Escherichia coli Genome Plasticity and Evolution
David W. Lacher, Michael L. Kotewicz, Mark K. Mammel and Christopher A. Elkins
from: Pathogenic Escherichia coli: Evolution, Omics, Detection and Control (Edited by: Pina M. Fratamico, Yanhong Liu and Christopher H. Sommers). Caister Academic Press, U.K. (2018) Pages: 15-28.
Escherichia coli are associated with environmental, commensal, and emergent pathogenic niches. Extensive genome sequencing has expanded and refined the landscape for this microbial species beyond traditional taxonomy reliant on fragmented phenotypic and genetic data. Core genome sequences provide a new standard to investigate clonal relationships, diversity, species definition, and strain classification. Specifically, major phylogroups originally established by multilocus enzyme electrophoresis are recapitulated with greater resolution than previously reported and new environmental cryptic lineages sharpen perspectives on species definition. Shigella species are interwoven across this high resolution landscape again providing further evidence to reject their species distinction. We use E. coli O157:H7 as a paradigm for pathogen evolution and offer critical analyses of associated clade and lineage models with respect to core genome phylogenetics. This perspective is further stratified and extended to the strain level to highlight the plasticity of genome architectures in these pathogens. In aggregate, the species landscape is expectedly well-populated from a clinical perspective but is under-represented from environmental and commensal niches. Regardless, the robustness in framework and fundamental architecture of core genome analysis should be foundational for future molecular systematic applications read more ...