Genomics for classification, nomenclature and identification of entero-invasive Escherichia coli and Shigella species.

In this study, draft genomes of EIEC and Shigella strains are sequenced and analyzed, both reference isolates and clinically encountered isolates. With this set of genomes, the current classification of Shigella spp. and EIEC is evaluated using genomic taxonomy, by assessing 16S-23S rDNA sequences, Average Nucleotide Identity (ANI), Average Amino-acid Identity (AAI) and in-silico DNA-DNA hybridization (DDH). Second, proposed essays for identification of Shigella spp. and EIEC, that are described, are assessed by evaluating them in-silico. Third, new targets for identification are explored by applying comparative genomics of the non-coding and coding regions, in particular Mobile Genetic Elements (MGE), since the genes encoding for most virulence traits of E. coli and Shigella spp. are located on MGEs. Lastly, core genome MLST (cgMLST) is evaluated as phylogenic technique for species specific clustering of Shigella spp. and EIEC.