Genomic Epidemiology of Salmonella Isolated from Meat Products in China: Population Structure, Phylodynamics, and Antimicrobial Resistance

Salmonella is a major foodborne pathogen, and its increasing antimicrobial resistance poses a significant public health challenge. In this study, we conducted a comprehensive genomic epidemiological investigation of Salmonella isolates recovered from meat products across multiple provinces in China. A total of 141 isolates were collected and subjected to antimicrobial susceptibility testing and whole-genome sequencing. Core genome MLST and hierarchical clustering (HierCC) were performed using EnteroBase, while SNP phylogeny and phylodynamic analyses were conducted to characterize the evolutionary dynamics of Salmonella populations. The predominant serovars were Enteritidis and Infantis, with a high proportion of multidrug-resistant isolates. Potentially transferable plasmids carrying ARGs, such as blaCTX-M, qnrS1, sul2, and mcr-1.1, were frequently detected, indicating a risk of horizontal transfer during transmission. Genomic epidemiological investigation of our sequenced strains and their associated cgMLST HierCC clusters revealed both persistent Salmonella lineages, such as Enteritidis HC50-87 and Agona HC20-419, and emerging China-specific lineages, including Enteritidis HC20-10145 and Typhimurium HC50-2304. The estimated divergence times of these lineages mostly dated to the late mid-20th century, coinciding with the intensification of poultry farming in China. These findings highlight the power of genomic epidemiology in uncovering antimicrobial resistance patterns and transmission dynamics, underscoring the need for strengthened Salmonella surveillance.