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Year : 2017  |  Volume : 146  |  Issue : 1  |  Page : 11-14

Molecular epidemiology of tuberculosis: Opportunities & challenges in disease control

1 Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, New Delhi 110 007, India
2 Department of Microbiology, Vardhman Mahavir Medical College & Safdarjung Hospital, New Delhi 110 007, India

Date of Submission06-Jul-2017
Date of Web Publication22-Nov-2017

Correspondence Address:
Mandira Varma-Basil
Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, New Delhi 110 007
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Source of Support: None, Conflict of Interest: None

DOI: 10.4103/ijmr.IJMR_941_17

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How to cite this article:
Varma-Basil M, Nair D. Molecular epidemiology of tuberculosis: Opportunities & challenges in disease control. Indian J Med Res 2017;146:11-4

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Varma-Basil M, Nair D. Molecular epidemiology of tuberculosis: Opportunities & challenges in disease control. Indian J Med Res [serial online] 2017 [cited 2021 Sep 26];146:11-4. Available from:

A pathogen Mycobacterium tuberculosis that produces nearly 10.4 million new infections and 1.4 million deaths in a year and is one of the top 10 causes of death worldwide[1], remains one of the most successful human pathogens today with enormous health and economic problems in both the developing and high-income countries. The success of propagation of tuberculosis (TB) is directly linked to the social and hygiene conditions of human populations. The M. tuberculosis complex (MTBC) emerged about 70,000 yrs ago as a genetic bottleneck and spread globally by clonal expansion. Increase in population during the Neolithic period and the accompanying migration of humans are believed to be some of the factors that led to the spread of this pathogen[2]. The organism has undergone several changes over the centuries; thus, though a genetically homogenous group, the genetic diversity of MTBC may be greater than previously envisaged[3]. This diversity may in turn impact the biological properties of the organism[4], which may further impact TB control programmes. The emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB has increased the challenges faced by TB control programmes manifold. Moreover, several studies have shown that diverse molecular types of the organism may have different abilities to acquire drug resistance. Hence, the increase in drug resistance has added to our need to understand new clones that are developing and about the clones that have become extinct.

The global impact of TB can, thus, be reduced only with a concerted effort by not only clinicians and laboratory specialists but also epidemiologists and public health officials. This implies that we need coordinated efforts to promptly diagnose TB, adequately treat the disease and detect outbreaks accurately[2]. The latter requires the use of a combination of conventional and molecular epidemiological tools.

Molecular epidemiology has gained importance in recent times as a resource to understand crucial issues in spread of TB, particularly MDR and XDR-TB, and has emerged as a combination of molecular typing techniques and classical epidemiological approaches. Proper control of TB requires knowledge of the strains circulating in a region, being able to differentiate between relapse and reinfection, identifying incidence of recent transmission, the risk factors involved, the ability to track geographic distribution and clonal expansion of specific strains. There is increasing evidence that genetic differences in MTBC strains are linked to the outcome of the disease and thus patient management[5]. Hence, information about the strain can help in disease control, especially during outbreaks.

Although, initially, the identification and discrimination of mycobacteria were dependent on individual strain phenotype, susceptibility to antimicrobial agents, biochemical differences and serological reactivity, the introduction of molecular techniques in the field of TB has improved our understanding of the dissemination dynamics and evolutionary genetics of the pathogen. The first molecular typing methods used for M. tuberculosis were based on restriction fragment length polymorphism (RFLP) analysis of bacterial DNA. Later, insertion sequences such as IS6110 were used[6]. IS6110 RFLP-based fingerprinting has been used extensively to study the mycobacterial population structure in several parts of the world, including India[7],[8],[9],[10],[11]. However, IS6110 fingerprinting is of limited use since a significant proportion (40-44%) of isolates of M. tuberculosis in certain regions of the world including several parts of India have been reported with low copy numbers or lack of IS6110[7],[8],[12],[13]. Furthermore, IS6110 typing is labour intensive and requires several weeks for culturing the M. tuberculosis isolates. Molecular typing methods targeting spacer sequences in the direct repeat region, including spoligotyping, have also been used. However, these methods if used alone may underestimate the clonal diversity of M. tuberculosis[14], though spoligotyping has been found to be useful in identifying strains belonging to different clades or lineages[2]. Methods based on variable-number tandem repeats (VNTRs) of genetic elements such as mycobacterial interspersed repetitive unit (MIRU) typing can also be used to differentiate between M. tuberculosis isolates with low copy number IS6110 elements[15]. MIRU-VNTR has a discriminating power greater than that of spoligotyping. In fact, when used together, MIRU-VNTR and spoligotyping offer a powerful molecular epidemiological tool. In addition, these techniques are less cumbersome than IS6110 and the results are available faster. Although these techniques target sequences that are genetically variable, these interrogate less than one per cent of the genome of M. tuberculosis.

