Whole Genome Sequencing-Based Identification and Comparative Analysis of Major and Putative Virulence Genes of Escherichia coli O103 of Bovine Fecal Origin

Introduction: Escherichia coli serogroup O103 is a common foodborne pathogen that can present as both potentially deadly Enterohemorrhagic E. coli (EHEC) and, less severely, Enteropathogenic E. coli (EPEC). Potential differences in disease outcomes, particularly serious complications, can be attributed to the diverse make-up of major and putative E. coli O103 virulence factors. Whole genome sequencing (WGS) has been used to analyze and characterize phylogenic relationships, virulence, and antimicrobial resistance gene profiles of EHEC, particularly of E. coli O157:H7. However, genome variations including those that encode for virulence genes of O103 serogroup are less characterized.

Purpose: Our objective was to utilize WGS to identify and compare major and putative virulence genes of EHEC and EPEC O103 isolates of bovine fecal origin.

Methods: A total of 69 O103 strains, previously identified by PCR as positive for stx1 (Shiga-toxin 1) and eae (intimin) (EHEC; n=43), negative for stx1 and positive for eae (EPEC; n=13) and negative for both stx1 and eae (n=13), were sequenced using WGS (Illumina MiSeq). Virulence genes, common and unique to O103 isolates, were identified using Virulence Finder 1.5.  

Results: All EHEC and a majority (92.3%) of non-EHEC strains were O103:H2 serotype.  The following genes differed between the EHEC and EPEC strains:  EHEC adherence factor (efa1; 81.4 vs 7.7%), non-LEE encoded effector A (nleA, 100 vs. 53.8%) and C (53.5 vs. 0%), catalase peroxidase (katP2; 67.4 vs. 7.7%), type III secretion system effector (espJ; 88.4 vs. 7.7%), and EAST-1 heat-stable toxin (astA; 0 vs. 76.9%). Strains negative for stx1 and eae were negative for all above-mentioned virulence genes. 

Significance: The WGS data indicate that bovine strains of O103 are diverse, but key gene patterns evolutionarily differentiate O103 EHEC from EPEC. The information can be used to increase the specificity of detection methods for risk assessment.