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Dale K, Globan M, Horan K, Sherry N, Ballard S, Tay EL, Bittmann S, Meagher N, Price DJ, Howden BP, Williamson DA, Denholm J. Whole genome sequencing for tuberculosis in Victoria, Australia: A genomic implementation study from 2017 to 2020. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2022; 28:100556. [PMID: 36034164 PMCID: PMC9405109 DOI: 10.1016/j.lanwpc.2022.100556] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
BACKGROUND Whole genome sequencing (WGS) is increasingly used by tuberculosis (TB) programs to monitor Mycobacterium tuberculosis (Mtb) transmission. We aimed to characterise the molecular epidemiology of TB and Mtb transmission in the low-incidence setting of Victoria, Australia, and assess the utility of WGS. METHODS WGS was performed on all first Mtb isolates from TB cases from 2017 to 2020. Potential clusters (≤12 single nucleotide polymorphisms [SNPs]) were investigated for epidemiological links. Transmission events in highly-related (≤5 SNPs) clusters were classified as likely or possible, based on the presence or absence of an epidemiological link, respectively. Case characteristics and transmission settings (as defined by case relationship) were summarised. Poisson regression was used to examine associations with secondary case number. FINDINGS Of 1844 TB cases, 1276 (69.2%) had sequenced isolates, with 182 (14.2%) in 54 highly-related clusters, 2-40 cases in size. Following investigation, 140 cases (11.0% of sequenced) were classified as resulting from likely/possible local-transmission, including 82 (6.4%) for which transmission was likely. Common identified transmission settings were social/religious (26.4%), household (22.9%) and family living in different households (7.1%), but many were uncertain (41.4%). While household transmission featured in many clusters (n = 24), clusters were generally smaller (median = 3 cases) than the fewer that included transmission in social/religious settings (n = 12, median = 7.5 cases). Sputum-smear-positivity was associated with higher secondary case numbers. INTERPRETATION WGS results suggest Mtb transmission commonly occurs outside the household in our low-incidence setting. Further work is required to optimise the use of WGS in public health management of TB. FUNDING The Victorian Tuberculosis Program receives block funding for activities including case management and contact tracing from the Victorian Department of Health. No specific funding for this report was received by manuscript authors or the Victorian Tuberculosis Program, and the funders had no role in the study design, data collection, data analysis, interpretation or report writing.
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Affiliation(s)
- Katie Dale
- Victorian Tuberculosis Program, Melbourne Health, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Maria Globan
- Victorian Infectious Diseases Reference Laboratory (VIDRL), at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kristy Horan
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Norelle Sherry
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Susan Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ee Laine Tay
- Communicable Disease Epidemiology and Surveillance, Health Protection Branch, Public Health Division, Department of Health, Victoria, Australia
| | - Simone Bittmann
- Victorian Tuberculosis Program, Melbourne Health, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Niamh Meagher
- Department of Infectious Diseases at the Doherty Institute for Infection & Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - David J. Price
- Department of Infectious Diseases at the Doherty Institute for Infection & Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Deborah A. Williamson
- Victorian Infectious Diseases Reference Laboratory (VIDRL), at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Justin Denholm
- Victorian Tuberculosis Program, Melbourne Health, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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Keikha M, Majidzadeh M. Beijing genotype of Mycobacterium tuberculosis is associated with extensively drug-resistant tuberculosis: A global analysis. New Microbes New Infect 2021; 43:100921. [PMID: 34466269 PMCID: PMC8383003 DOI: 10.1016/j.nmni.2021.100921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/05/2021] [Accepted: 07/15/2021] [Indexed: 02/08/2023] Open
Abstract
We found that the frequency of Beijing genotype among XDR-TB strains was high. The data in this study would help guide the TB control program, and we however need further investigation to confirm the reliability of the present findings.
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Affiliation(s)
- M Keikha
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - M Majidzadeh
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Diversity of Mycobacterium tuberculosis Complex Lineages Associated with Pulmonary Tuberculosis in Southwestern, Uganda. Tuberc Res Treat 2021; 2021:5588339. [PMID: 34306752 PMCID: PMC8264515 DOI: 10.1155/2021/5588339] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/05/2021] [Indexed: 11/23/2022] Open
Abstract
Uganda is among the 22 countries in the world with a high burden of tuberculosis. The southwestern region of the country has consistently registered a high TB/HIV incidence rate. This study is aimed at characterizing the Mycobacterium tuberculosis complex (MTBC) genotypic diversity in southwestern Uganda. A total of 283 sputum samples from patients with pulmonary tuberculosis were genotyped using specific single nucleotide polymorphism markers for lineages 3 and 4. Most of the patients were males with a mean age of 34. The lineage 4 Ugandan family was found to be the most dominant strains accounting for 59.7% of all cases followed by lineage 3 at 15.2%. The lineage 4 non-Ugandan family accounted for 14.5% of all cases while 4.2% showed amplification for both lineage 4 and lineage 3. Eighteen samples (6.4%) of the strains remained unclassified since they could not be matched to any lineage based on the genotyping technique used. This study demonstrates that a wide diversity of strains is causing pulmonary tuberculosis in this region with those belonging to the lineage 4 Ugandan family being more predominant. However, to confirm this, further studies using more discriminative genotyping methods are necessary.
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Mokrousov I. Ubiquitous and multifaceted: SIT53 spoligotype does not correlate with any particular family of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2020; 126:102024. [PMID: 33242765 DOI: 10.1016/j.tube.2020.102024] [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: 09/26/2020] [Revised: 10/23/2020] [Accepted: 11/15/2020] [Indexed: 01/17/2023]
Abstract
Euro-American lineage (Lineage 4) of Mycobacterium tuberculosis comprises genetically and geographically diverse families that differ in their clinical and/or epidemiological capacities. Due to the characteristic structure of the CRISPR locus (presence of almost all 43 classical spacers except for deleted signals 33-36), spoligotype SIT53 takes the basal position in the evolution of this lineage. In the SITVIT database, it is assigned to the "ill-defined" T family and T1 subfamily. Here, I analyzed the phylogenetic diversity of SIT53 isolates and discussed interconnected terminological issues concerning M. tuberculosis population structure. The 24-MIRU-VNTR profiles of 266 SIT53 isolates from Europe, Asia, Africa, and South America were submitted to the phylogenetic analysis jointly with reference profiles of different families from MIRU-VNTRplus database. Under this analysis, SIT53 isolates were clustered within different and distant families such as Ghana, NEW-1 (L4.5), TUR (L4.2.2.1), etc whereas many remained unclassified within L4. This confirms the evolutionarily basal position of this spoligotype and in its turn, this demonstrates that SIT53 does not correspond to any particular family of M. tuberculosis. Instead, different SIT53 subpopulations with evolutionarily stable and unchanged CRISPR locus gave rise to different and distant families that in many instances evolved through long-term allopatric evolution.
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Affiliation(s)
- Igor Mokrousov
- St. Petersburg Pasteur Institute, 14 Mira Street, St. Petersburg, 197101, Russia.
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5
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Solo ES, Suzuki Y, Kaile T, Bwalya P, Lungu P, Chizimu JY, Shah Y, Nakajima C. Characterization of Mycobacterium tuberculosis genotypes and their correlation to multidrug resistance in Lusaka, Zambia. Int J Infect Dis 2020; 102:489-496. [PMID: 33059094 DOI: 10.1016/j.ijid.2020.10.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/04/2020] [Accepted: 10/06/2020] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES The burden of multidrug-resistant tuberculosis (MDR-TB) has been reported to be increasing in Zambia. The reasons for the increase are still unclear. This study determined the diversity of Mycobacterium tuberculosis genotypes among isolates in Lusaka, the capital city, and investigated their association with MDR-TB. METHODS Spoligotyping, large sequence polymorphism (LSP) analysis, and sequencing of MDR associated genes were performed on a total of 274 M. tuberculosis clinical isolates stored at the University Teaching Hospital from 2013 to 2017. Of these, 134 were MDR-TB while 126 were pan-susceptible. RESULTS Spoligotyping showed the LAM family as the most predominant genotype (149/274, 54.4%) followed by the CAS family (44/274, 16.1%), T family (39/274, 14.2%), and minor proportions of X, S, Harleem, EAI and Beijing spoligofamilies were identified. Three M. bovis isolates were also observed. Among those, CAS1-Kili (SIT 21) and LAM1 (SIT 20) subfamilies showed a propensity for MDR-TB with p = 0.0001 and p = 0.001, respectively. CONCLUSIONS This phenomenon might explain the future increase in the MDR-TB burden caused by specific lineages in Zambia. Therefore, it is recommended that the National TB control program in the country complements conventional control strategies with molecular analysis for monitoring and surveillance of MDR-TB epidemiology.
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Affiliation(s)
- Eddie Samuneti Solo
- Department of Pathology and Microbiology, University Teaching Hospital, RW 1X, Ministry of Health, Lusaka, Zambia
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Trevor Kaile
- University of Zambia, School of Medicine, Lusaka, Zambia
| | - Precious Bwalya
- Department of Pathology and Microbiology, University Teaching Hospital, RW 1X, Ministry of Health, Lusaka, Zambia; Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Patrick Lungu
- National TB Control Program, Ministry of Health, Zambia
| | - Joseph Yamweka Chizimu
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Zambia National Public Health Institute, Ministry of Health, Zambia
| | - Yogendra Shah
- 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; International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.
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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: 4] [Impact Index Per Article: 1.0] [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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Sharma SK, Upadhyay V. Epidemiology, diagnosis & treatment of non-tuberculous mycobacterial diseases. Indian J Med Res 2020; 152:185-226. [PMID: 33107481 PMCID: PMC7881820 DOI: 10.4103/ijmr.ijmr_902_20] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Indexed: 12/13/2022] Open
Abstract
Non-tuberculous mycobacteria (NTM) are ubiquitously present in the environment, but NTM diseases occur infrequently. NTM are generally considered to be less virulent than Mycobacterium tuberculosis, however, these organisms can cause diseases in both immunocompromised and immunocompetent hosts. As compared to tuberculosis, person-to-person transmission does not occur except with M. abscessus NTM species among cystic fibrosis patients. Lung is the most commonly involved organ, and the NTM-pulmonary disease (NTM-PD) occurs frequently in patients with pre-existing lung disease. NTM may also present as localized disease involving extrapulmonary sites such as lymph nodes, skin and soft tissues and rarely bones. Disseminated NTM disease is rare and occurs in individuals with congenital or acquired immune defects such as HIV/AIDS. Rapid molecular tests are now available for confirmation of NTM diagnosis at species and subspecies level. Drug susceptibility testing (DST) is not routinely done except in non-responsive disease due to slowly growing mycobacteria ( M. avium complex, M. kansasii) or infection due to rapidly growing mycobacteria, especially M. abscessus. While the decision to treat the patients with NTM-PD is made carefully, the treatment is given for 12 months after sputum culture conversion. Additional measures include pulmonary rehabilitation and correction of malnutrition. Treatment response in NTM-PD is variable and depends on isolated NTM species and severity of the underlying PD. Surgery is reserved for patients with localized disease with good pulmonary functions. Future research should focus on the development and validation of non-culture-based rapid diagnostic tests for early diagnosis and discovery of newer drugs with greater efficacy and lesser toxicity than the available ones.
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Affiliation(s)
- Surendra K. Sharma
- Department of Molecular Medicine, Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard (Deemed-to-be-University), New Delhi, India
| | - Vishwanath Upadhyay
- Department of Molecular Medicine, Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard (Deemed-to-be-University), New Delhi, India
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Alshukairi AN, Moalim HM, Alsaedi A, Almansouri WY, Al-Zahrani M, Aljuaid A, Alraddadi BM, Altorkistani HH, Alrajhi AA, Al-Hajoj SA. Family cluster of multi-drug resistant tuberculosis in Kingdom of Saudi Arabia. J Infect Public Health 2019; 13:154-157. [PMID: 31431418 DOI: 10.1016/j.jiph.2019.07.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 06/25/2019] [Accepted: 07/28/2019] [Indexed: 10/26/2022] Open
Abstract
We describe the clinical and genetic characteristics of multi-drug resistant tuberculosis (MDR-TB) in a family cluster in the western region of Kingdom of Saudi Arabia diagnosed between 2012 and 2016. All cases had risk factors for tuberculosis acquisition and they were not household contacts of the index case. Genetic analysis detected both MDR-TB and pre-extensively drug-resistant tuberculosis (pre-XDR TB) strains in the index case and confirmed tuberculosis transmission between two cases. Lack of early diagnosis of MDR-TB by molecular testing and lack of extended contact tracing contributed to the transmission of MDR-TB among this family cluster over four years.
