Genomic Surveillance and Multidrug Resistance Profiles of SalmonellaClinical Isolates in Fujian, China

Salmonella is a major foodborne pathogen imposes a substantial global disease burden. The rising prevalence of cephalosporin and quinolone resistance in Salmonella highlights the need for continued surveillance of resistance profiles and mechanisms. Here, we investigated the prevalence and antimicrobial resistance of Salmonella isolated from clinical patients in Fuzhou, China, between 2017 and 2020. Among 139 culture-positive cases, the male-to-female ratio was 1.53:1 and detections peaked from May to October. Twenty-nine serotypes were identified, with S. Enteritidis, S. Typhimurium, and S. Rissen being predominant. The overall resistance rate was 85.6%, with 64.0% of isolates were multidrug resistance (MDR). Isolates were highly resistance to ampicillin, tetracycline, and nalidixic acid, showed moderate resistance to ceftazidime, gentamicin, and ciprofloxacin, and were uniformly susceptibility to imipenem. All 58 nalidixic acid-resistant isolates carried QRDR mutations, most commonly gyrA : Asp87Tyr , gyrA : Asp87Asn , and parC : Thr57Ser , whereas only two S. Typhimurium isolates harbored PMQR genes aac(6')-Ib-cr and oqxAB . Whole-genome sequencing of 61 S. Typhimurium isolates revealed ST34 as the dominant sequence type, with bla CTX-M ESBL genes and multiple mobile genetic elements facilitating resistance gene transfer. Phylogenomic analysis of 122 S. Typhimurium and monophasic variant isolates from Fujian Province revealed a bipartite population structure comprising two major lineages, ST19 and ST34, with further sublineage differentiation driven by key resistance genes including qnrS1 , bla CTX-M-55 , and bla OXA-1. Despite an overall sporadic epidemiological pattern, the detection of multiple highly related isolate pairs (≤5 cgSNP differences)–including household-linked transmission and farm-level persistent contamination–strongly suggests that undiagnosed small-scale foodborne transmission events are substantially under-recognized. This study confirms high prevalence of MDR among clinical Salmonella in Fujian, with distinct serotype-specific patterns, and underscores the need for sustained local genomic surveillance. Clinical trial number: not applicable.