Journal
ANNALS OF THE NEW YORK ACADEMY OF SCIENCES
Volume 1388, Issue 1, Pages 59-77Publisher
WILEY
DOI: 10.1111/nyas.13273
Keywords
tuberculosis; transmission; genomics; resistance
Categories
Funding
- Frederick Banting and Charles Best Canada Graduate Scholarships program
- Canada Research Chairs and Michael Smith Foundation
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Genomics is now firmly established as a technique for the investigation and reconstruction of communicable disease outbreaks, with many genomic epidemiology studies focusing on revealing transmission routes of Mycobacterium tuberculosis. In this primer, we introduce the basic techniques underlying transmission inference fromgenomic data, using illustrative examples from M. tuberculosis and other pathogens routinely sequenced by public health agencies. We describe the laboratory and epidemiological scenarios under which genomics may or may not be used, provide an introduction to sequencing technologies and bioinformatics approaches to identifying transmission-informative variation and resistance-associated mutations, and discuss how variation must be considered in the light of available clinical and epidemiological information to infer transmission.
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