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Shibabaw A, Gelaw B, Ghanem M, Legall N, Schooley AM, Soehnlen MK, Salvador LCM, Gebreyes W, Wang SH, Tessema B. Molecular epidemiology and transmission dynamics of multi-drug resistant tuberculosis strains using whole genome sequencing in the Amhara region, Ethiopia. BMC Genomics 2023; 24:400. [PMID: 37460951 DOI: 10.1186/s12864-023-09502-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Drug resistant Mycobacterium tuberculosis prevention and care is a major challenge in Ethiopia. The World health organization has designated Ethiopia as one of the 30 high burden multi-drug resistant tuberculosis (MDR-TB) countries. There is limited information regarding genetic diversity and transmission dynamics of MDR-TB in Ethiopia. OBJECTIVE To investigate the molecular epidemiology and transmission dynamics of MDR-TB strains using whole genome sequence (WGS) in the Amhara region. METHODS Forty-five MDR-TB clinical isolates from Amhara region were collected between 2016 and 2018, and characterized using WGS and 24-loci Mycobacterium Interspersed Repetitive Units Variable Number of Tandem Repeats (MIRU-VNTR) typing. Clusters were defined based on the maximum distance of 12 single nucleotide polymorphisms (SNPs) or alleles as the upper threshold of genomic relatedness. Five or less SNPs or alleles distance or identical 24-loci VNTR typing is denoted as surrogate marker for recent transmission. RESULTS Forty-one of the 45 isolates were analyzed by WGS and 44% (18/41) of the isolates were distributed into 4 clusters. Of the 41 MDR-TB isolates, 58.5% were classified as lineage 4, 36.5% lineage 3 and 5% lineage 1. Overall, TUR genotype (54%) was the predominant in MDR-TB strains. 41% (17/41) of the isolates were clustered into four WGS groups and the remaining isolates were unique strains. The predominant cluster (Cluster 1) was composed of nine isolates belonging to lineage 4 and of these, four isolates were in the recent transmission links. CONCLUSIONS Majority of MDR-TB strain cluster and predominance of TUR lineage in the Amhara region give rise to concerns for possible ongoing transmission. Efforts to strengthen TB laboratory to advance diagnosis, intensified active case finding, and expanded contact tracing activities are needed in order to improve rapid diagnosis and initiate early treatment. This would lead to the interruption of the transmission chain and stop the spread of MDR-TB in the Amhara region.
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Affiliation(s)
- Agumas Shibabaw
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia.
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA.
- Department of Medical Microbiology, School of Medical Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia.
- Michigan Department of Health and Human Services, Infectious disease, Lansing, MI, USA.
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA.
| | - Baye Gelaw
- Department of Medical Microbiology, School of Medical Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Mostafa Ghanem
- Department of Veterinary Medicine, Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, MD, USA
| | - Noah Legall
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Angie M Schooley
- Michigan Department of Health and Human Services, Infectious disease, Lansing, MI, USA
| | - Marty K Soehnlen
- Michigan Department of Health and Human Services, Infectious disease, Lansing, MI, USA
| | - Liliana C M Salvador
- School of Animal and Comparative Biomedical Sciences, College of Agriculture and life sciences, University of Arizona, Tucson, AZ, USA
| | - Wondwossen Gebreyes
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Shu-Hua Wang
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA
- Department of Internal Medicine, Division of Infectious Diseases, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Belay Tessema
- Department of Medical Microbiology, School of Medical Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
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Gürer Giray B, Aslantürk A, Şimşek H, Özgür D, Kılıç S, Aslan G. Determination of genetic diversity of multidrug-resistant Mycobacterium tuberculosis strains in Turkey using 15 locus MIRU-VNTR and spoligotyping methods. Pathog Glob Health 2023; 117:85-91. [PMID: 35642888 PMCID: PMC9848327 DOI: 10.1080/20477724.2022.2084807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Tuberculosis (TB) remains the leading cause of deaths from infectious disease worldwide. Nowadays, the tendency of Mycobacterium tuberculosis complex (MTBC) to spread between continents due to uncontrolled migration movements shows that TB is a global health problem. The number of studies for the detection of MTBC strains' epidemiological features in areas with TB spread risk using molecular-based methods such as spoligotyping and Mycobacterial Interspersed Repetitive Unit (MIRU) Variable Number Tandem Repeats (VNTR) at the clonal level is insufficient. In this study, it was aimed to determine the phylogenetic relationships of MTBC strains at the species level by spoligotyping and 15 locus MIRU-VNTR (MIRU-VNTR15) molecular methods of 96 multidrug-resistant (MDR) MTBC strains isolated from sputum samples of patients with a preliminary diagnosis of pulmonary TB or suspected contact history those sent to National Tuberculosis Reference Laboratory from the centers that are members of the Tuberculosis Laboratory Surveillance Network. The phylogenetic relationship between 96 MDR-TB strains was investigated with the combination of bead-based spoligotyping and MIRU-VNTR15 methods on the MAGPIX® Milliplex Map device. In this study, it was determined that the T1 family is more common in our country and LAM7-TUR family is less common than the Beijing family unlike other studies. It was determined that the strains in the same cluster had different locus profiles, and there was no transmission from the same clone in the clonal typing we performed with spoligotyping and MIRU-VNTR15.
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Affiliation(s)
- Burcu Gürer Giray
- Ankara Provincial Health Directorate Public Health Molecular Diagnosis Laboratory, Ankara, Turkey,CONTACT Burcu Gürer Giray Molecular Diagnosis Laboratory, Public Health Institution of Ankara, Turkey
| | - Ahmet Aslantürk
- National Tuberculosis Reference Laboratory, Public Health Institution of Turkey (PHIT), Ankara, Turkey
| | - Hülya Şimşek
- Faculty of Medicine, Department of Medical Microbiology, Yozgat Bozok University, Yozgat, Turkey
| | - Didem Özgür
- Department of Medical Microbiology, Kafkas University, Kars, Turkey
| | - Selçuk Kılıç
- Department of Medical CBRN, University of Health Sciences, Institute of Dedenxe Health Sciences, Ankara, Turkey
| | - Gönül Aslan
- Mersin University Faculty of Medicine, Department of Medical Microbiology, Mersin, Turkey
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Asgharzadeh M, Rashedi J, Poor BM, Kafil HS, Zadeh HM, Ahmadpour E. How Molecular Epidemiology Can Affect Tuberculosis Control in the Middle East Countries: A Systematic Review and Meta-Analysis. Infect Disord Drug Targets 2021; 21:28-37. [PMID: 31903887 DOI: 10.2174/1871526520666200106123619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/13/2019] [Accepted: 12/24/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Nowadays, due to the incidence of specific strains of Mycobacterium tuberculosis and also an increase in the rate of drug resistant-TB, the mortality rate has been increased by this disease. The identification of common strains in the region, as well as the sources of transmission, is essential to control the disease, which is possible by using molecular epidemiology. OBJECTIVES In this survey, the studies utilizing the spoligotyping method in Muslim Middle East countries are reviewed to determine their role in the control of TB. METHODS All studies conducted from 2005 to June 2016 were considered systematically in three electronic databases out of which 23 studies were finally selected. RESULTS The average rate of clustering was 84% and the rate of recent transmission varied from 21.7% to 92.4%. The incidence of Beijing strains has been found to be rising in the abovementioned countries. In Iran and Saudi Arabia known as immigration and labour-hosting countries, respectively, rapid transmittable and drug-resistant Beijing strains were higher than those in other Muslim Middle East countries. CONCLUSION Considering the incidence of highly virulent strains, due to the increase in immigration and people infected with HIV, tuberculosis, especially drug-resistant form, careful monitoring is needed.
