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Bakuła Z, Wuyep VB, Bartocha Ł, Vyazovaya A, Ikeh EI, Bielecki J, Mokrousov I, Jagielski T. Molecular snapshot of drug-resistant Mycobacterium tuberculosis strains from the Plateau State, Nigeria. PLoS One 2022; 17:e0266837. [PMID: 35609028 PMCID: PMC9129033 DOI: 10.1371/journal.pone.0266837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 03/29/2022] [Indexed: 11/18/2022] Open
Abstract
Nigeria ranks 1st in Africa and 6th globally with the highest burden of tuberculosis (TB). However, only a relatively few studies have addressed the molecular epidemiology of Mycobacterium tuberculosis in this country. The aim of this work was to analyze the genetic structure of drug-resistant (DR) M. tuberculosis population in the Plateau State (central Nigeria), with the results placed in the broader context of West Africa. The study sample included 67 DR M. tuberculosis isolates, recovered from as many TB patients between November 2015 and January 2016, in the Plateau State. The isolates were subjected to spoligotyping and MIRU-VNTR typing. A total of 20 distinct spoligotypes were obtained, split into 3 clusters (n = 50, 74.6%, 2–33 isolates per cluster) and 17 (25.4%) unique patterns. The Cameroon clade was the largest lineage (62.7%) followed by T (28.3%), LAM (3%), and Haarlem (3%) clades. Upon MIRU-VNTR typing, the isolates produced 31 profiles, i.e. 7 clusters (n = 43, 64.2%, 2–17 isolates per cluster) and 24 singletons. A combined spoligotyping and MIRU-VNTR typing analysis showed 20.9% of the cases clustered and estimated the recent transmission rate at 11.9%. In conclusion, two lineages, namely Cameroon, and T accounted for the majority (91%) of cases. No association was observed between the most prevalent Cameroon lineage and drug resistance, including multidrug resistant (MDR) phenotype, or any of the patient demographic characteristics.
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Affiliation(s)
- Zofia Bakuła
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | | | - Łukasz Bartocha
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Anna Vyazovaya
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Eugene I. Ikeh
- Department of Medical Microbiology, School of Medical and Health Sciences, College of Medical Sciences, University of Jos, Jos, Nigeria
| | - Jacek Bielecki
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
- * E-mail: (IM); (TJ)
| | - Tomasz Jagielski
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- * E-mail: (IM); (TJ)
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Singh J, Singh N, Suresh G, Srivastava R, Aggarwal U, Behera D, Munisamy M, Malhotra AG, Singh S. A comparative analysis of molecular genotypes of Mycobacterium tuberculosis isolates from HIV-positive and HIV-negative patients. Front Cell Infect Microbiol 2022; 12:953443. [PMID: 36310875 PMCID: PMC9597297 DOI: 10.3389/fcimb.2022.953443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/30/2022] [Indexed: 02/05/2023] Open
Abstract
SETTING Tuberculosis Research Laboratory, Division of Clinical Microbiology and Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences, and the National Institute of Tuberculosis and Respiratory Diseases (NITRD), both situated in New Delhi. OBJECTIVES We aimed to identify the distribution of various genotypes of M. tuberculosis among HIV-positive and HIV-negative patients suspected of having Tuberculosis, seen at the National Institute of Tuberculosis and Respiratory Diseases, New Delhi, which is a tertiary care dedicated TB hospital. PATIENTS AND METHODS Genotyping by Spoligotyping and 24 loci MIRU-VNTR was performed and analyzed using SITVITWEB and MIRU-VNTRplus. Drug susceptibility patterns were also analyzed. RESULTS A total of 503 subjects who were PTB/EPTB suspected were recruited and 287 were culture positive. Among them, 276 had growth of Mycobacterium tuberculosis (MTB) and in 11 patients non-tuberculous mycobacteria (NTM) were grown. The isolation rate of NTM was predominantly from HIV positive [10 of 130 (7.6%)] patients. Of the total isolates of MTB, 156 (56.5%) were from HIV negative patients and 120 (43.5%) were from HIV positive patients. All 276 M. tuberculosis isolates were genotyped and tested for drug susceptibility patterns. The CAS genotype was most predominant [153 (55.4%)], followed by Beijing lineage [44 (15.9%)], East African India [25 (9.1%)] and others [54 (19.6%)]. Beijing genotype was significantly more common in HIV positive patients (22.5%) than in HIV negative patients (10.9%). In MIRU-VNTR analysis, clustering was found to be more frequent in CAS strains irrespective of HIV status. In the HIV positive group, spoligotyping could differentiate various genotypes in 90% of isolates and MIRU-VNTR analysis in 84.2% of isolates. The clustering of various MTB strains was more associated with drug resistance. CONCLUSION The Beijing lineage was predominant in HIV-TB coinfected cases, even though the Central Asian Strain (CAS) was overall more predominant in the region.
