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Rickman HM, Kamchedzera W, Schwalb A, Phiri MD, Ruhwald M, Shanaube K, Dodd PJ, Houben RMGJ, Corbett EL, MacPherson P. Know your tuberculosis epidemic-Is it time to add Mycobacterium tuberculosis immunoreactivity back into global surveillance? PLOS GLOBAL PUBLIC HEALTH 2022; 2:e0001208. [PMID: 36962621 PMCID: PMC10021854 DOI: 10.1371/journal.pgph.0001208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Tuberculosis (TB) still causes 1.5 million deaths globally each year. Over recent decades, slow and uneven declines in TB incidence have resulted in a falling prevalence of TB disease, which increasingly concentrates in vulnerable populations. Falling prevalence, while welcome, poses new challenges for TB surveillance. Cross-sectional disease surveys require very large sample sizes to accurately estimate disease burden, and even more participants to detect trends over time or identify high-risk areas or populations, making them prohibitively resource-intensive. In the past, tuberculin skin surveys measuring Mycobacterium tuberculosis (Mtb) immunoreactivity were widely used to monitor TB epidemiology in high-incidence settings, but were limited by challenges with both delivering and interpreting the test. Here we argue that the shifting epidemiology of tuberculosis, and the development of new tests for Mtb infection, make it timely and important to revisit the strategy of TB surveillance based on infection or immunoreactivity. Mtb infection surveys carry their own operational challenges and fundamental questions, for example: around survey design and frequency; which groups should be included; how the prevalence of immunoreactivity in a population should be used to estimate force of infection; how individual results should be interpreted and managed; and how surveillance can be delivered efficiently and ethically. However, if these knowledge gaps are addressed, the relative feasibility and lower costs of Mtb infection surveillance offer a powerful and affordable opportunity to better "know your TB epidemic", understand trends, identify high-risk and underserved communities, and tailor public health responses to dynamic epidemiology.
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Affiliation(s)
- Hannah M Rickman
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
| | | | - Alvaro Schwalb
- TB Modelling Group, TB Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mphatso D Phiri
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Morten Ruhwald
- FIND, the Global Alliance for Diagnostics, Geneva, Switzerland
| | | | - Peter J Dodd
- School of Health and Related Research, University of Sheffield, Sheffield, United Kingdom
| | - Rein M G J Houben
- TB Modelling Group, TB Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Elizabeth L Corbett
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
| | - Peter MacPherson
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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Whole-Genome Sequencing Reveals Recent Transmission of Multidrug-Resistant Mycobacterium tuberculosis CAS1-Kili Strains in Lusaka, Zambia. Antibiotics (Basel) 2021; 11:antibiotics11010029. [PMID: 35052906 PMCID: PMC8773284 DOI: 10.3390/antibiotics11010029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/16/2021] [Accepted: 12/21/2021] [Indexed: 11/17/2022] Open
Abstract
Globally, tuberculosis (TB) is a major cause of death due to antimicrobial resistance. Mycobacterium tuberculosis CAS1-Kili strains that belong to lineage 3 (Central Asian Strain, CAS) were previously implicated in the spread of multidrug-resistant (MDR)-TB in Lusaka, Zambia. Thus, we investigated recent transmission of those strains by whole-genome sequencing (WGS) with Illumina MiSeq platform. Twelve MDR CAS1-Kili isolates clustered by traditional methods (MIRU-VNTR and spoligotyping) were used. A total of 92% (11/12) of isolates belonged to a cluster (≤12 SNPs) while 50% (6/12) were involved in recent transmission events, as they differed by ≤5 SNPs. All the isolates had KatG Ser315Thr (isoniazid resistance), EmbB Met306 substitutions (ethambutol resistance) and several kinds of rpoB mutations (rifampicin resistance). WGS also revealed compensatory mutations including a novel deletion in embA regulatory region (−35A > del). Several strains shared the same combinations of drug-resistance-associated mutations indicating transmission of MDR strains. Zambian strains belonged to the same clade as Tanzanian, Malawian and European strains, although most of those were pan-drug-susceptible. Hence, complimentary use of WGS to traditional epidemiological methods provides an in-depth insight on transmission and drug resistance patterns which can guide targeted control measures to stop the spread of MDR-TB.
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Genetic Diversity and Transmission of Multidrug Resistant Mycobacterium tuberculosis strains in Lusaka, Zambia. Int J Infect Dis 2021; 114:142-150. [PMID: 34718155 DOI: 10.1016/j.ijid.2021.10.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVE Zambia is among the 30 high tuberculosis burden countries in the world. Despite increasing reports of multidrug resistant tuberculosis (MDR-TB) in routine surveillance, information on the transmission of MDR Mycobacterium tuberculosis strains is largely unknown. This study elucidated genetic diversity and transmission of MDR M. tuberculosis strains in Lusaka, Zambia. METHODS Eighty-five MDR M. tuberculosis samples collected from the year 2013 to 2017 at the University Teaching Hospital were used. Drug-resistance associated gene sequencing, spoligotyping, 24-loci mycobacterial interspersed repetitive units-variable number of tandem repeats, and multiplex PCR for RD-Rio sub-lineage identification were applied. RESULTS Clades identified were LAM (48%), CAS (29%), T (14%), X (6%) and Harlem (2%). Strains belonging to SITs 21/CAS1-Kili and 20/LAM1 formed the largest clonal complexes. Combined spoligotyping and 24 loci-MIRU-VNTR revealed 47 genotypic patterns with clustering rate of 63%. Ninety five percent of LAM strains belonged to RD-Rio sub-lineage. CONCLUSION The high clustering rate suggested that a large proportion of MDR-TB was due to recent transmission rather than independent acquisition of MDR. This spread was attributed to clonal expansion of SIT21/CAS1-Kili and SIT20/LAM1 strains. Therefore, TB control programs recommending genotyping coupled with conventional epidemiological methods can guide measures for stopping the spread of MDR-TB.
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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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Salazar-Austin N, Dowdy DW, Chaisson RE, Golub JE. Seventy Years of Tuberculosis Prevention: Efficacy, Effectiveness, Toxicity, Durability, and Duration. Am J Epidemiol 2019; 188:2078-2085. [PMID: 31364692 DOI: 10.1093/aje/kwz172] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 01/12/2023] Open
Abstract
Tuberculosis (TB) has been a leading infectious cause of death worldwide for much of human history, with 1.6 million deaths estimated in 2017. The Department of Epidemiology at the Johns Hopkins Bloomberg School of Public Health has played an important role in understanding and responding to TB, and it has made particularly substantial contributions to prevention of TB with chemoprophylaxis. TB preventive therapy is highly efficacious in the prevention of TB disease, yet it remains underutilized by TB programs worldwide despite strong evidence to support its use in high-risk groups, such as people living with HIV and household contacts, including those under 5 years of age. We review the evidence for TB preventive therapy and discuss the future of TB prevention.
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Muvunyi CM, Ngabonziza JCS, Uwimana I, Harelimana JDD, Mucyo Y, Sebatunzi OR, Muvunyi TZ, Seruyange E, Masaisa F, Mazarati JB, Gasana M. Highly successful treatment outcome of multidrug-resistant and genetic diversity of multidrug-resistant Mycobacterium tuberculosis strains in Rwanda. Trop Med Int Health 2019; 24:879-887. [PMID: 31066112 DOI: 10.1111/tmi.13245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To determine prevalent MDR-TB genotypes and describe treatment outcome and bacteriology conversion in MDR-TB patients. METHODS Review of laboratory records of 173 MDR-TB patients from all over Rwanda who initiated treatment under programmatic management of MDR-TB (PMDT) between 2014 and 2015. Fifty available archived isolates were genotyped by mycobacterial interspersed repetitive units - variable number of tandem repeats (MIRU-VNTR) genotyping. RESULT Of the 170 patients whose outcome was known, 114 (66.3%) were cured and 36 (21%) completed the treatment, giving a successful outcome (cured and completed) of 150 (87.3%) patients. Of 20 MDR-TB patients with unfavourable treatment outcome, 18 died, one failed and one defaulted/stopped treatment. Of the 18 patients who died, 11 (61%) were HIV-coinfected. The treatment outcome was successful for 93.9% among HIV negative and 81.8% among HIV-coinfected patients (P = 0.02). Sputum smear conversion occurred in 3, 46, 57 and 78 patients before 2, 3, 4 and 6 months, respectively, with median time of sputum smear and culture conversion at 3 months. The 44 MDR-TB isolates with MIRU-VNTR result, showed high genetic diversity with low clustering rate (9.09%) and Uganda II being the most prevalent sub-family lineage detected in 68.2% of isolates. Beijing family was the least common genotype detected (2.3%, 1 isolate). CONCLUSION The high success rates for MDR-TB treatment achieved in Rwanda were comparable to outcomes observed in resource-rich settings with HIV being an independent risk factor for poor treatment outcome. High genetic diversity and low clustering rate reported here suggest that reactivation of previous disease plays an important role in the transmission of MDR-TB in Rwanda.
