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

Journal Article · · Microbial Genomics
 [1];  [2];  [2];  [2];  [2];  [2];  [2];  [2]
  1. U.S. Food and Drug Administration (FDA), College Park, MD (United States). Center for Food Safety and Applied Nutrition; DOE/OSTI
  2. U.S. Food and Drug Administration (FDA), College Park, MD (United States). Center for Food Safety and Applied Nutrition
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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.

Research Organization:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Sponsoring Organization:
USDOE Office of Science (SC); USFDA
Grant/Contract Number:
AC05-76RL01830
OSTI ID:
1625605
Journal Information:
Microbial Genomics, Journal Name: Microbial Genomics Journal Issue: 7 Vol. 4; ISSN 2057-5858
Publisher:
Society for General MicrobiologyCopyright Statement
Country of Publication:
United States
Language:
English

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59 BASIC BIOLOGICAL SCIENCES
GenomeTrakr
foodborne pathogen
genetics & heredity
microbiology
molecular epidemiology
outbreak detection
proficiency test
whole-genome sequencing