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Scandurra G, Degeling C, Douglas P, Dobler CC, Marais B. Tuberculosis in migrants - screening, surveillance and ethics. Pneumonia (Nathan) 2020; 12:9. [PMID: 32923311 PMCID: PMC7473829 DOI: 10.1186/s41479-020-00072-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 07/29/2020] [Indexed: 12/13/2022] Open
Abstract
Tuberculosis (TB) is the leading infectious cause of human mortality and is responsible for nearly 2 million deaths every year. It is often regarded as a 'silent killer' because it predominantly affects the poor and marginalized, and disease outbreaks occur in 'slow motion' compared to Ebola or coronavirus 2 (COVID-19). In low incidence countries, TB is predominantly an imported disease and TB control in migrants is pivotal for countries to progress towards TB elimination in accordance with the World Health Organisations (WHO's) End TB strategy. This review provides a brief overview of the different screening approaches and surveillance processes that are in place in low TB incidence countries. It also includes a detailed discussion of the ethical issues related to TB screening of migrants in these settings and the different interests that need to be balanced. Given recognition that a holistic approach that recognizes and respects basic human rights is required to end TB, the review considers the complexities that require consideration in low-incidence countries that are aiming for TB elimination.
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Affiliation(s)
- Gabriella Scandurra
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
| | - Chris Degeling
- Australian Centre for Health Engagement Evidence and Values, University of Wollongong, Wollongong, Australia
| | - Paul Douglas
- International Organization for Migration (IOM), Geneva, Switzerland
| | - Claudia C. Dobler
- Institute for Evidenced-Based Healthcare, Bond University, Gold Coast, Australia
| | - Ben Marais
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
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Outhred AC, Gurjav U, Jelfs P, McCallum N, Wang Q, Hill-Cawthorne GA, Marais BJ, Sintchenko V. Extensive Homoplasy but No Evidence of Convergent Evolution of Repeat Numbers at MIRU Loci in Modern Mycobacterium tuberculosis Lineages. Front Public Health 2020; 8:455. [PMID: 32974265 PMCID: PMC7481465 DOI: 10.3389/fpubh.2020.00455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 07/22/2020] [Indexed: 11/13/2022] Open
Abstract
More human deaths have been attributable to Mycobacterium tuberculosis than any other pathogen, and the epidemic is sustained by ongoing transmission. Various typing schemes have been developed to identify strain-specific differences and track transmission dynamics in affected communities, with recent introduction of whole genome sequencing providing the most accurate assessment. Mycobacterial interspersed repetitive unit (MIRU) typing is a family of variable number tandem repeat schemes that have been widely used to study the molecular epidemiology of M. tuberculosis. MIRU typing was used in most well-resourced settings to perform routine molecular epidemiology. Instances of MIRU homoplasy have been observed in comparison with sequence-based phylogenies, limiting its discriminatory value. A fundamental question is whether the observed homoplasy arises purely through stochastic processes, or whether there is evidence of natural selection. We compared repeat numbers at 24 MIRU loci with a whole genome sequence-based phylogeny of 245 isolates representing three modern M. tuberculosis lineages. This analysis demonstrated extensive homoplasy of repeat numbers, but did not detect any evidence of natural selection of repeat numbers, at least since the ancestral branching of the three modern lineages of M. tuberculosis. In addition, we observed good sensitivity but poor specificity and positive predictive values of MIRU-24 to detect clusters of recent transmission, as defined by whole-genome single nucleotide polymorphism analysis. These findings provide mechanistic insight, and support a transition away from VNTR-based typing toward sequence-based typing schemes for both research and public health purposes.