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Affiliation(s)
- Jitendra Singh
- Division of Clinical Microbiology and Molecular Medicine, All India Institute of Medical Sciences, New Delhi, India
- Translational Medicine Centre, All India Institute of Medical Sciences, Bhopal, India
| | - Niti Singh
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases (NITRD), New Delhi, India
| | - Gayatri Suresh
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases (NITRD), New Delhi, India
| | - Rahul Srivastava
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases (NITRD), New Delhi, India
| | - Upasna Aggarwal
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases (NITRD), New Delhi, India
| | - Digamber Behera
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases (NITRD), New Delhi, India
- Department of Pulmonary Medicine, PGIMER, Chandigarh, India
| | - Murali Munisamy
- Translational Medicine Centre, All India Institute of Medical Sciences, Bhopal, India
| | | | - Sarman Singh
- Division of Clinical Microbiology and Molecular Medicine, All India Institute of Medical Sciences, New Delhi, India
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal, India
- Medical Science and Engineering Research Centre, Indian Institute of Science Education and Research, Bhopal, India
- *Correspondence: Sarman Singh, ;
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Olawoye IB, Uwanibe JN, Kunle-Ope CN, Davies-Bolorunduro OF, Abiodun TA, Audu RA, Salako BL, Happi CT. Whole genome sequencing of clinical samples reveals extensively drug resistant tuberculosis (XDR TB) strains from the Beijing lineage in Nigeria, West Africa. Sci Rep 2021; 11:17387. [PMID: 34462504 PMCID: PMC8405707 DOI: 10.1038/s41598-021-96956-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022] Open
Abstract
Multi-drug (MDR) and extensively drug-resistant (XDR) tuberculosis (TB) continues to be a global public health problem especially in high TB burden countries like Nigeria. Many of these cases are undetected and go on to infect high risk individuals. Clinical samples from positive rifampicin resistant Xpert®MTB/Rif assay were subjected to direct whole genome sequencing and bioinformatics analysis to identify the full antibiotics resistance and lineage profile. We report two (2) XDR TB samples also belonging to the East-Asian/Beijing family of lineage 2 Mycobacterium tuberculosis complex from clinical samples in Nigeria. Our findings further reveal the presence of mutations that confer resistance to first-line drugs (rifampicin, isoniazid, ethambutol and pyrazanimide), second-line injectables (capreomycin, streptomycin, kanamycin and/or amikacin) and at least one of the fluoroquinolones (ofloxacin, moxifloxacin, levofloxacin and/or ciprofloxacin) in both samples. The genomic sequence data from this study not only provide the first evidence of XDR TB in Nigeria and West Africa, but also emphasize the importance of WGS in accurately detecting MDR and XDR TB, to ensure adequate and proper management treatment regimens for affected individuals. This will greatly aid in preventing the spread of drug resistance TB in high burden countries.
