Nouws, StephanieBogaerts, BertVerhaegen, BavoDenayer, SarahCrombe, FlorenceDe Rauw, KlaraPierard, DenisMarchal, KathleenVanneste, KevinRoosens, Nancy H.C.De Keersmaecker, Sigrid C.J.2020-10-062020-10-062020-08-01Nouws et al. 2020, 'The benefits of whole genome sequencing for foodborne outbreak investigation from the Perspective of a National Reference laboratory in a smaller country', Foods, vol. 9, no. 1030, pp. 1-21.2304-8158 (online)10.3390/foods9081030http://hdl.handle.net/2263/76353Supplementary Material: Table S1: Characteristics of all background isolates determined with conventional methods and WGS, Table S2: WGS-based serotype determination, Table S3: WGS-based virulence allele typing, Table S4: NCBI SRA accession numbers of WGS data of all isolates, Figure S1: Conventional typing results of the Limburg 2012 outbreak, Methods: Conventional ISO workflows for STEC detection, isolation and identification from food samples, as performed during the initial outbreak investigation.Gradually, conventional methods for foodborne pathogen typing are replaced by whole genome sequencing (WGS). Despite studies describing the overall benefits, National Reference Laboratories of smaller countries often show slower uptake of WGS, mainly because of significant investments required to generate and analyze data of a limited amount of samples. To facilitate this process and incite policy makers to support its implementation, a Shiga toxin-producing Escherichia coli (STEC) O157:H7 (stx1+, stx2+, eae+) outbreak (2012) and a STEC O157:H7 (stx2+, eae+) outbreak (2013) were retrospectively analyzed using WGS and compared with their conventional investigations. The corresponding results were obtained, with WGS delivering even more information, e.g., on virulence and antimicrobial resistance genotypes. Besides a universal, all-in-one workflow with less hands-on-time (five versus seven actual working days for WGS versus conventional), WGS-based cgMLST-typing demonstrated increased resolution. This enabled an accurate cluster definition, which remained unsolved for the 2013 outbreak, partly due to scarce epidemiological linking with the suspect source. Moreover, it allowed detecting two and one earlier circulating STEC O157:H7 (stx1+, stx2+, eae+) and STEC O157:H7 (stx2+, eae+) strains as closely related to the 2012 and 2013 outbreaks, respectively, which might have further directed epidemiological investigation initially. Although some bottlenecks concerning centralized data-sharing, sampling strategies, and perceived costs should be considered, we delivered a proof-of-concept that even in smaller countries, WGS o ers benefits for outbreak investigation, if a su cient budget is available to ensure its implementation in surveillance. Indeed, applying a database with background isolates is critical in interpreting isolate relationships to outbreaks, and leveraging the true benefit of WGS in outbreak investigation and/or prevention.en© 2020 by the authors. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license.Foodborne outbreak investigationFood safetySurveillanceWhole genome sequencing (WGS)Shiga toxin-producing Escherichia coli (STEC)Article