Currrent Issue: Volume 3, Number 4, 2015


16S rRNA Amplicons Survey Revealed Unprecedented Bacterial Community in Solid Biomedical Wastes

1The Nelson Mandela African Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania

2BecA-ILRI Hub International Livestock Research Institute, P. O. Box 30709, Nairobi, Kenya

3Departments of Biochemistry and Molecular Biology, W238A Millennium Science Complex University Park, PA 16802, Penn State University, USA

4Huck Institutes of Life Sciences, Department of Veterinary and Biomedical Sciences, 205 Wartik Laboratories, The Pennsylvania State University, University Park, PA 16802, USA

5Genome Sciences Centre, Faculty of Veterinary Medicine, Sokoine University of Agriculture, Morogoro, Tanzania

American Journal of Microbiological Research. 2015, 3(4), 135-143
doi: 10.12691/ajmr-3-4-3
Copyright © 2015 Science and Education Publishing

Cite this paper:
Kilaza Samson MWAIKONO, Solomon Maina, Aswathy Sebastian, Vivek Kapur, Paul Gwakisa. 16S rRNA Amplicons Survey Revealed Unprecedented Bacterial Community in Solid Biomedical Wastes. American Journal of Microbiological Research. 2015; 3(4):135-143. doi: 10.12691/ajmr-3-4-3.

Correspondence to: Kilaza  Samson MWAIKONO, The Nelson Mandela African Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania. Email:


Despite known risks of inappropriate disposal of biomedical solid waste; most cities in developing countries are still disposing unsorted and untreated solid biomedical waste in common dumpsites. While many studies reported the presence of pathogens in fresh biomedical waste from hospitals, none has reported on the abundance and diversity of bacterial community in aged solid biomedical waste from a common dumpsite. A qualitative survey was done to identify types of solid biomedical waste on the dumpsite. Soils, sludge or washings of biomedical wastes were sampled. Total DNA was extracted and v4 region of 16S rRNA amplicons were sequenced using an Illumina MiSeq platform. A total of 1,706,442 sequences from 15 samples passed quality control. The number of sequences per sample ranged from 70664 to 174456 (mean 121765, SD 35853). Diversity was high with an InvSimpson index of 63 (Range 5 – 496, SD 121). Thirty five phyla were identified, but only 9 accounted for 96% of all sequences. The dominant phyla were Proteobacteria 37.4%, Firmicutes 34.4%, Bacteroidetes 14.1 %, Actinobacteria 5.6% and Chloroflex 1.7%. Catchall analysis predicted a mean of 9399 species per sample. Overall, 31402 operational taxonomic units (OTUs) were detected, however, only 19.8% (6,202) OTUs were found more than ten times. The most predominant OTUs were Proteinclasticum (10.4%), Acinetobacter (6.9), Halomonas (3.9), Pseudomonas (1.7%), Escherichia/Shigella 1.5% and Planococcus (1.3%). Proteiniclasticum spp and Acinetobacter spp were found in 67% (10/15) of all samples at relative abundance of 1%. Taxonomic-to-phenotype mapping revealed the presence of 36.2% related to bacteria involved in dehalogenation, 11.6% degraders of aromatic hydrocarbons, 14.8% chitin degraders, 8.5% chlorophenol degradation and Atrazine metabolism 8.3%. Taxonomy-to human pathogen mapping found 34% related to human pathogens and 39.4% were unknown. Conclusions There’s rich and diverse bacterial community in aged solid biomedical waste. Some of the predominant OTUs are related to bacteria of industrial use. We found a good number of OTUs mapping to human pathogens. Most of OTUs mapped to unknown metabolism and also to group unknown whether they human pathogens or not. To our knowledge, this is the first reports on bacteria related to industrial use from solid biomedical waste. This finding will facilitate to design further research using functional metagenomics to better understand the potential of bacteria from aged solid biomedical waste.



