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Hadifar S, Kargarpour Kamakoli M, Eybpoosh S, Nakhaeizadeh M, Kargarpour Kamakoli MA, Ebrahimifard N, Fateh A, Siadat SD, Vaziri F. The shortcut of mycobacterial interspersed repetitive unit-variable number tandem repeat typing for Mycobacterium tuberculosis differentiation. Front Microbiol 2022; 13:978355. [PMID: 36160200 PMCID: PMC9493315 DOI: 10.3389/fmicb.2022.978355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
The 24-loci mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) genotyping has been used as an international standard method for Mycobacterium tuberculosis (Mtb) genotyping. However, different optimized VNTR loci sets for improving the discrimination of specific Mtb genotypes have been proposed. In this regard, we investigated the efficacy of accumulation of the percentage differences (APDs) compared with the least absolute shrinkage and selection operator (LASSO) regression strategy to identify a customized genotype-specific VNTR loci set which provides a resolution comparable to 24-loci MIRU-VNTR in divergent Mtb populations. We utilized Spoligotyping and 24-loci MIRU-VNTR typing for genotyping 306 Mtb isolates. The APD and LASSO regression approaches were used to identify a customized VNTR set in our studied isolates. Besides, the Hunter-Gaston discriminatory index (HGDI), sensitivity, and specificity of each selected loci set were calculated based on both strategies. The selected loci based on LASSO regression compared with APD-based loci showed a better discriminatory power for identifying all studied genotypes except for T genotype, which APD-based loci showed promising discriminative power. Our findings suggested the LASSO regression rather than the APD approach is more effective in the determination of possible discriminative VNTR loci set to precise discrimination of our studied Mtb population and may be beneficial to be used in finding reduced number loci sets in other Mtb genotypes or sublineages. Moreover, we proposed customized genotype-specific MIRU-VNTR loci sets based on the LASSO regression and APD approaches for precise Mtb strains identification. As the proposed VNTR sets offered a comparable discriminatory power to the standard 24 MIRU-VNTR loci set could be promising alternatives to the standard genotyping for using in resource-limited settings.
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Affiliation(s)
- Shima Hadifar
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mansour Kargarpour Kamakoli
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Sana Eybpoosh
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Mehran Nakhaeizadeh
- Modeling in Health Research Center, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
- Department of Biostatistics and Epidemiology, School of Public Health, Kerman University of Medical Sciences, Kerman, Iran
| | | | - Nasim Ebrahimifard
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
- *Correspondence: Farzam Vaziri, ,
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Maghradze N, Jugheli L, Borrell S, Tukvadze N, Kempker RR, Blumberg HM, Gagneux S. Developing customized stepwise MIRU-VNTR typing for tuberculosis surveillance in Georgia. PLoS One 2022; 17:e0264472. [PMID: 35231041 PMCID: PMC8887741 DOI: 10.1371/journal.pone.0264472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 02/10/2022] [Indexed: 11/19/2022] Open
Abstract
Introduction
Mycobacterial Interspersed Repetitive Units–Variable Tandem Repeats (MIRU-VNTR) typing has been widely used for molecular epidemiological studies of tuberculosis (TB). However, genotyping tools for Mycobacterium tuberculosis (Mtb) may be limiting in some settings due to high cost and workload. In this study developed a customized stepwise MIRU-VNTR typing that prioritizes high discriminatory loci and validated this method using penitentiary system cohort in the country of Georgia.
Methods
We used a previously generated MIRU-VNTR dataset from recurrent TB cases (32 cases) in Georgia and a new dataset of TB cases from the penitentiary system (102 cases) recruited from 2014 to 2015. A Hunter-Gaston Discriminatory Index (HGDI) was calculated utilizing a 24 standard loci panel, to select high discriminatory power loci, subsequently defined as the customized Georgia-specific set of loci for initial typing. The remaining loci were scored and hierarchically grouped for second and third step typing of the cohort. We then compared the processing time and costs of the customized stepwise method to the standard 24-loci method.
Results
For the customized Georgia-specific set that was used for initial typing, 10 loci were selected with a minimum value of 0.32 to the highest HGDI score locus. Customized 10 loci (step 1) typing of 102 Mtb patient isolates revealed 35.7% clustered cases. This proportion was reduced to 19.5% after hierarchical application of 2nd and 3rd step typing with the corresponding groups of loci. Our customized stepwise MIRU-VNTR genotyping approach reduced the quantity of samples to be typed and therefore overall processing time and costs by 42.6% each.
Conclusion
Our study shows that our customized stepwise MIRU-VNTR typing approach is a valid alternative of standard MIRI-VNTR typing panels for molecular epidemiological investigation in Georgia that saves time, workload and costs. Similar approaches could be developed for other settings.