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Affiliation(s)
- Alexander C. Outhred
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
- Children's Hospital at Westmead, Sydney, NSW, Australia
- Center for Infectious Diseases and Microbiology—Public Health, Westmead Hospital, Sydney, NSW, Australia
| | - Ulziijargal Gurjav
- Department of Microbiology and Immunology, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | - Peter Jelfs
- Center for Infectious Diseases and Microbiology—Public Health, Westmead Hospital, Sydney, NSW, Australia
- NSW Mycobacterium Reference Laboratory, Center for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research—NSW Health Pathology, Sydney, NSW, Australia
| | - Nadine McCallum
- Deep Seq Lab, Queen's Medical Center, University of Nottingham, Nottingham, United Kingdom
| | - Qinning Wang
- Center for Infectious Diseases and Microbiology—Public Health, Westmead Hospital, Sydney, NSW, Australia
| | - Grant A. Hill-Cawthorne
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
- School of Public Health, University of Sydney, Sydney, NSW, Australia
| | - Ben J. Marais
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
- Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Vitali Sintchenko
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
- Center for Infectious Diseases and Microbiology—Public Health, Westmead Hospital, Sydney, NSW, Australia
- NSW Mycobacterium Reference Laboratory, Center for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research—NSW Health Pathology, Sydney, NSW, Australia
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3
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Karmakar M, Trauer JM, Ascher DB, Denholm JT. Hyper transmission of Beijing lineage Mycobacterium tuberculosis: Systematic review and meta-analysis. J Infect 2019; 79:572-581. [PMID: 31585190 DOI: 10.1016/j.jinf.2019.09.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/30/2019] [Accepted: 09/27/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVES The globally distributed "Beijing" lineage of Mycobacterium tuberculosis has been associated with outbreaks worldwide. Laboratory based studies have suggested that Beijing lineage may have increased fitness; however, it has not been established whether these differences are of epidemiological significance with regards to transmission. Therefore, we undertook a systematic review of epidemiological studies of tuberculosis clustering to compare the transmission dynamics of Beijing lineages versus the non-Beijing lineages. METHODS We systematically searched Embase and MEDLINE before 31st December 2018, for studies which provided information on the transmission dynamics of the different M. tuberculosis lineages. We included articles that conducted population-based cross-sectional or longitudinal molecular epidemiological studies reporting information about extent of transmission of different lineages. The protocol for this systematic review was prospectively registered with PROSPERO (CDR42018088579). RESULTS Of 2855 records identified by the search, 46 were included in the review, containing 42,700 patients from 27 countries. Beijing lineage was the most prevalent and highly clustered strain in 72.4% of the studies and had a higher likelihood of transmission than non-Beijing lineages (OR 1·81 [95% 1·28-2·57], I2 = 94·0%, τ2 = 0·59, p < 0·01). CONCLUSIONS Despite considerable heterogeneity across epidemiological contexts, Beijing lineage appears to be more transmissible than other lineages.
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Affiliation(s)
- Malancha Karmakar
- Victorian Tuberculosis Program, Melbourne Health, 792 Elizabeth Street, Melbourne, Victorian 3000 Australia; Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria 3010, Australia; Department of Microbiology and Immunology, at the Doherty Institute of Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia; Structural Biology and Bioinformatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - James M Trauer
- Victorian Tuberculosis Program, Melbourne Health, 792 Elizabeth Street, Melbourne, Victorian 3000 Australia; School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - David B Ascher
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria 3010, Australia; Structural Biology and Bioinformatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Department of Biochemistry, University of Cambridge, CB2 1GA, UK
| | - Justin T Denholm
- Victorian Tuberculosis Program, Melbourne Health, 792 Elizabeth Street, Melbourne, Victorian 3000 Australia; Department of Microbiology and Immunology, at the Doherty Institute of Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.