[1]  Acharya A, Gokhale VA, Joshi D: Impact of Biomedical Waste on City Environment: Case Study of Pune, India. Applied Chemistry (IOSR-JAC) 2014, 6(6):7.
[2]  Gidarakos E, Petrantonaki M, Anastasiadou K, Schramm K-W: Characterization and hazard evaluation of bottom ash produced from incinerated hospital waste. Journal of hazardous materials 2009, 172(2):935-942.
[3]  Hossain MS, Santhanam A, Norulaini NN, Omar AM: Clinical solid waste management practices and its impact on human health and environment–A review. Waste Management 2011, 31(4):754-766.
[4]  DeRoos R: Environmental concerns in hospital waste disposal. Hospitals 1974, 48(4):88 passim.
[5]  Hassan MM, Ahmed S, Rahman KA, Biswas T: Pattern of medical waste management: existing scenario in Dhaka City, Bangladesh. BMC Public Health 2008, 8(1):36.
Show More References
[6]  Rastogi V, Rastogi P, Bhatia S: Bacteriological Profile of Biomedical Waste: Management Guidelines. Journal of Indian Academy of Forensic Medicine 2011, 33(2):145-148.
[7]  Boss U, Moli G, Roy G, Prasad K: Biomedical waste generation in Puducherry Government General Hospital and its management implications. Journal of environmental health 2009, 71(9):54-58.
[8]  Yadavannavar M, Berad AS, Jagirdar P: Biomedical waste management: A study of knowledge, attitude, and practices in a tertiary health care institution in Bijapur. Indian journal of community medicine: official publication of Indian Association of Preventive & Social Medicine 2010, 35(1):170.
[9]  Wallace L, Zaltzman R, Burchinal I: Where solid waste comes from; where it goes. Modem hospitals 1972, 121(3):92-95.
[10]  Saini S, Das BK, Kapil A, Nagarajan SS, Sarma R: The study of bacterial flora of different types in hospital waste: evaluation of waste treatment at AIIMS Hospital, New Delhi. Southeast Asian Journal of Tropical Medicine & Public Health 2004, 35(4):986.
[11]  Anitha J, JAYRAAJ IA: Isolation and identification of bacteria in biomedical wastes (BMW). International journal of pharmacy and pharmaceutical sciences 2012, 4(5):386-388.
[12]  Vandecandelaere I, Matthijs N, Van Nieuwerburgh F, Deforce D, Vosters P, De Bus L, Nelis HJ, Depuydt P, Coenye T: Assessment of Microbial Diversity in Biofilms Recovered from Endotracheal Tubes Using Culture Dependent and Independent Approaches. PloS one 2012, 7(6):e38401.
[13]  Riesenfeld CS, Goodman RM, Handelsman J: Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environmental Microbiology 2004, 6(9):981-989.
[14]  Oyeleke S, Istifanus N: The microbiological effects of hospital wastes on the environment. African Journal of Biotechnology 2009, 8(7).
[15]  Illumina: 16S Metagenomic Sequencing Library preparation Guide: 2013.
[16]  Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R: Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the national academy of sciences 2011, 108(Supplement 1):4516-4522.
[17]  Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ: Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and environmental microbiology 2009, 75(23):7537-7541.
[18]  Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO: The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic acids research 2013, 41(D1):D590-D596.
[19]  Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R: UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011, 27(16):2194-2200.
[20]  Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM: Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic acids research 2014, 42(D1):D633-D642.
[21]  Chao A: Nonparametric estimation of the number of classes in a community. Scand J Stat 1984, 11:265–270.
[22]  Chao A, Lee S-M: Estimating the number of classes via sample coverage. Journal of the American statistical Association 1992, 87(417):210-217.
[23]  Chao A, Shen T-J: Nonparametric estimation of Shannon’s index of diversity when there are unseen species in sample. Environmental and ecological statistics 2003, 10(4):429-443.
