Escherichia coli (E. coli) strains are normal flora of human gastrointestinal tract. The evolution encoded by horizontally-transferred genetic (HGT) elements has been perceived in several species. E. coli strains have acquired virulence potential factors by attainment of particular loci through HGT, transposons or phages. The heterogeneous nature of these strains is because of HGT through mobile genetic elements. These genetic exchanges that occur in bacteria provide the genetic diversity. A diverse enterobacterial species of E. coli is classified into (i) commensal nonpathogenic, (ii) intestinal and (iii) extraintestinal pathogenic strains. This is related to the presence or absence of regions which are associated with certain pathotypes. The genetic information belongs to the flexible E. coli genome and it has been horizontally acquired by plasmids, bacteriophages and genomic islands. The rapid evolution of E. coli variants results from the genomic regions, contribute to frequently rearrangements, excision and transfer as well as acquisition of additional genome thus resulting to the creation of new (pathogenic) variants. HGT is a key step in the evolution of bacterial pathogens. This study is focused on determining the common virulence factors as a signature at the genetic level to use for classification, diversity and evolution of E. coli.

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Diarrheagenic and uropathogenic E. coli types are mainly characterized by the expression of distinctive bacterial virulent factors. stx1, stx2 (Shiga toxins), and cdt (cytolethal distending toxin) genes have been acquired by horizontal gene transfer. Some virulent genes such as espP (serine protease), etpD (part of secretion pathway), and katP (catalase-peroxidase), or sfpA gene (Sfp fimbriae), are on plasmids and the others like fliC (flagellin) and the fimH gene (fimbriae type-I) are located on chromosome. Genomic pathogenicity islands (PAIs) carry some virulent genes such as hly gene. To determine the existence of virulence genes in cdt clinical isolates, genes including stx1, stx2, cdt, hly, espP, katP, sfpA, etpD, fliC, and fimH were assessed by Polymerase Chain Reaction (PCR). The most prevalent isolates for etpD and katP genes were 85.7% in cdtII. katP gene was also observed 83.3% in cdtI. However, in 42.85% of cdtIII isolates, espP gene was the most detected. Moreover, hly gene was also the most prominent gene in cdtIII (71.42%). sfpA gene was observed in 66.6% of cdtV. stx1 gene was detected in 100% of cdtII, cdtIV, and cdtV types. Presence and pattern of virulence genes were considered among cdt positive isotypes and used for their clustering and profiling.

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Highlights A cross-reactive multi-epitope vaccine stimulates the immune system against ExPEC, P. mirabilis , and K. pneumonia strains. A potential vaccine through in silico strategy uses anti-virulent compounds. The designed constructs managed to induce significant immunity (CD8+ and CD4+ T cells) and protection against UTI infection. In a murine model, it reduces UTI bacterial burdens, and it provides a multi-epitope vaccine to prevent pathogenesis.