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4
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Mai TQ, Martinez E, Menon R, Van Anh NT, Hien NT, Marais BJ, Sintchenko V. Mycobacterium tuberculosis Drug Resistance and Transmission among Human Immunodeficiency Virus-Infected Patients in Ho Chi Minh City, Vietnam. Am J Trop Med Hyg 2019; 99:1397-1406. [PMID: 30382014 DOI: 10.4269/ajtmh.18-0185] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Vietnam has a high burden of tuberculosis (TB) and multidrug-resistant (MDR) TB, but drug resistance patterns and TB transmission dynamics among TB/human immunodeficiency virus (HIV) coinfected patients are not well described. We characterized 200 Mycobacterium tuberculosis isolates from TB/HIV coinfected patients diagnosed at the main TB referral hospital in Ho Chi Minh City, Vietnam. Phenotypic drug susceptibility testing (DST) for first-line drugs, spoligotyping, and 24-locus mycobacterial interspersed repetitive unit (MIRU-24) analysis was performed on all isolates. The 24-locus mycobacterial interspersed repetitive unit clusters and MDR isolates were subjected to whole genome sequencing (WGS). Most of the TB/HIV coinfected patients were young (162/174; 93.1% aged < 45 years) males (173; 86.5% male). Beijing (98; 49.0%) and Indo-Oceanic (70; 35.0%) lineage strains were most common. Phenotypic drug resistance was detected in 84 (42.0%) isolates, of which 17 (8.5%) were MDR; three additional MDR strains were identified on WGS. Strain clustering was reduced from 84.0% with spoligotyping to 20.0% with MIRU-24 typing and to 13.5% with WGS. Whole genome sequencing identified five additional clusters, or members of clusters, not recognized by MIRU-24. In total, 13 small (two to three member) WGS clusters were identified, with less clustering among drug susceptible (2/27; 7.4%) than among drug-resistant strains (25/27; 92.6%). On phylogenetic analysis, strains from TB/HIV coinfected patients were interspersed among strains from the general community; no major clusters indicating transmission among people living with HIV were detected. Tuberculosis/HIV coinfection in Vietnam was associated with high rates of drug resistance and limited genomic evidence of ongoing M. tuberculosis transmission among HIV-infected patients.
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Affiliation(s)
- Trinh Quynh Mai
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam.,Sydney Medical School and Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia.,Centre for Infectious Disease and Microbiology-Public Health, ICPMR, Westmead Hospital, Sydney, Australia
| | - Elena Martinez
- Centre for Infectious Disease and Microbiology-Public Health, ICPMR, Westmead Hospital, Sydney, Australia.,Sydney Medical School and Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
| | - Ranjeeta Menon
- Centre for Infectious Disease and Microbiology-Public Health, ICPMR, Westmead Hospital, Sydney, Australia.,Sydney Medical School and Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
| | | | | | - Ben J Marais
- Sydney Medical School and Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
| | - Vitali Sintchenko
- Centre for Infectious Disease and Microbiology-Public Health, ICPMR, Westmead Hospital, Sydney, Australia.,Sydney Medical School and Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
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Prediction of Local Transmission of Mycobacterium tuberculosis Isolates of a Predominantly Beijing Lineage by Use of a Variable-Number Tandem-Repeat Typing Method Incorporating a Consensus Set of Hypervariable Loci. J Clin Microbiol 2017; 56:JCM.01016-17. [PMID: 29046413 DOI: 10.1128/jcm.01016-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/05/2017] [Indexed: 01/08/2023] Open
Abstract
Strain genotyping based on the variable-number tandem repeat (VNTR) is widely applied for identifying the transmission of Mycobacterium tuberculosis A consensus set of four hypervariable loci (1982, 3232, 3820, and 4120) has been proposed to improve the discrimination of Beijing lineage strains. Herein, we evaluated the utility of these four hypervariable loci for tracing local tuberculosis transmission in 981 cases over a 14-month period in Japan (2010 to 2011). We used six different VNTR systems, with or without the four hypervariable loci. Patient ages and weighted standard distances (a measure of the dispersion of genotype-clustered cases) were used as proxies for estimating local tuberculosis transmission. The highest levels of isolate discrimination were achieved with VNTR systems that incorporated the four hypervariable loci (i.e., the Japan Anti-Tuberculosis Association [JATA]18-VNTR, mycobacterial interspersed repetitive unit [MIRU]28-VNTR, and 24Beijing-VNTR). The clustering rates by JATA12-VNTR, MIRU15-VNTR, JATA15-VNTR, JATA18-VNTR, MIRU28-VNTR, and 24Beijing-VNTR systems were 52.2%, 51.0%, 39.0%, 24.1%, 23.1%, and 22.0%, respectively. As the discriminative power increased, the median weighted standard distances of the clusters tended to decrease (from 311 to 80 km, P < 0.001, Jonckheere-Terpstra trend test). Concurrently, the median ages of patients in the clusters tended to decrease (from 68 to 60 years, P < 0.001, Jonckheere-Terpstra trend test). These findings suggest that strain typing using the four hypervariable loci improves the prediction of active local tuberculosis transmission. The four-locus set can therefore contribute to the targeted control of tuberculosis in settings with high prevalence of Beijing lineage strains.
