Genomic epidemiology and antimicrobial resistance of non-typhoidal Salmonella from retail meats in Beijing, China: implications for foodborne transmission and phage susceptibility.

OBJECTIVES: To investigate the prevalence, antimicrobial resistance (AMR) profiles, genomic characteristics and phage susceptibility of non-typhoidal Salmonella (NTS) isolated from retail meats in Beijing, China, and to assess the potential for foodborne transmission and risks associated with phage application. METHODS: A total of 583 retail meat samples (pork, chicken, beef, mutton) were collected across Beijing (2021-2022). NTS isolates were identified by serotyping and MALDI-TOF. Antimicrobial susceptibility was tested by broth microdilution. Whole-genome sequencing was performed on 153 isolates for resistome, virulome, plasmid typing and core-genome MLST (cgMLST). Phage lysis assays used 46 phages against representative isolates, and prophages were predicted in silico. RESULTS: NTS prevalence was highest in pork (52.4%) and chicken (43.8%). Dominant serotypes were S. London and S. Enteritidis. Resistance rates were high for sulfisoxazole (74.6%), ampicillin (68.6%) and tetracycline (68.6%); 64.4% of isolates were multidrug-resistant (MDR). Genomic analysis revealed widespread resistance genes (e.g. bla CTX-M-55, sul, mph(A)) associated with mobile genetic elements (ISEcp1, IS91). cgMLST showed high genetic similarity between foodborne isolates and contemporaneous human clinical isolates from multiple provinces. Phage lysis was highly effective against S. Enteritidis (83.3%) but limited against S. Kentucky; 34.0% of isolates carried prophages containing transposons. CONCLUSIONS: Retail meats in Beijing, particularly pork and chicken, represent an important reservoir of multidrug-resistant NTS. Comparative genomic analysis revealed close genomic relatedness between retail meat isolates and human clinical isolates, suggesting the potential for foodborne transmission along the food chain. In vitro phage lysis assays demonstrated serotype-dependent susceptibility patterns, highlighting the potential of phage-based control strategies for specific Salmonella serotypes. However, prophages containing transposon-associated sequences were identified in a subset of isolates, and their contribution to horizontal gene transfer warrants further investigation. Enhanced surveillance integrating food, animal, environmental and human clinical Salmonella monitoring, together with serotype-targeted intervention strategies, is needed to support a One Health approach to foodborne disease control.