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

## TL;DR

This study analyzed Salmonella strains from a chicken farm in China, finding high prevalence and multidrug resistance, with clonal spread within the farm.

## Contribution

The study provides insights into the clonal dissemination and antimicrobial resistance of Salmonella in a homebred chicken farm setting.

## Key findings

- Salmonella prevalence was 26.20% in chicken swabs, with no environmental contamination detected.
- High resistance rates to erythromycin, amoxicillin, and ampicillin were observed, with some strains resistant to eight agents.
- Genomic analysis revealed clonal dissemination and strong phylogenetic clustering by serotype and building.

## Abstract

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). Differences 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, aph3'-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 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 Salmonella in chicken farms and underscore the need for improved surveillance and infection control measures in agricultural environments.