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Guthrie JL, Marchand-Austin A, Cronin K, Lam K, Pyskir D, Kong C, Jorgensen D, Rodrigues M, Roth D, Tang P, Cook VJ, Johnston J, Jamieson FB, Gardy JL. Universal genotyping reveals province-level differences in the molecular epidemiology of tuberculosis. PLoS One 2019; 14:e0214870. [PMID: 30943250 PMCID: PMC6447219 DOI: 10.1371/journal.pone.0214870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/21/2019] [Indexed: 11/21/2022] Open
Abstract
OBJECTIVES Compare the molecular epidemiology of tuberculosis (TB) between two large Canadian provinces-Ontario and British Columbia (BC)-to identify genotypic clusters within and across both provinces, allowing for an improved understanding of genotype data and providing context to more accurately identify clusters representing local transmission. DESIGN We compared 24-locus Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) genotyping for 3,314 Ontario and 1,602 BC clinical Mycobacterium tuberculosis isolates collected from 2008 through 2014. Laboratory data for each isolate was linked to case-level records to obtain clinical and demographic data. RESULTS The demographic characteristics of persons with TB varied between provinces, most notably in the proportion of persons born outside Canada, which was reflected in the large number of unique genotypes (n = 3,461). The proportion of clustered isolates was significantly higher in BC. Substantial clustering amongst non-Lineage 4 TB strains was observed within and across the provinces. Only two large clusters (≥10 cases/cluster) representing within province transmission had interprovincial genotype matches. CONCLUSION We recommend expanding analysis of shared genotypes to include neighbouring jurisdictions, and implementing whole genome sequencing to improve identification of TB transmission, recognize outbreaks, and monitor changing trends in TB epidemiology.
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Affiliation(s)
- Jennifer L. Guthrie
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
- Public Health Ontario, Toronto, Canada
| | | | - Kirby Cronin
- Public Health Ontario, Toronto, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Karen Lam
- Public Health Ontario, Toronto, Canada
| | | | - Clare Kong
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, Canada
| | - Danielle Jorgensen
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, Canada
| | - Mabel Rodrigues
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, Canada
| | - David Roth
- British Columbia Centre for Disease Control, Vancouver, Canada
| | - Patrick Tang
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Victoria J. Cook
- British Columbia Centre for Disease Control, Vancouver, Canada
- Respiratory Medicine, University of British Columbia, Vancouver, Canada
| | - James Johnston
- British Columbia Centre for Disease Control, Vancouver, Canada
- Respiratory Medicine, University of British Columbia, Vancouver, Canada
| | - Frances B. Jamieson
- Public Health Ontario, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Jennifer L. Gardy
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
- British Columbia Centre for Disease Control, Vancouver, Canada
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2
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Rindi L, Alì G, Fabiani B, Fontanini G, Garzelli C. Detection of Mycobacterium tuberculosis from paraffin-embedded tissues by GeneXpert MTB/RIF. Tuberculosis (Edinb) 2017; 106:53-55. [PMID: 28802405 DOI: 10.1016/j.tube.2017.06.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 06/28/2017] [Accepted: 06/30/2017] [Indexed: 11/19/2022]
Abstract
GeneXpert MTB/RIF (Xpert) assay, a rapid and automated system based on real-time PCR and molecular beacon technology, proved to be a sensitive and specific tool capable of detecting Mycobacterium tuberculosis and rifampin resistance in clinical specimens. In this study we provide a Xpert-dedicated successful protocol for processing paraffin-embedded tissue and assess the feasibility of the Xpert assay-based tuberculosis (TB) diagnosis on these specimens, thus proving the Xpert assay as a valuable TB diagnostic tool in supporting conventional histopathological methods.