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Affiliation(s)
- Mohammad Asgharzadeh
- Biotechnology Research Center, Faculty of Paramedicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jalil Rashedi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behroz Mahdavi Poor
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Moharram Zadeh
- Women's Reproduction Health Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ehsan Ahmadpour
- Department of Medical Parasitology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Molecular epidemiology of clinical Mycobacterium tuberculosis complex isolates in South Omo, Southern Ethiopia. BMC Infect Dis 2020; 20:750. [PMID: 33050903 PMCID: PMC7557052 DOI: 10.1186/s12879-020-05394-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 09/02/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is caused by Mycobacterium tuberculosis complex (MTBC). Mapping the genetic diversity of MTBC in high TB burden country like Ethiopia is important to understand principles of the disease transmission and to strengthen the regional TB control program. The aim of this study was to investigate the genetic diversity of Mycobacterium tuberculosis complex (MTBC) isolates circulating in the South Omo, southern Ethiopia. METHODS MTBC isolates (N = 156) were genetically analyzed using spacer oligotyping (spoligotyping) and mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) typing. Major lineages and lineages were identified using MTBC databases. Logistic regression was used to correlate patient characteristics with strain clustering. RESULTS The study identified Euro-American (EA), East-African-Indian (EAI), Indo-Oceanic (IO), Lineage_7/Aethiops vertus, Mycobacterium bovis and Mycobacterium africanum major lineages in proportions of 67.3% (105/156), 22.4% (35/156), 6.4% (10/156), 1.9% (3/156), 1.3% (2/156) and 0.6% (1/156), respectively. Lineages identified were Delhi/CAS 23.9% (37/155), Ethiopia_2 20.6% (32/155), Haarlem 14.2% (22/155), URAL 14.2%(22/155), Ethiopia_3 8.4% (13/155), TUR 6.5% (10/155), Lineage_7/Aethiops vertus 1.9% (3/155), Bovis 1.3% (2/155), LAM 1.3% (2/155), EAI 0.6% (1/155), X 0.6% (1/155) and Ethiopia H37Rv-like strain 0.6% (1/155). Of the genotyped isolates 5.8% (9/155) remained unassigned. The recent transmission index (RTI) was 3.9%. Orphan strains compared to shared types (AOR: 0.09, 95% CI: 0.04-0.25) were associated with reduced odds of clustering. The dominant TB lineage in pastoral areas was EAI and in non-pastoral areas was EA. CONCLUSION The epidemiological data, highly diverse MTBC strains and a low RTI in South Omo, provide information contributing to the TB Control Program of the country.
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Molecular typing of drug-resistant Mycobacterium tuberculosis strains from Turkey. J Glob Antimicrob Resist 2020; 23:130-134. [PMID: 32956873 DOI: 10.1016/j.jgar.2020.08.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/03/2020] [Accepted: 08/18/2020] [Indexed: 11/21/2022] Open
Abstract
OBJECTIVES Appropriate antibiotic therapy and prevention of cross-contamination are the most important subjects in tuberculosis (TB) control. The aim of this study was to investigate the major phylogenetic clades and transmission rate of multidrug-resistant (MDR) Mycobacterium tuberculosis isolates (n = 200) from patients with TB in Sivas and Konya Provinces of Turkey. METHODS The phylogenetic relationship among the isolates was investigated by spoligotyping method. In addition, the 24-locus mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) typing method was used to reveal cross-contamination. RESULTS Spoligotyping revealed 13 different spoligotypes. A total of 188 strains (94.0%) were included in the cluster. The most prominent spoligofamily was the T family (43.0% of strains), followed by LAM (26.0%), H (8.0%), X and S (both 6.0%) and U (5.0%). Also, 12 strains (6.0%) belonged to the Beijing profile. MIRU-VNTR results showed 176 (88.0%) different genotypes among the isolates. In total, 24 strains (12.0%) were in the cluster. CONCLUSIONS According to spoligotyping, there is a heterogeneous M. tuberculosis population in Turkey. MIRU-VNTR results showed that cross-contamination observed between MDR M. tuberculosis isolates in Turkey is controllable.
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Bhembe NL, Nwodo UU, Okoh AI, Obi CL, Mabinya LV, Green E. Clonality and genetic profiles of drug-resistant Mycobacterium tuberculosis in the Eastern Cape Province, South Africa. Microbiologyopen 2019; 8:e00449. [PMID: 30801981 PMCID: PMC6436438 DOI: 10.1002/mbo3.449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/15/2016] [Accepted: 12/20/2016] [Indexed: 01/05/2023] Open
Abstract
In this study, we investigated the diversity of drug-resistant Mycobacterium tuberculosis isolates from families who own cattle in the Eastern Cape Province of South Africa using spoligotyping and mycobacterial interspersed repetitive-unit-variable number tandem repeat (MIRU-VNTR) typing. The Mycobacterium tuberculosis was investigated using MIRU-VNTR and the Mycobacterium tuberculosis families were evaluated using spoligotyping. Spoligotyping grouped 91% of the isolates into seven clusters, while 9% of the deoxyribonucleic acid (DNA) from TB isolates were unclustered from a total of 154 DNA used. Previously described shared types were observed in 89.6% of the isolates, with the Beijing family, SIT1, the principal genotype in the province, while the families T, SIT53 and X1, SIT1329 were the least detected genotypes. MIRU-VNTR grouped 81% of the isolates in 23 clusters while 19% were unclustered. A combination of the VNTR and spoligotyping grouped 79% of the isolates into 23 clusters with 21% unclustered. The low level of diversity and the clonal spread of drug-resistant Mycobacterium tuberculosis isolates advocate that the spread of TB in this study may be instigated by the clonal spread of Beijing genotype. The results from this study provide vital information about the lack of TB control and distribution of Mycobacterium tuberculosis complex strain types in the Eastern Cape Province of South Africa.
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Affiliation(s)
- Nolwazi L Bhembe
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa.,Molecular Pathogenesis and Molecular Epidemiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
| | - Uchechukwu U Nwodo
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa.,Molecular Pathogenesis and Molecular Epidemiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
| | - Anthony I Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa.,Molecular Pathogenesis and Molecular Epidemiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
| | - Chikwelu L Obi
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa.,Academic and Research Division, University of Fort Hare, Alice, South Africa
| | - Leonard V Mabinya
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa.,Molecular Pathogenesis and Molecular Epidemiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
| | - Ezekiel Green
- Department of Biotechnology and Food Science, Faculty of Science, University of Johannesburg, Doornfontein, South Africa
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Weerasekera D, Pathirane H, Madegedara D, Dissanayake N, Thevanesam V, Magana-Arachchi DN. Evaluation of the 15 and 24-loci MIRU-VNTR genotyping tools with spoligotyping in the identification of Mycobacterium tuberculosis strains and their genetic diversity in molecular epidemiology studies. Infect Dis (Lond) 2019; 51:206-215. [PMID: 30689510 DOI: 10.1080/23744235.2018.1551619] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
BACKGROUND The transmission dynamics of Mycobacterium tuberculosis (Mtb) using various genotyping tools has been studied globally and a particular tool for genotyping Mtb is the mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR). Tuberculosis (TB) remains an important public health problem worldwide and Sri Lanka being a country of tourist destination; because of major development projects undergoing, it has a high proportion of tourists and immigrants from Asia and Europe that are characterized with highest TB incidences and drug-resistant clinical isolates. Hence, in order to address the question of Mtb genetic diversity, we investigated the discriminatory power of both MIRU-VNTR typing of 15 and 24 loci with spoligotyping to differentiate Mtb isolates. METHOD Acid-fast bacilli positive sputum samples (n = 150) from first visit patients were collected. Decontamination of sputum and extraction of genomic DNA were carried out using standard techniques. The isolates were characterized by MIRU-VNTR for both the 15 and 24 loci and spoligotyping. RESULTS In our study population, MIRU-VNTR 15 and 24 loci did not show a significant difference among the identified M. tuberculosis strains. However, MIRU 24 loci yielded an additional strain LAM, which is of T1 origin. 15 loci strain grouping had more clusters of strains grouped together while 24 loci differentiated the same cluster of strains into distinct strain types. CONCLUSION We conclude that the use of 15-locus MIRU-VNTR typing is sufficient for a first-line epidemiological study to genotype M. tuberculosis, but the additional discriminatory power of 24 loci MIRU-VNTR has been able to differentiate samples within highly homologous groups.
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Affiliation(s)
| | | | | | - Neranjan Dissanayake
- c Consultant Respiratory Unit , District General Hospital , Nuwara-Eliya , Sri Lanka
| | - Vasanthi Thevanesam
- d Department of Microbiology, Faculty of Medicine , University of Peradeniya , Peradeniya , Sri Lanka
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Role of Molecular Epidemiology on Tuberculosis Control in the Middle East Countries: a Systematic Review and Meta-Analysis. TANAFFOS 2018; 17:223-232. [PMID: 31143212 PMCID: PMC6534806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Tuberculosis (TB) is a public health problem in developing countries and yet the numbers of people with the disease are abundant. Early detection of transmission sources and effective treatment of the cases is essential to control the disease which will be possible by application of molecular epidemiology approaches. Studies conducted based on Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) method in Muslim Middle East countries were evaluated to determine their role in TB control. MATERIALS AND METHODS All studies from January 2005 to April 2016 were systematically reviewed in four electronic databases and finally 16 articles were found eligible to be included in this study. The mean clustering rate was determined as 44% and the recent transmission rate was 12.3 to 78.8% with average of 33%. RESULTS The results showed that both reactivation and recent transmission were important in developing new cases of TB in Middle East countries; but, reactivation plays a more critical role. CONCLUSION Regarding to ongoing war and immigration in the region along with the increasing of drug-resistant TB, in the case of improper supervision in the future, the disease, especially drug- resistant TB, will be problematic.
