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Hoffner S, Sahebi L, Ansarin K, Sabour S, Mohajeri P. Mycobacterium tuberculosis of the Beijing Genotype in Iran and the World Health Organization Eastern Mediterranean Region: A Meta-Analysis. Microb Drug Resist 2017; 24:693-698. [PMID: 29058526 DOI: 10.1089/mdr.2017.0160] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
OBJECTIVE The Beijing genotype is a distinct genetic lineage of Mycobacterium tuberculosis, which is distributed worldwide, and may cause large outbreaks of multidrug resistance-tuberculosis (MDR-TB). The distribution of such strains in the Eastern Mediterranean region (EMR) is unclear, and clarifying the data is our purpose apart from the presence of Beijing TB in Iran. METHODS We searched Published literature from CINAHL Cochrane Library, Current Contents, Database of Abstracts of Reviews of Effects (DARE), ProQuest Google Scholar PubMed, PsycINFO, Thomson Reuters, (SID), and Medical Library (MedLib) to detect relevant studies from the year 2000 to July 2015 with the following keywords: M. tuberculosis, Beijing genotype, EMR, and drug resistance. Random-effect models were used to estimate the proportion of Beijing strains in STATA 14. Heterogeneity was investigated by subgroup analysis and meta-regression. RESULTS AND CONCLUSION The meta-prevalence of Beijing strains was 4% (CI 95% = 3-5). The prevalence was different based on types of detection techniques (spoligotyping = 4% vs. other techniques = 6%; p = 0.003) and years of study (before the year 2000 = 2% vs. after year 2000 = 4%, p = 0.004). The Beijing family was most prevalent in Iran and Pakistan. A strong relationship with drug resistance was reported in Pakistan and Iran, and an increasing trend was seen in Pakistan. Additional studies of drug-resistant TB distribution among Beijing strains in EMR countries are needed as well as a time-trend analysis of the Beijing strain infection in the region.
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Affiliation(s)
- Sven Hoffner
- 1 Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet , Stockholm, Sweden
| | - Leyla Sahebi
- 2 Maternal/Fetal and Neonatal Research Center, Tehran University of Medical Sciences , Tehran, Iran .,3 Department of Epidemiology, Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Science , Tabriz, Iran
| | - Khalil Ansarin
- 4 Department of Medicine, Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | - Siamak Sabour
- 5 Department of Clinical Epidemiology, Safety Promotion and Injury Prevention Research Center, School of Health, Shahid Beheshti University of Medical Sciences , Tehran, Iran
| | - Parviz Mohajeri
- 6 Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences , Kermanshah, Iran
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Genetic Diversity of Mycobacterium tuberculosis Complex Isolated from Tuberculosis Patients in Bahir Dar City and Its Surroundings, Northwest Ethiopia. BIOMED RESEARCH INTERNATIONAL 2015; 2015:174732. [PMID: 26491657 PMCID: PMC4600926 DOI: 10.1155/2015/174732] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 08/08/2015] [Accepted: 08/17/2015] [Indexed: 11/17/2022]
Abstract
The knowledge of the diversity of strains of Mycobacterium tuberculosis complex (MTBC) species in a specific geographical region can contribute to the control of tuberculosis (TB). This study was conducted to identify the MTBC isolates to the species and spoligotype international type (SIT) level by spoligotyping. A total of 168 MTBC isolates were recovered from TB patients, spoligotyped, and their patterns were compared with those of the strains registered in the SITVIT2 database. Of 168 isolates spoligotyped, 89 patterns were identified. Ninety-eight isolates were clustered into 19 strain groups with clustering percentage of 58.3%. Forty-four strains matched the preexisting SITs in the SITVIT2 database. The dominant strains were SIT289, SIT134, and SIT3411, comprising 16.7% (28/168), 7.14% (12/168), and 4.76% (8/168) of the isolates, respectively. Euro-American (51.2%), East-African-Indian (34.5%), and M. africanum (9.52%) were the major lineages identified. Two strains of M. bovis were isolated from TB lymphadenitis cases. The high percentage of clustered strains of M. tuberculosis could suggest that a small number of lineages of M. tuberculosis are causing the disease in the area while isolation of M. bovis could suggest its zoonotic potential. Additionally, identification of M. africanum requires further confirmation by tools with a better discriminatory power.
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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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Strain diversity of Mycobacterium tuberculosis isolates from pulmonary tuberculosis patients in Afar pastoral region of Ethiopia. BIOMED RESEARCH INTERNATIONAL 2014; 2014:238532. [PMID: 24734230 PMCID: PMC3966356 DOI: 10.1155/2014/238532] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 01/22/2014] [Indexed: 12/02/2022]
Abstract
Data on genotypic diversity of Mycobacterium tuberculosis complex (MTBC) is important to understand its epidemiology, human adaptation, clinical phenotypes, and drug resistance.
This study aimed to characterize MTBC clinical isolates circulating in a predominantly pastoralist area in Ethiopia, a country where tuberculosis is the second leading cause of mortality.
Culture of sputum samples collected from a total of 325 pulmonary TB suspects was done to isolate MTBC. Spoligotyping was used to characterize 105 isolates from culture positive
slopes and the result was compared with an international database. Forty-four spoligotype patterns were observed to correspond to 35 shared-types (SITs) containing 96 isolates and
9 orphan patterns; 27 SITs containing 83 isolates matched a preexisting shared-type in the database, whereas 8 SITs (n = 13 isolates) were newly created. A total of 19 SITs containing
80 isolates were clustered within this study (overall clustering of 76.19%). Three dominant lineages (T, CAS, and Manu) accounted for 76.19% of the isolates. SIT149/T3-ETH was one
of the two most dominant sublineages. Unlike previous reports, we show that Manu lineage strains not only constitute a dominant lineage, but are also associated with HIV infection in
Afar region of Ethiopia. The high level of clustering suggests the presence of recent transmission that should be further studied using additional genotyping markers.
