Genomic epidemiology of multidrug-resistant and non-multidrug-resistant clinical Salmonella enterica isolates in Guangdong, China

Abstract

Salmonella enterica ( S. enterica ) is a major foodborne pathogen that threatens human health. Multidrug resistance (MDR) has complicated the prevention and treatment of salmonellosis. The present study aimed to characterize the antimicrobial resistance patterns, population structure, and genomic features of clinical S. enterica isolates from Guangdong, China. Among 4413 isolates collected between 2022 and 2024, 1084 underwent antimicrobial susceptibility testing and 170 were further analyzed by whole-genome sequencing. MDR was defined as resistance to at least three antimicrobial classes and was identified in 71.13% of the tested isolates. Genomic analyses included serotyping, multilocus sequence typing, resistance and virulence gene analyses, and core-genome phylogenetic analysis. XGBoost and LASSO were used to prioritize genomic features associated with MDR phenotype. Serovar I 4,[5],12:i:- was the predominant serovar among MDR isolates, while ST34 and ST19 were the most common sequence types. Compared with non-MDR isolates, MDR isolates more frequently carried several resistance genes, including CTX-M-55 , qnrS1 , tet(A) , floR , sul2 , sul3 , and TEM-1. Differences in virulence gene content were also observed between the two groups. Both XGBoost and LASSO consistently prioritized floR and CTX-M-55 as candidate genomic features associated with the MDR phenotype. Overall, MDR and non-MDR clinical S. enterica isolates from Guangdong differed markedly in lineage distribution and gene carriage, providing a genomic basis for regional surveillance of MDR S. enterica .