The availability of genomic sequences of M. tuberculosis led to a new phase in the molecular epidemiological investigations of TB. Earlier studies used Sanger sequencing[16]. However, next generation sequencing (NGS) or high throughput platforms metamorphosed a mere research tool into a large-scale diagnostic and molecular typing platform since millions of DNA fragments could be sequenced at the same time[16].

With these new technological advances, the clinical implications of molecular epidemiological studies have increased[16]. Molecular typing of MTBC cannot only inform investigators about the strains circulating in a particular country or region but can also be used to monitor the spread of specific genotypes in a community or between patients. Moreover, molecular typing can be used to identify cross contamination in laboratories and thus avoid false detection of pseudo-outbreaks[16]. More importantly, genotyping data have provided important information on the risk factors involved in TB transmission. Risk factors that have been identified for recent transmission of TB are pulmonary TB, smear-positive disease, HIV, alcohol abuse, intravenous drug use and residence in urban settings[17],[18]. Molecular typing can thus be used by health authorities to plan or modify TB control programmes.

In this issue, Pasechnik et al[19] have used spoligotyping and MIRU typing to identify M. tuberculosis strains circulating in Omsk, Siberia. They reported that a large number of their isolates belonged to the Beijing family which is known to have a high rate of multidrug resistance. It has been hypothesized that drug resistance leads to reduced virulence and transmissibility of M. tuberculosis. However, as in Omsk, large regions of the world have been seen to harbour drug-resistant isolates, the most notable being, India, China and Russia. It is believed that epistasis may play a role in the compensation of the fitness cost that is believed to be associated with drug resistance[14]. The spread of MDR strains differs in various regions. In Europe, though the predominant MDR strains vary between countries, the T, LAM and Haarlem families have been seen to harbour the maximum numbers of MDR strains, while in East Asia, the Beijing isolates make up the most MDR isolates[16].

India is a vast land with enormous genetic and ethnic diversities and contributes to one-fourth of the global incident TB cases[20]. The distribution of M. tuberculosis lineages globally and in India emphasizes the spread of TB linked to human travel. Studies from India showed that the Central Asian strain (CAS), a modern lineage, was predominant in the western, central and northern parts of India[10],[11],[21],[22],[23]. The Manu lineage has been found in West Central India, while the East African Indian lineage has been predominantly found in south India[21]. Beijing is the third most predominant lineage, but the dominant lineage in North Eastern India[21].

It has also been found that the modern lineages have acquired mutations faster than ancient lineages. Beijing has been significantly associated with MDR as compared to other lineages. Many studies have linked the M. tuberculosis genotypes with the clinical manifestations of disease. For example, CAS strains have been found to be associated with extrapulmonary disease[24]. Euro American lineage was associated more with pulmonary TB than extrapulmonary TB[25].