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Refrégier G, Abadia E, Matsumoto T, Ano H, Takashima T, Tsuyuguchi I, Aktas E, Cömert F, Gomgnimbou MK, Panaiotov S, Phelan J, Coll F, McNerney R, Pain A, Clark TG, Sola C. Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor. INFECTION GENETICS AND EVOLUTION 2016; 45:461-473. [PMID: 27746295 DOI: 10.1016/j.meegid.2016.10.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/23/2016] [Accepted: 10/12/2016] [Indexed: 12/19/2022]
Abstract
Two geographically distant M. tuberculosis sublineages, Tur from Turkey and T3-Osaka from Japan, exhibit partially identical genotypic signatures (identical 12-loci MIRU-VNTR profiles, distinct spoligotyping patterns). We investigated T3-Osaka and Tur sublineages characteristics and potential genetic relatedness, first using MIRU-VNTR locus analysis on 21 and 25 samples of each sublineage respectively, and second comparing Whole Genome Sequences of 8 new samples to public data from 45 samples uncovering human tuberculosis diversity. We then tried to date their Most Recent Common Ancestor (MRCA) using three calibrations of SNP accumulation rate (long-term=0.03SNP/genome/year, derived from a tuberculosis ancestor of around 70,000years old; intermediate=0.2SNP/genome/year derived from a Peruvian mummy; short-term=0.5SNP/genome/year). To disentangle between these scenarios, we confronted the corresponding divergence times with major human history events and knowledge on human genetic divergence. We identified relatively high intrasublineage diversity for both T3-Osaka and Tur. We definitively proved their monophyly; the corresponding super-sublineage (referred to as "T3-Osa-Tur") shares a common ancestor with T3-Ethiopia and Ural sublineages but is only remotely related to other Euro-American sublineages such as X, LAM, Haarlem and S. The evolutionary scenario based on long-term evolution rate being valid until T3-Osa-Tur MRCA was not supported by Japanese fossil data. The evolutionary scenario relying on short-term evolution rate since T3-Osa-Tur MRCA was contradicted by human history and potential traces of past epidemics. T3-Osaka and Tur sublineages were found likely to have diverged between 800y and 2000years ago, potentially at the time of Mongol Empire. Altogether, this study definitively proves a strong genetic link between Turkish and Japanese tuberculosis. It provides a first hypothesis for calibrating TB Euro-American lineage molecular clock; additional studies are needed to reliably date events corresponding to intermediate depths in tuberculosis phylogeny.
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Affiliation(s)
- Guislaine Refrégier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
| | - Edgar Abadia
- Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Venezuela
| | - Tomoshige Matsumoto
- Department of Clinical Research and Development, Osaka Prefectural Hospital Organization, Osaka Prefectural Medical Center for Respiratory and Allergic Diseases, Habikino-city, Japan
| | - Hiromi Ano
- Department of Clinical Research and Development, Osaka Prefectural Hospital Organization, Osaka Prefectural Medical Center for Respiratory and Allergic Diseases, Habikino-city, Japan
| | - Tetsuya Takashima
- Department of Clinical Research and Development, Osaka Prefectural Hospital Organization, Osaka Prefectural Medical Center for Respiratory and Allergic Diseases, Habikino-city, Japan
| | - Izuo Tsuyuguchi
- Department of Clinical Research and Development, Osaka Prefectural Hospital Organization, Osaka Prefectural Medical Center for Respiratory and Allergic Diseases, Habikino-city, Japan
| | - Elif Aktas
- Şişli Etfal Research and Training Hopital, Istanbul, Turkey
| | - Füsun Cömert
- Faculty of Medicine, Bülent Ecevit University, Zonguldak, Turkey
| | - Michel Kireopori Gomgnimbou
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Stefan Panaiotov
- National Center of Parasitic and Infectious Diseases, Sofia, Bulgaria
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Infection and Immunity Unit, UCT Lung Institute, University of Cape Town, Old Main Building, Groote Schuur Hospital, Cape Town,South Africa
| | - Arnab Pain
- Pathogen Genomics Group, Biological, Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Christophe Sola
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
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Genetic diversity of the Mycobacterium tuberculosis Beijing family based on multiple genotyping profiles. Epidemiol Infect 2015; 144:1728-35. [PMID: 26667080 DOI: 10.1017/s095026881500312x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Among the most prevalent Mycobacterium tuberculosis (Mtb) strains worldwide is the Beijing genotype, which has caused large outbreaks of tuberculosis (TB). Characteristics facilitating the dissemination of Beijing family strains remain unknown, but they are presumed to have been acquired through evolution of the lineage. To explore the genetic diversity of the Beijing family Mtb and explore the discriminatory ability of mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) loci in several regions of East Asia, a cross-sectional study was conducted with a total of 163 Beijing strains collected from registered TB patients between 1 June 2009 and 31 November 2010 in Funing County, China. The isolated strains were analysed by 15-MIRU-VNTR loci typing and compared with published MIRU-VNTR profiles of Beijing strains. Synonymous single nucleotide polymorphisms at 10 chromosomal positions were also analysed. The combination of SNP and MIRU-VNTR typing may be used to assess Mtb genotypes in areas dominated by Beijing strains. The modern subfamily in Shanghai overlapped with strains from other countries, whereas the ancient subfamily was genetically differentiated across several countries. Modern subfamilies, especially ST10, were prevalent. Qub11b and four other loci (MIRU 26, Mtub21, Qub26, Mtub04) could be used to discriminate Beijing strains.
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Ahmed MM, Mohammed SH, Nasurallah HAA, Ali MM, Couvin D, Rastogi N. Snapshot of the genetic diversity of Mycobacterium tuberculosis isolates in Iraq. Int J Mycobacteriol 2014; 3:184-96. [DOI: 10.1016/j.ijmyco.2014.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 07/17/2014] [Indexed: 10/24/2022] Open
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Diversity of Mycobacterium tuberculosis isolates from new pulmonary tuberculosis cases in Addis Ababa, Ethiopia. Tuberc Res Treat 2012; 2012:892079. [PMID: 23227330 PMCID: PMC3513727 DOI: 10.1155/2012/892079] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Accepted: 10/18/2012] [Indexed: 11/18/2022] Open
Abstract
Understanding the genetic diversity of Mycobacterium tuberculosis is needed for a better understanding of the epidemiology of TB and could have implications for the development of new diagnostics, drugs, and vaccines. M. tuberculosis isolates were characterized using spoligotyping and were compared with the SpoIDB4 database of the Pasteur Institute of Guadeloupe. A total of 53 different patterns were identified among 192 isolates examined. 169 of the isolates were classified into one of the 33 shared SITs, whereas the remaining 23 corresponded to 20 orphan patterns. 54% of the isolates were ascribed to the T family, a family which has not been well defined to date. Other prominent families were CAS, Haarlem, LAM, Beijing, and Unknown comprising 26%, 13%, 2.6%, 0.5%, and 2.1%, respectively. Among HIV-positive patients, 10 patterns were observed among 25 isolates. The T (38.5%), H (26.9%), and CAS (23.1%) families were the most common among HIV-positive individuals. The diversity of the M. tuberculosis strains found in this study is very high, and there was no difference in the distribution of families in HIV-positive and HIV-negative TB patients except the H family. Tuberculosis transmission in Addis Ababa is due to only the modern M. tuberculosis families (CAS, LAM, T, Beijing, Haarlem, and U).