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Affiliation(s)
- Claude Mambo Muvunyi
- Department of Clinical Biology, School of Medicine and Pharmacy, University of Rwanda, Kigali, Rwanda
| | | | - Innocent Uwimana
- National Reference Laboratory Division, Rwanda Biomedical Centre, Kigali, Rwanda
| | - Jean De Dieu Harelimana
- Department of Biomedical Laboratory Science, School of Health Science, University of Rwanda, Kigali, Rwanda
| | - Yves Mucyo
- Tuberculosis and Other Respiratory Diseases Division, Rwanda Biomedical Centre, Kigali, Rwanda
| | - Osee Rurambya Sebatunzi
- Department of Internal Medicine, School of Medicine and Pharmacy, University of Rwanda, Kigali, Rwanda
| | | | - Eric Seruyange
- Department of Internal Medicine, School of Medicine and Pharmacy, University of Rwanda, Kigali, Rwanda
| | - Florence Masaisa
- Department of Clinical Biology, School of Medicine and Pharmacy, University of Rwanda, Kigali, Rwanda.,Department of Internal Medicine, School of Medicine and Pharmacy, University of Rwanda, Kigali, Rwanda
| | | | - Michel Gasana
- Tuberculosis and Other Respiratory Diseases Division, Rwanda Biomedical Centre, Kigali, Rwanda
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Maguga-Phasha NTC, Munyai NS, Mashinya F, Makgatho ME, Mbajiorgu EF. Genetic diversity and distribution of Mycobacterium tuberculosis genotypes in Limpopo, South Africa. BMC Infect Dis 2017; 17:764. [PMID: 29233106 PMCID: PMC5727936 DOI: 10.1186/s12879-017-2881-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 12/04/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tuberculosis remains a major health problem and knowledge of the diversity of Mycobacterium tuberculosis strains in specific geographical regions can contribute to the control of the disease. This study describes the genetic profile of M. tuberculosis in five districts of Limpopo Province. METHODS A total 487 isolates were collected from the National Health Laboratory Services from all regions/districts of Limpopo Province. Only 215 isolates were confirmed to be M. tuberculosis by Bactec Mycobacterium Growth Indicator Tube 960® and Rhodamine-Auramine staining. Isolates were subcultured on Löwenstein-Jensen medium agar slants to validate purity. They were spoligotyped and data analysed using the international spoligotyping database 4 (SpolDB4). RESULTS Of the 215 isolates, 134 (62.3%) were genotyped into 21 genotype families while 81 (37.7%) were orphans. The 81 orphans were further subjected to resolution employing SpolDB3/RIM. Overall, the study revealed a high diversity of strains of 32 predominantly the non-Beijing lineages: the LAM- LAM3 (9.8%), LAM9 (4.7%) and LAM11- ZWE (3.3%), the T-T1(15.0%), T2 (0.9%), T2-T3 (1.4%), the CAS-CAS1-Delhi 5 (1.9%) and CAS1-KILI (1.4%) the MANU2 (1.4%), U (0.5%), X-X1(1.4%), X3 (1.9%), S (9.8%), CAS (1.4%), LAM7(0.9%), T3(0.5%), LAM8(4.7%), T4(1.4%), X2(0.4%), AI5(1.9%), LAM1(0.5%), FAMILY33 (1.9%), EAI4(1.4%), M. microti (1.9%). The Beijing and Beijing-like families were (14.9%) and (0.9%), respectively. A total of 28(13%) clusters and 77(36%) unique cases were identified. Beijing strain (SIT 1) formed the biggest cluster constituting 14%, followed by LAM3 (SIT 33), T1 (SIT 53) and LAM4 (SIT 811) with 7%, 5.1% and 2.8%, respectively. The Beijing family was the only genotype found in all the five districts and was predominant in Mopani (18.8%), Sekhukhune (23.7%) and Vhembe (23.3%). Dominant genotypes in Capricorn and Waterberg were LAM3 (11.9%) and T1 (13.3%), respectively. CONCLUSION A wide diversity of lineages was demonstrated at district level. A high number of clusters per district provided evidence of on-going transmission in this Province.
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Affiliation(s)
- N T C Maguga-Phasha
- Department of Pathology and Medical Sciences, University of Limpopo, Private Bag X1107, Sovenga, Mankweng, 0727, South Africa.
| | - N S Munyai
- Department of Pathology and Medical Sciences, University of Limpopo, Private Bag X1107, Sovenga, Mankweng, 0727, South Africa
| | - F Mashinya
- Department of Pathology and Medical Sciences, University of Limpopo, Private Bag X1107, Sovenga, Mankweng, 0727, South Africa
| | - M E Makgatho
- Department of Pathology and Medical Sciences, University of Limpopo, Private Bag X1107, Sovenga, Mankweng, 0727, South Africa
| | - E F Mbajiorgu
- School of Anatomical Sciences Faculty of Health Sciences University of the Witwatersrand, 7 York Road, Wits Medical School, Parktown, Johannesburg, 2193, South Africa
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Egbe NF, Muwonge A, Ndip L, Kelly RF, Sander M, Tanya V, Ngwa VN, Handel IG, Novak A, Ngandalo R, Mazeri S, Morgan KL, Asuquo A, de C Bronsvoort BM. Molecular epidemiology of Mycobacterium bovis in Cameroon. Sci Rep 2017; 7:4652. [PMID: 28680043 PMCID: PMC5498612 DOI: 10.1038/s41598-017-04230-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 05/11/2017] [Indexed: 11/28/2022] Open
Abstract
We describe the largest molecular epidemiological study of Bovine Tuberculosis (bTB) in a sub-Saharan African country with higher spatial resolution providing new insights into bTB. Four hundred and ninety-nine samples were collected for culture from 201 and 179 cattle with and without bTB-like lesions respectively out of 2,346 cattle slaughtered at Bamenda, Ngaoundere, Garoua and Maroua abattoirs between 2012–2013. Two hundred and fifty-five M. bovis were isolated, identified and genotyped using deletion analysis, Hain® Genotype MTBC, spoligotyping and MIRU-VNTR. African 1 was the dominant M. bovis clonal complex, with 97 unique genotypes including 19 novel spoligotypes representing the highest M. bovis genetic diversity observed in Africa to date. SB0944 and SB0953 dominated (63%) the observed spoligotypes. A third of animals with multiple lesions had multiple strain infections. Higher diversity but little evidence of recent transmission of M. bovis was more common in Adamawa compared to the North-West Region. The Adamawa was characterised by a high frequency of singletons possibly due to constant additions from an active livestock movement network compared to the North-West Region where a local expansion was more evident. The latter combined with population-based inferences suggest an unstable and stable bTB-endemic status in the North-West and Adamawa Regions respectively.
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Affiliation(s)
- N F Egbe
- Division of Genetics and Genomics, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.,Microbiology and Parasitology Unit, Faculty of Allied Medical Sciences, University of Calabar, Calabar, Nigeria
| | - A Muwonge
- Division of Genetics and Genomics, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| | - L Ndip
- Laboratory for Emerging Infectious Diseases, University of Buea, Buea, Cameroon.,Department of Biomedical Sciences, Faculty of Health Sciences, University of Buea, Buea, Cameroon
| | - R F Kelly
- Division of Genetics and Genomics, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.,Farm Animal Clinical Sciences, School of Veterinary Medicine, University of Glasgow, Glasgow, G61 1QH, UK
| | - M Sander
- Tuberculosis Reference Laboratory, Bamenda, P.O. Box 586, Cameroon
| | - V Tanya
- Cameroon Academy of Sciences, P.O. Box 1457, Yaoundé, Cameroon
| | - V Ngu Ngwa
- School of Veterinary Medicine and Sciences, University of Ngaoundere, B.P. 454, Ngaoundere, Cameroon
| | - I G Handel
- Division of Genetics and Genomics, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - A Novak
- Division of Genetics and Genomics, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - R Ngandalo
- Laboratoire de Recherches Vétérinaires et Zootechniques de Farcha, N'Djaména, Chad
| | - S Mazeri
- Division of Genetics and Genomics, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - K L Morgan
- Institute of Ageing and Chronic Disease, University of Liverpool, Leahurst Campus, Neston, Wirral, CH64 7TE, UK
| | - A Asuquo
- Microbiology and Parasitology Unit, Faculty of Allied Medical Sciences, University of Calabar, Calabar, Nigeria
| | - B M de C Bronsvoort
- Division of Genetics and Genomics, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.,Centre for Tropical Livestock Genetics and Health, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
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Genotyping of Mycobacterium tuberculosis Isolates from Hormozgan Province of Iran Based on 15-Locus MIRU-VNTR and Spoligotyping. INTERNATIONAL JOURNAL OF BACTERIOLOGY 2016; 2016:7146470. [PMID: 27819023 PMCID: PMC5081880 DOI: 10.1155/2016/7146470] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 09/25/2016] [Indexed: 11/17/2022]
Abstract
Background. Considering that Hormozgan province in Iran (southern part of Iran on the Persian Gulf) is among the areas with high prevalence of MDR-MTB and attracts so many sailors and tourists, genetic diversity of MTB isolates circulating in this part of Iran was evaluated. Pattern of TB transmission was also examined. Methods and Material. A total of 38 isolates of MTB were cultured from TB patients from Hormozgan province of Iran and standard MIRU-VNTR typing and spoligotyping were applied to genotype these isolates. Drug susceptibility testing was performed using proportion method. Results. There were 28 VNTR profiles comprising 5 clusters and 23 unique isolates compared to 21 spoligotyping profiles, which contained 9 clusters and 12 unique isolates. Latin American-Mediterranean (n = 9, 23.6%) was found to be the most predominant lineage. MIRU-VNTR analysis, with an HGDI of 0.975, was more discriminating than spoligotyping, which had an HGDI of 0.955. The estimated proportion of TB cases due to recent transmission was 26.3% and 44.7% by MIRU-VNTR and spoligotyping, respectively. The rates of monodrug resistance and MDR were 15.8% and 7.9%, respectively. Two of 3 MDR strains were found to be related to MIRU-VNTR and belonged to the same spoligotyping cluster characterized with T1/SIT53 genotype. Conclusions. The high genetic diversity among MTB isolates suggests that transmission occurred from different sources to this area. Reactivation of a priori, latent MTB infection was found to contribute mainly to TB cases in this geographic region.
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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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Genetic Diversity of Mycobacterium tuberculosis Complex Isolated from Tuberculosis Patients in Bahir Dar City and Its Surroundings, Northwest Ethiopia. BIOMED RESEARCH INTERNATIONAL 2015; 2015:174732. [PMID: 26491657 PMCID: PMC4600926 DOI: 10.1155/2015/174732] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 08/08/2015] [Accepted: 08/17/2015] [Indexed: 11/17/2022]
Abstract
The knowledge of the diversity of strains of Mycobacterium tuberculosis complex (MTBC) species in a specific geographical region can contribute to the control of tuberculosis (TB). This study was conducted to identify the MTBC isolates to the species and spoligotype international type (SIT) level by spoligotyping. A total of 168 MTBC isolates were recovered from TB patients, spoligotyped, and their patterns were compared with those of the strains registered in the SITVIT2 database. Of 168 isolates spoligotyped, 89 patterns were identified. Ninety-eight isolates were clustered into 19 strain groups with clustering percentage of 58.3%. Forty-four strains matched the preexisting SITs in the SITVIT2 database. The dominant strains were SIT289, SIT134, and SIT3411, comprising 16.7% (28/168), 7.14% (12/168), and 4.76% (8/168) of the isolates, respectively. Euro-American (51.2%), East-African-Indian (34.5%), and M. africanum (9.52%) were the major lineages identified. Two strains of M. bovis were isolated from TB lymphadenitis cases. The high percentage of clustered strains of M. tuberculosis could suggest that a small number of lineages of M. tuberculosis are causing the disease in the area while isolation of M. bovis could suggest its zoonotic potential. Additionally, identification of M. africanum requires further confirmation by tools with a better discriminatory power.
