Insights into Microbial Contamination and Antibiotic Resistome Traits in Pork Wholesale Market: An Evaluation of the Disinfection Effect of Sodium Hypochlorite

This study evaluated the efficacy of NaClO disinfection by examining the alterations in the microbiome and resistome of a pork wholesale market (PWM), and bacteria isolation and analysis were performed to validate the findings. As expected, the taxonomic compositions of bacteria were significantly different before and after disinfection. While it is worth mentioning that Salmonella enterica, Salmonella bongori, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa can be observed in all surfaces, indicating the application of NaClO disinfection treatment in PMW environment on pathogenic bacteria was limited. Correlations were identified between antibiotic resistance genes (ARGs) associated with aminoglycosides (aph(3’’)-I, aph(6’)-I), quinolone (qnrB, abaQ), polymyxin (arnA, mcr-4) and disinfectant resistance genes (emrA/BD, mdtA/B/C/E/F). Futhermore, correlations were found between risk Rank I ARGs associated with aminoglycoside (aph(3’)-I), tetracycline (tetH), beta_lactam (TEM-171), and disinfectant resistance genes (mdtB/C/E/F, emrA, acrB, qacG). Importantly, we found that Acinetobacter and Salmonella were main hosts of disinfectant resistance genes. The proportion of genes encoding efflux pumps increased in the PMW resistome after disinfection. Microbial cultures demonstrated that the traits of microbial contamination and antibiotic resistome were consistent with the observed in metagenomic sequencing.