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Affiliation(s)
- Idowu B Olawoye
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Jessica N Uwanibe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Chioma N Kunle-Ope
- Centre for Tuberculosis Research (CTBR), Microbiology Department, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos State, Nigeria
| | - Olabisi F Davies-Bolorunduro
- Centre for Tuberculosis Research (CTBR), Microbiology Department, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos State, Nigeria
| | - Temitope A Abiodun
- Centre for Tuberculosis Research (CTBR), Microbiology Department, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos State, Nigeria
| | - Rosemary A Audu
- Centre for Tuberculosis Research (CTBR), Microbiology Department, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos State, Nigeria
| | - Babatunde L Salako
- Centre for Tuberculosis Research (CTBR), Microbiology Department, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos State, Nigeria
| | - Christian T Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria.
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Kone B, Somboro AM, Holl JL, Baya B, Togo AACG, Sarro YDS, Diarra B, Kodio O, Murphy RL, Bishai W, Maiga M, Doumbia S. Exploring the usefulness of molecular epidemiology of tuberculosis in Africa: a systematic review. INTERNATIONAL JOURNAL OF MOLECULAR EPIDEMIOLOGY AND GENETICS 2020; 11:1-15. [PMID: 32714498 PMCID: PMC7373718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 06/05/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Tuberculosis (TB) is caused by Mycobacterium tuberculosis complex (MTBC) and remains a serious global public health threat, especially in resource-limited settings such as the African region. Recent developments in molecular epidemiology tools have significantly improved our understanding of TB transmission patterns and revealed the high genetic diversity of TB isolates across geographical entities in Africa. This study reports the results of a systematic review of current knowledge about MTBC strain diversity and geographical distribution in African regions. METHODS Search tools (PubMed, Embase, Popline, OVID and Africa Wide Information) were employed to identify the relevant literature about prevalence, strain diversity, and geographic distribution of MTBC infection in Africa. RESULTS A total of 59 articles from 739 citations met our inclusion criteria. Most articles reported about patients with presumptive pulmonary TB (73%), fewer reports were on retreatment and treatment failure cases (12%), and presumptive drug resistance cases (3%). Spoligotyping was the most used, alone in 21 studies and in parallel with either the Mycobacterial Interspersed Repetitive Units Variable Number of Tandem Repeats or the Restriction Fragment Length Polymorphism. Various TB lineages were observed across the African continent, with the originally European lineage 4 spotted in all countries studied. CONCLUSION TB molecular epidemiology tools have substantially improved our understanding of the MTBC circulating isolates, their evolution, and diversity in this highly endemic region of Africa. We found that only TB lineage 4 is present throughout all the continent and the clusters identified provides an extended insight into the disease transmission dynamics.
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Affiliation(s)
- Bourahima Kone
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB)Bamako, Mali
| | - Anou M Somboro
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB)Bamako, Mali
- Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurban, South Africa
| | | | - Bocar Baya
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB)Bamako, Mali
| | - Antieme ACG Togo
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB)Bamako, Mali
| | - Yeya Dit Sadio Sarro
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB)Bamako, Mali
| | - Bassirou Diarra
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB)Bamako, Mali
| | - Ousmane Kodio
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB)Bamako, Mali
| | - Robert L Murphy
- Institute for Global Health, Northwestern UniversityChicago, Illinois, USA
| | - William Bishai
- Center for TB Research, Johns Hopkins UniversityBaltimore, MD, USA
| | - Mamoudou Maiga
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB)Bamako, Mali
- Institute for Global Health, Northwestern UniversityChicago, Illinois, USA
| | - Seydou Doumbia
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB)Bamako, Mali
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Adesokan HK, Streicher EM, van Helden PD, Warren RM, Cadmus SIB. Genetic diversity of Mycobacterium tuberculosis complex strains isolated from livestock workers and cattle in Nigeria. PLoS One 2019; 14:e0211637. [PMID: 30785899 PMCID: PMC6382159 DOI: 10.1371/journal.pone.0211637] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 01/17/2019] [Indexed: 12/02/2022] Open
Abstract
