Antimicrobial resistance genes of fermented red pepper (FRP) related food in a large-scale environment: distribution pattern and risk assessment

Abstract

Abstract Background Antibiotic resistance genes (ARGs) are rapidly increasing numbers of difficult-to-treat infections and have been taken as a severe global health threat, which is estimated that the number of approximately 700,000 annual deaths and will exceed 10 million deaths per year by 2050 due to ARGs. Recently, ARGs involved in fermented foods have been taken more attention due to the spread of ARGs throughout the food chain. As well known, fermented red pepper (FRP) foods have been consumed widely as their unique flavor and health beneficial effects. However, knowledge gaps are still in the risk assessment of FRPs and their dissemination patterns on a large scale, which limited the development of effective methods to control and monitor the ARGs in fermented food. Here, a combination of read- and assembly-based whole genome sequencing methods as well as amplicon sequences analysis was used to investigate and reveal the ARGs dissemination patterns and risk assessment in FRPs related foods on a large-scale metagenomic data. Results 65.38% of FRP samples contained high-risk ARGs need to be concerned. Multidrug resistant (MDR) was the highest abundant type. On average, tetL and tetracycline resistance protein account for 81.8%, followed by multidrug (7.5%), beta-lactam (5.5%), colistin (1.5%), aminoglycoside (1.1%), and macrolide-lincosamide-streptogramin (1.1%) in the highest risk level, and the corresponding host range crossed from genus to bacteria indicating high mobility. Bacillus, Enterobacter, and Pantoea were the predominant host of carrying ARGs, which involved three major classes of resistance mechanism, that is, antibiotic efflux, antibiotic inactivation, and antibiotic target alteration. In addition, various ARGs and virulence factors with significant positive or negative relationships have been revealed. Conclusion Our findings demonstrated various ARGs were present in FRPs and high-risk ARGs such as tetL, tetracycline resistance protein, multidrug, beta-lactam, colistin, aminoglycoside, and macrolide-lincosamide-streptogramin has high mobility from genus to bacteria, which were significantly positively or negatively related to virulence factors. These results not only pave a way for understanding distribution patterns of ARGs in FRP foods on a large scale but also provide valuable knowledge to monitor and mitigate the ARGs.