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Varghese B, Shoukri M, Memish Z, Abuljadayel N, Alhakeem R, Alrabiah F, Al-Hajoj S. Occurrence of diverse mutations in isoniazid- and rifampicin-resistant Mycobacterium tuberculosis isolates from autochthonous and immigrant populations of Saudi Arabia. Microb Drug Resist 2015; 20:623-31. [PMID: 25014484 DOI: 10.1089/mdr.2014.0065] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
For the first time in Saudi Arabia, the impact of a patient's ethnic background on mutations conferring resistance to rifampicin (RIF) and isoniazid (INH) in Mycobacterium tuberculosis isolates was analyzed on a nationwide sample collection. Four hundred fifteen isolates were subjected to drug susceptibility testing, mutation analysis, spoligotyping, and 24 loci-based Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeat typing, respectively. Phenotypically, 41 (9.9%) isolates were resistant to RIF, 239 (57.6%) to INH, and 135 (32.5%) to both RIF and INH, respectively. Forty (9.6%), 236 (56.8%), and 133 (32%) isolates were determined as resistant to RIF, INH, and to both by molecular assay. Codon 531 (S531L) mutations (69.4%) in the rpoB gene and codon 315 (S315T) mutations (67.2%) in the katG gene were the most prominent among RIF- and INH-resistant isolates, respectively. The autochthonous population showed a predominance of rpoB codon 516 and 526 mutations, while the inhA promoter position -15 and -8 mutations were prominent among immigrants. A strain cluster ratio of 32% (30 clusters) was observed and 24 clusters displayed identical mutations. Overall, Euro-American lineages were predominant. However, Beijing (56.7%) and EAI (42.7%) were noticed with the highest cluster rate. In Saudi Arabia, the occurrence of mutations responsible for INH and RIF resistance was significantly associated with the ethnic origin of the patient.
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Affiliation(s)
- Bright Varghese
- 1 Mycobacteriology Research Section, Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre , Riyadh, Saudi Arabia
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152
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Transmission and Progression to Disease of Mycobacterium tuberculosis Phylogenetic Lineages in The Netherlands. J Clin Microbiol 2015. [PMID: 26224845 DOI: 10.1128/jcm.01370-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The aim of this study was to determine if mycobacterial lineages affect infection risk, clustering, and disease progression among Mycobacterium tuberculosis cases in The Netherlands. Multivariate negative binomial regression models adjusted for patient-related factors and stratified by patient ethnicity were used to determine the association between phylogenetic lineages and infectivity (mean number of positive contacts around each patient) and clustering (as defined by number of secondary cases within 2 years after diagnosis of an index case sharing the same fingerprint) indices. An estimate of progression to disease by each risk factor was calculated as a bootstrapped risk ratio of the clustering index by the infectivity index. Compared to the Euro-American reference, Mycobacterium africanum showed significantly lower infectivity and clustering indices in the foreign-born population, while Mycobacterium bovis showed significantly lower infectivity and clustering indices in the native population. Significantly lower infectivity was also observed for the East African Indian lineage in the foreign-born population. Smear positivity was a significant risk factor for increased infectivity and increased clustering. Estimates of progression to disease were significantly associated with age, sputum-smear status, and behavioral risk factors, such as alcohol and intravenous drug abuse, but not with phylogenetic lineages. In conclusion, we found evidence of a bacteriological factor influencing indicators of a strain's transmissibility, namely, a decreased ability to infect and a lower clustering index in ancient phylogenetic lineages compared to their modern counterparts. Confirmation of these findings via follow-up studies using tuberculin skin test conversion data should have important implications on M. tuberculosis control efforts.
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153
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Ssengooba W, Cobelens FG, Nakiyingi L, Mboowa G, Armstrong DT, Manabe YC, Joloba ML, de Jong BC. High Genotypic Discordance of Concurrent Mycobacterium tuberculosis Isolates from Sputum and Blood of HIV-Infected Individuals. PLoS One 2015; 10:e0132581. [PMID: 26176604 PMCID: PMC4503667 DOI: 10.1371/journal.pone.0132581] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/16/2015] [Indexed: 11/19/2022] Open
Abstract
Background Among HIV-infected individuals with CD4 less than 200 cells/mm3, tuberculosis often has an atypical presentation, is more likely to be disseminated and is diagnostically challenging. We sought to understand the genotypic discordance of concurrent sputum and blood M. tuberculosis (MTB) isolates from HIV-infected individuals. Methods From a prospective diagnostic accuracy study with 182 HIV-infected culture-positive TB adults, isolates were obtained from 51 of 66 participants who were MTB culture-positive by both sputum and blood. Isolates were subjected to susceptibility testing to 1st line drugs, spoligotyping and 24 locus- MIRU-VNTR. Results The median age of the participants was 31 (IQR; 27–38) years and 51% were male. The median CD4 count was 29 (IQR; 10–84) cells/mm3 with 20% taking ART; 8.0% were previously treated for TB, and 63% were AFB smear-negative. The isolates belonged to two of the main global MTB-lineages; East-African-Indian (L3) 17 (16.7%) and Euro-American (L4) 85 (83.3%). We identified 26 (51.0%) participants with discordant MTB-genotypes between sputum and blood, including two patients with evidence of mixed infection in either compartment. Having discordant MTB-genotypes was not predicted by the MTB-lineage in either blood or sputum, CD4 cell count, or any other clinical characteristic. Conclusions There is a high genotypic discordance among M. tuberculosis concurrently isolated from sputum and blood of HIV-infected individuals. These findings suggest that infection with more than one strain of M. tuberculosis occurs in at least half of patients with advanced HIV infection.
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Affiliation(s)
- Willy Ssengooba
- Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda
- Department of Global Health and Amsterdam Institute of Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Unit of Mycobacteriology Institute of Tropical Medicine, Antwerp, Belgium
| | - Frank G. Cobelens
- Department of Global Health and Amsterdam Institute of Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
- KNCV Tuberculosis Foundation, The Hague, Netherlands
| | - Lydia Nakiyingi
- Infectious Diseases Institute, College of Health Sciences Makerere University, Kampala, Uganda
| | - Gerald Mboowa
- Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda
| | - Derek T. Armstrong
- Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Yukari C. Manabe
- Infectious Diseases Institute, College of Health Sciences Makerere University, Kampala, Uganda
- Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Moses L. Joloba
- Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda
- Infectious Diseases Institute, College of Health Sciences Makerere University, Kampala, Uganda
| | - Bouke C. de Jong
- Unit of Mycobacteriology Institute of Tropical Medicine, Antwerp, Belgium
- Division of Infectious Diseases, New York University, New York, NY, United States of America
- * E-mail:
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154
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Khandkar C, Harrington Z, Jelfs PJ, Sintchenko V, Dobler CC. Epidemiology of Peripheral Lymph Node Tuberculosis and Genotyping of M. tuberculosis Strains: A Case-Control Study. PLoS One 2015; 10:e0132400. [PMID: 26177546 PMCID: PMC4503442 DOI: 10.1371/journal.pone.0132400] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/13/2015] [Indexed: 11/19/2022] Open
Abstract
Background This study examined potential risk factors of lymph node tuberculosis (LNTB), including phylogenetic lineages of Mycobacterium tuberculosis (MTB), in comparison to pulmonary tuberculosis (PTB) in a setting with an ethnically diverse population. Methods We conducted a case-control study at a major tuberculosis clinic in Sydney, Australia, which included all patients with peripheral LNTB seen at the clinic between 2000 and 2012. Controls were randomly selected patients with PTB seen at the same clinic during the study period. Epidemiological data were extracted from the hospital electronic database and medical records. Associations between LNTB and age, sex, ethnicity, comorbidities and phylogenetic lineages of MTB in comparison to PTB were examined using logistic regression in univariate and multivariate analyses. Results There were 212 cases with LNTB and 424 randomly selected controls with PTB. Among patients with LNTB, 74% were female and the mean age (standard deviation, SD) was 42 (16) years. Among patients with PTB, 43% were female and the mean age was 44 (22) years. Females, 45 to 64-year-olds and Southern Asians had an increased risk for LNTB (OR 3.13, 95% CI 2.10-4.67; OR 2.50, 95% CI 1.29-4.84; OR 3.95, 95% CI 1.54-10.12 respectively). Patients with diabetes were at a higher risk of PTB (OR 0.40, 95% CI 0.19 – 0.83 for LNTB). A subset analysis showed that patients infected with the East African Indian strain of MTB were more likely to develop LNTB (OR 10.07, 95% CI 2.37-42.77). Conclusions An increased risk for LNTB (but still lower rates than for PTB) was found among females, people aged 45 to 64 years and people born in Southern Asia. An increased risk for PTB was found among patients with diabetes. The East African Indian strain of MTB was significantly associated with a higher likelihood of LNTB compared to other MTB strains.
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Affiliation(s)
- Chinmay Khandkar
- South Western Sydney Clinical School, University of New South Wales, Sydney, New South Wales, Australia
- * E-mail:
| | - Zinta Harrington
- South Western Sydney Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Peter J. Jelfs
- NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Sydney, New South Wales, Australia
| | - Vitali Sintchenko
- NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Sydney, New South Wales, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, New South Wales, Australia
| | - Claudia C. Dobler
- South Western Sydney Clinical School, University of New South Wales, Sydney, New South Wales, Australia
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155
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Fløe A, Hilberg O, Thomsen VØ, Lillebaek T, Wejse C. Shortening Isolation of Patients With Suspected Tuberculosis by Using Polymerase Chain Reaction Analysis: A Nationwide Cross-sectional Study. Clin Infect Dis 2015; 61:1365-73. [PMID: 26175524 DOI: 10.1093/cid/civ563] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 07/02/2015] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Isolation of patients suspected for pulmonary tuberculosis is guided by serial sputum smears. This can result in isolation for days for patients with noncontagious tuberculosis. To determine whether a single sample negative for Mycobacterium tuberculosis complex at polymerase chain reaction (PCR) can guide isolation. METHODS We retrospectively evaluated sputum samples analyzed for M. tuberculosis complex at the International Reference Laboratory of Mycobacteriology, Copenhagen, Denmark in 2002-2011. We selected culture-confirmed tuberculosis cases with ≥3 samples within 14 days before or after the initial culture-positive sample. We repeated the process for those with ≥2 samples within 28 days. The primary outcome was PCR-negative, smear-positive patients. RESULTS We included 53 533 sputum samples from 20 928 individuals; 1636 had culture-confirmed tuberculosis. Of these, 856 had ≥3 sputum samples analyzed within the 28 days, and 482 had ≥1 PCR result. Nine patients (2.5% of smear-positive patients) were smear positive/PCR negative; 8 of the 9 had a smear-positive result in only 1 of 3 samples, and 5 had a low smear grade. Of 722 patients with 2 samples, 7 (1.3% of smear-positive patients) were smear positive/PCR negative. Overall, none were smear positive for the sample that produced the negative PCR result. CONCLUSIONS Primary PCR identified >97% of serial smear-positive cases. The majority of the missed cases had low-grade smears. Nevertheless, the occurrence of smear-positive/PCR-negative cases underlines the importance of increasing the quantity and quality of samples. Moreover, it is important that samples analyzed with PCR are cultured, owing to higher-sensitivity drug susceptibility testing, differential diagnosis, and surveillance.
