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

Abstract

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 harborthat 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 252isolates 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 thatEnteritidis was the dominant serotype, accounting for 92.85% of all isolates. AllEnteritidis isolates belonged to ST11. The drug-resistant gene among the 252with the highest carrying rate was the fluoroquinolone resistance gene(93.68%), followed by theantibiotic resistance gene(86.56%), the aminoglycoside resistance genes(81.82%) and(81.82%), the sulfonamide resistance gene(80.63%) and the tetracycline resistance gene(40.32%). The plasmids with the highest carrying rates are(90.91%) and(90.91%). Among single-point mutations,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 genedecreased significantly from 72 to 26%. SNP distance calculations showed that among the 234Enteritidis strains, 163 (69.7%) were homologous to at least one other isolate, with a total of 1,047 clonal transmission events.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 ofin breeder farms, providing a genomic basis for formulating targeted biosecurity prevention and control strategies as well as antibiotic reduction programs.