Although India is a diverse land, the number of epidemiological studies available does not do justice to the repertoire of strains circulating in the country. In addition, the number of isolates included in most of the studies is only a few. Moreover, though the relapse rate of TB in India is 10 per cent, there are no data on whether the relapse is due to reactivation of a previous infection or due to reinfection[26]. The need of the hour is large multisite studies that include strains from large parts of India. Given the recent increase in travel related to work and leisure, a continuous vigil is required to be able to arrest the spread of TB and the emergence of new clones. In addition, it is now widely clear that missed diagnostic opportunities, particularly that of drug-resistant M. tuberculosis, can lead to the evolution of more transmissible organisms that may become increasingly drug resistant. Molecular typing tools can help public health officials to identify transmission links with confidence. In the future, we may see powerful high throughput technologies such as NGS being used for complete strain characterization, detection of drug resistance, monitoring emergence of new drug resistance mutations and mechanisms and outbreak investigation through identification of clades and lineages that will transform disease management and target interventions and resources for TB control more appropriately.

   References Top

World Health Organization. Global Tuberculosis Report 2016. Available from:, accessed on June 7, 2017.  Back to cited text no. 1
Cannas A, Mazzarelli A, Di Caro A, Delogu G, Girardi E. Molecular typing of Mycobacterium tuberculosis strains: A fundamental tool for tuberculosis control and elimination. Infect Dis Rep 2016; 8 : 6567.  Back to cited text no. 2
Hershberg R, Lipatov M, Small PM, Sheffer H, Niemann S, Homolka S, et al. High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol 2008; 6 : e311.  Back to cited text no. 3
Gao Q, Kripke KE, Saldanha AJ, Yan W, Holmes S, Small PM, et al. Gene expression diversity among Mycobacterium tuberculosis clinical isolates. Microbiology 2005; 151 : 5-14.  Back to cited text no. 4
Coleman PG, Perry BD, Woolhouse ME. Endemic stability - A veterinary idea applied to human public health. Lancet 2001; 357 : 1284-6.  Back to cited text no. 5
McAdam RA, Hermans PW, van Soolingen D, Zainuddin ZF, Catty D, van Embden JD, et al. Characterization of a Mycobacterium tuberculosis insertion sequence belonging to the IS3 family. Mol Microbiol 1990; 4 : 1607-13.  Back to cited text no. 6
Das S, Paramasivan CN, Lowrie DB, Prabhakar R, Narayanan PR. IS6110 restriction fragment length polymorphism typing of clinical isolates of Mycobacterium tuberculosis from patients with pulmonary tuberculosis in Madras, South India. Tuber Lung Dis 1995; 76 : 550-4.  Back to cited text no. 7
Radhakrishnan I, Manju YK, Kumar RA, Mundayoor S. Implications of low frequency of IS6110 in fingerprinting field isolates of Mycobacterium tuberculosis from Kerala, India. J Clin Microbiol 2001; 39 : 1683.  Back to cited text no. 8
Siddiqi N, Shamim M, Amin A, Chauhan DS, Das R, Srivastava K, et al. Typing of drug resistant isolates of Mycobacterium tuberculosis from India using the IS6110 element reveals substantive polymorphism. Infect Genet Evol 2001; 1 : 109-16.  Back to cited text no. 9
Bhanu NV, van Soolingen D, van Embden JD, Dar L, Pandey RM, Seth P, et al. Predominace of a novel Mycobacterium tuberculosis genotype in the Delhi region of India. Tuberculosis (Edinb) 2002; 82 : 105-12.  Back to cited text no. 10
Varma-Basil M, Kumar S, Arora J, Angrup A, Zozio T, Banavaliker JN, et al. Comparison of spoligotyping, mycobacterial interspersed repetitive units typing and IS6110-RFLP in a study of genotypic diversity of Mycobacterium tuberculosis in Delhi, North India. Mem Inst Oswaldo Cruz 2011; 106 : 524-35.  Back to cited text no. 11