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Affiliation(s)
| | - Ole Hilberg
- Departments of Respiratory Diseases and Allergy
| | | | - Troels Lillebaek
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Christian Wejse
- Infectious Diseases, Aarhus University Hospital GloHAU Center for Global Health, Department of Public Health, Aarhus University
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156
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Zelner JL, Murray MB, Becerra MC, Galea J, Lecca L, Calderon R, Yataco R, Contreras C, Zhang Z, Manjourides J, Grenfell BT, Cohen T. Identifying Hotspots of Multidrug-Resistant Tuberculosis Transmission Using Spatial and Molecular Genetic Data. J Infect Dis 2015; 213:287-94. [PMID: 26175455 DOI: 10.1093/infdis/jiv387] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 07/08/2015] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND We aimed to identify and determine the etiology of "hotspots" of concentrated multidrug-resistant tuberculosis (MDR-tuberculosis) risk in Lima, Peru. METHODS From 2009 to 2012, we conducted a prospective cohort study among households of tuberculosis cases from 106 health center (HC) areas in Lima, Peru. All notified tuberculosis cases and their household contacts were followed for 1 year. Symptomatic individuals were screened by microscopy and culture; positive cultures were tested for drug susceptibility (DST) and genotyped by 24-loci mycobacterial interspersed repetitive units-variable-number tandem repeats (MIRU-VNTR). RESULTS 3286 individuals with culture-confirmed disease, DST, and 24-loci MIRU-VNTR were included in our analysis. Our analysis reveals: (1) heterogeneity in annual per-capita incidence of tuberculosis and MDR-tuberculosis by HC, with a rate of MDR-tuberculosis 89 times greater (95% confidence interval [CI], 54,185) in the most-affected versus the least-affected HC; (2) high risk for MDR-tuberculosis in a region spanning several HCs (odds ratio = 3.19, 95% CI, 2.33, 4.36); and (3) spatial aggregation of MDR-tuberculosis genotypes, suggesting localized transmission. CONCLUSIONS These findings reveal that localized transmission is an important driver of the epidemic of MDR-tuberculosis in Lima. Efforts to interrupt transmission may be most effective if targeted to this area of the city.
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Affiliation(s)
- Jonathan L Zelner
- Robert Wood Johnson Foundation Health and Society Scholars Program, Interdisciplinary Center for Innovative Theory and Empirics (INCITE) & Mailman School of Public Health, Columbia University, New York, New York
| | - Megan B Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Department of Epidemiology, Harvard School of Public Health
| | - Mercedes C Becerra
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts
| | | | | | | | | | | | - Zibiao Zhang
- Division of Global Health Equity, Brigham and Women's Hospital
| | - Justin Manjourides
- Department of Health Sciences, Bouvé College of Health Sciences, Northeastern University, Boston, Massachusetts
| | - Bryan T Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, New Jersey Fogarty International Center, National Institutes of Health, Bethesda, Maryland
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut
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157
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Azé J, Sola C, Zhang J, Lafosse-Marin F, Yasmin M, Siddiqui R, Kremer K, van Soolingen D, Refrégier G. Genomics and Machine Learning for Taxonomy Consensus: The Mycobacterium tuberculosis Complex Paradigm. PLoS One 2015; 10:e0130912. [PMID: 26154264 PMCID: PMC4496040 DOI: 10.1371/journal.pone.0130912] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 05/25/2015] [Indexed: 11/18/2022] Open
Abstract
Infra-species taxonomy is a prerequisite to compare features such as virulence in different pathogen lineages. Mycobacterium tuberculosis complex taxonomy has rapidly evolved in the last 20 years through intensive clinical isolation, advances in sequencing and in the description of fast-evolving loci (CRISPR and MIRU-VNTR). On-line tools to describe new isolates have been set up based on known diversity either on CRISPRs (also known as spoligotypes) or on MIRU-VNTR profiles. The underlying taxonomies are largely concordant but use different names and offer different depths. The objectives of this study were 1) to explicit the consensus that exists between the alternative taxonomies, and 2) to provide an on-line tool to ease classification of new isolates. Genotyping (24-VNTR, 43-spacers spoligotypes, IS6110-RFLP) was undertaken for 3,454 clinical isolates from the Netherlands (2004-2008). The resulting database was enlarged with African isolates to include most human tuberculosis diversity. Assignations were obtained using TB-Lineage, MIRU-VNTRPlus, SITVITWEB and an algorithm from Borile et al. By identifying the recurrent concordances between the alternative taxonomies, we proposed a consensus including 22 sublineages. Original and consensus assignations of the all isolates from the database were subsequently implemented into an ensemble learning approach based on Machine Learning tool Weka to derive a classification scheme. All assignations were reproduced with very good sensibilities and specificities. When applied to independent datasets, it was able to suggest new sublineages such as pseudo-Beijing. This Lineage Prediction tool, efficient on 15-MIRU, 24-VNTR and spoligotype data is available on the web interface “TBminer.” Another section of this website helps summarizing key molecular epidemiological data, easing tuberculosis surveillance. Altogether, we successfully used Machine Learning on a large dataset to set up and make available the first consensual taxonomy for human Mycobacterium tuberculosis complex. Additional developments using SNPs will help stabilizing it.
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Affiliation(s)
- Jérôme Azé
- LIRMM UM CNRS, UMR 5506, 860 rue de St Priest, 34095 Montpellier cedex 5, France
| | - Christophe Sola
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, rue Gregor Mendel, Bât 400, 91405 Orsay cedex, France
| | - Jian Zhang
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, rue Gregor Mendel, Bât 400, 91405 Orsay cedex, France
| | - Florian Lafosse-Marin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, rue Gregor Mendel, Bât 400, 91405 Orsay cedex, France
| | - Memona Yasmin
- Pakistan Institute for Engineering and Applied Sciences (PIEAS), Lehtrar Road, Nilore, Islamabad, Pakistan
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box # 577, Jhang Road, Faisalabad, Pakistan
| | - Rubina Siddiqui
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box # 577, Jhang Road, Faisalabad, Pakistan
| | - Kristin Kremer
- National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven, The Netherlands
| | - Dick van Soolingen
- National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven, The Netherlands
- Department of Pulmonary Diseases and Department of Microbiology, Radbout University Nijmegen Medical Centre, University Lung Centre Dekkerswald, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Guislaine Refrégier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, rue Gregor Mendel, Bât 400, 91405 Orsay cedex, France
- * E-mail:
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158
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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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Couvin D, Rastogi N. Tuberculosis – A global emergency: Tools and methods to monitor, understand, and control the epidemic with specific example of the Beijing lineage. Tuberculosis (Edinb) 2015; 95 Suppl 1:S177-89. [DOI: 10.1016/j.tube.2015.02.023] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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160
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Rabna P, Ramos J, Ponce G, Sanca L, Mané M, Armada A, Machado D, Vieira F, Gomes VF, Martins E, Colombatti R, Riccardi F, Perdigão J, Sotero J, Portugal I, Couto I, Atouguia J, Rodrigues A, Viveiros M. Direct Detection by the Xpert MTB/RIF Assay and Characterization of Multi and Poly Drug-Resistant Tuberculosis in Guinea-Bissau, West Africa. PLoS One 2015; 10:e0127536. [PMID: 26017968 PMCID: PMC4446334 DOI: 10.1371/journal.pone.0127536] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 04/16/2015] [Indexed: 11/18/2022] Open
Abstract
Background This study aimed to evaluate the usefulness of the Xpert MTB/RIF assay for the rapid direct detection of M. tuberculosis complex (MTBC) strains and rifampicin resistance associated mutations in a resource-limited setting such as Guinea-Bissau and its implications in the management of tuberculosis (TB) and drug resistant tuberculosis, complementing the scarce information on resistance and genotypic diversity of MTBC strains in this West African country. Methods and Results This cross-sectional prospective study included 100 consecutive TB patients with positive acid-fast smears at two months of anti-tuberculosis treatment or in a re-treatment situation, between May and December 2012. Resistance to rifampicin was detected using the GeneXpert system and the Xpert MTB/RIF assay. MTBC isolates obtained with the BACTEC MGIT 960 system were tested for susceptibility to first- and second-line anti-tuberculosis drugs. Overall, the prevalence of multidrug-resistant tuberculosis (MDR-TB) was found to be 9 cases. Of these, 67% (6 patients) of confirmed MDR-TB cases had no past history of TB treatment and 33% (3 patients) were previously treated cases. Extensively drug-resistant TB was not found. Molecular typing of the MDR-TB strains revealed recent transmission patterns of imported MDR strains. Conclusions The Xpert MTB/RIF assay was reliable for the detection of rifampicin resistant MTBC strains directly from sputum samples of patients undergoing first-line treatment for two months, being more trustworthy than the simple presence of acid-fast bacilli in the smear. Its implementation is technically simple, does not require specialized laboratory infrastructures and is suitable for resource-limited settings when a regular source of electricity and maintenance is available as well as financial and operation sustainability is guaranteed by the health authorities. A high prevalence of MDR-TB among patients at risk of MDR-TB after two months of first-line treatment was found, in support of the WHO recommendations for its use in the management of this risk group.
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Affiliation(s)
- Paulo Rabna
- Instituto Nacional de Saúde Pública/Projecto de Saúde de Bandim (INASA/PSB), Bissau, Guiné-Bissau
| | - Jorge Ramos
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical, Universidade NOVA de Lisboa (IHMT, UNL), Lisboa, Portugal
| | - Gema Ponce
- Unidade de Clínica Tropical, Instituto de Higiene e Medicina Tropical de Lisboa/Universidade NOVA de Lisboa (IHMT/UNL), Lisboa, Portugal
| | - Lilica Sanca
- Instituto Nacional de Saúde Pública/Projecto de Saúde de Bandim (INASA/PSB), Bissau, Guiné-Bissau
| | - Morto Mané
- Instituto Nacional de Saúde Pública/Projecto de Saúde de Bandim (INASA/PSB), Bissau, Guiné-Bissau
| | - Ana Armada
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical, Universidade NOVA de Lisboa (IHMT, UNL), Lisboa, Portugal
- Centro de Malária e Outras Doenças Tropicais (CMDT), Instituto de Higiene e Medicina Tropical de Lisboa/Universidade NOVA de Lisboa (IHMT/UNL), Lisboa, Portugal
| | - Diana Machado
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical, Universidade NOVA de Lisboa (IHMT, UNL), Lisboa, Portugal
| | - Fina Vieira
- Hospital Raoul Follereau, Bissau, Guiné-Bissau
| | - Victor F. Gomes
- Ministério da Saúde/Programa Nacional de Luta contra a Tuberculose, Bissau, Guiné-Bissau
| | | | | | - Fabio Riccardi
- Aid, Health and Development-Onlus—Ahead-Onlus, Rome, Italy
| | - João Perdigão
- Centro de Patogénese Molecular, URIA, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Joana Sotero
- Centro de Patogénese Molecular, URIA, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Isabel Portugal
- Centro de Patogénese Molecular, URIA, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Isabel Couto
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical, Universidade NOVA de Lisboa (IHMT, UNL), Lisboa, Portugal
| | - Jorge Atouguia
- Unidade de Clínica Tropical, Instituto de Higiene e Medicina Tropical de Lisboa/Universidade NOVA de Lisboa (IHMT/UNL), Lisboa, Portugal
- Centro de Malária e Outras Doenças Tropicais (CMDT), Instituto de Higiene e Medicina Tropical de Lisboa/Universidade NOVA de Lisboa (IHMT/UNL), Lisboa, Portugal
| | - Amabélia Rodrigues
- Instituto Nacional de Saúde Pública/Projecto de Saúde de Bandim (INASA/PSB), Bissau, Guiné-Bissau
| | - Miguel Viveiros
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical, Universidade NOVA de Lisboa (IHMT, UNL), Lisboa, Portugal
- Centro de Malária e Outras Doenças Tropicais (CMDT), Instituto de Higiene e Medicina Tropical de Lisboa/Universidade NOVA de Lisboa (IHMT/UNL), Lisboa, Portugal
- * E-mail:
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161
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Eldholm V, Monteserin J, Rieux A, Lopez B, Sobkowiak B, Ritacco V, Balloux F. Four decades of transmission of a multidrug-resistant Mycobacterium tuberculosis outbreak strain. Nat Commun 2015; 6:7119. [PMID: 25960343 PMCID: PMC4432642 DOI: 10.1038/ncomms8119] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 04/08/2015] [Indexed: 01/06/2023] Open
Abstract
The rise of drug-resistant strains is a major challenge to containing the tuberculosis (TB) pandemic. Yet, little is known about the extent of resistance in early years of chemotherapy and when transmission of resistant strains on a larger scale became a major public health issue. Here we reconstruct the timeline of the acquisition of antimicrobial resistance during a major ongoing outbreak of multidrug-resistant TB in Argentina. We estimate that the progenitor of the outbreak strain acquired resistance to isoniazid, streptomycin and rifampicin by around 1973, indicating continuous circulation of a multidrug-resistant TB strain for four decades. By around 1979 the strain had acquired additional resistance to three more drugs. Our results indicate that Mycobacterium tuberculosis (Mtb) with extensive resistance profiles circulated 15 years before the outbreak was detected, and about one decade before the earliest documented transmission of Mtb strains with such extensive resistance profiles globally. The early origin and evolution of multidrug resistant strains of Mycobacterium tuberculosis are poorly understood. Here, the authors perform genomic and phylogenetic analyses of 252 clinical isolates from a tuberculosis outbreak in Argentina and reconstruct the timeline of the acquisition of antibiotic resistance.
