Genetic methods in molecular epidemiology of tuberculosis
More details
Hide details
Department of Microbiology, National Research Institute of Tuberculosis and Lung Diseases, Warsaw, Poland
Ewa Augustynowicz-Kopeć   

Department of Microbiology, National Research Institute of Tuberculosis and Lung Diseases, Warsaw, Poland
J Pre Clin Clin Res. 2012;6(1):1–6
Epidemiological studies of tuberculosis cover a number of medical disciplines, such as clinical medicine, pathology, microbiology, medical statistics, as well as biochemistry and genetics. The rapid development of modern techniques in molecular biology observed in recent years has also allowed their use in the studies of the epidemiology of tuberculosis. These techniques are based on the detection in the mycobacterial genome of characteristic sequences, their organization and polymorphism, and also the identification of genes which determine virulence factors and antibiotic resistance.

Characteristics of the main genotyping methods applied in molecular epidemiological investigations of tuberculosis.

Brief description of the state of knowledge:
Genome sequencing allows the determination of molecular patterns (fingerprinting) of Mycobacterium tuberculosis strains analyzed and their discrimination. This is crucial when defining the findings of epidemiological investigations and, above all, recognizing the source of tuberculosis and routes of its transmission. Before molecular methods for epidemiological investigations had been developed, most of the research was limited to discriminating on the basis of biochemical and serological features, phage typing and drug resistance phenotype. With the advent of molecular techniques, epidemiologists began using effective markers to track the transmission and to identify the phylogenetic characteristics of M. tuberculosis strains.

The most important criteria for selection of the method of typing are: the nature of the sample, its size, and the time at which the material was collected. The methods currently used are characterized by varied discriminatory power, the value of which is determined by the degree of clustering/grouping of strains into potential epidemiological groups within which the transmission occurred.

