Abstract
Pathogen monitoring is becoming more precise as sequencing technologies become more affordable and accessible worldwide. This transition is especially apparent in the field of food safety, which has demonstrated how whole-genome sequencing (WGS) can be used on a global scale to protect public health. GenomeTrakr coordinates the WGS performed by public-health agencies and other partners by providing a public database with real-time cluster analysis for foodborne pathogen surveillance. Because WGS is being used to support enforcement decisions, it is essential to have confidence in the quality of the data being used and the downstream data analyses that guide these decisions. Routine proficiency tests, such as the one described here, have an important role in ensuring the validity of both data and procedures. In 2015, the GenomeTrakr proficiency test distributed eight isolates of common foodborne pathogens to participating laboratories, who were required to follow a specific protocol for performing WGS. Resulting sequence data were evaluated for several metrics, including proper labelling, sequence quality and new single nucleotide polymorphisms (SNPs). Illumina MiSeq sequence data collected for the same set of strains across 21 different laboratories exhibited high reproducibility, while revealing a narrow range of technical and biological variance. The numbers of SNPs reported for sequencing runs of the same isolates across multiple laboratories support the robustness of our cluster analysis pipeline in that each individual isolate cultured and resequenced multiple times in multiple places are all easily identifiable as originating from the same source.
Highlights
Foodborne pathogen surveillance in the USA is transitioning from pulsed-field gel electrophoresis (PFGE) to wholegenome sequencing (WGS) for subtyping and disease surveillance
Microbial food and environmental isolates collected by the GenomeTrakr network laboratories (FDA field labs, state and local publichealth labs, academic labs and others) are submitted to the public GenomeTrakr database hosted at the National Center for Biotechnology Information (NCBI)
We provide the analytical results of the entire exercise in Table S1; from these results, we developed further correlation studies and graphics
Summary
Foodborne pathogen surveillance in the USA is transitioning from pulsed-field gel electrophoresis (PFGE) to wholegenome sequencing (WGS) for subtyping and disease surveillance. Administration (FDA), tasked with ensuring a safe food supply, began piloting this technology in 2012 with the formation of the GenomeTrakr network [1]. Microbial food and environmental isolates collected by the GenomeTrakr network laboratories (FDA field labs, state and local publichealth labs, academic labs and others) are submitted to the public GenomeTrakr database hosted at the National Center for Biotechnology Information (NCBI). WGS data collection for foodborne pathogens is part of the standard operating protocol (SOP) across the three federal agencies working in food safety [the FDA, the Centers for Disease Control and Prevention (CDC) and the United States Department of Agriculture – Food Safety and Inspection Service (USDA-FSIS)]. As of April 13th 2018, approximately 210 000 genomes have been submitted from all over the world to this public pathogen surveillance network, including from the USA’s GenomeTrakr and PulseNet [6, 7] networks
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