GenomeTrakr proficiency testing for foodborne pathogen surveillance: an exercise from 2015

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.

Genomic Comparison Reveals Natural Occurrence of Clinically Relevant Multidrug-Resistant Extended-Spectrum-β-Lactamase-Producing Escherichia coli Strains

“…Antibiotic-resistant bacteria are widespread through multiple routes, including human travel, precipitation, and migratory birds (34). Phylogenetic analyses have been widely used to determine the relatedness of isolates and trace the sources of potential reservoirs of pathogens (24,25,35). In this study, having less than 10 SNPs in the core genome, we could not identify clonal variants among the strains isolated from two farms (Fig.…”

“…Recently, efforts have been made for outbreak investigation of infectious diseases by targeting a variety of pathogens through the use of wholegenome-sequence data (24). First, genomes of MDR E. coli isolates were submitted to the NCBI GenomeTrakr pathogen detection system to generate phylogenetic trees with 55,062 E. coli/Shigella genomes (25). Although none of the MDR E. coli strains were identified as clonal variants of known outbreak-associated pathogens, isolates were closely clustered with clinically relevant E. coli strains ( Fig.…”

“…The number of SNPs in each phylogenetic clade was calculated by using NCBI Pathogen Detection (https://www.ncbi.nlm.nih.gov/pathogens/) (54). The phylogenetic trees of each representative strain were generated using Genome Workbench (https:// www.ncbi.nlm.nih.gov/tools/gbench/) after uploading the raw reads to GenomeTrakr (25).…”

Precision epidemiology for infectious disease control

“…Genome sequencing of foodborne bacterial pathogens now forms part of many surveillance systems, and outbreak investigations in the United States are routinely performed by the Food and Drug Administration's GenomeTrackr Network. In recent years, this network has grown into an international collaboration among 63 government, private, and academic research laboratories 40,41 . Through near-real-time genome sequencing and public data deposition of clinical, environmental, and foodrelated bacterial isolates, this network is streamlining the process of recognizing, investigating, and reducing the impact of foodborne disease outbreaks 42,43 .…”

Phylogenomic Pipeline Validation for Foodborne Pathogen Disease Surveillance

“…Either way, these data show a minimum of 99.99992% platform accuracy and thus are in agreement with the numbers reported by Kozyreva et al, which provides confidence in the use of this technology in decision making for public health applications such as outbreak detection, outbreak management, food facility inspection positives analysis, and monitoring for antibiotic resistance elements. The raw data, complete reference genomes, and a table of metrics summarized in the PT were made publicly available for the PT study (52), so this exercise can be fully replicated in a new lab looking to compare their sequencing quality to the data collected in this exercise.…”