Van der Zanden AGM, Kremer K, Schouls LM, Caimi K, Cataldi A, Hulleman A, et al. Improvement of differentiation and interpretability of spoligotyping for Mycobacterium tuberculosis complex isolates by introduction of nem spacer oligonucleotides. J Clin Microbiol. 2002; 4: 4628-39.
Grange JM, Laszlo A. Serodiagnostic tests for tuberculosis: a need for assessment of their operational predictive accuracy and acceptability. Bull World Health Organ 1990; 68: 571-6.
Hoffner SE, Svenson SB, Norberg R, Dias F, Ghebremichael S, Kallenius G. Biochemical heterogeneity of Mycobacterium tuberculosis complex isolates in Guinea-Bissau. J Clin Microbiol. 1993; 31: 2215-7.
Jones WD. Jr. Bacteriophage typing of Mycobacterium tuberculosis cultures from incidents of suspected laboratory cross-contamination. Tubercle 1988; 69: 43-6.
Kanduma E, McHugh TD, Gillespie SH. Molecular methods for Mycobacterium tuberculosis strain typing: a users’ guide. J Appl Microbiol. 2003; 94: 781-91.
Collins DM, de Lisle GW. DNA restriction endonuclease analysis of Mycobacterium tuberculosis and Mycobacterium bovis BCG. J Gen Microbiol. 1984; 130: 1019-21.
Varnerot A, Clement F, Gheorghiu M, Vincent-Levy-Frebault V. Pulsed field gel electrophoresis of representatives of Mycobacterium tuberculosis and Mycobacterium bovis BCG strains. FEMS Microbiol Lett. 1992; 77: 155-60.
Dale JW. Mobile genetic elements in mycobacteria. Eur Respir J Suppl. 1995; 20: 633-648.
Eisenach KD, Cave MD, Bates JH, Crawford JT. Polymerase chain reaction amplification of a repetitive DNA sequence specific for Mycobacterium tuberculosis. J Infect Dis. 1990; 161: 977-81.
Hermans PW, van Soolingen D, Bik EM, de Haas PE, Dale JW, van Embden JD. Insertion element IS987 from Mycobacterium bovis BCG is located in a hot-spot integration region for insertion elements in Mycobacterium tuberculosis complex strains. Infect Immun. 1991; 59: 2695-705.
Maguire H, Dale JW, McHugh TD, Butcher PD, Gillespie SH, Costetsos A, et al. Molecular epidemiology of tuberculosis in London 1995-7 showing low rate of active transmission. Thorax 2002; 57: 617-22.
McHugh TD, Newport LE, Gillespie SH. IS6110 homologs are present in multiple copies in mycobacteria other than tuberculosis-causing mycobacteria. J Clin Microbiol. 1997; 35: 1769-71.
van Soolingen D, Hermans PW, de Haas PE, van Embden JD. Insertion element IS1081-associated restriction fragment length polymorphisms in Mycobacterium tuberculosis complex species: a reliable tool for recognizing Mycobacterium bovis BCG. J Clin Microbiol. 1992; 30: 1772-7.
De Wit D, Steyn L, Shoemaker S, Sogin M. Direct detection of Mycobacterium tuberculosis in clinical specimens by DNA amplification. J Clin Microbiol. 1990; 28: 2437-41.
Ross BC, Raios K, Jackson K, Dwyer B. Molecular cloning of a highly repeated DNA element from Mycobacterium tuberculosis and its use as an epidemiological tool. J Clin Microbiol. 1992; 30: 942-6.
Kotłowski R, Shamputa IC, El Aila NA, Sajduda A, Rigouts L, van Deun A, et al. PCR-based genotyping of Mycobacterium tuberculosis with new GC-rich repeated sequences and IS6110 inverted repeats used as primers. J Clin Microbiol. 2004; 42: 372-7.
Kozińska M, Augustynowicz-Kopeć E, Zwolska Z, Brzezińska S, Zabost A, Anielak M, et al. Transmission of Mycobacterium tuberculosis among household contacts of patients with tuberculosis. Przegl Epidemiol. 2008; 62: 55-62.
van Soolingen D, de Haas PE, Hermans PW, Groenen PM, van Embden JD. Comparison of various repetitive DNA elements as genetic markers for strain differentiation and epidemiology of Mycobacterium tuberculosis. J Clin Microbiol. 1993; 31: 1987-95.
Hermans PW, Schuitema AR, Van Soolingen D, Verstynen CP, Bik EM, Thole JE, et al. Specific detection of Mycobacterium tuberculosis complex strains by polymerase chain reaction. J Clin Microbiol. 1990; 28: 1204-13.
Kremer K, van Soolingen D, Frothingham R, Haas WH, Hermans PW, Martin 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.
Yuen KY, Chan CM, Chan KS, Yam WC, Ho PL, Chau PY. IS6110 based amplityping assay and RFLP fingerprinting of clinical isolates of Mycobacterium tuberculosis. J Clin Pathol. 1995; 48: 924-8.
Graham SM, Gie RP, Schaaf HS, Coulter JB, Espinal MA, Beyers N. Childhood tuberculosis: clinical research needs. Int J Tuberc Lung Dis. 2004; 8: 648-57.
Prod’hom G, Guilhot C, Gutierrez MC, Varnerot A, Gicquel B, Vincent V. Rapid discrimination of Mycobacterium tuberculosis complex strains by ligation-mediated PCR fingerprint analysis. J Clin Microbiol. 1997; 35: 3331-4.
Reisig F, Kremer K, Amthor B, van Soolingen D, Haas WH. Fast ligationmediated PCR, a fast and reliable method for IS6110-based typing of Mycobacterium tuberculosis complex. J Clin Microbiol. 2005; 43: 5622-7.
Abed Y, Davin-Regli A, Bollet C, De Micco P. Efficient discrimination of Mycobacterium tuberculosis strains by 16S-23S spacer region-based random amplified polymorphic DNA analysis. J Clin Microbiol. 1995; 33: 1418-20.
Vitol I, Driscoll J, Kreiswirth B, Kurepina N, Bennett KP. Identifying Mycobacterium tuberculosis complex strain families using spoligotypes. Infect Genet Evol. 2006; 6: 491-504.
Kamerbeek J, Schouls L, Kolk A, van Agterveld M, van Soolingen D, Kuijper S, et al. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol. 1997; 35: 907-14.
Filliol I, Driscoll JR, van Soolingen D, Kreiswirth BN, Kremer K, Valetudie G, et al. Global distribution of Mycobacterium tuberculosis spoligotypes. Emerg Infect Dis. 2002;8:1347-9.
Frothingham R, Meeker-O’Connell WA. Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats. Microbiology 1998; 144: 1189-96.
Alonso-Rodriguez N, Martinez-Lirola M, Herranz M, Sanchez-Benitez M, Barroso P. Evaluation of the new advanced 15-loci MIRU-VNTR genotyping tool in Mycobacterium tuberculosis molecular epidemiology studies. BMC Microbiol. 2008; 8: 34.
Valcheva V, Mokrousov I, Narvskaya O, Rastogi N, Markova N. Utility of New 24-Locus Variable-Number Tandem-Repeat Typing for Discriminating Mycobacterium tuberculosis Clinical Isolates Collected in Bulgaria. J Clin Microbiol. 2008; 46: 3005-11.
Centers for Disease Control and Prevention (CDC). Trends in tuberculosis – United States, 2007. MMWR Morb Mortal Wkly Rep. 2008; 57: 281-5.
Hawkey PM, Smith EG, Evans JT, Monk P, Bryan G, Mohamed HH, et al. Mycobacterial interspersed repetitive unit typing of Mycobacterium tuberculosis compared to IS6110-based restriction fragment length polymorphism analysis for investigation of apparently clustered cases of tuberculosis. J Clin Microbiol. 2003; 41: 3514-20.
Supply P, Lesjean S, Savine E, Kremer K, van Soolingen D, Locht C. Automated high-throughput genotyping for study of global epidemiology of Mycobacterium tuberculosis based on mycobacterial interspersed repetitive units J Clin Microbiol. 2001; 39: 3563-71.
Mathema B, Kurepina NE, Bifani PJ, Kreiswirth BN. Molecular epidemiology of tuberculosis: current insights. Clin Microbiol Rev. 2006; 19: 658-85.
Barlow RE, Gascoyne-Binzi DM, Gillespie I. Comparison of variable number tandem repeat and IS6110-restriction fragment length polymorphism analyses for discrimination of high- and low-copynumber IS6110 Mycobacterium tuberculosis isolates. J Clin Microbiol. 2001; 39: 2453-2457.
Cowan LS, Mosher L, Diem L. Variable-number tandem repeat typing of Mycobacterium tuberculosis isolates with low copy numbers of IS6110 by using mycobacterial interspersed repetitive units. J Clin Microbiol. 2002; 40: 1592-1602.
Kulkarni S, Sola C, Filliol I, et al. Spoligotyping of Mycobacterium tuberculosis isolates from patients with pulmonary tuberculosis in Mumbai, India. Res Microbiol. 2005; 156: 588-596.
Allix-Beguec C, Harmsen D, Weniger T. Evaluation and strategy for use of MIRU-VNTRplus, a multifunctional database for online analysis of genotyping data and phylogenetic identification of Mycobacterium tuberculosis complex isolates. J Clin Microbiol. 2008; 46: 2692-2699.