Fluoroquinolone resistance in Escherichia coli in the broiler production chain: the role of parent stock and hatchery

Fluoroquinolone (FQ) resistance has a major impact on human and animal health by complicating treatment of infections. In Belgium, the use of FQ in the agricultural chain is restricted, but high levels of resistance have nevertheless been observed. The spread of resistant strains and their genomic resistance determinants throughout the poultry production chain remain poorly understood. This study investigated the role of the parental flocks and hatchery in the spread of FQ resistance towards broiler farms. Samples were collected from four parental farms and corresponding hatcheries in Belgium. E. coli and FQ-resistant E.coli isolates were recovered from the samples using non-selective and FQ-selective media. Isolates were identified using MALDI-TOF mass spectrometry. A selection of 79 isolates were analyzed using whole genome sequencing (WGS) to determine antimicrobial resistance and to identify phylogenetically related isolates. FQ-resistant E. coli were detected in the faeces of the parent stock on all four farms, with 70.3% of all E. coli positive samples showing FQ resistance. No FQ-resistant E. coli were detected in the egg samples. All environmental samples from the sorting belt of the hatcheries carried FQ-resistant E. coli. Of the sampled day-old chicks at the hatchery, 3 out of 4 batches were positive. The WGS analysis could not identify any genomic links between isolates from parent stock and the day-old chicks. Additionally, WGS revealed high genomic diversity among the collected strains, with 13 different sequence types and a wide range of genomic AMR determinants. In conclusion, our findings highlight the complexity of FQ resistance transmission in broiler production. The presence of FQ-resistant E. coli in the hatchery and their spread among day-old chicks stress the need for critical interventions at multiple stages, which should include enhanced, batch-level cleaning and disinfection protocols in hatcheries, and minimizing antimicrobial usage across the whole broiler production chain.