ReviewOne health outlook2020
Typing methods based on whole genome sequencing data.
Review in One health outlook, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 121 papers, 1 of them a synthesis that pooled it.
What it found
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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
121 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Tracking of multidrug-resistant pathogen clones in Ghana: a systematic review and meta-analysis.BMC medical genomics · 2025Pooled it
- Whole Genome Characterisation of Non-O1/Non-O139Microorganisms · 2026Article
- cgDist: Nucleotide-level distance calculation from cgMLST allelic profiles.NAR genomics and bioinformatics · 2026Article
- A new core-genome MLST approach for Chlamydia trachomatis genomic surveillance and research.Nature communications · 2026Article
- Near-real-time whole-genome sequencing in hospital infection control: a narrative review.Infection · 2026Review
- SEVA: structural and evolutionary feature integration for predicting virulence factors and antibiotic resistance genes.Microbiome · 2026Article
- Phylo-Plex: a phylogenetically informed, low-cost amplicon sequencing platform for deployable high-resolution genomic epidemiology.Nature communications · 2026Article
- Spatial ecology meets quality control: a GIS-integrated strategy for visualizing and managing microbial contamination in sterile pharmaceutical cleanrooms.Microbiology spectrum · 2026Article
- Machine Learning-Based Prediction of Antimicrobial Resistance inDiagnostics (Basel, Switzerland) · 2026Article
- Implementing the CRISPR 2.1 array for genotyping enhances identification of uropathogenic Escherichia coli in Colombian pediatric patients.Biomedica : revista del Instituto Nacional de Salud · 2026Article
- chewBBACA 3: lowering the barrier for scalable and detailed whole- and core-genome multilocus sequence typing.Genome medicine · 2026Article
- Prediction of genetic relatedness ofAntimicrobial agents and chemotherapy · 2026Article
- Article
- Consanguinity-linked genetic variants in Algerian patients with steroid-resistant nephrotic syndrome: a familial study.Pediatric nephrology (Berlin, Germany) · 2026Article
- Ribotyping for Accurate Identification of Infectious Bacteria in Animal-Derived Foods and Laboratory Samples: Implications for Human Health.Journal of tropical medicine · 2026Review
- Population structure and phylogenetic analysis of Vibrio cholerae non-O1/O139 by whole genome sequencing.PloS one · 2026Article
- Leveraging whole-genome sequencing for microbial contamination tracking and risk assessment in pharmaceutical manufacturing.Frontiers in microbiology · 2026Article
- Molecular insights into antimicrobial resistance in human bacterial pathogens: mechanisms, resistance genes, and translational diagnostic applications.Frontiers in microbiology · 2026Review
- Global epidemiological insights on the antimicrobial resistance ofMicrobial genomics · 2025Article
- Typing ofMicroorganisms · 2025Article
61 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole genome sequencing (WGS) of foodborne pathogens has become an effective method for investigating the information contained in the genome sequence of bacterial pathogens. In addition, its highly discriminative power enables the comparison of genetic relatedness between bacteria even on a sub-species level. For this reason, WGS is being implemented worldwide and across sectors (human, veterinary, food, and environment) for the investigation of disease outbreaks, source attribution, and improved risk characterization models. In order to extract relevant information from the large quantity and complex data produced by WGS, a host of bioinformatics tools has been developed, allowing users to analyze and interpret sequencing data, starting from simple gene-searches to complex phylogenetic studies. Depending on the research question, the complexity of the dataset and their bioinformatics skill set, users can choose between a great variety of tools for the analysis of WGS data. In this review, we describe the relevant approaches for phylogenomic studies for outbreak studies and give an overview of selected tools for the characterization of foodborne pathogens based on WGS data. Despite the efforts of the last years, harmonization and standardization of typing tools are still urgently needed to allow for an easy comparison of data between laboratories, moving towards a one health worldwide surveillance system for foodborne pathogens.
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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.