{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T13:24:14Z","timestamp":1788269054499,"version":"build-2803163510"},"reference-count":44,"publisher":"American Society for Microbiology","issue":"9","license":[{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2026,9,1]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      <jats:italic toggle=\"yes\">Escherichia coli<\/jats:italic>\n                      is a highly diverse bacterial species that includes avian pathogenic\n                      <jats:italic toggle=\"yes\">E. coli<\/jats:italic>\n                      (APEC), one of the most prevalent causative agents of disease in poultry worldwide. Rapid and accurate discrimination of\n                      <jats:italic toggle=\"yes\">E. coli<\/jats:italic>\n                      strains 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\n                      <jats:italic toggle=\"yes\">E. coli<\/jats:italic>\n                      isolates, originating from four poultry rearing farms in the Netherlands. From each farm, we sampled 10 one-day-old meat type rearing chicks, and from every chick, we isolated 5\n                      <jats:italic toggle=\"yes\">E. coli<\/jats:italic>\n                      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\u20130.92). While Nanopore and Illumina sequencing provided the highest genetic resolution, FTIR offered a faster (max 6 vs 12\u201328 days for 200 isolates) and more cost-effective alternative for assessing clonality. Across all methods, multiple strains were detected per farm, whereas most birds carried a single dominant\n                      <jats:italic toggle=\"yes\">E. coli<\/jats:italic>\n                      strain. Our findings demonstrate that FTIR provides a reliable and scalable phenotypic method for rapid strain discrimination in\n                      <jats:italic toggle=\"yes\">E. coli<\/jats:italic>\n                      , complementing WGS in diagnostic, surveillance, and epidemiological settings where speed and throughput are critical.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      <jats:italic toggle=\"yes\">Escherichia coli<\/jats:italic>\n                      is a major pathogen in poultry and a potential zoonotic risk for humans. Rapid and accurate discrimination of avian pathogenic\n                      <jats:italic toggle=\"yes\">E. coli<\/jats:italic>\n                      (APEC) strains is critical for outbreak management, antimicrobial resistance surveillance, and the design of effective autogenous vaccines. In this study, we compared Fourier Transform Infrared (FTIR) spectroscopy with Nanopore and Illumina whole-genome sequencing for strain typing of\n                      <jats:italic toggle=\"yes\">E. coli<\/jats:italic>\n                      isolates originating from poultry. The results show that FTIR provides comparable clustering accuracy to genomic approaches at a fraction of the time and costs. This work demonstrates that FTIR can serve as a practical, high-throughput alternative for routine monitoring of\n                      <jats:italic toggle=\"yes\">E. coli<\/jats:italic>\n                      in veterinary diagnostics and food safety of poultry meat, enabling faster decision-making and more targeted interventions across the poultry production chain.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.00513-26","type":"journal-article","created":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T13:00:55Z","timestamp":1785330055000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Performance of the IR Biotyper, Nanopore, and Illumina sequencing to discriminate\n                    <i>Escherichia coli<\/i>\n                    strains originating from poultry"],"prefix":"10.1128","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-8437-0648","authenticated-orcid":false,"given":"Jeroen","family":"Leus","sequence":"first","affiliation":[{"name":"Demetris DierGezondheid","place":["Duiven, the Netherlands"]},{"id":[{"id":"https:\/\/ror.org\/056vnsb08","id-type":"ROR","asserted-by":"publisher"}],"name":"Royal GD","place":["Deventer, the Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-7658-1208","authenticated-orcid":true,"given":"Annet","family":"Heuvelink","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/056vnsb08","id-type":"ROR","asserted-by":"publisher"}],"name":"Royal GD","place":["Deventer, the Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Max","family":"Schellekens","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/056vnsb08","id-type":"ROR","asserted-by":"publisher"}],"name":"Royal 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