Investigating the dynamics of S. Enteritidis serotype spread in breeder poultry company using a whole genome sequencing approach

Salmonella is a globally prevalent foodborne zoonotic pathogen, with poultry and its products serving as the primary epidemiological reservoirs. As a core upstream component of the poultry industry chain, breeder farms can harbor Salmonella that contaminates breeder eggs via vertical transmission or spreads to hatcheries and downstream commercial flocks through horizontal transmission, resulting in cross-generational and cross-regional dissemination of the pathogen. From 2013 to 2022, this study conducted a molecular epidemiological investigation on 252 Salmonella isolates from grandparent (GG) and parent (PG) chicken flocks of an integrated breeder poultry enterprise in Shandong Province using whole-genome sequencing (WGS) technology. The results showed that S. Enteritidis was the dominant serotype, accounting for 92.85% of all isolates. All S. Enteritidis isolates belonged to ST11. The drug-resistant gene among the 252 Salmonella with the highest carrying rate was the fluoroquinolone resistance gene gyrA (93.68%), followed by the β-lactam antibiotic resistance gene blaTEM-1B (86.56%), the aminoglycoside resistance genes aph(3″)-Ib (81.82%) and aph(6)-Id (81.82%), the sulfonamide resistance gene sul2 (80.63%) and the tetracycline resistance gene tet(A) (40.32%). The plasmids with the highest carrying rates are IncFIB (90.91%) and IncFII (90.91%). Among single-point mutations, gyrA D87Y had the highest amino acid substitution rate (80.63%). The drug resistance gene carrier rates were similar between GG and PG isolates. After the comprehensive ban on antibiotics in animal feed implemented in 2020, the carriage rate of the tetracycline resistance gene tet(A) decreased significantly from 72 to 26%. SNP distance calculations showed that among the 234 S. Enteritidis strains, 163 (69.7%) were homologous to at least one other isolate, with a total of 1,047 clonal transmission events. S. Enteritidis underwent extensive clonal transmission across different regions, different generations of culture, and different time periods. This study clarified the transmission patterns and antimicrobial resistance evolution characteristics of Salmonella in breeder farms, providing a genomic basis for formulating targeted biosecurity prevention and control strategies as well as antibiotic reduction programs.