Prevalence and genomic characterization of Salmonella enterica serovar Typhimurium across a duck breeder-hatchery-grow-out production system in China.

Non-typhoidal Salmonella (NTS) is a leading bacterial pathogen responsible for foodborne outbreaks worldwide, with poultry products being a major source of human salmonellosis. While previous studies have predominantly focused on Salmonella transmission in the chicken production chain, ducks have received comparatively little attention as a potential reservoir host. In this study, we investigated Salmonella contamination across a commercial duck breeder-hatchery-grow-out (BHG) production system in Inner Mongolia, Hebei, and Shandong, China, comprising five breeder duck farms, one hatchery, and one commercial grow-out duck farm. From January 2022 to July 2025, a total of 7765 samples were collected across the duck BHG production system, from which 796 Salmonella isolates were recovered, yielding an overall prevalence of 10.25%. Serotyping analysis identified 16 serovars, dominated by S. Typhimurium (52.51%, 418/796), followed by S. Anatum (18.72%, 149/796) and S. Enteritidis (16.21%, 129/796). To further explore genomic relationships and potential transmission routes, 212 of the 418 S. Typhimurium isolates, representing diverse sampling time points, production stages, sample sources, locations, and antimicrobial-resistance profiles, were selected for whole-genome sequencing (WGS). Core-genome single nucleotide polymorphism (cgSNP) analysis revealed the presence of both vertical and horizontal transmission of S. Typhimurium from breeder ducks to commercial ducks. Antimicrobial susceptibility testing showed that 83 S. Typhimurium isolates (26.35%) exhibited antimicrobial resistance (AMR) to more than three classes of antibiotics. These isolates exhibited high resistance rates to ampicillin, amoxicillin, tetracycline, nalidixic acid, and streptomycin. A comparative genomic analysis of multidrug resistance genes identified an IS26-mediated chromosomal replacement event, leading to the replacement of a chromosomal region with a multidrug resistance region (MRR). This genomic rearrangement may contribute to the persistence and dissemination of multidrug-resistant clones within the production system. Overall, these findings demonstrate that Salmonella circulating in breeder ducks and farm environments can disseminate through eggs and the hatchery to commercial meat ducks, suggesting that the hatchery may serve as key points for amplification and cross-contamination. These results underscore the need for strengthened hatchery biosecurity, including routine surveillance, strict workflow separation, and enhanced cleaning and disinfection, to reduce the dissemination of antimicrobial-resistant Salmonella along the duck production chain.