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Affiliation(s)
- Abeer N Alshukairi
- Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia.
| | - Hanan M Moalim
- Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Asim Alsaedi
- Department of Medicine, King Abdulaziz Medical City, Jeddah, Saudi Arabia
| | - Walaa Y Almansouri
- Department of Pediatrics, King Abdulaziz Medical City, Jeddah, Saudi Arabia
| | | | - Alaa Aljuaid
- Department of Pediatrics, King Abdulaziz Medical City, Jeddah, Saudi Arabia
| | - Basem M Alraddadi
- Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Hanan H Altorkistani
- Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Abdulrahman A Alrajhi
- Department of Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sahal A Al-Hajoj
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
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Couvin D, David A, Zozio T, Rastogi N. Macro-geographical specificities of the prevailing tuberculosis epidemic as seen through SITVIT2, an updated version of the Mycobacterium tuberculosis genotyping database. INFECTION GENETICS AND EVOLUTION 2018; 72:31-43. [PMID: 30593925 DOI: 10.1016/j.meegid.2018.12.030] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/23/2018] [Accepted: 12/25/2018] [Indexed: 02/01/2023]
Abstract
In order to provide a global overview of genotypic, epidemiologic, demographic, phylogeographical, and drug resistance characteristics related to the prevailing tuberculosis (TB) epidemic, we hereby report an update of the 6th version of the international genotyping database SITVIT2. We also make all the available information accessible through a dedicated website (available at http://www.pasteur-guadeloupe.fr:8081/SITVIT2). Thanks to the public release of SITVIT2 which is currently the largest international multimarker genotyping database with a compilation of 111,635 clinical isolates from 169 countries of patient origin (131 countries of isolation, representing 1032 cities), our major aim is to highlight macro- and micro-geographical cleavages and phylogeographical specificities of circulating Mycobacterium tuberculosis complex (MTBC) clones worldwide. For this purpose, we retained strains typed by the most commonly used PCR-based methodology for TB genotyping, i.e., spoligotyping based on the polymorphism of the direct repeat (DR) locus, 5-loci Exact Tandem Repeats (ETRs), and MIRU-VNTR minisatellites used in 12-, 15-, or 24-loci formats. We describe the SITVIT2 database and integrated online applications that permit to interrogate the database using easy drop-down menus to draw maps, graphics and tables versus a long list of parameters and variables available for individual clinical isolates (year and place of isolation, origin, sex, and age of patient, drug-resistance, etc.). Available tools further allow to generate phylogenetical snapshot of circulating strains as Lineage-specific WebLogos, as well as minimum spanning trees of their genotypes in conjunction with their geographical distribution, drug-resistance, demographic, and epidemiologic characteristics instantaneously; whereas online statistical analyses let a user to pinpoint phylogeographical specificities of circulating MTBC lineages and conclude on actual demographic trends. Available associated information on gender (n = 18,944), age (n = 16,968), drug resistance (n = 19,606), and HIV serology (n = 2673), allowed to draw some important conclusions on TB geo-epidemiology; e.g. a positive correlation exists between certain Mycobacterium tuberculosis lineages (such as CAS and Beijing) and drug resistance (p-value<.001), while other lineages (such as LAM, X, and BOV) are more frequently associated with HIV-positive serology (p-value<.001). Besides, availability of information on the year of isolation of strains (range 1759-2012), also allowed to make tentative correlations between drug resistance information and lineages - portraying probable evolution trends over time and space. To conclude, the present approach of geographical mapping of predominant clinical isolates of tubercle bacilli causing the bulk of the disease both at country and regional level in conjunction with epidemiologic and demographic characteristics allows to shed new light on TB geo-epidemiology in relation with the continued waves of peopling and human migration.
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Affiliation(s)
- David Couvin
- WHO Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes, Guadeloupe, France.
| | - Audrey David
- WHO Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes, Guadeloupe, France
| | - Thierry Zozio
- WHO Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes, Guadeloupe, France
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes, Guadeloupe, France.
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Shi J, Zheng D, Zhu Y, Ma X, Wang S, Li H, Xing J. Role of MIRU-VNTR and spoligotyping in assessing the genetic diversity of Mycobacterium tuberculosis in Henan Province, China. BMC Infect Dis 2018; 18:447. [PMID: 30176820 PMCID: PMC6122615 DOI: 10.1186/s12879-018-3351-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 08/21/2018] [Indexed: 01/31/2023] Open
Abstract
Background Tuberculosis remains a serious threat to human health as an infectious disease in China. Henan, a most populated province in China, has a high incidence of tuberculosis (TB). Though the genetic diversity of Mycobacterium tuberculosis (MTB) has been investigated in many regions, there have been only a few studies on the molecular characteristics and drug resistance phenotypes in Henan. This is the first study on the genetic profile of MTB from Henan. Methods A total of 668 MTB isolates from various areas were genotyped with spoligotyping and 26-locus MIRU-VNTR (classical 24-locus MIRU-VNTR and 2 other loci). The association between TB spoligotype signatures and drug-resistant profiles was analysed. Results Our data revealed that MTB isolates circulating in Henan had a high degree of genetic variation. The Beijing family was the most predominant genotype (83.53%,n = 558), and the typical Beijing type(ST1) was the major sublineage (81.73%,n = 546). In total,668 isolates were divided into 567 different types, forming 38 clusters (2–15 isolates per cluster), and 529 unique types by 26-locus MIRU-VNTR analysis. There was no correlation between the Beijing family and gender, age at diagnosis or treatment history, whereas the Beijing family was significantly associated with all four first-line drug resistance and multidrug-resistant phenotypes. For these samples, 15 of 26 MIRU-VNTR loci had high or moderate discriminatory power according to the Hunter-Gaston discriminatory index. A combination of the 10 most polymorphic loci had similar discriminatory power as the 26-locus set. Conclusion The Beijing genotype is the most prevalent family. Ten-locus MIRU-VNTR in combination with spoligotyping can efficiently classify the molecular type of MTB in Henan Province. Electronic supplementary material The online version of this article (10.1186/s12879-018-3351-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jie Shi
- Henan Province Center for Disease Control and Prevention, Zheng Zhou, 450016, Henan, People's Republic of China.
| | - Danwei Zheng
- Henan Province Center for Disease Control and Prevention, Zheng Zhou, 450016, Henan, People's Republic of China
| | - Yankun Zhu
- Henan Province Center for Disease Control and Prevention, Zheng Zhou, 450016, Henan, People's Republic of China
| | - Xiaoguang Ma
- Henan Province Center for Disease Control and Prevention, Zheng Zhou, 450016, Henan, People's Republic of China
| | - Shaohua Wang
- Henan Province Center for Disease Control and Prevention, Zheng Zhou, 450016, Henan, People's Republic of China
| | - Hui Li
- Henan Province Center for Disease Control and Prevention, Zheng Zhou, 450016, Henan, People's Republic of China.
| | - Jin Xing
- Henan Province Center for Disease Control and Prevention, Zheng Zhou, 450016, Henan, People's Republic of China
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Kohl TA, Utpatel C, Niemann S, Moser I. Mycobacterium bovis Persistence in Two Different Captive Wild Animal Populations in Germany: a Longitudinal Molecular Epidemiological Study Revealing Pathogen Transmission by Whole-Genome Sequencing. J Clin Microbiol 2018; 56:e00302-18. [PMID: 29950330 PMCID: PMC6113487 DOI: 10.1128/jcm.00302-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 06/15/2018] [Indexed: 11/20/2022] Open
Abstract
Bovine tuberculosis (bTB) caused by Mycobacterium bovis is a transmissible disease notifiable to the World Organization for Animal Health and to the European Union, with ongoing efforts of surveillance and eradication in every EU member state. In Germany, a country which has been declared officially free from bovine tuberculosis since 1997 by the EU, M. bovis infections still occur sporadically in cattle and other mammals, including humans. Here, the transmission routes of a bTB outbreak in a wildlife park in Germany affecting different cervid species, bison, lynx, and pot-bellied pigs were followed by employing whole-genome sequencing (WGS) combined with spoligotyping and mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing. One single M. bovis strain persisted from 2002 to 2015, and transmission between the park and a distantly located captive cervid farm was verified. The spoligotyping patterns remained identical, while MIRU-VNTR typing of 24 loci of the standardized panel and locus 2163a as an additional locus revealed one change at locus 2165 in a strain from a fallow deer and one at locus 2461 in isolates from red deer over the whole time period. WGS analysis confirmed the close relatedness of the isolates, with a maximum of 12 single nucleotide polymorphisms (SNPs) detected between any two sequenced isolates. In conclusion, our data confirm a longitudinal outbreak of M. bovis in a German wildlife park and provide the first insights into the dynamics of different genotyping markers in M. bovis.
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Affiliation(s)
- Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, TTU-TB, Borstel, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, TTU-TB, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, TTU-TB, Borstel, Germany
| | - Irmgard Moser
- Friedrich-Loeffler-Institut, Federal Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany
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Chihota VN, Niehaus A, Streicher EM, Wang X, Sampson SL, Mason P, Källenius G, Mfinanga SG, Pillay M, Klopper M, Kasongo W, Behr MA, Gey van Pittius NC, van Helden PD, Couvin D, Rastogi N, Warren RM. Geospatial distribution of Mycobacterium tuberculosis genotypes in Africa. PLoS One 2018; 13:e0200632. [PMID: 30067763 PMCID: PMC6070189 DOI: 10.1371/journal.pone.0200632] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/29/2018] [Indexed: 11/24/2022] Open
Abstract
Objective To investigate the distribution of Mycobacterium tuberculosis genotypes across Africa. Methods The SITVIT2 global repository and PUBMED were searched for spoligotype and published genotype data respectively, of M. tuberculosis from Africa. M. tuberculosis lineages in Africa were described and compared across regions and with those from 7 European and 6 South-Asian countries. Further analysis of the major lineages and sub-lineages using Principal Component analysis (PCA) and hierarchical cluster analysis were done to describe clustering by geographical regions. Evolutionary relationships were assessed using phylogenetic tree analysis. Results A total of 14727 isolates from 35 African countries were included in the analysis and of these 13607 were assigned to one of 10 major lineages, whilst 1120 were unknown. There were differences in geographical distribution of major lineages and their sub-lineages with regional clustering. Southern African countries were grouped based on high prevalence of LAM11-ZWE strains; strains which have an origin in Portugal. The grouping of North African countries was due to the high percentage of LAM9 strains, which have an origin in the Eastern Mediterranean region. East African countries were grouped based on Central Asian (CAS) and East-African Indian (EAI) strain lineage possibly reflecting historic sea trade with Asia, while West African Countries were grouped based on Cameroon lineage of unknown origin. A high percentage of the Haarlem lineage isolates were observed in the Central African Republic, Guinea, Gambia and Tunisia, however, a mixed distribution prevented close clustering. Conclusions This study highlighted that the TB epidemic in Africa is driven by regional epidemics characterized by genetically distinct lineages of M. tuberculosis. M. tuberculosis in these regions may have been introduced from either Europe or Asia and has spread through pastoralism, mining and war. The vast array of genotypes and their associated phenotypes should be considered when designing future vaccines, diagnostics and anti-TB drugs.
