Molecular Strain Typing ofMycobacterium tuberculosis: a Review of Frequently Used Methods

Abstract

Tuberculosis, caused by the bacterium Mycobacterium tuberculosis, remains one of the most serious global health problems. Molecular typing of M. tuberculosis has been used for various epidemiologic purposes as well as for clinical management. Currently, many techniques are available to type M. tuberculosis. Choosing the most appropriate technique in accordance with the existing laboratory conditions and the specific features of the geographic region is important. Insertion sequence IS6110-based restriction fragment length polymorphism (RFLP) analysis is considered the gold standard for the molecular epidemiologic investigations of tuberculosis. However, other polymerase chain reaction-based methods such as spacer oligonucleotide typing (spoligotyping), which detects 43 spacer sequence-interspersing direct repeats (DRs) in the genomic DR region; mycobacterial interspersed repetitive units–variable number tandem repeats, (MIRU-VNTR), which determines the number and size of tandem repetitive DNA sequences; repetitive-sequence-based PCR (rep-PCR), which provides high-throughput genotypic fingerprinting of multiple Mycobacterium species; and the recently developed genome-based whole genome sequencing methods demonstrate similar discriminatory power and greater convenience. This review focuses on techniques frequently used for the molecular typing of M. tuberculosis and discusses their general aspects and applications.

Insights into Recurrent Tuberculosis: Relapse Versus Reinfection and Related Risk Factors

“…The former occur throughout the genome in the form of direct repeats and insertion sequences, while the latter are a series of head-to-tail direct uninterrupted repeats in the form of variable number tandem repeats (VNTR). The most common techniques used to distinguish between the two mechanisms of TB recurrence include IS6110-restriction fragment length polymorphism (IS6110-RFLP) analysis, mycobacterial interspersed repetitive-unit variable number of tandem repeats (MIRU-VNTR) typing, and spacer oligonucleotide genotyping (spoligotyping) [4,23]. More recently, whole genome sequencing (WGS) has been used to compare strains representing different episodes of TB infection.…”

Identification and Molecular Epidemiology of Mycobacterial Isolates in Kayseri/Turkey

“…In particular, some NTM species, especially MAC members, are frequently isolated from clinical laboratories. Molecular methods have also found wide application in the identification of mycobacteria in clinical specimens and at species level [14,15]. Koh, et al [16] in 2006, isolated NTMs from respiratory tract specimens which were defined mainly as MAC (48%) and M. abscessus (33%).…”

“…The rep-PCR lonae, 4.4% M. gordonae, 3.2% M. terrae, 1.8% M. scrofuloceum, 1.3% M. kansasii and M. szulgai [11]. In the study by Couto, et al [14], NTMs isolated from clinical samples [15] were identified mainly as follows 24.8% MAC, 15.4% M. gordonae, 9.4% M. fortuitum, 6.7% M chelonae, 6% M. xenopi, 4.7% M. peregrinum and 4% M. abscessus. In our study, 66.7% of cases were found to be M. tuberculosis by the rep-PCR method.…”

“…Genotyping methods are used to determine disease source and transmission time. Genotyping, which provides information about infection, is needed for epidemiological and clinical purposes with TB control [8,15]. Genotypic analysis of M. tuberculosis isolates has been implemented to support TB epidemic control activities.…”

Predominance of Central Asian strain (ST 26) in Mycobacterium tuberculosis isolates from Balochistan by spoligotyping

“…This is despite effective treatments, diagnostic and preventive measures that have become available in the last few decades. Molecular based typing techniques for the causative Mycobacterium tuberculosis (M. tuberculosis) complex have emerged as effective tools based on variation in insertion sequences and repetitive genomic sequences [1][2][3]. M. tuberculosis has a highly conserved genome containing useful markers that can be exploited in different typing techniques, such as those using Insertion Sequence IS6110 [4], Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) [5], Large Sequence Polymorphism (LSP) [6], Restriction Fragment Length Polymorphism (RFLP) [7] and reverse line dot blot spoligotyping [8,9].…”