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Sadegh H, Kargarpour Kamakoli M, Farmanfarmaei G, Masoumi M, Abdolrahimi F, Fateh A, Ebrahimzadeh N, Rahimi Jamnani F, Vaziri F, Siadat SD. Pros and cons of direct genotyping on tuberculosis clinical samples. Microb Pathog 2016; 103:135-138. [PMID: 28034830 DOI: 10.1016/j.micpath.2016.12.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 12/16/2016] [Accepted: 12/16/2016] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Prompt genotyping of Mycobacterium tuberculosis (M. tuberculosis) is crucial for improving molecular epidemiological investigation of tuberculosis (TB). METHODS We performed a retrospective study to evaluate the use of 24 loci MIRU-VNTR (mycobacterial interspersed repetitive unit-variable number of tandem-repeat) directly on 135 clinical samples from 84 TB patients. RESULTS There was a direct correlation between genotyping on clinical samples by MIRU-VNTR and bacterial load (P = 0.001). VNTR loci were amplified successfully for 41.5% of the clinical samples (19-24 loci), 32.6% (13-18 loci), 23.7% (7-12 loci) and 2.2% (1-6 loci). Loci of 2401, 577, 2996 and 154 had the highest power to show the mixed strains infection in clinical samples. CONCLUSIONS Direct MIRU-VNTR is partially successful in complete genotyping of M. tuberculosis strains. On the other hand, detection of polyclonal infection is undoubtedly reliable based on the direct MIRU-VNTR.
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Affiliation(s)
- Hamidreza Sadegh
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Ghazaleh Farmanfarmaei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Morteza Masoumi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Farid Abdolrahimi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Nayereh Ebrahimzadeh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Rahimi Jamnani
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
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Gurjav U, Outhred AC, Jelfs P, McCallum N, Wang Q, Hill-Cawthorne GA, Marais BJ, Sintchenko V. Whole Genome Sequencing Demonstrates Limited Transmission within Identified Mycobacterium tuberculosis Clusters in New South Wales, Australia. PLoS One 2016; 11:e0163612. [PMID: 27737005 PMCID: PMC5063377 DOI: 10.1371/journal.pone.0163612] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 09/12/2016] [Indexed: 11/18/2022] Open
Abstract
Australia has a low tuberculosis incidence rate with most cases occurring among recent immigrants. Given suboptimal cluster resolution achieved with 24-locus mycobacterium interspersed repetitive unit (MIRU-24) genotyping, the added value of whole genome sequencing was explored. MIRU-24 profiles of all Mycobacterium tuberculosis culture-confirmed tuberculosis cases diagnosed between 2009 and 2013 in New South Wales (NSW), Australia, were examined and clusters identified. The relatedness of cases within the largest MIRU-24 clusters was assessed using whole genome sequencing and phylogenetic analyses. Of 1841 culture-confirmed TB cases, 91.9% (1692/1841) had complete demographic and genotyping data. East-African Indian (474; 28.0%) and Beijing (470; 27.8%) lineage strains predominated. The overall rate of MIRU-24 clustering was 20.1% (340/1692) and was highest among Beijing lineage strains (35.7%; 168/470). One Beijing and three East-African Indian (EAI) clonal complexes were responsible for the majority of observed clusters. Whole genome sequencing of the 4 largest clusters (30 isolates) demonstrated diverse single nucleotide polymorphisms (SNPs) within identified clusters. All sequenced EAI strains and 70% of Beijing lineage strains clustered by MIRU-24 typing demonstrated distinct SNP profiles. The superior resolution provided by whole genome sequencing demonstrated limited M. tuberculosis transmission within NSW, even within identified MIRU-24 clusters. Routine whole genome sequencing could provide valuable public health guidance in low burden settings.