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Affiliation(s)
- Violet N. Chihota
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research /SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
- The Aurum Institute, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- * E-mail:
| | - Antoinette Niehaus
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research /SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Elizabeth M. Streicher
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research /SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Xia Wang
- Department of Mathematical Sciences, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Samantha L. Sampson
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research /SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Peter Mason
- Biomedical Research and Training Institute, Harare, Zimbabwe
| | - Gunilla Källenius
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Sayoki G. Mfinanga
- National Institute for Medical Research Muhimbili Medical Research Centre, Dar es Saalam, Tanzania
| | - Marnomorney Pillay
- Department of Medical Microbiology University of KwaZulu Natal, Durban, South Africa
| | - Marisa Klopper
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research /SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | | | - Marcel A. Behr
- Division of Infectious Diseases, Department of Medicine McGill University Health Centre, Montreal, Quebec, Canada
| | - Nicolaas C. Gey van Pittius
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research /SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Paul D. van Helden
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research /SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - David Couvin
- WHO Supranational TB Reference Laboratory, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
| | - Robin M. Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research /SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
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Nahid P, Jarlsberg LG, Kato-Maeda M, Segal MR, Osmond DH, Gagneux S, Dobos K, Gold M, Hopewell PC, Lewinsohn DM. Interplay of strain and race/ethnicity in the innate immune response to M. tuberculosis. PLoS One 2018; 13:e0195392. [PMID: 29787561 PMCID: PMC5963792 DOI: 10.1371/journal.pone.0195392] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/21/2018] [Indexed: 11/19/2022] Open
Abstract
Background The roles of host and pathogen factors in determining innate immune responses to M. tuberculosis are not fully understood. In this study, we examined host macrophage immune responses of 3 race/ethnic groups to 3 genetically and geographically diverse M. tuberculosis lineages. Methods Monocyte-derived macrophages from healthy Filipinos, Chinese and non-Hispanic White study participants (approximately 45 individuals/group) were challenged with M. tuberculosis whole cell lysates of clinical strains Beijing HN878 (lineage 2), Manila T31 (lineage 1), CDC1551 (lineage 4), the reference strain H37Rv (lineage 4), as well as with Toll-like receptor 2 agonist lipoteichoic acid (TLR2/LTA) and TLR4 agonist lipopolysaccharide (TLR4/LPS). Following overnight incubation, multiplex assays for nine cytokines: IL-1β, IL-2, IL-6, IL-8, IL-10, IL-12p70, IFNγ, TNFα, and GM-CSF, were batch applied to supernatants. Results Filipino macrophages produced less IL-1, IL-6, and more IL-8, compared to macrophages from Chinese and Whites. Race/ethnicity had only subtle effects or no impact on the levels of IL-10, IL-12p70, TNFα and GM-CSF. In response to the Toll-like receptor 2 agonist lipoteichoic acid (TLR2/LTA), Filipino macrophages again had lower IL-1 and IL-6 responses and a higher IL-8 response, compared to Chinese and Whites. The TLR2/LTA-stimulated Filipino macrophages also produced lower amounts of IL-10, TNFα and GM-CSF. Race/ethnicity had no impact on IL-12p70 levels released in response to TLR2/LTA. The responses to TLR4 agonist lipopolysaccharide (TLR4/LPS) were similar to the TLR2/LTA responses, for IL-1, IL-6, IL-8, and IL-10. However, TLR4/LPS triggered the release of less IL-12p70 from Filipino macrophages, and less TNFα from White macrophages. Conclusions Both host race/ethnicity and pathogen strain influence the innate immune response. Such variation may have implications for the development of new tools across TB therapeutics, immunodiagnostics and vaccines.
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Affiliation(s)
- P. Nahid
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, University of California, San Francisco, United States of America
- * E-mail: (PN); (DML)
| | - L. G. Jarlsberg
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, University of California, San Francisco, United States of America
| | - M. Kato-Maeda
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, University of California, San Francisco, United States of America
| | - M. R. Segal
- Department of Epidemiology & Biostatistics, University of California, San Francisco, United States of America
| | - D. H. Osmond
- Department of Epidemiology & Biostatistics, University of California, San Francisco, United States of America
| | - S. Gagneux
- Swiss Tropical and Public Health Institute, Department of Medical Parasitology and Infection Biology, University of Basel, Basel, Switzerland
| | - K. Dobos
- Colorado State University, Department of Microbiology, Immunology & Pathology, Fort Collins, CO, United States of America
| | - M. Gold
- Department of Research, Veterans Affairs Portland Health Care Center, Portland, Oregon, United States of America
| | - P. C. Hopewell
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, University of California, San Francisco, United States of America
| | - D. M. Lewinsohn
- Department of Pulmonary and Critical Care Medicine, Oregon Health and Sciences University, Portland, Oregon
- Department of Research, Veterans Affairs Portland Health Care Center, Portland, Oregon, United States of America
- * E-mail: (PN); (DML)
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On sunspots, click science and molecular iconography. Tuberculosis (Edinb) 2018; 110:91-95. [PMID: 29779780 DOI: 10.1016/j.tube.2018.04.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/02/2018] [Accepted: 04/06/2018] [Indexed: 01/21/2023]
Abstract
CRISPR-spoligotyping and MIRU-VNTR typing, SITVIT_WEB and MIRU-VNTRplus are the methods and online resources most widely used for Mycobacterium tuberculosis genotype family assignment and clustering analysis. They have been proven invaluable for molecular epidemiological studies of this important human pathogen in setting up the terminology and classification framework. However, they are inherently limited by insufficient knowledge of evolution of the targeted genome loci (especially, CRISPR). The situation is aggravated by the dogmatic, iconographic perception of these increasingly user-friendly online tools. Here, I present a critical essay on hot practical aspects related to the use of SITVIT_WEB and MIRU-VNTRplus, in particular, partly inadequate (sub)clade assignment due to imperfect decision rules, partly outdated methodological options offered to the users that permit to build scientifically unsound phylogenies from spoligotyping data. A confusing terminology, misclassification and false clustering are not abstract issues but make a scientific discussion meaningless, and I propose some courses for improvement.
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Diversity of Mycobacterium tuberculosis Complex from Cattle Lymph Nodes in Eastern Cape Province. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3683801. [PMID: 29850506 PMCID: PMC5914149 DOI: 10.1155/2018/3683801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/10/2018] [Indexed: 02/04/2023]
Abstract
Tuberculosis (TB) remains a major health challenge in South Africa and the condition in humans has been well researched and documented. However, investigations on the circulating Mycobacterium tuberculosis complex (MTBC) strains from cattle in the Eastern Cape Province of South Africa are insufficient. This study delineated the diversity of MTBC isolates from cows' lymph nodes. A total of 162 MTBC isolates, collected over a one-year period from cattle lymph nodes from two abattoirs, were submitted to spoligotyping and 12 MIRU-VNTR typing. The spoligotyping results were matched with isolates in the universal spoligotyping database (SITVIT2). Our study identified 27 spoligotype patterns, with 10 shared types assigned to five lineages: the East-Asian (Beijing) was predominant, 17.9%, and East-Asian (Microti) and Latin-American-Mediterranean S were the least detected with 0.6%. Spoligotyping showed a higher clustering rate of 82.1%, with the lowest being the Hunter-Gaston Diversity Index (HGDI) of 0.485; 12 MIRU-VNTR resulted in a clustering rate of 64.8%, showing a higher HGDI of 0.671. The results of this study show a high diversity of MTBC strains in the Eastern Cape Province and clustering rate, which indicates ongoing transmission in the province.
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Hijikata M, Keicho N, Duc LV, Maeda S, Hang NTL, Matsushita I, Kato S. Spoligotyping and whole-genome sequencing analysis of lineage 1 strains of Mycobacterium tuberculosis in Da Nang, Vietnam. PLoS One 2017; 12:e0186800. [PMID: 29049400 PMCID: PMC5648229 DOI: 10.1371/journal.pone.0186800] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 10/06/2017] [Indexed: 11/18/2022] Open
Abstract
Background Spacer oligonucleotide typing (spoligotyping), a widely used, classical genotyping method for Mycobacterium tuberculosis complex (MTBC), is a PCR-based dot-blot hybridization technique to detect the genetic diversity of the direct repeat (DR) region. Of the seven major MTBC lineages in the world, lineage 1 (Indo-Oceanic) mostly corresponds to the East African–Indian (EAI) spoligotype family in East Africa and Southeast Asia. Objectives We investigated the genomic features of Vietnamese lineage 1 strains, comparing spoligotype patterns using whole-genome sequencing (WGS) data. Methods M. tuberculosis strains isolated in Da Nang, Vietnam were subjected to conventional spoligotyping, followed by WGS analysis using a high-throughput sequencer. Vietnamese lineage 1 strains were further analyzed with other lineage 1 strains obtained from a public database. Results Indicating a major spoligotype in Da Nang, 86 (46.2%) of the 186 isolates belonged to the EAI family or lineage 1. Although typical EAI4-VNM strains are characterized by the deletion of spacers 26 and 27, 65 (75.6%) showed ambiguous signals on spacer 26. De novo assembly of the entire DR region and in silico spoligotyping analysis suggested the absence of spacer 26, and direct sequencing revealed that the 17th spacer sequence not used for conventional typing, was cross-hybridized to the spacer 26 probe. Vietnamese EAI4-VNM, other EAI-like strains, and those showing a non-EAI pattern lacking many spacers formed a monophyletic group separate from other EAI families in the world. Conclusion Information about the alignment of spacers in the entire DR region obtained from WGS data provides a clue for the determination of experimentally ambiguous spoligo patterns. WGS data also helped to analyze the hidden relationships between apparently distinct spoligo patterns.
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Affiliation(s)
- Minako Hijikata
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Tokyo, Japan
| | - Naoto Keicho
- The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Tokyo, Japan
- * E-mail:
| | | | - Shinji Maeda
- Hokkaido Pharmaceutical University School of Pharmacy, Sapporo, Hokkaido, Japan
| | | | - Ikumi Matsushita
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Tokyo, Japan
| | - Seiya Kato
- The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Tokyo, Japan
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Zhang H, Huang H, Liu C, Jia T, Zhang L, Zhou D, Wei S, Wang C. Genotyping and drug-resistance epidemiology of mycobacterium tuberculosis in Xuzhou, China. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2017; 10:9675-9682. [PMID: 31966848 PMCID: PMC6965968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/09/2017] [Indexed: 06/10/2023]
Abstract
BACKGROUND To explore the genetic diversity and drug resistance status of MTB in Xuzhou, China. METHODS A total of 325 clinical MTB strains were genotyped by spacer-oligonucleotide typing (spoligotyping) and mycobacterial interspersed repetitive unit variable number of tandem repeats (MIRU-VNTR). Phenotypic resistance was assessed by drug susceptibility testing (DST). RESULT Based on the spoligotyping method, 325 MTB isolates were classified into 5 known genotypes and 12 unknown genotypes, and the largest branch comprised 268 strains belonging to the Beijing family. Based on the 15-loci VNTR typing method, 325 MTB isolates were divided into 35 clusters and 220 unique patterns. Compared to the low discriminatory power of spoligotyping genotyping (HGDI = 0.3444), 15-loci VNTR genotyping had a significantly higher discriminatory power for all strains (HGDI = 0.9980), particularly for the Beijing family strains (HGDI = 0.9892). When spoligotyping and 15-loci VNTR methods were used together, the discriminatory power increased to 0.9991. The Beijing family strain presented increased risks for developing multi-drug resistance TB (P < 0.05). CONCLUSION The Beijing family isolates is the most prevalent strains in Xuzhou. Spoligotyping, in combination with 15-loci MIRU-VNTR, is useful for epidemiological analysis of MTB transmission in Xuzhou.
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Affiliation(s)
- Haiqing Zhang
- Department of Tuberculosis, Xuzhou Infectious Disease HospitalXuzhou, China
| | - Haibin Huang
- Department of Tuberculosis, Xuzhou Infectious Disease HospitalXuzhou, China
| | - Chengyong Liu
- Department of Tuberculosis, Xuzhou Infectious Disease HospitalXuzhou, China
| | - Tong Jia
- Department of Tuberculosis, Xuzhou Infectious Disease HospitalXuzhou, China
| | - Limao Zhang
- Department of Tuberculosis, Xuzhou Infectious Disease HospitalXuzhou, China
| | - Dongqing Zhou
- Department of Tuberculosis, Xuzhou Infectious Disease HospitalXuzhou, China
| | - Sumei Wei
- Department of Tuberculosis, Xuzhou Infectious Disease HospitalXuzhou, China
| | - Chunying Wang
- Department of Infectious Diseases, Xuzhou Infectious Disease HospitalXuzhou, China
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Agarwal S, Nguyen DT, Teeter LD, Graviss EA. Spatial-temporal distribution of genotyped tuberculosis cases in a county with active transmission. BMC Infect Dis 2017; 17:378. [PMID: 28569145 PMCID: PMC5452388 DOI: 10.1186/s12879-017-2480-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/22/2017] [Indexed: 11/11/2022] Open
Abstract
Background Harris County, Texas is the third most populous county in the United States and consistently has tuberculosis rates above the national average. Understanding jurisdictional epidemiologic characteristics for the most common Mycobacterium tuberculosis genotyped clusters is needed for tuberculosis prevention programs. Our objective is to describe the demographic, laboratory, clinical, temporal and geospatial characteristics for the most common Mycobacterium tuberculosis GENType clusters in Harris County from 2009 to 2015. Methods We analyzed data from the Centers for Disease Control and Prevention (CDC) Tuberculosis Genotyping Information Management System (TB GIMS). Chi-square analyses were used to determine associations between selected clusters and specific characteristics of interest. Geographical Information System (GIS) point density and hot spot maps were generated and analyzed with ArcGIS 10.4. Results In Harris County from 2009 to 2015, 1655 of 1705 (97.1%) culture positive tuberculosis cases were genotyped and assigned a GENType, and 1058 different GENTypes were identified. The analyzed genotype clusters represent 14.1% (233/1655) of all genotyped cases: G00010 (n = 118), G00014 (n = 38), G00769 (n = 33), G01521 (n = 26), and G08964 (n = 18). Male gender (p = 0.002), ethnicity (p < 0.001), homelessness (p < 0.001), excessive alcohol use (p = 0.002), and U.S.-birth (p = 0.004) were associated with the 5 GENTypes. Hot and cold spots were identified as geographic areas having high and low TB incidence. Conclusions Of more than 1000 distinct GENTypes identified in Harris County, there were 5 common Mycobacterium tuberculosis GENType clusters seen from 2009 to 2015. The common genotypes were observed primarily in U.S.-born populations despite the large foreign-born population residing in Harris County. GENType was significant distributed spatially and temporally in Harris County in the analyzed time period indicating that there may be outbreaks caused by transmission.