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Affiliation(s)
- Nino Maghradze
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- National Center for Tuberculosis and Lung Diseases (NCTLD), Tbilisi, Georgia
| | - Levan Jugheli
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- National Center for Tuberculosis and Lung Diseases (NCTLD), Tbilisi, Georgia
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Nestani Tukvadze
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- National Center for Tuberculosis and Lung Diseases (NCTLD), Tbilisi, Georgia
| | - Russell R. Kempker
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, United States of America
| | - Henry M. Blumberg
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, United States of America
- Departments of Epidemiology and Global Health, Rollins School of Public Health of Emory University, Atlanta, GA, United States of America
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- * E-mail:
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Qiu B, Tao B, Liu Q, Li Z, Song H, Tian D, Wu J, Wu Z, Zhan M, Lu W, Wang J. A Prospective Cohort Study on the Prevalent and Recurrent Tuberculosis Isolates Using the MIRU-VNTR Typing. Front Med (Lausanne) 2021; 8:685368. [PMID: 34595184 PMCID: PMC8476766 DOI: 10.3389/fmed.2021.685368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/23/2021] [Indexed: 11/30/2022] Open
Abstract
The study aims to describe the clustering characteristics of Mycobacterium tuberculosis (M.tb) strains circulating in eastern China and determine the ratio of relapse and reinfection in recurrent patients. We recruited sputum smear-positive pulmonary tuberculosis cases from five cities of Jiangsu Province, China, during August 2013 and December 2015. Patients were followed for the treatment outcomes and recurrence based on a cohort design. M.tb strains were isolated and genotyped using the 12-locus MIRU-VNTR. The Beijing family was identified by the extended Region of Difference (RD) analysis. The Hunter-Gaston Discriminatory Index (HGDI) was used to judge the resolution ability of MIRU-VNTR. The odds ratio (OR) together with 95% confidence interval (CI) were used to estimate the strength of association. We performed a cluster analysis on 2098 M.tb isolates and classified them into 545 genotypes and five categories (I, 0.19%; II, 0.43%; III, 3.34%; IV, 77.46%; V, 18.59%). After adjusting for potential confounders, the Beijing family genotype (OR = 118.63, 95% CI: 79.61–176.79, P = 0.001) was significantly related to the dominant strain infections. Patients infected with non-dominant strains had a higher risk of the pulmonary cavity (OR = 1.39, 95% CI: 1.01–1.91, P = 0.046). Among 37 paired recurrent cases, 22 (59.46%) were determined as endogenous reactivation, and 15 (40.54%) were exogenous reinfection. The type of M.tb strains prevalent in Jiangsu Province is relatively single. Beijing family strains infection is dominant in local tuberculosis cases. Endogenous reactivation appears to be a major cause of recurrent tuberculosis in Eastern China. This finding emphasizes the importance of case follow-up and monitoring after the completion of antituberculosis treatment.
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Affiliation(s)
- Beibei Qiu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Bilin Tao
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qiao Liu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, China
| | - Zhongqi Li
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Huan Song
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Dan Tian
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jizhou Wu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhuchao Wu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Mengyao Zhan
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Wei Lu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, China
| | - Jianming Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
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Hadifar S, Kamakoli MK, Fateh A, Siadat SD, Vaziri F. Enhancing the differentiation of specific genotypes in Mycobacterium tuberculosis population. Sci Rep 2019; 9:17946. [PMID: 31784605 PMCID: PMC6884525 DOI: 10.1038/s41598-019-54393-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 11/14/2019] [Indexed: 12/18/2022] Open
Abstract
Today, significant attention is directed towards the global lineages and sublineages of Mycobacterium tuberculosis (Mtb). NEW-1 (SIT 127) and CAS1-Delhi (SIT 26) strains are recognized as growing and circulating Mtb genotypes, especially in Asian countries. It is crucial to develop or enhance Mtb genotyping methods for a more accurate and simple differentiation of these families. We used 24-loci mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing for genotyping 217 Mtb isolates. To select the optimal MIRU-VNTR loci, we calculated the Hunter-Gaston discriminatory index (HGDI), allelic diversity, and accumulation of percentage differences (APDs) between the strains among different groups of genotypes (NEW-1 and non-NEW-1; CAS1-Delhi and non-CAS). Finally, the minimum spanning tree was constructed for clustering analysis. In the NEW-1 population, loci with APD > 60% were found to have a high discriminatory power. VNTR loci with APD > 50% showed high discrimination power for the CAS population. Our findings suggest that APDs, which are valuable for the selection of VNTR loci sets, may improve the discriminatory power of MIRU-VNTR typing for identification of Mtb genotypes in specific regions.
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Affiliation(s)
- Shima Hadifar
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Mansour Kargarpour Kamakoli
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran. .,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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Díaz Acosta CC, Russomando G, Candia N, Ritacco V, Vasconcellos SEG, de Berrêdo Pinho Moreira M, de Romero NJ, Morcillo N, De Waard JH, Gomes HM, Suffys PN. Exploring the "Latin American Mediterranean" family and the RD Rio lineage in Mycobacterium tuberculosis isolates from Paraguay, Argentina and Venezuela. BMC Microbiol 2019; 19:131. [PMID: 31195979 PMCID: PMC6567603 DOI: 10.1186/s12866-019-1479-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 05/07/2019] [Indexed: 11/21/2022] Open
Abstract
Background The Latin American & Mediterranean (LAM) spoligotype family is one of the most successful genotype of Mycobacterium tuberculosis worldwide and particularly prevalent in South-America. Within this family, a sublineage named Region of Difference Rio (RDRio) was reported initially in Brazil and is characterized by a genomic deletion of about 26.3 kb. This lineage seems to show a specific adaptation to the Euro-Latin American population. In this context, we sought to evaluate the LAM family and the presence of the RDRio genotype in samples from three Latin American countries including Paraguay, Venezuela and Argentina. To detect LAM strains reliably we applied a typing scheme using spoligotyping, 12 loci MIRU-VNTR, the Ag85C103 SNP and the regions of difference RDRio and RD174. IS6110-RFLP results were also used when available. Results Genotyping of 413 M. tuberculosis isolates from three Latin-American countries detected LAM (46%) and the ill-defined T clade (16%) as the most frequent families. The highest clustering rate was detected in the sample population from the city of Caracas in Venezuela. We observed considerable differences in the presence of the RDRio lineage, with high frequency in Caracas-Venezuela (55%) and low frequency in Buenos Aires-Argentina (11%) and Paraguay (10%). The molecular markers (RD174, Ag85C103, MIRU02-MIRU40 signature) of the RDRio lineage were essentially confirmed. For the LAM family, the most polymorphic loci were MIRU40, MIRU31, MIRU10, MIRU26, MIRU16 and the least polymorphic MIRU24, MIRU20, MIRU04, MIRU23. Conclusions Our results suggest a differential adaptation of LAM-sublineages in neighboring populations and that RDRio strains spread regionally with different rates of distribution. The Ag85C SNP and RDs (RD174, RDRio) tested in this study can in fact facilitate molecular epidemiological studies of LAM strains in endemic settings and low-income countries. Electronic supplementary material The online version of this article (10.1186/s12866-019-1479-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chyntia Carolina Díaz Acosta
- Departamento de Biología Molecular y Biotecnología. Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Asunción, Paraguay.,Laboratório de Biologia Molecular aplicada às Micobactérias, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21045-900, Brazil
| | - Graciela Russomando
- Departamento de Biología Molecular y Biotecnología. Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Asunción, Paraguay
| | - Norma Candia
- Departamento de Biología Molecular y Biotecnología. Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Asunción, Paraguay
| | - Viviana Ritacco
- Servicio de Micobacterias, Instituto Nacional de Enfermedades Infecciosas, ANLIS "Carlos G. Malbran", Buenos Aires, Argentina
| | - Sidra E G Vasconcellos
- Laboratório de Biologia Molecular aplicada às Micobactérias, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21045-900, Brazil
| | | | | | - Nora Morcillo
- Instituto Nacional de Enfermedades Respiratorias Emilio Coni, Buenos Aires, Argentina
| | - Jacobus Henri De Waard
- Laboratorio de Tuberculosis, Instituto de Biomedicina, Caracas, Venezuela.,Present Address: One Health Research Group. Facultad de Ciencias de la Salud, Universidad de Las Américas (UDLA), Quito, Ecuador
| | - Harrison Magdinier Gomes
- Laboratório de Biologia Molecular aplicada às Micobactérias, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21045-900, Brazil
| | - Philip Noel Suffys
- Laboratório de Biologia Molecular aplicada às Micobactérias, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21045-900, Brazil.