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Affiliation(s)
- Vegard Eldholm
- Division of Infectious Disease Control, Norwegian Institute of Public Health, Lovisenberggata 8, Oslo 0456, Norway
| | - Johana Monteserin
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Vélez Sarsfield 563, Buenos Aires 1281, Argentina
| | - Adrien Rieux
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Beatriz Lopez
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Vélez Sarsfield 563, Buenos Aires 1281, Argentina
| | - Benjamin Sobkowiak
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Viviana Ritacco
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Vélez Sarsfield 563, Buenos Aires 1281, Argentina
| | - Francois Balloux
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
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Is the Beijing strain of Mycobacterium tuberculosis associated with cavitary lung disease? INFECTION GENETICS AND EVOLUTION 2015; 33:1-5. [PMID: 25891279 DOI: 10.1016/j.meegid.2015.04.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 03/31/2015] [Accepted: 04/10/2015] [Indexed: 11/24/2022]
Abstract
We conducted a cross-sectional study to describe clinical characteristics of patients with pulmonary tuberculosis with and without evidence of pulmonary cavitation on chest radiography and assess whether cavitation is associated with infection with Mycobacterium tuberculosis Beijing strain. Cases were selected from the Tuberculosis Registry (January 1, 2008-November 1, 2011) of the Florida Department of Health (FDOH). Molecular characterization was performed by spoligotyping and MIRU-VNTR. We analyzed 975 cases, where 144 (14.8%) were infected with the Beijing strain. Cavitation was not associated with disease caused by the Beijing strain. Alcohol use (OR = 1.7; 95%CI: 1.249-2.313) was associated with increased risk of cavitation in the unadjusted analyses. Multivariable analyses showed that older age (⩾ 65 years) (OR = 0.5; 95%CI: 0.233-0.871), Hispanic ethnicity (OR = 0.6; 95%CI: 0.312-0.962), and co-infection with HIV (OR = 0.1; 95%CI: 0.068-0.295) demonstrated protective effects to cavitation. Understanding the factors associated with cavitation among pulmonary cases is essential toward improved tuberculosis management and control.
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163
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Mycobacterium pinnipedii tuberculosis in a free-ranging Australian fur seal (Arctocephalus pusillus doriferus) in South Australia. J Zoo Wildl Med 2015; 45:970-2. [PMID: 25632695 DOI: 10.1638/2014-0054.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This report describes the first case in South Australia, Australia, of Mycobacterium pinnipedii tuberculosis in a free-ranging Australian fur seal (Arctocephalus pusillus doriferus). Severe pyogranulomatous pleuropneumonia with intrahistocytic acid-fast beaded filamentous bacilli was seen on histology. M. pinnipedii was confirmed by full 24-loci mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing. Spillover concerns for public health and cattle are discussed.
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164
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Yu-Feng W, Chao J, Xian-Feng C. Drug-resistant tuberculosis can be predicted by Mycobacterial interspersed repetitive unit locus. Front Microbiol 2015; 6:147. [PMID: 25759689 PMCID: PMC4338821 DOI: 10.3389/fmicb.2015.00147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 02/09/2015] [Indexed: 11/25/2022] Open
Abstract
It is unknown whether MIRU-VNTR (Mycobacterial Interspersed Repetitive Unit-Variable Number of Tandem Repeat) is associated with drug resistance of Mycobacterium tuberculosis. The purpose of this study was to explore the ability of 24 MIRU loci to predict the drug resistance of Isoniazid (INH), Rifampicin (RFP), Streptomycin (SM), Ethambutol (EMB) and Pyrazinamide (PZA). We collected the drug resistance and MIRU loci information of 109 strains of M. tuberculosis from an open database. The results of multivariate logistic regression showed that the VNTR polymorphism of MTUB04 was related to INH resistance [odds ratio (OR) = 2.82, P = 0.00], RFP resistance (OR = 1.91, P = 0.02), SM resistance (OR = 1.98, P = 0.01) and EMB resistance (OR = 1.95, P = 0.03). MIRU40 was associated with INH resistance (OR = 2.22, P = 0.00). MTUB21 was connected with INH resistance (OR = 1.63, P = 0.02) and SM resistance (OR = 1.69, P = 0.01). MIRU26 was correlated with SM resistance (OR = 1.52, P = 0.04). MIRU39 was associated with EMB resistance (OR = 4.07, P = 0.02). The prediction power of MIRU loci were 0.84, 0.70, 0.85, and 0.74 respectively for INH (predicted by MTUB04, MIRU20, and MTUB21), RFP (predicted by MTUB04), SM (predicted by MTUB21 and MIRU26) and EMB (MTUB04 and MIRU39) through ROC analysis. Our results showed that MIRU loci were related to anti-tuberculosis drug and could predict the drug resistance of tuberculosis.
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Affiliation(s)
- Wen Yu-Feng
- School of Public Health, Wannan Medical College Wuhu, China
| | - Jiang Chao
- School of Public Health, Wannan Medical College Wuhu, China
| | - Cheng Xian-Feng
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Nanjing, China
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165
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Sola C. Clustured regularly interspersed short palindromic repeats (CRISPR) genetic diversity studies as a mean to reconstruct the evolution of the Mycobacterium tuberculosis complex. Tuberculosis (Edinb) 2015; 95 Suppl 1:S159-66. [PMID: 25748060 DOI: 10.1016/j.tube.2015.02.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The natural history of tuberculosis may be tackled by various means, among which the record of molecular scars that have been registered by the Mycobacterium tuberculosis complex (MTBC) genomes transmitted from patient to patient for tens of thousands years and possibly more. Recently discovered polymorphic loci, the CRISPR sequences, are indirect witnesses of the historical phage-bacteria struggle, and may be related to the time when the ancestor of today's tubercle bacilli were environmental bacteria, i.e. before becoming intracellular parasites. In this article, we present what are CRISPRs and try to summarize almost 20 years of research results obtained using the genetic diversity of the CRISPR loci in MTBC as a perspective for studying new models. We show that the study of the diversity of CRISPR sequences, thanks to «spoligotyping», has played a great role in our global understanding of the population structure of MTBC.
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Affiliation(s)
- Christophe Sola
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Saclay, Orsay, France.
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166
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A Rapid and Sensitive Diagnostic Screening Assay for Detection of Mycobacteria Including Mycobacterium tuberculosis Directly from Sputum without Extraction. INTERNATIONAL JOURNAL OF BACTERIOLOGY 2015; 2015:593745. [PMID: 26904747 PMCID: PMC4745473 DOI: 10.1155/2015/593745] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 12/04/2014] [Accepted: 12/15/2014] [Indexed: 12/05/2022]
Abstract
We report a novel approach utilising a real-time PCR screening assay targeting a 53 bp tandemly repeated element present at various loci within the Mycobacterium tuberculosis (Mtb) genome. Positive samples were identified within a discriminatory melting curve range of 90–94°C, with results obtained in under one hour directly from decontaminated sputum samples without extraction. A panel of 89 smear-positive sputa were used for analytical validation of the assay with 100% concordance, with sensitivity matching that of culture. Cross reactivity was detected within a narrow range of mycobacteria other than tuberculosis (MOTT) (five sputa, three in silico), with the highest sensitivity within M. avium complex (MAC). A year-long head to head evaluation of the test with the GeneXpert platform was carried out with 104 consecutive samples at the Royal Free Hospital, UK. Receiver operating characteristics (ROC) analysis of the data revealed that the two tests are approximately equivalent in sensitivity, with the area under the curve being 0.85 and 0.80 for the GeneXpert and our assay, respectively, indicating that the test would be a cost effective screen prior to GeneXpert testing.
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167
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A Snapshot of Drug-Resistant M. tuberculosis Strains in Croatia. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 901:103-8. [DOI: 10.1007/5584_2015_5019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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168
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Pouseele H, Supply P. Accurate Whole-Genome Sequencing-Based Epidemiological Surveillance of Mycobacterium Tuberculosis. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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169
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Global multilocus sequence typing analysis of Mycoplasma bovis isolates reveals two main population clusters. J Clin Microbiol 2014; 53:789-94. [PMID: 25540400 DOI: 10.1128/jcm.01910-14] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycoplasma bovis is a major bovine pathogen associated with bovine respiratory disease complex and is responsible for substantial economic losses worldwide. M. bovis is also associated with other clinical presentations in cattle, including mastitis, otitis, arthritis, and reproductive disorders. To gain a better understanding of the genetic diversity of this pathogen, a multilocus sequence typing (MLST) scheme was developed and applied to the characterization of 137 M. bovis isolates from diverse geographical origins, obtained from healthy or clinically infected cattle. After in silico analysis, a final set of 7 housekeeping genes was selected (dnaA, metS, recA, tufA, atpA, rpoD, and tkt). MLST analysis demonstrated the presence of 35 different sequence types (STs) distributed in two main clonal complexes (CCs), defined at the double-locus variant level, namely, CC1, which included most of the British and German isolates, and CC2, which was a more heterogeneous and geographically distant group of isolates, including European, Asian, and Australian samples. Index of association analysis confirmed the clonal nature of the investigated M. bovis population, based on MLST data. This scheme has demonstrated high discriminatory power, with the analysis showing the presence of genetically distant and divergent clusters of isolates predominantly associated with geographical origins.
