Genotyping of Pulmonary Mycobacterium tuberculosis Isolates from Sudan Using Spoligotyping

Muataz M. Eldirdery^1, , Intisar E. Alrayah^{1, 2}, Mona OA. Awad ElkareIm³, Fatima A. Khalid⁴, Asrar M A/Salam Elegail⁵, Nuha Y. Ibrahim⁵, Eman O M. Nour⁵, Rahma H. Ali⁵, Elena Hailu⁶, Markos Abebe⁶, Abraham Aseffa⁶, Najem Aldin M. Osman⁷, Maowia M. Mukhtar⁸, Nihad M A. Elhaj¹ and Atif A. Elagib¹

¹Tropical Medicine Research Institute, National Center for Research, Khartoum, Sudan

²College of Applied Medical Science, Shaqra University, Shaqra, KSA

³Blood Transfusion Service, National Blood Transfusion Center, Khartoum, Sudan

⁴Tuberculosis Research Center, University of Kassala, Kassala, Sudan

⁵National Tuberculosis Reference Laboratory, National Laboratory of Public Health, Khartoum, Sudan

⁶6Molecular biology Armauer Hansen Research Institute, Addis Ababa, Ethiopia

⁷Faculty of Science and Technology, Omdurman Islamic University, Khartoum, Sudan

⁸8Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan

Cite this paper:
Muataz M. Eldirdery, Intisar E. Alrayah, Mona OA. Awad ElkareIm, Fatima A. Khalid, Asrar M A/Salam Elegail, Nuha Y. Ibrahim, Eman O M. Nour, Rahma H. Ali, Elena Hailu, Markos Abebe, Abraham Aseffa, Najem Aldin M. Osman, Maowia M. Mukhtar, Nihad M A. Elhaj and Atif A. Elagib. Genotyping of Pulmonary Mycobacterium tuberculosis Isolates from Sudan Using Spoligotyping. American Journal of Microbiological Research. 2015; 3(4):125-128. doi: 10.12691/ajmr-3-4-1

Abstract

Tuberculosis (TB) remains a major public health problem worldwide due to its high risk of person-to-person transmission, morbidity and mortality [1]. Sudan has a high burden of tuberculosis. Spoligotyping (spacer oligonucleotide typing) a rapid method for genotyping of Mycobacterium tuberculosis using the principle of reverse hybridization. The ecology of the prevalent mycobacteria strain can vary depending on country and region. The aim of this study was to determine the genotyping of Mycobacterium tuberculosis isolated from Sudan using spoligotyping SPOLDB4. A total of 75 Mycobacterium tuberculosis sputum samples were collected from pulmonary Tuberculosis patients attending references Laboratories and diagnostic centers in Khartoum and Eastern Sudan in (2011-2013). The mycobacteria were genotyped using Spoligotyping technique and data obtained were analyzed and compared to the SPOLDB4 database. Among the 75 isolate analyzed, 57(76%) were identified by SPOLDB4 and 18 (24%) could not be matched to any lineages. The most prevalent genotype cluster was MANU2 38 (50.7%) followed by CASI Delhi 8 (10.7%). In the study SIT54 was the most common pattern 37 (49.3%) followed by SIT25 6(8%).

Keywords:
spoligotyping mycobacterium tuberculosis Sudan

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References:

