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Djunaedy HAK, Febinia CA, Hamers RL, Baird K, Elyazar I, Thuong NTT, Trimarsanto H, Malik SG, Thwaites G, van Crevel R, Alisjahbana B, Chaidir L, Ashton PM. A description of lineage 1 Mycobacterium tuberculosis from papua, Indonesia. Tuberculosis (Edinb) 2024; 149:102568. [PMID: 39321697 DOI: 10.1016/j.tube.2024.102568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 09/06/2024] [Accepted: 09/12/2024] [Indexed: 09/27/2024]
Abstract
Indonesia has the third highest number of tuberculosis (TB) patients infected with Mycobacterium tuberculosis (MTB) Lineage 1 (L1). Most of these MTB L1 cases can be found in Indonesia's remote easternmost province of Papua, one of Indonesia's most underdeveloped provinces with a particularly high burden for TB. In this study, we sequenced and described 42 MTB L1 isolates from a well-characterized cohort of patients. We found a genetically diverse MTB L1 population with no association between pathogen genetic relatedness and place of residence or pathogen genetic relatedness and patient ethnicity, which could reflect mixing between different locales and ethnicities or our low sampling fraction. Only a small number showed genetic variants associated with drug resistance (5/42, 11.9 %), probably due to a lack of effective treatment programs. The Papuan isolates showed similarities to other Island Southeast Asian Countries due to the high proportion of L1.2.1.2.1 (30/42, 71.4 %), especially East Timor and the Philippines. This study fills a research gap of MTB L1 in Indonesian Papua and should serve as a stepping stone for further research in the region.
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Affiliation(s)
- Hanif A K Djunaedy
- Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia; Research Center for Care and Control of Infectious Diseases, Universitas Padjadjaran, Bandung, Indonesia.
| | - Clarissa A Febinia
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; Division of Biological Anthropology, Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Raph L Hamers
- Oxford University Clinical Research Unit Indonesia, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Kevin Baird
- Oxford University Clinical Research Unit Indonesia, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Iqbal Elyazar
- Oxford University Clinical Research Unit Indonesia, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Nguyen Thuy Thuong Thuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Hidayat Trimarsanto
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; Menzies School of Health Research, Darwin, Australia
| | - Safarina G Malik
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; Mochtar Riady Institute for Nanotechnology, Banten, Indonesia
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Reinout van Crevel
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Bachti Alisjahbana
- Research Center for Care and Control of Infectious Diseases, Universitas Padjadjaran, Bandung, Indonesia; Department of Internal Medicine, Hasan Sadikin General Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Lidya Chaidir
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia; Center for Translational Biomarker Research, Universitas Padjadjaran, Bandung, Indonesia.
| | - Philip M Ashton
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
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2
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Ashton PM, Cha J, Anscombe C, Thuong NTT, Thwaites GE, Walker TM. Distribution and origins of Mycobacterium tuberculosis L4 in Southeast Asia. Microb Genom 2023; 9:mgen000955. [PMID: 36729036 PMCID: PMC9997747 DOI: 10.1099/mgen.0.000955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/21/2022] [Indexed: 02/03/2023] Open
Abstract
Molecular and genomic studies have revealed that Mycobacterium tuberculosis Lineage 4 (L4, Euro-American lineage) emerged in Europe before becoming distributed around the globe by trade routes, colonial migration and other historical connections. Although L4 accounts for tens or hundreds of thousands of tuberculosis (TB) cases in multiple Southeast Asian countries, phylogeographical studies have either focused on a single country or just included Southeast Asia as part of a global analysis. Therefore, we interrogated public genomic data to investigate the historical patterns underlying the distribution of L4 in Southeast Asia and surrounding countries. We downloaded 6037 genomes associated with 29 published studies, focusing on global analyses of L4 and Asian studies of M. tuberculosis. We identified 2256 L4 genomes including 968 from Asia. We show that 81 % of L4 in Thailand, 51 % of L4 in Vietnam and 9 % of L4 in Indonesia belong to sub-lineages of L4 that are rarely seen outside East and Southeast Asia (L4.2.2, L4.4.2 and L4.5). These sub-lineages have spread between East and Southeast Asian countries, with no recent European ancestor. Although there is considerable uncertainty about the exact direction and order of intra-Asian M. tuberculosis dispersal, due to differing sampling frames between countries, our analysis suggests that China may be the intermediate location between Europe and Southeast Asia for two of the three predominantly East and Southeast Asian L4 sub-lineages (L4.2.2 and L4.5). This new perspective on L4 in Southeast Asia raises the possibility of investigating host population-specific evolution and highlights the need for more structured sampling from Southeast Asian countries to provide more certainty of the historical and current routes of dispersal.
