title: Genotype diversity of Mycobacterium isolates from children in Jimma, Ethiopia.
abstract: BACKGROUND
  Paediatric tuberculosis (TB) is poorly addressed in Ethiopia and information about its magnitude and the genotype distribution of the causative Mycobacterium tuberculosis strains responsible for its spread are scanty.
  
  
  METHODS
  Gastric lavage or sputum samples were collected from consecutively enrolled TB suspect children visiting Jimma University Hospital in 2011 and cultured on Middlebrook 7H11 and Löwenstein-Jensen media. Acid fast bacterial (AFB) isolates were subjected to molecular typing targeting regions of difference (RDs), 16S rDNA gene and the direct repeat (DR) region using multiplex polymerase chain reaction (mPCR), gene sequencing and spoligotyping, respectively. Molecular drug susceptibility testing of M. tuberculosis isolates was performed by Genotype®MTBDRplus line probe assay (LPA) (Hain Life Sciences, Germany).
  
  
  RESULTS
  Gastric lavage (n = 43) or sputum (n = 58) samples were collected from 101 children and 31.7% (32/101) of the samples were positive for AFB by microscopy, culture and/or PCR. Out of 25 AFB isolates, 60% (15/25) were identified as M. tuberculosis by PCR, and 40% isolates (10/25) were confirmed to be non-tuberculous mycobacteria (NTM) by genus typing and 16S rDNA gene sequencing. Lineage classification assigned the M. tuberculosis strains into Euro-American (EUA, 66.7%; 10/15), East-African-Indian (EAI; 2/15), East-Asian (EA; 1/15) and Indio-Oceanic (IO; 1/15) lineages. Seven M. tuberculosis strains were new to the SpolDB4 database. All of the M. tuberculosis isolates were susceptible to isoniazid (INH) and rifampicin (RIF), except for one strain (of spoligotype SIT-149 or T3_ETH family) which had a mutation at the inhA locus which often confers resistance to INH (low level) and ethionamide.
  
  
  CONCLUSIONS
  Analysis of the genetic population structure of paediatric M. tuberculosis strains suggested similarity with that of adults, indicating an on-going and active transmission of M. tuberculosis from adults to children in Ethiopia. There were no multidrug-resistant TB (MDR-TB) strains among the isolates.
authors.affiliation: Armauer Hansen Research Institute (AHRI/ALERT), Addis Ababa, Ethiopia. bekicho@gmail.com.
authors.forename: Bereket
authors.initials: B
authors.lastname: Workalemahu
authors.forename: Stefan
authors.initials: S
authors.lastname: Berg
authors.forename: Wondewosen
authors.initials: W
authors.lastname: Tsegaye
authors.forename: Alemseged
authors.initials: A
authors.lastname: Abdissa
authors.forename: Tsinuel
authors.initials: T
authors.lastname: Girma
authors.forename: Markos
authors.initials: M
authors.lastname: Abebe
authors.forename: Abraham
authors.initials: A
authors.lastname: Aseffa
mesh_terms: D000293:Adolescent; D000328:Adult; D000995:Antitubercular Agents / Q000627:therapeutic use; D015373:Bacterial Typing Techniques; D002648:Child; D002675:Child, Preschool; D024881:Drug Resistance, Bacterial; D005002:Ethiopia / Q000453:epidemiology; D005751:Gastric Lavage; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D007223:Infant; D007538:Isoniazid / Q000627:therapeutic use; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012293:Rifampin / Q000627:therapeutic use; D013183:Sputum / Q000382:microbiology; D014397:Tuberculosis, Pulmonary / Q000188:drug therapy / Q000453:epidemiology* / Q000382:microbiology / Q000635:transmission
chemical_list: D000995:Antitubercular Agents; D012336:RNA, Ribosomal, 16S; D007538:Isoniazid; D012293:Rifampin