Metagenomics reveals the risk of antibiotic resistance genes and co-occurrence in Chinese traditional fermented bean products

The natural symbiotic fermentation by diverse microorganisms significantly influences the quality and safety of traditional fermented soybean products, imparting them with distinct flavor and nutrition. Economic growth, population increase, and intensive production practices in crop-producing regions have altered bacterial communities and facilitated the accumulation of antibiotic resistance genes. Although shotgun metagenomic sequencing is widely employed for resistance gene analysis in environmental studies, the comprehensive understanding of bacterial communities, epidemiological distribution, coexistence patterns, and host information related to antibiotic resistance genes in fermented bean products remains incompletely elucidated. We performed a comprehensive metagenomic sequencing study on locally characteristic traditional fermented bean products (such as sufu and bean paste) across 10 provinces and cities in China. Our investigation systematically analyzed microbial communities and antibiotic resistance profiles in fermented bean products, shedding light on the coexistence patterns and host information of resistance genes. The study findings revealed the presence of bacteria with potential health risks. We identified 1854 distinct subtypes of antibiotic resistance genes (ARGs) resistant to over 20 antibiotics. To assess the potential harm of these ARGs, we established a "Risk ARG Library for Fermented Bean Products" comprising 87 ARGs primarily hosted by Escherichia, Citrobacter, and Raoultella. This suggests their significant role in hosting and potentially transmitting these harmful resistance genes. In summary, our study enhances the comprehensive understanding of resistance profiles in fermented bean products, crucial for preventing and managing foodborne multidrug-resistant bacteria.