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Affiliation(s)
- Philip M. Ashton
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jaeyoon Cha
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Catherine Anscombe
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nguyen T. T. Thuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Guy E. Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Timothy M. Walker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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3
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Guernier-Cambert V, Diefenbach-Elstob T, Klotoe BJ, Burgess G, Pelowa D, Dowi R, Gula B, McBryde ES, Refrégier G, Rush C, Sola C, Warner J. Diversity of Mycobacterium tuberculosis in the Middle Fly District of Western Province, Papua New Guinea: microbead-based spoligotyping using DNA from Ziehl-Neelsen-stained microscopy preparations. Sci Rep 2019; 9:15549. [PMID: 31664101 PMCID: PMC6820861 DOI: 10.1038/s41598-019-51892-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/25/2019] [Indexed: 11/29/2022] Open
Abstract
Tuberculosis remains the world's leading cause of death from an infectious agent, and is a serious health problem in Papua New Guinea (PNG) with an estimated 36,000 new cases each year. This study describes the genetic diversity of Mycobacterium tuberculosis among tuberculosis patients in the Balimo/Bamu region in the Middle Fly District of Western Province in PNG, and investigates rifampicin resistance-associated mutations. Archived Ziehl-Neelsen-stained sputum smears were used to conduct microbead-based spoligotyping and assess genotypic resistance. Among the 162 samples included, 80 (49.4%) generated spoligotyping patterns (n = 23), belonging predominantly to the L2 Lineage (44%) and the L4 Lineage (30%). This is consistent with what has been found in other PNG regions geographically distant from Middle Fly District of Western Province, but is different from neighbouring South-East Asian countries. Rifampicin resistance was identified in 7.8% of the successfully sequenced samples, with all resistant samples belonging to the L2/Beijing Lineage. A high prevalence of mixed L2/L4 profiles was suggestive of polyclonal infection in the region, although this would need to be confirmed. The method described here could be a game-changer in resource-limited countries where large numbers of archived smear slides could be used for retrospective (and prospective) studies of M. tuberculosis genetic epidemiology.
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Affiliation(s)
- Vanina Guernier-Cambert
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland, Australia.
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, 50010, IA, USA.