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Wyllie DH, Davidson JA, Grace Smith E, Rathod P, Crook DW, Peto TEA, Robinson E, Walker T, Campbell C. A Quantitative Evaluation of MIRU-VNTR Typing Against Whole-Genome Sequencing for Identifying Mycobacterium tuberculosis Transmission: A Prospective Observational Cohort Study. EBioMedicine 2018; 34:122-130. [PMID: 30077721 PMCID: PMC6116353 DOI: 10.1016/j.ebiom.2018.07.019] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/13/2018] [Accepted: 07/15/2018] [Indexed: 12/24/2022] Open
Abstract
Background Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeat (MIRU-VNTR) typing is widely used in high-income countries to determine Mycobacterium tuberculosis relatedness. Whole-genome sequencing (WGS) is known to deliver greater specificity, but no quantitative prospective comparison has yet been undertaken. Methods We studied isolates from the English Midlands, sampled consecutively between 1 January 2012 and 31 December 2015. In addition to routinely performed MIRU-VNTR typing, DNA was extracted from liquid cultures and sequenced using Illumina technology. Demographic and epidemiological data for the relevant patients were extracted from the Enhanced Tuberculosis Surveillance system run by Public Health England. Closely related samples, defined using a threshold of five single nucleotide variants (SNVs), were compared to samples with identical MIRU-VNTR profiles, to samples from individuals with shared epidemiological risk factors, and to those with both characteristics. Findings 1999 patients were identified for whom at least one M. tuberculosis isolate had been MIRU-VNTR typed and sequenced. Comparing epidemiological risk factors with close genetic relatedness, only co-residence had a positive predictive value of over 5%. Excluding co-resident individuals, 18.6% of patients with identical MIRU-VNTR profiles were within 5 SNVs. Where patients also shared social risk factors and ethnic group, this rose to 48%. Only 8% of MIRU-VNTR linked pairs in lineage 1 were within 5 SNV, compared to 31% in lineage 4. Interpretation In the setting studied, this molecular epidemiological study shows MIRU-VNTR typing and epidemiological risk factors are poorly predictive of close genomic relatedness, assessed by SNV. MIRU-VNTR performance varies markedly by lineage. Funding Public Health England, Health Innovation Challenge Fund, NIHR Health Protection Research Unit Oxford, NIHR Oxford Biomedical Research Centre. M. tuberculosis relatedness was measured by MIRU-VNTR typing and single nucleotide variants (SNV). In consecutive isolates in England, only 20% of samples with identical MIRU-VNTR profiles were within 5 SNVs. MIRU-VNTR is more predictive of close relatedness in lineage 4 (Euro-American) lineages than in other lineages.
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Affiliation(s)
- David H Wyllie
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; Public Health England Academic Collaborating Centre, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; The National Institute for Health Research, Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, UK.
| | - Jennifer A Davidson
- Tuberculosis Section, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - E Grace Smith
- Public Health England National Regional Mycobacteriology Laboratory North and Midlands, Heartlands Hospital, Birmingham BS9 5SS
| | - Priti Rathod
- Public Health England National Regional Mycobacteriology Laboratory North and Midlands, Heartlands Hospital, Birmingham BS9 5SS
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; The National Institute for Health Research, Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, UK
| | - Tim E A Peto
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; The National Institute for Health Research, Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, UK
| | - Esther Robinson
- Public Health England National Regional Mycobacteriology Laboratory North and Midlands, Heartlands Hospital, Birmingham BS9 5SS
| | - Tim Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
| | - Colin Campbell
- Tuberculosis Section, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
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Asare P, Asante-Poku A, Prah DA, Borrell S, Osei-Wusu S, Otchere ID, Forson A, Adjapong G, Koram KA, Gagneux S, Yeboah-Manu D. Reduced transmission of Mycobacterium africanum compared to Mycobacterium tuberculosis in urban West Africa. Int J Infect Dis 2018; 73:30-42. [PMID: 29879521 PMCID: PMC6069673 DOI: 10.1016/j.ijid.2018.05.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 05/23/2018] [Accepted: 05/29/2018] [Indexed: 11/27/2022] Open
Abstract
OBJECTIVE Understanding transmission dynamics is useful for tuberculosis (TB) control. A population-based molecular epidemiological study was conducted to determine TB transmission in Ghana. METHODS Mycobacterium tuberculosis complex (MTBC) isolates obtained from prospectively sampled pulmonary TB patients between July 2012 and December 2015 were characterized using spoligotyping and standard 15-locus mycobacterial interspersed repetitive unit variable number tandem repeat (MIRU-VNTR) typing for transmission studies. RESULTS Out of 2309 MTBC isolates, 1082 (46.9%) unique cases were identified, with 1227 (53.1%) isolates belonging to one of 276 clusters. The recent TB transmission rate was estimated to be 41.2%. Whereas TB strains of lineage 4 belonging to M. tuberculosis showed a high recent transmission rate (44.9%), reduced recent transmission rates were found for lineages of Mycobacterium africanum (lineage 5, 31.8%; lineage 6, 24.7%). CONCLUSIONS The study findings indicate high recent TB transmission, suggesting the occurrence of unsuspected outbreaks in Ghana. The observed reduced transmission rate of M. africanum suggests other factor(s) (host/environmental) may be responsible for its continuous presence in West Africa.