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Smit PW, Haanperä M, Rantala P, Couvin D, Lyytikäinen O, Rastogi N, Ruutu P, Soini H. Genotypic characterization and historical perspective of Mycobacterium tuberculosis among older and younger Finns, 2008-2011. Clin Microbiol Infect 2015; 20:1134-9. [PMID: 24944074 DOI: 10.1111/1469-0691.12725] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 06/03/2014] [Accepted: 06/12/2014] [Indexed: 12/16/2022]
Abstract
The Mycobacterium tuberculosis genotypes obtained from elderly Finns were assessed and compared with those obtained from younger Finns to comprehend the epidemiology of tuberculosis (TB) in Finland. From 2008 to 2011, a total of 1021 M. tuberculosis isolates were characterized by spoligotyping and 15-locus mycobacterial interspersed repetitive units-variable number tandem repeat typing. In total, 733 Finnish-born cases were included in the study, of which 466 (64%) were born before 1945 (older Finns). Of these, 63 (14%) shared an M. tuberculosis genotype with foreign-born or younger Finnish cases (born after 1945), and 59 (13%) shared a genotype with older Finnish cases. Eighty-five per cent had a unique genotypic profile while 70% belonged to T or Haarlem families, suggesting that ongoing transmission is infrequent among young and elderly Finns. Simultaneous reactivation of TB among older Finns was the most likely cause for clustering. As most isolates belonged to Haarlem or T, Finland was most likely affected by a similar TB epidemic at the beginning of the twentieth century as that seen in Sweden and Norway. Younger Finns were significantly more likely to be clustered (56% versus 27%, p<0.001), have pulmonary TB (87% versus 71%, p<0.001) and to be sputum smear positive (57% versus 48%, p<0.05) indicating that the risk of TB transmission from younger Finns is likely to be larger than from older Finns. The M. tuberculosis isolates from elderly Finns were associated with dominant lineages of the early twentieth century and differed from the heterogeneous lineages found among younger TB patients. Additionally, younger TB patients were more likely to transmit TB than elderly Finns.
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Affiliation(s)
- P W Smit
- European Public Health Microbiology Training Programme (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden; Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Helsinki, Finland
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Mycobacterium africanum is associated with patient ethnicity in Ghana. PLoS Negl Trop Dis 2015; 9:e3370. [PMID: 25569290 PMCID: PMC4287525 DOI: 10.1371/journal.pntd.0003370] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 10/24/2014] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium africanum is a member of the Mycobacterium tuberculosis complex (MTBC) and an important cause of human tuberculosis in West Africa that is rarely observed elsewhere. Here we genotyped 613 MTBC clinical isolates from Ghana, and searched for associations between the different phylogenetic lineages of MTBC and patient variables. We found that 17.1% (105/613) of the MTBC isolates belonged to M. africanum, with the remaining belonging to M. tuberculosis sensu stricto. No M. bovis was identified in this sample. M. africanum was significantly more common in tuberculosis patients belonging to the Ewe ethnic group (adjusted odds ratio: 3.02; 95% confidence interval: 1.67–5.47, p<0.001). Stratifying our analysis by the two phylogenetic lineages of M. africanum (i.e. MTBC Lineages 5 and 6) revealed that this association was mainly driven by Lineage 5 (also known as M. africanum West Africa 1). Our findings suggest interactions between the genetic diversity of MTBC and human diversity, and offer a possible explanation for the geographical restriction of M. africanum to parts of West Africa. Tuberculosis remains one of the main global public health problems. Human tuberculosis is caused by bacteria known as the Mycobacterium tuberculosis complex (MTBC). The MTBC includes a variant called Mycobacterium africanum, which causes up to half of all tuberculosis cases in West Africa. For reasons unknown, M. africanum does not occur in other parts of the world. To explore the possible reasons for this geographic restriction of M. africanum, we analysed a large collection of bacterial strains isolated from tuberculosis patients in Ghana. We genetically characterized these bacterial isolates and collected relevant socio-demographic and epidemiological data. We found tuberculosis patients infected with M. africanum were more likely to belong to the Ewe ethnic group, compared to patients carrying other MTBC bacteria. The Ewes are indigenous inhabitants of coastal regions in West Africa that have previously been shown to harbour a high prevalence of M. africanum. Our findings support the hypothesis that different variants of MTBC have adapted to different human populations, and offer a possible explanation for the geographical restriction of M. africanum to West Africa.
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Malama S, Muma J, Munyeme M, Mbulo G, Muwonge A, Shamputa IC, Djønne B, Godfroid J, Johansen TB. Isolation and molecular characterization of Mycobacterium tuberculosis from humans and cattle in Namwala District, Zambia. ECOHEALTH 2014; 11:564-570. [PMID: 24845573 DOI: 10.1007/s10393-014-0940-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 03/25/2014] [Accepted: 03/27/2014] [Indexed: 05/28/2023]
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis in humans, is considered primarily a human pathogen. It has, however, been reported in a wide range of domestic and wild animals, often living in close prolonged contact with humans. Sputum samples in which acid fast bacteria were detected in smears were collected from patients at three health facilities in Namwala district, Zambia. Samples from cattle presenting gross lesions compatible with bovine tuberculosis were collected at a local abattoir in the same district. Isolated mycobacteria were identified and genotyped using classical molecular methods. From a total of 33 isolates of M. tuberculosis detected (30 from humans and 3 from cattle), two cattle isolates shared the same spoligotype and MIRU-VNTR pattern with a human patient. This study has for the first time documented the isolation of M. tuberculosis from cattle in Zambia and provides molecular evidence of an epidemiological link between M. tuberculosis isolates from humans and cattle in Namwala district. A possible spill back of M. tuberculosis to humans cannot be excluded and therefore further studies documenting to what extent M. tuberculosis is shed in cattle milk are needed. This finding further suggests that veterinary public health measures to control human TB, should also take into account the bovine reservoir.
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Affiliation(s)
- Sydney Malama
- Institute of Economic and Social Research, University of Zambia, P.O. Box 30900, Munali Road, Lusaka, Zambia,
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Suitability of IS6110-RFLP and MIRU-VNTR for differentiating spoligotyped drug-resistant mycobacterium tuberculosis clinical isolates from Sichuan in China. BIOMED RESEARCH INTERNATIONAL 2014; 2014:763204. [PMID: 24724099 PMCID: PMC3958788 DOI: 10.1155/2014/763204] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 01/19/2014] [Accepted: 01/19/2014] [Indexed: 11/17/2022]
Abstract
Genotypes of Mycobacterium tuberculosis complex (MTBC) vary with the geographic origin of the patients and can affect tuberculosis (TB) transmission. This study was aimed to further differentiate spoligotype-defined clusters of drug-resistant MTBC clinical isolates split in Beijing (n = 190) versus non-Beijing isolates (n = 84) from Sichuan region, the second high-burden province in China, by IS6110-restriction fragment length polymorphism (RFLP) and 24-locus MIRU-VNTRs. Among 274 spoligotyped isolates, the clustering ratio of Beijing family was 5.3% by 24-locus MIRU-VNTRs versus 2.1% by IS6110-RFLP, while none of the non-Beijing isolates were clustered by 24-locus MIRU-VNTRs versus 9.5% by IS6110-RFLP. Hence, neither the 24-locus MIRU-VNTR was sufficient enough to fully discriminate the Beijing family, nor the IS6110-RFLP for the non-Beijing isolates. A region adjusted scheme combining 12 highly discriminatory VNTR loci with IS6110-RFLP was a better alternative for typing Beijing strains in Sichuan than 24-locus MIRU-VNTRs alone. IS6110-RFLP was for the first time introduced to systematically genotype MTBC in Sichuan and we conclude that the region-adjusted scheme of 12 highly discriminative VNTRs might be a suitable alternative to 24-locus MIRU-VNTR scheme for non-Beijing strains, while the clusters of the Beijing isolates should be further subtyped using IS6110-RFLP for optimal discrimination.
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Smit PW, Haanperä M, Rantala P, Couvin D, Lyytikäinen O, Rastogi N, Ruutu P, Soini H. Molecular epidemiology of tuberculosis in Finland, 2008-2011. PLoS One 2013; 8:e85027. [PMID: 24386443 PMCID: PMC3873426 DOI: 10.1371/journal.pone.0085027] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 11/20/2013] [Indexed: 01/21/2023] Open
Abstract
In industrialized countries the majority of tuberculosis (TB) cases are linked to immigration. In Finland, most cases are still Finnish born but the number of foreign born cases is steadily increasing. In this 4-year population based study, the TB situation in Finland was characterized by a genotypic analysis of Mycobacterium tuberculosis isolates. A total of 1048 M. tuberculosis isolates (representing 99.4% of all culture positive cases) were analyzed by spoligotyping and MIRU. Spoligotype lineages belonging to the Euro-American family were predominant among the Finnish isolates, particularly T (n=346, 33.0%) and Haarlem (n=237, 22.6%) strains. The lineage signature was unknown for 130 (12.4%) isolates. Out of the 17 multi-drug resistant TB strains, 10 (58.8%) belonged to the Beijing lineage. In total, 23 new SIT designations were given and 51 orphan strains were found, of which 58 patterns were unique to Finland. Phylogeographical TB mapping as compared to neighboring countries showed that the population structure in Finland most closely resembled that observed in Sweden. By combining spoligotyping and MIRU results, 98 clusters comprising 355 isolates (33.9%) were found. Only 10 clusters contained both Finnish and foreign born cases. In conclusion, a large proportion of the M. tuberculosis isolates were from Finnish born elderly patients. Moreover, many previously unidentified spoligotype profiles and isolates belonging to unknown lineages were encountered.
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Affiliation(s)
- Pieter Willem Smit
- European Public Health Microbiology Training Programme, (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
- Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Helsinki, Finland
- * E-mail:
| | - Marjo Haanperä
- Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Helsinki, Finland
| | - Pirre Rantala
- Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Helsinki, Finland
| | - David Couvin
- WHO Supranational TB Reference Laboratory, Tuberculosis & Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Abymes, France
| | - Outi Lyytikäinen
- Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Helsinki, Finland
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Tuberculosis & Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Abymes, France
| | - Petri Ruutu
- Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Helsinki, Finland
| | - Hanna Soini
- Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Helsinki, Finland
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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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Yimer SA, Hailu E, Derese Y, Bjune GA, Holm-Hansen C. Spoligotyping of Mycobacterium tuberculosis isolates among pulmonary tuberculosis patients in Amhara Region, Ethiopia. APMIS 2013; 121:878-85. [PMID: 23336257 DOI: 10.1111/apm.12046] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 12/07/2012] [Indexed: 11/28/2022]
Abstract
The aim of this study was to characterize Mycobacterium tuberculosis isolates circulating in the Amhara Region of Ethiopia. Sputum samples were collected from new pulmonary tuberculosis (TB) patients in the Region. Genotyping of mycobacterial DNA was performed by spoligotyping and isolates were assigned to families using the SpolDB4 and the model-based program 'Spotclust'. A high level of diversity was found among the 237 isolates. Sixty-five different spoligopatterns were obtained. The T (30.8%), Central Asian (CAS; 21.1%) and U (17.7%) families were the predominant isolates comprising 69.6% of the total strains. Eighty-five per cent of the U lineage belonged to Spoligo-International-Type (SIT) 910 and SIT 1729. Only a few of these strains are included in SpolDB4 to date. Of the total strains, 41 (17.3%) were unique and have not been described in SpolDB4 to date. This study indicated that the TB epidemic in Amhara Region, Ethiopia, is characterized by the circulation of numerous M. tuberculosis strain families. The high proportion of SIT 910 and SIT 1729 strains may indicate an increase in the importance of these lineages in the transmission of TB in the study region.