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170
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Cáceres O, Rastogi N, Bartra C, Couvin D, Galarza M, Asencios L, Mendoza-Ticona A. Characterization of the genetic diversity of extensively-drug resistant Mycobacterium tuberculosis clinical isolates from pulmonary tuberculosis patients in Peru. PLoS One 2014; 9:e112789. [PMID: 25489950 PMCID: PMC4260790 DOI: 10.1371/journal.pone.0112789] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 10/20/2014] [Indexed: 11/18/2022] Open
Abstract
Background Peru holds the fourth highest burden of tuberculosis in the Americas. Despite an apparently well-functioning DOTS control program, the prevalence of multidrug resistant tuberculosis (MDR-TB) continues to increase. To worsen this situation, cases of extensively drug resistance tuberculosis (XDR-TB) have been detected. Little information exists about the genetic diversity of drug-susceptible vs. MDR-TB and XDR-TB. Methods Cryopreserved samples of XDR strains from 2007 to 2009 (second semester), were identified and collected. Starting from 227 frozen samples, a total of 142 XDR-TB strains of Mycobacterium tuberculosis complex (MTBC; 1 isolate per patient) were retained for this study. Each strain DNA was analyzed by spoligotyping and the 15-loci Mycobacterial Interspersed Repetitive Unit (MIRU-15). Results Among the 142 isolates analyzed, only 2 samples (1.41%) could not be matched to any lineage. The most prevalent sublineage was Haarlem (43.66%), followed by T (27.46%), LAM (16.2%), Beijing (9.15%), and X clade (1.41%). Spoligotype analysis identified clustering for 128/142 (90.1%) isolates vs. 49/142 (34.5%) with MIRUs. Of the samples, 90.85% belonged to retreated patients. The drug resistant profile demonstrated that 62.67% showed resistance to injectable drugs capreomycin (CAP) and kanamycin (KAN) vs. 15.5% to CAP alone and 21.8% to KAN alone. The SIT219/T1 and SIT50/H3 were the most prevalent patterns in our study. The spoligoforest analysis showed that SIT53/T1 was at the origin of many of the T lineage strains as well as a big proportion of Haarlem lineage strains (SIT50/H3, followed by SIT47/H1, SIT49/H3, and SIT2375/H1), as opposed to the SIT1/Beijing strains that did not appear to evolve into minor Beijing sublineages among the XDR-TB strains. Conclusion In contrast with other Latin-American countries where LAM sublineage is the most predominant, we found the Haarlem to be the most common followed by T sublineage among the XDR-TB strains.
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Affiliation(s)
- Omar Cáceres
- Biotechnology and Molecular Biology Laboratory, Instituto Nacional de Salud, Lima, Peru
- * E-mail:
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, TB and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Guadeloupe, France
| | - Carlos Bartra
- Mycobacterias National Reference Laboratory, Instituto Nacional de Salud, Lima, Peru
| | - David Couvin
- WHO Supranational TB Reference Laboratory, TB and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Guadeloupe, France
| | - Marco Galarza
- Biotechnology and Molecular Biology Laboratory, Instituto Nacional de Salud, Lima, Peru
| | - Luis Asencios
- Mycobacterias National Reference Laboratory, Instituto Nacional de Salud, Lima, Peru
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171
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Mbugi EV, Katale BZ, Siame KK, Keyyu JD, Kendall SL, Dockrell HM, Streicher EM, Michel AL, Rweyemamu MM, Warren RM, Matee MI, van Helden PD. Genetic diversity of Mycobacterium tuberculosis isolated from tuberculosis patients in the Serengeti ecosystem in Tanzania. Tuberculosis (Edinb) 2014; 95:170-8. [PMID: 25522841 PMCID: PMC4364622 DOI: 10.1016/j.tube.2014.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 11/20/2014] [Accepted: 11/24/2014] [Indexed: 11/05/2022]
Abstract
This study was part of a larger cross-sectional survey that was evaluating tuberculosis (TB) infection in humans, livestock and wildlife in the Serengeti ecosystem in Tanzania. The study aimed at evaluating the genetic diversity of Mycobacterium tuberculosis isolates from TB patients attending health facilities in the Serengeti ecosystem. DNA was extracted from 214 sputum cultures obtained from consecutively enrolled newly diagnosed untreated TB patients aged ≥18 years. Spacer oligonucleotide typing (spoligotyping) and Mycobacterium Interspersed Repetitive Units and Variable Number Tandem Repeat (MIRU-VNTR) were used to genotype M. tuberculosis to establish the circulating lineages. Of the214 M. tuberculosis isolates genotyped, 55 (25.7%) belonged to the Central Asian (CAS) family, 52 (24.3%) were T family (an ill-defined family), 38 (17.8%) belonged to the Latin American Mediterranean (LAM) family, 25 (11.7%) to the East-African Indian (EAI) family, 25 (11.7%) comprised of different unassigned (‘Serengeti’) strain families, while 8 (3.7%) belonged to the Beijing family. A minority group that included Haarlem, X, U and S altogether accounted for 11 (5.2%) of all genotypes. MIRU-VNTR typing produced diverse patterns within and between families indicative of unlinked transmission chains. We conclude that, in the Serengeti ecosystem only a few successful families predominate namely CAS, T, LAM and EAI families. Other types found in lower prevalence are Beijing, Haarlem, X, S and MANU. The Haarlem, EAI_Somalia, LAM3 and S/convergent and X2 subfamilies found in this study were not reported in previous studies in Tanzania.
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Affiliation(s)
- Erasto V Mbugi
- Department of Biochemistry, Muhimbili University of Health and Allied Sciences, P. O. Box 65001 Dar es Salaam, Tanzania; Departments of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001 Dar es Salaam, Tanzania.
| | - Bugwesa Z Katale
- Departments of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001 Dar es Salaam, Tanzania; Tanzania Wildlife Research Institute (TAWIRI), P.O. Box 661, Arusha, Tanzania.
| | - Keith K Siame
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ Medical Research Council (MRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, P. O. Box 19063, Tygerberg, 7505, South Africa.
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), P.O. Box 661, Arusha, Tanzania.
| | - Sharon L Kendall
- The Royal Veterinary College, Royal College Street, London, NW1 0TU, United Kingdom.
| | - Hazel M Dockrell
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom.
| | - Elizabeth M Streicher
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ Medical Research Council (MRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, P. O. Box 19063, Tygerberg, 7505, South Africa.
| | - Anita L Michel
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, South Africa.
| | - Mark M Rweyemamu
- Southern African Centre for Infectious Disease Surveillance, Sokoine University of Agriculture, Morogoro, Tanzania.
| | - Robin M Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ Medical Research Council (MRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, P. O. Box 19063, Tygerberg, 7505, South Africa.
| | - Mecky I Matee
- Departments of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001 Dar es Salaam, Tanzania.
| | - Paul D van Helden
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ Medical Research Council (MRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, P. O. Box 19063, Tygerberg, 7505, South Africa.
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High-throughput mycobacterial interspersed repetitive-unit-variable-number tandem-repeat genotyping for Mycobacterium tuberculosis epidemiological studies. J Clin Microbiol 2014; 53:498-503. [PMID: 25428144 DOI: 10.1128/jcm.01611-14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The emergence of drug-resistant forms of tuberculosis (TB) represents a major public health concern. Understanding the transmission routes of the disease is a key factor for its control and for the implementation of efficient interventions. Mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) marker typing is a well-described method for lineage identification and transmission tracking. However, the conventional manual genotyping technique is cumbersome and time-consuming and entails many risks for errors, thus hindering its implementation and dissemination. We describe here a new approach using the QIAxcel system, an automated high-throughput capillary electrophoresis system that also carries out allele calling. This automated method was assessed on 1,824 amplicons from 82 TB isolates and tested with sets of markers of 15 or 24 loci. Overall allele-calling concordance between the methods from 140 to 1,317 bp was 98.9%. DNA concentrations and repeatability and reproducibility performances showed no biases in allele calling. Furthermore, turnaround time using this automated system was reduced by 81% compared to the conventional manual agarose gel method. In sum, this new automated method facilitates MIRU-VNTR genotyping and provides reliable results. Therefore, it is well suited for field genotyping. The implementation of this method will help to achieve accurate and cost-effective epidemiological studies, especially in countries with a high prevalence of TB, where the high number of strains complicates the surveillance of circulating lineages and requires efficient interventions to be carried out in an urgent manner.
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173
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Molecular confirmation of Bacillus Calmette Guerin vaccine related adverse events among Saudi Arabian children. PLoS One 2014; 9:e113472. [PMID: 25409184 PMCID: PMC4237431 DOI: 10.1371/journal.pone.0113472] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 10/23/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Bacillus Calmette Guerin (BCG) is the only available vaccine for tuberculosis (TB). Low grade complications in healthy recipients and disseminated vaccine associated complications among immuno-suppressed individuals were noticed globally after administration. Recently a series of clinically suspected BCG associated suppurative and non-suppurative lymphadenitis cases were reported from different regions of Saudi Arabia. However a molecular confirmative analysis was lacking to prove these claims. METHODOLOGY During 2009-2010, 42 Mycobacterium bovis BCG suspected clinical isolates from children diagnosed with suppurative lymphadenitis from different provinces of the country were collected and subjected to 24 loci based MIRU-VNTR typing, spoligotyping and first line anti-TB drugs susceptibility testing. PRINCIPAL FINDINGS Of the total 42 cases, 41 (97.6%) were Saudi nationals and particularly male (64.3%). Majority of the cases were aged below 6 months (83.3%) with a median of age 4 months. All the enrolled subjects showed left axillary mass which suppurated in a median of 4 months after vaccination. Among the study subjects, 1 (2.4%) case was reactive to HIV antigen and 2 (4.8%) case had severe combined immunodeficiency. Genotyping results showed that, 41 (97.6%) isolates were identical to the vaccine strain Danish 1331 and one to Tokyo 172-1. Phylogenetic analysis revealed all the Danish 1331 isolates in a single cluster. CONCLUSION Elevated proportion of suppurative lymphadenitis caused by M. bovis BCG reported in the country recently is majorly related to the vaccine strain Danish 1331. However lack of nationwide data on real magnitude of BCG related adverse events warrants population centric, long term future studies.
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Toit K, Altraja A, Acosta CD, Viiklepp P, Kremer K, Kummik T, Danilovitš M, Van den Bergh R, Harries AD, Supply P. A four-year nationwide molecular epidemiological study in Estonia: risk factors for tuberculosis transmission. Public Health Action 2014; 4:S34-40. [PMID: 26393096 PMCID: PMC4547518 DOI: 10.5588/pha.14.0045] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 07/27/2014] [Indexed: 02/03/2023] Open
Abstract
SETTING Estonia has a high proportion of multidrug-resistant tuberculosis (MDR-TB). It is important to link molecular and epidemiological data to understand TB transmission patterns. OBJECTIVE To use 24-locus variable numbers of tandem repeat (VNTR) typing and national TB registry data in Estonia from 2009 to 2012 to identify the distribution of drug resistance patterns, Mycobacterium tuberculosis isolate clustering as an index for recent transmission, socio-demographic and clinical characteristics associated with recent transmission, and the distribution of transmission between index and secondary cases. DESIGN A retrospective nationwide cross-sectional study. RESULTS Of 912 cases with isolate and patient information, 39.1% of isolates were from the Beijing lineage. Cluster analysis identified 87 clusters encompassing 69.1% of isolates. The largest cluster comprised 178 isolates from the Beijing lineage, of which 92.1% were MDR- or extensively drug-resistant TB (XDR-TB). Factors associated with recent transmission were polyresistant TB, MDR- and XDR-TB, human immunodeficiency virus positivity, Russian ethnicity, non-permanent living situation, alcohol abuse and detention. XDR-TB cases had the highest risk of recent transmission. The majority of transmission cases involved individuals aged 30-39 years. CONCLUSION Recent TB transmission in Estonia is high and is particularly associated with MDR- and XDR-TB and the Beijing lineage.