| | - Tanya Diefenbach-Elstob
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
| | - Bernice J Klotoe
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, Orsay, France
| | - Graham Burgess
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
| | - Daniel Pelowa
- Balimo District Hospital, Balimo, Western Province, Papua New Guinea
| | - Robert Dowi
- Balimo District Hospital, Balimo, Western Province, Papua New Guinea
| | - Bisato Gula
- Balimo District Hospital, Balimo, Western Province, Papua New Guinea
| | - Emma S McBryde
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland, Australia
- Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Melbourne, Victoria, Australia
| | - Guislaine Refrégier
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, Orsay, France
| | - Catherine Rush
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
| | - Christophe Sola
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, Orsay, France
| | - Jeffrey Warner
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
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4
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Klotoe BJ, Kacimi S, Costa-Conceicão E, Gomes HM, Barcellos RB, Panaiotov S, Haj Slimene D, Sikhayeva N, Sengstake S, Schuitema AR, Akhalaia M, Alenova A, Zholdybayeva E, Tarlykov P, Anthony R, Refrégier G, Sola C. Genomic characterization of MDR/XDR-TB in Kazakhstan by a combination of high-throughput methods predominantly shows the ongoing transmission of L2/Beijing 94-32 central Asian/Russian clusters. BMC Infect Dis 2019; 19:553. [PMID: 31234780 PMCID: PMC6592005 DOI: 10.1186/s12879-019-4201-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 06/18/2019] [Indexed: 12/27/2022] Open
Abstract
Background Kazakhstan remains a high-burden TB prevalence country with a concomitent high-burden of multi-drug resistant tuberculosis. For this reason, we performed an in depth genetic diversity and population structure characterization of Mycobacterium tuberculosis complex (MTC) genetic diversity in Kazakhstan with both patient and community benefit. Methods A convenience sample of 700 MTC DNA cultures extracts from 630 tuberculosis patients recruited from 12 out of 14 regions in Kazakhstan, between 2010 and 2015, was independently studied by high-throughput hybridization-based methods, TB-SPRINT (59-Plex, n = 700), TB-SNPID (50-Plex, n = 543). DNA from 391 clinical isolates was successfully typed by two methods. To resolve the population structure of drug-resistant clades in more detail two complementary assays were run on the L2 isolates: an IS6110-NTF insertion site typing assay and a SigE SNP polymorphism assay. Results Strains belonged to L2/Beijing and L4/Euro-American sublineages; L2/Beijing prevalence totaled almost 80%. 50% of all samples were resistant to RIF and to INH., Subtyping showed that: (1) all L2/Beijing were “modern” Beijing and (2) most of these belonged to the previously described 94–32 sublineage (Central Asian/Russian), (3) at least two populations of the Central Asian/Russian sublineages are circulating in Kazakhstan, with different evolutionary dynamics. Conclusions For the first time, the global genetic diversity and population structure of M. tuberculosis genotypes circulating in Kazakhstan was obtained and compared to previous local studies. Results suggest a region-specific spread of a very limited number of L2/Beijing clonal complexes in Kazakhstan many strongly associated with an MDR phenotype. Electronic supplementary material The online version of this article (10.1186/s12879-019-4201-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- B J Klotoe
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - S Kacimi
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - E Costa-Conceicão
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - H M Gomes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.,Laboratory of Molecular Biology Applied to Mycobacteria, FIOCRUZ, Rio de Janeiro, Brazil
| | - R B Barcellos
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.,Center of Scientific and Technological Development (CDCT), Secretary of Health of Rio Grande do Sul State (SES/RS), Porto Alegre, Brazil
| | - S Panaiotov
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.,National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - D Haj Slimene
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.,Institut Pasteur de Tunisie, Tunis, Tunisie
| | - N Sikhayeva
- National Centre for Biotechnology, Astana, Kazakhstan
| | - S Sengstake
- Royal Tropical Institute (KIT), Amsterdam, The Netherlands
| | - A R Schuitema
- Royal Tropical Institute (KIT), Amsterdam, The Netherlands
| | - M Akhalaia
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - A Alenova
- National Centre for Tuberculosis Problems, Almaty, Kazakhstan
| | | | - P Tarlykov
- National Centre for Biotechnology, Astana, Kazakhstan
| | - R Anthony
- Royal Tropical Institute (KIT), Amsterdam, The Netherlands
| | - G Refrégier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - C Sola
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
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5
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Chaidir L, Ruesen C, Dutilh BE, Ganiem AR, Andryani A, Apriani L, Huynen MA, Ruslami R, Hill PC, van Crevel R, Alisjahbana B. Use of whole-genome sequencing to predict Mycobacterium tuberculosis drug resistance in Indonesia. J Glob Antimicrob Resist 2019; 16:170-177. [DOI: 10.1016/j.jgar.2018.08.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 06/06/2018] [Accepted: 08/23/2018] [Indexed: 10/28/2022] Open