Molecular typing techniques are useful in understanding tuberculosis epidemiology; yet, they have been under-utilised at the human-animal interface in Nigeria. Sixty-four Mycobacterium tuberculosis complex (MTBC) isolates including 42 M. tuberculosis, 13 M. bovis and nine M. africanum obtained from livestock workers (LW, n = 47) and their cattle (n = 17) in three geographical zones of Nigeria were genotyped to identify and evaluate the genetic diversity of the circulating MTBC using spoligotyping. Distribution into clades of M. tuberculosis revealed; 45.3% Uganda I- [SIT46- cattle: 1; LW: 28], 14.1% Latin American Mediterranean- [SIT61, cattle: 1; LW: 8], and 1.6% T- [SIT53—LW: 1]. The M. bovis strains were 6.3% SB0944 [cattle: 4] and 1.6% each of SB0300, SB1026, SB1027 and SB1439 [cattle: 4]. Seventeen MTBC isolates [cattle: 7; LW: 10] yielded 14 new spoligotype patterns including three M. tuberculosis strains (three isolates), five M. bovis strains (five isolates) and six M. africanum strains (nine isolates), two of which belonged to MAF1. Only few families namely, the not previously described Uganda I-, LAM and SB0944 are predominant among the LW and cattle, with other types in lower prevalences. The strain population structure indicates an intriguing diversity and possible zoonotic linkage with consequences for TB control in the country. The need to employ newer molecular techniques such as Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeats and whole genome sequence to decipher circulating MTBC strains in Nigeria is advocated.
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Affiliation(s)
- Hezekiah K. Adesokan
- Department of Veterinary Public Health and Preventive Medicine, University of Ibadan, Ibadan, Nigeria
- * E-mail: (HKA); (SIBC)
| | - 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, Cape Town, 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, Cape Town, South Africa
| | - Rob 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, Cape Town, South Africa
| | - Simeon I. B. Cadmus
- Department of Veterinary Public Health and Preventive Medicine, University of Ibadan, Ibadan, Nigeria
- Centre for Control and Prevention of Zoonoses, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
- * E-mail: (HKA); (SIBC)
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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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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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Winglee K, Manson McGuire A, Maiga M, Abeel T, Shea T, Desjardins CA, Diarra B, Baya B, Sanogo M, Diallo S, Earl AM, Bishai WR. Whole Genome Sequencing of Mycobacterium africanum Strains from Mali Provides Insights into the Mechanisms of Geographic Restriction. PLoS Negl Trop Dis 2016; 10:e0004332. [PMID: 26751217 PMCID: PMC4713829 DOI: 10.1371/journal.pntd.0004332] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 12/05/2015] [Indexed: 01/05/2023] Open
Abstract
Background Mycobacterium africanum, made up of lineages 5 and 6 within the Mycobacterium tuberculosis complex (MTC), causes up to half of all tuberculosis cases in West Africa, but is rarely found outside of this region. The reasons for this geographical restriction remain unknown. Possible reasons include a geographically restricted animal reservoir, a unique preference for hosts of West African ethnicity, and an inability to compete with other lineages outside of West Africa. These latter two hypotheses could be caused by loss of fitness or altered interactions with the host immune system. Methodology/Principal Findings We sequenced 92 MTC clinical isolates from Mali, including two lineage 5 and 24 lineage 6 strains. Our genome sequencing assembly, alignment, phylogeny and average nucleotide identity analyses enabled us to identify features that typify lineages 5 and 6 and made clear that these lineages do not constitute a distinct species within the MTC. We found that in Mali, lineage 6 and lineage 4 strains have similar levels of diversity and evolve drug resistance through similar mechanisms. In the process, we identified a putative novel streptomycin resistance mutation. In addition, we found evidence of person-to-person transmission of lineage 6 isolates and showed that lineage 6 is not enriched for mutations in virulence-associated genes. Conclusions This is the largest collection of lineage 5 and 6 whole genome sequences to date, and our assembly and alignment data provide valuable insights into what distinguishes these lineages from other MTC lineages. Lineages 5 and 6 do not appear to be geographically restricted due to an inability to transmit between West African hosts or to an elevated number of mutations in virulence-associated genes. However, lineage-specific mutations, such as mutations in cell wall structure, secretion systems and cofactor biosynthesis, provide alternative mechanisms that may lead to host specificity. Mycobacterium africanum consists of two lineages, lineages 5 and 6, within the Mycobacterium tuberculosis complex (MTC) that cause human tuberculosis in West Africa, but are found rarely outside of this region. Our analysis of the whole genome sequences of 26 lineage 5 and 6 isolates, and 66 isolates from other lineages within the MTC, reveal that M. africanum does not meet modern criteria to be considered an independent species. We analyzed drug resistance-associated genes and found that drug resistance evolves within these lineages through similar mechanisms as observed for the rest of the MTC in Mali. Though we did not see an elevated number of mutations in virulence-associated genes in these two lineages, we identified a number of lineage-specific mutations, pseudogenes and changes in gene content that may impact virulence and host specificity, and improve, overall, our understanding of what make these lineages unique.