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Affiliation(s)
| | - Duc T Nguyen
- , Houston Methodist Research Institute, Houston, Texas, USA
| | - Larry D Teeter
- Forensic Research and Analysis, 425 NW 10th Avenue, Ste 306, Portland, OR, 97209, USA
| | - Edward A Graviss
- Institute of Academic Medicine, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Mail Station: R6-414, 6670 Bertner Ave, Houston, TX, 77030, USA.
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Moraes EB, Slompo L, Finardi AJ, Silveira HPPD, Ruiz L, Gomes HM, Richini VB, Suffys P, Fortaleza CMCB, Cavalcanti R, Baptista IMFD. Tuberculosis associated factors caused by Mycobacterium tuberculosis of the RDRio genotype. Mem Inst Oswaldo Cruz 2017; 112:182-187. [PMID: 28225901 PMCID: PMC5319367 DOI: 10.1590/0074-02760160347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 11/07/2016] [Indexed: 11/22/2022] Open
Affiliation(s)
- Eloise Brasil Moraes
- Instituto Lauro de Souza Lima, Brasil; Universidade Estadual Paulista Júlio de Mesquita Filho, Brasil
| | | | - Amanda Juliane Finardi
- Instituto Lauro de Souza Lima, Brasil; Universidade Estadual Paulista Júlio de Mesquita Filho, Brasil
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Freidlin PJ, Nissan I, Luria A, Goldblatt D, Schaffer L, Kaidar-Shwartz H, Chemtob D, Dveyrin Z, Head SR, Rorman E. Structure and variation of CRISPR and CRISPR-flanking regions in deleted-direct repeat region Mycobacterium tuberculosis complex strains. BMC Genomics 2017; 18:168. [PMID: 28201993 PMCID: PMC5310062 DOI: 10.1186/s12864-017-3560-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 02/07/2017] [Indexed: 12/16/2022] Open
Abstract
Background CRISPR and CRISPR-flanking genomic regions are important for molecular epidemiology of Mycobacterium tuberculosis complex (MTBC) strains, and potentially for adaptive immunity to phage and plasmid DNA, and endogenous roles in the bacterium. Genotyping in the Israel National Mycobacterium Reference Center Tel-Aviv of over 1500 MTBC strains from 2008–2013 showed three strains with validated negative 43-spacer spoligotypes, that is, with putatively deleted direct repeat regions (deleted-DR/CRISPR regions). Two isolates of each of three negative spoligotype MTBC (a total of 6 isolates) were subjected to Next Generation Sequencing (NGS). As positive controls, NGS was performed for three intact-DR isolates belonging to T3_Eth, the largest multiple-drug-resistant (MDR)-containing African-origin cluster in Israel. Other controls consisted of NGS reads and complete whole genome sequences from GenBank for 20 intact-DR MTBC and for 1 deleted-DR MTBC strain recognized as CAS by its defining RD deletion. Results NGS reads from negative spoligotype MTBC mapped to reference H37Rv NC_000962.3 suggested that the DR/CRISPR regions were completely deleted except for retention of the middle IS6110 mobile element. Clonally specific deletion of CRISPR-flanking genes also was observed, including deletion of at least cas2 and cas1 genes. Genomic RD deletions defined lineages corresponding to the major spoligotype families Beijing, EAI, and Haarlem, consistent with 24 loci MIRU-VNTR profiles. Analysis of NGS reads, and analysis of contigs obtained by manual PCR confirmed that all 43 gold standard DR/CRISPR spacers were missing in the deleted-DR genomes. Conclusions Although many negative spoligotype strains are recorded as spoligotype-international-type (SIT) 2669 in the SITVIT international database, this is the first time to our knowledge that it has been shown that negative spoligotype strains are found in at least 4 different 24 loci MIRU-VNTR and RD deletion families. We report for the first time negative spoligotype-associated total loss of CRISPR region spacers and repeats, with accompanying clonally specific loss of flanking genes, including at least CRISPR-associated genes cas2 and cas1. Since cas1 deleted E.coli shows increased sensitivity to DNA damage and impaired chromosomal segregation, we discussed the possibility of a similar phenotype in the deleted-DR strains and Beijing family strains as both lack the cas1 gene. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3560-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paul Jeffrey Freidlin
- National Mycobacterium Reference Center, National Public Health Laboratory Tel Aviv, Ministry of Health, Tel Aviv, Israel.
| | - Israel Nissan
- National Mycobacterium Reference Center, National Public Health Laboratory Tel Aviv, Ministry of Health, Tel Aviv, Israel
| | - Anna Luria
- National Mycobacterium Reference Center, National Public Health Laboratory Tel Aviv, Ministry of Health, Tel Aviv, Israel.,current address: Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Drora Goldblatt
- National Mycobacterium Reference Center, National Public Health Laboratory Tel Aviv, Ministry of Health, Tel Aviv, Israel
| | | | - Hasia Kaidar-Shwartz
- National Mycobacterium Reference Center, National Public Health Laboratory Tel Aviv, Ministry of Health, Tel Aviv, Israel
| | - Daniel Chemtob
- Department of Tuberculosis and AIDS, Ministry of Health, Jerusalem, Israel
| | - Zeev Dveyrin
- National Public Health Laboratory Tel Aviv, Ministry of Health, Tel Aviv, Israel
| | | | - Efrat Rorman
- National Public Health Laboratory Tel Aviv, Ministry of Health, Tel Aviv, Israel
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22
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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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Emergence of mixed infection of Beijing/Non-Beijing strains among multi-drug resistant Mycobacterium tuberculosis in Pakistan. 3 Biotech 2016; 6:108. [PMID: 28330178 PMCID: PMC4837763 DOI: 10.1007/s13205-016-0423-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 03/30/2016] [Indexed: 11/17/2022] Open
Abstract
Tuberculosis (TB) remains as one of the deadliest diseases after HIV globally with 95 % of deaths confined to low-and-middle income countries. Pakistan is fifth among the 22 high-burden TB countries with the incidence rate of 230/100,000 persons, however, studies related to prevalent Mycobacterium tuberculosis strains and their spread, drug resistance pattern and evolutionary genetics are inadequate. The present study was undertaken to highlight the circulation of M. tuberculosis strains causing drug resistant TB in our community by targeting the molecular marker IS6110 and then characterization of these strains as Beijing and Non-Beijing genotypes. Sputum samples from 102 MDR TB suspects from different cities of Punjab were collected and their record was stored in a database. Sputum samples were evaluated by Ziehl Neelson staining and cultured on Lownstein Jensen medium by Modified Petroff’s method. DST was performed for first-line anti-mycobacterial drugs by indirect proportion method. Mycobacterium tuberculosis isolates were investigated for the presence of IS6110 and further identification as Beijing, Non-Beijing or mixed genotype. Percentage of male and female patients was found to be 58.8 and 41.2 % respectively. DST showed resistance of 93 % of isolates to isoniazid and rifampicin. All of the isolates showed positive results for IS6110 amplification. Based on PCR amplification of Beijing and non-Beijing primer sets 4.9 % of the patients showed infection with pure Beijing isolates, 14.7 % with both Beijing and non-Beijing isolates and 80.3 % with pure non-Beijing isolates. Analysis of IS6110 and Beijing sequences showed the presence of putative transposase conserved domain while non-Beijing sequences were epitomized with RAMP_I_III superfamily domain (CRISPR-associated protein family). TB in Pakistan is predominantly caused by Non-Beijing genotypes, but Beijing strains showed incessant circulation in our community as both single and mixed (co-infecting Non-Beijing and Beijing) strains.
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Mbugi EV, Katale BZ, Streicher EM, Keyyu JD, Kendall SL, Dockrell HM, Michel AL, Rweyemamu MM, Warren RM, Matee MI, van Helden PD, Couvin D, Rastogi N. Mapping of Mycobacterium tuberculosis Complex Genetic Diversity Profiles in Tanzania and Other African Countries. PLoS One 2016; 11:e0154571. [PMID: 27149626 PMCID: PMC4858144 DOI: 10.1371/journal.pone.0154571] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/15/2016] [Indexed: 11/23/2022] Open
Abstract
The aim of this study was to assess and characterize Mycobacterium tuberculosis complex (MTBC) genotypic diversity in Tanzania, as well as in neighbouring East and other several African countries. We used spoligotyping to identify a total of 293 M. tuberculosis clinical isolates (one isolate per patient) collected in the Bunda, Dar es Salaam, Ngorongoro and Serengeti areas in Tanzania. The results were compared with results in the SITVIT2 international database of the Pasteur Institute of Guadeloupe. Genotyping and phylogeographical analyses highlighted the predominance of the CAS, T, EAI, and LAM MTBC lineages in Tanzania. The three most frequent Spoligotype International Types (SITs) were: SIT21/CAS1-Kili (n = 76; 25.94%), SIT59/LAM11-ZWE (n = 22; 7.51%), and SIT126/EAI5 tentatively reclassified as EAI3-TZA (n = 18; 6.14%). Furthermore, three SITs were newly created in this study (SIT4056/EAI5 n = 2, SIT4057/T1 n = 1, and SIT4058/EAI5 n = 1). We noted that the East-African-Indian (EAI) lineage was more predominant in Bunda, the Manu lineage was more common among strains isolated in Ngorongoro, and the Central-Asian (CAS) lineage was more predominant in Dar es Salaam (p-value<0.0001). No statistically significant differences were noted when comparing HIV status of patients vs. major lineages (p-value = 0.103). However, when grouping lineages as Principal Genetic Groups (PGG), we noticed that PGG2/3 group (Haarlem, LAM, S, T, and X) was more associated with HIV-positive patients as compared to PGG1 group (Beijing, CAS, EAI, and Manu) (p-value = 0.03). This study provided mapping of MTBC genetic diversity in Tanzania (containing information on isolates from different cities) and neighbouring East African and other several African countries highlighting differences as regards to MTBC genotypic distribution between Tanzania and other African countries. This work also allowed underlining of spoligotyping patterns tentatively grouped within the newly designated EAI3-TZA lineage (remarkable by absence of spacers 2 and 3, and represented by SIT126) which seems to be specific to Tanzania. However, further genotyping information would be needed to confirm this specificity.
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Affiliation(s)
- Erasto V. Mbugi
- Department of Biochemistry, Muhimbili University of Health and Allied Sciences, P. O. Box 65001, Dar es Salaam, Tanzania
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania
| | - Bugwesa Z. Katale
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania
- Tanzania Wildlife Research Institute (TAWIRI), P.O. Box 661, Arusha, Tanzania
| | - Elizabeth M. Streicher
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ South African Medical Research Council (MRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa
| | - Julius D. Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), P.O. Box 661, Arusha, Tanzania
| | - Sharon L. Kendall
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
| | - Hazel M. Dockrell
- The Royal Veterinary College, Royal College Street, London, NW1 0TU, United Kingdom
| | - Anita L. Michel
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Mark M. Rweyemamu
- Southern African Centre for Infectious Disease Surveillance, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Robin M. Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ South African Medical Research Council (MRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa
| | - Mecky I. Matee
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania
| | - Paul D. van Helden
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ South African Medical Research Council (MRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa
| | - David Couvin
- WHO Supranational TB Reference Laboratory, Tuberculosis & Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Morne Joliviere, BP 484, 97183, Abymes, Guadeloupe
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Tuberculosis & Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Morne Joliviere, BP 484, 97183, Abymes, Guadeloupe
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Diverse Molecular Genotypes of Mycobacterium tuberculosis Complex Isolates Circulating in the Free State, South Africa. Int J Microbiol 2016; 2016:6572165. [PMID: 27073397 PMCID: PMC4814679 DOI: 10.1155/2016/6572165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 02/08/2016] [Accepted: 02/25/2016] [Indexed: 11/17/2022] Open
Abstract
Tuberculosis is a serious public health concern especially in Africa and Asia. Studies describing strain diversity are lacking in the Free State region of South Africa. The aim of the study was to describe the diversity of Mycobacterium tuberculosis (M. tuberculosis) strain families in the Free State province of South Africa. A total of 86 M. tuberculosis isolates were genotyped using spoligotyping. A 12-locus mycobacterial interspersed repetitive units-variable-number tandem repeats (MIRU-VNTRs) typing was used to further characterize the resulting spoligotyping clusters. SITVITWEB identified 49 different patterns with allocation to six lineages including Latin-American-Mediterranean (LAM) (18 isolates), T (14 isolates), Beijing (five isolates), S (six isolates), Haarlem (one isolate), and X (five isolates), while 37 (43.0%) orphans were identified. Eight clusters included 37 isolates with identical spoligotypes (2 to 13/cluster). MIRU-VNTR typing further differentiated three spoligotyping clusters: SIT1/Beijing/MIT17, SIT33/LAM3/MIT213, and confirmed one SIT34/S/MIT311. In addition, SpolDB3/RIM assignment of the orphan strains resulted in a further 10 LAM and 13 T families. In total, LAM (28 isolates) and T (27 isolates) cause 63% of the individual cases of MTB in our study. The Free State has a highly diverse TB population with LAM being predominant. Further studies with inclusion of multidrug-resistant strains with larger sample size are warranted.