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Affiliation(s)
- Prince Asare
- Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana, Legon, Ghana; West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana; Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
| | - Adwoa Asante-Poku
- Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana, Legon, Ghana
| | - Diana Ahu Prah
- Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana, Legon, Ghana
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Stephen Osei-Wusu
- Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana, Legon, Ghana
| | - Isaac Darko Otchere
- Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana, Legon, Ghana
| | | | | | - Kwadwo Ansah Koram
- Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana, Legon, Ghana
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana, Legon, Ghana.
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Rasoahanitralisoa R, Rakotosamimanana N, Stucki D, Sola C, Gagneux S, Rasolofo Razanamparany V. Evaluation of spoligotyping, SNPs and customised MIRU-VNTR combination for genotyping Mycobacterium tuberculosis clinical isolates in Madagascar. PLoS One 2017; 12:e0186088. [PMID: 29053711 PMCID: PMC5650158 DOI: 10.1371/journal.pone.0186088] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 09/25/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Combining different molecular typing methods for Mycobacterium tuberculosis complex (MTBC) can be a powerful tool for molecular epidemiology-based investigation of TB. However, the current standard method that provides high discriminatory power for such a combination, mycobacterial interspersed repetitive units-variable numbers of tandem repeats typing (MIRU-VNTR), is laborious, time-consuming and often too costly for many resource-limited laboratories. We aimed to evaluate a reduced set of loci for MIRU-VNTR typing in combination with spoligotyping and SNP-typing for routine molecular epidemiology of TB. METHOD Spoligotyping and SNP-typing, in combination with the 15 loci MIRU-VNTR typing, were first used to type clinical MTBC isolates (n = 158) from Madagascar. A step by step reduction of MIRU-VNTR loci number was then performed according to the Hunter and Gaston Discriminatory Index (HGDI) and to the Principal component analysis (PCA) correlation with the spoligotype profiles to evaluate the discrimination power inside the generated spoligotype clusters. The 15 MIRU-VNTR was used as reference and SNP-typing was used to determine the main MTBC lineages. RESULTS Of the 158 clinical isolates studied, the SNP-typing classified 23 into Lineage 1 (14.6%), 31 into Lineage 2 (19.6%), 23 into Lineage 3 (14.6%) and 81 into Lineage 4 strains (51.3%). 37 different spoligotypes profiles were obtained, 15 of which were unique and 20 in clusters. 15-loci MIRU-VNTR typing revealed 144 different genotypes: 132 isolates had a unique MIRU-VNTR profile and 27 isolates were grouped into 12 clusters. After a stepwise reduction of the MIRU-VNTR loci number within each main spoligotype families, three different sets composed of 5 customised MIRU-VNTR loci had a similar discrimination level to the reference 15 loci MIRU-VNTR in lineage 1, lineage 2 and lineage 3. For lineage 4, a set of 4 and 3 MIRU-VNTR loci were proposed to subtype the Harleem and LAM spoligotype families, respectively. For the T spoligotype family, a set of 5 MIRU-VNTR loci was proposed. CONCLUSION According to the lineages and the spoligotype families, the number of MIRU-VNTR loci can be reduced to get an optimal classification of MTBC. These customized sets of MIRU-VNTR loci reduce workload and save resources while maintaining optimal discriminatory power.
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Affiliation(s)
- Rondroarivelo Rasoahanitralisoa
- Mycobacteria Unit, Institut Pasteur of Madagascar, Antananarivo, Madagascar, Ecole Doctorale Science de la Vie et de l'Environnement, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
| | | | - David Stucki
- Department of Medical Parasitology and infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Sebastien Gagneux
- Department of Medical Parasitology and infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,Institut for Integrative Cell Biology, I2BC, UMR9198 CEA-CNRS-UP Saclay, Orsay, France
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9
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Abascal E, Herrera DM, Herranz M, Santantón S, Martínez-Lirola M, Tudó G, Gonzalez J, Bouza E, Pérez-Lago L, García-de-Viedma D. A deletion hampering appropriate typing of Mycobacterium africanum. Tuberculosis (Edinb) 2017; 103:24-27. [PMID: 28237030 DOI: 10.1016/j.tube.2016.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 12/22/2016] [Accepted: 12/24/2016] [Indexed: 11/26/2022]
Abstract
Molecular epidemiology analysis of tuberculosis transmission is based mostly on the application of MIRU-VNTR. In certain isolates a complete 24-loci genotype is not obtained and these incompletely genotyped isolates can not be used in the definition of clusters. In a population-based molecular epidemiology study performed in Almería, Southeast Spain, a context with a high proportion of immigrants, we found that an 88-bp deletion in isolates of Mycobacterium africanum Lineage 5 hampers MIRU-VNTR analysis. A more extensive analysis revealed that this deletion was shared by all the Lineage 5 isolates in certain countries of origin of immigrants, such as Equatorial Guinea, and is likely present in several other African countries and also in the USA. A procedure is proposed to enable epidemiological analysis of these isolates.