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MESH Headings
- Antibiotics, Antitubercular/pharmacology
- Automation, Laboratory
- Bacteriological Techniques
- Biopsy
- Case-Control Studies
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- Drug Resistance, Bacterial/genetics
- Humans
- Microbial Sensitivity Tests
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/isolation & purification
- Paraffin Embedding
- Predictive Value of Tests
- Real-Time Polymerase Chain Reaction/methods
- Rifampin/pharmacology
- Tuberculosis, Lymph Node/diagnosis
- Tuberculosis, Lymph Node/genetics
- Tuberculosis, Lymph Node/pathology
- Tuberculosis, Pleural/diagnosis
- Tuberculosis, Pleural/genetics
- Tuberculosis, Pleural/pathology
- Tuberculosis, Pulmonary/diagnosis
- Tuberculosis, Pulmonary/genetics
- Tuberculosis, Pulmonary/pathology
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Affiliation(s)
- Laura Rindi
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, I-56127, Pisa, Italy.
| | - Greta Alì
- Unit of Pathological Anatomy, University Hospital of Pisa, I-56126, Pisa, Italy
| | - Barbara Fabiani
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, I-56127, Pisa, Italy
| | - Gabriella Fontanini
- Department of Surgical, Medical and Molecular Pathology and Critical Area, University of Pisa, I-56126, Pisa, Italy
| | - Carlo Garzelli
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, I-56127, Pisa, Italy
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Garzelli C, Lari N, Rindi L. Genomic diversity of Mycobacterium tuberculosis Beijing strains isolated in Tuscany, Italy, based on large sequence deletions, SNPs in putative DNA repair genes and MIRU-VNTR polymorphisms. Tuberculosis (Edinb) 2016; 97:147-53. [DOI: 10.1016/j.tube.2015.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 10/15/2015] [Accepted: 10/20/2015] [Indexed: 12/28/2022]
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Gebrezgabiher G, Romha G, Ameni G. Spoligotyping of Mycobacterium tuberculosis isolates from tuberculosis diagnosed patients at Dilla University Referral Hospital and other private clinics, Southern Ethiopia. ASIAN PACIFIC JOURNAL OF TROPICAL DISEASE 2015. [DOI: 10.1016/s2222-1808(14)60792-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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5
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Balcells ME, García P, Meza P, Peña C, Cifuentes M, Couvin D, Rastogi N. A first insight on the population structure of Mycobacterium tuberculosis complex as studied by spoligotyping and MIRU-VNTRs in Santiago, Chile. PLoS One 2015; 10:e0118007. [PMID: 25671320 PMCID: PMC4324903 DOI: 10.1371/journal.pone.0118007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/05/2015] [Indexed: 02/04/2023] Open
Abstract
Tuberculosis (TB) remains a significant public health problem worldwide, but the ecology of the prevalent mycobacterial strains, and their transmission, can vary depending on country and region. Chile is a country with low incidence of TB, that has a geographically isolated location in relation to the rest of South American countries due to the Andes Mountains, but recent migration from neighboring countries has changed this situation. We aimed to assess the genotypic diversity of Mycobacterium tuberculosis complex (MTBC) strains in Santiago, Chile, and compare with reports from other Latin-American countries. We analyzed MTBC isolates from pulmonary tuberculosis cases collected between years 2008 and 2013 in Central Santiago, using two genotyping methods: spoligotyping and 12-loci mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTRs). Data obtained were analyzed and compared to the SITVIT2 database. Mean age of the patients was 47.5 years and 61% were male; 11.6% were migrants. Of 103 strains (1 isolate/patient) included, there were 56 distinct spoligotype patterns. Of these, 16 strains (15.5%) corresponded to orphan strains in the SITVIT2 database, not previously reported. Latin American and Mediterranean (LAM) (34%) and T (33%) lineages were the most prevalent strains, followed by Haarlem lineage (16.5%). Beijing family was scarcely represented with only two cases (1.9%), one of them isolated from a Peruvian migrant. The most frequent clustered spoligotypes were SIT33/LAM3 (10.7%), SIT53/T1 (8.7%), SIT50/H3 (7.8%), and SIT37/T3 (6.8%). We conclude that LAM and T genotypes are the most prevalent genotypes of MTBC in Santiago, Chile, and together correspond to almost two thirds of analyzed strains, which is similar to strain distribution reported from other countries of Latin America. Nevertheless, the high proportion of SIT37/T3, which was rarely found in other Latin American countries, may underline a specific history or demographics of Chile related to probable human migrations and evolutions.
