WGS-A Useful Tool to Genotype Mycobacterium Tuberculosis

Currently, the genotyping of M. tuberculosis is crucial for epidemiologic studies. There are lot of ways to type the Tuberculosis (TB), however, each of them has their disadvantages.

According to the phenotypic and biochemical analysis, so-called routine identification method, time-consuming of course. Then various PCR-based methods have been developed. An old gold standard method, called IS6110-RFLP, its main disadvantages are the necessity of high concentration of a high quality of input DNA, sophisticated procedure, and expensive computer software and most importantly the stability of the insertion sequence. And PGRS-RFLP, only need low input amount of DNA (1% of IS6110-RFLP needed), however, lower discrimination power is reported. Also, DNA extracted from a pure culture is required, and some PCR may result negative for some loci in a specific strain, which limiting the use of MIRU-VNTR method. Other types of methods are used very rarely due to their low differential ability or difficult implementation. Compare with Sanger sequencing method which is not suitable for routine sequencing of common isolates, because of labor intensity and cost.

Next generation sequencing (NGS) is the possibility to simultaneous sequence multiple DNA samples during the same run. Whole genome sequencing (WGS), one aspect application of the NGS, which process is starts by DNA extraction and purification, then library preparation and applied on the sequencer. After the run is finished, enormous reads is generated, these reads can be assembled by whether VELVET, A5MISEQ, SPADES, etc., or some other online software.

For TB genotyping, WGS always is a good choice, which could acquire short read data but high sequence quality (low error rate), and the previously collected data may be used for historical description of M. tuberculosis evolution, furthermore, NGS is able to differentiate isolates in outbreaks or reinfections.

Even the price of the NGS is still relatively high limiting the use of the method with low TB incidence and specialized data analysis is also required, NGS is a useful tool of M. tuberculosis Genotyping.

• Jana Amlerova et al. Genotyping of Mycobacterium tuberculosis using whole genome sequencing. Science. Folia Microbiol (2018) 63:537–545.