Using whole genome sequencing data to study the molecular relationship between Shigella and enteroinvasive Escherichia coli
Shigellosis, or bacillary dysentery, is caused by ingestion of as few as ten to two hundred Shigella or one million enteroinvasive Escherichia coli (EIEC) cells and continues to pose a threat to public health. Those enteric bacteria share the same mechanism of pathogenesis and appear to be human specific. They are traditionally screened and identified by laborious biochemical testing and by serology. Shigella strains were separated from E. coli in the 1940s. Shigella genus is divided into four species: S. boydii, S. dysenteriae, S. flexneri and S. sonnei. The first three species are typed into multiple serotypes, based on antigenic variation in their O antigens only since they lack H and K antigens. About fourteen different O antigen types have been found in EIEC strains, three being identical to O antigens present in Shigella. Making a distinction between EIEC and Shigella spp. is difficult and depends on a very limited number of physiological traits, EIEC strains tending to show a higher metabolic activity than Shigella.
Current molecular assays for the diagnosis of Shigella do not differentiate between Shigella and EIEC. Initially, we developed PCR fingerprinting assays that grouped Shigella and EIEC isolates into distinct clusters and identified molecular markers for S. sonnei and for all S. flexneri but one serotype. These clusters correlated with those previously identified by phylogenetic analyses using the sequence data of four or twenty-three housekeeping genes. We extended this work by including whole genome sequencing technologies. Interestingly, the strain clustering from phylogenetic analyses using core SNPs, or the analyses of gene functions in metabolism, physiology and antibiotic resistance was still similar to the one observed with the PCR fingerprinting assays. Cluster specific genetic markers are now being explored to assist in rapid identification of specific groups of Shigella or EIEC.