Chauhan A, Chauhan DS, Parashar D, Gupta P, Sharma VD, Sachan AS, et al. DNA fingerprinting of Mycobacterium tuberculosis isolates from Agra region by IS6110 probe. Indian J Med Microbiol 2004; 22 : 238-40.  Back to cited text no. 12
Mathuria JP, Sharma P, Prakash P, Samaria JK, Katoch VM, Anupurba S, et al. Role of spoligotyping and IS6110-RFLP in assessing genetic diversity of Mycobacterium tuberculosis in India. Infect Genet Evol 2008; 8 : 346-51.  Back to cited text no. 13
Kremer K, van Soolingen D, Frothingham R, Haas WH, Hermans PW, Martín C, et al. Comparison of methods based on different molecular epidemiological markers for typing of Mycobacterium tuberculosis complex strains: Interlaboratory study of discriminatory power and reproducibility. J Clin Microbiol 1999; 37 : 2607-18.  Back to cited text no. 14
Supply P, Mazars E, Lesjean S, Vincent V, Gicquel B, Locht C, et al. Variable human minisatellite-like regions in the Mycobacterium tuberculosis genome. Mol Microbiol 2000; 36 : 762-71.  Back to cited text no. 15
Jagielski T, Minias A, van Ingen J, Rastogi N, Brzostek A, Żaczek A, et al. Methodological and clinical aspects of the molecular epidemiology of Mycobacterium tuberculosis and other mycobacteria. Clin Microbiol Rev 2016; 29 : 239-90.  Back to cited text no. 16
Van Soolingen D, Borgdorff MW, de Haas PE, Sebek MM, Veen J, Dessens M, et al. Molecular epidemiology of tuberculosis in the Netherlands: A nationwide study from 1993 through 1997. J Infect Dis 1999; 180 : 726-36.  Back to cited text no. 17
Fok A, Numata Y, Schulzer M, FitzGerald MJ. Risk factors for clustering of tuberculosis cases: A systematic review of population-based molecular epidemiology studies. Int J Tuberc Lung Dis 2008; 12 : 480-92.  Back to cited text no. 18
Pasechnik O, Dymora MA, Stasenko VL, Blokh AI, Tatarintsera MP, Pavlovna LK, et al. Molecular and genetic characteristics of Mycobacterium tuberculosis strains circulating in the southern part of West Siberia. Indian J Med Res 2017; 146 : 49-55.  Back to cited text no. 19
Ministry of Health and Family Welfare, India. TB INDIA 2016: Revised National TB Control Programme; Annual Status Report. Available from:, accessed on May 15, 2016.  Back to cited text no. 20
Singh J, Sankar MM, Kumar P, Couvin D, Rastogi N, Singh S, et al. Genetic diversity and drug susceptibility profile of Mycobacterium tuberculosis isolated from different regions of India. J Infect 2015; 71 : 207-19.  Back to cited text no. 21
Singh UB, Arora J, Suresh N, Pant H, Rana T, Sola C, et al. Genetic biodiversity of Mycobacterium tuberculosis isolates from patients with pulmonary tuberculosis in India. Infect Genet Evol 2007; 7 : 441-8.  Back to cited text no. 22
Arora J, Singh UB, Suresh N, Rana T, Porwal C, Kaushik A, et al. Characterization of predominant Mycobacterium tuberculosis strains from different subpopulations of India. Infect Genet Evol 2009; 9 : 832-9.  Back to cited text no. 23
Lari N, Rindi L, Cristofani R, Rastogi N, Tortoli E, Garzelli C, et al. Association of Mycobacterium tuberculosis complex isolates of BOVIS and Central Asian (CAS) genotypic lineages with extrapulmonary disease. Clin Microbiol Infect 2009; 15 : 538-43.  Back to cited text no. 24
Caws M, Thwaites G, Dunstan S, Hawn TR, Lan NT, Thuong NT, et al. The influence of host and bacterial genotype on the development of disseminated disease with Mycobacterium tuberculosis. PLoS Pathog 2008; 4 : e1000034.  Back to cited text no. 25
Behera D. Issues in the management of drug resistant tuberculosis in India. Lung India 2013; 30 : 269-72.  Back to cited text no. 26

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