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Affiliation(s)
- Estefanía Abascal
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Diana Maricela Herrera
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Grupo de Investigación en Sanidad Animal y Humana, Departamento de Ciencias de la Vida y la Agricultura Universidad de las Fuerzas Armadas ESPE, Sangolquí, Ecuador
| | - Marta Herranz
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER Enfermedades respiratorias, CIBERES, Spain
| | - Sheila Santantón
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | | | - Griselda Tudó
- Servei de Microbiologia, Hospital Clinic-CDB, Barcelona, Spain; IS Global, Barcelona, Spain
| | - Juliá Gonzalez
- Servei de Microbiologia, Hospital Clinic-CDB, Barcelona, Spain; IS Global, Barcelona, Spain
| | - Emilio Bouza
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER Enfermedades respiratorias, CIBERES, Spain
| | - Laura Pérez-Lago
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER Enfermedades respiratorias, CIBERES, Spain.
| | - Darío García-de-Viedma
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER Enfermedades respiratorias, CIBERES, Spain.
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10
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Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria. Clin Microbiol Rev 2016; 29:239-90. [PMID: 26912567 DOI: 10.1128/cmr.00055-15] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Molecular typing has revolutionized epidemiological studies of infectious diseases, including those of a mycobacterial etiology. With the advent of fingerprinting techniques, many traditional concepts regarding transmission, infectivity, or pathogenicity of mycobacterial bacilli have been revisited, and their conventional interpretations have been challenged. Since the mid-1990s, when the first typing methods were introduced, a plethora of other modalities have been proposed. So-called molecular epidemiology has become an essential subdiscipline of modern mycobacteriology. It serves as a resource for understanding the key issues in the epidemiology of tuberculosis and other mycobacterial diseases. Among these issues are disclosing sources of infection, quantifying recent transmission, identifying transmission links, discerning reinfection from relapse, tracking the geographic distribution and clonal expansion of specific strains, and exploring the genetic mechanisms underlying specific phenotypic traits, including virulence, organ tropism, transmissibility, or drug resistance. Since genotyping continues to unravel the biology of mycobacteria, it offers enormous promise in the fight against and prevention of the diseases caused by these pathogens. In this review, molecular typing methods for Mycobacterium tuberculosis and nontuberculous mycobacteria elaborated over the last 2 decades are summarized. The relevance of these methods to the epidemiological investigation, diagnosis, evolution, and control of mycobacterial diseases is discussed.
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11
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Hoza AS, Mfinanga SG, Moser I, König B. Molecular characterization of Mycobacterium tuberculosis isolates from Tanga, Tanzania: First insight of MIRU-VNTR and microarray-based spoligotyping in a high burden country. Tuberculosis (Edinb) 2016; 98:116-24. [PMID: 27156627 DOI: 10.1016/j.tube.2016.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 02/12/2016] [Accepted: 02/13/2016] [Indexed: 11/26/2022]
Abstract
Molecular typing of Mycobacterium tuberculosis(MTB) has greatly enhanced the understanding of the population structure of MTB isolates and epidemiology of tuberculosis (TB). To characterize prevalent genotypes of MTB, microarrays‑based spoligotyping and mycobacterial interspersed repetitive unit‑variable number of tandem repeats (MIRU‑VNTR) were applied on 80 isolates collected from primary health care facilities in Tanga, North‑eastern Tanzania. A total of 18 distinct spoligotypes were identified. The lineages by order of their predominance were EAI and CAS families (26.25%, 21 isolates each), LAM family and T super‑family (10%, 8 isolates each), MANU family (3.75%, 3 isolates), Beijing family (2.5%, 2 isolates) and S family (1.25%, 1 isolate). Overall, sixteen (20%) strains could not be allocated to any lineage according to the SITVIT_WEB database. The allelic diversity (h) for specific MIRU‑VNTR loci showed a considerable variation ranging from 0.826 of VNTR locus 3192 to 0.141 of VNTR locus 2059. The allelic diversity for 11 loci (VNTR 3192, 2996, 2165, 960, 4052, 424, 4156, 2531, 1644, 802 and 3690) exceeded 0.6, indicating highly discriminatory power. Seven loci (VNTR 2163b, 2401, 1955, 577, 4348, 2687 and 580) showed moderate discrimination (0.3 ≤ h ≥ 0.6), and three loci (VNTR3007, 154 and 2059) were less polymorphic. The present study suggests that the TB cases in Tanga might be caused by a diverse array of MTB strain families that may be indicative of a cosmopolitan population with frequent migration and travel. Microarray‑based spoligotyping and MIRU‑VNTR could be reliable tools in detecting different MTB genotypes in high burden settings.
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Affiliation(s)
- Abubakar S Hoza
- Department of Medical Microbiology and Epidemiology of Infectious Diseases, Medical Faculty, University of Leipzig, Liebig Str. 21, 04103 Leipzig, Germany; Department of Veterinary Microbiology and Parasitology, Sokoine University of Agriculture, P.O. Box 3019, Morogoro, Tanzania.