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6
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Feyisa SG, Abdurahman AA, Jimma W, Chaka EE, Kardan-Yamchi J, Kazemian H. Resistance of Mycobacterium tuberculosis strains to Rifampicin: A systematic review and meta-analysis. Heliyon 2019; 5:e01081. [PMID: 30619960 PMCID: PMC6314001 DOI: 10.1016/j.heliyon.2018.e01081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 11/15/2018] [Accepted: 12/18/2018] [Indexed: 12/01/2022] Open
Abstract
Introduction Antitubercular drug resistance strain is a horrifying barrier to effective TB treatment and prevention. The present study aimed to determine the prevalence and geographical distribution of rifampicin-resistance M. tuberculosis (MTB) strains. Methods We searched two electronic databases, PubMed and EMBASE, until 26 March 2017 and updated our search on 27 April 2018 and accessed all prevalence studies of MTB strain and their drug susceptibility patterns to rifampicin. The pooled prevalence estimate was determined using random effects model. Results We identified 23 studies satisfying the inclusion criteria. The proportion of rifampicin resistance strains was diverged depending on the type of strains, country and Regions. The pooled estimate of rifampicin-resistance strains of MTB for the included studies was 4% (95% CI: 3–5%). In subgroup analysis based on World Health Organization (WHO) Regions, the pooled estimate of rifampicin-resistance strains of MTB was 11% (95% CI: 9–13%) with the Western Pacific Region 24%, Europian Region 10%, South-East Asian Region 6%, African Region 3% and Region of American 1%. Beijing family was the most dominant strain resistance to rifampicin with pooled prevalence of 14% (95% CI: 10–18%). The pooled prevalence of other families, i.e. EAI, T, CAS, MANU, Haarlem, LAM and Ural, was ≤2% for each. Conclusion High burden of rifampicin resistance MTB strains was identified in the Western Pacific Region. Of these, Beijing family was predominantly resistance to rifampicin in Western Pacific Region and South-East Asian Region and also spread to European Region and Region of American.
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Affiliation(s)
- Seifu Gizaw Feyisa
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, International Campus, Tehran, Iran.,Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Department of Biology, College of Natural Sciences, Jimma University, Ethiopia
| | - Ahmed Abdulahi Abdurahman
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences, Tehran, Iran
| | - Worku Jimma
- Department of Health Information Management, School of School of Allied Medical Sciences, Tehran University of Medical Sciences, International Campus, Tehran, Iran.,Department of Information Science, Jimma Institute of Technology, Jimma University, Ethiopia
| | - Eshetu Ejeta Chaka
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, International Campus, Tehran, Iran.,Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Department of Public Health, College of Medical and Health Sciences, Ambo University, Ethiopia
| | - Jalil Kardan-Yamchi
- Department of Pathobiology, Division of Microbiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Kazemian
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran.,Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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7
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Santos PFGD, Costa ERD, Ramalho DM, Rossetti ML, Barcellos RB, Nunes LDS, Esteves LS, Rodenbusch R, Anthony RM, Bergval I, Sengstake S, Viveiros M, Kritski A, Oliveira MM. Detection of tuberculosis drug resistance: a comparison by Mycobacterium tuberculosis MLPA assay versus Genotype®MTBDRplus. Mem Inst Oswaldo Cruz 2017; 112:396-403. [PMID: 28591399 PMCID: PMC5446228 DOI: 10.1590/0074-02760160376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 02/21/2017] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND To cope with the emergence of multidrug-resistant tuberculosis (MDR-TB), new molecular methods that can routinely be used to screen for a wide range of drug resistance related genetic markers in the Mycobacterium tuberculosis genome are urgently needed. OBJECTIVE To evaluate the performance of multiplex ligaton-dependent probe amplification (MLPA) against Genotype® MTBDRplus to detect resistance to isoniazid (INHr) and rifampicin (RIFr). METHOD 96 culture isolates characterised for identification, drug susceptibility testing (DST) and sequencing of rpoB, katG, and inhA genes were evaluated by the MLPA and Genotype®MTBDRplus assays. RESULTS With sequencing as a reference standard, sensitivity (SE) to detect INHr was 92.8% and 85.7%, and specificity (SP) was 100% and 97.5%, for MLPA and Genotype®MTBDRplus, respectively. In relation to RIFr, SE was 87.5% and 100%, and SP was 100% and 98.8%, respectively. Kappa value was identical between Genotype®MTBDRplus and MLPA compared with the standard DST and sequencing for detection of INHr [0.83 (0.75-0.91)] and RIFr [0.93 (0.88-0.98)]. CONCLUSION Compared to Genotype®MTBDRplus, MLPA showed similar sensitivity to detect INH and RIF resistance. The results obtained by the MLPA and Genotype®MTBDRplus assays indicate that both molecular tests can be used for the rapid detection of drug-resistant TB with high accuracy. MLPA has the added value of providing information on the circulating M. tuberculosis lineages.
