title: Genomic diversity among Beijing and non-Beijing Mycobacterium tuberculosis isolates from Myanmar.
abstract: BACKGROUND
  The Beijing family of Mycobacterium tuberculosis is dominant in countries in East Asia. Genomic polymorphisms are a source of diversity within the M. tuberculosis genome and may account for the variation of virulence among M. tuberculosis isolates. Till date there are no studies that have examined the genomic composition of M. tuberculosis isolates from the high TB-burden country, Myanmar.
  
  
  RESULTS
  Twenty-two M. tuberculosis isolates from Myanmar were screened on whole-genome arrays containing genes from M. tuberculosis H37Rv, M. tuberculosis CDC1551 and M. bovis AF22197. Screening identified 198 deletions or extra regions in the clinical isolates compared to H37Rv. Twenty-two regions differentiated between Beijing and non-Beijing isolates and were verified by PCR on an additional 40 isolates. Six regions (Rv0071-0074 [RD105], Rv1572-1576c [RD149], Rv1585c-1587c [RD149], MT1798-Rv1755c [RD152], Rv1761c [RD152] and Rv0279c) were deleted in Beijing isolates, of which 4 (Rv1572-1576c, Rv1585c-1587c, MT1798-Rv1755c and Rv1761c) were variably deleted among ST42 isolates, indicating a closer relationship between the Beijing and ST42 lineages. The TbD1 region, Mb1582-Mb1583 was deleted in Beijing and ST42 isolates. One M. bovis gene of unknown function, Mb3184c was present in all isolates, except 11 of 13 ST42 isolates. The CDC1551 gene, MT1360 coding for a putative adenylate cyclase, was present in all Beijing and ST42 isolates (except 1). The pks15/1 gene, coding for a putative virulence factor, was intact in all Beijing and non-Beijing isolates, except in ST42 and ST53 isolates.
  
  
  CONCLUSIONS
  This study describes previously unreported deletions/extra regions in Beijing and non-Beijing M. tuberculosis isolates. The modern and highly frequent ST42 lineage showed a closer relationship to the hypervirulent Beijing lineage than to the ancient non-Beijing lineages. The pks15/1 gene was disrupted only in modern non-Beijing isolates. This is the first report of an in-depth analysis on the genomic diversity of M. tuberculosis isolates from Myanmar.
authors.affiliation: Section for Microbiology and Immunology, The Gade Institute, University of Bergen, Bergen, Norway.
authors.forename: Ruth
authors.initials: R
authors.lastname: Stavrum
authors.forename: Håvard
authors.initials: H
authors.lastname: Valvatne
authors.forename: Trond H
authors.initials: TH
authors.lastname: Bø
authors.forename: Inge
authors.initials: I
authors.lastname: Jonassen
authors.forename: Jason
authors.initials: J
authors.lastname: Hinds
authors.forename: Philip D
authors.initials: PD
authors.lastname: Butcher
authors.forename: Harleen M S
authors.initials: HM
authors.lastname: Grewal
mesh_terms: D002681:China; D017353:Gene Deletion; D014644:Genetic Variation; D016680:Genome, Bacterial; D002052:Myanmar; D009169:Mycobacterium tuberculosis / Q000378:metabolism* / Q000472:pathogenicity; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D018088:Tuberculosis, Multidrug-Resistant / Q000382:microbiology*; D014774:Virulence