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Affiliation(s)
- Ulziijargal Gurjav
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Sydney, Australia
| | - Alexander C. Outhred
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
- Children's Hospital at Westmead, Sydney, Australia
| | - Peter Jelfs
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Sydney, Australia
- NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research–Pathology West, Sydney, Australia
| | - Nadine McCallum
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Sydney, Australia
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Sydney, Australia
| | - Grant A. Hill-Cawthorne
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
- School of Public Health and Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia
| | - Ben J. Marais
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
- Children's Hospital at Westmead, Sydney, Australia
| | - Vitali Sintchenko
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Sydney, Australia
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Gurjav U, Erkhembayar B, Burneebaatar B, Narmandakh E, Tumenbayar O, Hill-Cawthorne GA, Marais BJ, Sintchenko V. Transmission of multi-drug resistant tuberculosis in Mongolia is driven by Beijing strains of Mycobacterium tuberculosis resistant to all first-line drugs. Tuberculosis (Edinb) 2016; 101:49-53. [PMID: 27865397 DOI: 10.1016/j.tube.2016.07.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/17/2016] [Accepted: 07/19/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND Mongolia has high and rising rates of multi-drug resistant tuberculosis (MDR-TB). Spatio-temporal and programmatic evidence suggests a major contribution from MDR-TB transmission, but genotypic evidence has not been assessed. METHODS All MDR-TB cases identified during 2012 were examined. Demographic and bacteriological data were obtained from the National Tuberculosis Reference Laboratory. Isolates of Mycobacterium tuberculosis from culture-confirmed category 1 treatment failures were genotyped using 24-loci mycobacterium interspersed repetitive unit (MIRU-24) analysis. RESULTS Of the 210 MDR-TB cases identified, 115 (54.8%) were treatment failures (34.8% category 1; 20.0% category 2). Streptomycin resistance was present in 156 (74.3%) cases; including 55/73 (75.3%) category 1 treatment failures who had never been exposed to streptomycin. Among category 1 treatment failures, Beijing lineage strains predominated (88.0%; 59/67 of genotyped isolates). MIRU-24 clustering was documented in 62.7% (42/67) of strains; 55.2% (37/67) remained clustered when drug susceptibility test results were considered. In total 59.5% (25/42) of clustered strains were Beijing lineage and demonstrated in-vitro resistance to all first-line drugs tested. CONCLUSION The MDR-TB epidemic in Mongolia appears to be driven by primary transmission of Beijing lineage strains resistant to all first-line drugs. Enhanced infection control strategies together with early MDR-TB case detection and appropriate treatment are necessary to limit escalation of the MDR-TB epidemic.
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Affiliation(s)
- Ulziijargal Gurjav
- Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Sydney, Australia.
| | - Baasansuren Erkhembayar
- National Tuberculosis Reference Laboratory, National Center for Communicable Diseases, Ulaanbaatar, Mongolia
| | - Buyankhishig Burneebaatar
- National Tuberculosis Reference Laboratory, National Center for Communicable Diseases, Ulaanbaatar, Mongolia
| | - Erdenegerel Narmandakh
- National Tuberculosis Reference Laboratory, National Center for Communicable Diseases, Ulaanbaatar, Mongolia
| | - Oyuntuya Tumenbayar
- National Tuberculosis Reference Laboratory, National Center for Communicable Diseases, Ulaanbaatar, Mongolia
| | - Grant A Hill-Cawthorne
- Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia; Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia
| | - Ben J Marais
- Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
| | - Vitali Sintchenko
- Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Sydney, Australia
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Wang T, Feng GD, Pang Y, Liu JY, Zhou Y, Yang YN, Dai W, Zhang L, Li Q, Gao Y, Chen P, Zhan LP, Marais BJ, Zhao YL, Zhao G. High rate of drug resistance among tuberculous meningitis cases in Shaanxi province, China. Sci Rep 2016; 6:25251. [PMID: 27143630 PMCID: PMC4855176 DOI: 10.1038/srep25251] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 04/12/2016] [Indexed: 11/18/2022] Open
Abstract
The clinical and mycobacterial features of tuberculous meningitis (TBM) cases in China are not well described; especially in western provinces with poor tuberculosis control. We prospectively enrolled patients in whom TBM was considered in Shaanxi Province, northwestern China, over a 2-year period (September 2010 to December 2012). Cerebrospinal fluid specimens were cultured for Mycobacterium tuberculosis; with phenotypic and genotypic drug susceptibility testing (DST), as well as genotyping of all positive cultures. Among 350 patients included in the study, 27 (7.7%) had culture-confirmed TBM; 84 (24.0%) had probable and 239 (68.3%) had possible TBM. DST was performed on 25/27 (92.3%) culture positive specimens; 12/25 (48.0%) had "any resistance" detected and 3 (12.0%) were multi-drug resistant (MDR). Demographic and clinical features of drug resistant and drug susceptible TBM cases were similar. Beijing was the most common genotype (20/25; 80.0%) with 9/20 (45%) of the Beijing strains exhibiting drug resistance; including all 3 MDR strains. All (4/4) isoniazid resistant strains had mutations in the katG gene; 75% (3/4) of strains with phenotypic rifampicin resistance had mutations in the rpoB gene detected by Xpert MTB/RIF®. High rates of drug resistance were found among culture-confirmed TBM cases; most were Beijing strains.