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Affiliation(s)
- Paula Fernanda Gonçalves Dos Santos
- Universidade Federal do Rio de Janeiro, Faculdade de Medicina, Programa Acadêmico de Tuberculose, Programa de Pós-Graduação em Clínica Médica, Rio de Janeiro, RJ, Brasil
| | - Elis Regina Dalla Costa
- Fundação Estadual de Produção e Pesquisa em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil.,Rede Brasileira de Pesquisa em Tuberculose, Rio de Janeiro, RJ, Brasil
| | - Daniela M Ramalho
- Universidade Federal do Rio de Janeiro, Faculdade de Medicina, Programa Acadêmico de Tuberculose, Programa de Pós-Graduação em Clínica Médica, Rio de Janeiro, RJ, Brasil
| | - Maria Lucia Rossetti
- Fundação Estadual de Produção e Pesquisa em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil.,Universidade Luterana do Brasil, Porto Alegre, RS, Brasil
| | - Regina Bones Barcellos
- Universidade Federal do Rio de Janeiro, Faculdade de Medicina, Programa Acadêmico de Tuberculose, Programa de Pós-Graduação em Clínica Médica, Rio de Janeiro, RJ, Brasil.,Fundação Estadual de Produção e Pesquisa em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil.,Rede Brasileira de Pesquisa em Tuberculose, Rio de Janeiro, RJ, Brasil
| | - Luciana de Souza Nunes
- Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Porto Alegre, RS, Brasil
| | - Leonardo Souza Esteves
- Fundação Estadual de Produção e Pesquisa em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil
| | - Rodrigo Rodenbusch
- Fundação Estadual de Produção e Pesquisa em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil
| | - Richard M Anthony
- Royal Tropical Institute, KIT Biomedical Research, Amsterdam, The Netherlands
| | - Indra Bergval
- Royal Tropical Institute, KIT Biomedical Research, Amsterdam, The Netherlands
| | - Sarah Sengstake
- Royal Tropical Institute, KIT Biomedical Research, Amsterdam, The Netherlands
| | - Miguel Viveiros
- Universidade Nova de Lisboa, Instituto de Higiene e Medicina Tropical, Unidade de Microbiologia Médica, Global Health and Tropical Medicine, Lisboa, Portugal
| | - Afrânio Kritski
- Universidade Federal do Rio de Janeiro, Faculdade de Medicina, Programa Acadêmico de Tuberculose, Programa de Pós-Graduação em Clínica Médica, Rio de Janeiro, RJ, Brasil.,Rede Brasileira de Pesquisa em Tuberculose, Rio de Janeiro, RJ, Brasil
| | - Martha M Oliveira
- Universidade Federal do Rio de Janeiro, Faculdade de Medicina, Programa Acadêmico de Tuberculose, Programa de Pós-Graduação em Clínica Médica, Rio de Janeiro, RJ, Brasil.,Rede Brasileira de Pesquisa em Tuberculose, Rio de Janeiro, RJ, Brasil
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8
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Pan XL, Zhang CL, Nakajima C, Fu J, Shao CX, Zhao LN, Cui JY, Jiao N, Fan CL, Suzuki Y, Hattori T, Li D, Ling H. A quantitative and efficient approach to select MIRU-VNTR loci based on accumulation of the percentage differences of strains for discriminating divergent Mycobacterium tuberculosis sublineages. Emerg Microbes Infect 2017; 6:e68. [PMID: 28745309 PMCID: PMC5567172 DOI: 10.1038/emi.2017.58] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 05/11/2017] [Accepted: 06/04/2017] [Indexed: 11/09/2022]
Abstract
