Abstract
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 offers benefits for outbreak investigation, if a sufficient 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.
Highlights
Safety of the food chain is assured, amongst others, by regular sampling of a broad diversity of food matrices
A first outbreak was situated in North-East Limburg, Belgium, in 2012, for which the applied conventional methods combined with the epidemiological data succeeded to detect the outbreak, define its cluster, and identify the causal source, resulting in outbreak management
Our study demonstrated that whole genome sequencing (WGS)-based core genome MLST (cgMLST) typing delivered a higher discriminatory power compared to conventional methods, enabling more accurate phylogenetic analysis, as reported before [4,51,52,53,54,55]
Summary
Safety of the food chain is assured, amongst others, by regular sampling of a broad diversity of food matrices. When the detection of pathogens with similar characteristics in the human population is exceeding expected numbers [1] within a limited time period or geographical area, an outbreak is suspected. In this case, the goal lies in its rapid confinement by tracing and eliminating the causal food source. The goal lies in its rapid confinement by tracing and eliminating the causal food source This is based on epidemiological interrogation of cases, sampling of suspect food matrices, and matching strains isolated from patients with those collected from suspect food. By virtue of its single nucleotide resolution, the ultimate level of discriminatory power is acquired to investigate phylogenetic relationships between isolates, as part of foodborne outbreak investigations
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