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Affiliation(s)
- K. Toit
- United Laboratories, Tartu University Hospital, Tartu, Estonia
- Department of Pulmonary Medicine, University of Tartu, Tartu, Estonia
| | - A. Altraja
- Department of Pulmonary Medicine, University of Tartu, Tartu, Estonia
- Lung Clinic, Tartu University Hospital, Tartu, Estonia
| | - C. D. Acosta
- Tuberculosis and M/XDR-TB Programme, Division of Communicable Diseases, Health Security & Environment, World Health Organization Regional Office for Europe, Copenhagen, Denmark
| | - P. Viiklepp
- National Institute for Health Development, Tallinn, Estonia
| | - K. Kremer
- Tuberculosis and M/XDR-TB Programme, Division of Communicable Diseases, Health Security & Environment, World Health Organization Regional Office for Europe, Copenhagen, Denmark
- Centre for Infectious Diseases Control, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | - T. Kummik
- United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - M. Danilovitš
- Lung Clinic, Tartu University Hospital, Tartu, Estonia
| | - R. Van den Bergh
- Medical Department, Brussels Operational Center, Médecins Sans Frontières MSF-Luxembourg, Luxembourg
| | - A. D. Harries
- International Union Against Tuberculosis and Lung Disease, Paris, France
- London School of Hygiene & Tropical Medicine, London, UK
| | - P. Supply
- Institut National de la Santé et de la Recherche Médicale 1019, Lille, France
- Unités Mixtes de Recherche 8204, Centre national de la Recherche scientifique, Lille, France
- Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Lille, France
- University Nord de France, Lille, France
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175
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Abstract
Pyrazinamide (PZA) is a prodrug that is converted to pyrazinoic acid by the enzyme pyrazinamidase, encoded by the pncA gene in Mycobacterium tuberculosis. Molecular identification of mutations in pncA offers the potential for rapid detection of pyrazinamide resistance (PZAr). However, the genetic variants are highly variable and scattered over the full length of pncA, complicating the development of a molecular test. We performed a large multicenter study assessing pncA sequence variations in 1,950 clinical isolates, including 1,142 multidrug-resistant (MDR) strains and 483 fully susceptible strains. The results of pncA sequencing were correlated with phenotype, enzymatic activity, and structural and phylogenetic data. We identified 280 genetic variants which were divided into four classes: (i) very high confidence resistance mutations that were found only in PZAr strains (85%), (ii) high-confidence resistance mutations found in more than 70% of PZAr strains, (iii) mutations with an unclear role found in less than 70% of PZAr strains, and (iv) mutations not associated with phenotypic resistance (10%). Any future molecular diagnostic assay should be able to target and identify at least the very high and high-confidence genetic variant markers of PZAr; the diagnostic accuracy of such an assay would be in the range of 89.5 to 98.8%. Conventional phenotypic testing for pyrazinamide resistance in Mycobacterium tuberculosis is technically challenging and often unreliable. The development of a molecular assay for detecting pyrazinamide resistance would be a breakthrough, directly overcoming both the limitations of conventional testing and its related biosafety issues. Although the main mechanism of pyrazinamide resistance involves mutations inactivating the pncA enzyme, the highly diverse genetic variants scattered over the full length of the pncA gene and the lack of a reliable phenotypic gold standard hamper the development of molecular diagnostic assays. By analyzing a large number of strains collected worldwide, we have classified the different genetic variants based on their predictive value for resistance which should lead to more rapid diagnostic tests. This would assist clinicians in improving treatment regimens for patients.
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176
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Verdugo C, Pleydell E, Price-Carter M, Prattley D, Collins D, de Lisle G, Vogue H, Wilson P, Heuer C. Molecular epidemiology of Mycobacterium avium subsp. paratuberculosis isolated from sheep, cattle and deer on New Zealand pastoral farms. Prev Vet Med 2014; 117:436-46. [PMID: 25315761 DOI: 10.1016/j.prevetmed.2014.09.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 09/26/2014] [Accepted: 09/26/2014] [Indexed: 10/24/2022]
Abstract
The present study aimed to describe the molecular diversity of Mycobacterium avium subsp. paratuberculosis (MAP) isolates obtained from sheep, cattle (beef and dairy) and deer farms in New Zealand. A total of 206 independent MAP isolates (15 beef cattle, 89 dairy cattle, 35 deer, 67 sheep) were sourced from 172 species-mobs (15 beef cattle, 66 dairy cattle, 31 deer, 60 sheep). Seventeen subtypes were identified, using a combination of variable number of tandem repeats (VNTR) and short sequence repeat (SSR) methods. Rarefaction analysis, analysis of molecular variance (AMOVA), Fst pairwise comparisons and proportional similarity index (PSI) were used to describe subtype population richness, genetic structure and potential associations between livestock sectors and New Zealand two main islands (North and South). The rarefaction analysis suggests a significantly higher subtype richness in dairy cattle herds when compared to the other livestock sectors. AMOVA results indicate that the main source of subtype variation is attributable to the livestock sector from which samples were sourced suggesting that subtypes are generally sector-specific. The pairwise Fst results were similar, with low Fst values for island differences within a livestock sector when compared to between sector analyses, representing a low subtype differentiation between islands. However, for a given island, potential associations were seen between dominant subtypes and specific livestock sectors. Three subtypes accounted for 76% of the isolates. The most common of these was isolated from sheep and beef cattle in the North Island, the second most frequent subtype was mainly isolated from dairy cattle (either island), while the third most common subtype was associated with deer farmed in the South Island. The PSI analysis suggests similarities in subtypes sourced from sheep and beef cattle. This contrasted with the isolates sourced from other livestock sectors, which tended to present sector-specific subtypes. Sheep and beef cattle were mainly infected with MAP Type I, while dairy cattle and deer were almost exclusively infected with MAP Type II. However, when beef cattle and deer were both present at farm level, they harboured similar subtypes. This study indicates that cross-species transmission of MAP occurs on New Zealand farms although close contact between species appears to be required, as in the case of sheep and beef cattle which are commonly grazed together in New Zealand.
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Affiliation(s)
- Cristobal Verdugo
- Instituto de Medicina Preventiva Veterinaria, Universidad Austral de Chile, Valdivia, Chile; EpiCentre, Massey University, Private Bag 11-222, Palmerston North, New Zealand.
| | - Eve Pleydell
- Infectious Disease Research Centre, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - Marian Price-Carter
- AgResearch, National Centre for Biosecurity and Infectious Disease, Wallaceville, P.O. Box 40063, Upper Hutt, New Zealand
| | - Deborah Prattley
- Infectious Disease Research Centre, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - Desmond Collins
- AgResearch, National Centre for Biosecurity and Infectious Disease, Wallaceville, P.O. Box 40063, Upper Hutt, New Zealand
| | - Geoffrey de Lisle
- AgResearch, National Centre for Biosecurity and Infectious Disease, Wallaceville, P.O. Box 40063, Upper Hutt, New Zealand
| | - Hinrich Vogue
- Livestock Improvement Corporation, Private Bag 3016, Hamilton, New Zealand
| | - Peter Wilson
- Institute of Veterinary, Animal, and Biomedical Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - Cord Heuer
- EpiCentre, Massey University, Private Bag 11-222, Palmerston North, New Zealand
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177
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Rindi L, Medici C, Bimbi N, Buzzigoli A, Lari N, Garzelli C. Genomic variability of Mycobacterium tuberculosis strains of the Euro-American lineage based on large sequence deletions and 15-locus MIRU-VNTR polymorphism. PLoS One 2014; 9:e107150. [PMID: 25197794 PMCID: PMC4157836 DOI: 10.1371/journal.pone.0107150] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 08/11/2014] [Indexed: 11/19/2022] Open
Abstract
A sample of 260 Mycobacterium tuberculosis strains assigned to the Euro-American family was studied to identify phylogenetically informative genomic regions of difference (RD). Mutually exclusive deletions of regions RD115, RD122, RD174, RD182, RD183, RD193, RD219, RD726 and RD761 were found in 202 strains; the RDRio deletion was detected exclusively among the RD174-deleted strains. Although certain deletions were found more frequently in certain spoligotype families (i.e., deletion RD115 in T and LAM, RD174 in LAM, RD182 in Haarlem, RD219 in T and RD726 in the “Cameroon” family), the RD-defined sublineages did not specifically match with spoligotype-defined families, thus arguing against the use of spoligotyping for establishing exact phylogenetic relationships between strains. Notably, when tested for katG463/gyrA95 polymorphism, all the RD-defined sublineages belonged to Principal Genotypic Group (PGG) 2, except sublineage RD219 exclusively belonging to PGG3; the 58 Euro-American strains with no deletion were of either PGG2 or 3. A representative sample of 197 isolates was then analyzed by standard 15-locus MIRU-VNTR typing, a suitable approach to independently assess genetic relationships among the strains. Analysis of the MIRU-VNTR typing results by using a minimum spanning tree (MST) and a classical dendrogram showed groupings that were largely concordant with those obtained by RD-based analysis. Isolates of a given RD profile show, in addition to closely related MIRU-VNTR profiles, related spoligotype profiles that can serve as a basis for better spoligotype-based classification.
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Affiliation(s)
- Laura Rindi
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
- * E-mail:
| | - Chiara Medici
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
| | - Nicola Bimbi
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
| | - Andrea Buzzigoli
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
| | - Nicoletta Lari
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
| | - Carlo Garzelli
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
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178
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Diversity and evolution of Mycobacterium tuberculosis: moving to whole-genome-based approaches. Cold Spring Harb Perspect Med 2014; 4:a021188. [PMID: 25190252 DOI: 10.1101/cshperspect.a021188] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Genotyping of clinical Mycobacterium tuberculosis complex (MTBC) strains has become a standard tool for epidemiological tracing and for the investigation of the local and global strain population structure. Of special importance is the analysis of the expansion of multidrug (MDR) and extensively drug-resistant (XDR) strains. Classical genotyping and, more recently, whole-genome sequencing have revealed that the strains of the MTBC are more diverse than previously anticipated. Globally, several phylogenetic lineages can be distinguished whose geographical distribution is markedly variable. Strains of particular (sub)lineages, such as Beijing, seem to be more virulent and associated with enhanced resistance levels and fitness, likely fueling their spread in certain world regions. The upcoming generalization of whole-genome sequencing approaches will expectedly provide more comprehensive insights into the molecular and epidemiological mechanisms involved and lead to better diagnostic and therapeutic tools.
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179
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Dymova MA, Cherednichenko AG, Alkhovik OI, Khrapov EA, Petrenko TI, Filipenko ML. Characterization of extensively drug-resistant Mycobacterium tuberculosis isolates circulating in Siberia. BMC Infect Dis 2014; 14:478. [PMID: 25186134 PMCID: PMC4161839 DOI: 10.1186/1471-2334-14-478] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 08/29/2014] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The spread of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mycobacterium tuberculosis compromises effective control of tuberculosis (TB) in Siberia. Early identification of drug-resistant isolates is, therefore, crucial for effective treatment of this disease. The aim of this study was to conduct drug susceptibility testing and identify mutations in drug resistance genes in clinical isolates of M. tuberculosis from some TB patients presenting for treatment in Siberia. METHODS Thirty randomly selected clinical isolates of M. tuberculosis were obtained from the Novosibirsk Research Institute of Tuberculosis, Russia. Isolates were screened for drug resistance and characterized by variable number of tandem repeats (VNTR)-typing using 15 standard and four additional loci. Deligotyping on multiple large sequences was performed using 10 loci. RESULTS Twenty-nine of the isolates were assigned XDR status. Twenty-eight isolates belonged to the M. tuberculosis Beijing family, from which 11 isolates were considered the M11 type (39%), two the M2 type (7%), and one the M33 type (3%). Seventeen isolates (60.7%) from this family exhibited unique genetic patterns. The remaining two isolates belonged to the Latino-American Mediterranean family. Gene sequences (rpoB, katG, rrs, rpsL, tlyA, gidB, gyrA, gyrB) were analyzed to identify mutations that confer resistance to rifampicin, isoniazid, amikacin, kanamycin, capreomycin, and ofloxacin. The most common mutations among the XDR isolates were S531L in RpoB, S315T in KatG, various codon 94 mutations in gyrA, A90V in GyrA, K43R in RpsL, and 1401 A → G in rrs; these confer resistance to rifampicin, isoniazid, ofloxacin, streptomycin and kanamycin/capreomycin, respectively. There was high congruence between the two typing methods (VNTR typing and deligotyping) and RD105, RD149, RD152, RD181, and RD207 regions of difference were absent from the 28 Beijing family isolates. CONCLUSIONS Deligotyping can be used for rapid and reliable screening of M. tuberculosis isolates, followed by more in-depth genotyping. Identification of Beijing family isolates with extensive drug resistance confirms that such strains have epidemiological importance in Siberia. Rapid detection of mutations that lead to drug resistance should facilitate selection of effective drug therapies, and the development of early prevention strategies to combat this infection.