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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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David S, Mateus ARA, Duarte EL, Albuquerque J, Portugal C, Sancho L, Lavinha J, Gonçalves G. Determinants of the Sympatric Host-Pathogen Relationship in Tuberculosis. PLoS One 2015; 10:e0140625. [PMID: 26529092 PMCID: PMC4631367 DOI: 10.1371/journal.pone.0140625] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 09/29/2015] [Indexed: 01/04/2023] Open
Abstract
Major contributions from pathogen genome analysis and host genetics have equated the possibility of Mycobacterium tuberculosis co-evolution with its human host leading to more stable sympatric host–pathogen relationships. However, the attribution to either sympatric or allopatric categories depends on the resolution or grain of genotypic characterization. We explored the influence on the sympatric host-pathogen relationship of clinical (HIV infection and multidrug-resistant tuberculosis [MDRTB]) and demographic (gender and age) factors in regards to the genotypic grain by using spacer oligonucleotide typing (spoligotyping) for classification of M. tuberculosis strains within the Euro-American lineage. We analyzed a total of 547 tuberculosis (TB) cases, from six year consecutive sampling in a setting with high TB-HIV coinfection (32.0%). Of these, 62.0% were caused by major circulating pathogen genotypes. The sympatric relationship was defined according to spoligotype in comparison to the international spoligotype database SpolDB4. While no significant association with Euro-American lineage was observed with any of the factors analyzed, increasing the resolution with spoligotyping evidenced a significant association of MDRTB with sympatric strains, regardless of the HIV status. Furthermore, distribution curves of the prevalence of sympatric and allopatric TB in relation to patients’ age showed an accentuation of the relevance of the age of onset in the allopatric relationship, as reflected in the trimodal distribution. On the contrary, sympatric TB was characterized by the tendency towards a typical (standard) distribution curve. Our results suggest that within the Euro-American lineage a greater degree of genotyping fine-tuning is necessary in modeling the biological processes behind the host-pathogen interplay. Furthermore, prevalence distribution of sympatric TB to age was suggestive of host genetic determinisms driven by more common variants.
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Affiliation(s)
- Susana David
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge (INSA), Lisboa, Portugal
- * E-mail:
| | - A. R. A. Mateus
- Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Elsa L. Duarte
- Escola de Ciências e Tecnologia/ Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal
| | - José Albuquerque
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge (INSA), Lisboa, Portugal
| | - Clara Portugal
- Serviço de Patologia Clínica, Hospital Fernando Fonseca, Amadora, Portugal
| | - Luísa Sancho
- Serviço de Patologia Clínica, Hospital Fernando Fonseca, Amadora, Portugal
| | - João Lavinha
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge (INSA), Lisboa, Portugal
| | - Guilherme Gonçalves
- Unidade Multidisciplinar de Investigação Biomédica (UMIB), Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Porto, Portugal
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Lisdawati V, Puspandari N, Rif'ati L, Soekarno T, M M, K S, Ratnasari L, Izzatun N, Parwati I. Molecular epidemiology study of Mycobacterium tuberculosis and its susceptibility to anti-tuberculosis drugs in Indonesia. BMC Infect Dis 2015; 15:366. [PMID: 26297576 PMCID: PMC4546281 DOI: 10.1186/s12879-015-1101-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 08/12/2015] [Indexed: 12/21/2022] Open
Abstract
Background Genotyping of Mycobacterium tuberculosis helps to understand the molecular epidemiology of tuberculosis and to address evolutionary questions about the disease spread. Certain genotypes also have implications for the spread of infection and treatment. Indonesia is a very diverse country with a population with multiple ethnicities and cultures and a history of many trade and tourism routes. This study describes the first attempt to map the molecular epidemiology of TB in the Indonesian archipelago. Method From 2008 to 2011, 404 clinical specimens from sputum-smear (SS+) TB patients, age ≥15 years, were collected from 16 TB referral primary health centers (PHC) in 16 provincial capitals in Indonesia. Susceptibility testing to first line drugs was conducted for 262 samples using the agar proportion method as per WHO guidelines. Spoligotyping was done on all samples. Results Ninety-three of the 404 samples (23 %) were from the Beijing family, making it the predominant family in the country. However, the geographic distribution of the family varied by region with 86/294 (29.3 %) in the western region, 6/72 (8.3 %) in the central region, and 2/72 (2.8 %) in the eastern region (p < 0.001). The predominant genotype in the central and eastern regions was from the East-African-Indian (EAI) family, comprising 15.3 % (11/72), and 26.3 % (10/38) of the isolates, respectively. Drug susceptibility to first-line anti-TB drugs was tested in 262 isolates. 162 (61.8 %) isolates were susceptible to all TB drugs, 70 (26.7 %) were mono-resistant 16 (6.1 %) were poly-resistant, and 14 (5.4 %) were multi-drug resistant (MDR). The proportion of Beijing family isolates in the susceptible, mono-resistant, poly-resistant, and MDR groups was 33/162 (20.4 %), 28/70 (40.0 %), 6/16 (37.5 %), and 3/14 (21.4 %), respectively. Overall, resistance of the Beijing family isolates to any of the first line TB drugs was significantly higher than non-Beijing families [37/71 (52.1 %) vs. 63/191 (33.0 %) (p-value = 0.003)]. Conclusion The distribution of Mycobacterium tuberculosis genotypes in Indonesia showed high genetic diversity and tended to vary by geographic regions. Drug susceptibility testing confirmed that the Beijing family of M.tb in Indonesia exhibited greater resistance to first line anti-TB drugs than did other families.
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Affiliation(s)
- Vivi Lisdawati
- Institute for Vector and Reservoir Disease Control Research and Development (IVRDCRD), Salatiga, Indonesia.
| | - Nelly Puspandari
- Center for Biomedical and Basic Technology of Health (CBBTH), NIHRD, MoH-RI, Jakarta, Indonesia.
| | - Lutfah Rif'ati
- Center for Biomedical and Basic Technology of Health (CBBTH), NIHRD, MoH-RI, Jakarta, Indonesia.
| | - Triyani Soekarno
- Center for Biomedical and Basic Technology of Health (CBBTH), NIHRD, MoH-RI, Jakarta, Indonesia.
| | - Melatiwati M
- Center for Biomedical and Basic Technology of Health (CBBTH), NIHRD, MoH-RI, Jakarta, Indonesia.
| | - Syamsidar K
- Center for Biomedical and Basic Technology of Health (CBBTH), NIHRD, MoH-RI, Jakarta, Indonesia.
| | - Lies Ratnasari
- Department of Clinical Pathology, Dr. Hasan Sadikin Hospital, Bandung, Indonesia.
| | - Nur Izzatun
- Department of Clinical Pathology, Dr. Hasan Sadikin Hospital, Bandung, Indonesia.
| | - Ida Parwati
- Department of Clinical Pathology, Dr. Hasan Sadikin Hospital, Bandung, Indonesia.
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Azé J, Sola C, Zhang J, Lafosse-Marin F, Yasmin M, Siddiqui R, Kremer K, van Soolingen D, Refrégier G. Genomics and Machine Learning for Taxonomy Consensus: The Mycobacterium tuberculosis Complex Paradigm. PLoS One 2015; 10:e0130912. [PMID: 26154264 PMCID: PMC4496040 DOI: 10.1371/journal.pone.0130912] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 05/25/2015] [Indexed: 11/18/2022] Open
Abstract
Infra-species taxonomy is a prerequisite to compare features such as virulence in different pathogen lineages. Mycobacterium tuberculosis complex taxonomy has rapidly evolved in the last 20 years through intensive clinical isolation, advances in sequencing and in the description of fast-evolving loci (CRISPR and MIRU-VNTR). On-line tools to describe new isolates have been set up based on known diversity either on CRISPRs (also known as spoligotypes) or on MIRU-VNTR profiles. The underlying taxonomies are largely concordant but use different names and offer different depths. The objectives of this study were 1) to explicit the consensus that exists between the alternative taxonomies, and 2) to provide an on-line tool to ease classification of new isolates. Genotyping (24-VNTR, 43-spacers spoligotypes, IS6110-RFLP) was undertaken for 3,454 clinical isolates from the Netherlands (2004-2008). The resulting database was enlarged with African isolates to include most human tuberculosis diversity. Assignations were obtained using TB-Lineage, MIRU-VNTRPlus, SITVITWEB and an algorithm from Borile et al. By identifying the recurrent concordances between the alternative taxonomies, we proposed a consensus including 22 sublineages. Original and consensus assignations of the all isolates from the database were subsequently implemented into an ensemble learning approach based on Machine Learning tool Weka to derive a classification scheme. All assignations were reproduced with very good sensibilities and specificities. When applied to independent datasets, it was able to suggest new sublineages such as pseudo-Beijing. This Lineage Prediction tool, efficient on 15-MIRU, 24-VNTR and spoligotype data is available on the web interface “TBminer.” Another section of this website helps summarizing key molecular epidemiological data, easing tuberculosis surveillance. Altogether, we successfully used Machine Learning on a large dataset to set up and make available the first consensual taxonomy for human Mycobacterium tuberculosis complex. Additional developments using SNPs will help stabilizing it.
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Affiliation(s)
- Jérôme Azé
- LIRMM UM CNRS, UMR 5506, 860 rue de St Priest, 34095 Montpellier cedex 5, France
| | - Christophe Sola
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, rue Gregor Mendel, Bât 400, 91405 Orsay cedex, France
| | - Jian Zhang
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, rue Gregor Mendel, Bât 400, 91405 Orsay cedex, France
| | - Florian Lafosse-Marin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, rue Gregor Mendel, Bât 400, 91405 Orsay cedex, France
| | - Memona Yasmin
- Pakistan Institute for Engineering and Applied Sciences (PIEAS), Lehtrar Road, Nilore, Islamabad, Pakistan
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box # 577, Jhang Road, Faisalabad, Pakistan
| | - Rubina Siddiqui
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box # 577, Jhang Road, Faisalabad, Pakistan
| | - Kristin Kremer
- National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven, The Netherlands
| | - Dick van Soolingen
- National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven, The Netherlands
- Department of Pulmonary Diseases and Department of Microbiology, Radbout University Nijmegen Medical Centre, University Lung Centre Dekkerswald, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Guislaine Refrégier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, rue Gregor Mendel, Bât 400, 91405 Orsay cedex, France
- * E-mail:
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30
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Vasconcellos SEG, Acosta CC, Gomes LL, Conceição EC, Lima KV, de Araujo MI, Leite MDL, Tannure F, Caldas PCDS, Gomes HM, Santos AR, Gomgnimbou MK, Sola C, Couvin D, Rastogi N, Boechat N, Suffys PN. Strain classification of Mycobacterium tuberculosis isolates in Brazil based on genotypes obtained by spoligotyping, mycobacterial interspersed repetitive unit typing and the presence of large sequence and single nucleotide polymorphism. PLoS One 2014; 9:e107747. [PMID: 25314118 PMCID: PMC4196770 DOI: 10.1371/journal.pone.0107747] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Accepted: 08/21/2014] [Indexed: 11/26/2022] Open
Abstract
Rio de Janeiro is endemic for tuberculosis (TB) and presents the second largest prevalence of the disease in Brazil. Here, we present the bacterial population structure of 218 isolates of Mycobacterium tuberculosis, derived from 186 patients that were diagnosed between January 2008 and December 2009. Genotypes were generated by means of spoligotyping, 24 MIRU-VNTR typing and presence of fbpC103, RDRio and RD174. The results confirmed earlier data that predominant genotypes in Rio de Janeiro are those of the Euro American Lineages (99%). However, we observed differences between the classification by spoligotyping when comparing to that of 24 MIRU-VNTR typing, being respectively 43.6% vs. 62.4% of LAM, 34.9% vs. 9.6% of T and 18.3% vs. 21.5% of Haarlem. Among isolates classified as LAM by MIRU typing, 28.0% did not present the characteristic spoligotype profile with absence of spacers 21 to 24 and 32 to 36 and we designated these conveniently as “LAM-like”, 79.3% of these presenting the LAM-specific SNP fbpC103. The frequency of RDRio and RD174 in the LAM strains, as defined both by spoligotyping and 24 MIRU-VNTR loci, were respectively 11% and 15.4%, demonstrating that RD174 is not always a marker for LAM/RDRio strains. We conclude that, although spoligotyping alone is a tool for classification of strains of the Euro-American lineage, when combined with MIRU-VNTRs, SNPs and RD typing, it leads to a much better understanding of the bacterial population structure and phylogenetic relationships among strains of M. tuberculosis in regions with high incidence of TB.
