Diversity of tetracycline- and sulfamethoxazole-resistant bacteria on surface of cold fresh chicken

Abstract: The increased use of antimicrobial-resistant (AR) bacteria in agricultural production has posed a great threat to human health, as AR pathogens could spread from agricultural product to human body via food chain. The antimicrobial resistance (ART) genes in animal- and environment-derived bacteria can migrates to human commensal bacteria through horizontal gene transfer (HGT). Increased evidences have shown the critical role of commensal bacteria in HGT of ART genes, affected by both size and species of ART bacteria. Because of the horizontal gene transfer, it is essential to understand antimicrobial resistance in bacterial community rather than in several species. Currently, there is a knowledge gap in our understanding of tendentious carriers of ART gene as most existing studies focused only on a limited pathogenic bacteria. Cold fresh chicken is consumed worldwide, and our previous work had found existence of tetracycline-resistant (Tetr) bacteria and sulfamethoxazole-resistant (Sulr) bacteria in chicken products which might harbor a pool of AR gene, offering a potential avenue for transmission of antimicrobial resistant bacteria and AR genes to human beings. Motivated by these findings, we randomly selected 18 cold fresh chicken samples from six supermarkets in Shanghai from September to October in 2018 to investigate possible existence of Tetr and Sulr bacteria, as well as the potential risk of antimicrobial resistance migration. The culturable Tetr and Sulr bacteria on the surface of the chicken samples were recovered by brain heart infusion (BHI) agar, containing 48 μg/mL tetracycline or 228 μg/mL sulfamethoxazole plus 12 μg/mL trimethoprim. Their diversity was analyzed by the IonS5TM XL sequencing platform. The results showed that the top three phyla with highest relative abundance of ART bacteria were Proteobacteria, Bacteroidetes and Firmicutes. In Tetr and Sulr bacteria, 59 and 58 specific genera were identified respectively. Compared with the literature report on diversity of total bacteria on surface of cold fresh chicken, the genera of the two ART bacteria found in our study accounted for a high proportion of the total microbial population, indicating that many bacteria on the surface of cold fresh chicken were resistant to the two antimicrobials. The results of shared floras found 18 genera (56 OUTs) and 19 genera (63 OUTs) in Tetr and Sulr bacteria respectively, among which the multi-drug resistance of avian and human Acinetobacter spp., Pseudomonas spp., Proteus spp., Citrobacter spp. and Myroides spp. had been well established. Thus, the potential risk of horizontal transfer of AR genes from avian to human need to further investigation. However, the characteristics of antimicrobial resistance in other 16 genera of shared floras isolated from avian, including Serratia spp., Aeromonas spp., Buttiauxella spp., Comamonas spp., Pseudochrobactrum spp., Stenotrophomonas spp., Moellerella spp., Providencia spp., Sphingomonas spp., Anaeromyxobacter spp., Empedobacter spp., Soonwooa spp., Carnobacterium spp., Weissella spp., Kurthia spp. and Lysinibacillus spp., have not been reported yet. We found that the specific floras of ART bacteria differed from each sample, and 5 to 39 unique OTUs, from three to 32 genus, were identified in samples taken from all supermarkets. The specific ART floras data could be used to trace the origin of the ART bacteria during the processing chain. Overall, our results identified existence of ART bacteria on surface of cold fresh chicken and provided reference for further investigation into their potential risk and control. Since separation of bacteria could be affected by cultural method, our diversity analysis was limited to a single culture condition and relied on establishment of analytical techniques of culture-independent in the future.