Chapter 7. Whole-Genome Sequencing for Rapid and Accurate Identification of Bacterial Transmission Pathways

• Published in: Methods in microbiology Vol. 41; pp. 123 - 152
• Main Authors: Harris, Simon R, Okoro, Chinyere K
• Format: Journal Article
• Language: English
• Published: 01.01.2014
• Subjects: Bacteria
• ISSN: 0580-9517
• DOI: 10.1016/bs.mim.2014.07.003

The advent of DNA sequencing technologies with the capability to sequence the entire genomes of large numbers of bacteria in clinically relevant timescales has opened up the opportunity of using whole-genome sequencing as an epidemiological tool. With costs of sequencing also reducing, we are on the verge of a genomic epidemiology revolution that will provide a method that is both more widely applicable and more detailed than any other current bacterial typing technique. However, the wealth of information provided by whole-genome sequencing requires novel analysis techniques and a review of the current ways of interpreting epidemiological relatedness. This will entail a shift from a same-versus-different methodology to a hierarchical approach that provides a more realistic representation of bacterial evolution. In this chapter, we describe some of the methods by which sequence data can be analysed to identify genomic variation and how genomic relatedness of bacteria can be used alongside traditional epidemiological evidence to draw conclusions about the nature of bacterial disease outbreaks and transmission chains.