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Affiliation(s)
- Sidra E. G. Vasconcellos
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
- Multidisciplinary Research Laboratory, University Hospital Clementino Fraga Filho – HUCFF, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Chyntia Carolina Acosta
- Laboratory of Cellular Microbiology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lia Lima Gomes
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Karla Valéria Lima
- Instituto Evandro Chagas, Section of Bacteriology and Mycology, Belém, Pará, Brazil
| | - Marcelo Ivens de Araujo
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maria de Lourdes Leite
- Hospital Municipal Rafael de Paula Souza, Municipal Secretary of Health, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Flávio Tannure
- Hospital Municipal Rafael de Paula Souza, Municipal Secretary of Health, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulo Cesar de Souza Caldas
- Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Publica Sergio Arouca, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Harrison M. Gomes
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Adalberto Rezende Santos
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Michel K. Gomgnimbou
- CNRS–Université Paris–Sud, Institut de Génétique et Microbiologie–Infection Genetics Emerging Pathogens Evolution Team, Orsay, France
| | - Christophe Sola
- CNRS–Université Paris–Sud, Institut de Génétique et Microbiologie–Infection Genetics Emerging Pathogens Evolution Team, Orsay, France
| | - David Couvin
- Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes, Guadeloupe, France
| | - Nalin Rastogi
- Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes, Guadeloupe, France
| | - Neio Boechat
- Multidisciplinary Research Laboratory, University Hospital Clementino Fraga Filho – HUCFF, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Graduate Program in Clinical Medicine, Faculty of Medicine, University Hospital Clementino Fraga Filho, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Philip Noel Suffys
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail:
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Mixed Mycobacterium tuberculosis complex infections and false-negative results for rifampin resistance by GeneXpert MTB/RIF are associated with poor clinical outcomes. J Clin Microbiol 2014; 52:2422-9. [PMID: 24789181 DOI: 10.1128/jcm.02489-13] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The Xpert MTB/RIF (Xpert) assay is becoming a principal screening tool for diagnosing rifampin-resistant Mycobacterium tuberculosis complex (MTBC) infection. However, little is known about the performance of the Xpert assay in infections with both drug-sensitive and drug-resistant strains (mixed MTBC infections). We assessed the performance of the Xpert assay for detecting rifampin resistance using phenotypic drug sensitivity testing (DST) as the reference standard in 370 patients with microbiologically proven pulmonary tuberculosis. Mixed MTBC infections were identified genetically through 24-locus mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) analysis. Logistic regression was used to identify the factors associated with poor (defined as treatment failure, default, and death from any cause) or good (defined as cure or successful treatment completion) clinical outcomes. The analytic sensitivity of the Xpert assay for detecting rifampin resistance was assessed in vitro by testing cultures containing different ratios of drug-sensitive and drug-resistant organisms. Rifampin resistance was detected by the Xpert assay in 52 (14.1%) and by phenotypic DST in 55 (14.9%) patients. Mixed MTBC infections were identified in 37 (10.0%) patients. The Xpert assay was 92.7% (95% confidence interval [CI], 82.4% to 97.9%) sensitive for detecting rifampin resistance and 99.7% (95% CI, 98.3% to 99.9%) specific. When restricted to patients with mixed MTBC infections, Xpert sensitivity was 80.0% (95% CI, 56.3 to 94.3%). False-negative Xpert results (adjusted odds ratio [aOR], 6.6; 95% CI,1.2 to 48.2) and mixed MTBC infections (aOR, 6.5; 95% CI, 2.1 to 20.5) were strongly associated with poor clinical outcome. The Xpert assay failed to detect rifampin resistance in vitro when <90% of the organisms in the sample were rifampin resistant. Our study indicates that the Xpert assay has an increased false-negative rate for detecting rifampin resistance with mixed MTBC infections. In hyperendemic settings where mixed infections are common, the Xpert results might need further confirmation.
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Prevalence and molecular characteristics of drug-resistant Mycobacterium tuberculosis in Hunan, China. Antimicrob Agents Chemother 2014; 58:3475-80. [PMID: 24733464 DOI: 10.1128/aac.02426-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To determine the prevalence and molecular characteristics of drug-resistant tuberculosis in Hunan province, drug susceptibility testing and spoligotyping methods were performed among 171 M. tuberculosis isolates. In addition, the mutated characteristics of 12 loci, including katG, inhA, rpoB, rpsL, nucleotides 388 to 1084 of the rrs gene [rrs(388-1084)], embB, pncA, tlyA, eis, nucleotides 1158 to 1674 of the rrs gene [rrs(1158-1674)], gyrA, and gyrB, among drug-resistant isolates were also analyzed by DNA sequencing. Our results indicated that the prevalences of isoniazid (INH), rifampin (RIF), streptomycin (SM), ethambutol (EMB), pyrazinamide (PZA), capreomycin (CAP), kanamycin (KAN), amikacin (AKM), and ofloxacin (OFX) resistance in Hunan province were 35.7%, 26.9%, 20.5%, 9.9% 15.2%, 2.3%, 1.8%, 1.2%, and 10.5%, respectively. The previously treated patients presented significantly increased risks for developing drug resistance. The majority of M. tuberculosis isolates belonged to the Beijing family. Almost all the drug resistance results demonstrated no association with genotype. The most frequent mutations of drug-resistant isolates were katG codon 315 (katG315), inhA15, rpoB531, rpoB526, rpoB516, rpsL43, rrs514, embB306, pncA96, rrs1401, gyrA94, and gyrA90. These results contribute to the knowledge of the prevalence of drug resistance in Hunan province and also expand the molecular characteristics of drug resistance in China.
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Molecular characterization of multidrug-resistant Mycobacterium tuberculosis isolates from China. Antimicrob Agents Chemother 2014; 58:1997-2005. [PMID: 24419342 DOI: 10.1128/aac.01792-13] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To investigate the molecular characterization of multidrug-resistant tuberculosis (MDR-TB) isolates from China and the association of specific mutations conferring drug resistance with strains of different genotypes, we performed spoligotyping and sequenced nine loci (katG, inhA, the oxyR-ahpC intergenic region, rpoB, tlyA, eis, rrs, gyrA, and gyrB) for 128 MDR-TB isolates. Our results showed that 108 isolates (84.4%) were Beijing family strains, 64 (59.3%) of which were identified as modern Beijing strains. Compared with the phenotypic data, the sensitivity and specificity of DNA sequencing were 89.1% and 100.0%, respectively, for isoniazid (INH) resistance, 93.8% and 100.0% for rifampin (RIF) resistance, 60.0% and 99.4% for capreomycin (CAP) resistance, 84.6% and 99.4% for kanamycin (KAN) resistance, and 90.0% and 100.0% for ofloxacin (OFX) resistance. The most prevalent mutations among the MDR-TB isolates were katG315, inhA15, rpoB531, -526, and -516, rrs1401, eis-10, and gyrA94, -90, and -91. Furthermore, there was no association between specific resistance-conferring mutations and the strain genotype. These findings will be helpful for the establishment of rapid molecular diagnostic methods to be implemented in China.
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Mozafari M, Farnia P, Afraei M, Derakhshani-Nezhad Z, Masjedi MR, Velayati AA. Molecular diversity of Mycobacterium tuberculosis strains indifferent provinces of Iran. IRANIAN JOURNAL OF MICROBIOLOGY 2013; 5:366-73. [PMID: 25848506 PMCID: PMC4385162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND AND OBJECTIVES Molecular epidemiology tools are widely used in determining epidemiology of tuberculosis. Spoligotyping is a molecular epidemiology method that is used for characterization and typing of Mycobacterium tuberculosis complex strains. The method is based on polymorphism of the chromosomal DR locus consisting of identical 36-bp DRs alternating with 35-41 unique spacers. The objective of this study was to investigate the prevalence of M. tuberculosis spoligotypes in different provinces of Iran. MATERIALS AND METHODS M. tuberculosis strains were isolated from TB patients of Mycobacteriology Research center (MRC). DNA was extracted from patient's clinical samples. PCR was performed by using of specific primers for DR region. The amplified DNA was hybridized to the spoligotyping Membrane. Hybridized DNA was detected with ECL detection kit and by exposing ECL Hyperfilm to the membrane. The obtained result was entered to a binary format and was analyzed using SpolDB4 database. RESULTS Spoligotyping resulted in 136 different patterns. Out of 1242 M. tuberculosis strains, 1165 strains (93.8%) were classified into 59 clusters and the remaining strains (6.2 %) were singleton. CONCLUSIONS The results of present study showed that strains of CAS family were more prevalent than other strains in Iran. Other prevalent families were Haarlem, T and Beijing, respectively.
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Affiliation(s)
- Mohadese Mozafari
- Corresponding author: Mohadese Mozafari M.Sc, Address: National Research Institute of Tuberculosis and Lung Disease, Shahid Beheshti University of Medical Sciences, Darabad, Tehran, Iran. Tel/Fax: +98-21-26109505,
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Mycobacterium tuberculosis is the causative agent of tuberculosis in the southern ecological zones of Cameroon, as shown by genetic analysis. BMC Infect Dis 2013; 13:431. [PMID: 24028382 PMCID: PMC3851856 DOI: 10.1186/1471-2334-13-431] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 09/03/2013] [Indexed: 11/10/2022] Open
Abstract
Background Tuberculosis (TB) is a major cause of mortality and suffering worldwide, with over 95% of TB deaths occurring in low- and middle-income countries. In recent years, molecular typing methods have been widely used in epidemiological studies to aid the control of TB, but this usage has not been the case with many African countries, including Cameroon. The aims of the present investigation were to identify and evaluate the diversity of the Mycobacterium tuberculosis complex (MTBC) isolates circulating in two ecological zones of Cameroon, seven years after the last studies in the West Region, and after the re-organization of the National TB Control Program (NTBCP). These were expected to shed light also on the transmission of TB in the country. The study was conducted from February to July 2009. During this period, 169 patients with symptomatic disease and with sputum cultures that were positive for MTBC were randomly selected for the study from amongst 964 suspected patients in the savannah mosaic zone (West and North West regions) and the tropical rainforest zone (Central region). After culture and diagnosis, DNA was extracted from each of the MTBC isolates and transported to the BecA-ILRI Hub in Nairobi, Kenya for molecular analysis. Methods Genetic characterization was done by mycobacterial interspersed repetitive unit–variable number tandem repeat typing (MIRU-VNTR) and Spoligotyping. Results Molecular analysis showed that all TB cases reported in this study were caused by infections with Mycobacterium tuberculosis (98.8%) and Mycobacterium africanum (M. africanum) (1.2%) respectively. We did not detect any M. bovis. Comparative analyses using spoligotyping revealed that the majority of isolates belong to major clades of M. tuberculosis: Haarlem (7.6%), Latin American-Mediterranean (34.4%) and T clade (26.7%); the remaining isolates (31.3%) where distributed among the minor clades. The predominant group of isolates (34.4%) corresponded to spoligotype 61, previously described as the “Cameroon family. Further analysis based on MIRU-VNTR profiles had greater resolving power than spoligotyping and defined additional genotypes in the same spoligotype cluster. Conclusion The molecular characterization of MTBC strains from humans in two ecological regions of Cameroon has shown that M. tuberculosis sensu stricto is the predominant agent of TB cases in the zones. Three decades ago, TB was reported to be caused by M. africanum in 56.0% of cases. The present findings are consistent with a major shift in the prevalence of M. tuberculosis in Cameroon.
