubljana, Slovenia) through the young researchers program (grant numbers 6316-1/2017-273, 603-1/2017-13), the research project J4-1769, and the research program P4-0097.