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Bergval I, Sengstake S, Brankova N, Levterova V, Abadía E, Tadumaze N, Bablishvili N, Akhalaia M, Tuin K, Schuitema A, Panaiotov S, Bachiyska E, Kantardjiev T, de Zwaan R, Schürch A, van Soolingen D, van ‘t Hoog A, Cobelens F, Aspindzelashvili R, Sola C, Klatser P, Anthony R. Combined species identification, genotyping, and drug resistance detection of Mycobacterium tuberculosis cultures by MLPA on a bead-based array. PLoS One 2012; 7:e43240. [PMID: 22916230 PMCID: PMC3423362 DOI: 10.1371/journal.pone.0043240] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 07/18/2012] [Indexed: 11/29/2022] Open
Abstract
The population structure of Mycobacterium tuberculosis is typically clonal therefore genotypic lineages can be unequivocally identified by characteristic markers such as mutations or genomic deletions. In addition, drug resistance is mainly mediated by mutations. These issues make multiplexed detection of selected mutations potentially a very powerful tool to characterise Mycobacterium tuberculosis. We used Multiplex Ligation-dependent Probe Amplification (MLPA) to screen for dispersed mutations, which can be successfully applied to Mycobacterium tuberculosis as was previously shown. Here we selected 47 discriminative and informative markers and designed MLPA probes accordingly to allow analysis with a liquid bead array and robust reader (Luminex MAGPIX technology). To validate the bead-based MLPA, we screened a panel of 88 selected strains, previously characterised by other methods with the developed multiplex assay using automated positive and negative calling. In total 3059 characteristics were screened and 3034 (99.2%) were consistent with previous molecular characterizations, of which 2056 (67.2%) were directly supported by other molecular methods, and 978 (32.0%) were consistent with but not directly supported by previous molecular characterizations. Results directly conflicting or inconsistent with previous methods, were obtained for 25 (0.8%) of the characteristics tested. Here we report the validation of the bead-based MLPA and demonstrate its potential to simultaneously identify a range of drug resistance markers, discriminate the species within the Mycobacterium tuberculosis complex, determine the genetic lineage and detect and identify the clinically most relevant non-tuberculous mycobacterial species. The detection of multiple genetic markers in clinically derived Mycobacterium tuberculosis strains with a multiplex assay could reduce the number of TB-dedicated screening methods needed for full characterization. Additionally, as a proportion of the markers screened are specific to certain Mycobacterium tuberculosis lineages each profile can be checked for internal consistency. Strain characterization can allow selection of appropriate treatment and thereby improve treatment outcome and patient management.
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Affiliation(s)
- Indra Bergval
- KIT Biomedical Research, Royal Tropical Institute, Amsterdam, The Netherlands
| | - Sarah Sengstake
- KIT Biomedical Research, Royal Tropical Institute, Amsterdam, The Netherlands
| | - Nadia Brankova
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | - Edgar Abadía
- Institute of Genetics and Microbiology UMR 8621 CNRS/UPS11, Orsay, France
- Venezuelan Institute of Scientific Research, Caracas, Venezuela
| | - Nino Tadumaze
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis and Lung Diseases, Tbilisi, Georgia
| | - Nino Bablishvili
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis and Lung Diseases, Tbilisi, Georgia
| | - Maka Akhalaia
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis and Lung Diseases, Tbilisi, Georgia
| | - Kiki Tuin
- MRC-Holland, Amsterdam, The Netherlands
| | - Anja Schuitema
- KIT Biomedical Research, Royal Tropical Institute, Amsterdam, The Netherlands
| | - Stefan Panaiotov
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | - Todor Kantardjiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Rina de Zwaan
- Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Anita Schürch
- Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Dick van Soolingen
- Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Departments of Microbiology and of Pulmonary Diseases, Radboud University Nijmegen Medical Centre/University Lung Centre Dekkerswald, Nijmegen, The Netherlands
| | - Anja van ‘t Hoog
- Amsterdam Institute of Global Health and Development, Amsterdam, The Netherlands
| | - Frank Cobelens
- Amsterdam Institute of Global Health and Development, Amsterdam, The Netherlands
| | - Rusudan Aspindzelashvili
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis and Lung Diseases, Tbilisi, Georgia
| | - Christophe Sola
- Institute of Genetics and Microbiology UMR 8621 CNRS/UPS11, Orsay, France
| | - Paul Klatser
- KIT Biomedical Research, Royal Tropical Institute, Amsterdam, The Netherlands
| | - Richard Anthony
- KIT Biomedical Research, Royal Tropical Institute, Amsterdam, The Netherlands
- * E-mail:
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Kisa O, Tarhan G, Gunal S, Albay A, Durmaz R, Saribas Z, Zozio T, Alp A, Ceyhan I, Tombak A, Rastogi N. Distribution of spoligotyping defined genotypic lineages among drug-resistant Mycobacterium tuberculosis complex clinical isolates in Ankara, Turkey. PLoS One 2012; 7:e30331. [PMID: 22279583 PMCID: PMC3261197 DOI: 10.1371/journal.pone.0030331] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 12/14/2011] [Indexed: 11/18/2022] Open
Abstract
Background Investigation of genetic heterogeneity and spoligotype-defined lineages of drug-resistant Mycobacterium tuberculosis clinical isolates collected during a three-year period in two university hospitals and National Tuberculosis Reference and Research Laboratory in Ankara, Turkey. Methods and Findings A total of 95 drug-resistant M. tuberculosis isolates collected from three different centers were included in this study. Susceptibility testing of the isolates to four major antituberculous drugs was performed using proportion method on Löwenstein–Jensen medium and BACTEC 460-TB system. All clinical isolates were typed by using spoligotyping and IS6110-restriction fragment length polymorphism (RFLP) methods. Seventy-three of the 95 (76.8%) drug resistant M. tuberculosis isolates were isoniazid-resistant, 45 (47.4%) were rifampicin-resistant, 32 (33.7%) were streptomycin-resistant and 31 (32.6%) were ethambutol-resistant. The proportion of multidrug-resistant isolates (MDR) was 42.1%. By using spoligotyping, 35 distinct patterns were observed; 75 clinical isolates were grouped in 15 clusters (clustering rate of 79%) and 20 isolates displayed unique patterns. Five of these 20 unique patterns corresponded to orphan patterns in the SITVIT2 database, while 4 shared types containing 8 isolates were newly created. The most prevalent M. tuberculosis lineages were: Haarlem (23/95, 24.2%), ill-defined T superfamily (22/95, 23.2%), the Turkey family (19/95, 20%; previously designated as LAM7-TUR), Beijing (6/95, 6.3%), and Latin-America & Mediterranean (LAM, 5/95 or 5.3%), followed by Manu (3/95, 3.2%) and S (1/95, 1%) lineages. Four of the six Beijing family isolates (66.7%) were MDR. A combination of IS6110-RFLP and spoligotyping reduced the clustering rate from 79% to 11.5% among the drug resistant isolates. Conclusions The results obtained showed that ill-defined T, Haarlem, the Turkey family (previously designated as LAM7-TUR family with high phylogeographical specifity for Turkey), Beijing and LAM were predominant lineages observed in almost 80% of the drug-Resistant M. tuberculosis complex clinical isolates in Ankara, Turkey.
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Affiliation(s)
- Ozgul Kisa
- Department of Medical Microbiology, Gulhane Military Medical Academy and School of Medicine, Ankara, Turkey.
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Mokrousov I. The quiet and controversial: Ural family of Mycobacterium tuberculosis. INFECTION GENETICS AND EVOLUTION 2011; 12:619-29. [PMID: 22036706 DOI: 10.1016/j.meegid.2011.09.026] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 09/29/2011] [Accepted: 09/30/2011] [Indexed: 12/15/2022]
Abstract
The absence of lateral gene exchange is a characteristic feature defining the genome evolution and clonal population structure of Mycobacterium tuberculosis. Certain of its lineages have justly attracted more attention due to their global dissemination and/or remarkable pathogenic properties. In this critical review, I discuss the population structure and genetic geography of the less 'popular' but in some aspects no less noteworthy M. tuberculosis lineage, Ural family. Its specific signature was initially defined by single copy in MIRU26, and large (>6) copy number in MIRU10 loci, and by 43-spoligotyping as absence of signals 29-31 and 33-36. Here, I suggest to subdivide Ural strains with present and absent spoligosignal 2 into primary Ural-1 and secondary Ural-2 sublineages, respectively, while 1 copy in MIRU26 is specific of Ural-1. Furthermore, three copies were recently described in MIRU10 in Ural-1 strains which highlights a high diversity of this locus in Ural genotype. The data on the two Ural sublineages were extracted from SpolDB4 database and original publications in order to trace their distribution at global and within-country levels. Importantly, the rigorous reanalysis suggested the true rate of the Ural genotype in the Ural area in Russia to be only 7%. In contrast, the frequencies of the Ural sublineages peak elsewhere: in South Ukraine and Georgia/Abkhazia (Ural-1, up to 14-19%), and in southwestern Iran (Ural-2, up to 26%). However, as this name is used since 2005, it seems most parsimonious to continue its use even if misleading. The forest graph was built on the available spoligoprofiles of Ural family strains from Eurasia. It helped to suggest routes of their primary dispersal that are discussed in the context of the known human migrations also influenced by natural barriers. The north/east Pontic area may have been an area of origin and primary dispersal of the Ural (Ural-1) genotype in Eurasia, whereas political and natural borders may have influenced its subsequent dissemination throughout Central Asia. Studies of phenotypic properties in different models, comparison with host genetics give evidence that the Ural family strains are not associated with increased capacity to acquire drug resistance, pathogenicity or transmissibility. Instead since Ural family is rather moderately widespread in Eurasia beyond the hypothesized areas of origin, this situation may be a result of its low contagiosity as a consequence of long-term co-adaptation with human host. Future research should be focused on whole-genome sequencing in order to identify Ural-specific SNP and/or deletion, to resolve its phylogenetic and phylogeographic uncertainty and to elucidate biological features underlying its circulation and co-evolution with the human species.