| | - Sayoki G Mfinanga
- National Institute for Medical Research, Muhimbili Medical Research Centre, P.O. Box 3436 Dar es Salaam, Tanzania
| | - Irmgard Moser
- Friedrich Loeffler Institut, Institute of Molecular Pathogenesis, Naumburger Str. 96a, 07743 Jena, Germany
| | - Brigitte König
- Department of Medical Microbiology and Epidemiology of Infectious Diseases, Medical Faculty, University of Leipzig, Liebig Str. 21, 04103 Leipzig, Germany
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12
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Diab HM, Nakajima C, Kotb SA, Mokhtar A, Khder NFM, Abdelaal ASA, Hegazy A, Poudel A, Shah Y, Suzuki Y. First insight into the genetic population structure of Mycobacterium tuberculosis isolated from pulmonary tuberculosis patients in Egypt. Tuberculosis (Edinb) 2015; 96:13-20. [PMID: 26786649 DOI: 10.1016/j.tube.2015.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 10/31/2015] [Accepted: 11/08/2015] [Indexed: 11/19/2022]
Abstract
The present study aimed to assess the population structure of Mycobacterium tuberculosis (MTB) isolates from Egypt. A total of 230 MTB isolates were analysed using spoligotyping, large sequence polymorphism (LSPs), mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing and multi-locus sequence typing (MLST). The majority of isolates (93.0%) belonged to lineage 4, including 44.3, 13.4 and 10.8% of the ill-defined T clade, LAM and Haarlem families, respectively, and lineage 3 was identified in 7.0% of the isolates. MIRU-VNTRs typing allowed efficient discrimination of the spoligotype-defined clusters, including spoligo-international types (SIT) 53, 34, and 4, into 56 patterns, including 13 clusters and 43 unique patterns. A new SNP at position 311614 was identified in all six isolates to form the biggest MIRU-VNTR cluster, which suggested a recent clonal expansion. This SNP could possibly be used as a genetic marker for robust discriminations of Egyptian MTB isolates belonging to SIT53. The combination of spoligotyping, 12 MIRU-VNTRs loci and MLST provided insight into the genetic diversity and transmission dynamics of the Egyptian MTB genotypes and could be a key to implementation of effective control measures by public health authorities.
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Affiliation(s)
- Hassan Mahmoud Diab
- Department of Animal Hygiene, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt; Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Hokkaido University, The Global Station for Zoonosis Control, Sapporo, Japan
| | - Saber A Kotb
- Department of Animal Hygiene, Faculty of Veterinary Medicine, Assiut University, Egypt
| | - Alaa Mokhtar
- National Tuberculosis Control Program, Ministry of Health and Population, Egypt
| | - Nagwa F M Khder
- TB Supranational Reference Laboratory, Central Public Health Laboratories, Clinical Microbiology Department, Ministry of Health and Population, Egypt
| | - Ahmed S A Abdelaal
- TB Supranational Reference Laboratory, Central Public Health Laboratories, Clinical Microbiology Department, Ministry of Health and Population, Egypt
| | - Azza Hegazy
- TB Supranational Reference Laboratory, Central Public Health Laboratories, Clinical Microbiology Department, Ministry of Health and Population, Egypt
| | - Ajay Poudel
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Yogendra Shah
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Hokkaido University, The Global Station for Zoonosis Control, Sapporo, Japan.
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13
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Abstract
Until recently, bioinformatics, an important discipline in the biological sciences, was largely limited to countries with advanced scientific resources. Nonetheless, several developing countries have lately been making progress in bioinformatics training and applications. In Africa, leading countries in the discipline include South Africa, Nigeria, and Kenya. However, one country that is less known when it comes to bioinformatics is Ghana. Here, I provide a first description of the development of bioinformatics activities in Ghana and how these activities contribute to the overall development of the discipline in Africa. Over the past decade, scientists in Ghana have been involved in publications incorporating bioinformatics analyses, aimed at addressing research questions in biomedical science and agriculture. Scarce research funding and inadequate training opportunities are some of the challenges that need to be addressed for Ghanaian scientists to continue developing their expertise in bioinformatics.
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Affiliation(s)
- Thomas K. Karikari
- Department of Science Laboratory Technology, School of Applied Science and Technology, Wa Polytechnic, Wa, Ghana
- * E-mail:
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14
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Dantas NGT, Suffys PN, Carvalho WDS, Gomes HM, de Almeida IN, de Assis LJ, Augusto CJ, Gomgnimbou MK, Refregier G, Sola C, de Miranda SS. Genetic diversity and molecular epidemiology of multidrug-resistant Mycobacterium tuberculosis in Minas Gerais State, Brazil. BMC Infect Dis 2015; 15:306. [PMID: 26231661 PMCID: PMC4521345 DOI: 10.1186/s12879-015-1057-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 07/23/2015] [Indexed: 11/22/2022] Open
Abstract
Background We aimed to characterize the genetic diversity of drug-resistant Mycobacterium tuberculosis (MTb) clinical isolates and investigate the molecular epidemiology of multidrug-resistant (MDR) tuberculosis from Minas Gerais State, Brazil. Methods One hundred and four MTb clinical isolates were assessed by IS6110-RFLP, 24-locus mycobacterial interspersed repetitive units variable-number tandem repeats (MIRU-VNTR), TB-SPRINT (simultaneous spoligotyping and rifampicin-isoniazid drug-resistance mutation analysis) and 3R-SNP-typing (analysis of single-nucleotide polymorphisms in the genes involved in replication, recombination and repair functions). Results Fifty-seven different IS6110-RFLP patterns were found, among which 50 had unique patterns and 17 were grouped into seven clusters. The discriminatory index (Hunter and Gaston, HGDI) for RFLP was 0.9937. Ninety-nine different MIRU-VNTR patterns were found, 95 of which had unique patterns and nine isolates were grouped into four clusters. The major allelic diversity index in the MIRU-VNTR loci ranged from 0.6568 to 0.7789. The global HGDI for MIRU-VNTR was 0.9991. Thirty-two different spoligotyping profiles were found: 16 unique patterns (n = 16) and 16 clustered profiles (n = 88). The HGDI for spoligotyping was 0.9009. The spoligotyped clinical isolates were phylogenetically classified into Latin-American Mediterranean (66.34 %), T (14.42 %), Haarlem (5.76 %), X (1.92 %), S (1.92 %) and U (unknown profile; 8.65 %). Among the U isolates, 77.8 % were classified further by 3R-SNP-typing as 44.5 % Haarlem and 33.3 % LAM, while the 22.2 % remaining were not classified. Among the 104 clinical isolates, 86 were identified by TB-SPRINT as MDR, 12 were resistant to rifampicin only, one was resistant to isoniazid only, three were susceptible to both drugs, and two were not successfully amplified by PCR. A total of 42, 28 and eight isolates had mutations in rpoB positions 531, 526 and 516, respectively. Correlating the cluster analysis with the patient data did not suggest recent transmission of MDR-TB. Conclusions Although our results do not suggest strong transmission of MDR-TB in Minas Gerais (using a classical 100 % MDR-TB identical isolates cluster definition), use of a smoother cluster definition (>85 % similarity) does not allow us to fully eliminate this possibility; hence, around 20–30 % of the isolates we analyzed might be MDR-TB transmission cases.
