title: Predominance of modern Mycobacterium tuberculosis strains and active transmission of Beijing sublineage in Jayapura, Indonesia Papua.
abstract: Mycobacterium tuberculosis genotype distribution is different between West and Central Indonesia, but there are no data on the most Eastern part, Papua. We aimed to identify the predominant genotypes of M. tuberculosis responsible for tuberculosis in coastal Papua, their transmission, and the association with patient characteristics. A total of 199 M. tuberculosis isolates were collected. Spoligotyping was applied to describe the population structure of M. tuberculosis, lineage identification was performed using a combination of lineage-specific markers, and genotypic clusters were identified using a combination of 24-locus-MIRU-VNTR and spoligotyping. A high degree of genetic diversity was observed among isolates based on their spoligopatterns. Strains from modern lineage 4 made up almost half of strains (46.9%), being more abundant than the ancient lineage 1 (33.7%), and modern lineage 2 (19.4%). Thirty-five percent of strains belonged to genotypic clusters, especially strains in the Beijing genotype. Previous TB treatment and mutations associated with drug resistance were more common in patients infected with strains of the Beijing genotype. Papua shows a different distribution of M. tuberculosis genotypes compared to other parts of Indonesia. Clustering and drug resistance of modern strains recently introduced to Papua may contribute to the high tuberculosis burden in this region.
authors.affiliation: Faculty of Medicine, Universitas Padjadjaran, Eijkman 38 Bandung, Indonesia. Electronic address: lidya.chaidir@gmail.com.
authors.forename: Lidya
authors.initials: L
authors.lastname: Chaidir
authors.affiliation: KIT Biomedical Research, Royal Tropical Institute, Mauritskade 63, 1092 AD, Amsterdam, The Netherlands.
authors.forename: Sarah
authors.initials: S
authors.lastname: Sengstake
authors.affiliation: Tuberculosis Reference Laboratory, Center for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA, Bilthoven, The Netherlands.
authors.forename: Jessica
authors.initials: J
authors.lastname: de Beer
authors.affiliation: Papua Biomedical Research Center, National Institute for Health Research, Indonesian Ministry of Health, Jl Kesehatan 10, Dok II, Jayapura, Papua, Indonesia.
authors.forename: Antonius
authors.initials: A
authors.lastname: Oktavian
authors.affiliation: Papua Biomedical Research Center, National Institute for Health Research, Indonesian Ministry of Health, Jl Kesehatan 10, Dok II, Jayapura, Papua, Indonesia.
authors.forename: Hana
authors.initials: H
authors.lastname: Krismawati
authors.affiliation: Department of Pulmonology, Jayapura General Hospital, Jl Kesehatan 1, Dok II, Jayapura, Papua, Indonesia.
authors.forename: Erfin
authors.initials: E
authors.lastname: Muhapril
authors.affiliation: Faculty of Medicine, Universitas Padjadjaran, Eijkman 38 Bandung, Indonesia.
authors.forename: Inri
authors.initials: I
authors.lastname: Kusumadewi
authors.affiliation: Faculty of Medicine, Universitas Padjadjaran, Eijkman 38 Bandung, Indonesia.
authors.forename: Jessi
authors.initials: J
authors.lastname: Annisa
authors.affiliation: KIT Biomedical Research, Royal Tropical Institute, Mauritskade 63, 1092 AD, Amsterdam, The Netherlands.
authors.forename: Richard
authors.initials: R
authors.lastname: Anthony
authors.affiliation: Tuberculosis Reference Laboratory, Center for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA, Bilthoven, The Netherlands; Department of Medical Microbiology, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6500 HB, Nijmegen, The Netherlands.
authors.forename: Dick
authors.initials: D
authors.lastname: van Soolingen
authors.affiliation: Faculty of Medicine, Universitas Padjadjaran, Eijkman 38 Bandung, Indonesia.
authors.forename: Tri Hanggono
authors.initials: TH
authors.lastname: Achmad
authors.affiliation: Eijkman Institute for Molecular Biology, Jl Diponegoro 69, Jakarta, Indonesia.
authors.forename: Sangkot
authors.initials: S
authors.lastname: Marzuki
authors.affiliation: Faculty of Medicine, Universitas Padjadjaran, Eijkman 38 Bandung, Indonesia; Department of Internal Medicine, Hasan Sadikin Hospital, Jl Pasteur 38, Bandung, Indonesia.
authors.forename: Bachti
authors.initials: B
authors.lastname: Alisjahbana
authors.affiliation: Department of Medicine, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6500 HB Nijmegen, The Netherlands.
authors.forename: Reinout
authors.initials: R
authors.lastname: van Crevel
mesh_terms: D000328:Adult; D019143:Evolution, Molecular; D005260:Female; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D007214:Indonesia / Q000453:epidemiology; D008297:Male; D018598:Minisatellite Repeats; D058889:Molecular Typing; D009169:Mycobacterium tuberculosis / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny; D014376:Tuberculosis / Q000453:epidemiology / Q000382:microbiology* / Q000635:transmission*; D055815:Young Adult
keywords: 24-Locus MIRU-VNTR; Genotype distribution; M. tuberculosis lineage; Spoligotyping; Transmission