Fitness factors and siderophores influence the survival of E. coli in reused broiler litter

Escherichia coli (E. coli) is a common bacterium in poultry that can exhibit virulence toward poultry and humans, and harbor antimicrobial resistance (AMR) and virulence factor (VF) genes. This study characterized 217 E. coli isolates recovered from reused broiler litter across three successive flocks from four broiler houses to identify associations between fitness factors (AMR and VF genes) and management (flock cohort, house, section, area, and grow-out period) or environmental (house temperature, litter pH, and moisture content) factors. Different E. coli strains were identified across flocks, with phylogenetic groups A and B1 being the most prevalent. A few sequence types such as ST10, ST212, and ST117 were frequently observed across flocks. Isolates from the first flock harbored more fitness factors, including siderophore biosynthesis operons such as yersiniabactin (ybt, 15/64), aerobactin (iuc, 32/64), and salmochelin (iro, 23/64), ColV plasmids (28/64), class 1 integrase gene (intI1) (12/64) and metal resistance genes than flock 2 and 3 (p < 0.05), suggesting that these genetic elements may be required for adaptation to a naïve environment. Transcriptional and proteome analyses found that the majority of ST117 strains repressed siderophore gene expression and proteins needed for growth and acid/oxidative stress response under acidified CuSO₄ exposure, except for one strain (TE207) that showed significantly enhanced fitness. This study highlights the heterogeneity of fitness factors that E. colimay employ to persist in broiler chicken houses and underscores the role of litter management practices in controlling pathogens in poultry production.