Comparative genomic analysis of cyclomodulin-producing Escherichia coli strains of animal origin

Cytolethal distending toxin (CDT), a cyclomodulin and genotoxin produced by many Gram-negative bacteria including pathogenic Escherichia coli, disrupts the eukaryotic host cell cycle to facilitate bacterial colonization. In a survey of dairy cows in Hungary, 7 % of of sampled animal and farm environment isolates carried CDT-producing E. coli (CTEC). Whole genome sequencing (WGS) performed on six recent isolates and three historical CTEC strains revealed association with diverse pathotypes, including enteropathogenic- (EPEC) and necrotoxigenic- (NTEC) types, as well as several unclassified atypical strains. Four of the six strains isolated in this study carried plasmid encoding cdt-III+ NTEC, while a prophage based cdt-V allele was present in the remaining two strains which were of unknown pathotype. These isolates exhibited significant variability in their supplementary virulence genes (SVGs) content as well as in multiple prophage regions linked to virulence or fitness factors. They were phylogenetically distinct and comprised of only distantly related sequence types (STs) that include two novel STs. Several isolates also carried other genotoxic cyclomodulins such as the cytotoxic necrotizing factor (cnf), the cycle inhibiting factor (cif), and colibactin (polyketide synthase, pks) which is located on a genomic island, indicating multiple mechanisms for dysplastic damage of the eukaryotic host cells exist and highlight the role of horizontal gene transfer in the zoonotic and pathogenic potential of CTEC.