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Affiliation(s)
- María Elvira Balcells
- Infectious Diseases Department, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Patricia García
- Microbiology Laboratory, Clinical Laboratory Department, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Paulina Meza
- Microbiology Laboratory, Clinical Laboratory Department, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carlos Peña
- Respiratory Division and Microbiology Laboratory, Hospital San Borja Arriarán, Santiago, Chile
| | - Marcela Cifuentes
- Respiratory Division and Microbiology Laboratory, Hospital San Borja Arriarán, Santiago, Chile
| | - David Couvin
- WHO Supranational TB Reference Laboratory, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
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Andersen P, Woodworth JS. Tuberculosis vaccines--rethinking the current paradigm. Trends Immunol 2014; 35:387-95. [PMID: 24875637 DOI: 10.1016/j.it.2014.04.006] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/09/2014] [Accepted: 04/30/2014] [Indexed: 11/16/2022]
Abstract
The vaccine discovery paradigm in tuberculosis (TB) has been to mimic the natural immune response to infection. With an emphasis on interferon (IFN)-γ as the main protective cytokine, researchers have selected dominant antigens and administered them in delivery systems to promote strong T helper (Th)1 responses. However, the Bacillus Calmette-Guérin (BCG) vaccine is a strong inducer of Th1 cells, yet has limited protection in adults, and further boosting by the Modified-Vaccinia-Ankara (MVA)85A vaccine failed to enhance efficacy in a clinical trial. We review the current understanding of host-pathogen interactions in TB infection and propose that rather than boosting Th1 responses, we should focus on understanding protective immune responses that are lacking or insufficiently promoted by BCG that can intervene at critical stages of the TB life cycle.
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Affiliation(s)
- Peter Andersen
- Statens Serum Institut, Department of Infectious Disease Immunology, Artillerivej 5, 2300 Copenhagen S, Denmark.
| | - Joshua S Woodworth
- Statens Serum Institut, Department of Infectious Disease Immunology, Artillerivej 5, 2300 Copenhagen S, Denmark
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Liu M, Jiang W, Liu Y, Zhang Y, Wei X, Wang W. Increased genetic diversity of the Mycobacterium tuberculosis W-Beijing genotype that predominates in eastern China. INFECTION GENETICS AND EVOLUTION 2014; 22:23-9. [PMID: 24412724 DOI: 10.1016/j.meegid.2013.12.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 12/28/2013] [Accepted: 12/28/2013] [Indexed: 12/30/2022]
Abstract
OBJECTIVES To determine the genetic diversity of Mycobacterium tuberculosis (M. tuberculosis) strains in a Chinese population predominately infected with strains of the W-Beijing family. METHODS A cross-sectional study was conducted in three counties of eastern China. M. tuberculosis strains were collected at TB clinics, and patients were interviewed by trained physicians at the time of TB diagnosis. RD105 and RD181 were used to identify W-Beijing and modern W-Beijing strains, respectively, while seven-locus variable numbers of tandem repeat-mycobacterial interspersed repetitive unit (VNTR-MIRU) analysis was employed to differentiate the genotypes of these strains. RESULTS Of 441 strains studied, 394 (89.3%) were identified as W-Beijing family strains; of them, 299 were modern W-Beijing strains. VNTR-MIRU identified 409 genotypes from 426 strains, including 395 unique patterns and 14 clusters. Ancestral W-Beijing strains were more likely to be clustered (OR=1.32, 95%CI: 0.58-2.97) compared to modern W-Beijing strains. The proportions of clustered strains were 14.6%, 4.2% and 0% at sites Funing (FN), Deqing (DQ) and Yinzhou (YZ), respectively. Of the seven MIRU loci, VNTR3820 was found to have the highest discriminatory power and allelic diversity. CONCLUSIONS VNTR-MIRU typing appears to be a reliable method for analyzing M. tuberculosis transmission in relatively closed populations. The low clustering proportions indicate that endogenous relapse may be a main source of TB cases in eastern China. Furthermore, our results indicate that migration has played may play an important role in the recent transmission of the W-Beijing family of M. tuberculosis.