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Affiliation(s)
- Ting Wang
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
- Department of Neurology, Kunming Medical University affiliated Yan’an Hospital, 245 Renming East Road, Kunming, Yunnan, 650200, P.R.China
| | - Guo-Dong Feng
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
| | - Yu Pang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, no.155 Changbai Road, Beijing, 102206, P.R.China
| | - Jia-Yun Liu
- Department of Inspection, Xijing Hospital, Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
| | - Yang Zhou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, no.155 Changbai Road, Beijing, 102206, P.R.China
| | - Yi-Ning Yang
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
| | - Wen Dai
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
| | - Lin Zhang
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
| | - Qiao Li
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
| | - Yu Gao
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
| | - Ping Chen
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
| | - Li-Ping Zhan
- Department of Neurology, Kunming Medical University affiliated Yan’an Hospital, 245 Renming East Road, Kunming, Yunnan, 650200, P.R.China
| | - Ben J Marais
- The Children’s Hospital at Westmead and the Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Australia
| | - Yan-Lin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, no.155 Changbai Road, Beijing, 102206, P.R.China
| | - Gang Zhao
- Department of Neurology, Xijing Hospital, the Fourth Military Medical University, no.169 Changle West Road, Xi’an, Shaanxi, 710032, P.R.China
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Outhred AC, Holmes N, Sadsad R, Martinez E, Jelfs P, Hill-Cawthorne GA, Gilbert GL, Marais BJ, Sintchenko V. Identifying Likely Transmission Pathways within a 10-Year Community Outbreak of Tuberculosis by High-Depth Whole Genome Sequencing. PLoS One 2016; 11:e0150550. [PMID: 26938641 PMCID: PMC4777479 DOI: 10.1371/journal.pone.0150550] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 02/15/2016] [Indexed: 12/29/2022] Open
Abstract
Background Improved tuberculosis control and the need to contain the spread of drug-resistant strains provide a strong rationale for exploring tuberculosis transmission dynamics at the population level. Whole-genome sequencing provides optimal strain resolution, facilitating detailed mapping of potential transmission pathways. Methods We sequenced 22 isolates from a Mycobacterium tuberculosis cluster in New South Wales, Australia, identified during routine 24-locus mycobacterial interspersed repetitive unit typing. Following high-depth paired-end sequencing using the Illumina HiSeq 2000 platform, two independent pipelines were employed for analysis, both employing read mapping onto reference genomes as well as de novo assembly, to control biases in variant detection. In addition to single-nucleotide polymorphisms, the analyses also sought to identify insertions, deletions and structural variants. Results Isolates were highly similar, with a distance of 13 variants between the most distant members of the cluster. The most sensitive analysis classified the 22 isolates into 18 groups. Four of the isolates did not appear to share a recent common ancestor with the largest clade; another four isolates had an uncertain ancestral relationship with the largest clade. Conclusion Whole genome sequencing, with analysis of single-nucleotide polymorphisms, insertions, deletions, structural variants and subpopulations, enabled the highest possible level of discrimination between cluster members, clarifying likely transmission pathways and exposing the complexity of strain origin. The analysis provides a basis for targeted public health intervention and enhanced classification of future isolates linked to the cluster.