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Affiliation(s)
- Maya A Dymova
- />Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of The Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
- />Novosibirsk State University (NSU), Novosibirsk, Russia
| | - Andrey G Cherednichenko
- />Ministry of Public Health and Social Development of The Russian Federation (NRIT), Novosibirsk Research Institute of Tuberculosis, Novosibirsk, Russia
| | - Olga I Alkhovik
- />Ministry of Public Health and Social Development of The Russian Federation (NRIT), Novosibirsk Research Institute of Tuberculosis, Novosibirsk, Russia
| | - Eugeny A Khrapov
- />Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of The Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - Tatjana I Petrenko
- />Ministry of Public Health and Social Development of The Russian Federation (NRIT), Novosibirsk Research Institute of Tuberculosis, Novosibirsk, Russia
| | - Maxim L Filipenko
- />Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of The Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
- />Novosibirsk State University (NSU), Novosibirsk, Russia
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180
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Abstract
SUMMARY We analysed Mycobacterium tuberculosis strains from children, hospitalized from January 2004 to July 2008 in the largest paediatric hospital complex in Cambodia. Specimens were tested for drug susceptibility and genotypes. From the 260 children, 161 strains were available. The East African-Indian genotype family was the most common (59.0%), increasing in frequency with distance from the Phnom Penh area, while the frequency of the Beijing genotype family strains decreased. The drug resistance pattern showed a similar geographical gradient: lowest in the northwest (4.6%), intermediate in the central (17.1%), and highest in the southeastern (30.8%) parts of the country. Three children (1.9%) had multidrug-resistant tuberculosis. The Beijing genotype and streptomycin resistance were significantly associated (P < 0.001). As tuberculosis in children reflects recent transmission patterns in the community, multidrug resistance levels inform about the current quality of the tuberculosis programme.
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181
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Sengstake S, Bablishvili N, Schuitema A, Bzekalava N, Abadia E, de Beer J, Tadumadze N, Akhalaia M, Tuin K, Tukvadze N, Aspindzelashvili R, Bachiyska E, Panaiotov S, Sola C, van Soolingen D, Klatser P, Anthony R, Bergval I. Optimizing multiplex SNP-based data analysis for genotyping of Mycobacterium tuberculosis isolates. BMC Genomics 2014; 15:572. [PMID: 25001491 PMCID: PMC4117977 DOI: 10.1186/1471-2164-15-572] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 06/19/2014] [Indexed: 11/10/2022] Open
Abstract
Background Multiplex ligation-dependent probe amplification (MLPA) is a powerful tool to identify genomic polymorphisms. We have previously developed a single nucleotide polymorphism (SNP) and large sequence polymorphisms (LSP)-based MLPA assay using a read out on a liquid bead array to screen for 47 genetic markers in the Mycobacterium tuberculosis genome. In our assay we obtain information regarding the Mycobacterium tuberculosis lineage and drug resistance simultaneously. Previously we called the presence or absence of a genotypic marker based on a threshold signal level. Here we present a more elaborate data analysis method to standardize and streamline the interpretation of data generated by MLPA. The new data analysis method also identifies intermediate signals in addition to classification of signals as positive and negative. Intermediate calls can be informative with respect to identifying the simultaneous presence of sensitive and resistant alleles or infection with multiple different Mycobacterium tuberculosis strains. Results To validate our analysis method 100 DNA isolates of Mycobacterium tuberculosis extracted from cultured patient material collected at the National TB Reference Laboratory of the National Center for Tuberculosis and Lung Diseases in Tbilisi, Republic of Georgia were tested by MLPA. The data generated were interpreted blindly and then compared to results obtained by reference methods. MLPA profiles containing intermediate calls are flagged for expert review whereas the majority of profiles, not containing intermediate calls, were called automatically. No intermediate signals were identified in 74/100 isolates and in the remaining 26 isolates at least one genetic marker produced an intermediate signal. Conclusion Based on excellent agreement with the reference methods we conclude that the new data analysis method performed well. The streamlined data processing and standardized data interpretation allows the comparison of the Mycobacterium tuberculosis MLPA results between different experiments. All together this will facilitate the implementation of the MLPA assay in different settings. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-572) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sarah Sengstake
- KIT Biomedical Research, Royal Tropical Institute, Meibergdreef 39, 1105 AZ Amsterdam, The Netherlands.
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182
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Genetic diversity of Mycobacterium tuberculosis isolates obtained from patients with pulmonary tuberculosis in Beira city, Mozambique. Int J Mycobacteriol 2014; 3:94-100. [DOI: 10.1016/j.ijmyco.2014.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 03/27/2014] [Accepted: 03/31/2014] [Indexed: 11/23/2022] Open
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183
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Nebenzahl-Guimaraes H, Borgdorff MW, Murray MB, van Soolingen D. A novel approach - the propensity to propagate (PTP) method for controlling for host factors in studying the transmission of Mycobacterium tuberculosis. PLoS One 2014; 9:e97816. [PMID: 24849817 PMCID: PMC4029888 DOI: 10.1371/journal.pone.0097816] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 04/24/2014] [Indexed: 11/18/2022] Open
Abstract
Rationale Understanding the genetic variations among Mycobacterium tuberculosis (MTB) strains with differential ability to transmit would be a major step forward in preventing transmission. Objectives To describe a method to extend conventional proxy measures of transmissibility by adjusting for patient-related factors, thus strengthening the causal association found with bacterial factors. Methods Clinical, demographic and molecular fingerprinting data were obtained during routine surveillance of verified MTB cases reported in the Netherlands between 1993 and 2011, and the phylogenetic lineages of the isolates were inferred. Odds ratios for host risk factors for clustering were used to obtain a measure of each patient's and cluster's propensity to propagate (CPP). Mean and median cluster sizes across different categories of CPP were compared amongst four different phylogenetic lineages. Results Both mean and median cluster size grew with increasing CPP category. On average, CPP values from Euro-American lineage strains were higher than Beijing and EAI strains. There were no significant differences between the mean and median cluster sizes among the four phylogenetic lineages within each CPP category. Conclusions Our finding that the distribution of CPP scores was unequal across four different phylogenetic lineages supports the notion that host-related factors should be controlled for to attain comparability in measuring the different phylogenetic lineages' ability to propagate. Although Euro-American strains were more likely to be in clusters in an unadjusted analysis, no significant differences among the four lineages persisted after we controlled for host factors.
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Affiliation(s)
- Hanna Nebenzahl-Guimaraes
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
- ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
- * E-mail:
| | - Martien W. Borgdorff
- Public Health Service, Amsterdam, Netherlands
- Department of Clinical Epidemiology, Academic Medical Centre, University of Amsterdam, Amsterdam, Netherlands
| | - Megan B. Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, United States of America
| | - Dick van Soolingen
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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184
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Prevalence of Extensively Drug Resistant Tuberculosis among Archived Multidrug Resistant Tuberculosis Isolates in Zimbabwe. Tuberc Res Treat 2014; 2014:349141. [PMID: 24967101 PMCID: PMC4054961 DOI: 10.1155/2014/349141] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Revised: 04/27/2014] [Accepted: 04/28/2014] [Indexed: 11/17/2022] Open
Abstract
We conducted a cross-sectional study of second line drug resistance patterns and genetic diversity of MDR-TB isolates archived at the BRTI-TB Laboratory, Harare, between January 2007 and December 2011. DSTs were performed for second line antituberculosis drugs. XDR-TB strains were defined as MDR-TB strains with resistance to either kanamycin and ofloxacin or capreomycin and ofloxacin. Strain types were identified by spoligotyping. No resistance to any second line drugs was shown in 73% of the isolates, with 23% resistant to one or two drugs but not meeting the definition of XDR-TB. A total of 26 shared types were identified, and 18 (69%) matched preexisting shared types in the current published spoligotype databases. Of the 11 out of 18 clustered SITs, 4 predominant (>6 isolates per shared type) were identified. The most and least abundant types were SIT 1468 (LAM 11-ZWE) with 12 (18%) isolates and SIT 53 (T1) with 6 (9%) isolates, respectively. XDR-TB strains are rare in Zimbabwe, but the high proportion of “pre-XDR-TB” strains and treatment failure cases is of concern. The genetic diversity of the MDR-TB strains showed no significant association between SITs and drug resistance.
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185
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Mixed Mycobacterium tuberculosis complex infections and false-negative results for rifampin resistance by GeneXpert MTB/RIF are associated with poor clinical outcomes. J Clin Microbiol 2014; 52:2422-9. [PMID: 24789181 DOI: 10.1128/jcm.02489-13] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The Xpert MTB/RIF (Xpert) assay is becoming a principal screening tool for diagnosing rifampin-resistant Mycobacterium tuberculosis complex (MTBC) infection. However, little is known about the performance of the Xpert assay in infections with both drug-sensitive and drug-resistant strains (mixed MTBC infections). We assessed the performance of the Xpert assay for detecting rifampin resistance using phenotypic drug sensitivity testing (DST) as the reference standard in 370 patients with microbiologically proven pulmonary tuberculosis. Mixed MTBC infections were identified genetically through 24-locus mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) analysis. Logistic regression was used to identify the factors associated with poor (defined as treatment failure, default, and death from any cause) or good (defined as cure or successful treatment completion) clinical outcomes. The analytic sensitivity of the Xpert assay for detecting rifampin resistance was assessed in vitro by testing cultures containing different ratios of drug-sensitive and drug-resistant organisms. Rifampin resistance was detected by the Xpert assay in 52 (14.1%) and by phenotypic DST in 55 (14.9%) patients. Mixed MTBC infections were identified in 37 (10.0%) patients. The Xpert assay was 92.7% (95% confidence interval [CI], 82.4% to 97.9%) sensitive for detecting rifampin resistance and 99.7% (95% CI, 98.3% to 99.9%) specific. When restricted to patients with mixed MTBC infections, Xpert sensitivity was 80.0% (95% CI, 56.3 to 94.3%). False-negative Xpert results (adjusted odds ratio [aOR], 6.6; 95% CI,1.2 to 48.2) and mixed MTBC infections (aOR, 6.5; 95% CI, 2.1 to 20.5) were strongly associated with poor clinical outcome. The Xpert assay failed to detect rifampin resistance in vitro when <90% of the organisms in the sample were rifampin resistant. Our study indicates that the Xpert assay has an increased false-negative rate for detecting rifampin resistance with mixed MTBC infections. In hyperendemic settings where mixed infections are common, the Xpert results might need further confirmation.
