Metagenomics reveals differences in the composition of bacterial antimicrobial resistance and antibiotic resistance genes in pasteurized yogurt and probiotic bacteria yogurt from China

Abstract

Antimicrobial resistance has become a global public health concern, and antibiotic resistance genes (ARGs) in food are a research focus. In China, probiotics and pasteurized yogurts are the 2 main types of commercially available yogurt, but the distribution and differences of antibiotic-resistant bacteria and gene types in these products are not well known. This study used a shotgun metagenomic approach to analyze 22 different types of yogurt collected from 9 main yogurt-producing areas in China, each type of yogurt includes 8 different batches of samples. The abundance and diversity of bacteria identified in probiotic yogurt were significantly higher than those in pasteurized yogurt, with Acetobacter, Raoultella, and Burkholderia identified as unique and highly abundant genera in probiotic yogurt. Similarly, ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) abundance was higher than that in pasteurized yogurt. A total of 1149 ARG subtypes belonging to 16 ARG types were identified, with the highest abundance of rifampicin, multidrug efflux pumps, and quinolone resistance genes detected. Network analysis revealed significant non-random co-occurrence relationships between different types and subtypes of ARGs in yogurt samples. Forty-four ARG subtypes in pasteurized yogurt were potentially hosted by 36 bacterial genera, and in probiotic yogurt, 63 ARGs were expected to be hosted by 86 bacterial species from 37 genera. These findings speculate on potential safety issues in fermented dairy products and emphasize the need for a more hygienic environment when processing probiotic yogurt.