title: Mycobacterium tuberculosis genotypic drug resistance patterns and clustering in Jayapura, Papua, Indonesia.
abstract: BACKGROUND
  Little is known about drug-resistant tuberculosis (TB) and its transmission in Papua, which has one of the highest rates of TB in Indonesia.
  
  
  METHODS
  We examined genotypic drug resistance patterns using multiplex ligation-dependent probe amplification and the degree of molecular clustering using 24-locus mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) among 199 consecutive pulmonary TB patients in Jayapura, Papua.
  
  
  RESULTS
  Drug resistance mutations were present in 30/198 (15.2%) patients: 16/144 (11.1%) primary cases and 14/51 (27.5%) retreatment cases. Genotypic resistance to rifampicin was found in 15 (7.6%) patients, to isoniazid in 19 (9.6%), to ethambutol in 7 (3.5%), and to streptomycin and second-line injectable drugs in 5 (2.5%) patients. Eight (4.0%) patients had multidrug-resistant TB, while no mutations were found for fluoroquinolones. The most common lineage found among all isolates was East-African Indian (n = 66, 33.7%), followed by Euro-American (n = 38, 19.4%). Drug resistance mutations were more common among Beijing strains than other lineages. Of the 30 drug-resistant isolates, 12 (40.0%) fell into four clusters that were separate from drug-susceptible clusters as determined using MIRU-VNTR.
  
  
  CONCLUSIONS
  These are the first genotypic drug resistance data from Jayapura, Papua, showing moderate rates of resistance to first-line drugs and likely transmission of drug-resistant TB.
authors: Laboratory for Health Research and Community Service, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia.
authors: L
authors: L
authors: Chaidir
authors: KIT Biomedical Research, Royal Tropical Institute (KIT), Amsterdam, The Netherlands.
authors: S
authors: S
authors: Sengstake
authors: Tuberculosis Reference Laboratory, Center for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the Environment, Bilthoven, The Netherlands.
authors: J
authors: J
authors: de Beer
authors: Papua Biomedical Research Centre, National Institute of Health Research and Development, The Indonesian Ministry of Health, Jayapura, Papua, Indonesia.
authors: H
authors: H
authors: Krismawati
authors: Jayapura General Hospital, Jayapura, Papua, Indonesia.
authors: F D
authors: FD
authors: Lestari
authors: Papua Provincial Referral Laboratory, Jayapura, Papua, Indonesia.
authors: S
authors: S
authors: Ayawaila
authors: Tuberculosis Reference Laboratory, Center for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the Environment, Bilthoven, The Netherlands; Department of Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands.
authors: D
authors: D
authors: van Soolingen
authors: KIT Biomedical Research, Royal Tropical Institute (KIT), Amsterdam, The Netherlands.
authors: R
authors: R
authors: Anthony
authors: Department of Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands.
authors: R
authors: R
authors: van Crevel
authors: Laboratory for Health Research and Community Service, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia.
authors: B
authors: B
authors: Alisjahbana
mesh_terms: D000328:Adult; D000995:Antitubercular Agents / Q000627:therapeutic use*; D016000:Cluster Analysis; D005260:Female; D005838:Genotype; D006801:Humans; D007214:Indonesia; D008297:Male; D058889:Molecular Typing; D060885:Multiplex Polymerase Chain Reaction; D009154:Mutation; D009169:Mycobacterium tuberculosis / Q000187:drug effects* / Q000235:genetics* / Q000302:isolation & purification; D018088:Tuberculosis, Multidrug-Resistant / Q000382:microbiology*; D014397:Tuberculosis, Pulmonary / Q000382:microbiology*; D055815:Young Adult
chemical_list: D000995:Antitubercular Agents