title: Temporal dynamics of Mycobacterium tuberculosis genotypes in New South Wales, Australia.
abstract: BACKGROUND
  Molecular epidemiology of Mycobacterium tuberculosis, its transmission dynamics and population structure have become important determinants of targeted tuberculosis control programs. Here we describe recent changes in the distribution of M. tuberculosis genotypes in New South Wales (NSW), Australia and compared strain types with drug resistance, site of disease and demographic data.
  
  
  METHODS
  We evaluated all culture-confirmed newly identified tuberculosis cases in NSW, Australia, from 2010-2012. M. tuberculosis population structure and clustering rates were assessed using 24-loci Mycobacterial interspersed repetitive unit (MIRU) analysis and compared to MIRU data from 2006-2008.
  
  
  RESULTS
  Of 1177 tuberculosis cases, 1128 (95.8%) were successfully typed. Beijing and East African Indian (EAI) lineage strains were most common (27.6% and 28.5%, respectively) with EAI strains increasing in relative abundance from 11.8% in 2006-2008 to 28.5% in 2010-2012. Few cases of multi-drug resistant tuberculosis were identified (18; 1.7%). Compared to 12-loci, 24-loci MIRU provided improved cluster resolution with 695 (61.6%) and 227 (20.1%) clustered cases identified, respectively. Detailed analysis of the largest cluster identified (an 11 member Beijing cluster) revealed wide geographic diversity in the absence of documented social contact.
  
  
  CONCLUSIONS
  EAI strains of M. tuberculosis recently overtook Beijing family as a prevalent cause of tuberculosis in NSW, Australia. This lineage appeared to be less commonly related to multi-drug resistant tuberculosis as compared to Beijing strain lineage. The resolution provided by 24-loci MIRU typing was insufficient for reliable assessment of transmissions, especially of Beijing family strains.
authors.forename: Ulziijargal
authors.initials: U
authors.lastname: Gurjav
authors.forename: Peter
authors.initials: P
authors.lastname: Jelfs
authors.forename: Nadine
authors.initials: N
authors.lastname: McCallum
authors.forename: Ben J
authors.initials: BJ
authors.lastname: Marais
authors.affiliation: Sydney Medical School and the Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia. vitali.sintchenko@sydney.edu.au.
authors.forename: Vitali
authors.initials: V
authors.lastname: Sintchenko
mesh_terms: D000293:Adolescent; D000328:Adult; D015373:Bacterial Typing Techniques; D005838:Genotype; D006801:Humans; D008875:Middle Aged; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D009517:New South Wales / Q000453:epidemiology; D010802:Phylogeny; D015995:Prevalence; D014376:Tuberculosis / Q000453:epidemiology / Q000382:microbiology*; D018088:Tuberculosis, Multidrug-Resistant / Q000453:epidemiology / Q000382:microbiology; D055815:Young Adult