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Affiliation(s)
- Igor Mokrousov
- Laboratory of Molecular Microbiology, St. Petersburg Pasteur Institute, St. Petersburg, Russia.
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16
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Borile C, Labarre M, Franz S, Sola C, Refrégier G. Using affinity propagation for identifying subspecies among clonal organisms: lessons from M. tuberculosis. BMC Bioinformatics 2011; 12:224. [PMID: 21635750 PMCID: PMC3126747 DOI: 10.1186/1471-2105-12-224] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 06/02/2011] [Indexed: 12/26/2022] Open
Abstract
Background Classification and naming is a key step in the analysis, understanding and adequate management of living organisms. However, where to set limits between groups can be puzzling especially in clonal organisms. Within the Mycobacterium tuberculosis complex (MTC), the etiological agent of tuberculosis (TB), experts have first identified several groups according to their pattern at repetitive sequences, especially at the CRISPR locus (spoligotyping), and to their epidemiological relevance. Most groups such as "Beijing" found good support when tested with other loci. However, other groups such as T family and T1 subfamily (belonging to the "Euro-American" lineage) correspond to non-monophyletic groups and still need to be refined. Here, we propose to use a method called Affinity Propagation that has been successfully used in image categorization to identify relevant patterns at the CRISPR locus in MTC. Results To adequately infer the relative divergence time between strains, we used a distance method inspired by the recent evolutionary model by Reyes et al. We first confirm that this method performs better than the Jaccard index commonly used to compare spoligotype patterns. Second, we document the support of each spoligotype family among the previous classification using affinity propagation on the international spoligotyping database SpolDB4. This allowed us to propose a consensus assignation for all SpolDB4 spoligotypes. Third, we propose new signatures to subclassify the T family. Conclusion Altogether, this study shows how the new clustering algorithm Affinity Propagation can help building or refining clonal organims classifications. It also describes well-supported families and subfamilies among M. tuberculosis complex, especially inside the modern "Euro-American" lineage.
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Affiliation(s)
- Claudio Borile
- LPTMS, CNRS and Univ. Paris-Sud, UMR8626, Bat. 100, 91405 Orsay, France
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Tanveer M, Hasan Z, Siddiqui AR, Ali A, Kanji A, Ghebremicheal S, Hasan R. Genotyping and drug resistance patterns of M. tuberculosis strains in Pakistan. BMC Infect Dis 2008; 8:171. [PMID: 19108722 PMCID: PMC2630917 DOI: 10.1186/1471-2334-8-171] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2007] [Accepted: 12/24/2008] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The incidence of tuberculosis in Pakistan is 181/100,000 population. However, information about transmission and geographical prevalence of Mycobacterium tuberculosis strains and their evolutionary genetics as well as drug resistance remains limited. Our objective was to determine the clonal composition, evolutionary genetics and drug resistance of M. tuberculosis isolates from different regions of the country. METHODS M. tuberculosis strains isolated (2003-2005) from specimens submitted to the laboratory through collection units nationwide were included. Drug susceptibility was performed and strains were spoligotyped. RESULTS Of 926 M. tuberculosis strains studied, 721(78%) were grouped into 59 "shared types", while 205 (22%) were identified as "Orphan" spoligotypes. Amongst the predominant genotypes 61% were Central Asian strains (CAS ; including CAS1, CAS sub-families and Orphan Pak clusters), 4% East African-Indian (EAI), 3% Beijing, 2% poorly defined TB strains (T), 2% Haarlem and LAM (0.2). Also TbD1 analysis (M. tuberculosis specific deletion 1) confirmed that CAS1 was of "modern" origin while EAI isolates belonged to "ancestral" strain types.Prevalence of CAS1 clade was significantly higher in Punjab (P < 0.01, Pearsons Chi-square test) as compared with Sindh, North West Frontier Province and Balochistan provinces. Forty six percent of isolates were sensitive to five first line antibiotics tested, 45% were Rifampicin resistant, 50% isoniazid resistant. MDR was significantly associated with Beijing strains (P = 0.01, Pearsons Chi-square test) and EAI (P = 0.001, Pearsons Chi-square test), but not with CAS family. CONCLUSION Our results show variation of prevalent M. tuberculosis strain with greater association of CAS1 with the Punjab province. The fact that the prevalent CAS genotype was not associated with drug resistance is encouraging. It further suggests a more effective treatment and control programme should be successful in reducing the tuberculosis burden in Pakistan.
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Affiliation(s)
- Mahnaz Tanveer
- Department of Pathology and Microbiology, The Aga Khan University, Stadium Road Karachi, Pakistan
| | - Zahra Hasan
- Department of Pathology and Microbiology, The Aga Khan University, Stadium Road Karachi, Pakistan
| | - Amna R Siddiqui
- Department of Community Health Sciences, The Aga Khan University, Stadium Road Karachi, Pakistan
| | - Asho Ali
- Department of Pathology and Microbiology, The Aga Khan University, Stadium Road Karachi, Pakistan
| | - Akbar Kanji
- Department of Pathology and Microbiology, The Aga Khan University, Stadium Road Karachi, Pakistan
| | - Solomon Ghebremicheal
- Department of Bacteriology, Swedish Institute for Infectious Diseases Control, Stockholm, Sweden
| | - Rumina Hasan
- Department of Pathology and Microbiology, The Aga Khan University, Stadium Road Karachi, Pakistan
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Wada T, Iwamoto T, Maeda S. Genetic diversity of the Mycobacterium tuberculosis Beijing family in East Asia revealed through refined population structure analysis. FEMS Microbiol Lett 2008; 291:35-43. [PMID: 19054072 DOI: 10.1111/j.1574-6968.2008.01431.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The Beijing/W family is the endemic lineage of Mycobacterium tuberculosis in East Asia: it has disseminated worldwide. To elucidate its genetic diversity in Japan, phylogenetic reconstruction was performed using 403 M. tuberculosis Beijing family clinical isolates. Variable number of tandem repeats analysis revealed the strains from Japan to be dispersed mainly among five subgroups in a phylogenetic tree. Interestingly, the genotypes of the strains from China and Mongolia were restricted mainly to a single branch; they exhibited high clonality. IS6110 insertion in the NTF region was also analyzed. The majority (78.6%) of Japanese isolates belonged to the ancient sublineage. The modern Beijing strains were observed to correspond to the branch containing the foreign strains, although the ancient Beijing strains were dispersed among the tree's other branches. Our results reflect the singular genetic diversity and the epidemiological pattern of Beijing M. tuberculosis in Japan.
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Affiliation(s)
- Takayuki Wada
- Department of Microbiology, Osaka City Institute of Public Health and Environmental Sciences, Osaka, Japan.
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Namouchi A, Karboul A, Mhenni B, Khabouchi N, Haltiti R, Ben Hassine R, Louzir B, Chabbou A, Mardassi H. Genetic profiling of Mycobacterium tuberculosis in Tunisia: predominance and evidence for the establishment of a few genotypes. J Med Microbiol 2008; 57:864-872. [PMID: 18566145 DOI: 10.1099/jmm.0.47483-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Typing analyses of 378 Mycobacterium tuberculosis isolates collected between the years 2001 and 2005 from three northern representative regions of Tunisia revealed a highly homogeneous population. Indeed, 84.9 % of all tuberculosis (TB) cases were attributed to the Haarlem, LAM or T families. Strikingly, within each family, more than 60 % of TB cases were due to a single genotype. ST50 (Haarlem3) and ST42 (LAM9) genotypes were exceptionally predominant, representing 46.3 % of all typed isolates. ST50 showed an increased tendency for clustering and was more predominant in the extreme north of the country. By contrast, the more widespread ST42, which was apparently prevalent 17 years ago, displayed weak cluster individualization and a low transmission rate, consistent with its stable association with the Tunisian population. It is believed that both mass BCG vaccination, strictly applied for four decades, and the high endogamy rate that characterizes the Tunisian population could have profoundly shaped the population structure of M. tuberculosis by concurrently favouring the selection and accommodation of particular genotypes.