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Affiliation(s)
- Kathryn Winglee
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Abigail Manson McGuire
- Genome Sequencing and Analysis Program, The Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America
| | - Mamoudou Maiga
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
- Project SEREFO (Centre de Recherche et de Formation sur le VIH/Sida et la Tuberculose)/University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Thomas Abeel
- Genome Sequencing and Analysis Program, The Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Terrance Shea
- Genome Sequencing and Analysis Program, The Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America
| | - Christopher A. Desjardins
- Genome Sequencing and Analysis Program, The Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America
| | - Bassirou Diarra
- Project SEREFO (Centre de Recherche et de Formation sur le VIH/Sida et la Tuberculose)/University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bocar Baya
- Project SEREFO (Centre de Recherche et de Formation sur le VIH/Sida et la Tuberculose)/University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Moumine Sanogo
- Project SEREFO (Centre de Recherche et de Formation sur le VIH/Sida et la Tuberculose)/University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Souleymane Diallo
- Project SEREFO (Centre de Recherche et de Formation sur le VIH/Sida et la Tuberculose)/University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Ashlee M. Earl
- Genome Sequencing and Analysis Program, The Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (AME); (WRB)
| | - William R. Bishai
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail: (AME); (WRB)
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10
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Ejo M, Gehre F, Barry MD, Sow O, Bah NM, Camara M, Bah B, Uwizeye C, Nduwamahoro E, Fissette K, De Rijk P, Merle C, Olliaro P, Burgos M, Lienhardt C, Rigouts L, de Jong BC. First insights into circulating Mycobacterium tuberculosis complex lineages and drug resistance in Guinea. INFECTION GENETICS AND EVOLUTION 2015; 33:314-9. [PMID: 26004194 PMCID: PMC4503999 DOI: 10.1016/j.meegid.2015.05.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/19/2015] [Accepted: 05/20/2015] [Indexed: 11/23/2022]
Abstract
First insight into resistance levels and genetic diversity of TB in Guinea. Rapid expansion of drug-resistance prone LAM10 Cameroon family. Population structure reveals less ‘ancestral’ TB than in surrounding countries. Knowledge of genetic diversity is relevant for tuberculosis control programs.
In this study we assessed first-line anti-tuberculosis drug resistance and the genotypic distribution of Mycobacterium tuberculosis complex (MTBC) isolates that had been collected from consecutive new tuberculosis patients enrolled in two clinical trials conducted in Guinea between 2005 and 2010. Among the total 359 MTBC strains that were analyzed in this study, 22.8% were resistant to at least one of the first line anti-tuberculosis drugs, including 2.5% multidrug resistance and 17.5% isoniazid resistance, with or without other drugs. In addition, further characterization of isolates from a subset of the two trials (n = 184) revealed a total of 80 different spoligotype patterns, 29 “orphan” and 51 shared patterns. We identified the six major MTBC lineages of human relevance, with predominance of the Euro-American lineage. In total, 132 (71.7%) of the strains were genotypically clustered, and further analysis (using the DESTUS model) suggesting significantly faster spread of LAM10_CAM family (p = 0.00016). In conclusion, our findings provide a first insight into drug resistance and the population structure of the MTBC in Guinea, with relevance for public health scientists in tuberculosis control programs.