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Gafirita J, Umubyeyi AN, Asiimwe BB. A first insight into the genotypic diversity of Mycobacterium tuberculosis from Rwanda. BMC Clin Pathol 2012; 12:20. [PMID: 23131092 PMCID: PMC3520741 DOI: 10.1186/1472-6890-12-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 11/01/2012] [Indexed: 11/21/2022] Open
Abstract
Background Mycobacterium tuberculosis complex (MTC) is the causative agent of tuberculosis (TB). Globally, increasing evidence shows that in M. tuberculosis, transmission varies from strain to strain and that different strains exhibit a range of geographical and host specificities, pathogenicity, and drug susceptibility. Therefore rapid and accurate differentiation of the members of MTC is critical in guiding treatment and public health decisions. We carried out a study at different health units and the National Reference Laboratory in Rwanda identify Mycobacterium tuberculosis complex species prevalent in TB patients in Rwanda. We further characterized the isolates using spoligotyping in order to gain an insight into the strain diversity of drug resistant and susceptible isolates of M. tuberculosis in this setting. Methods A total of 151 isolates from culture positive sputum samples were harvested, heat killed at 80°C for two hours, and then shipped to Makerere University College of Health Sciences, Uganda, for speciation and typing. Species identification was achieved by regions of difference (RD) analysis, while Spoligotyping was done to identify strain types. Results Region of difference analysis identified all the 151 isolates as M. tuberculosis. Spoligotyping revealed predominance of the T2 family (58.3%, 88/151), with SIT 52 being the most prevalent strain (31.8%, 48/151). Among the 151 isolates, 64 (42.4%) were multidrug resistant (MDR) with 3 cases on mono-resistance. Of 94 retreatment cases, 48 (51.1%) were MDR and of 46 newly presenting cases 14 (30.4%) were MDR. There was a significant difference (p=0.01) in anti-TB drug resistance between new and retreatment cases in the sample. However, there was no significant relationship between HIV serostatus and the two major strain types SIT 52 (p =0.15and SIT 152 (p = 0.41). Conclusion Mycobacterium tuberculosis is the most prevalent species of Mycobacterium tuberculosis complex in Rwanda, and SIT 52 (T2) the predominant strain. There is significantly more MDR in the retreatment cases but no significant difference was observed by HIV status in relation to any spoligotypes.
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Affiliation(s)
- James Gafirita
- Department of Medical Microbiology, College of Health Sciences, Makerere University, P O Box 7072, Kampala, Uganda.
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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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Heterogeneity in tuberculosis transmission and the role of geographic hotspots in propagating epidemics. Proc Natl Acad Sci U S A 2012; 109:9557-62. [PMID: 22645356 DOI: 10.1073/pnas.1203517109] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The importance of high-incidence "hotspots" to population-level tuberculosis (TB) incidence remains poorly understood. TB incidence varies widely across countries, but within smaller geographic areas (e.g., cities), TB transmission may be more homogeneous than other infectious diseases. We constructed a steady-state compartmental model of TB in Rio de Janeiro, replicating nine epidemiological variables (e.g., TB incidence) within 1% of their observed values. We estimated the proportion of TB transmission originating from a high-incidence hotspot (6.0% of the city's population, 16.5% of TB incidence) and the relative impact of TB control measures targeting the hotspot vs. the general community. If each case of active TB in the hotspot caused 0.5 secondary transmissions in the general community for each within-hotspot transmission, the 6.0% of people living in the hotspot accounted for 35.3% of city-wide TB transmission. Reducing the TB transmission rate (i.e., number of secondary infections per infectious case) in the hotspot to that in the general community reduced city-wide TB incidence by 9.8% in year 5, and 29.7% in year 50-an effect similar to halving time to diagnosis for the remaining 94% of the community. The importance of the hotspot to city-wide TB control depended strongly on the extent of TB transmission from the hotspot to the general community. High-incidence hotspots may play an important role in propagating TB epidemics. Achieving TB control targets in a hotspot containing 6% of a city's population can have similar impact on city-wide TB incidence as achieving the same targets throughout the remaining community.
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First insight into the genetic diversity of Mycobacterium tuberculosis strains from patients in Duhok, Iraq. Int J Mycobacteriol 2012; 1:13-20. [DOI: 10.1016/j.ijmyco.2012.01.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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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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Ani AE, Diarra B, Dahle UR, Lekuk C, Yetunde F, Somboro AM, Anatole T, Idoko J. Identification of mycobacteria and other acid fast organisms associated with pulmonary disease. ASIAN PACIFIC JOURNAL OF TROPICAL DISEASE 2011. [DOI: 10.1016/s2222-1808(11)60061-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Thumamo BP, Asuquo AE, Abia-Bassey LN, Lawson L, Hill V, Zozio T, Emenyonu N, Eko FO, Rastogi N. Molecular epidemiology and genetic diversity of Mycobacterium tuberculosis complex in the Cross River State, Nigeria. INFECTION GENETICS AND EVOLUTION 2011; 12:671-7. [PMID: 21878397 DOI: 10.1016/j.meegid.2011.08.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 08/11/2011] [Accepted: 08/15/2011] [Indexed: 01/18/2023]
Abstract
This study provides with a first insight on Mycobacterium tuberculosis complex epidemiology and genetic diversity in the Cross River State, Nigeria. Starting with 137 smear positive patients recruited over a period of 12months (June 2008 to May 2009), we obtained 97 pure mycobacterial isolates out of which 81 (83.5%) were identified as M. tuberculosis complex. Genotyping revealed a total of 27 spoligotypes patterns with 10 clusters (n=64% or 79% of clustered isolates, 2-32 isolates/cluster), with patients in the age group range 25-34 years being significantly associated with shared-type pattern SIT61 (p=0.019). Comparison with SITVIT2 database showed that with the exception of a single cluster (SIT727/H1), all other clusters observed were representative of West Africa; the two main lineages involved were LAM10-CAM (n=42/81% or 51.8%) of M. tuberculosis and AFRI_2 sublineage of Mycobacterium africanum (n=27/81% or 33.3%). Subsequent 12-loci MIRU typing resulted in a total of 13 SIT/MIT clusters (n=52 isolates, 2-9 isolates per cluster), with a resulting recent n-1 transmission rate of 48.1%. Available drug-susceptibility testing (DST) results for 58/81 clinical isolates revealed 6/58% or 10.4% cases of multiple drug-resistance (MDR); 5/6 MDR cases were caused by strains belonging to LAM10-CAM lineage (a specific cluster SIT61/MIT266 in 4/6 cases, and an orphan spoligotype pattern in 1/6 case). Additionally, MIT266 was associated with streptomycin resistance (p=0.016). All the six MDRTB isolates were concomitantly resistance to streptomycin and ethambutol; however, 4/6 MDR strains with identical MIRU patterns were characterized by consecutive strain numbers hence the possibility of laboratory cross contamination could not be excluded in 3/4 serial cases. The present preliminary study underlines the usefulness of spoligotyping and 12-loci MIRU-VNTRs to establish a baseline of circulating genotypic lineages of M. tuberculosis complex in Nigeria.
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Affiliation(s)
- Benjamin P Thumamo
- Department of Medical Laboratory Science, University of Calabar, Calabar, Nigeria
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Yeboah-Manu D, Asante-Poku A, Bodmer T, Stucki D, Koram K, Bonsu F, Pluschke G, Gagneux S. Genotypic diversity and drug susceptibility patterns among M. tuberculosis complex isolates from South-Western Ghana. PLoS One 2011; 6:e21906. [PMID: 21779354 PMCID: PMC3133566 DOI: 10.1371/journal.pone.0021906] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Accepted: 06/14/2011] [Indexed: 11/18/2022] Open
Abstract
Objective The aim of this study was to use spoligotyping and large sequence polymorphism (LSP) to study the population structure of M. tuberculosis complex (MTBC) isolates. Methods MTBC isolates were identified using standard biochemical procedures, IS6110 PCR, and large sequence polymorphisms. Isolates were further typed using spoligotyping, and the phenotypic drug susceptibility patterns were determined by the proportion method. Result One hundred and sixty-two isolates were characterised by LSP typing. Of these, 130 (80.25%) were identified as Mycobacterium tuberculosis sensu stricto (MTBss), with the Cameroon sub-lineage being dominant (N = 59/130, 45.38%). Thirty-two (19.75%) isolates were classified as Mycobacterium africanum type 1, and of these 26 (81.25%) were identified as West-Africa I, and 6 (18.75%) as West-Africa II. Spoligotyping sub-lineages identified among the MTBss included Haarlem (N = 15, 11.53%), Ghana (N = 22, 16.92%), Beijing (4, 3.08%), EAI (4, 3.08%), Uganda I (4, 3.08%), LAM (2, 1.54%), X (N = 1, 0.77%) and S (2, 1.54%). Nine isolates had SIT numbers with no identified sub-lineages while 17 had no SIT numbers. MTBss isolates were more likely to be resistant to streptomycin (p<0.008) and to any drug resistance (p<0.03) when compared to M. africanum. Conclusion This study demonstrated that overall 36.4% of TB in South-Western Ghana is caused by the Cameroon sub-lineage of MTBC and 20% by M. africanum type 1, including both the West-Africa 1 and West-Africa 2 lineages. The diversity of MTBC in Ghana should be considered when evaluating new TB vaccines.
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Affiliation(s)
- Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana.