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Affiliation(s)
- Alexander C. Outhred
- NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research–Pathology West, Sydney, Australia
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Sydney, Australia
- Centre for Research Excellence in Tuberculosis and the Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
- Children’s Hospital at Westmead, Sydney, Australia
- * E-mail:
| | - Nadine Holmes
- NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research–Pathology West, Sydney, Australia
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Sydney, Australia
| | - Rosemarie Sadsad
- NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research–Pathology West, Sydney, Australia
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Sydney, Australia
| | - Elena Martinez
- NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research–Pathology West, Sydney, Australia
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Sydney, Australia
| | - Peter Jelfs
- NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research–Pathology West, Sydney, Australia
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Sydney, Australia
| | - Grant A. Hill-Cawthorne
- Centre for Research Excellence in Tuberculosis and the Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
- School of Public Health, University of Sydney, Sydney, Australia
| | - Gwendolyn L. Gilbert
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Sydney, Australia
- Centre for Research Excellence in Tuberculosis and the Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
| | - Ben J. Marais
- Centre for Research Excellence in Tuberculosis and the Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
- Children’s Hospital at Westmead, Sydney, Australia
| | - Vitali Sintchenko
- NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research–Pathology West, Sydney, Australia
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Sydney, Australia
- Centre for Research Excellence in Tuberculosis and the Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
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Genotype heterogeneity of Mycobacterium tuberculosis within geospatial hotspots suggests foci of imported infection in Sydney, Australia. INFECTION GENETICS AND EVOLUTION 2015; 40:346-351. [PMID: 26187743 DOI: 10.1016/j.meegid.2015.07.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 07/06/2015] [Accepted: 07/13/2015] [Indexed: 01/11/2023]
Abstract
In recent years the State of New South Wales (NSW), Australia, has maintained a low tuberculosis incidence rate with little evidence of local transmission. Nearly 90% of notified tuberculosis cases occurred in people born in tuberculosis-endemic countries. We analyzed geographic, epidemiological and genotypic data of all culture-confirmed tuberculosis cases to identify the bacterial and demographic determinants of tuberculosis hotspot areas in NSW. Standard 24-loci mycobacterium interspersed repetitive unit-variable number tandem repeat (MIRU-24) typing was performed on all isolates recovered between 2009 and 2013. In total 1692/1841 (91.9%) cases with confirmed Mycobacterium tuberculosis infection had complete MIRU-24 and demographic data and were included in the study. Despite some year-to-year variability, spatio-temporal analysis identified four tuberculosis hotspots. The incidence rate and the relative risk of tuberculosis in these hotspots were 2- to 10-fold and 4- to 8-fold higher than the state average, respectively. MIRU-24 profiles of M. tuberculosis isolates associated with these hotspots revealed high levels of heterogeneity. This suggests that these spatio-temporal hotspots, within this low incidence setting, can represent areas of predominantly imported infection rather than clusters of cases due to local transmission. These findings provide important epidemiological insight and demonstrate the value of combining tuberculosis genotyping and spatiotemporal data to guide better-targeted public health interventions.
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Osman DA, Phelippeau M, Drancourt M, Musso D. Diversity of Mycobacterium tuberculosis lineages in French Polynesia. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2015; 50:199-206. [PMID: 26271142 DOI: 10.1016/j.jmii.2015.05.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 05/01/2015] [Accepted: 05/28/2015] [Indexed: 11/19/2022]
Abstract
BACKGROUND/PURPOSE French Polynesia is an overseas territory located in the South Pacific. The incidence of tuberculosis in French Polynesia has been stable since 2000 with an average of 20 cases/y/100,000 inhabitants. Molecular epidemiology of Mycobacterium tuberculosis in French Polynesia is unknown because M. tuberculosis isolates have not been routinely genotyped. METHODS From 2009 to 2012, 34 isolates collected from 32 French Polynesian patients were identified as M. tuberculosis by probe hybridization. These isolates were genotyped using spoligotyping and 24-loci mycobacterial interspersed repetitive units (MIRUs)-variable number of tandem repeat (VNTR). Spoligotype patterns obtained using commercial kits were compared with the online international database SITVIT. MIRU-VNTR genotyping was performed using an in-house protocol based on capillary electrophoresis sizing for 24-loci MIRU-VNTR genotyping. RESULTS The results of the spoligotyping method revealed that 25 isolates grouped into six previously described spoligotypes [H1, H3, U likely (S), T1, Manu, and Beijing] and nine isolates grouped into six new spoligotypes. Comparison with the international database MIRU-VNTRplus distributed 30 isolates into five lineages (Haarlem, Latin American Mediterranean, S, X, and Beijing) and four as unassigned isolates. CONCLUSION Genotyping identified four phylogenetic lineages belonging to the modern Euro-American subgroup, one Beijing genotype responsible for worldwide pandemics, including remote islands in the South Pacific, and one Manu genotype of the ancestral lineage of M. tuberculosis.