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Affiliation(s)
- Mebrat Ejo
- Institute of Tropical Medicine (ITM), Antwerp, Belgium; University of Gondar, Gondar, Ethiopia
| | - Florian Gehre
- Institute of Tropical Medicine (ITM), Antwerp, Belgium; Medical Research Council (MRC), Fajara, Gambia.
| | | | - Oumou Sow
- Reference Laboratory for Mycobacteria, Conakry, Guinea; National University Hospital IgnaceDeen, Conakry, Guinea
| | | | - Mory Camara
- Reference Laboratory for Mycobacteria, Conakry, Guinea
| | - Boubacar Bah
- National University Hospital IgnaceDeen, Conakry, Guinea
| | | | | | | | - Pim De Rijk
- Institute of Tropical Medicine (ITM), Antwerp, Belgium
| | - Corinne Merle
- London School of Hygiene and Tropical Medicine, London, UK; UNICEF/UNDP/World Bank/WHO Special Programme for Research and Training in Tropical Diseases (TDR), Geneva, Switzerland
| | - Piero Olliaro
- UNICEF/UNDP/World Bank/WHO Special Programme for Research and Training in Tropical Diseases (TDR), Geneva, Switzerland; Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Marcos Burgos
- Division of Infectious Diseases, Department of Internal Medicine, University of New Mexico, Albuquerque, United States
| | - Christian Lienhardt
- Clinical Trial Division, International Union against Tuberculosis and Lung Disease, Paris, France; World Health Organization, Geneva, Switzerland
| | - Leen Rigouts
- Institute of Tropical Medicine (ITM), Antwerp, Belgium; University of Antwerp, Antwerp, Belgium
| | - Bouke C de Jong
- Institute of Tropical Medicine (ITM), Antwerp, Belgium; Medical Research Council (MRC), Fajara, Gambia; New York University (NYU), New York, United States
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11
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Viegas SO, Machado A, Groenheit R, Ghebremichael S, Pennhag A, Gudo PS, Cuna Z, Langa E, Miotto P, Cirillo DM, Rastogi N, Warren RM, van Helden PD, Koivula T, Källenius G. Mycobacterium tuberculosis Beijing genotype is associated with HIV infection in Mozambique. PLoS One 2013; 8:e71999. [PMID: 23940801 PMCID: PMC3737140 DOI: 10.1371/journal.pone.0071999] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 07/08/2013] [Indexed: 11/19/2022] Open
Abstract
The Beijing genotype is a lineage of Mycobacterium tuberculosis that is distributed worldwide and responsible for large epidemics, associated with multidrug-resistance. However, its distribution in Africa is less understood due to the lack of data. Our aim was to investigate the prevalence and possible transmission of Beijing strains in Mozambique by a multivariate analysis of genotypic, geographic and demographic data. A total of 543 M. tuberculosis isolates from Mozambique were spoligotyped. Of these, 33 were of the Beijing lineage. The genetic relationship between the Beijing isolates were studied by identification of genomic deletions within some Regions of Difference (RD), Restriction Fragment Length Polymorphism (RFLP) and Mycobacterial Interspersed Repetivie Unit – variable number tandem repeat (MIRU-VNTR). Beijing strains from South Africa, representing different sublineages were included as reference strains. The association between Beijing genotype, Human Immunodeficiency Virus (HIV) serology and baseline demographic data was investigated. HIV positive serostatus was significantly (p=0.023) more common in patients with Beijing strains than in patients with non-Beijing strains in a multivariable analysis adjusted for age, sex and province (14 (10.9%) of the 129 HIV positive patients had Beijing strains while 6/141 (4.3%) of HIV negative patients had Beijing strains). The majority of Beijing strains were found in the Southern region of Mozambique, particularly in Maputo City (17%). Only one Beijing strain was drug resistant (multi-drug resistant). By combined use of RD and spoligotyping, three genetic sublineages could be tentatively identified where a distinct group of four isolates had deletion of RD150, a signature of the “sublineage 7” recently emerging in South Africa. The same group was very similar to South African “sublineage 7” by RFLP and MIRU-VNTR, suggesting that this sublineage could have been recently introduced in Mozambique from South Africa, in association with HIV infection.
