A Simple and Robust Statistical Method to Define Genetic Relatedness of Samples Related to Outbreaks at the Genomic Scale – Application to Retrospective Salmonella Foodborne Outbreak Investigations

A Simple and Robust Statistical Method to Define Genetic Relatedness of Samples Related to Outbreaks at the Genomic Scale – Application to Retrospective Salmonella Foodborne Outbreak Investigations

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-in...

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Bibliographic Details
Main Authors: Nicolas Radomski, Sabrina Cadel-Six, Emeline Cherchame, Arnaud Felten, Pauline Barbet, Federica Palma, Ludovic Mallet, Simon Le Hello, François-Xavier Weill, Laurent Guillier, Michel-Yves Mistou
Format: Article
Language:English
Published: Frontiers Media S.A. 2019-10-01
Series:Frontiers in Microbiology
Subjects:
outbreak investigation
Salmonella Typhimurium
monophasic S. Typhimurium (S. 1
4
[5]
12:i:-)
Online Access:https://www.frontiersin.org/article/10.3389/fmicb.2019.02413/full

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