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186
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The T2 Mycobacterium tuberculosis genotype, predominant in Kampala, Uganda, shows negative correlation with antituberculosis drug resistance. Antimicrob Agents Chemother 2014; 58:3853-9. [PMID: 24777100 DOI: 10.1128/aac.02338-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Surveillance of the circulating Mycobacterium tuberculosis complex (MTC) strains in a given locality is important for understanding tuberculosis (TB) epidemiology. We performed molecular epidemiological studies on sputum smear-positive isolates that were collected for anti-TB drug resistance surveillance to establish the variability of MTC lineages with anti-TB drug resistance and HIV infection. Spoligotyping was performed to determine MTC phylogenetic lineages. We compared patients' MTC lineages with drug susceptibility testing (DST) patterns and HIV serostatus. Out of the 533 isolates, 497 (93.2%) had complete DST, PCR, and spoligotyping results while 484 (90.1%) participants had results for HIV testing. Overall, the frequency of any resistance was 75/497 (15.1%), highest among the LAM (34.4%; 95% confidence interval [CI], 18.5 to 53.2) and lowest among the T2 (11.5%; 95% CI, 7.6 to 16.3) family members. By multivariate analysis, LAM (adjusted odds ratio [OR(adj)], 5.0; 95% CI, 2.0 to 11.9; P < 0.001) and CAS (OR(adj), 2.9; 95% CI, 1.4.0 to 6.3; P = 0.006) families were more likely to show any resistance than was T2. All other MTC lineages combined were more likely to be resistant to any of the anti-TB drugs than were the T2 strains (OR(adj), 1.7; 95% CI, 1.0 to 2.9; P = 0.040). There were no significant associations between multidrug resistance and MTC lineages, but numbers of multidrug-resistant TB strains were small. No association was established between MTC lineages and HIV status. In conclusion, the T2 MTC lineage negatively correlates with anti-TB drug resistance, which might partly explain the reported low levels of anti-TB drug resistance in Kampala, Uganda. Patients' HIV status plays no role with respect to the MTC lineage distribution.
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187
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Cross GB, Coles K, Nikpour M, Moore OA, Denholm J, McBryde ES, Eisen DP, Warigi B, Carter R, Pandey S, Harino P, Siba P, Coulter C, Mueller I, Phuanukoonnon S, Pellegrini M. TB incidence and characteristics in the remote gulf province of Papua New Guinea: a prospective study. BMC Infect Dis 2014; 14:93. [PMID: 24555577 PMCID: PMC3936911 DOI: 10.1186/1471-2334-14-93] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 02/18/2014] [Indexed: 11/10/2022] Open
Abstract
Background The incidence and characteristics of tuberculosis (TB) in remote areas of Papua New Guinea (PNG) are largely unknown. The purpose of our study was to determine the incidence of TB in the Gulf Province of PNG and describe disease characteristics, co-morbidities and drug resistance profiles that could impact on disease outcomes and transmission. Methods Between March 2012 and June 2012, we prospectively collected data on 274 patients presenting to Kikori Hospital with a presumptive diagnosis of TB, and on hospital inpatients receiving TB treatment during the study period. Sputum was collected for microscopy, GeneXpert analysis, culture and genotyping of isolates. Results We estimate the incidence of TB in Kikori to be 1290 per 100,000 people (95% CI 1140 to 1460) in 2012. The proportion of TB patients co-infected with HIV was 1.9%. Three of 32 TB cases tested were rifampicin resistant. Typing of nine isolates demonstrated allelic diversity and most were related to Beijing strains. Conclusions The incidence of TB in Kikori is one of the highest in the world and it is not driven by HIV co-infection. The high incidence and the presence of rifampicin resistant warrant urgent attention to mitigate substantial morbidity in the region.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Suparat Phuanukoonnon
- Infection and Immunity Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.
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The seal tuberculosis agent, Mycobacterium pinnipedii, infects domestic cattle in New Zealand: epidemiologic factors and DNA strain typing. J Wildl Dis 2014; 50:180-7. [PMID: 24484478 DOI: 10.7589/2013-09-237] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The fur seal (Arctocephalus forsteri), which is abundant in coastal areas of New Zealand, harbors several zoonotic pathogens, including Mycobacterium pinnipedii, a member of the Mycobacterium tuberculosis complex. We describe the microbiology and epidemiology of seven cases of M. pinnipedii infection in beef cattle (Bos primigenius) in coastal areas of New Zealand in 1991-2011. Epidemiologic factors were analyzed on six case farms and a telephone survey of 55 neighboring farms. A DNA-strain typing, using analysis of variable number tandem repeats and the direct repeats (VNTR/DR) of those isolates, was used to compare them to M. bovis isolates commonly found in New Zealand cattle and wildlife. In all cases of M. pinnipedii in cattle, only one animal in the herd was found to be infected. In six of seven cases, the lesions were in the thoracic lymph nodes, indicating a likely aerosol pathway. The lack of multiple cases within a herd suggests that cow-to-cow transmission is uncommon, if it occurs at all. There was no significant difference between case and control farms in distance to sea, herd size, herd type, or farming practice. The odds ratio for access to the beach for cattle on the Chatham Islands was significantly higher than it was for farms on the mainland coastal areas (odds ratio [OR] = 3.6, 95% CI = 1.1-11.4) Likewise, the odds ratio for acquiring tuberculosis was increased when farmers had seen seals on the property (OR = 9, 95% CI = 1.4-56.1 ). In all case farms, cattle had access to seals by beach grazing areas or waterways connecting directly with the ocean. The VNTR/DR typing of the isolates showed some variation in the M. pinnipedii isolates, with only two being identical; all isolates were easily distinguishable from M. bovis isolates.
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Current methods in the molecular typing of Mycobacterium tuberculosis and other mycobacteria. BIOMED RESEARCH INTERNATIONAL 2014; 2014:645802. [PMID: 24527454 PMCID: PMC3914561 DOI: 10.1155/2014/645802] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 11/18/2013] [Indexed: 11/18/2022]
Abstract
In the epidemiology of tuberculosis (TB) and nontuberculous mycobacterial (NTM) diseases, as in all infectious diseases, the key issue is to define the source of infection and to disclose its routes of transmission and dissemination in the environment. For this to be accomplished, the ability of discerning and tracking individual Mycobacterium strains is of critical importance. Molecular typing methods have greatly improved our understanding of the biology of mycobacteria and provide powerful tools to combat the diseases caused by these pathogens. The utility of various typing methods depends on the Mycobacterium species under investigation as well as on the research question. For tuberculosis, different methods have different roles in phylogenetic analyses and person-to-person transmission studies. In NTM diseases, most investigations involve the search for environmental sources or phylogenetic relationships. Here, too, the type of setting determines which methodology is most suitable. Within this review, we summarize currently available molecular methods for strain typing of M. tuberculosis and some NTM species, most commonly associated with human disease. For the various methods, technical practicalities as well as discriminatory power and accomplishments are reviewed.
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190
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Lu W, Lu B, Liu Q, Dong H, Shao Y, Jiang Y, Song H, Chen C, Li G, Xu W, Zhao X, Wan K, Zhu L. Genotypes of Mycobacterium tuberculosis isolates in rural China: using MIRU-VNTR and spoligotyping methods. ACTA ACUST UNITED AC 2013; 46:98-106. [PMID: 24359517 DOI: 10.3109/00365548.2013.858182] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND The genotypes of Mycobacterium tuberculosis (MTB) have been found to be related to the risk of transmission and the development of drug resistance of this pathogen. Thus, exploring the molecular characteristics of MTB is helpful for understanding and controlling the spread of strains in areas with a high incidence of tuberculosis. METHODS We recruited 512 sputum smear-positive tuberculosis patients from 30 counties from 1 April to 30 June 2010; 503 MTB strains were isolated and 497 were successfully genotyped. We genotyped the strains based on a new 15-locus mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR) method in combination with spacer-oligonucleotide typing (spoligotyping) technology. RESULTS Based on spoligotyping, 487 strains displayed known patterns, and 10 were absent from the current global spoligotyping database (SpolDB4). The predominant spoligotypes belonged to the Beijing or Beijing-like family (81.1%). When we used the new 15-locus (MIRU-15) set for the MIRU-VNTR analysis, 388 different patterns were identified, including 46 clusters and 342 unique patterns. The combination of spoligotyping and MIRU-15 demonstrated a high discriminatory power. The proportion of clusters varied significantly between the Beijing and non-Beijing family strains, but no significant association was observed between multidrug resistance and Beijing family strains. CONCLUSIONS The present study demonstrated that the Beijing family strains are the most prevalent in rural China. Spoligotyping in combination with the new MIRU-15 technique is useful for the epidemiological analysis of MTB transmission and could be used as a first-line method for the large-scale genotyping of MTB.
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Affiliation(s)
- Wei Lu
- From the Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province , Nanjing
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Molecular epidemiology of Mycobacterium tuberculosis complex in Singapore, 2006-2012. PLoS One 2013; 8:e84487. [PMID: 24367667 PMCID: PMC3867517 DOI: 10.1371/journal.pone.0084487] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 11/14/2013] [Indexed: 01/20/2023] Open
Abstract
Background Tuberculosis remains common in Singapore, increasing in incidence since 2008. We attempted to determine the molecular epidemiology of Mycobacterium tuberculosis complex (MTC) isolates locally, identifying major circulating genotypes and obtaining a glimpse of transmission dynamics. Methodology Non-duplicate MTC isolates archived between 2006 and 2012 at the larger clinical tuberculosis laboratory in Singapore were sampled for spoligotyping and MIRU-VNTR typing, with case data obtained from the Singapore Tuberculosis Elimination Program registry database. Isolates between 2008 and 2012 were selected because of either multidrug-resistance or potential epidemiological linkage, whereas earlier isolates were randomly selected. Separate analyses were performed for the early (2006-2007) and later (2008-2012) study phases in view of potential selection bias. Principal Findings A total of 1,612 MTC isolates were typed, constituting 13.1% of all culture-positive tuberculosis cases during this period. Multidrug-resistance was present in 91 (5.6%) isolates – higher than the national prevalence in view of selection bias. The majority of isolates belonged to the Beijing (45.8%) and EAI (22.8%) lineages. There were 347 (30.7%) and 133 (27.5%) cases clustered by combined spoligotyping and MIRU-VNTR typing from the earlier and later phases respectively. Patients within these clusters tended to be of Chinese ethnicity, Singapore resident, and have isolates belonging to the Beijing lineage. A review of prior contact investigation results for all patients with clustered isolates failed to reveal epidemiological links for the majority, suggesting either unknown transmission networks or inadequate specificity of the molecular typing methods in a country with a moderate incidence of tuberculosis. Conclusion Our work demonstrates that Singapore has a large and heterogeneous distribution of MTC strains, and with possible cross-transmission over the past few years based on our molecular typing results. A universal MTC typing program coupled with enhanced contact investigations may be useful in further understanding the transmission dynamics of tuberculosis locally.
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192
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Soares RO, de Macedo MB, von Groll A, da Silva PEA. Mycobacterium tuberculosis belonging to family LAM and sublineage RD(Rio): common strains in Southern Brazil for over 10 years. Braz J Microbiol 2013; 44:1251-5. [PMID: 24688519 PMCID: PMC3958195 DOI: 10.1590/s1517-83822013000400032] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 04/04/2013] [Indexed: 11/21/2022] Open
Abstract
A sublineage of Mycobacterium tuberculosis called RD(Rio) was described in 2007. Although only recently described, this strain may have been present previously in the population, and its identification in clinical isolates will elucidate bacterial transmission dynamics and host-pathogen interactions. This study evaluated the clonal diversity of the RD(Rio) sublineage in clinical isolates from Rio Grande-RS obtained between 1998 and 2001. Among the 45 samples analyzed by the MIRU-VNTR method, there were six clusters with two samples each and 33 orphan strains with unique pattern. The strains were distributed across several different lineages including LAM (34.04%), × (14.89%), Haarlem (12.77%), UgandaI (10.64%), S (4.26%), NEW-1 (2.13%) and Cameroon (2.13%); 14.89% of the strains matched to multiple lineages. RD(Rio) strains were present in 28.9% of the samples and 81.25% of the identified strains belonged to the LAM family. The high clonal diversity observed in this study is a constant feature in this region. The RD(Rio) sublineage has been in Rio Grande-RS since 1998. The continued monitoring of RD(Rio) in clinical isolates will enhance the understanding of its epidemiological significance.
