In addition, a set of 22 accessory genome genes was recently used to reassign Shigella serotypes to eight clusters 16. flexneri serotype-converting prophages, to ensure serotype specificity 14, 15. The genomic methods used mostly target the O-antigen gene cluster ( rfb) or the S. In an increasing number of countries, the laboratory surveillance of Shigella infections has now passed from conventional serotyping to real-time genomic surveillance 10, 14. boydii serotype 13, for example, was withdrawn from the classification, because it was shown to belong to another species, Escherichia albertii, and lacked the VP 12, 13. However, some molecular data have been taken into account in an update of the Shigella serotyping scheme. More recent molecular approaches have shown that the current standardised Shigella typing scheme does not accurately reflect the population structure of this pathogen 8. In parallel, these host-restricted pathogens converged independently on the Shigella phenotype (non-motility, no decarboxylation of lysine, no use of citrate and malonate, and other characteristics, as reported by Pupo and coworkers 8) through genome degradation. coli, from which they emerged following the acquisition of a large virulence plasmid (VP) enabling the bacterium to invade intestinal cells 8, 9, 10, 11. However, modern population genetics methods based on bacterial DNA sequences, such as multilocus sequence typing (MLST) analysis (which analyses the allelic profiles of - generally seven - housekeeping genes), and, more recently, core-genome single-nucleotide variant (cgSNV) analysis, have shown that shigellae form distinct lineages within the species E. sonnei these four serogroups are then subdivided into more than 50 serotypes. ![]() It splits the Shigella genus into four serogroups (originally considered to be species): Shigella dysenteriae, S. This scheme, which is still in use today, is based on biochemical tests and serotyping (slide agglutination with typing sera directed against the different Shigella lipopolysaccharide O-antigens). Laboratory surveillance of Shigella infections was initiated several decades ago, and was facilitated by the adoption of a standardised Shigella typing scheme in the late 1940s 7. sonnei isolates have been found in the US, England and Australia 3. Since 2016, highly drug-resistant (i.e., resistant to at least ciprofloxacin, azithromycin and third-generation cephalosporins) S. The morbidity of these infections is currently increasing due to growing resistance to antimicrobial drugs in these bacteria 2, 3, 5, 6. In high-income countries, Shigella infections also occur in travellers and in some high-risk groups, such as men who have sex with men (MSM) and Orthodox Jewish communities 2, 3, 4, 5. It has been estimated that this intracellular human pathogen, which is transmitted via the faecal-oral route with a very low infectious dose (10–100 cells), is responsible for over 210,000 deaths per year, mostly in children under the age of 5 years 1, 2, 3. Shigella belongs to the Enterobacteriaceae family, and causes bacillary dysentery, a common cause of diarrhoea in low- and middle-income countries. 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. 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 cgMLST hierarchical clustering (HC) analysis at different levels of resolution (HC2000 to HC400) recognises the natural population structure of Shigella. The Shigella genomes are grouped into eight phylogenetically distinct clusters, within the E. ![]() 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). Real-time genomic surveillance of Shigella infections has been implemented in several countries, but without the use of a standardised typing scheme. ![]() ![]() 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.
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