Accurate whole-genome sequencing-based epidemiological surveillance of mycobacterium tuberculosis

Publication date: Available online 19 May 2015 Source:Methods in Microbiology Author(s): Hannes Pouseele , Philip Supply Efficient molecular-guided epidemiological control of tuberculosis is especially important, because of the complex epidemiology, the insidious transmission and the specific biological features of its etiologic agent Mycobacterium tuberculosis. The most used typing system for epidemiological tracing of the pathogen is MIRU-VNTR typing, which has been internationally standardised under two formats (standard 24-locus based and 4 hypervariable locus based), optionally combined with spoligotyping. This generalised use has been facilitated by the portable numerical genotypes that are generated, the precisely calibrated molecular cluster definition and the option to use published protocols or ready-to-go kits directly compatible with multifunctional web-based databases. However, such classical typing systems can inherently not capture all possible micro-variation that can occur in the genome. Near complete capture of the available genetic information is increasingly performed by whole-genome sequencing (WGS). Such approaches take advantage of the rapid advances and increasing affordability of next-generation sequencing technologies, including benchtop platforms meeting the needs of routine clinical microbiology. However, such technologies rely on a number of key technical steps that are important, including in particular the critical bioinformatics analysis ...
Source: Methods in Microbiology - Category: Microbiology Source Type: research