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Affiliation(s)
- Amine Namouchi
- Unit of Typing and Genetics of Mycobacteria, Institut Pasteur de Tunis (Tunisia), 13 Place Pasteur, BP 74, Tunis, Tunisia
| | - Anis Karboul
- Unit of Typing and Genetics of Mycobacteria, Institut Pasteur de Tunis (Tunisia), 13 Place Pasteur, BP 74, Tunis, Tunisia
| | - Besma Mhenni
- Unit of Typing and Genetics of Mycobacteria, Institut Pasteur de Tunis (Tunisia), 13 Place Pasteur, BP 74, Tunis, Tunisia
| | - Neila Khabouchi
- Unit of Typing and Genetics of Mycobacteria, Institut Pasteur de Tunis (Tunisia), 13 Place Pasteur, BP 74, Tunis, Tunisia
| | - Raja Haltiti
- Hôpital Régional de Menzel-Bourguiba, Menzel-Bourguiba, Tunisia
| | | | | | | | - Helmi Mardassi
- Unit of Typing and Genetics of Mycobacteria, Institut Pasteur de Tunis (Tunisia), 13 Place Pasteur, BP 74, Tunis, Tunisia
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Molecular characterization of Mycobacterium tuberculosis isolates from different regions of Bulgaria. J Clin Microbiol 2008; 46:1014-8. [PMID: 18199794 DOI: 10.1128/jcm.01841-07] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis isolates from different regions of Bulgaria were studied by a variety of molecular typing tools. Based on spacer oligonucleotide typing (spoligotyping), the 113 strains were subdivided into 35 spoligotypes: 5 unique profiles and 15 profiles shared by two to 29 strains; the Hunter-Gaston diversity index (HGI) was 0.9. Comparison with the international database SITVIT2 at the Institut Pasteur de Guadeloupe showed the presence of two globally distributed shared types, ST53 (25.7%) and ST47 (6.2%). Nineteen (16.8%) and six (5.3%) strains belonged to the ST125 (LAM/S subfamily) and ST41 (LAM7_TUR subfamily) types described in SITVIT2 as ubiquitous/rare and ubiquitous/common types, respectively. Seven spoligoprofiles (12 strains) were not found in the database; two of them constituted new shared types. The Beijing genotype strains were not found in the studied collection in spite of close contacts with Russia in the recent and historical past. Additional subtyping by IS6110-restriction fragment length polymorphism (RFLP) and 12-locus mycobacterial interspersed repetitive unit (MIRU)-variable number of tandem repeat analyses were performed within selected spoligotypes. In particular, MIRU typing showed better discrimination within ST125 than IS6110-RFLP typing (HGI = 0.83 versus 0.39). A high gradient for ST125 in Bulgaria compared to its negligible presence in the global database and neighboring countries leads us to suggest a Bulgarian phylogeographic specificity of this spoligotype. To conclude, this first study of the Bulgarian M. tuberculosis population demonstrated its heterogeneity and predominance of several worldwide-distributed and Balkan-specific spoligotypes.
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Aktaş E, Zozio T, Cömert FB, Külah C, Aydin O, Rastogi N, Sola C. A first insight into the genetic diversity and population structure of Mycobacterium tuberculosis in Zonguldak, Turkey. Clin Microbiol Infect 2007; 14:55-9. [PMID: 18034858 DOI: 10.1111/j.1469-0691.2007.01882.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This study evaluated the molecular epidemiology and biodiversity of Mycobacterium tuberculosis isolates in Zonguldak, Turkey, and investigated the presence and significance of the LAM7-TUR clone by spoligotyping and mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) analysis. In total, 128 isolates were tested by spoligotyping; 25 selected isolates representative of the LAM7-TUR clone and similar types were also tested by MIRU-VNTR analysis. In total, 47 distinct patterns were revealed by spoligotyping, represented by 13 clusters containing between two and 28 isolates (94 isolates in total), and 34 unique patterns (a clustering rate of 73%). Using MIRU-VNTR analysis, the clustering relationships revealed by spoligotyping were confirmed. The most common spoligotyping profile was SIT53, followed by SIT41 (LAM7-TUR) and SIT50. The SIT284 clone was another phylogeographically specific clonal complex whose presence in Turkey may be endemic. The LAM7-TUR genotype was highly prevalent in Zonguldak.
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Affiliation(s)
- E Aktaş
- Faculty of Medicine, Department of Microbiology and Clinical Microbiology, Zonguldak Karaelmas University, Zonguldak, Turkey.
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Population-based molecular epidemiological study of tuberculosis in Malatya, Turkey. J Clin Microbiol 2007; 45:4027-35. [PMID: 17928426 DOI: 10.1128/jcm.01308-07] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This investigation describes drug resistance patterns and genotyping data on a total of 145 Mycobacterium tuberculosis strains isolated between 2000 and 2004 in Malatya, Turkey. Drug susceptibility results indicated a total of 20% resistant and 4.8% of multidrug-resistant isolates. Spoligotyping resulted in 25 unique patterns and 120 strains in 19 clusters (2 to 33 strains per cluster). When the results were compared to an international spoligotyping database, 19 of 25 unique patterns matched existing shared spoligotype international types (SITs). This led to the description of 38 SITs with 139 strains and 6 orphan patterns (not previously reported). Five of the SITs (SIT759, SIT1936, SIT1937, SIT1938, and SIT2285) were newly created. The most prevalent spoligotype was SIT41 (LAM7-TUR) with 33 (23.9%) isolates. The repartition of strains according to major M. tuberculosis clades (in decreasing order) was as follows: ill-defined T clade (45.7%) > Latin American and Mediterranean (LAM; 29%) > Haarlem (15.9%). Strains belonging to Central Asian (CAS), East-African Indian (EAI), Beijing, and Africanum clades were absent in this setting. IS6110-restriction fragment length polymorphism (RFLP) resulted in 19 clusters (52 strains), with a final clustering rate of 35.9% and a recent transmission rate of 22.8%. Typing based on mycobacterial interspersed repetitive units (MIRUs) permitted us to identify 65 patterns (23 orphan patterns and 42 patterns that matched existing MIRU international types in an updated database). The combination of the three typing methods allowed us to calculate a final clustering rate of 22% and a significantly lower transmission rate of 13.1%. The discrimination achieved by IS6110-RFLP/MIRUs was not significantly improved by adding spoligotyping results (1.4%). We conclude that our patient population is infected by diverse M. tuberculosis populations; however, the majority of the ongoing transmission is due to "evolutionary recent" tuberculosis lineages belonging to principal genetic group 2 (PGG2; Haarlem and LAM) and PGG3 (ill-defined T clade), and most of it is attributable to the LAM7-TUR sublineage with an enhanced phylogeographical specificity for Turkey. An absence of lineages belonging to PGG1 clones (EAI, CAS, and Beijing, essentially found in Central, South, and Southeast Asia), is noteworthy.
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Millet J, Miyagi-Shiohira C, Yamane N, Sola C, Rastogi N. Assessment of mycobacterial interspersed repetitive unit-QUB markers to further discriminate the Beijing genotype in a population-based study of the genetic diversity of Mycobacterium tuberculosis clinical isolates from Okinawa, Ryukyu Islands, Japan. J Clin Microbiol 2007; 45:3606-15. [PMID: 17898160 PMCID: PMC2168487 DOI: 10.1128/jcm.00348-07] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The present investigation focused on genetic diversity and drug resistance of 101 Mycobacterium tuberculosis strains isolated between July 2003 and February 2005 in the Okinawa prefecture, Ryukyu Islands, Japan. A high rate of clustering (87%, eight clusters, 2 to 69 strains/cluster) was observed upon spoligotyping; most of it was due to the lower discriminatory power of this method for the Beijing lineage (n = 72; 71.3% of the isolates). The remaining diversity was limited to seven clusters (two to five isolates/cluster), with the following distribution of major lineages: ill-defined T (n = 13; 12.8%), ancestral East African-Indian (n = 6; 5.9%), Haarlem (n = 4; 4%), Latin American-Mediterranean (n = 2; 2%), X1 (n = 1; 1%), and a total absence of the central Asian clade. Three remaining strains could not be classified on the basis of their spoligotype pattern and were labeled "unknown." Subtyping with mycobacterial interspersed repetitive units (MIRUs) in association with additional QUB minisatellites was performed to discriminate among the Beijing strains. Based on an "in-house" spoligotyping/MIRU database (n = 694 Beijing strains), eight highly discriminative MIRU loci for Beijing strains were selected (loci numbered 10, 16, 23, 26, 27, 31, 39, and 40). The highest discriminatory power (h) observed in our sample (n = 72; M-26, 0.385; M-10, 0.38; M-31, 0.255; M-16, 0.238) was too low, and 73.6% of the Beijing strains from Okinawa remained clustered. Typing of Beijing strains with additional QUB loci (with the exception of "one-copy" QUB-1451) resulted in higher discriminatory powers: QUB-11b, 0.68; QUB-11a, 0.656; QUB-26, 0.644; QUB-18, 0.553; QUB-4156, 0.5; and QUB-1895, 0.453. A definitive algorithm on the use of QUB markers to subtype Beijing isolates in expanded studies would shed light on their hypervariability, which may sometimes blur recognition between epidemiologically linked Beijing isolates. The total absence of multiple drug resistance among Beijing isolates from Okinawa, as well as the relatively older ages of the patients (majority above 60 years), shows that tuberculosis (TB) is a declining disease in Okinawa, and an adequate TB control program has successfully avoided both the emergence and the spread of multidrug-resistant TB in this insular setting.
