ORIGINAL RESEARCH article
Front. Vet. Sci.
Sec. Veterinary Infectious Diseases
Prevalence and whole genome sequencing analysis of Salmonella isolated from a homebred chicken farm in Jiangsu Province
Provisionally accepted
- 1Shandong Agricultural University, Tai'an, China
- 2Shandong Province Animal Disease Prevention and Control Center, Jinan, China
- 3Shandong Center for Quality Control of Feed and Veterinary Drug, Jinan, China
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Salmonella 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 Salmonella strains were isolated (isolation rate: 26.20%), with no isolates detected in environmental samples (n = 60). Significant Ddifferences in prevalence were observed among chicken breeds within the same building. All isolates belonged to two serotypes: S. Enteritidis (SE, 56.67%) and S. Kentucky (SK, 43.33%). Multilocus sequence typing (MLST) classified the strains into two sequence types: ST11 (n = 34) and ST198 (n = 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 gyrA (S83F, D87G, D87Y) and parC (S80I). Additionally, aph(3'')-Ib and aph(6)-Id 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 disseminationrecent transmission events. Homologous strain analysis (SNP distance ≤10) further revealed within-farmcross-host transmission of closely related strains. These findings highlight the clonal spread of multidrug-resistant Salmonella in chicken farms and underscore the need for improved surveillance and infection control measures in agricultural environments.
Keywords: antibiotic resistance genes, homebred chicken, Salmonella, sequence type, whole genome sequencing
Received: 17 Dec 2025; Accepted: 03 Feb 2026.
Copyright: © 2026 Liu, Wu, Huang, Cui, Song, Tang and Sun. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Wenli Tang
Shuhong Sun
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