Genomic Epidemiology of Salmonella and Campylobacter in Poultry Production: Quantifying the Contribution of Primary Breeders

The US broiler production system processes over 9.3 billion chickens annually through a highly integrated pyramid structure where two primary breeding companies supply genetic stock to approximately 40 major integrators operating nationwide. To provide a quantitative, system-wide estimate of contamination origins, I analyzed whole genome sequences from Salmonella and Campylobacter isolates collected from over 800 processing facilities as part of the USDA’s Food Safety Inspection Service (FSIS) verification sampling (2019-2024). Single-linkage clustering identified isolates sharing common origins (≤2, 4, or 8 SNPs genome-wide), which were categorized by facility, company, and geographical distributions to infer contamination sources. Among the isolates analyzed, geographically dispersed multi-company clusters implying a primary breeder origin accounted for 78% of Campylobacter , 77% of non-Enteritidis Salmonella , and 96% of Salmonella Enteritidis isolates. Geographic spread analysis revealed that Enteritidis isolates matched a random distribution model consistent with contamination originating from the highest levels of the breeding pyramid. Campylobacter showed regional clustering implying sources at lower levels of the breeding pyramid. Cluster persistence exceeded multiple production cycles (median >4 years for Campylobacter , >4.5 years for 75% of Enteritidis isolates), indicating stable contamination reservoirs upstream of processing. These results demonstrate that the primary breeders are a major source of broiler contamination and suggest that upstream interventions targeting breeding stock, in particular for Enteritidis, may represent an efficient strategy for further reducing clinical cases of foodborne illness.