Development of a high throughput phylogenomic framework for outbreak investigations and virulence studies of Escherichia coli O157:H7 serotype
The non-sorbitol fermenting enterohemorrhagic Escherichia coli (EHEC) O157:H7 serotype is a major water- and food-borne enteric pathogen responsible for approximately 75,000 cases of human infection per year in North America alone. Shiga toxin production is the major virulence hallmark of EHEC and is encoded within the lambdoid Shiga toxin-encoding bacteriophages. The genetic polymorphisms underlying the diversity observed in O157:H7 pathogenicity remain to be elucidated. To gain further insight into the genetic heterogeneity that exists within the O157:H7 serotype, a spatiotemporally diverse collection of O157:H7 outbreaks were subjected to comparative genomics and genome-wide association studies and investigated for genetic polymorphisms in the core genome, as well as the highly virulent Stx-encoding bacteriophages. The genotypic studies of diverse O157:H7 strains revealed the degree of heterogeneity and variations observed among eight different outbreaks. These findings were further analyzed by conducting phenotypic studies of an epidemiologically diverse collection of O157:H7 strains that represented the different lineages and clades of this serotype. Investigations of the diversity present within the transcriptome or proteome of different O157:H7 strains contributed to a deeper understanding of the phenotypic variation found in this serotype and allowed for the potential linking of such findings to underlying genetic polymorphisms. The characterization of Stx virulence phenotypes can ultimately serve as an indicator of potential virulence and disease severity. The gathered phenotypes allowed us to relate the limited, yet important genomic plasticity in this genetically homogenous lineage to altered toxin profiles and provide the basis to identify variants leading to increased Stx production. In addition to the O157:H7 serotype, the genetic diversity of emerging enteropathogenic E. coli (EPEC) O157:non-H7 serotypes was characterized and its phylogenetic relationship to the highly virulent O157:H7 serotype was investigated. Whole genome-based analysis of epidemiologically diverse O157:non-H7 strains revealed a non-monophyletic genome make-up within and across the non-H7 serotypes. EPEC O157:non-H7 serotypes exhibit a distant phylogenetic relatedness to the EHEC O157:H7 and its ancestral EPEC O55:H7 serotype. The availability of complete genome sequences of O157:non-H7 strains placed these isolates into their phylogenomic context. Whole genome-based characterization and typing was important for developing a refined phylogenomic framework and assessment of the individual pathogenic potential of circulating extant non-H7 strains.