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Bedrossian N, Rahmo A, Karam W, Hamze M. Mycobacterium tuberculosis spoligotypes circulating in the Syrian population: A retrospective study. Int J Mycobacteriol 2013; 2:141-7. [DOI: 10.1016/j.ijmyco.2013.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 05/26/2013] [Indexed: 11/15/2022] Open
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Genetic variability of Mycobacterium tuberculosis complex in patients with no known risk factors for MDR-TB in the North-Eastern part of Lima, Peru. BMC Infect Dis 2013; 13:397. [PMID: 23984854 PMCID: PMC3765759 DOI: 10.1186/1471-2334-13-397] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 08/21/2013] [Indexed: 11/12/2022] Open
Abstract
Background The aim of this study was to investigate the genetic diversity among Mycobacterium tuberculosis complex circulating in patients with no known risk factors for multi-drug resistant (MDR) tuberculosis (TB) living in a high MDR burden area and analyze the relationship between genotypes, primary drug resistance and age. Methods Samples were collected during January-July 2009. Isolates were tested for drug susceptibility to first-line drugs and were genotyped by spoligotyping and the 15-loci Mycobacterial Interspersed Repetitive Unit (MIRU15). Results Among the 199 isolates analyzed, 169 (84.9%) were identified in the SpolDB4.0 and 30 (15.1%) could not be matched to any lineage. The most prevalent lineage was Haarlem (29.6%), followed by T (15.6%), Beijing (14.1%), Latin American Mediterranean (12.6%) and U (8.5%). A few isolates belonged to the X and S clades (4.5%). Spoligotype analysis identified clustering among 148 of 169 isolates, whereas with MIRU15 all isolates were unique. Out of 197 strains; 31.5% were resistant to at least one drug, 7.5% were MDR and 22.3% showed any resistance to isoniazid. Conclusion In contrast with other Latin-American countries where LAM lineage is the most predominant, we found the spoligotype 50 from the Haarlem lineage as the most common. None of the prevailing lineages showed a significant association with age or resistance to isoniazid and/or rifampicin.
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Huyen MNT, Buu TN, Tiemersma E, Lan NTN, Dung NH, Kremer K, Soolingen DV, Cobelens FGJ. Tuberculosis relapse in Vietnam is significantly associated with Mycobacterium tuberculosis Beijing genotype infections. J Infect Dis 2013; 207:1516-24. [PMID: 23408848 DOI: 10.1093/infdis/jit048] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND In Vietnam, the Mycobacterium tuberculosis Beijing genotype is associated with multi-drug resistance and is emerging. A possible explanation for this genotype's success is an increased rate of relapse. METHODS In a prospective cohort study, isolates from patients with smear-positive tuberculosis were subjected to drug susceptibility testing and to spoligotyping and variable number of tandem repeats typing before treatment and after recurrence of tuberculosis. RESULTS Among 1068 patients who were actively followed up over 18 months for recurrence, 23 relapse cases occurred (1.39 cases/100 person-years). After adjustment for genotype, tuberculosis treatment history, and drug resistance, relapse was significantly associated with the Beijing genotype (adjusted hazard ratio [aHR], 5.48; 95% confidence interval [CI], 2.06-14.55) and isoniazid resistance (aHR, 5.91; 95% CI, 2.16-16.16). CONCLUSIONS The strongly increased relapse rate in tuberculosis cases caused by Beijing strains probably contributes to the successful spread of this genotype in Vietnam and elsewhere.
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Characterization of extensively drug-resistant Mycobacterium tuberculosis in Nepal. Tuberculosis (Edinb) 2012; 93:84-8. [PMID: 23146281 DOI: 10.1016/j.tube.2012.10.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Revised: 10/12/2012] [Accepted: 10/15/2012] [Indexed: 11/21/2022]
Abstract
The emergence of extensively drug-resistant tuberculosis (XDR-TB) has raised public health concern for global control of TB. Although molecular characterization of drug resistance-associated mutations in multidrug-resistant isolates in Nepal has been made, mutations in XDR isolates and their genotypes have not been reported previously. In this study, we identified and characterized 13 XDR Mycobacterium tuberculosis isolates from clinical isolates in Nepal. The most prevalent mutations involved in rifampicin, isoniazid, ofloxacin, and kanamycin/capreomycin resistance were Ser531Leu in rpoB gene (92.3%), Ser315Thr in katG gene (92.3%), Asp94Gly in gyrA gene (53.9%) and A1400G in rrs gene (61.5%), respectively. Spoligotyping and multilocus sequence typing revealed that 69% belonged to Beijing family, especially modern types. Further typing with 26-loci variable number of tandem repeats suggested the current spread of XDR M. tuberculosis. Our result highlights the need to reinforce the TB policy in Nepal with regard to control and detection strategies.
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Lahlou O, Millet J, Chaoui I, Sabouni R, Filali-Maltouf A, Akrim M, El Mzibri M, Rastogi N, El Aouad R. The genotypic population structure of Mycobacterium tuberculosis complex from Moroccan patients reveals a predominance of Euro-American lineages. PLoS One 2012; 7:e47113. [PMID: 23077552 PMCID: PMC3471964 DOI: 10.1371/journal.pone.0047113] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 09/12/2012] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) remains a major health problem in Morocco. Characterization of circulating Mycobacterium tuberculosis genotypic lineages, important to understand the dynamic of the disease, was hereby addressed for the first time at a national level. METHODOLOGY/PRINCIPAL FINDINGS Spoligotyping was performed on a panel of 592 M. tuberculosis complex strains covering a 2-year period (2004-2006). It identified 129 patterns: 105 (n = 568 strains) corresponded to a SIT number in the SITVIT2 database, while 24 patterns were labeled as orphan. A total of 523 (88.3%) strains were clustered vs. 69 or 11.7% unclustered. Classification of strains within 3 large phylogenetical groups was as follows: group 1- ancestral/TbD1+/PGG1 (EAI, Bovis, Africanum), group 2- modern/TbD1-/PGG1 group (Beijing, CAS), group 3- evolutionary recent/TbD1-/PGG2/3 (Haarlem, X, S, T, LAM; alternatively designated as the Euro-American lineage). As opposed to group 3 strains (namely LAM, Haarlem, and T) that predominated (86.5% of all isolates), 6 strains belonged to group 2 (Beijing n = 5, CAS n = 1), and 3 strains (BOV_1 n = 2, BOV_4-CAPRAE) belonged to ancestral group 1 (EAI and AFRI lineage strains were absent). 12-loci MIRU-VNTR typing of the Casablanca subgroup (n = 114 strains) identified 71 patterns: 48 MITs and 23 orphan patterns; it allowed to reduce the clustering rate from 72.8% to 29.8% and the recent transmission rate from 64% to 20.2%. CONCLUSION The M. tuberculosis population structure in Morocco is highly homogeneous, and is characterized by the predominance of the Euro-American lineages, namely LAM, Haarlem, and T, which belong to the "evolutionary recent" TbD1-/PGG2/3 phylogenetic group. The combination of spoligotyping and MIRUs decreased the clustering rate significantly, and should now be systematically applied in larger studies. The methods used in this study appear well suited to monitor the M. tuberculosis population structure for an enhanced TB management program in Morocco.
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Affiliation(s)
- Ouafae Lahlou
- National Tuberculosis Reference Laboratory, National Institute of Hygiene, Rabat, Morocco
| | - Julie Millet
- WHO Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes, Guadeloupe, France
| | - Imane Chaoui
- Biology and Medical Research Unit, National Centre of Energy, Nuclear Sciences and Techniques, Rabat, Morocco
| | - Radia Sabouni
- National Tuberculosis Reference Laboratory, National Institute of Hygiene, Rabat, Morocco
| | - Abdelkarim Filali-Maltouf
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, University of Mohammed V-Agdal, Rabat, Morocco
| | - Mohammed Akrim
- National Tuberculosis Reference Laboratory, National Institute of Hygiene, Rabat, Morocco
| | - Mohammed El Mzibri
- Biology and Medical Research Unit, National Centre of Energy, Nuclear Sciences and Techniques, Rabat, Morocco
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes, Guadeloupe, France
| | - Rajae El Aouad
- National Tuberculosis Reference Laboratory, National Institute of Hygiene, Rabat, Morocco
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Zhao Y, Li H, Xing J, Yang H, Ma X, Xu J, Shi J, Yan G. Molecular typing of Mycobacterium tuberculosis isolates circulating in Henan, central China. Exp Ther Med 2012; 4:949-953. [PMID: 23226754 PMCID: PMC3493818 DOI: 10.3892/etm.2012.699] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 09/03/2012] [Indexed: 11/06/2022] Open
Abstract
The aim of this study was to characterize the genotypes of Mycobacterium tuberculosis (MT) in isolates obtained from Henan, China, and to study the distribution features of Beijing strains in Henan. A total of 443 MT strains isolated in Henan Province were tested for susceptibility to isonicotinylhydrazide (INH), rifampicin (RFP), ethambutol (EMB) and streptomycin (SM), and genotyped by spoligotyping. The clustering of genotypes revealed 4 gene clusters (Beijing and Beijing-like, T, Manu, and S and LAM3) and 24 genotypes. In total, 387 (87.4%) of the strains were Beijing strains. The frequency of multidrug-resistant (MDR) strains was significantly higher in the Beijing and Beijing-like strains than in the other strains (χ(2)=4.6564, P<0.05). However, the percentages of drug resistance and sensitivity in the Beijing strains were almost the same as those in the non-Beijing strains. The proportion of Beijing strains in the ≤60-year-old TB patients was significantly higher than in the >60-year-old TB patients (χ(2)=32.053, P<0.001). The distribution of Beijing strains deceased gradually from the east to the west in Henan Province (P<0.0001). The data demonstrate that the Beijing genotype is a major type in the area and may be related to enhanced transmissibility. The transmission of Beijing family strains has increased in Henan and its incidence is highest in the east of Henan. The MDR strains were significant in the spread of MT.
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Affiliation(s)
- Yuling Zhao
- Center for Disease Control and Prevention of Henan Province, Zhengzhou, Henan 450016, P.R. China
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Mihret A, Bekele Y, Aytenew M, Assefa Y, Abebe M, Wassie L, Loxton GA, Yamuah L, Aseffa A, Walzl G, Howe R. Modern lineages of Mycobacterium tuberculosis in Addis Ababa, Ethiopia: implications for the tuberculosis control programe. Afr Health Sci 2012; 12:339-44. [PMID: 23382750 DOI: 10.4314/ahs.v12i3.15] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND The genotyping of Mycobacterium tuberculosis strains is important to have unique insights into the dissemination dynamics and evolutionary genetics of this pathogen and for TB control as it allows the detection of suspected outbreaks and the tracing of transmission chains. OBJECTIVE To characterize M. tuberculois isolates collected from newly diagnosed pulmonary TB patients in Addis Ababa METHODS One hundred and ninety two sputum samples were cultured on Löwenstein-Jensen (LJ) slants and isolates were heat killed for molecular genotyping. The isolates were characterized using spoligotyping and were compared with the International SpoIDB4 database. RESULT T genotype constitutes the most predominant in our study (95, 49.5%) followed by the CAS genotype (42, 21.9%). Other genotypes found were Haarlem (H) (24, 12.5%), the LAM (3, 1.5%), the Beijing genotype (1, 0.5%); four (2.1%) isolates were designated as Unknown. CONCLUSION All the isolates belong to the modern lineage and there is high clustering in the genotype of isolates which indicated the presence of recent TB transmission. Therefore, the Tuberculosis Control Programme needs to do more in advocating and strengthening the health system for early detection and treatment of active TB cases as delay in treatment is the key factor in disease transmission.
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Affiliation(s)
- A Mihret
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia.
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Sürücüoğlu S, Günal S, Ozkütük N, Biçmen C, Ozsöz A, Gazi H, Durmaz R. Molecular diversity of drug resistant mycobacterium tuberculosis strains in Western Turkey. Balkan Med J 2012; 29:160-5. [PMID: 25206987 DOI: 10.5152/balkanmedj.2012.012] [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: 06/20/2011] [Accepted: 02/14/2012] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE The aim of this study was to investigate the molecular diversity and clonal relationship of drug resistant Mycobacterium tuberculosis strains isolated in Western Turkey. MATERIALS AND METHODS A total of 87 strains isolated between 2006 and 2009, eight of which were rifampicin monoresistant and 79 were multidrug resistant, were analyzed with IS6110 RFLP and spoligotyping methods. RESULTS The results of spoligotyping showed that 7% of the strains were orphans, and 8% were undefined for family in the SpolDB4 database. Major families of the strains were LAM (38%), T (35%), Haarlem (7%), Beijing (2%), S (2%) and U (1%) families. The clustering rate by spoligotyping was calculated as 75%. The most predominant SIT cluster was SIT41 (29%). According to the results of IS6110 RFLP, 71 different patterns of IS6110 were observed. Low copy number was found in 26% of the strains. When the results of two methods were combined, the final clustering rate was calculated as 26%. CONCLUSIONS The genotypical distribution of drug resistant tuberculosis isolates in our region indicates genetic diversity and the clustering rate was found low in our region. However, more comprehensive and long-term molecular epidemiological studies are needed to control the drug resistant strains.