[24]  Hunter PR, Gaston MA: Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity. Journal of clinical microbiology 1988, 26(11):2465-2466.
[25]  Bunge J: Estimating the number of species with CatchAll. In: Pacific Symposium on Biocomputing: 2011: World Scientific; 2011: 121-130.
[26]  McMurdie PJ, Holmes S: phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PloS one 2013, 8(4):e61217.
[27]  Meadow JF, Altrichter AE, Kembel SW, Moriyama M, O’Connor TK, Womack AM, Brown G, Green JL, Bohannan BJ: Bacterial communities on classroom surfaces vary with human contact. Microbiome 2014, 2(1):7.
[28]  Mitra S, Stärk M, Huson DH: Analysis of 16S rRNA environmental sequences using MEGAN. BMC genomics 2011, 12(Suppl 3):S17.
[29]  Hossain MS, Rahman NNNA, Balakrishnan V, Puvanesuaran VR, Sarker MZI, Kadir MOA: Infectious Risk Assessment of Unsafe Handling Practices and Management of Clinical Solid Waste. International journal of environmental research and public health 2013, 10(2):556-567.
[30]  Costa MC, Arroyo LG, Allen-Vercoe E, Stämpfli HR, Kim PT, Sturgeon A, Weese JS: Comparison of the fecal microbiota of healthy horses and horses with colitis by high throughput sequencing of the V3-V5 region of the 16S rRNA gene. PloS one 2012, 7(7):e41484.
[31]  Suchodolski JS, Markel ME, Garcia-Mazcorro JF, Unterer S, Heilmann RM, Dowd SE, Kachroo P, Ivanov I, Minamoto Y, Dillman EM: The fecal microbiome in dogs with acute diarrhea and idiopathic inflammatory bowel disease. PloS one 2012, 7(12):e51907.
[32]  Suchodolski JS, Xenoulis PG, Paddock CG, Steiner JM, Jergens AE: Molecular analysis of the bacterial microbiota in duodenal biopsies from dogs with idiopathic inflammatory bowel disease. Veterinary Microbiology 2010, 142(3):394-400.
[33]  Bouchotroch S, Quesada E, Izquierdo I, Rodríguez M, Béjar V: Bacterial exopolysaccharides produced by newly discovered bacteria belonging to the genus Halomonas, isolated from hypersaline habitats in Morocco. Journal of Industrial Microbiology and Biotechnology 2000, 24(6):374-378.
[34]  Schwibbert K, Marin‐Sanguino A, Bagyan I, Heidrich G, Lentzen G, Seitz H, Rampp M, Schuster SC, Klenk HP, Pfeiffer F: A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581T. Environmental Microbiology 2011, 13(8):1973-1994.
[35]  Omer MI, Gumaa SA, Hassan AA, Idris KH, Ali OA, Osman MM, Saleh MS, Mohamed NA, Khaled MM: Prevalence and Resistance Profile of Acinetobacter baumannii Clinical Isolates from a Private Hospital in Khartoum, Sudan. American Journal of Microbiological Research 2015, 3(2):76-79.
[36]  Bhattacharya A, Gupta A: Evaluation of Acinetobacter sp. B9 for Cr (VI) resistance and detoxification with potential application in bioremediation of heavy-metals-rich industrial wastewater. Environmental Science and Pollution Research 2013, 20(9):6628-6637.
[37]  Franzetti A, Gandolfi I, Fracchia L, Van Hamme J, Gkorezis P, Marchant R, Banat IM: Biosurfactant use in heavy metal removal from industrial effluents and contaminated sites. Biosurfactants: Production and Utilization—Processes, Technologies, and Economics 2014, 159:361.
[38]  Hossain MS, Santhanam A, Nik Norulaini NA, Omar AKM: Clinical solid waste management practices and its impact on human health and environment – A review. Waste Management 2011, 31(4):754-766.
[39]  Oviasogie FE, Ajuzie CU, Ighodaro UG: Bacterial Analysis of Soil From Waste Dumpsite. Archives of Applied Science Research 2010, 2(5):161-167.
[40]  Pfeifer Y, Cullik A, Witte W: Resistance to cephalosporins and carbapenems in Gram-negative bacterial pathogens. International Journal of Medical Microbiology 2010, 300(6):371-379.
[41]  Ndugulile F, Jureen R, Harthug S, Urassa W, Langeland N: Extended Spectrum β-Lactamases among Gram-negative bacteria of nosocomial origin from an Intensive Care Unit of a tertiary health facility in Tanzania. BMC infectious Diseases 2005, 5(1):86.
