title: Genetic markers, genotyping methods & next generation sequencing in Mycobacterium tuberculosis.
abstract: Molecular epidemiology (ME) is one of the main areas in tuberculosis research which is widely used to study the transmission epidemics and outbreaks of tubercle bacilli. It exploits the presence of various polymorphisms in the genome of the bacteria that can be widely used as genetic markers. Many DNA typing methods apply these genetic markers to differentiate various strains and to study the evolutionary relationships between them. The three widely used genotyping tools to differentiate Mycobacterium tuberculosis strains are IS6110 restriction fragment length polymorphism (RFLP), spacer oligotyping (Spoligotyping), and mycobacterial interspersed repeat units - variable number of tandem repeats (MIRU-VNTR). A new prospect towards ME was introduced with the development of whole genome sequencing (WGS) and the next generation sequencing (NGS) methods, where the entire genome is sequenced that not only helps in pointing out minute differences between the various sequences but also saves time and the cost. NGS is also found to be useful in identifying single nucleotide polymorphisms (SNPs), comparative genomics and also various aspects about transmission dynamics. These techniques enable the identification of mycobacterial strains and also facilitate the study of their phylogenetic and evolutionary traits.
authors.forename: Srinidhi
authors.initials: S
authors.lastname: Desikan
authors.affiliation: Department of Immunology, National Institute of Research in Tuberculosis (ICMR), Chennai, India.
authors.forename: Sujatha
authors.initials: S
authors.lastname: Narayanan
mesh_terms: D015373:Bacterial Typing Techniques; D004251:DNA Transposable Elements / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D005819:Genetic Markers; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D018598:Minisatellite Repeats / Q000235:genetics; D017720:Molecular Epidemiology; D009169:Mycobacterium tuberculosis / Q000235:genetics* / Q000472:pathogenicity; D010802:Phylogeny; D014376:Tuberculosis / Q000453:epidemiology / Q000235:genetics* / Q000382:microbiology
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D005819:Genetic Markers