Skip to Main content Skip to Navigation
Journal articles

Population structure analysis and laboratory monitoring of Shigella by core-genome multilocus sequence typing

Abstract : The laboratory surveillance of bacillary dysentery is based on a standardised Shigella typing scheme that classifies Shigella strains into four serogroups and more than 50 serotypes on the basis of biochemical tests and lipopolysaccharide O-antigen serotyping. Real-time genomic surveillance of Shigella infections has been implemented in several countries, but without the use of a standardised typing scheme. Here, we study over 4000 reference strains and clinical isolates of Shigella, covering all serotypes, with both the current serotyping scheme and the standardised EnteroBase core-genome multilocus sequence typing scheme (cgMLST). The Shigella genomes are grouped into eight phylogenetically distinct clusters, within the E. coli species. The cgMLST hierarchical clustering (HC) analysis at different levels of resolution (HC2000 to HC400) recognises the natural population structure of Shigella. By contrast, the serotyping scheme is affected by horizontal gene transfer, leading to a conflation of genetically unrelated Shigella strains and a separation of genetically related strains. The use of this cgMLST scheme will facilitate the transition from traditional phenotypic typing to routine whole-genome sequencing for the laboratory surveillance of Shigella infections.
Complete list of metadata

https://hal-pasteur.archives-ouvertes.fr/pasteur-03694335
Contributor : Maria Pardos de la Gandara Connect in order to contact the contributor
Submitted on : Monday, June 13, 2022 - 3:51:14 PM
Last modification on : Saturday, June 25, 2022 - 3:44:10 AM

File

08.Yassine_NatComm_2022.pdf
Publication funded by an institution

Licence


Distributed under a Creative Commons Attribution 4.0 International License

Identifiers

Collections

Citation

Iman Yassine, Sophie Lefèvre, Elisabeth E. Hansen, Corinne Ruckly, Isabelle Carle, et al.. Population structure analysis and laboratory monitoring of Shigella by core-genome multilocus sequence typing. Nature Communications, Nature Publishing Group, 2022, 13 (1), pp.551. ⟨10.1038/s41467-022-28121-1⟩. ⟨pasteur-03694335⟩

Share

Metrics

Record views

0

Files downloads

0