[42]  Jensen LB, Baloda S, Boye M, Aarestrup FM: Antimicrobial resistance among Pseudomonas spp. and the Bacillus cereus group isolated from Danish agricultural soil. Environment international 2001, 26(7):581-587.
[43]  Odjadjare EE, Igbinosa EO, Mordi R, Igere B, Igeleke CL, Okoh AI: Prevalence of Multiple Antibiotics Resistant (MAR) Pseudomonas Species in the Final Effluents of Three Municipal Wastewater Treatment Facilities in South Africa. International journal of environmental research and public health 2012, 9(6):2092-2107.
[44]  Khannous L, Jrad M, Dammak M, Miladi R, Chaaben N, Khemakhem B, Gharsallah N, Fendri I: Isolation of a novel amylase and lipase-producing Pseudomonas luteola strain: study of amylase production conditions. Lipids in health and disease 2014, 13(1):9.
[45]  Miyazaki R, Bertelli C, Benaglio P, Canton J, De Coi N, Gharib WH, Gjoksi B, Goesmann A, Greub G, Harshman K et al: Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds. Environmental Microbiology 2015, 17(1):91-104.
[46]  Wasi S, Tabrez S, Ahmad M: Use of Pseudomonas spp. for the bioremediation of environmental pollutants: a review. Environmental monitoring and assessment 2013, 185(10):8147-8155.
[47]  Nandi RG, Joshi M, Shriwastva K: Biodegradation of polyethylene by microorganism isolated from garbage soil. Indian J Applied & Pure Bio Vol 2013, 28(2):279-281.
[48]  48.Xu G, Zheng W, Li Y, Wang S, Zhang J, Yan Y: Biodegradation of chlorpyrifos and 3, 5, 6-trichloro-2-pyridinol by a newly isolated Paracoccus sp. strain TRP. International biodeterioration & biodegradation 2008, 62(1):51-56.
[49]  Dziewit L, Dmowski M, Baj J, Bartosik D: The plasmid pAMI2 of Paracoccus aminophilus JCM 7686 carries genes for the degradation of N, N-dimethylformamide (DMF), whose expression is activated by a LuxR-family regulator. Applied and environmental microbiology 2010.
[50]  Huang C-J, Lin H, Yang X: Industrial production of recombinant therapeutics in Escherichia coli and its recent advancements. Journal of industrial microbiology & biotechnology 2012, 39(3):383-399.
[51]  Thakker C, Martínez I, San KY, Bennett GN: Succinate production in Escherichia coli. Biotechnology journal 2012, 7(2):213-224.
[52]  Na D, Yoo SM, Chung H, Park H, Park JH, Lee SY: Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nature biotechnology 2013, 31(2):170-174.
[53]  Zhang K, Song L, Dong X: Proteiniclasticum ruminis gen. nov., sp. nov., a strictly anaerobic proteolytic bacterium isolated from yak rumen. International journal of systematic and evolutionary microbiology 2010, 60(9): 2221-2225.
[54]  Desta AF, Assefa F, Leta S, Stomeo F, Wamalwa M, Njahira M, Appolinaire D: Microbial Community Structure and Diversity in an Integrated System of Anaerobic-Aerobic Reactors and a Constructed Wetland for the Treatment of Tannery Wastewater in Modjo, Ethiopia. PloS one 2014, 9(12): e115576.
[55]  Khan NH, Bondici VF, Medihala PG, Lawrence JR, Wolfaardt GM, Warner J, Korber DR: Bacterial diversity and composition of an alkaline uranium mine tailings-water interface. Journal of Microbiology 2013, 51(5): 558-569.
[56]  Vester JK, Glaring MA, Stougaard P: Discovery of novel enzymes with industrial potential from a cold and alkaline environment by a combination of functional metagenomics and culturing. Microb Cell Fact 2014, 13:72.
[57]  Subramanian S: Bioprospecting of moderately halophilic bacteria planococcus sp vitp21 for cr vi reduction under high salt condition. 2015.
[58]  Vennila R, Kannan V: Bioremediation of petroleum refinery effluent by Planococcus halophilus. African Journal of Biotechnology 2013, 10(44): 8829-8833.
[59]  Essghaier B, Rouaissi M, Boudabous A, Jijakli H, Sadfi-Zouaoui N: Production and partial characterization of chitinase from a halotolerant Planococcus rifitoensis strain M2-26. World Journal of Microbiology and Biotechnology 2010, 26(6): 977-984.
Show Less References


