Oxford Nanopore Technologies as an ISO accredited single platform solution for Salmonella surveillance
Citations
Abstract
The rapid and accurate identification of Salmonella enterica serotypes is critical for public health monitoring and timely case management. Particularly in the poultry sector, both national and EU legislation imply laboratories qualified for Salmonella serotyping to report results within five days of sample receipt. Traditional methods such as agglutination and biochemical tests, are labor-intensive, require expensive antisera, and rely on skilled personnel. While target-based molecular genoserotyping (qPCR, μ-array) 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 (€80-100 per sample) and lengthy turnaround time associated with Illumina sequencing — especially when outsourced — prevent its routine use for all required serotyping in Belgium. Recent advancements in Oxford Nanopore Technologies (ONT), notably the R10.4.1 flow cells paired with V14 chemistry, enabled the validation under ISO 16140-6 of ONT in combination with an in-house developed bioinformatic pipeline as a cost-effective solution for Salmonella surveillance, including (sub)species identification, serotyping, and outbreak detection.
