AbstractThe laboratory surveillance of bacillary dysentery is based on a standardisedShigellatyping scheme that classifiesShigellastrains into four serogroups and more than 50 serotypes on the basis of biochemical tests and lipopolysaccharide O-antigen serotyping. Real-time genomic surveillance ofShigellainfections 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 ofShigella, covering all serotypes, with both the current serotyping scheme and the standardised EnteroBase core-genome multilocus sequence typing scheme (cgMLST). TheShigellagenomes are grouped into eight phylogenetically distinct clusters, within theE. colispecies. The cgMLST hierarchical clustering (HC) analysis at different levels of resolution (HC2000 to HC400) recognises the natural population structure ofShigella. By contrast, the serotyping scheme is affected by horizontal gene transfer, leading to a conflation of genetically unrelatedShigellastrains 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 ofShigellainfections.