Genomic epidemiology and antimicrobial resistance of nontyphoidal Salmonella in retail meats in Hong Kong: A comprehensive surveillance study using whole-genome sequencing

Nontyphoidal Salmonella (NTS) is a major foodborne pathogen, and rising antimicrobial resistance (AMR) threatens treatment efficacy. Salmonella remained the leading cause of bacterial foodborne outbreaks in Hong Kong, but data regarding its prevalence in retail meats are limited. This study investigated the prevalence, serotype distribution, AMR patterns, and genetic relationships of Salmonella in retail pork, beef, and chicken collected across Hong Kong from July 2022 to June 2023. We found a high overall Salmonella prevalence (27.6 %), particularly in pork (50.6 %) and fresh, non-chilled meat (46.2 %), suggesting potential contamination during slaughter, with the non-chilled conditions potentially promoting further bacterial growth. The dominant serotypes (S. typhimurium, S. Rissen, S. Derby, S. London), mainly from pork and beef, mirrored the top serotypes and key AMR profiles (ciprofloxacin, ceftriaxone) found in local human clinical cases, highlighting the food chain's relevance. High rates of multidrug non-susceptibility (68.7 %) and non-susceptibility to critical antibiotics like ciprofloxacin (69.6 %), ceftriaxone (7.8 %), and azithromycin (8.3 %) were observed. Phylogenetic analysis identified multiple genetically related clusters containing both human and food isolates, with clonal spread predominant in pork/beef serotypes and plasmid-mediated AMR determinants in chicken serotypes. Notably, several clusters showed non-susceptibility to multiple first-line antimicrobials, highlighting concerning transmission patterns from retail meats to clinical cases. This study provides crucial baseline data and identifies high-risk transmission pathways between food sources and clinical cases, underscoring the need for integrated genomic surveillance to combat AMR Salmonella in Hong Kong's food supply.