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Samandari T, Agizew TB, Nyirenda S, Tedla Z, Sibanda T, Shang N, Mosimaneotsile B, Motsamai OI, Bozeman L, Davis MK, Talbot EA, Moeti TL, Moffat HJ, Kilmarx PH, Castro KG, Wells CD. 6-month versus 36-month isoniazid preventive treatment for tuberculosis in adults with HIV infection in Botswana: a randomised, double-blind, placebo-controlled trial. Lancet 2011; 377:1588-98. [PMID: 21492926 DOI: 10.1016/s0140-6736(11)60204-3] [Citation(s) in RCA: 242] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
BACKGROUND In accordance with WHO guidelines, people with HIV infection in Botswana receive daily isoniazid preventive therapy against tuberculosis without obtaining a tuberculin skin test, but duration of prophylaxis is restricted to 6 months. We aimed to assess effectiveness of extended isoniazid therapy. METHODS In our randomised, double-blind, placebo-controlled trial we enrolled adults infected with HIV aged 18 years or older at government HIV-care clinics in Botswana. Exclusion criteria included current illness such as cough and an abnormal chest radiograph without antecedent tuberculosis or pneumonia. Eligible individuals were randomly allocated (1:1) to receive 6 months' open-label isoniazid followed by 30 months' masked placebo (control group) or 6 months' open-label isoniazid followed by 30 months' masked isoniazid (continued isoniazid group) on the basis of a computer-generated randomisation list with permuted blocks of ten at each clinic. Antiretroviral therapy was provided if participants had CD4-positive lymphocyte counts of fewer than 200 cells per μL. We used Cox regression analysis and the log-rank test to compare incident tuberculosis in the groups. Cox regression models were used to estimate the effect of antiretroviral therapy. The trial is registered at ClinicalTrials.gov, number NCT00164281. FINDINGS Between Nov 26, 2004, and July 3, 2009, we recorded 34 (3·4%) cases of incident tuberculosis in 989 participants allocated to the control group and 20 (2·0%) in 1006 allocated to the continued isoniazid group (incidence 1·26% per year vs 0·72%; hazard ratio 0·57, 95% CI 0·33-0·99, p=0·047). Tuberculosis incidence in those individuals receiving placebo escalated approximately 200 days after completion of open-label isoniazid. Participants who were tuberculin skin test positive (ie, ≥5 mm induration) at enrolment received a substantial benefit from continued isoniazid treatment (0·26, 0·09-0·80, p=0·02), whereas participants who were tuberculin skin test-negative received no significant benefit (0·75, 0·38-1·46, p=0·40). By study completion, 946 (47%) of 1995 participants had initiated antiretroviral therapy. Tuberculosis incidence was reduced by 50% in those receiving 360 days of antiretroviral therapy compared with participants receiving no antiretroviral therapy (adjusted hazard ratio 0·50, 95% CI 0·26-0·97). Severe adverse events and death were much the same in the control and continued isoniazid groups. INTERPRETATION In a tuberculosis-endemic setting, 36 months' isoniazid prophylaxis was more effective for prevention of tuberculosis than was 6-month prophylaxis in individuals with HIV infection, and chiefly benefited those who were tuberculin skin test positive. FUNDING US Centers for Disease Control and Prevention and US Agency for International Development.
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Affiliation(s)
- Taraz Samandari
- Botswana-USA Partnership (BOTUSA), Gaborone and Francistown, Botswana.
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Mycobacterium tuberculosis spoligotypes and drug susceptibility pattern of isolates from tuberculosis patients in South-Western Uganda. BMC Infect Dis 2011; 11:81. [PMID: 21453482 PMCID: PMC3100262 DOI: 10.1186/1471-2334-11-81] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Accepted: 03/31/2011] [Indexed: 11/18/2022] Open
Abstract
Background Determination of the prevalence and drug susceptibility of the M. tuberculosis strains is important in tuberculosis control. We determined the genetic diversity and susceptibility profiles of mycobacteria isolated from tuberculosis patients in Mbarara, South Western Uganda. Methods We enrolled, consecutively; all newly diagnosed and previously treated smear-positive TB patients aged ≥ 18 years. The isolates were characterized using regions of difference (RD) analysis and spoligotyping. Drug resistance against rifampicin and isoniazid were tested using the Genotype® MDRTBplus assay and the indirect proportion method on Lowenstein-Jensen media. HIV-1 testing was performed using two rapid HIV tests. Results A total of 125 isolates from 167 TB suspects (60% males) with a mean age 33.7 years and HIV prevalence of 67.9% (55/81) were analyzed. Majority (92.8%) were new cases while only 7.2% were retreatment cases. All the 125 isolates were identified as M. tuberculosis strict sense with the majority (92.8%) of the isolates being modern strains while seven (7.2%) isolates were ancestral strains. Spoligotyping revealed 79 spoligotype patterns, with an overall diversity of 63.2%. Sixty two (49.6%) of the isolates formed 16 clusters consisting of 2-15 isolates each. A majority (59.2%) of the isolates belong to the Uganda genotype group of strains. The major shared spoligotypes in our sample were SIT 135 (T2-Uganda) with 15 isolates and SIT 128 (T2) with 3 isolates. Sixty nine (87%) of the 79 patterns had not yet been defined in the SpolDB4.0.database. Resistance mutations to either RIF or INH were detected in 6.4% of the isolates. Multidrug resistance, INH and RIF resistance was 1.6%, 3.2% and 4.8%, respectively. The rpoβ gene mutations seen in the sample were D516V, S531L, H526Y H526D and D516V, while one strain had a Δ1 mutation in the wild type probes. There were three strains with katG (codon 315) gene mutations only while one strain showed the inhA promoter gene mutation. Conclusion The present study shows that the TB epidemic in Mbarara is caused by modern M. tuberculosis strains mainly belonging to the Uganda genotype and anti-TB drug resistance rate in the region is low.
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Bazira J, Matte M, Asiimwe BB, Joloba LM. Genetic diversity of Mycobacterium tuberculosis in Mbarara, South Western Uganda. Afr Health Sci 2010; 10:306-311. [PMID: 21416030 PMCID: PMC3052804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023] Open
Abstract
BACKGROUND We determined the genetic diversity of mycobacteria isolated from tuberculosis patients in Mbarara Uganda, using region of difference (RD) analysis and spacer oligonucleotide typing (spoligotyping). METHODS Sputum samples were cultured on Lowenstein Jensen media. The isolates were characterized using RD analysis and spoligotyping. RESULTS The majority (92.8%) of the patients were new cases, 60% were males and 44% were HIV positive with a mean age of 33.7 years. All the 125 isolates were identified as M.tuberculosis sensu stricto. Most (92.8%) of the isolates were modern strains. Spoligotyping revealed 79 spoligotype patterns, with an overall diversity of 63.2%. Sixty (48%) isolates formed 16 clusters each consisting of 2-15 isolates. Mst (59.2 %) of the isolates were Uganda genotype strains. The major shared spoligotypes in our sample were SIT 135 (T2-Uganda) with 12 isolates and SIT 128 (T2) with 5 isolates. Sixty nine (87%) patterns had not yet been defined in the SpolDB4.0.database. CONCLUSION The TB epidemic in Mbarara is caused mainly by modern M.tuberculosis strains of the Uganda genotype. The wide diversity of strains may indicate that the majority of the TB cases are reactivation rather than re-infection. However this needs to be ascertained with more discriminative finger printing techniques.
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Affiliation(s)
- J Bazira
- Department of Microbiology, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda.
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Glynn JR, Alghamdi S, Mallard K, McNerney R, Ndlovu R, Munthali L, Houben RM, Fine PEM, French N, Crampin AC. Changes in Mycobacterium tuberculosis genotype families over 20 years in a population-based study in Northern Malawi. PLoS One 2010; 5:e12259. [PMID: 20808874 PMCID: PMC2923199 DOI: 10.1371/journal.pone.0012259] [Citation(s) in RCA: 20] [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: 05/18/2010] [Accepted: 07/26/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Despite increasing interest in possible differences in virulence and transmissibility between different genotypes of M. tuberculosis, very little is known about how genotypes within a population change over decades, or about relationships to HIV infection. METHODS AND PRINCIPAL FINDINGS In a population-based study in rural Malawi we have examined smears and cultures from tuberculosis patients over a 20-year period using spoligotyping. Isolates were grouped into spoligotype families and lineages following previously published criteria. Time trends, HIV status, drug resistance and outcome were examined by spoligotype family and lineage. In addition, transmissibility was examined among pairs of cases with known epidemiological contact by assessing the proportion of transmissions confirmed for each lineage, on the basis of IS6110 RFLP similarity of the M tuberculosis strains. 760 spoligotypes were obtained from smears from 518 patients from 1986-2002, and 377 spoligotypes from cultures from 347 patients from 2005-2008. There was good consistency in patients with multiple specimens. Among 781 patients with first episode tuberculosis, the majority (76%) had Lineage 4 ("European/American") strains; 9% had Lineage 3 ("East-African/Indian"); 8% Lineage 1 ("Indo-Oceanic"); and 2% Lineage 2 ("East-Asian"); others unclassifiable. Over time the proportion of Lineage 4 decreased from >90% to 60%, with an increase in the other 3 lineages (p<0.001). Lineage 1 strains were more common in those with HIV infection, even after adjusting for age, sex and year. There were no associations with drug resistance or outcome, and no differences by lineage in the proportion of pairs in which transmission was confirmed. CONCLUSIONS This is the first study to describe long term trends in the four M. tuberculosis lineages in a population. Lineage 4 has probably been longstanding in this population, with relatively recent introductions and spread of Lineages1-3, perhaps influenced by the HIV epidemic.
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Affiliation(s)
- Judith R Glynn
- London School of Hygiene & Tropical Medicine, London, United Kingdom.
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Viegas SO, Machado A, Groenheit R, Ghebremichael S, Pennhag A, Gudo PS, Cuna Z, Miotto P, Hill V, Marrufo T, Cirillo DM, Rastogi N, Källenius G, Koivula T. Molecular diversity of Mycobacterium tuberculosis isolates from patients with pulmonary tuberculosis in Mozambique. BMC Microbiol 2010; 10:195. [PMID: 20663126 PMCID: PMC2914001 DOI: 10.1186/1471-2180-10-195] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Accepted: 07/21/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mozambique is one of the countries with the highest burden of tuberculosis (TB) in Sub-Saharan Africa, and information on the predominant genotypes of Mycobacterium tuberculosis circulating in the country are important to better understand the epidemic. This study determined the predominant strain lineages that cause TB in Mozambique. RESULTS A total of 445 M. tuberculosis isolates from seven different provinces of Mozambique were characterized by spoligotyping and resulting profiles were compared with the international spoligotyping database SITVIT2.The four most predominant lineages observed were: the Latin-American Mediterranean (LAM, n = 165 or 37%); the East African-Indian (EAI, n = 132 or 29.7%); an evolutionary recent but yet ill-defined T clade, (n = 52 or 11.6%); and the globally-emerging Beijing clone, (n = 31 or 7%). A high spoligotype diversity was found for the EAI, LAM and T lineages. CONCLUSIONS The TB epidemic in Mozambique is caused by a wide diversity of spoligotypes with predominance of LAM, EAI, T and Beijing lineages.
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Affiliation(s)
- Sofia O Viegas
- Faculty of Veterinary, Eduardo Mondlane University, Maputo Mozambique.