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Affiliation(s)
- Julie Millet
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, BP484, 97183, Abymes, Guadeloupe
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Durmaz R, Zozio T, Gunal S, Yaman A, Cavusoglu C, Guney C, Sola C, Rastogi N. Genetic diversity and major spoligotype families of drug-resistant Mycobacterium tuberculosis clinical isolates from different regions of Turkey. INFECTION GENETICS AND EVOLUTION 2007; 7:513-9. [PMID: 17462962 DOI: 10.1016/j.meegid.2007.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Revised: 03/21/2007] [Accepted: 03/22/2007] [Indexed: 11/18/2022]
Abstract
To highlight the transmission rate and major phylogenetic clades of drug-resistant Mycobacterium tuberculosis isolates, a total of 200 drug-resistant strains isolated in four different regions of Turkey (Marmara n=81; Mediterranean n=39; Aegean n=42; East Anatolia n=38), were typed by spoligotyping and IS6110-restriction fragment length polymorphism (RFLP). The major spoligotyping-defined shared-types (STs) and corresponding lineages were, ST 41 (22.5%, LAM7-TUR), ST53 (19.5%, ill-defined T super-family), ST 50 (6.5%, Haarlem 3), ST 1261 (4.5%, LAM7-TUR), ST 47 (3.5%, Haarlem 1), as well as two STs that belonged to undefined clades (ST 284, 3%, and ST 2067, 2.5%). The global distribution of major M. tuberculosis lineages among drug-resistant strains was as follows: T super-family (29%), Latin-American & Mediterranean (33.5%), Haarlem (14%), and the S lineage (3%). A high number of strains (n=29, 14.5%) showed patterns that did not fall within major clades described so far. A combination of spoligotyping and IS6110-RFLP fingerprinting methods resulted in a final clustering rate of 38.5% and a recent transmission rate of 25.5%. Our results underline the highly diverse nature of drug-resistant tuberculosis in our study population, as well as its ongoing transmission with lineages that are specific to these regions, the most predominant being the LAM7-TUR lineage which shows an enhanced phylogeographical specificity for Turkey.
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Affiliation(s)
- Riza Durmaz
- Department of Clinical Microbiology, Faculty of Medicine, Inonu University, Malatya, Turkey.
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Kisa O, Albay A, Baylan O, Tozkoparan E, Acikel CH, Doganci L. Genetic diversity of Mycobacterium tuberculosis isolates at the Military Medical Academy in Ankara, Turkey. Res Microbiol 2007; 158:318-23. [PMID: 17398073 DOI: 10.1016/j.resmic.2007.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2006] [Revised: 12/01/2006] [Accepted: 01/25/2007] [Indexed: 11/23/2022]
Abstract
Genotyping of Mycobacterium tuberculosis isolates from infected individuals can play an important role in tracking the source of infection and unraveling the epidemiology of a tuberculosis pandemic. A total of 114 M. tuberculosis isolates were genotyped by spoligotyping and results were compared with an international spoligotype database (SpoIDB4). Twenty-one spoligotyping-defined clusters including 97 patients were established, and an additional 17 unique patterns were found. Ninety-eight (85.9%) isolates belonged to previously defined shared types (STs). The ST53 (ill-defined T1 superfamily, n=31), ST41 (LAM7-TUR family, n=9), ST118 (T undefined, n=8) and ST50 (Haarlem 3, n=6) were four major clusters of our isolates. After comparison with the international SpoIDB4 database, two new intrafile clusters, ST2136 and ST2139, were created and two new interfile clusters, ST2135 and ST2140, were defined. Eight (7%) of the 17 isolates with unique patterns were found to be orphans, whereas the STs of 9 isolates had previously been deposited in the international SpoIDB4 database. In addition, two isolates with an ST pattern characteristic of the Beijing family of M. tuberculosis were found. This study shows that, although ubiquitous spoligotypes are common, several spoligotypes specific to Turkey also exist. Thus, our study may help us to better understand the spread of M. tuberculosis genotypes to Turkey.
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Affiliation(s)
- Ozgul Kisa
- Department of Microbiology and Clinical Microbiology, Gulhane Military Medical Academy and School of Medicine, 06018 Ankara, Turkey.
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Streicher EM, Victor TC, van der Spuy G, Sola C, Rastogi N, van Helden PD, Warren RM. Spoligotype signatures in the Mycobacterium tuberculosis complex. J Clin Microbiol 2006; 45:237-40. [PMID: 17065260 PMCID: PMC1828946 DOI: 10.1128/jcm.01429-06] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Evolution of the direct repeat region in Mycobacterium tuberculosis has created unique spoligotype signatures specifically associated with IS6110-defined strain families. Spoligotyping signatures may enable the analysis of the strain population structure in different settings and will enable the rapid identification of strain families that acquire drug resistance or escape protective immunity in drug and vaccine trials.
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Affiliation(s)
- E M Streicher
- DST/NRF Centre of Excellence in Biomedical TB Research, Department of Medical Biochemistry, Stellenbosch University, Tygerberg, South Africa 7505
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Ergun I, Ekmekci Y, Sengul S, Kutlay S, Dede F, Canbakan B, Erbay B. Mycobacterium tuberculosis Infection in Renal Transplant Recipients. Transplant Proc 2006; 38:1344-5. [PMID: 16797298 DOI: 10.1016/j.transproceed.2006.03.029] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2005] [Indexed: 10/24/2022]
Abstract
Mycobacterium tuberculosis (TB) infection is more common among renal allograft recipients compared with the general population due to immunosuppression. The epidemiological risk in a country is an important determinant of transplant TB after transplantation. We retrospectively analyzed 283 renal transplant recipients who underwent renal transplantation between 1990 and 2004. We evaluated the incidence, patient and disease characteristics, prognosis, and outcome of TB infection. Tuberculosis developed in 10 (seven men and three women of mean age of 41+/-9 years) among 283 patients (3.1%). All patients were culture-positive for M tuberculosis. Although pulmonary TB was the most common presentation in the general population, 50% of patients in the study group developed extrapulmonary TB. The mean elapsed time from renal transplantation was 38 months. Three patients (1%) developed TB in the first year after transplantation. All patients were treated with a quartet of anti-TB therapy. One patient developed isoniazid-related reversible hepatotoxicity. No acute allograft rejection occurred during the anti-TB therapy. Two patients (20%) with pulmonary TB died due to dissemination of the disease. In conclusion, extrapulmonary presentations of TB are more common among renal transplant recipients with the increased risk of mortality.
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Affiliation(s)
- I Ergun
- Department of Nephrology, Ankara University School of Medicine, Ankara, Turkey.