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Affiliation(s)
- Süheyla Sürücüoğlu
- Department of Medical Microbiology, Faculty of Medicine, Celal Bayar University, Manisa, Turkey
| | - Selami Günal
- Department of Medical Microbiology, Faculty of Medicine, İnönü University, Malatya, Turkey
| | - Nuri Ozkütük
- Department of Medical Microbiology, Faculty of Medicine, Celal Bayar University, Manisa, Turkey
| | - Can Biçmen
- Department of Medical Microbiology, Dr. Suat Seren Chest Diseases and Surgery Training and Research Hospital, İzmir, Turkey
| | - Ayşe Ozsöz
- Department of Tuberculosis and Chest Diseases, Dr. Suat Seren Chest Diseases and Surgery Training and Research Hospital, İzmir, Turkey
| | - Hörü Gazi
- Department of Medical Microbiology, Faculty of Medicine, Celal Bayar University, Manisa, Turkey
| | - Rıza Durmaz
- Department of Medical Microbiology, Faculty of Medicine, İnönü University, Malatya, Turkey
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Garzelli C, Rindi L. Molecular epidemiological approaches to study the epidemiology of tuberculosis in low-incidence settings receiving immigrants. INFECTION GENETICS AND EVOLUTION 2012; 12:610-8. [DOI: 10.1016/j.meegid.2011.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Revised: 10/17/2011] [Accepted: 10/18/2011] [Indexed: 10/15/2022]
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Molecular characterization and second-line antituberculosis drug resistance patterns of multidrug-resistant Mycobacterium tuberculosis isolates from the northern region of South Africa. J Clin Microbiol 2012; 50:2857-62. [PMID: 22649019 DOI: 10.1128/jcm.00358-12] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite South Africa being one of the high-burden multidrug-resistant tuberculosis (MDR-TB) countries, information regarding the population structure of drug-resistant Mycobacterium tuberculosis strains is limited from many regions of South Africa. This study investigated the population structure and transmission patterns of drug-resistant M. tuberculosis isolates in a high-burden setting of South Africa as well as the possible association of genotypes with drug resistance and demographic characteristics. A total of 336 consecutive MDR-TB isolates from four provinces of South Africa were genotyped using spoligotyping and mycobacterial interspersed repetitive-unit-variable number tandem repeat (MIRU-VNTR) typing. Drug susceptibility testing for ofloxacin, kanamycin, and capreomycin was performed using the agar proportion method. The results showed that 4.8% of MDR-TB isolates were resistant to ofloxacin, 2.7% were resistant to kanamycin, and 4.5% were resistant to capreomycin, while 7.1% were extensively drug resistant (XDR), and the remaining 83.6% were susceptible to all of the second-line drugs tested. Spoligotyping grouped 90.8% of the isolates into 25 clusters, while 9.2% isolates were unclustered. Ninety-one percent of the 336 isolates were assigned to 21 previously described shared types, with the Beijing family being the predominant genotype in the North-West and Limpopo Provinces, while the EAI1_SOM family was the predominant genotype in the Gauteng and Mpumalanga Provinces. No association was found between genotypes and specific drug resistance patterns or demographic information. The high level of diversity and the geographical distribution of the drug-resistant M. tuberculosis isolates in this study suggest that the transmission of TB in the study settings is not caused by the clonal spread of a specific M. tuberculosis strain.
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Shabbeer A, Cowan LS, Ozcaglar C, Rastogi N, Vandenberg SL, Yener B, Bennett KP. TB-Lineage: an online tool for classification and analysis of strains of Mycobacterium tuberculosis complex. INFECTION GENETICS AND EVOLUTION 2012; 12:789-97. [PMID: 22406225 DOI: 10.1016/j.meegid.2012.02.010] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 02/18/2012] [Accepted: 02/21/2012] [Indexed: 11/19/2022]
Abstract
This paper formulates a set of rules to classify genotypes of the Mycobacterium tuberculosis complex (MTBC) into major lineages using spoligotypes and MIRU-VNTR results. The rules synthesize prior literature that characterizes lineages by spacer deletions and variations in the number of repeats seen at locus MIRU24 (alias VNTR2687). A tool that efficiently and accurately implements this rule base is now freely available at http://tbinsight.cs.rpi.edu/run_tb_lineage.html. When MIRU24 data is not available, the system utilizes predictions made by a Naïve Bayes classifier based on spoligotype data. This website also provides a tool to generate spoligoforests in order to visualize the genetic diversity and relatedness of genotypes and their associated lineages. A detailed analysis of the application of these tools on a dataset collected by the CDC consisting of 3198 distinct spoligotypes and 5430 distinct MIRU-VNTR types from 37,066 clinical isolates is presented. The tools were also tested on four other independent datasets. The accuracy of automated classification using both spoligotypes and MIRU24 is >99%, and using spoligotypes alone is >95%. This online rule-based classification technique in conjunction with genotype visualization provides a practical tool that supports surveillance of TB transmission trends and molecular epidemiological studies.
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Affiliation(s)
- Amina Shabbeer
- Computer Science Dept., Rensselaer Polytechnic Institute, Troy, NY, USA.
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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: 27] [Impact Index Per Article: 2.3] [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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48
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Characterization of mutations conferring extensive drug resistance to Mycobacterium tuberculosis isolates in Pakistan. Antimicrob Agents Chemother 2011; 55:5654-9. [PMID: 21911575 DOI: 10.1128/aac.05101-11] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The increasing incidence of extensively drug-resistant (XDR) Mycobacterium tuberculosis in high-tuberculosis-burden countries further highlights the need for improved rapid diagnostic assays. An increasing incidence of XDR M. tuberculosis strains in Pakistan has been reported, but drug resistance-associated mutations in these strains have not been evaluated previously. We sequenced the "hot-spot" regions of rpoB, katG, inhA, ahpC, gyrA, gyrB, and rrs genes in 50 XDR M. tuberculosis strains. It was observed that 2% of rifampin, 6% of isoniazid, 24% of fluoroquinolone, and 32% of aminoglycoside/capreomycin resistance in XDR M. tuberculosis strains would be undetected if only these common hot-spot regions were tested. The frequencies of resistance-conferring mutations were found to be comparable among all XDR M. tuberculosis strain families present, including the Central Asian Strain, Beijing, and East African Indian genogroups and the Unique isolates. Additional genetic loci need to be tested for detection of mutations conferring fluoroquinolone, aminoglycoside, and capreomycin resistance in order to improve molecular diagnosis of regional XDR M. tuberculosis strains.
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Shabbeer A, Ozcaglar C, Yener B, Bennett KP. Web tools for molecular epidemiology of tuberculosis. INFECTION GENETICS AND EVOLUTION 2011; 12:767-81. [PMID: 21903179 DOI: 10.1016/j.meegid.2011.08.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 08/14/2011] [Accepted: 08/19/2011] [Indexed: 01/03/2023]
Abstract
In this study we explore publicly available web tools designed to use molecular epidemiological data to extract information that can be employed for the effective tracking and control of tuberculosis (TB). The application of molecular methods for the epidemiology of TB complement traditional approaches used in public health. DNA fingerprinting methods are now routinely employed in TB surveillance programs and are primarily used to detect recent transmissions and in outbreak investigations. Here we present web tools that facilitate systematic analysis of Mycobacterium tuberculosis complex (MTBC) genotype information and provide a view of the genetic diversity in the MTBC population. These tools help answer questions about the characteristics of MTBC strains, such as their pathogenicity, virulence, immunogenicity, transmissibility, drug-resistance profiles and host-pathogen associativity. They provide an integrated platform for researchers to use molecular epidemiological data to address current challenges in the understanding of TB dynamics and the characteristics of MTBC.
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Affiliation(s)
- Amina Shabbeer
- Department of Mathematical Science, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
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50
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Mendes NH, Melo FAF, Santos ACB, Pandolfi JRC, Almeida EA, Cardoso RF, Berghs H, David S, Johansen FK, Espanha LG, Leite SRA, Leite CQF. Characterization of the genetic diversity of Mycobacterium tuberculosis in São Paulo city, Brazil. BMC Res Notes 2011; 4:269. [PMID: 21801364 PMCID: PMC3160979 DOI: 10.1186/1756-0500-4-269] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 07/29/2011] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Tuberculosis is a major health problem in São Paulo, Brazil, which is the most populous and one of the most cosmopolitan cities in South America. To characterize the genetic diversity of Mycobacterium tuberculosis in the population of this city, the genotyping techniques of spoligotyping and MIRU were applied to 93 isolates collected in two consecutive years from 93 different tuberculosis patients residing in São Paulo city and attending the Clemente Ferreira Institute (the reference clinic for the treatment of tuberculosis). FINDINGS Spoligotyping generated 53 different spoligotype patterns. Fifty-one isolates (54.8%) were grouped into 13 spoligotyping clusters. Seventy- two strains (77.4%) showed spoligotypes described in the international databases (SpolDB4, SITVIT), and 21 (22.6%) showed unidentified patterns. The most frequent spoligotype families were Latin American Mediterranean (LAM) (26 isolates), followed by the T family (24 isolates) and Haarlem (H) (11 isolates), which together accounted for 65.4% of all the isolates. These three families represent the major genotypes found in Africa, Central America, South America and Europe. Six Spoligo-International-types (designated SITs by the database) comprised 51.8% (37/72) of all the identified spoligotypes (SIT53, SIT50, SIT42, SIT60, SIT17 and SIT1). Other SITs found in this study indicated the great genetic diversity of M. tuberculosis, reflecting the remarkable ethnic diversity of São Paulo city inhabitants. The MIRU technique was more discriminatory and did not identify any genetic clusters with 100% similarity among the 93 isolates. The allelic analysis showed that MIRU loci 26, 40, 23 and 10 were the most discriminatory. When MIRU and spoligotyping techniques were combined, all isolates grouped in the 13 spoligotyping clusters were separated. CONCLUSIONS Our data indicated the genomic stability of over 50% of spoligotypes identified in São Paulo and the great genetic diversity of M. tuberculosis isolates in the remaining SITs, reflecting the large ethnic mix of the São Paulo city inhabitants. The results also indicated that in this city, M. tuberculosis isolates acquired drug resistance independently of genotype and that resistance was more dependent on the selective pressure of treatment failure and the environmental circumstances of patients.
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Affiliation(s)
- Natália H Mendes
- Laboratory of Micobacteriology, Faculty of Pharmacy, São Paulo State University at Araraquara, UNESP. Araraquara-Jaú Road Km 01, Araraquara, SP, 14801-902, Brazil
| | - Fernando AF Melo
- Clemente Ferreira Institute. 717 Consolação St, São Paulo, SP, 01301-000, Brazil
| | - Adolfo CB Santos
- Laboratory of Micobacteriology, Faculty of Pharmacy, São Paulo State University at Araraquara, UNESP. Araraquara-Jaú Road Km 01, Araraquara, SP, 14801-902, Brazil
| | - José RC Pandolfi
- Laboratory of Micobacteriology, Faculty of Pharmacy, São Paulo State University at Araraquara, UNESP. Araraquara-Jaú Road Km 01, Araraquara, SP, 14801-902, Brazil
| | - Elisabete A Almeida
- Clemente Ferreira Institute. 717 Consolação St, São Paulo, SP, 01301-000, Brazil
| | - Rosilene F Cardoso
- State University of Maringá. 5790 Colombo Ave, Maringá, PR, 87020-900, Brazil
| | - Henri Berghs
- Fairport Ltda. 293 Jacarandá St, São Paulo, SP, 04926-160, Brazil
| | - Suzana David
- National Institute of Heath Dr. Ricardo Jorge. Padre Cruz Ave, Lisbon, 1649-016, Portugal
| | - Faber K Johansen
- Laboratory of Micobacteriology, Faculty of Pharmacy, São Paulo State University at Araraquara, UNESP. Araraquara-Jaú Road Km 01, Araraquara, SP, 14801-902, Brazil
| | - Lívia G Espanha
- Laboratory of Micobacteriology, Faculty of Pharmacy, São Paulo State University at Araraquara, UNESP. Araraquara-Jaú Road Km 01, Araraquara, SP, 14801-902, Brazil
| | - Sergio RA Leite
- Institute of Chemistry, São Paulo State University at Araraquara, UNESP, 55 Prof. Francisco Degni St, Araraquara, SP, 14800-060, Brazil
| | - Clarice QF Leite
- Laboratory of Micobacteriology, Faculty of Pharmacy, São Paulo State University at Araraquara, UNESP. Araraquara-Jaú Road Km 01, Araraquara, SP, 14801-902, Brazil
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