title: Molecular typing of Mycobacterium tuberculosis complex isolated from pulmonary tuberculosis patients in central Ethiopia.
abstract: Identification of the types of strains of Mycobacterium tuberculosis (M. tuberculosis) complex causing tuberculosis (TB) could contribute to TB control program of specific geographic region as well as it could add knowledge onto the existing literature on TB worldwide. The objective of the present study was to identify the species and strains of M. tuberculosis complex causing pulmonary tuberculosis in central Ethiopia.
  
  
  
  A health institution- based cross-sectional study was conducted on 338 smear positive TB cases visiting three hospitals between October 2012 and September 2013. Morning and spot sputum samples were collected before the starting of treatment regimens. Thus, a total of 338 pooled sputum samples collected from these cases. Samples were cultured on Löwenstein Jensen media and the isolates were identified by the region of difference (RD) 9 based polymerase chain reaction (PCR) and spoligotyping.
  
  
  
  Of the total isolates 98.6% of the isolates were identified to be M. tuberculosis while the remaining 1.4% were identified as M. africanum. Further, typing of M. tuberculosis using spoligotyping lead to the identification of 90 different strains of M. tuberculosis. Of these strains, 32 were clustered consisting of more than one isolate while the remaining 58 strains were unique consisting of single isolate. Thus, 79.3% (223/281) of the isolates were found in the clustered while only 20.6% (58/281) of the strains were unique. Forty-five of the spolgotyping patterns were registeredin the SITVIT2 or SpolDB4 database in while the remaining 45 were notfound in the database and hence were orphan strains. The dominant strains were SIT53, SIT149, and SIT54, consisting of 43, 37 and 34 isolates, respectively. Classification of the spoligotype patterns using TB-insight RUN TB-Lineage showed that 86.8, 6.4, 5, 1.4% ofthe isolatesbelonged to the Euro-American lineage, East-African-Indian, Indo-oceanic and M. africanum, respectively.
  
  
  
  The identification of clustered and new strains using spolygotyping in present study does not give conclusive finding as spoligotyping has low discriminatory power. Thus, further identification of these isolates using mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VENTR) and or whole genome sequencing (WGS) recommended.
authors.affiliation: Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia.|College of Natural Sciences, Microbial, Cellular and Molecular Biology Department, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia.|College of Natural Science and Computational Science, Department of Biology, Hawassa University, P.O. Box 05, Hawassa, Ethiopia.
authors.forename: Zufan
authors.initials: Z
authors.lastname: Bedewi
authors.affiliation: Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia.
authors.forename: Adane
authors.initials: A
authors.lastname: Worku
authors.affiliation: College of Natural Sciences, Microbial, Cellular and Molecular Biology Department, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia.
authors.forename: Yalemtsehay
authors.initials: Y
authors.lastname: Mekonnen
authors.affiliation: College of Health Sciences, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia.
authors.forename: Getnet
authors.initials: G
authors.lastname: Yimer
authors.affiliation: Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia.
authors.forename: Girmay
authors.initials: G
authors.lastname: Medhin
authors.affiliation: College of Veterinary Medicine and Agriculture, Addis Ababa University, P.O. Box 34, DebreZeit, Ethiopia.
authors.forename: Gezahegne
authors.initials: G
authors.lastname: Mamo
authors.affiliation: J.Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, USA.
authors.forename: Rembert
authors.initials: R
authors.lastname: Pieper
authors.affiliation: Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia. gobena.ameni@aau.edu.et.
authors.forename: Gobena
authors.initials: G
authors.lastname: Ameni
mesh_terms: D000328:Adult; D003430:Cross-Sectional Studies; D016208:Databases, Factual; D005002:Ethiopia; D005260:Female; D005838:Genotype; D006801:Humans; D008297:Male; D008875:Middle Aged; D058889:Molecular Typing; D009169:Mycobacterium tuberculosis / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D016133:Polymerase Chain Reaction; D014397:Tuberculosis, Pulmonary / Q000382:microbiology*
keywords: Central Ethiopia; Diversity of strain; M. tuberculosis