Phylogenomic Pipeline Validation for Foodborne Pathogen Disease Surveillance

Abstract

Foodborne pathogen surveillance in the United States is transitioning from strain identification using restriction digest technology (pulsed-field gel electrophoresis [PFGE]) to shotgun sequencing of the entire genome (whole-genome sequencing [WGS]). WGS requires a new suite of analysis tools, some of which have long histories in academia but are new to the field of public health and regulatory decision making. Although the general workflow is fairly standard for collecting and analyzing WGS data for disease surveillance, there are a number of differences in how the data are collected and analyzed across public health agencies, both nationally and internationally. This impedes collaborative public health efforts, so national and international efforts are underway to enable direct comparison of these different analysis methods. Ultimately, the harmonization efforts will allow the (mutually trusted and understood) production and analysis of WGS data by labs and agencies worldwide, thus improving outbreak response capabilities globally. This review provides a historical perspective on the use of WGS for pathogen tracking and summarizes the efforts underway to ensure the major steps in phylogenomic pipelines used for pathogen disease surveillance can be readily validated. The tools for doing this will ensure that the results produced are sound, reproducible, and comparable across different analytic approaches.

Genomic Analyses of Human Sapoviruses Detected over a 40-Year Period Reveal Disparate Patterns of Evolution among Genotypes and Genome Regions

“…The use of whole, versus short, genome sequences can enhance those studies, particularly in viruses that can rapidly acquire mutations [25,26]. The application of metagenomic analyses using whole genome sequencing is increasing in use in clinical settings, because of the power and potential for obtaining longer nucleotide sequence reads of a pathogen's genome [27]. However, in most cases, the performance of these metagenomic analyses are greatly affected by the concentration of the viral contaminant and the complexity of the food and/or water matrix [28].…”

Phylogenomic Analysis of Salmonella enterica subsp. enterica Serovar Bovismorbificans from Clinical and Food Samples Using Whole Genome Wide Core Genes and kmer Binning Methods to Identify Two Distinct Polyphyletic Genome Pathotypes

“…Genome-wide and core genome analysis of Salmonella serovars using WGS datasets has been proven to be capable of profiling underlying evolutionary processes contributing to the genome backbone differences among different lineages constituting a conventionally typed serovar [19][20][21][22]46,47]. The application of WGS technology for sequence-based serotyping [25,48], characterization of outbreak isolates [49,50], source-tracking in the epidemiological investigation of foodborne outbreaks, and phylogenetic relationships [51][52][53][54][55] have been well documented. The robust bioinformatic workflow from this study utilizes an ad hoc set of complete genome assemblies for high-resolution phylogenetic analysis and adds to the existing S. enterica core-genes (cgMLST) and whole genome MLST (wgMLST) typing schema hosted on public resources such as EnteroBase and SISTR [46,48].…”

Precision Food Safety: a Paradigm Shift in Detection and Control of Foodborne Pathogens

“…The implementation of whole-genome sequencing (WGS) in foodborne pathogen surveillance in the United States resulted in a rapid increase in public availability of foodborne pathogen whole-genome sequences (5). By the end of the first quarter of 2019, GenomeTrakr and PulseNet networks have sequenced over 317,000 foodborne pathogen genomes, according to the fact sheet published on the GenomeTrakr website (https://www.fda.gov/Food/FoodScienceResearch/WholeGenomeSequencingProgramWGS/ucm403550.htm).…”

“…The critical component of successful implementation of such enhanced surveillance programs is national and international data sharing and methods standardization. The data analyses and storage are supported by the National Center for Biotechnology Information, and the latter is currently coordinated by the Genomics for Food Safety (Gen-FS) within the United States and by the Global Microbial Identifier at international scale (5). Global standardization still represents a significant challenge and is a work in progress, while the positive impacts of the increased global availability of WGS are already evident.…”