title: Strain diversity of Mycobacterium tuberculosis isolates from pulmonary tuberculosis patients in Afar pastoral region of Ethiopia.
abstract: Data on genotypic diversity of Mycobacterium tuberculosis complex (MTBC) is important to understand its epidemiology, human adaptation, clinical phenotypes, and drug resistance. This study aimed to characterize MTBC clinical isolates circulating in a predominantly pastoralist area in Ethiopia, a country where tuberculosis is the second leading cause of mortality. Culture of sputum samples collected from a total of 325 pulmonary TB suspects was done to isolate MTBC. Spoligotyping was used to characterize 105 isolates from culture positive slopes and the result was compared with an international database. Forty-four spoligotype patterns were observed to correspond to 35 shared-types (SITs) containing 96 isolates and 9 orphan patterns; 27 SITs containing 83 isolates matched a preexisting shared-type in the database, whereas 8 SITs (n = 13 isolates) were newly created. A total of 19 SITs containing 80 isolates were clustered within this study (overall clustering of 76.19%). Three dominant lineages (T, CAS, and Manu) accounted for 76.19% of the isolates. SIT149/T3-ETH was one of the two most dominant sublineages. Unlike previous reports, we show that Manu lineage strains not only constitute a dominant lineage, but are also associated with HIV infection in Afar region of Ethiopia. The high level of clustering suggests the presence of recent transmission that should be further studied using additional genotyping markers.
authors.affiliation: Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia ; Section for International Health, Department of Community Medicine, Institute for Health and Society, University of Oslo, P.O. Box 1130, Blindern, 0318 Oslo, Norway.
authors.forename: Mulugeta
authors.identifier: 0000-0001-6901-0037
authors.initials: M
authors.lastname: Belay
authors.affiliation: Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia.
authors.forename: Gobena
authors.initials: G
authors.lastname: Ameni
authors.affiliation: Section for International Health, Department of Community Medicine, Institute for Health and Society, University of Oslo, P.O. Box 1130, Blindern, 0318 Oslo, Norway.
authors.forename: Gunnar
authors.initials: G
authors.lastname: Bjune
authors.affiliation: WHO Supranational TB Reference Laboratory, TB & Mycobacteria Unit, Institut Pasteur de la Guadeloupe, 97183 Abymes, France.
authors.forename: David
authors.identifier: 0000-0002-7897-9023
authors.initials: D
authors.lastname: Couvin
authors.affiliation: WHO Supranational TB Reference Laboratory, TB & Mycobacteria Unit, Institut Pasteur de la Guadeloupe, 97183 Abymes, France.
authors.forename: Nalin
authors.identifier: 0000-0002-7199-7747
authors.initials: N
authors.lastname: Rastogi
authors.affiliation: Section for International Health, Department of Community Medicine, Institute for Health and Society, University of Oslo, P.O. Box 1130, Blindern, 0318 Oslo, Norway.
authors.forename: Fekadu
authors.identifier: 0000-0002-4368-1593
authors.initials: F
authors.lastname: Abebe
mesh_terms: D000328:Adult; D003430:Cross-Sectional Studies; D016208:Databases, Factual; D005002:Ethiopia / Q000453:epidemiology; D005260:Female; D005819:Genetic Markers; D005838:Genotype; D015658:HIV Infections / Q000150:complications; D006801:Humans; D008297:Male; D017720:Molecular Epidemiology; D009169:Mycobacterium tuberculosis / Q000378:metabolism*; D010641:Phenotype; D013045:Species Specificity; D013183:Sputum / Q000378:metabolism; D014397:Tuberculosis, Pulmonary / Q000453:epidemiology* / Q000382:microbiology*; D055815:Young Adult
chemical_list: D005819:Genetic Markers
references.citation: Ecohealth. 2012 Jun;9(2):139-49
references.pmid: 22526748
references.citation: J Clin Microbiol. 2009 Sep;47(9):2794-801
references.pmid: 19553569
references.citation: Infect Genet Evol. 2003 Jul;3(2):125-33
references.pmid: 12809807
references.citation: Lancet. 2003 Sep 13;362(9387):887-99
references.pmid: 13678977
references.citation: Bioinformatics. 2008 Oct 15;24(20):2414-5
references.pmid: 18710872
references.citation: Infect Genet Evol. 2012 Jun;12(4):798-806
references.pmid: 21920466
references.citation: J Clin Microbiol. 2006 Dec;44(12):4498-510
references.pmid: 17005759
references.citation: BMC Public Health. 2012 May 23;12:369
references.pmid: 22621312
references.citation: Tuberc Res Treat. 2012;2012:892079
references.pmid: 23227330
references.citation: J Clin Microbiol. 2013 Jan;51(1):299-302
references.pmid: 23115266
references.citation: Curr Opin Pulm Med. 2000 May;6(3):174-9
references.pmid: 10782699
references.citation: Vet Med Int. 2012;2012:869146
references.pmid: 22852105
references.citation: Nat Genet. 2013 Oct;45(10):1176-82
references.pmid: 23995134
references.citation: PLoS Pathog. 2005 Sep;1(1):e5
references.pmid: 16201017
references.citation: PLoS One. 2011 Jan 24;6(1):e15862
references.pmid: 21283668
references.citation: BMC Bioinformatics. 2008 Nov 27;9:496
references.pmid: 19036166
references.citation: Clin Microbiol Infect. 2010 Jul;16(7):1023-6
references.pmid: 19694762
references.citation: PLoS One. 2012;7(1):e30331
references.pmid: 22279583
references.citation: J Clin Microbiol. 1997 Apr;35(4):907-14
references.pmid: 9157152
references.citation: Science. 2010 May 14;328(5980):856-61
references.pmid: 20466923
references.citation: J Clin Microbiol. 2001 Oct;39(10):3563-71
references.pmid: 11574573
references.citation: J Clin Microbiol. 2002 Nov;40(11):4230-4
references.pmid: 12409403
references.citation: Emerg Infect Dis. 2013 Mar;19(3):460-3
references.pmid: 23622814
references.citation: BMC Infect Dis. 2013 Mar 11;13:131
references.pmid: 23496968
references.citation: Infect Genet Evol. 2012 Jun;12(4):755-66
references.pmid: 22365971
references.citation: BMC Infect Dis. 2012 Mar 13;12:54
references.pmid: 22414165
references.citation: Int J Tuberc Lung Dis. 2010 Oct;14(10):1259-65
references.pmid: 20843416
references.citation: Int J Tuberc Lung Dis. 2013 Aug;17(8):1076-81
references.pmid: 23827032
references.citation: PLoS One. 2012;7(12):e52841
references.pmid: 23300794