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Affiliation(s)
- Sofia O Viegas
- National Institute of Health, Ministry of Health, Maputo, Mozambique.
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12
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Sankar MM, Singh J, Diana SCA, Singh S. Molecular characterization of Mycobacterium tuberculosis isolates from North Indian patients with extrapulmonary tuberculosis. Tuberculosis (Edinb) 2013; 93:75-83. [PMID: 23140853 DOI: 10.1016/j.tube.2012.10.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 10/11/2012] [Accepted: 10/12/2012] [Indexed: 02/07/2023]
Abstract
Genotypic studies are important to understand the molecular epidemiology and transmission routes of Mycobacterium tuberculosis. In the first and largest study from India, spoligotyping and 24 loci mycobacterial interspersed repetitive units (MIRU) were performed to find genetic profiles of 125 M. tuberculosis strains isolated from patients with extrapulmonary tuberculosis (EPTB) and their drug susceptibility test was performed using BACTEC-MGIT 960. Spoligotyping results were compared with the world Spoligotyping Database of Institute Pasteur de Guadeloupe (SpolDB4). The spoligotyping results showed that 110 (88%) displayed known patterns while 15 (12%) isolates had no matching database. Predominant spoligotypes belonged to CAS family (57.27%). The largest clade comprised of 38 isolates belonging to the CAS1_DEL lineage. Though there was no significant association between specific mycobacterial lineage and extrapulmonary site, a significantly high (p < 0.001) number of Beijing type isolates (28.6%) were isolated from bone and joint samples as compared to cerebrospinal fluid (5%). There was a significant association between Beijing family isolates and multi-drug-resistance, while all MANU genotypes were pan-drug sensitive. The CAS family lineage was most prevalent genotype in the EPTB cases in our population.
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Affiliation(s)
- Manimuthu Mani Sankar
- Clinical Microbiology Division, Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi 110029, India
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13
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Lawson L, Zhang J, Gomgnimbou MK, Abdurrahman ST, Le Moullec S, Mohamed F, Uzoewulu GN, Sogaolu OM, Goh KS, Emenyonu N, Refrégier G, Cuevas LE, Sola C. A molecular epidemiological and genetic diversity study of tuberculosis in Ibadan, Nnewi and Abuja, Nigeria. PLoS One 2012; 7:e38409. [PMID: 22723859 PMCID: PMC3377642 DOI: 10.1371/journal.pone.0038409] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 05/05/2012] [Indexed: 11/22/2022] Open
Abstract
Background Nigeria has the tenth highest burden of tuberculosis (TB) among the 22 TB high-burden countries in the world. This study describes the biodiversity and epidemiology of drug-susceptible and drug-resistant TB in Ibadan, Nnewi and Abuja, using 409 DNAs extracted from culture positive TB isolates. Methodology/Principal Findings DNAs extracted from clinical isolates of Mycobacterium tuberculosis complex were studied by spoligotyping and 24 VNTR typing. The Cameroon clade (CAM) was predominant followed by the M. africanum (West African 1) and T (mainly T2) clades. By using a smooth definition of clusters, 32 likely epi-linked clusters related to the Cameroon genotype family and 15 likely epi-linked clusters related to other “modern” genotypes were detected. Eight clusters concerned M. africanum West African 1. The recent transmission rate of TB was 38%. This large study shows that the recent transmission of TB in Nigeria is high, without major regional differences, with MDR-TB clusters. Improvement in the TB control programme is imperative to address the TB control problem in Nigeria.