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Affiliation(s)
- Nayanne Gama Teixeira Dantas
- Post-Graduate Program in Infectious Diseases and Tropical Medicine, Department of Internal medicine, Faculty of Medicine, Federal University of Minas Gerais, Belo Horizonte, Brazil.
| | - Phillip Noel Suffys
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Wânia da Silva Carvalho
- Laboratory of Molecular Biology and Public Health, Department of Social Pharmacy, Faculty of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Brazil.
| | - Harrison Magdinier Gomes
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Isabela Neves de Almeida
- Post-Graduate Program in Infectious Diseases and Tropical Medicine, Department of Internal medicine, Faculty of Medicine, Federal University of Minas Gerais, Belo Horizonte, Brazil.
| | - Lida Jouca de Assis
- Laboratory of Molecular Biology and Public Health, Department of Social Pharmacy, Faculty of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Brazil.
| | | | - Michel Kireopori Gomgnimbou
- Institut for Integrative Cell Biology, I2BC, UMR9198 CEA-CNRS-UPSaclay, Orsay, France. .,Centre Muraz, Bobo-Dioulasso, Burkina Faso.
| | - Guislaine Refregier
- Institut for Integrative Cell Biology, I2BC, UMR9198 CEA-CNRS-UPSaclay, Orsay, France.
| | - Christophe Sola
- Institut for Integrative Cell Biology, I2BC, UMR9198 CEA-CNRS-UPSaclay, Orsay, France.
| | - Silvana Spíndola de Miranda
- Post-Graduate Program in Infectious Diseases and Tropical Medicine, Department of Internal medicine, Faculty of Medicine, Federal University of Minas Gerais, Belo Horizonte, Brazil.
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15
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Seto J, Wada T, Iwamoto T, Tamaru A, Maeda S, Yamamoto K, Hase A, Murakami K, Maeda E, Oishi A, Migita Y, Yamamoto T, Ahiko T. Phylogenetic assignment of Mycobacterium tuberculosis Beijing clinical isolates in Japan by maximum a posteriori estimation. INFECTION GENETICS AND EVOLUTION 2015. [PMID: 26220897 DOI: 10.1016/j.meegid.2015.07.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Intra-species phylogeny of Mycobacterium tuberculosis has been regarded as a clue to estimate its potential risk to develop drug-resistance and various epidemiological tendencies. Genotypic characterization of variable number of tandem repeats (VNTR), a standard tool to ascertain transmission routes, has been improving as a public health effort, but determining phylogenetic information from those efforts alone is difficult. We present a platform based on maximum a posteriori (MAP) estimation to estimate phylogenetic information for M. tuberculosis clinical isolates from individual profiles of VNTR types. This study used 1245 M. tuberculosis clinical isolates obtained throughout Japan for construction of an MAP estimation formula. Two MAP estimation formulae, classification of Beijing family and other lineages, and classification of five Beijing sublineages (ST11/26, STK, ST3, and ST25/19 belonging to the ancient Beijing subfamily and modern Beijing subfamily), were created based on 24 loci VNTR (24Beijing-VNTR) profiles and phylogenetic information of the isolates. Recursive estimation based on the formulae showed high concordance with their authentic phylogeny by multi-locus sequence typing (MLST) of the isolates. The formulae might further support phylogenetic estimation of the Beijing lineage M. tuberculosis from the VNTR genotype with various geographic backgrounds. These results suggest that MAP estimation can function as a reliable probabilistic process to append phylogenetic information to VNTR genotypes of M. tuberculosis independently, which might improve the usage of genotyping data for control, understanding, prevention, and treatment of TB.
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Affiliation(s)
- Junji Seto
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, 1-6-6 Toka-machi, Yamagata-shi, Yamagata 990-0031, Japan.
| | - Takayuki Wada
- Department of International Health, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan.