Immunomodulator Potential of Miana Leaves(Coleus scutellarioides (L) Benth) in Prevention of Tuberculosis Infection

1Health Technology Department, Ministry of Health, Makasssar, Indonesia

2Faculty of Public Health, Airlangga University, Surabaya, Indonesia

3Faculty of Life Sciences and Technology, Airlangga University, Surabaya, Indonesia

4Department of Microbiology, Faculty of Medicine, Tadulako University, Palu, Indonesia

5Molecular Biology and Immunology Laboratory for Infectious Diseases, Microbiology Department, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia

6Department of Microbiology and Immunology, Faculty of Medicine, Mulawarman University, Samarinda, Indonesia

American Journal of Microbiological Research. 2015, 3(4), 129-134
doi: 10.12691/ajmr-3-4-2
Copyright © 2015 Science and Education Publishing

Cite this paper:
Sesilia Rante Pakadang, Chatarina Umbul Wahjuni, Hari Basuki Notobroto, Dwi Winarni, Ressy Dwiyanti, Yadi, Muhammad Sabir, Mochammad Hatta. Immunomodulator Potential of Miana Leaves(Coleus scutellarioides (L) Benth) in Prevention of Tuberculosis Infection. American Journal of Microbiological Research. 2015; 3(4):129-134. doi: 10.12691/ajmr-3-4-2.

Correspondence to: Mochammad  Hatta, Molecular Biology and Immunology Laboratory for Infectious Diseases, Microbiology Department, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia. Email:


Aim, The aim of this study to investigate the immunonomodulator effects of miana leaves (Coleus scutellarioides (L) Benth) on prevention of tuberculosis in wistar rats, Method, Samples of white male Wistar rats were divided into 4 groups, the samples were treated with miana leaves extract (EDM) and then infected by intra tracheal M. tuberculosis H37Rv strain and subsequently given a placebo, EDM and GAB (combined Rifampicin and EDM) and healthy control animals were treated with EDM. In this study we measure the level of Immunomodulatory parameter; the number of T-lymphocytes and CD4 T-cells measured by flowcytometry method, the levels of IFN-γ and TNF-α were measured by ELISA and the number of M. tuberculosis colonies derived from the rat lung in LJ media. Result, Results showed the increasing of T-lymphocytes, CD4 T-Cells, the levels of IFN-γ, TNF-α and decreasing in the number of M. tuberculosis colonies after EDM treatment. Conclusion, Miana leaves extract (Coleus scutellarioides, (L) Benth.) increased the number of T-lymphocytes, CD4 T-cell counts, levels of IFN-γ and TNF-α and decreased in the number of M. tuberculosis colony in infected wistar lung.