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Ani A, Bruvik T, Okoh Y, Agaba P, Agbaji O, Idoko J, Dahle UR. Genetic diversity of Mycobacterium tuberculosis Complex in Jos, Nigeria. BMC Infect Dis 2010; 10:189. [PMID: 20579382 PMCID: PMC2902480 DOI: 10.1186/1471-2334-10-189] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Accepted: 06/26/2010] [Indexed: 11/18/2022] Open
Abstract
Background Nigeria has a high tuberculosis incidence, and genotyping studies of Mycobacterium tuberculosis Complex (MTC) in the country are necessary in order to improve our understanding of the epidemic. Methods Isolates of MTC were isolated from cases of pulmonary tuberculosis in Jos, North Central region of Nigeria during 2006-2008. Drug susceptibility test (DST) was performed on 77 of 111 isolates by proportion method on Lowenstein Jensen (LJ) slope while genotyping of mycobacterial DNA was performed by spoligotyping. The SpolDB4 database and the model-based program 'spotclust' were used to assign isolates to families, subfamilies and variants. Results A total of 111 pulmonary isolates from consecutive tuberculosis patients in the city of Jos, Plateau State, Nigeria were spoligotyped. A total of 84 (76%) of the isolates belonged to the Latin American Mediterranean (LAM) family. Of these, 78 isolates were assigned to the LAM10 lineage. Among these, 66 exhibited identical spoligopatterns. Drug susceptibility profiles obtained were not consistently associated with any spoligopattern. Conclusions The dominance of few M. tuberculosis lineages suggests either a high rate of transmission, frequent import of closely related strains, or a highly conserved genotype. It remains to be confirmed whether the predominance of identical LAM10 represent an outbreak. Spoligotyping was useful to gain an overall understanding of the local TB epidemic. This study demonstrated that the incidence of TB in Jos, Nigeria may be caused by a few successful M. tuberculosis families, dominated by the LAM10 family.
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Affiliation(s)
- Agatha Ani
- Division of Infectious Disease Control, Norwegian Institute of Public Health, Oslo, Norway
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Mulenga C, Shamputa IC, Mwakazanga D, Kapata N, Portaels F, Rigouts L. Diversity of Mycobacterium tuberculosis genotypes circulating in Ndola, Zambia. BMC Infect Dis 2010; 10:177. [PMID: 20565802 PMCID: PMC2906459 DOI: 10.1186/1471-2334-10-177] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Accepted: 06/17/2010] [Indexed: 11/10/2022] Open
Abstract
Background Tuberculosis (TB) is one of the major public health problems in Zambia. However, information about lineages of M. tuberculosis complex (MTBC) isolates useful for epidemiology investigations is unknown. In this study, we investigated the diversity of MTBC isolates from Ndola, a typical Zambian urbanized city with a documented high HIV prevalence. Methods This was part of a prospective cohort study in subjects with sputum smear-positive pulmonary TB. Spoligotyping was used to genotype the MTBC isolates and establish the circulating lineages. The 15-locus Mycobacterial Interspersed Repetitive Units - Variable Number Tandem Repeats (MIRU-VNTR) typing was used to study recent transmission. Results A total of 98 different spoligotypes were identified among 273 MTBC isolates. The majority (64.8%) of the isolates belonged to 9 known families, while 96 (35.2%) of the isolates were orphans. While LAM (41.8%) was the largest spoligotype family observed, most of the isolates (87.7%) belonging to the SAF1 family, with a significant portion coming from the T (13.6%), and X (5.9%) families. A few isolates (3.6%) belonged to the CAS, EAI, H, S, X1-LAM9 or U families. MIRU-VNTR typing was highly discriminatory (h = 0.988) among the 156 isolates tested in our sample, and increased the discrimination among 82 SAF1 isolates from 6 to 46 distinct patterns. In addition, 3.2% (5/156) of cases with available MIRU-VNTR results harbored more than one MTBC strain. Conclusions Our findings show a limited diversity of MTBC in Ndola with a high clustering rate (37.7%), which indicates that recent transmission plays an appreciable role in the dynamics of TB disease in this setting. This conclusion emphasizes the importance of early diagnosis and timely treatment. The results also confirm that MIRU-VNTR typing is suitable for studying the molecular epidemiology of TB in Ndola.
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Isoniazid tuberculosis preventive therapy in HIV-infected adults accessing antiretroviral therapy: a Botswana Experience, 2004-2006. J Acquir Immune Defic Syndr 2010; 54:71-7. [PMID: 19934764 DOI: 10.1097/qai.0b013e3181c3cbf0] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES To describe reasons for exclusion from isoniazid tuberculosis preventive therapy (IPT) and outcomes of persons living with HIV (PLWH) during 6 months of IPT. METHODS In a clinical trial conducted in government clinics, first screening (screen 1) used National IPT Program guidelines and a second screening (screen 2) was trial specific. Adherence was defined as attending 6 monthly visits. RESULTS Between 2004 and 2006, at 4018 screening visits, 2934 (73%) PLWH met screen 1 criteria; 1995 (68%) met screen 2 criteria and were enrolled. Major reasons for exclusion were illness (66%) at screen 1 and abnormal chest radiographs (36%) at screen 2. Tuberculin skin tests were > or = 5 mm in 24% of those enrolled and 31% had CD4 lymphocyte counts <200 cells/mm(3). During the 6 months, 8 (0.40%) developed tuberculosis disease, 28 (1.4%) had severe adverse events (19/28 were hepatitis including one death probably isoniazid-associated), 20 others died, and 22% initiated antiretroviral therapy (ART). Although adherence was 86%, being on ART improved adherence: relative risk 1.41 (95% confidence limits 1.04-1.91). In multivariate analysis, ART was associated with a 4.38 greater odds of adherence to IPT. CONCLUSIONS Six months of IPT was relatively safe and well-tolerated by PLWH. Adherence to IPT was significantly better among those receiving ART with IPT.
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DNA restriction fragment length polymorphism analysis of Mycobacterium tuberculosis isolates from HIV-seropositive and HIV-seronegative patients in Kampala, Uganda. BMC Infect Dis 2009; 9:12. [PMID: 19196450 PMCID: PMC2645406 DOI: 10.1186/1471-2334-9-12] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2008] [Accepted: 02/05/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The identification and differentiation of strains of Mycobacterium tuberculosis by DNA fingerprinting has provided a better understanding of the epidemiology and tracing the transmission of tuberculosis. We set out to determine if there was a relationship between the risk of belonging to a group of tuberculosis patients with identical mycobacterial DNA fingerprint patterns and the HIV sero-status of the individuals in a high TB incidence peri-urban setting of Kampala, Uganda. METHODS One hundred eighty three isolates of Mycobacterium tuberculosis from 80 HIV seropositive and 103 HIV seronegative patients were fingerprinted by standard IS6110-RFLP. Using the BioNumerics software, strains were considered to be clustered if at least one other patient had an isolate with identical RFLP pattern. RESULTS One hundred and eighteen different fingerprint patterns were obtained from the 183 isolates. There were 34 clusters containing 54% (99/183) of the patients (average cluster size of 2.9), and a majority (96.2%) of the strains possessed a high copy number (> or = 5 copies) of the IS6110 element. When strains with <5 bands were excluded from the analysis, 50.3% (92/183) were clustered, and there was no difference in the level of diversity of DNA fingerprints observed in the two sero-groups (adjusted odds ratio [aOR] 0.85, 95%CI 0.46-1.56, P = 0.615), patients aged <40 years (aOR 0.53, 95%CI 0.25-1.12, P = 0.100), and sex (aOR 1.12, 95%CI 0.60-2.06, P = 0.715). CONCLUSION The sample showed evidence of a high prevalence of recent transmission with a high average cluster size, but infection with an isolate with a fingerprint found to be part of a cluster was not associated with any demographic or clinical characteristics, including HIV status.
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Crampin AC, Glynn JR, Fine PEM. What has Karonga taught us? Tuberculosis studied over three decades. Int J Tuberc Lung Dis 2009; 13:153-64. [PMID: 19146741 PMCID: PMC3272402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
This paper summarises tuberculosis (TB) research over almost 30 years in Karonga District, northern Malawi, an area typical of much of rural Africa. The dominant factor has been the human immunodeficiency virus (HIV), which arrived in the district about 1980, leading to an increase in TB incidence to a peak of approximately 65 smear-positive pulmonary cases per 100000 population in 2000. Tuberculin surveys indicate annual risks of Mycobacterium tuberculosis infection of approximately 1%; thus, most of the population is uninfected and at risk of primary infection and disease. Molecular epidemiological studies demonstrate that about two thirds of TB arises from recent infection, but recognisable recent contact is responsible for only about 10% of disease. By 2001, 57% of TB was directly attributable to HIV, implying that it would have declined were it not for HIV. HIV infection increases the risk of TB most among young adults, and greatly increases the risk of recurrence from new infection after treatment. Mortality rates in the HIV-infected are high, but there is no association of HIV with drug resistance. Other risk factors with relatively smaller effects include age and sex, contact, several genetic polymorphisms and area. Neither one nor two doses of the bacille Calmette-Guérin (BCG) vaccine provides protection against adult pulmonary TB, despite protecting against leprosy. Skin test surveys, cohort studies and comparative immunological studies with the UK suggest that exposure to environmental mycobacteria provides some protection against TB and that BCG's failure is attributable partly to this widespread heterologous exposure masking effects of the vaccine. Drug resistance has remained constant (<10%) over more than 20 years. Immunotherapy with M. vaccae provided no benefits, but treatment of HIV-positive patients with cotrimoxazole reduced mortality. The Karonga programme illustrates the value of long-term population-based studies to investigate the natural history of TB and to influence TB control policy. Current studies focus on immunological markers of infection, disease and protection, and on elucidating the impact of antiretroviral treatment on TB incidence at population level.
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Affiliation(s)
- A C Crampin
- London School of Hygiene & Tropical Medicine, London, UK.
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Reyes JF, Francis AR, Tanaka MM. Models of deletion for visualizing bacterial variation: an application to tuberculosis spoligotypes. BMC Bioinformatics 2008; 9:496. [PMID: 19036166 PMCID: PMC2620273 DOI: 10.1186/1471-2105-9-496] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Accepted: 11/27/2008] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Molecular typing methods are commonly used to study genetic relationships among bacterial isolates. Many of these methods have become standardized and produce portable data. A popular approach for analyzing such data is to construct graphs, including phylogenies. Inferences from graph representations of data assist in understanding the patterns of transmission of bacterial pathogens, and basing these graph constructs on biological models of evolution of the molecular marker helps make these inferences. Spoligotyping is a widely used method for genotyping isolates of Mycobacterium tuberculosis that exploits polymorphism in the direct repeat region. Our goal was to examine a range of models describing the evolution of spoligotypes in order to develop a visualization method to represent likely relationships among M. tuberculosis isolates. RESULTS We found that inferred mutations of spoligotypes frequently involve the loss of a single or very few adjacent spacers. Using a second-order variant of Akaike's Information Criterion, we selected the Zipf model as the basis for resolving ambiguities in the ancestry of spoligotypes. We developed a method to construct graphs of spoligotypes (which we call spoligoforests). To demonstrate this method, we applied it to a tuberculosis data set from Cuba and compared the method to some existing methods. CONCLUSION We propose a new approach in analyzing relationships of M. tuberculosis isolates using spoligotypes. The spoligoforest recovers a plausible history of transmission and mutation events based on the selected deletion model. The method may be suitable to study markers based on loci of similar structure from other bacteria. The groupings and relationships in the spoligoforest can be analyzed along with the clinical features of strains to provide an understanding of the evolution of spoligotypes.
