Understanding Pathogenic Escherichia coli Through Whole-genome Sequencing
Valeria Michelacci and Eelco Franz
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: 109-120.
Escherichia coli is a highly diverse microorganism with very different eco-evolutionary paths, ranging from commensalism to highly virulent intestinal and extra-intestinal pathovars. The recent broad access to whole-genome sequencing technology has expanded the understanding of the genomic basis of this diversity in an unprecedented way, but without undermining the prevailing views on E. coli diversity and phylogeny based on older low-resolution typing methods. Genomics indicate that in addition to recombination and mutation the acquisition and loss of genes is a major source for genetic variation in E. coli. The relatively small core-genome compared to a large pan-genome led to the recognition of continued diversification by gene acquisition. Genomics provides insights into the plasticity of the pathovars concept and led to the current viewpoint of the apparent continuum of pathogenic E. coli rather than strictly separated pathovars. The chimaeric and dynamic genome of E. coli provides a challenge to the useful application of genomics into public health (i.e. diagnostics, risk assessment, surveillance and disease-outbreak investigation). The combined study of the variation of different fractions of the genomes, which are subjected to different mutation rates such as the core and the accessory genome could eventually provide the best way forward to a consensus typing approach read more ...