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Affiliation(s)
- Meiling Liu
- School of Public Health & Key Laboratory of Public Health Safety (Ministry of Education), Fudan University, Shanghai, China; Hongkou District Center for Disease Control and Prevention, Shanghai, China
| | - Weili Jiang
- School of Public Health & Key Laboratory of Public Health Safety (Ministry of Education), Fudan University, Shanghai, China
| | - Yuan Liu
- School of Public Health & Key Laboratory of Public Health Safety (Ministry of Education), Fudan University, Shanghai, China
| | - Yue Zhang
- School of Public Health & Key Laboratory of Public Health Safety (Ministry of Education), Fudan University, Shanghai, China
| | - Xiaolin Wei
- School of Public Health and Primary Care, Chinese University of Hong Kong, China
| | - Weibing Wang
- School of Public Health & Key Laboratory of Public Health Safety (Ministry of Education), Fudan University, Shanghai, China.
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Sandgren A, Schepisi MS, Sotgiu G, Huitric E, Migliori GB, Manissero D, van der Werf MJ, Girardi E. Tuberculosis transmission between foreign- and native-born populations in the EU/EEA: a systematic review. Eur Respir J 2013; 43:1159-71. [PMID: 24114966 PMCID: PMC3971120 DOI: 10.1183/09031936.00117213] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Tuberculosis (TB) control programmes of many low TB incidence countries of the European Union/European Economic Area (EU/EEA) perceive challenges in controlling TB due to high numbers of TB in migrants from high-incidence countries. To assess the extent of TB transmission from the foreign-born to the native-born population, we quantitatively investigated the dynamics of TB transmission between these populations in the EU/EEA, using published molecular epidemiological studies. We searched PubMed and EMBASE databases from 1990 to August 2012. We identified 15 studies performed during 1992–2007 covering 12,366 cases, of which median (range) 49.2% (17.7%–86.4%) were foreign-born. The proportion of clustered isolates ranged between 8.5% and 49.1% of the total number of TB cases genotyped and among these, foreign-born cases were equally or more likely to have unique isolates compared to native-born cases. One third of the clusters were “mixed”, i.e. composed of foreign- and native-born cases, involving 0–34.2% of all genotyped cases. Cross-transmission among foreign and native populations was bidirectional, with wide differences across studies. This systematic review provides evidence that TB in a foreign-born population does not have a significant influence on TB in the native population in EU/EEA. TB in foreign-born cases does not have a significant influence on TB in the native population in EU/EEAhttp://ow.ly/pTTXv
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Affiliation(s)
- Andreas Sandgren
- European Centre for Disease Prevention and Control, Stockholm, Sweden
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Factors associated with genotype clustering of Mycobacterium tuberculosis isolates in an ethnically diverse region of southern California, United States. INFECTION GENETICS AND EVOLUTION 2012; 12:1917-25. [PMID: 22982156 DOI: 10.1016/j.meegid.2012.08.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 08/24/2012] [Accepted: 08/27/2012] [Indexed: 12/15/2022]
Abstract
Mycobacterium tuberculosis (Mtb) isolates with identical genotypes, found in different patients, are most likely the result of recent transmission. Mtb strains with closely related genotypes, called clonal complexes, are most likely derived from one another. We examined Mtb genotypes from southern California TB patients from 2005 through 2008 to complete the first comprehensive molecular epidemiology analysis of this complicated and ethnically diverse region. Mtb genotypes were characterized with spoligotype and MIRU-12 typing. MIRU-VNTRplus was utilized to assign genotypes to global lineages and complete cluster analyses. Associations between patient characteristics and genotype clustering and clonal complexes were evaluated using logistic regression and frequency analysis. Of 832 Mtb isolates analyzed, 480 (58%) fell into 94 strain clusters. The majority of isolates were identified as being in the EA1 (31%), LAM (17%) and Haarlem (15%) lineages, but 13 different lineages were found in this region. TB patients with clustered isolates were more likely to be homeless (AOR 3.44, 95% CI 1.65, 7.18) and male (AOR 1.57, 95% CI 1.17, 2.10). Of the 480 clustered strains, 388 aggregated into six clonal complexes. Over 45% of reported TB cases were clustered and likely resulted from recent transmission events. Patients with clustered Mtb isolates that were grouped into clonal complexes had unique socio-demographic characteristics. These data suggest that TB is being transmitted in relatively insular community networks defined by race/ethnicity and country of origin. The addition of clonal complex analysis to simple cluster analysis provides important public health insights into the local transmission of TB in ethnically diverse regions with diverse Mtb genotypes.
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