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Affiliation(s)
- Josephine F Reyes
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2052, Australia
- Evolution & Ecology Research Centre, University of New South Wales, Sydney 2052, Australia
| | - Andrew R Francis
- School of Computing and Mathematics, University of Western Sydney, South Penrith DC, NSW 1797, Australia
| | - Mark M Tanaka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2052, Australia
- Evolution & Ecology Research Centre, University of New South Wales, Sydney 2052, Australia
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Glynn JR, Crampin AC, Traore H, Chaguluka S, Mwafulirwa DT, Alghamdi S, Ngwira BMM, Yates MD, Drobniewski FD, Fine PEM. Determinants of cluster size in large, population-based molecular epidemiology study of tuberculosis, northern Malawi. Emerg Infect Dis 2008; 14:1060-6. [PMID: 18598626 PMCID: PMC2600342 DOI: 10.3201/eid1407.060468] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Both epidemiologic and strain-related factors may contribute to large clusters of tuberculosis patients. Tuberculosis patients with identical strains of Mycobacterium tuberculosis are described as clustered. Cluster size may depend on patient or strain characteristics. In a 7-year population-based study of tuberculosis in Karonga District, Malawi, clusters were defined by using IS6110 restriction fragment length polymorphism, excluding patterns with <5 bands. Spoligotyping was used to compare strains with an international database. Among 682 clustered patients, cluster size ranged from 2 to 37. Male patients, young adults, and town residents were over-represented in large clusters. Cluster size was not associated with HIV status or death from tuberculosis. Spoligotypes from 9 (90%) of 10 large cluster strains were identical or very similar (1 spacer different) to common spoligotypes found elsewhere, compared with 37 (66%) of 56 of those from nonclustered patients (p = 0.3). Large clusters were associated with factors likely to be related to social mixing, but spoligotypes of common strains in this setting were also common types elsewhere, consistent with strain differences in transmissibility.
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Affiliation(s)
- Judith R Glynn
- London School of Hygiene and Tropical Medicine, London, UK
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Asiimwe BB, Ghebremichael S, Kallenius G, Koivula T, Joloba ML. Mycobacterium tuberculosis spoligotypes and drug susceptibility pattern of isolates from tuberculosis patients in peri-urban Kampala, Uganda. BMC Infect Dis 2008; 8:101. [PMID: 18662405 PMCID: PMC2519071 DOI: 10.1186/1471-2334-8-101] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2008] [Accepted: 07/28/2008] [Indexed: 11/27/2022] Open
Abstract
Background The poor peri-urban areas of developing countries with inadequate living conditions and a high prevalence of HIV infection have been implicated in the increase of tuberculosis (TB). Presence of different lineages of Mycobacterium tuberculosis has been described in different parts of the world. This study determined the predominant strain lineages that cause TB in Rubaga division, Kampala, Uganda, and the prevalence of resistance to key anti-tuberculosis drugs in this community. Methods This was a cross-sectional study of newly diagnosed sputum smear-positive patients aged ≥ 18 years. A total of 344 isolates were genotyped by standard spoligotyping and the strains were compared with those in the international spoligotype database (SpolDB4). HIV testing and anti-tuberculosis drug susceptibility assays for isoniazid and rifampicin were performed and association with the most predominant spoligotypes determined. Results A total of 33 clusters were obtained from 57 spoligotype patterns. According to the SpolDB4 database, 241 (70%) of the isolates were of the T2 family, while CAS1-Kili (3.5%), LAM9 (2.6%), CAS1-Delhi (2.6%) were the other significant spoligotypes. Furthermore, a major spoligotype pattern of 17 (4.5%) strains characterized by lack of spacers 15–17 and 19–43 was not identified in SpolDB4. A total of 92 (26.7%) of the patients were HIV sero-positive, 176 (51.2%) sero-negative, while 76 (22.1%) of the patients did not consent to HIV testing. Resistance to isoniazid was found in 8.1% of strains, while all 15 (4.4%) strains resistant to rifampicin were multi-drug resistant. Additionally, there was no association between any strain types in the sample with either drug resistance or HIV sero-status of the patients. Conclusion The TB epidemic in Kampala is localized, mainly caused by the T2 family of strains. Strain types were neither associated with drug resistance nor HIV sero-status.
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Affiliation(s)
- Benon B Asiimwe
- Department of Medical Microbiology, Makerere University Medical School, Kampala, Republic of Uganda.
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40
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Oelemann MC, Fontes ANB, Pereira MADS, Bravin Y, Silva G, Degrave W, Carvalho ACC, Brito RC, Kritski AL, Suffys PN. Typing of Mycobacterium tuberculosis strains isolated in Community Health Centers of Rio de Janeiro City, Brazil. Mem Inst Oswaldo Cruz 2008; 102:455-62. [PMID: 17612765 DOI: 10.1590/s0074-02762007005000034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Accepted: 03/12/2007] [Indexed: 11/21/2022] Open
Abstract
Fingerprinting of Mycobacterium tuberculosis strains from tuberculosis (TB) patients attended in Community Health Centers (CHCs) of Rio de Janeiro was performed to verify possible risk factors for TB transmission. A prospective community-based study was performed during the period of July 1996 to December 1996 by collecting sputum samples of 489 patients in 11 different CHCs in four different planning areas (APs) of the city. Bacteriological, clinical, and epidemiological information was collected and M. tuberculosis genotypes defined after restriction fragment length polymorphism (IS6110-RFLP) and double repetitive element (DRE) fingerprinting of RFLP-clustered cases. Risk factors for TB transmission were looked for using three levels of cluster stringency. Among 349 (71%) positive cultures obtained, IS6110-RFLP typing could be performed on strains from 153 different patients. When using identity of RFLP patterns as cluster definition, 49 (32%) of the strains belonged to a cluster and none of the clinical or epidemiologic characteristics was associated with higher clustering levels. However, higher clustering level was observed in the AP including the central region of the city when compared to others. This strongly suggests that more recent transmission occurs in that area and this may be related with higher incidence of TB and HIV in this region.
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Affiliation(s)
- Maraníbia C Oelemann
- Departamento de Micobacterioses, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, 21045-900, Brasil
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Tazi L, Reintjes R, Bañuls AL. Tuberculosis transmission in a high incidence area: a retrospective molecular epidemiological study of Mycobacterium tuberculosis in Casablanca, Morocco. INFECTION GENETICS AND EVOLUTION 2007; 7:636-44. [PMID: 17689298 DOI: 10.1016/j.meegid.2007.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Revised: 06/26/2007] [Accepted: 06/28/2007] [Indexed: 11/19/2022]
Abstract
Like in most developing countries, tuberculosis represents a major public health problem in Morocco. This paper describes the first study combining molecular and conventional epidemiology of tuberculosis in Casablanca, the economic capital of this country. Molecular fingerprinting of the genomic DNA recovered from cultures of sputum of 150 patients was performed by MIRU-VNTR. This molecular marker revealed that 53.1% of the total cases were clustered. These cases were classified into 23 clusters ranging in size from 2 to 13 patients, suggesting a rate of 37% of recent transmission in the sample under study. In a multivariate analysis, there were no independent predictors of clustering. However, the clinical form was associated with drug resistance (odds ratio=9.9; P value=0.0006). The phylogenetic analysis showed that the heterogeneity found in this population includes also the members from a same patient family, and that the 2 major families distributed in Casablanca were the Latin-American-Mediterranean (LAM) and Haarlem families. All the results of this work allow to understand better the tuberculosis transmission in Casablanca, and suggest that different clones of M. tuberculosis seem to circulate in this city, and that the reactivation of latent infections would be mainly responsible for the endemic situation of this disease. These findings indicate also that the transmission of TB in Morocco is not optimally controlled, and that efforts for control strategies should be sustained in all developing countries where the incidence of TB is high and still raising.
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Affiliation(s)
- Loubna Tazi
- Centre IRD, Génétique et Evolution des Maladies Infectieuses (UMR CNRS/IRD 2724), 911 Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France.
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Kisa O, Albay A, Baylan O, Tozkoparan E, Acikel CH, Doganci L. Genetic diversity of Mycobacterium tuberculosis isolates at the Military Medical Academy in Ankara, Turkey. Res Microbiol 2007; 158:318-23. [PMID: 17398073 DOI: 10.1016/j.resmic.2007.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2006] [Revised: 12/01/2006] [Accepted: 01/25/2007] [Indexed: 11/23/2022]
Abstract
Genotyping of Mycobacterium tuberculosis isolates from infected individuals can play an important role in tracking the source of infection and unraveling the epidemiology of a tuberculosis pandemic. A total of 114 M. tuberculosis isolates were genotyped by spoligotyping and results were compared with an international spoligotype database (SpoIDB4). Twenty-one spoligotyping-defined clusters including 97 patients were established, and an additional 17 unique patterns were found. Ninety-eight (85.9%) isolates belonged to previously defined shared types (STs). The ST53 (ill-defined T1 superfamily, n=31), ST41 (LAM7-TUR family, n=9), ST118 (T undefined, n=8) and ST50 (Haarlem 3, n=6) were four major clusters of our isolates. After comparison with the international SpoIDB4 database, two new intrafile clusters, ST2136 and ST2139, were created and two new interfile clusters, ST2135 and ST2140, were defined. Eight (7%) of the 17 isolates with unique patterns were found to be orphans, whereas the STs of 9 isolates had previously been deposited in the international SpoIDB4 database. In addition, two isolates with an ST pattern characteristic of the Beijing family of M. tuberculosis were found. This study shows that, although ubiquitous spoligotypes are common, several spoligotypes specific to Turkey also exist. Thus, our study may help us to better understand the spread of M. tuberculosis genotypes to Turkey.
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Affiliation(s)
- Ozgul Kisa
- Department of Microbiology and Clinical Microbiology, Gulhane Military Medical Academy and School of Medicine, 06018 Ankara, Turkey.
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43
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Streicher EM, Victor TC, van der Spuy G, Sola C, Rastogi N, van Helden PD, Warren RM. Spoligotype signatures in the Mycobacterium tuberculosis complex. J Clin Microbiol 2006; 45:237-40. [PMID: 17065260 PMCID: PMC1828946 DOI: 10.1128/jcm.01429-06] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Evolution of the direct repeat region in Mycobacterium tuberculosis has created unique spoligotype signatures specifically associated with IS6110-defined strain families. Spoligotyping signatures may enable the analysis of the strain population structure in different settings and will enable the rapid identification of strain families that acquire drug resistance or escape protective immunity in drug and vaccine trials.
