Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing

Abstract

SUMMARYThe epidemiological investigation of a foodborne outbreak, including identification of related cases, source attribution, and development of intervention strategies, relies heavily on the ability to subtype the etiological agent at a high enough resolution to differentiate related from nonrelated cases. Historically, several different molecular subtyping methods have been used for this purpose; however, emerging techniques, such as single nucleotide polymorphism (SNP)-based techniques, that use whole-genome sequencing (WGS) offer a resolution that was previously not possible. With WGS, unlike traditional subtyping methods that lack complete information, data can be used to elucidate phylogenetic relationships and disease-causing lineages can be tracked and monitored over time. The subtyping resolution and evolutionary context provided by WGS data allow investigators to connect related illnesses that would be missed by traditional techniques. The added advantage of data generated by WGS is that these data can also be used for secondary analyses, such as virulence gene detection, antibiotic resistance gene profiling, synteny comparisons, mobile genetic element identification, and geographic attribution. In addition, several software packages are now available to generatein silicoresults for traditional molecular subtyping methods from the whole-genome sequence, allowing for efficient comparison with historical databases. Metagenomic approaches using next-generation sequencing have also been successful in the detection of nonculturable foodborne pathogens. This review addresses state-of-the-art techniques in microbial WGS and analysis and then discusses how this technology can be used to help support food safety investigations. Retrospective outbreak investigations using WGS are presented to provide organism-specific examples of the benefits, and challenges, associated with WGS in comparison to traditional molecular subtyping techniques.

Isolation and characterization of Salmonella in pork samples collected from retail and wholesale markets in each season from 2016 to 2018 in Wuhan, China

“…Multi‐locus sequence typing (MLST), which is based on the sequence variations of multiple Salmonella housekeeping genes, has been well‐established and has been considered as a replacement for Salmonella serotyping (Achtman et al ; Ranieri et al ; Cai et al ). Currently, whole‐genome sequencing is becoming more and more popular for Salmonella typing (Gimour et al ; Ronholm et al ; Ibrahim and Morin, ).…”

Use of multiple‐locus variable‐number of tandem repeats analysis (MLVA) to investigate genetic diversity of Salmonella enterica subsp. enterica serovar Typhimurium isolates from human, food, and veterinary sources

“…The currently existing phenotyping methods for Salmonella , including serotyping, phage typing, and antimicrobial resistance (AMR) determination, have several disadvantages, such as being time consuming and laborious, and having insufficient discriminatory power for certain purposes (Lindstedt, ; Wattiau, Boland, & Bertrand, ). Powerful genotyping methods, for example, multiple‐locus variable‐number of tandem repeats (VNTR) analysis (MLVA), pulsed‐field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and more recently whole genome sequencing (WGS), have been introduced into laboratory practice to solve some of the problems with the existing classical protocols (Ronholm, Nasheri, Petronella, & Pagotto, ; Wattiau et al., ). However, successful implementation of these techniques requires specialized equipment and training of personnel, thus making it a challenge in laboratories with limited resources.…”

Food Security: Microbiological and Chemical Risks

“…In recent years, next generation sequencing (NGS) including whole genome sequencing (WGS) and metagenomics testing have emerged with a great potential to revolutionize how microbiological food safety is managed. Particularly WGS has emerged as a new tool that has great potential within a One Health context [75][76][77][78][79]. WGS provides the highest possible microbial subtyping resolution available to public health authorities for the surveillance of and response to foodborne disease and AMR threats.…”

“…However, when both technologies are used in combination to close genomes, also known as hybrid sequencing, the short reads generate good quality contigs while the long reads can close the gaps that are between the contigs during scaffold assembly. For more information on the main sequencing platforms and their performance, refer to the brief summary (see Table 2; [87]) and the details [77,94,95] that are described in above cited excellent recent reviews.…”