Caister Academic Press

Use of Whole-genome Sequencing to Improve Investigations of Outbreaks of Escherichia coli

Claire Jenkins
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: 121-142.


The aim of this chapter is to evaluate the use of whole-genome sequencing (WGS) data for detecting and investigating outbreaks of Escherichia coli. The methods available for assessing the relatedness between isolates of E. coli, and their use in public health microbiology, are summarised. WGS typing methods are suitable for all pathotypes of E. coli and provide an unprecedented level of strain discrimination. WGS typing is robust and utilises stable genetic markers that can elucidate the evolutionary context of emerging pathogenic strains. The robustness of the approach ensures confidence in the microbiological identification of linked cases when epidemiological links are obscured. Long-read technology will facilitate the analysis of loss and acquisition of mobile genetic elements in the accessory genome, and improve our understanding of the impact of short-term evolutionary changes during outbreak investigations. There is increasing evidence that the geographical origin of an isolate can be inferred from the phylogeny. Expanding WGS-based typing analysis globally will improve trace-back investigations in the event of a foodborne outbreak, ensuring the rapid implementation of interventions to protect public health. The importance of publicly available WGS data linked to the clinical, epidemiological and environmental context of the sequenced strain cannot be underestimated read more ...
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