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Brudey K, Driscoll JR, Rigouts L, Prodinger WM, Gori A, Al-Hajoj SA, Allix C, Aristimuño L, Arora J, Baumanis V, Binder L, Cafrune P, Cataldi A, Cheong S, Diel R, Ellermeier C, Evans JT, Fauville-Dufaux M, Ferdinand S, de Viedma DG, Garzelli C, Gazzola L, Gomes HM, Guttierez MC, Hawkey PM, van Helden PD, Kadival GV, Kreiswirth BN, Kremer K, Kubin M, Kulkarni SP, Liens B, Lillebaek T, Ly HM, Martin C, Martin C, Mokrousov I, Narvskaïa O, Ngeow YF, Naumann L, Niemann S, Parwati I, Rahim Z, Rasolofo-Razanamparany V, Rasolonavalona T, Rossetti ML, Rüsch-Gerdes S, Sajduda A, Samper S, Shemyakin IG, Singh UB, Somoskovi A, Skuce RA, van Soolingen D, Streicher EM, Suffys PN, Tortoli E, Tracevska T, Vincent V, Victor TC, Warren RM, Yap SF, Zaman K, Portaels F, Rastogi N, Sola C. Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology. BMC Microbiol 2006; 6:23. [PMID: 16519816 PMCID: PMC1468417 DOI: 10.1186/1471-2180-6-23] [Citation(s) in RCA: 777] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Accepted: 03/06/2006] [Indexed: 12/04/2022] Open
Abstract
Background The Direct Repeat locus of the Mycobacterium tuberculosis complex (MTC) is a member of the CRISPR (Clustered regularly interspaced short palindromic repeats) sequences family. Spoligotyping is the widely used PCR-based reverse-hybridization blotting technique that assays the genetic diversity of this locus and is useful both for clinical laboratory, molecular epidemiology, evolutionary and population genetics. It is easy, robust, cheap, and produces highly diverse portable numerical results, as the result of the combination of (1) Unique Events Polymorphism (UEP) (2) Insertion-Sequence-mediated genetic recombination. Genetic convergence, although rare, was also previously demonstrated. Three previous international spoligotype databases had partly revealed the global and local geographical structures of MTC bacilli populations, however, there was a need for the release of a new, more representative and extended, international spoligotyping database. Results The fourth international spoligotyping database, SpolDB4, describes 1939 shared-types (STs) representative of a total of 39,295 strains from 122 countries, which are tentatively classified into 62 clades/lineages using a mixed expert-based and bioinformatical approach. The SpolDB4 update adds 26 new potentially phylogeographically-specific MTC genotype families. It provides a clearer picture of the current MTC genomes diversity as well as on the relationships between the genetic attributes investigated (spoligotypes) and the infra-species classification and evolutionary history of the species. Indeed, an independent Naïve-Bayes mixture-model analysis has validated main of the previous supervised SpolDB3 classification results, confirming the usefulness of both supervised and unsupervised models as an approach to understand MTC population structure. Updated results on the epidemiological status of spoligotypes, as well as genetic prevalence maps on six main lineages are also shown. Our results suggests the existence of fine geographical genetic clines within MTC populations, that could mirror the passed and present Homo sapiens sapiens demographical and mycobacterial co-evolutionary history whose structure could be further reconstructed and modelled, thereby providing a large-scale conceptual framework of the global TB Epidemiologic Network. Conclusion Our results broaden the knowledge of the global phylogeography of the MTC complex. SpolDB4 should be a very useful tool to better define the identity of a given MTC clinical isolate, and to better analyze the links between its current spreading and previous evolutionary history. The building and mining of extended MTC polymorphic genetic databases is in progress.
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Affiliation(s)
- Karine Brudey
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
| | | | - Leen Rigouts
- Mycobacteriology Unit, Prince Leopold Institute of Tropical Medicine, Antwerp, Belgium
| | - Wolfgang M Prodinger
- Dept. Hygiene Microbiology and Social Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Andrea Gori
- Dept of Infectious Diseases, Institut of Infectious Diseases, Milano, Italy
| | - Sahal A Al-Hajoj
- Department of Comparative Medicine, King Faisal specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Caroline Allix
- Laboratoire de la Tuberculose, Institut Pasteur de Bruxelles, Belgique
| | - Liselotte Aristimuño
- Universidad Centrooccidental Lisandro Alvarado, Barquisimeto, Venezuela and Universidad de Zaragoza, Spain
| | - Jyoti Arora
- All India Institute of Medical Sciences, New Delhi, India
| | | | - Lothar Binder
- Institut for Hygiene, Microbiologie and Tropical Medicine, Austria
| | | | - Angel Cataldi
- Instituto de Biotecnologia INTA, Castelar, Argentina
| | - Soonfatt Cheong
- Dept of Medical Microbiology and Pathology, faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia, School of Public Health
| | - Roland Diel
- University of Düsseldorf, Heinrich-Heine-University, Düsseldorf
| | | | - Jason T Evans
- Public Health Laboratory, Hearltlands Hospital, Birmingham, UK
| | | | - Séverine Ferdinand
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
| | - Dario Garcia de Viedma
- Dept of Clinical Microbiology and Infectious Diseases, Hospital Gregorio Marañon, Madrid, Spain
| | - Carlo Garzelli
- Dept. of Experimental Pathology, Medical Biotechnology, Infection and Epidemiology, Pisa University, Pisa, Italy
| | - Lidia Gazzola
- Dept of Infectious Diseases, Institut of Infectious Diseases, Milano, Italy
| | - Harrison M Gomes
- Laboratory of Molecular Biology applied to Mycobacteria, Dept. Mycobacteriosis, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | | | - Peter M Hawkey
- Public Health Laboratory, Hearltlands Hospital, Birmingham, UK
| | - Paul D van Helden
- MRC Centre for Molecular and Cellular Biology, Dept of medical Biochemistry, University of Stellenbosch, Tygerberg, South Africa
| | - Gurujaj V Kadival
- Laboratory Nuclear Medicine Section, Isotope group, Bhabha Atomic Research Centre c/T.M.H. Annexe, Parel, Mumbai-400012, India
| | | | - Kristin Kremer
- Mycobacteria reference unit, Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | - Milan Kubin
- Municipal Institute of Hygiene, Prague, Czech Republic
| | - Savita P Kulkarni
- Laboratory Nuclear Medicine Section, Isotope group, Bhabha Atomic Research Centre c/T.M.H. Annexe, Parel, Mumbai-400012, India
| | - Benjamin Liens
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
| | - Troels Lillebaek
- Statens Serum Institute, Int. Ref. lab. for Mycobacteriology, Copenhagen Denmark
| | - Ho Minh Ly
- Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | - Christian Martin
- Laboratoire de Bactério-virologie-hygiène, CHU Dupuytren, Limoges, France
| | - Igor Mokrousov
- Institut Pasteur de Saint-Petersbourg, Saint Petersbourg, Russia
| | - Olga Narvskaïa
- Institut Pasteur de Saint-Petersbourg, Saint Petersbourg, Russia
| | - Yun Fong Ngeow
- Dept of Medical Microbiology and Pathology, faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia, School of Public Health
| | - Ludmilla Naumann
- Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
| | - Stefan Niemann
- Forschungszentrum, National Reference Center for Mycobacteria, Borstel, Germany
| | - Ida Parwati
- Dept of Clinical Pathology, Padjadjaran University, Dr. Hasan Sadikin Hospital, Bandung, Indonesia
| | - Zeaur Rahim
- Tuberculosis Laboratory, International Centre for Diarrhoeal Research, Dhaka, Bangladesh
| | | | | | | | - Sabine Rüsch-Gerdes
- Forschungszentrum, National Reference Center for Mycobacteria, Borstel, Germany
| | - Anna Sajduda
- Dept of Genetics of Microorganisms, University of Lódz, Lodz, Poland
| | - Sofia Samper
- Servicio Microbiología, Hospital Universitario Miguel Servet, Zaragoza, Spain
| | - Igor G Shemyakin
- State Research Center for Applied Microbiology, Obolensk, Russian Federation
| | | | - Akos Somoskovi
- Dept. of Respiratory Medicine School of Medicine Semmelweis University, Budapest, Hungary
| | - Robin A Skuce
- Veterinary Sciences Division, Department of agriculture for Northern Ireland, Belfast, UK
| | - Dick van Soolingen
- Mycobacteria reference unit, Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | - Elisabeth M Streicher
- MRC Centre for Molecular and Cellular Biology, Dept of medical Biochemistry, University of Stellenbosch, Tygerberg, South Africa
| | - Philip N Suffys
- Laboratory of Molecular Biology applied to Mycobacteria, Dept. Mycobacteriosis, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | - Enrico Tortoli
- Centro regionale di Riferimento per i Micobatteri, Laboratorio de Microbiologia e Virologia, Ospedale Careggi, Firenze, Italy
| | | | - Véronique Vincent
- Centre National de Référence des Mycobactéries, Institut Pasteur, Paris, France
| | - Tommie C Victor
- MRC Centre for Molecular and Cellular Biology, Dept of medical Biochemistry, University of Stellenbosch, Tygerberg, South Africa
| | - Robin M Warren
- MRC Centre for Molecular and Cellular Biology, Dept of medical Biochemistry, University of Stellenbosch, Tygerberg, South Africa
| | - Sook Fan Yap
- Dept of Medical Microbiology and Pathology, faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia, School of Public Health
| | - Khadiza Zaman
- Tuberculosis Laboratory, International Centre for Diarrhoeal Research, Dhaka, Bangladesh
| | - Françoise Portaels
- Mycobacteriology Unit, Prince Leopold Institute of Tropical Medicine, Antwerp, Belgium
| | - Nalin Rastogi
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
| | - Christophe Sola
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
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