Prevalence and whole genome sequencing analysis of Salmonella isolated from a homebred chicken farm in Jiangsu province

<i>Salmonella</i> remains a significant zoonotic pathogen, and its antimicrobial resistance in agricultural settings poses a serious public health risk. In this study, we investigated the prevalence, serotype distribution, sequence types, and antimicrobial resistance profiles of Salmonella isolates from a homebred chicken farm in Jiangsu Province, China. Among 229 cloacal swab samples collected from two residential buildings, 60 <i>Salmonella</i> strains were isolated (isolation rate: 26.20%), with no isolates detected in environmental samples (<i>n</i> = 60). Differences in prevalence were observed among chicken breeds within the same building. All isolates belonged to two serotypes: <i>S</i>. Enteritidis (SE, 56.67%) and <i>S</i>. Kentucky (SK, 43.33%). Multilocus sequence typing (MLST) classified the strains into two sequence types: ST11 (<i>n</i> = 34) and ST198 (<i>n</i> = 26), with clear spatial clustering suggesting clonal dissemination within specific breeds. Antimicrobial susceptibility testing revealed high resistance rates to erythromycin (E), amoxicillin (AML), and ampicillin (AMP), exceeding 90%. All isolates were resistant to at least two antimicrobial agents, and one strain exhibited resistance to eight agents. Resistance gene screening showed that all isolates carried mutations in <i>gyrA</i> (S83F, D87G, D87Y) and <i>parC</i> (S80I). Additionally, <i>aph3'-Ib</i> and <i>aph(6)-Id</i> were detected in 68.33% of isolates. All strains harbored two or more antimicrobial resistance genes (ARGs). Whole-genome SNP analysis confirmed strong phylogenetic clustering by serotype and building, with ≤ 5 SNP differences within clades, indicating clonal persistence dissemination events. Homologous strain analysis (SNP distance ≤ 10) further revealed within-farm transmission of closely related strains. These findings highlight the clonal spread of multidrug-resistant <i>Salmonella</i> in chicken farms and underscore the need for improved surveillance and infection control measures in agricultural environments.