Performance of the IR Biotyper, Nanopore, and Illumina sequencing to discriminate Avian Pathogenic Escherichia coli clones

Escherichia coli is a highly diverse bacterial species that includes avian pathogenic E. coli (APEC), one of the most prevalent causative agents of disease in poultry worldwide. Rapid and accurate discrimination of E. coli clones is essential for outbreak management, antimicrobial resistance surveillance, and vaccine development. In this study, we compared the performance of Fourier Transform Infrared (FTIR) spectroscopy using the IR Biotyper system with Nanopore and Illumina whole-genome sequencing (WGS) for typing 200 E. coli isolates, originating from four poultry rearing farms in the Netherlands. From each farm we sampled ten one day old meat type rearing chicks, from every chick we isolated 5 E, coli strains. FTIR clustering showed strong concordance with WGS-based classifications, particularly serotyping and core-genome similarity determined by PopPUNK analysis (Adjusted Rand Index 0.75–0.92). While Nanopore and Illumina sequencing provided the highest genetic resolution, FTIR offered a faster (max 6 vs. 12–28 days for 200 isolates) and more cost-effective alternative for assessing clonality. Across all methods, multiple clones were detected per farm, whereas most birds carried a single dominant APEC clone. Our findings demonstrate that FTIR provides a reliable and scalable phenotypic method for rapid clone discrimination in E. coli, complementing WGS in diagnostic, surveillance, and epidemiological settings where speed and throughput are critical.