[1]	Martin, G., and Lazarus, A. (2000). Epidemiology and Diagnosis of Tuberculosis. Recognition of At-risk Patients is Key to Detection, Postgrad. Med. 108:42-44, 47-50, 53-54.
[2]	World Health Organization. 2014. Global Tuberculosis report.
[3]	World Health Organization. 2014. Multidrug resistant Tuberculosis (MDR-TB) Report.
[4]	World Health Organization/IUATLD. 2003. Global Project on Anti-tuberculosis drug resistance Surveillance, report No 3, Geneva.
[5]	Mostro¨m P., Gordon, M., Sola, C., Ridell, M., and Rastogi, N. 2002. Methods used in the molecular epidemiology of tuberculosis. Clin.Microbiol. Infect. 8:694-704.
[6]	van Soolingen, D. 2001. Molecular epidemiology of tuberculosis and other mycobacterial infections: main methodologies and achievements. J. Intern. Med. 249:1-26.
[7]	Al-Hajoj, S. A., Zozio, T., Al-Rabiah, F., Mohammad, V., Al-Nasser, M., Sola, C., and Rastogi, N. 2007. First insight into the population structure of Mycobacterium tuberculosis in Saudi Arabia. J. Clin. Microbiol. 45:2467 2473.
[8]	Brudey, K., Filliol, I., Ferdinand, S., Guernier, V., Duval, P., Maubert, B., Sola, C., and Rastogi, N. 2006. Long-term population-based genotyping study of Mycobacterium tuberculosis complex isolates in the French departments of the Americas. J. Clin. Microbiol. 44:183-191.
[9]	Mokrousov, I. 2007. Towards a quantitative perception of human-microbial co-evolution. Front. Biosci. 12:4818-4825.
[10]	Mokrousov, I., Ly, H. M., Otten, T., Lan, N. N., Vyshnevskyi, B., Hoffner S., and Narvskaya, O. 2005. Origin and primary dispersal of the Mycobacterium tuberculosis Beijing genotype: clues from human phylogeography. Genome Res. 15:1357-1364.
[11]	Mokrousov, I., Narvskaya, O. Limeschenko, E. Vyazovaya, A., Otten, T., and Vyshnevskiy, B. 2004. Analysis of the allelic diversity of the mycobacterial interspersed repetitive units in Mycobacterium tuberculosis strains of the Beijing family: practical implications and evolutionary considerations. J. Clin. Microbiol. 42:2438-2444.
[12]	Mostro¨m, P., Gordon, M., Sola, C., Ridell, M., and Rastogi, N. 2002. Methods used in the molecular epidemiology of tuberculosis. Clin. Microbiol. Infect. 8:694-704.
[13]	Narvskaya, O., Mokrousov, I., Otten, T., and Vishnevsky. B. 2005. Molecular markers: application for studies of the Mycobacterium tuberculosis population in Russia. ISBN 1-59454-372-0 Nova science publisher, Inc. p. 111-125.
[14]	Sola, C., Filliol, I., Legrand, E., Mokrousov, I., and Rastogi. N. 2001. Mycobacterium tuberculosis phylogeny reconstruction based on combined numerical analysis with IS1081, IS6110, VNTR, and DR-based spoligotyping suggests the existence of two new phylogeographical clades. J. Mol. 53: 680-689.
[15]	Zozio, T., Allix, C., Gunal, S., Saribas, Z., Alp, A., Durmaz, R., Fauville-Dufaux, M., Rastogi, N., and Sola. C. 2005. Genotyping of Mycobacterium tuberculosis clinical isolates in two cities of Turkey: description of a new family of genotypes that is phylogeographically specific for Asia Minor. BMC Microbiol. 5:44.
[16]	Brudey, K., Driscoll, J. R., Rigouts, L., Prodinger, W. M., Gori, A., Al-Hajoj, S. A., Allix, C., Aristimuno, L., Arora, J., Baumanis, V., Binder, L. et al., 2006. Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology. BMC Microbiol. 6:23.
[17]	Filliol, I., Driscoll, J. R., van Soolingen, D., Kreiswirth, B. N., Kremer, K., Valetudie, G., Dang, D. A., Barlow, R., Banerjee, D., Bifani, P. J., Brudey, K. et al., 2003. Snapshot of moving and expanding clones of Mycobacterium tuberculosis and their global distribution assessed by spoligotyping in an international study. J. Clin. Microbiol. 41:1963-1970.
[18]	Weniger, T., Harmsen, D., Supply, P. and Niemann, S. 2007. Mycobacteria MIRU VNTR plus: online database and analysis tool for MIRU, spoligo, and regions of difference data. Abstr. 107th Gen. Meet. Am. Soc. Microbiol. U-024. 688-689.
[19]	Hain Lifescience [http:/ / www.hain-lifescience.de/ en/ products/ microbiology/ mycobacteria/ genotype-mtbdrplus.html] webcite Genotype® MTBDRplus product insert. Version 1.
[20]	Kamerbeek, J., Schouls, L., Kolk, A., van Agterveld, M., van Soolingen, D., Kuijper, S., Bunschoten, A., Molhuizen, H., Shaw, R., Goyal, M., and van Embden, J. 1997. Rapid detection and simultaneous strain differentiation of Mycobacterium tuberculosis for diagnosis and tuberculosis control. J. Clin. Microbiol. 35:907-914.
[21]	Sharaf -Eldin, G S., Saeed, N S., Hamid, M E., Jordaan, A M., Van der Spuy, G D., Warren, R M., Van Helden, P D., and Victor, T C. 2002. Molecular analysis of clinical isolates of Mycobacterium tuberculosis collected from patients with persistent disease in the Khartoum region of Sudan. J. Infect. 44(4):244-251.
[22]	Sharaf Eldin, GS., Fadl-Elmula, I., Ali, MS., Ali, AB., Salih, AL., Mallard, K., Bottomley, C., and McNerney, R. 2011. Tuberculosis in Sudan: a study of Mycobacterium tuberculosis strain genotype and susceptibility to anti-tuberculosis drugs. BMC infectious Diseases. 11: 219.
[23]	Belay, M., Ameni,G., Bjune, G., Couvin, D., Rastogi, N., and Abebe, F. 2014. Strain Diversity of Mycobacterium tuberculosis Isolates from Pulmonary Tuberculosis Patients in Afar Pastoral Region of Ethiopia. BioMed Research International. Volume 2014 Article ID 238532, 12 pages.