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193
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Weile J, Eickmeyer H, Dreier J, Liebke M, Fuchs U, Wittke JW, Richter E, Gummert J, Knabbe C, Schulz U. First case of Mycobacterium tuberculosis transmission by heart transplantation from donor to recipient. Int J Med Microbiol 2013; 303:449-51. [DOI: 10.1016/j.ijmm.2013.06.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 05/28/2013] [Accepted: 06/02/2013] [Indexed: 10/26/2022] Open
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Zmak L, Obrovac M, Katalinic Jankovic V. First insights into the molecular epidemiology of tuberculosis in Croatia during a three-year period, 2009 to 2011. ACTA ACUST UNITED AC 2013; 46:123-9. [DOI: 10.3109/00365548.2013.855322] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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195
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Velayati AA, Farnia P, Mozafari M, Sheikholeslami MF, Karahrudi MA, Tabarsi P, Hoffner S. High prevelance of rifampin-monoresistant tuberculosis: a retrospective analysis among Iranian pulmonary tuberculosis patients. Am J Trop Med Hyg 2013; 90:99-105. [PMID: 24189362 DOI: 10.4269/ajtmh.13-0057] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We determined the prevalence of rifampin-monoresistant tuberculosis (RMR-TB) in Iran. Because development of RMR-TB is not common, we also identified the major risk factors associated with RMR-TB reported from different provinces of Iran. Data for 3,020 TB patients who remained or became smear positive after two, four, six, and nine months of standard first-line chemotherapy were retrospectively analyzed. Of 3,020 patients, 1,242 patients (41.1%) were culture and DNA positive for Mycobacterium tuberculosis. Of these patients, 73 (7.4%) patients had monoresistant isolates to rifampin, which was significantly higher than that for multidrug-resistant TB (5.8%). The average rate of RMR-TB in the studied population ranged from 5% to 10%. Classical investigation showed that 33.6% of patients had either a previous or family history of TB. Molecular epidemiology methods (i.e., spoligotyping and Mycobacterium interspersed repetitive unit-variable number tandem repeat), defined transmission link in three clusters (13%). These results outline the urgent need for a comprehensive plan for detection and treatment of RMR-TB cases.
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Affiliation(s)
- Ali Akbar Velayati
- Mycobacteriology Research Centre, Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran; World Health Organization Supranational Reference Laboratory for Tuberculosis, Swedish Institute for Communicable Disease Control, Stockholm, Sweden
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Proposal of a consensus set of hypervariable mycobacterial interspersed repetitive-unit-variable-number tandem-repeat loci for subtyping of Mycobacterium tuberculosis Beijing isolates. J Clin Microbiol 2013; 52:164-72. [PMID: 24172154 DOI: 10.1128/jcm.02519-13] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis Beijing strains represent targets of special importance for molecular surveillance of tuberculosis (TB), especially because they are associated with spread of multidrug resistance in some world regions. Standard 24-locus mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing lacks resolution power for accurately discriminating closely related clones that often compose Beijing strain populations. Therefore, we evaluated a set of 7 additional, hypervariable MIRU-VNTR loci for better resolution and tracing of such strains, using a collection of 535 Beijing isolates from six world regions where these strains are known to be prevalent. The typeability and interlaboratory reproducibility of these hypervariable loci were lower than those of the 24 standard loci. Three loci (2163a, 3155, and 3336) were excluded because of their redundant variability and/or more frequent noninterpretable results compared to the 4 other markers. The use of the remaining 4-locus set (1982, 3232, 3820, and 4120) increased the number of types by 52% (from 223 to 340) and reduced the clustering rate from 58.3 to 36.6%, when combined with the use of the standard 24-locus set. Known major clonal complexes/24-locus-based clusters were all subdivided, although the degree of subdivision varied depending on the complex. Only five single-locus variations were detected among the hypervariable loci of an additional panel of 92 isolates, representing 15 years of clonal spread of a single Beijing strain in a geographically restricted setting. On this calibrated basis, we propose this 4-locus set as a consensus for subtyping Beijing clonal complexes and clusters, after standard typing.
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197
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Tuberculosis transmission among immigrants and autochthonous populations of the eastern province of Saudi Arabia. PLoS One 2013; 8:e77635. [PMID: 24147042 PMCID: PMC3798324 DOI: 10.1371/journal.pone.0077635] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 09/12/2013] [Indexed: 11/19/2022] Open
Abstract
Background Eastern province of Saudi Arabia is an industrial zone with large immigrant population and high level of tuberculosis case notification among immigrants. The impact of immigration and current trends of tuberculosis transmission among immigrants and autochthonous population in the region had not been investigated so far using molecular tools. Methodology During 2009- 2011, a total of 524 Mycobacterium tuberculosis isolates were collected from the central tuberculosis reference laboratory, representing an estimated 79.2% of the culture-positive tuberculosis cases over the study period in the province. These isolates were genotyped by using 24 locus-based MIRU-VNTR typing and spoligotyping followed by first line drug susceptibility testing. The molecular clustering profiles and phylogenetic diversity of isolates were determined and compared to the geographical origins of the patients. Principle Findings Genotyping showed an overall predominance of Delhi/CAS (29.4%), EAI (23.8%) and Ghana (13.3%) lineages, with slightly higher proportions of Delhi/CAS among autochthonous population (33.3 %) and EAI (30.9%) among immigrants. Rate of any drug resistance was 20.2% with 2.5% of multi-drug resistance. Strain cluster analysis indicated 42 clusters comprising 210 isolates, resulting in a calculated recent transmission index of 32.1%. Overall shared cluster ratio was 78.6% while 75.8% were shared between autochthonous population and immigrant population with a predominance of immigrants from South east Asia (40.7%). In contrast, cross national transmission within the immigrant population was limited (24.2%). Younger age (15-30- p value-0.043, 16-45, p value 0.030), Saudi nationality (p value-0.004) and South East Asian origin (p value-0.011) were identified as significant predisposing factors for molecular strain clustering. Conclusions The high proportion of molecular clusters shared among the autochthonous and immigrant populations suggests a high permeability of tuberculosis transmission between both populations in the province. These results prompt for the need to strengthen the current tuberculosis control strategies and surveillance programs.
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Gehre F, Antonio M, Faïhun F, Odoun M, Uwizeye C, de Rijk P, de Jong BC, Affolabi D. The first phylogeographic population structure and analysis of transmission dynamics of M. africanum West African 1--combining molecular data from Benin, Nigeria and Sierra Leone. PLoS One 2013; 8:e77000. [PMID: 24143198 PMCID: PMC3797137 DOI: 10.1371/journal.pone.0077000] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 09/06/2013] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium africanum is an important cause of tuberculosis (TB) in West Africa. So far, two lineages called M. africanum West African 1 (MAF1) and M. africanum West African 2 (MAF2) have been defined. Although several molecular studies on MAF2 have been conducted to date, little is known about MAF1. As MAF1 is mainly present in countries around the Gulf of Guinea we aimed to estimate its prevalence in Cotonou, the biggest city in Benin. Between 2005–06 we collected strains in Cotonou/Benin and genotyped them using spoligo- and 12-loci-MIRU-VNTR-typing. Analyzing 194 isolates, we found that 31% and 6% were MAF1 and MAF2, respectively. Therefore Benin is one of the countries with the highest prevalence (37%) of M. africanum in general and MAF1 in particular. Moreover, we combined our data from Benin with publicly available genotyping information from Nigeria and Sierra Leone, and determined the phylogeographic population structure and genotypic clustering of MAF1. Within the MAF1 lineage, we identified an unexpected great genetic variability with the presence of at least 10 sub-lineages. Interestingly, 8 out of 10 of the discovered sub-lineages not only clustered genetically but also geographically. Besides showing a remarkable local restriction to certain regions in Benin and Nigeria, the sub-lineages differed dramatically in their capacity to transmit within the human host population. While identifying Benin as one of the countries with the highest overall prevalence of M. africanum, this study also contains the first detailed description of the transmission dynamics and phylogenetic composition of the MAF1 lineage.
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Affiliation(s)
- Florian Gehre
- Medical Research Council (MRC) Unit, Fajara, The Gambia
- Institute for Tropical Medicine (ITM), Antwerp, Belgium
- * E-mail:
| | | | - Frank Faïhun
- Laboratoire de Reference des Mycobacteries, Cotonou, Benin
| | - Mathieu Odoun
- Laboratoire de Reference des Mycobacteries, Cotonou, Benin
| | | | - Pim de Rijk
- Institute for Tropical Medicine (ITM), Antwerp, Belgium
| | - Bouke C. de Jong
- Medical Research Council (MRC) Unit, Fajara, The Gambia
- Institute for Tropical Medicine (ITM), Antwerp, Belgium
- New York University (NYU), New York, New York, United States of America
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Mycobacterium tuberculosis outbreak strain of Danish origin spreading at worrying rates among greenland-born persons in Denmark and Greenland. J Clin Microbiol 2013; 51:4040-4. [PMID: 24068008 DOI: 10.1128/jcm.01916-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transmission of Mycobacterium tuberculosis continues at high rates among Greenland-born persons in Greenland and Denmark, with 203 and 450 notified cases per 10(5) population, respectively, in the year 2010. Here, we document that the predominant M. tuberculosis outbreak strain C2/1112-15 of Danish origin has been transmitted to Greenland-born persons in Denmark and subsequently to Greenland, where it is spreading at worrying rates and adding to the already heavy tuberculosis burden in this population group. It is now clear that the C2/1112-15 strain is able to gain new territories using a new population group as the "vehicle." Thus, it might have the ability to spread even further, considering the potential clinical consequences of strain diversity such as that seen in the widely spread Beijing genotype. The introduction of the predominant M. tuberculosis outbreak strain C2/1112-15 into the Arctic circumpolar region is a worrying tendency which deserves attention. We need to monitor whether this strain already has, or will, spread to other countries.
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Genetic variability of Mycobacterium tuberculosis complex in patients with no known risk factors for MDR-TB in the North-Eastern part of Lima, Peru. BMC Infect Dis 2013; 13:397. [PMID: 23984854 PMCID: PMC3765759 DOI: 10.1186/1471-2334-13-397] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 08/21/2013] [Indexed: 11/12/2022] Open
Abstract
Background The aim of this study was to investigate the genetic diversity among Mycobacterium tuberculosis complex circulating in patients with no known risk factors for multi-drug resistant (MDR) tuberculosis (TB) living in a high MDR burden area and analyze the relationship between genotypes, primary drug resistance and age. Methods Samples were collected during January-July 2009. Isolates were tested for drug susceptibility to first-line drugs and were genotyped by spoligotyping and the 15-loci Mycobacterial Interspersed Repetitive Unit (MIRU15). Results Among the 199 isolates analyzed, 169 (84.9%) were identified in the SpolDB4.0 and 30 (15.1%) could not be matched to any lineage. The most prevalent lineage was Haarlem (29.6%), followed by T (15.6%), Beijing (14.1%), Latin American Mediterranean (12.6%) and U (8.5%). A few isolates belonged to the X and S clades (4.5%). Spoligotype analysis identified clustering among 148 of 169 isolates, whereas with MIRU15 all isolates were unique. Out of 197 strains; 31.5% were resistant to at least one drug, 7.5% were MDR and 22.3% showed any resistance to isoniazid. Conclusion In contrast with other Latin-American countries where LAM lineage is the most predominant, we found the spoligotype 50 from the Haarlem lineage as the most common. None of the prevailing lineages showed a significant association with age or resistance to isoniazid and/or rifampicin.
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