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Blouin Y, Hauck Y, Soler C, Fabre M, Vong R, Dehan C, Cazajous G, Massoure PL, Kraemer P, Jenkins A, Garnotel E, Pourcel C, Vergnaud G. Significance of the identification in the Horn of Africa of an exceptionally deep branching Mycobacterium tuberculosis clade. PLoS One 2012; 7:e52841. [PMID: 23300794 PMCID: PMC3531362 DOI: 10.1371/journal.pone.0052841] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 11/21/2012] [Indexed: 02/02/2023] Open
Abstract
Molecular and phylogeographic studies have led to the definition within the Mycobacterium tuberculosis complex (MTBC) of a number of geotypes and ecotypes showing a preferential geographic location or host preference. The MTBC is thought to have emerged in Africa, most likely the Horn of Africa, and to have spread worldwide with human migrations. Under this assumption, there is a possibility that unknown deep branching lineages are present in this region. We genotyped by spoligotyping and multiple locus variable number of tandem repeats (VNTR) analysis (MLVA) 435 MTBC isolates recovered from patients. Four hundred and eleven isolates were collected in the Republic of Djibouti over a 12 year period, with the other 24 isolates originating from neighbouring countries. All major M. tuberculosis lineages were identified, with only two M. africanum and one M. bovis isolates. Upon comparison with typing data of worldwide origin we observed that several isolates showed clustering characteristics compatible with new deep branching. Whole genome sequencing (WGS) of seven isolates and comparison with available WGS data from 38 genomes distributed in the different lineages confirms the identification of ancestral nodes for several clades and most importantly of one new lineage, here referred to as lineage 7. Investigation of specific deletions confirms the novelty of this lineage, and analysis of its precise phylogenetic position indicates that the other three superlineages constituting the MTBC emerged independently but within a relatively short timeframe from the Horn of Africa. The availability of such strains compared to the predominant lineages and sharing very ancient ancestry will open new avenues for identifying some of the genetic factors responsible for the success of the modern lineages. Additional deep branching lineages may be readily and efficiently identified by large-scale MLVA screening of isolates from sub-Saharan African countries followed by WGS analysis of a few selected isolates.
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Affiliation(s)
- Yann Blouin
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
| | - Yolande Hauck
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
| | - Charles Soler
- Laboratoire de biologie clinique, hôpital d'instruction des armées Percy, Clamart, France
| | - Michel Fabre
- Laboratoire de biologie clinique, hôpital d'instruction des armées Percy, Clamart, France
| | - Rithy Vong
- Laboratoire de biologie clinique, hôpital d'instruction des armées Percy, Clamart, France
| | | | | | | | - Philippe Kraemer
- Hôpital d'instruction des armées Alphonse Laveran, Marseille, France
| | - Akinbowale Jenkins
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, Pretoria, South Africa
| | - Eric Garnotel
- Hôpital d'instruction des armées Alphonse Laveran, Marseille, France
| | - Christine Pourcel
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
| | - Gilles Vergnaud
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
- DGA/MRIS- Mission pour la Recherche et l'Innovation Scientifique, Bagneux, France
- * E-mail:
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Taype CA, Agapito JC, Accinelli RA, Espinoza JR, Godreuil S, Goodman SJ, Bañuls AL, Shaw MA. Genetic diversity, population structure and drug resistance of Mycobacterium tuberculosis in Peru. INFECTION GENETICS AND EVOLUTION 2012; 12:577-85. [PMID: 22342744 DOI: 10.1016/j.meegid.2012.02.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Revised: 01/20/2012] [Accepted: 02/02/2012] [Indexed: 10/14/2022]
Abstract
This paper presents the first evaluation of the molecular epidemiology of Mycobacterium tuberculosis in Peru. We characterised 323 isolates using spoligotyping and mycobacterial interspersed repetitive units variable number tandem repeats (MIRU-VNTR) typing. We aimed to determine the levels of genetic diversity and genetic differentiation among and within Peruvian isolates and the epidemiological factors which may be driving patterns of population structure and evolution of M. tuberculosis in Peru. Our results compared to the fourth international spoligotyping database (SpolDB4) and MIRU-VNTRplus, show that the main M. tuberculosis families present are Latin American-Mediterranean, Haarlem, T, and Beijing. Bayesian clustering recovered 15 groups in the Peruvian M. tuberculosis isolates, among which two were composed mainly of orphans, implying the presence of native "Peruvian" strains not previously reported. Variable levels of association with drug resistance were observed, with Beijing genotypes not showing any association with multidrug resistance, while in other groups MIRU-VNTR loci 2, 23, 31, and 40 were found to be associated with the multidrug-resistant tuberculosis (MDR-TB) phenotype, suggesting that a linkage disequibrium between these MIRU and drug resistance loci may be present. Genetic differentiation was present among drug resistant and sensitive strains. Ethambutol appeared to be the main driver of differentiation, suggesting that strong selection pressure could have been exerted by drug treatment in Peru over recent years.
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Affiliation(s)
- C A Taype
- Institute of Integrative and Comparative Biology, University of Leeds, LS2 9JT, UK.
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