ArticleFrontiers in microbiology2019
A Simple and Robust Statistical Method to Define Genetic Relatedness of Samples Related to Outbreaks at the Genomic Scale - Application to Retrospective
Article in Frontiers in microbiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- cgDist: Nucleotide-level distance calculation from cgMLST allelic profiles.NAR genomics and bioinformatics · 2026Article
- Phenotypic and molecular characterization of Salmonella enterica isolated from retail beef in Peshawar, Pakistan.PloS one · 2026Article
- Lessons from 5 Years of Routine Whole-Genome Sequencing for Epidemiologic Surveillance of Shiga Toxin-Producing Escherichia coli, France, 2018-2022.Emerging infectious diseases · 2025Article
- Multi-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens.Nature communications · 2025Article
- Unraveling the impact of genome assembly on bacterial typing: a one health perspective.BMC genomics · 2024Article
- Genomic insights of Salmonella isolated from dry fermented sausage production chains in Spain and France.Scientific reports · 2024Article
- Isolation, Identification, Antimicrobial Resistance, Genotyping, and Whole-Genome Sequencing Analysis ofPolish journal of microbiology · 2024Article
- Virulence Factors and Antimicrobial Resistance of UropathogenicBioMed research international · 2023Article
- Tell me if you prefer bovine or poultry sectors and I'll tell you who you are: Characterization ofFrontiers in microbiology · 2023Article
- Large-scale comparative genomics to refine the organization of the globalMicrobial genomics · 2022Article
- A retrospective and regional approach assessing the genomic diversity ofNAR genomics and bioinformatics · 2022Article
- A European-wide dataset to uncover adaptive traits of Listeria monocytogenes to diverse ecological niches.Scientific data · 2022Article
- In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes.BMC genomics · 2022Article
- Salmonella enterica subsp. enterica Welikade: guideline for phylogenetic analysis of serovars rarely involved in foodborne outbreaks.BMC genomics · 2022Article
- Polyphyly in widespreadFrontiers in public health · 2022Article
- SARS-CoV-2 surveillance in Italy through phylogenomic inferences based on Hamming distances derived from pan-SNPs, -MNPs and -InDels.BMC genomics · 2021Article
- Decentralized Investigation of Bacterial Outbreaks Based on Hashed cgMLST.Frontiers in microbiology · 2021Article
- Serotyping, MLST, and Core Genome MLST Analysis ofFrontiers in microbiology · 2021Article
- Comparative phenotypic, genotypic and genomic analyses of Bacillus thuringiensis associated with foodborne outbreaks in France.PloS one · 2021Article
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Authors and funding
11 authors.
Funding
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Abstract
The investigation of foodborne outbreaks (FBOs) from genomic data typically relies on inspecting the relatedness of samples through a phylogenomic tree computed on either SNPs, genes, kmers, or alleles (i.e., cgMLST and wgMLST). The phylogenomic reconstruction is often time-consuming, computation-intensive and depends on hidden assumptions, pipelines implementation and their parameterization. In the context of FBO investigations, robust links between isolates are required in a timely manner to trigger appropriate management actions. Here, we propose a non-parametric statistical method to assert the relatedness of samples (i.e., outbreak cases) or whether to reject them (i.e., non-outbreak cases). With typical computation running within minutes on a desktop computer, we benchmarked the ability of three non-parametric statistical tests (i.e., Wilcoxon rank-sum, Kolmogorov-Smirnov and Kruskal-Wallis) on six different genomic features (i.e., SNPs, SNPs excluding recombination events, genes, kmers, cgMLST alleles, and wgMLST alleles) to discriminate outbreak cases (i.e., positive control: C+) from non-outbreak cases (i.e., negative control: C-). We leveraged four well-characterized and retrospectively investigated FBOs of
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