Oxford Nanopore Technologies as an ISO accredited single platform solution for Salmonella surveillance
Citations
Abstract
Rapid and accurate Salmonella enterica serotyping is critical for surveillance and timely case management. In the poultry sector, EU and national legislation require serotyping results within five days. Traditional typing methods such as agglutination and biochemical tests, are labor-intensive and depend upon expensive antisera. While targetbased molecular genoserotyping offers faster results, it introduces additional costs and operational complexity. These procedures remain the first-line approach for Salmonella characterization despite the growing reliance on short-read whole-genome sequencing (WGS) for source tracing and outbreak investigations. The high cost and lengthy turnaround time associated with Illumina sequencing — especially when outsourced — prevent its routine use for all serotyping in Belgium. Recent advancements in long-read sequencing by Oxford Nanopore Technologies (ONT), notably the R10.4 flow cells and v14 chemistry, enabled ISO 16140-6 validation of ONT and an in-house developed bioinformatics pipeline, providing a cost-effective solution for Salmonella surveillance, including (sub)species identification, serotyping, outbreak detection and vaccine differentiation.