| | - Tomotada Iwamoto
- Department of Microbiology, Kobe Institute of Health, 4-6 Minatojima-nakamachi, Chuo-ku, Kobe 650-0046, Japan
| | - Aki Tamaru
- Department of Microbiology, Osaka Prefectural Institute of Public Health, 1-3-69 Nakamichi, Higashinari-ku, Osaka 537-0025, Japan
| | - Shinji Maeda
- School of Pharmacy, Hokkaido Pharmaceutical University, 7-15-4-1 Maeda, Teine-ku, Sapporo, Hokkaido 006-8590, Japan
| | - Kaori Yamamoto
- Department of Microbiology, Osaka City Institute of Public Health and Environmental Sciences, 8-34 Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan; Department of International Health, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Atsushi Hase
- Department of Microbiology, Osaka City Institute of Public Health and Environmental Sciences, 8-34 Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan
| | - Koichi Murakami
- Department of Health Science, Fukuoka Institute of Health and Environmental Sciences, 39 Mukaizano, Dazaifu, Fukuoka 818-0135, Japan
| | - Eriko Maeda
- Department of Health Science, Fukuoka Institute of Health and Environmental Sciences, 39 Mukaizano, Dazaifu, Fukuoka 818-0135, Japan
| | - Akira Oishi
- Department of Health Science, Fukuoka Institute of Health and Environmental Sciences, 39 Mukaizano, Dazaifu, Fukuoka 818-0135, Japan
| | - Yuji Migita
- Department of Microbiology, Nagasaki Prefectural Institute for Environmental Research and Public Health, 2-1306-11 Ikeda, Ohmura, Nagasaki 856-0026, Japan
| | - Taro Yamamoto
- Department of International Health, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan; Department of International Health, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Tadayuki Ahiko
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, 1-6-6 Toka-machi, Yamagata-shi, Yamagata 990-0031, Japan
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16
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Yang L, Wang C, Wang H, Meng Q, Wang Q. Evaluation of MIRU-VNTR for typing of Mycobacterium bovis isolated from Sika deer in Northeast China. BMC Vet Res 2015; 11:93. [PMID: 25889075 PMCID: PMC4399248 DOI: 10.1186/s12917-015-0402-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 03/20/2015] [Indexed: 11/29/2022] Open
Abstract
Background Bovine tuberculosis has led to serious economic losses for Sika Deer producers in China. Strategies for controlling the spread of Mycobacterium bovis are often hampered by a lack of epidemiological data. Specifically, tracing infections requires the ability to trace back infections, which, in turn, requires the ability to determine isolates with a common source. This study was planned to assess the discriminatory power of each mycobacterial interspersed repetitive unit (MIRU)-variable number tandem repeats (VNTR) locus and evaluate the most appropriate combination of MIRU-VNTR loci for molecular epidemiological studies on Sika Deer in China. Results The discriminatory power of MIRU-VNTR typing based on 22 known loci (12 MIRUs, 2 ETRs, 4 QUBs, and 4 Mtubs) were assessed in 96 Mycobacterium bovis strains collected sequentially from Sika Deer at a slaughterhouse in northeastern China. We defined four loci (MIRU4, ETRA, QUB11b, and Mtub4) as highly discriminative, eight loci (MIRU2, MIRU23, MIRU27, MIRU31, MIRU39, MIRU40, QUB26, and Mtub21) as moderately discriminative, and three loci (MIRU16, Mtub30, and Mtub34) as poorly discriminative. The final locus showed no polymorphism between strains. MIRU-VNTR typing as a whole was highly discriminative, with an overall allelic diversity of 0.897. Of the loci tested, the four highly discriminative loci and eight moderately discriminative loci proved to be most appropriate for first line typing of M. bovis from Sika Deer, with the same resolving ability as all 22 loci (H = 0.897). Conclusions MIRU-VNTR typing is quick and effective for typing bovine tuberculosis isolates from Sika Deer in China. Electronic supplementary material The online version of this article (doi:10.1186/s12917-015-0402-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Li Yang
- College of Chinese Medicinal Materials, Jilin Agricultural University, Xincheng Street No.2888, 130118, Changchun, China.
| | - Chunyu Wang
- Jilin Entry-Exit Inspection and Quadrant Bureau, Puyang Street No.1301, Changchun, 130062, China.
| | - Haijun Wang
- College of Chinese Medicinal Materials, Jilin Agricultural University, Xincheng Street No.2888, 130118, Changchun, China.
| | - Qingfeng Meng
- Jilin Entry-Exit Inspection and Quadrant Bureau, Puyang Street No.1301, Changchun, 130062, China.
| | - Quankai Wang
- College of Chinese Medicinal Materials, Jilin Agricultural University, Xincheng Street No.2888, 130118, Changchun, China. .,Jilin Sino-ROK Academy of Animal Sciences, Donghua Street No.1699, Changchun, 130600, China.
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Wada T, Iwamoto T, Tamaru A, Seto J, Ahiko T, Yamamoto K, Hase A, Maeda S, Yamamoto T. Clonality and micro-diversity of a nationwide spreading genotype of Mycobacterium tuberculosis in Japan. PLoS One 2015; 10:e0118495. [PMID: 25734518 PMCID: PMC4348518 DOI: 10.1371/journal.pone.0118495] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 01/19/2015] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium tuberculosis transmission routes can be estimated from genotypic analysis of clinical isolates from patients. In Japan, still a middle-incidence country of TB, a unique genotype strain designated as ‘M-strain’ has been isolated nationwide recently. To ascertain the history of the wide spread of the strain, 10 clinical isolates from different areas were subjected to genome-wide analysis based on deep sequencers. Results show that all isolates possessed common mutations to those of referential strains. The greatest number of accumulated single nucleotide variants (SNVs) from the oldest coalescence was 13 nucleotides, indicating high clonality of these isolates. When an SNV common to the isolates was used as a surrogate marker of the clone, authentic clonal isolates with variation in a reliable subset of variable number of tandem repeat (VNTR) genotyping method can be selected successfully from clinical isolates populations of M. tuberculosis. When the authentic clones can also be assigned to sub-clonal groups by SNVs derived from the genomic comparison, they are classifiable into three sub-clonal groups with a bias of geographical origins. Feedback from genomic analysis of clinical isolates of M. tuberculosis to genotypic markers will be an efficient strategy for the big data in various settings for public health actions against TB.
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Affiliation(s)
- Takayuki Wada
- Department of International Health, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- * E-mail:
| | - Tomotada Iwamoto
- Department of Microbiology, Kobe Institute of Health, Kobe, Japan
| | - Aki Tamaru
- Department of Microbiology, Osaka Prefectural Institute of Public Health, Osaka, Japan
| | - Junji Seto
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata, Japan
| | - Tadayuki Ahiko
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata, Japan
| | - Kaori Yamamoto
- Department of Microbiology, Osaka City Institute of Public Health and Environmental Sciences, Osaka, Japan
| | - Atushi Hase
- Department of Microbiology, Osaka City Institute of Public Health and Environmental Sciences, Osaka, Japan
| | - Shinji Maeda
- Department of Mycobacterium Reference and Research, the Research Institute of Tuberculosis, Tokyo, Japan
| | - Taro Yamamoto
- Department of International Health, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
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