[1]  Summary of Health profile of South Sulawesi Province 2012. Makassar: Provincial Health Office of South Sulawesi; 2012.
[2]  (WHO) WHO: Global tuberculosis report 2014. In. Geneva: WHO; 2014.
[3]  Bannister B, Gillespie S, Jones J: Infection Microbiology and Management. Victoria Australia.: Blackwell Publishing Asia Pty Ltd, 2006.
[4]  Robbins C: Pocket companion to Robbins & Cotran Pathologic Basis of Disease,: Elsevier Inc.; 2009.
[5]  Raja A: Immunology of tuberculosis, Review article. Indian J Med Res 2004 120:213-232.
Show More References
[6]  RA. F, Perez TM., Aguilar LD., Rangel MJ., Garcia IE., Pando RH., Parra SE.: Transfer factors as immunotherapy and supplement of chemotherapy in experimental pulmonary tuberculosis. Clinical and Experimental Immunology 2004, 136(2):215-223.
[7]  van Zutphen LFM, Baumans V, Beynen AC: Principles of Laboratory Animal Science. In: A contribute to the humane use and care of animals and to the quality of experimental results. edn. Amsterdam, Netherlands.: Elsevier Science Publishers BV; 1993: 189-270.
[8]  Leon DA., Zumarraga MJ., Oopeza RJ., Gioffre AK., Bernardelli A., Estevez HO., Cataldi AA., Pando RH.: Mycobacterium bovis with different genotypes and from different hosts induce dissimilar immunopathological lesions in a mouse model of tuberculosis. Clinical and Experimental Immunology (2009), 157(1):139-147.
[9]  Arifa M: Mekanisme ekstrak etanol herba Centela asiatica (pegagan) dalam meningkatkan apoptosis sel alveolar makrofag dari jaringan paru tikus yang diinfeksi Mycobacterium tuberculosis,. Surabaya: Universitas Airlangga; 2012.
[10]  Smith J.B., Mangkoewidjojo S.: The Care Breeding and Management of Experimental Animals for Research in the Tropics. International Development Program of Australian Universities and Colleges Limited (IDP) 1987:36-38.
[11]  Singhal A., Aliouat EM, Herve´ M: Experimental Tuberculosis in the Wistar Rat: A Model for Protective Immunity and Control of Infection. PloS one 2011, 6(4):18632.
[12]  Espinosa DAM., Rodriguez VM., Leon DA., Rosales R., Casillas FC., Pando RH.: Therapeutic Effect of Recombinant Adenovirus Encoding Interferon-γ in a Murine Model of progressive Pulmonary Tuberculosis. Molecular Therapy 2008, 16(6):1065-1072.
[13]  Hidayat S, Wahyuni S, Andalusia S: Seri Tumbuhan Obat Berpotensi Hias,. Jakarta: PT. Elex Media Komputindo.; 2008.
[14]  Venkatesha S, Rajaiah R, Berman B: Immunomodulation of Autoimmune Arthritis by Herbal CAM. Evidence Based Complementary and Alternative Medicine; 2011.
[15]  Cooper A.M., Mayer-Barber K.D., Sher A.: Role of Innate Cytokines in Mycobacterial Infection, Review. Mucosal Immunology 2011, 4:232-260.
[16]  Curina G., Paternesi B., Cagiota M., de Gioseppe AM, Forti K., Mazzone P., Pasquali P.: Cellular immune response of mice experimentally infected with Mycobacterium bovis BCG. Oxford Journals; Life Sciences ; Intimm Meeting Abstracts 2010, 22(Suppl 1 Pt 3.):061-063.
[17]  Alvares: Immunoregulatory from IFN-γ,. In. Edited by Department of Biology DC. Davidson; 2005.
[18]  R.J. N, Yu J.J.: Immunity to tuberculosis. Annual Review of Immunology 2004, 22:599-617.
[19]  Kouakou K, Schepetkin I, Jun S, Kirpotina LN: Immunomodulatory activity of polysaccharides isolated from Clerodendrum splendens: Beneficial effects in experimental autoimmune encephalomyelitis. BMC complementary and alternative medicine 2013, 13(149): 1-19.
[20]  Reford P, Boonstra A, Read S, Pitt J: Enhanced protection to Mycobacterium tuberculosis infection in IL-10-deficient mice is accompanied by early and enhanced Th1 responses in the lung. Journal of Immunology 2010, 40(8):2200-2210.
[21]  Green A, DiFazio R: IFN-γ from CD4 T-Cells Is Essential for Host Survival and Enhances CD8 T-cell Function during Mycobacterium tuberculosis Infection. Journal of immunology 2013, 190(1):270-277.
[22]  Cavalcanti VWN, Brelaz M.C.A., de Andrade L.N.J.K., J.C. F, Pereira V.R.A.: Review Article, Role of TNF-Alpha, IFN-Gamma, and IL-10 in the Development of Pulmonary Tuberculosis,. Pulmonary Medicine Volume 2012.
[23]  Mattos AM, Almeida C: Increased IgG1, IFN-g, TNF-a and IL-6 responses to Mycobacterium tuberculosis antigens in patients with Tuberculosis are lower after chemotherapy.. International immunology 2010, 22(9):775-782.
[24]  O'Garra A., Redford P.S., McNab F.W., Bloom C.I., R.J. W, Berry M.P.R.: The Immune Response in Tuberculosis. Annual Review of Immunology 2013, 31:475-527.
Show Less References


Genotyping of Pulmonary Mycobacterium tuberculosis Isolates from Sudan Using Spoligotyping

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

American Journal of Microbiological Research. 2015, 3(4), 125-128
doi: 10.12691/ajmr-3-4-1
Copyright © 2015 Science and Education Publishing

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, 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.

Correspondence to: Muataz  M. Eldirdery, Tropical Medicine Research Institute, National Center for Research, Khartoum, Sudan. Email:


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%).



[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.
Show More References
[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:/ / 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.
Show Less References