ArticleMicrobial genomics2018
GenomeTrakr proficiency testing for foodborne pathogen surveillance: an exercise from 2015.
Article in Microbial genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
33 citing papers in PubMed.
- Meat-Borne Bacterial Pathogen Detection: Conventional, Molecular and Emerging AI-Based Strategies.Diagnostics (Basel, Switzerland) · 2026Review
- Review
- Establishing aMicrobiology spectrum · 2026Article
- Evaluation of capabilities of Chinese provincial veterinary laboratories in detection of African swine fever virus: a proficiency testing program.Frontiers in veterinary science · 2026Article
- Reference-guided assembly of metagenomes with MetaCompass.Cell reports methods · 2025Article
- Big data analytics in food industry: a state-of-the-art literature review.NPJ science of food · 2025Review
- Foodborne bacterial pathogens: genome-based approaches for enduring and emerging threats in a complex and changing world.Nature reviews. Microbiology · 2024Review
- Results of the 2020 Genomic Proficiency Test for the network of European Union Reference Laboratory for Antimicrobial Resistance assessing whole-genome-sequencing capacities.Microbial genomics · 2023Article
- Impact of wet-lab protocols on quality of whole-genome short-read sequences from foodborne microbial pathogens.Frontiers in microbiology · 2023Article
- Scaling neighbor joining to one million taxa with dynamic and heuristic neighbor joining.Bioinformatics (Oxford, England) · 2023Article
- PRAWNS: compact pan-genomic features for whole-genome population genomics.Bioinformatics (Oxford, England) · 2023Article
- Making microbial genomics work for clinical and public health microbiology.Microbial genomics · 2022Article
- A case report ofAccess microbiology · 2022Article
- Harmonization of whole-genome sequencing for outbreak surveillance ofMicrobial genomics · 2021Article
- Article
- Article
- Toward an Integrated Genome-Based Surveillance ofFrontiers in microbiology · 2021Article
- Genotypic and Phenotypic Characterization of Antimicrobial Resistance Profiles in Non-typhoidalFrontiers in microbiology · 2021Article
- Data structures based onGenome research · 2021Review
- Clinical Pathogen Genomics.Clinics in laboratory medicine · 2020Review
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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