ReviewJournal of clinical microbiology2019
Phylogenomic Pipeline Validation for Foodborne Pathogen Disease Surveillance.
Review in Journal of clinical microbiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
13 citing papers in PubMed, 29 citations in OpenAlex.
- Genomic Characterization of an O-Antigen-Deficient, Hydrogen Sulfide-NegativeMicroorganisms · 2026Article
- Big data analytics in food industry: a state-of-the-art literature review.NPJ science of food · 2025Review
- Traceability analysis of a foodborne disease outbreak caused byFrontiers in public health · 2025Article
- Advances in whole genome sequencing for foodborne pathogens: implications for clinical infectious disease surveillance and public health.Frontiers in cellular and infection microbiology · 2025Review
- Single Laboratory Evaluation of the Q20+ Nanopore Sequencing Kit for Bacterial Outbreak Investigations.International journal of molecular sciences · 2024Article
- Public health implementation of pathogen genomics: the role for accreditation and application of ISO standards.Microbial genomics · 2023Article
- Genetic diversity of Salmonella enterica isolated over 13 years from raw California almonds and from an almond orchard.PloS one · 2023Article
- Optimization and Validation of Candida auris Short Tandem Repeat Analysis.Microbiology spectrum · 2022Article
- Article
- Salmonella Genomics in Public Health and Food Safety.EcoSal Plus · 2021Article
- Article
- Article
- Precision Food Safety: a Paradigm Shift in Detection and Control of Foodborne Pathogens.mSystems · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.