Although several optimal mycobacterial interspersed repetitive units-variable number tandem repeat (MIRU-VNTR) loci have been suggested for genotyping homogenous Mycobacterium tuberculosis, including the Beijing genotype, a more efficient and convenient selection strategy for identifying optimal VNTR loci is needed. Here 281 M. tuberculosis isolates were analyzed. Beijing genotype and non-Beijing genotypes were identified, as well as Beijing sublineages, according to single nucleotide polymorphisms. A total of 22 MIRU-VNTR loci were used for genotyping. To efficiently select optimal MIRU-VNTR loci, we established accumulations of percentage differences (APDs) between the strains among the different genotypes. In addition, we constructed a minimum spanning tree for clustering analysis of the VNTR profiles. Our findings showed that eight MIRU-VNTR loci displayed disparities in h values of ≥0.2 between the Beijing genotype and non-Beijing genotype isolates. To efficiently discriminate Beijing and non-Beijing genotypes, an optimal VNTR set was established by adding loci with APDs ranging from 87.2% to 58.8%, resulting in the construction of a nine-locus set. We also found that QUB11a is a powerful locus for separating ST10s (including ST10, STF and STCH1) and ST22s (including ST22 and ST8) strains, whereas a combination of QUB11a, QUB4156, QUB18, Mtub21 and QUB26 could efficiently discriminate Beijing sublineages. Our findings suggested that two nine-locus sets were not only efficient for distinguishing the Beijing genotype from non-Beijing genotype strains, but were also suitable for sublineage genotyping with different discriminatory powers. These results indicate that APD represents a quantitative and efficient approach for selecting MIRU-VNTR loci to discriminate between divergent M. tuberculosis sublineages.
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Affiliation(s)
- Xin-Ling Pan
- Department of Microbiology, Wu Lien-Teh Institute, Harbin Medical University, Heilongjiang Provincial Key Laboratory of Infection and Immunity, Key Laboratory of Pathogen Biology, Harbin 150081, China
| | - Chun-Lei Zhang
- Department of Clinical Laboratory, Harbin Chest Hospital, Harbin 150081, China
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo 0010020, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo 0600808, Japan
| | - Jin Fu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150026, China
| | - Chang-Xia Shao
- Department of Microbiology, Wu Lien-Teh Institute, Harbin Medical University, Heilongjiang Provincial Key Laboratory of Infection and Immunity, Key Laboratory of Pathogen Biology, Harbin 150081, China
| | - Li-Na Zhao
- Department of Clinical Laboratory, Harbin Chest Hospital, Harbin 150081, China
| | - Jia-Yi Cui
- Department of Microbiology, Wu Lien-Teh Institute, Harbin Medical University, Heilongjiang Provincial Key Laboratory of Infection and Immunity, Key Laboratory of Pathogen Biology, Harbin 150081, China
| | - Na Jiao
- Department of Clinical Laboratory, Harbin Chest Hospital, Harbin 150081, China
| | - Chang-Long Fan
- Department of Clinical Laboratory, Harbin Chest Hospital, Harbin 150081, China
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo 0010020, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo 0600808, Japan
| | - Toshio Hattori
- Graduate School of Health Science Studies, Kibi International University, Takahashi 7168508, Japan
| | - Di Li
- Department of Microbiology, Wu Lien-Teh Institute, Harbin Medical University, Heilongjiang Provincial Key Laboratory of Infection and Immunity, Key Laboratory of Pathogen Biology, Harbin 150081, China
| | - Hong Ling
- Department of Microbiology, Wu Lien-Teh Institute, Harbin Medical University, Heilongjiang Provincial Key Laboratory of Infection and Immunity, Key Laboratory of Pathogen Biology, Harbin 150081, China
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