Genomic diversity, antimicrobial resistance, and virulence-associated characteristics of Escherichia coli recovered from poultry hatchery-box material

Abstract

Hatcheries are early points of exposure of newly hatched chicks to Escherichia coli from eggshell debris, dust, meconium, and the hatchery environment. This study used descriptive genomic surveillance to characterize population structure, antimicrobial resistance, virulence-associated genes, plasmid replicons, and genetic relatedness in a purposively selected collection of E. coli recovered from hatchery-box material in a Czech commercial poultry hatchery. From 83 samples collected between 2019 and 2023, 409 isolates were recovered. Following within-sample reduction based on antimicrobial susceptibility profiles and PCR screening for selected APEC-associated virulence genes, 91 isolates enriched for cefotaxime-medium recovery or APEC-associated gene profiles were selected for Illumina whole-genome sequencing. The sequenced collection comprised 35 sequence types across nine phylogenetic groups or clades; phylogroup B1 (59/91) and ST162 (28/91) predominated. ColV-associated markers were detected in 88 isolates, acquired resistance genes in 61, and a multidrug-resistant phenotype in 31. Seventeen isolates were resistant to ceftazidime; eight carried ESBL or plasmid-mediated AmpC determinants, while eight additional isolates had the chromosomal ampC promoter substitution C-42T as the only identified determinant associated with this phenotype. Closely related isolates, including ST131, ST162, and ST675, were recovered from different samples or parent-farm groups within restricted sampling periods. These findings document genomically diverse, resistance- and virulence-associated E. coli in hatchery-box material and identify genetically related isolates that warrant investigation through structured longitudinal sampling. Because sampling was unequal and isolates were purposively selected, the findings do not provide prevalence estimates or demonstrate source, transmission, persistence, or pathogenicity.