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Affiliation(s)
| | - Jian Zhang
- Institut de Génétique et Microbiologie UMR8621, CNRS-Université Paris-Sud, Orsay, France
| | - Michel K. Gomgnimbou
- Institut de Génétique et Microbiologie UMR8621, CNRS-Université Paris-Sud, Orsay, France
| | | | - Stéphanie Le Moullec
- Institut de Génétique et Microbiologie UMR8621, CNRS-Université Paris-Sud, Orsay, France
| | - Fatima Mohamed
- Institut de Génétique et Microbiologie UMR8621, CNRS-Université Paris-Sud, Orsay, France
| | | | | | - Khye Seng Goh
- Tuberculosis Laboratory Consultant, Les Abymes, Guadeloupe, France
| | | | - Guislaine Refrégier
- Institut de Génétique et Microbiologie UMR8621, CNRS-Université Paris-Sud, Orsay, France
| | - Luis E. Cuevas
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Christophe Sola
- Institut de Génétique et Microbiologie UMR8621, CNRS-Université Paris-Sud, Orsay, France
- * E-mail:
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14
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Reddington K, O'Grady J, Dorai-Raj S, Niemann S, van Soolingen D, Barry T. A novel multiplex real-time PCR for the identification of mycobacteria associated with zoonotic tuberculosis. PLoS One 2011; 6:e23481. [PMID: 21858140 PMCID: PMC3153498 DOI: 10.1371/journal.pone.0023481] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 07/18/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is the leading cause of death worldwide from a single infectious agent. An ability to detect the Mycobacterium tuberculosis complex (MTC) in clinical material while simultaneously differentiating its members is considered important. This allows for the gathering of epidemiological information pertaining to the prevalence, transmission and geographical distribution of the MTC, including those MTC members associated with zoonotic TB infection in humans. Also differentiating between members of the MTC provides the clinician with inherent MTC specific drug susceptibility profiles to guide appropriate chemotherapy. METHODOLOGY/PRINCIPAL FINDINGS The aim of this study was to develop a multiplex real-time PCR assay using novel molecular targets to identify and differentiate between the phylogenetically closely related M. bovis, M. bovis BCG and M. caprae. The lpqT gene was explored for the collective identification of M. bovis, M. bovis BCG and M. caprae, the lepA gene was targeted for the specific identification of M. caprae and a Region of Difference 1 (RD1) assay was incorporated in the test to differentiate M. bovis BCG. The multiplex real-time PCR assay was evaluated on 133 bacterial strains and was determined to be 100% specific for the members of the MTC targeted. CONCLUSIONS/SIGNIFICANCE The multiplex real-time PCR assay developed in this study is the first assay described for the identification and simultaneous differentiation of M. bovis, M. bovis BCG and M. caprae in one internally controlled reaction. Future validation of this multiplex assay should demonstrate its potential in the rapid and accurate diagnosis of TB caused by these three mycobacteria. Furthermore, the developed assay may be used in conjunction with a recently described multiplex real-time PCR assay for identification of the MTC and simultaneous differentiation of M. tuberculosis, M. canettii resulting in an ability to differentiate five of the eight members of the MTC.
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Affiliation(s)
- Kate Reddington
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
- Molecular Diagnostics Research Group, National Centre for Biomedical Engineering Science (NCBES), National University of Ireland, Galway, Ireland
| | - Justin O'Grady
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
- Molecular Diagnostics Research Group, National Centre for Biomedical Engineering Science (NCBES), National University of Ireland, Galway, Ireland
| | - Siobhan Dorai-Raj
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
- Molecular Diagnostics Research Group, National Centre for Biomedical Engineering Science (NCBES), National University of Ireland, Galway, Ireland
| | - Stefan Niemann
- Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Dick van Soolingen
- National Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Thomas Barry
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
- Molecular Diagnostics Research Group, National Centre for Biomedical Engineering Science (NCBES), National University of Ireland, Galway, Ireland
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