Comparative genomics reveals differences in mobile virulence genes of Escherichia coli O103 pathotypes of bovine fecal origin

Abstract

Escherichia coli O103, harbored in the hindgut and shed in the feces of cattle, can be enterohemorrhagic (EHEC), enteropathogenic (EPEC), or putative non-pathotype. The genetic diversity particularly that of virulence gene profiles within O103 serogroup is likely to be broad, considering the wide range in severity of illness. However, virulence descriptions of the E. coli O103 strains isolated from cattle feces have been primarily limited to major genes, such as Shiga toxin and intimin genes. Less is known about the frequency at which other virulence genes exist or about genes associated with the mobile genetic elements of E. coli O103 pathotypes. Our objective was to utilize whole genome sequencing (WGS) to identify and compare major and putative virulence genes of EHEC O103 (positive for Shiga toxin gene, stx1, and intimin gene, eae; n = 43), EPEC O103 (negative for stx1 and positive for eae; n = 13) and putative non-pathotype O103 strains (negative for stx and eae; n = 13) isolated from cattle feces. Six strains of EHEC O103 from human clinical cases were also included. All bovine EHEC strains (43/43) and a majority of EPEC (12/13) and putative non-pathotype strains (12/13) were O103:H2 serotype. Both bovine and human EHEC strains had significantly larger average genome sizes (P < 0.0001) and were positive for a higher number of adherence and toxin-based virulence genes and genes on mobile elements (prophages, transposable elements, and plasmids) than EPEC or putative non-pathotype strains. The genome size of the three pathotypes positively correlated (R2 = 0.7) with the number of genes carried on mobile genetic elements. Bovine strains clustered phylogenetically by pathotypes, which differed in several key virulence genes. The diversity of E. coli O103 pathotypes shed in cattle feces is likely reflective of the acquisition or loss of virulence genes carried on mobile genetic elements.

Fig 1. Scatterplot of genome sizes and number of genes on mobile elements^† of 75 strains of enterohemorrhagic (EHEC), enteropathogenic (EPEC) and putative non-pathotype (stx/eae negative) Escherichia coli O103.

^†Genome sizes and number of genes located on mobile elements (prophages, transposable elements and plasmids) were determined using Rapid Annotation Using Subsystem Technology (RAST; [25]).

Fig 2. Proportional branch transformed phylogenetic tree^† of 75 strains of enterohemorrhagic (EHEC), enteropathogenic (EPEC) and putative non-pathotype (stx/eae negative) Escherichia coli O103 of bovine and human origin using FigTree 1.4.

^†Numbers on the branches correspond to bootstrap values.

Fig 3. Multiple genome comparison of representative strains of enterohemorrhagic (EHEC), enteropathogenic (EPEC) and putative non-pathotype (stx/eae negative) Escherichia coli O103 strains of bovine and human origin using BLAST Ring Image Generator (BRIG) v0.95.

^†The nucleotide sequence (45,325 bp) of the locus of enterocyte effacement (LEE) pathogenicity island (GenBank accession no.: AF071034.1) was mapped for comparison of LEE between target strains.