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Affiliation(s)
- Djaltou Aboubaker Osman
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UMR CNRS 7278, IRD 198, INSERM 1095, Faculté de Médecine, Marseille, France; Institut de Recherche Médicinale (IRM), Centre d'études et de Recherche de Djibouti (CERD), Djibouti
| | - Michael Phelippeau
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UMR CNRS 7278, IRD 198, INSERM 1095, Faculté de Médecine, Marseille, France
| | - Michel Drancourt
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UMR CNRS 7278, IRD 198, INSERM 1095, Faculté de Médecine, Marseille, France.
| | - Didier Musso
- Pôle de recherche et de veille sur les maladies infectieuses émergente, Institut Louis Malardé, Tahiti, French Polynesia.
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Disratthakit A, Meada S, Prammananan T, Thaipisuttikul I, Doi N, Chaiprasert A. Genotypic diversity of multidrug-, quinolone- and extensively drug-resistant Mycobacterium tuberculosis isolates in Thailand. INFECTION GENETICS AND EVOLUTION 2015; 32:432-9. [DOI: 10.1016/j.meegid.2015.03.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 03/30/2015] [Accepted: 03/31/2015] [Indexed: 11/25/2022]
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Mears J, Abubakar I, Cohen T, McHugh TD, Sonnenberg P. Effect of study design and setting on tuberculosis clustering estimates using Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats (MIRU-VNTR): a systematic review. BMJ Open 2015; 5:e005636. [PMID: 25609667 PMCID: PMC4305070 DOI: 10.1136/bmjopen-2014-005636] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVES To systematically review the evidence for the impact of study design and setting on the interpretation of tuberculosis (TB) transmission using clustering derived from Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats (MIRU-VNTR) strain typing. DATA SOURCES MEDLINE, EMBASE, CINHAL, Web of Science and Scopus were searched for articles published before 21st October 2014. REVIEW METHODS Studies in humans that reported the proportion of clustering of TB isolates by MIRU-VNTR were included in the analysis. Univariable meta-regression analyses were conducted to assess the influence of study design and setting on the proportion of clustering. RESULTS The search identified 27 eligible articles reporting clustering between 0% and 63%. The number of MIRU-VNTR loci typed, requiring consent to type patient isolates (as a proxy for sampling fraction), the TB incidence and the maximum cluster size explained 14%, 14%, 27% and 48% of between-study variation, respectively, and had a significant association with the proportion of clustering. CONCLUSIONS Although MIRU-VNTR typing is being adopted worldwide there is a paucity of data on how study design and setting may influence estimates of clustering. We have highlighted study design variables for consideration in the design and interpretation of future studies.
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Affiliation(s)
- Jessica Mears
- Department of Infection and Population Health, University College London, London, UK
| | - Ibrahim Abubakar
- Department of Infection and Population Health, University College London, London, UK
- Centre for Infectious Disease Surveillance and Control, Public Health England, London, UK
- Clinical Trials Unit, Medical Research Council, London, UK
| | - Theodore Cohen
- Division of Global Health Equity, Brigham and Women's Hospital and Department of Epidemiology, Harvard School of Public Health, Harvard University, Boston, USA
| | - Timothy D McHugh
- Department of Infection, Centre for Clinical Microbiology, University College London, London, UK
| | - Pam Sonnenberg
- Department of Infection and Population Health, University College London, London, UK
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