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Affiliation(s)
- E M Streicher
- DST/NRF Centre of Excellence in Biomedical TB Research, Department of Medical Biochemistry, Stellenbosch University, Tygerberg, South Africa 7505
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44
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Abstract
The genotype, endemic in some areas and emerging in others, may be associated with drug-resistance. Beijing/W genotype Mycobacterium tuberculosis is widespread, may be increasing, and may have a predilection for drug resistance. Individual-level data on >29,000 patients from 49 studies in 35 countries were combined to assess the Beijing genotype’s prevalence worldwide, trends over time and with age, and associations with drug resistance. We found 4 patterns for Beijing/W genotype tuberculosis (TB): 1) endemic, not associated with drug resistance (high level in most of East Asia, lower level in parts of the United States); 2) epidemic, associated with drug resistance (high level in Cuba, the former Soviet Union, Vietnam, and South Africa, lower level in parts of Western Europe); 3) epidemic but drug sensitive (Malawi, Argentina); and 4) very low level or absent (parts of Europe, Africa). This study confirms that Beijing/W genotype TB is an emerging pathogen in several areas and a predominant endemic strain in others; it is frequently associated with drug resistance.
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45
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Eldholm V, Matee M, Mfinanga SGM, Heun M, Dahle UR. A first insight into the genetic diversity of Mycobacterium tuberculosis in Dar es Salaam, Tanzania, assessed by spoligotyping. BMC Microbiol 2006; 6:76. [PMID: 16970826 PMCID: PMC1592105 DOI: 10.1186/1471-2180-6-76] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2006] [Accepted: 09/13/2006] [Indexed: 11/10/2022] Open
Abstract
Background Tanzania has a high tuberculosis incidence, and genotyping studies of Mycobacterium tuberculosis in the country are necessary in order to improve our understanding of the epidemic. Spoligotyping is a potentially powerful genotyping method due to fast generation of genotyping results, high reproducibility and low operation costs. The recently constructed SpolDB4 database and the model-based program 'Spotclust' can be used to assign isolates to families, subfamilies and variants. The results of a study can thus be analyzed in a global context. Results One hundred forty-seven pulmonary isolates from consecutive tuberculosis patients in Dar es Salaam were spoligotyped. SpolDB4 and 'Spotclust' were used to assign isolates to families, subfamilies and variants. The CAS (37%), LAM (22%) and EAI (17%) families were the most abundant. Despite the dominance of these three families, diversity was high due to variation within M. tuberculosis families. Of the obtained spoligopatterns, 64% were previously unrecorded. Conclusion Spoligotyping is useful to gain an overall understanding of the local TB epidemic. This study demonstrates that the extensive TB epidemic in Dar es Salaam, Tanzania is caused by a few successful M. tuberculosis families, dominated by the CAS family. Import of strains was a minor problem.
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Affiliation(s)
- Vegard Eldholm
- Division of Infectious Disease Control, Norwegian Institute of Public Health, Oslo, Norway
- Institute of Nature Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Mecky Matee
- Muhimbili Medical Research Centre, Dar es Salaam, Tanzania
| | | | - Manfred Heun
- Institute of Nature Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Ulf R Dahle
- Division of Infectious Disease Control, Norwegian Institute of Public Health, Oslo, Norway
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46
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Brudey K, Filliol I, Ferdinand S, Guernier V, Duval P, Maubert B, Sola C, Rastogi N. Long-term population-based genotyping study of Mycobacterium tuberculosis complex isolates in the French departments of the Americas. J Clin Microbiol 2006; 44:183-91. [PMID: 16390968 PMCID: PMC1351934 DOI: 10.1128/jcm.44.1.183-191.2006] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The three French overseas departments of the Americas are characterized both by insular (Guadeloupe and Martinique) and continental (French Guiana) settings with a tuberculosis case detection rate that varies from less than 10 per 100,000 per year in insular areas to an estimated incidence of more than 55 per 100,000 in French Guiana. Under a long-term genotyping program, more than three-fourths of all the Mycobacterium tuberculosis isolates (n = 744) received from the three settings were fingerprinted over a 10-year period (1994 to 2003) by spoligotyping and variable number of tandem DNA repeats (VNTRs) in order to understand the current trends in their detection rates, drug resistance, and groups and subpopulations at risk of contracting the disease and to pinpoint the circulating phylogeographical clades of the bacilli. The major difference in the study populations was the nationality of the patients, with a high percentage of immigrants from high-incidence neighboring countries in French Guiana and a low but increasing percentage in the French Caribbean. The rate of recent transmission was calculated to be 49.3% in French Guiana, compared to 27.2% and 16.9% in Guadeloupe and Martinique, respectively. At the phylogeographic level, 77.9% of the isolates studied belonged to four major clades (Haarlem, Latin-American and Mediterranean, T, and X) which are already reported from neighboring Caribbean islands in an international database and may underline potential interregional transmission events.
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Affiliation(s)
- Karine Brudey
- Unité de la tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes, French Guiana
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47
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Brudey K, Driscoll JR, Rigouts L, Prodinger WM, Gori A, Al-Hajoj SA, Allix C, Aristimuño L, Arora J, Baumanis V, Binder L, Cafrune P, Cataldi A, Cheong S, Diel R, Ellermeier C, Evans JT, Fauville-Dufaux M, Ferdinand S, de Viedma DG, Garzelli C, Gazzola L, Gomes HM, Guttierez MC, Hawkey PM, van Helden PD, Kadival GV, Kreiswirth BN, Kremer K, Kubin M, Kulkarni SP, Liens B, Lillebaek T, Ly HM, Martin C, Martin C, Mokrousov I, Narvskaïa O, Ngeow YF, Naumann L, Niemann S, Parwati I, Rahim Z, Rasolofo-Razanamparany V, Rasolonavalona T, Rossetti ML, Rüsch-Gerdes S, Sajduda A, Samper S, Shemyakin IG, Singh UB, Somoskovi A, Skuce RA, van Soolingen D, Streicher EM, Suffys PN, Tortoli E, Tracevska T, Vincent V, Victor TC, Warren RM, Yap SF, Zaman K, Portaels F, Rastogi N, Sola C. Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology. BMC Microbiol 2006; 6:23. [PMID: 16519816 PMCID: PMC1468417 DOI: 10.1186/1471-2180-6-23] [Citation(s) in RCA: 777] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Accepted: 03/06/2006] [Indexed: 12/04/2022] Open
Abstract
Background The Direct Repeat locus of the Mycobacterium tuberculosis complex (MTC) is a member of the CRISPR (Clustered regularly interspaced short palindromic repeats) sequences family. Spoligotyping is the widely used PCR-based reverse-hybridization blotting technique that assays the genetic diversity of this locus and is useful both for clinical laboratory, molecular epidemiology, evolutionary and population genetics. It is easy, robust, cheap, and produces highly diverse portable numerical results, as the result of the combination of (1) Unique Events Polymorphism (UEP) (2) Insertion-Sequence-mediated genetic recombination. Genetic convergence, although rare, was also previously demonstrated. Three previous international spoligotype databases had partly revealed the global and local geographical structures of MTC bacilli populations, however, there was a need for the release of a new, more representative and extended, international spoligotyping database. Results The fourth international spoligotyping database, SpolDB4, describes 1939 shared-types (STs) representative of a total of 39,295 strains from 122 countries, which are tentatively classified into 62 clades/lineages using a mixed expert-based and bioinformatical approach. The SpolDB4 update adds 26 new potentially phylogeographically-specific MTC genotype families. It provides a clearer picture of the current MTC genomes diversity as well as on the relationships between the genetic attributes investigated (spoligotypes) and the infra-species classification and evolutionary history of the species. Indeed, an independent Naïve-Bayes mixture-model analysis has validated main of the previous supervised SpolDB3 classification results, confirming the usefulness of both supervised and unsupervised models as an approach to understand MTC population structure. Updated results on the epidemiological status of spoligotypes, as well as genetic prevalence maps on six main lineages are also shown. Our results suggests the existence of fine geographical genetic clines within MTC populations, that could mirror the passed and present Homo sapiens sapiens demographical and mycobacterial co-evolutionary history whose structure could be further reconstructed and modelled, thereby providing a large-scale conceptual framework of the global TB Epidemiologic Network. Conclusion Our results broaden the knowledge of the global phylogeography of the MTC complex. SpolDB4 should be a very useful tool to better define the identity of a given MTC clinical isolate, and to better analyze the links between its current spreading and previous evolutionary history. The building and mining of extended MTC polymorphic genetic databases is in progress.
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Affiliation(s)
- Karine Brudey
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
| | | | - Leen Rigouts
- Mycobacteriology Unit, Prince Leopold Institute of Tropical Medicine, Antwerp, Belgium
| | - Wolfgang M Prodinger
- Dept. Hygiene Microbiology and Social Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Andrea Gori
- Dept of Infectious Diseases, Institut of Infectious Diseases, Milano, Italy
| | - Sahal A Al-Hajoj
- Department of Comparative Medicine, King Faisal specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Caroline Allix
- Laboratoire de la Tuberculose, Institut Pasteur de Bruxelles, Belgique
| | - Liselotte Aristimuño
- Universidad Centrooccidental Lisandro Alvarado, Barquisimeto, Venezuela and Universidad de Zaragoza, Spain
| | - Jyoti Arora
- All India Institute of Medical Sciences, New Delhi, India
| | | | - Lothar Binder
- Institut for Hygiene, Microbiologie and Tropical Medicine, Austria
| | | | - Angel Cataldi
- Instituto de Biotecnologia INTA, Castelar, Argentina
| | - Soonfatt Cheong
- Dept of Medical Microbiology and Pathology, faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia, School of Public Health
| | - Roland Diel
- University of Düsseldorf, Heinrich-Heine-University, Düsseldorf
| | | | - Jason T Evans
- Public Health Laboratory, Hearltlands Hospital, Birmingham, UK
| | | | - Séverine Ferdinand
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
| | - Dario Garcia de Viedma
- Dept of Clinical Microbiology and Infectious Diseases, Hospital Gregorio Marañon, Madrid, Spain
| | - Carlo Garzelli
- Dept. of Experimental Pathology, Medical Biotechnology, Infection and Epidemiology, Pisa University, Pisa, Italy
| | - Lidia Gazzola
- Dept of Infectious Diseases, Institut of Infectious Diseases, Milano, Italy
| | - Harrison M Gomes
- Laboratory of Molecular Biology applied to Mycobacteria, Dept. Mycobacteriosis, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | | | - Peter M Hawkey
- Public Health Laboratory, Hearltlands Hospital, Birmingham, UK
| | - Paul D van Helden
- MRC Centre for Molecular and Cellular Biology, Dept of medical Biochemistry, University of Stellenbosch, Tygerberg, South Africa
| | - Gurujaj V Kadival
- Laboratory Nuclear Medicine Section, Isotope group, Bhabha Atomic Research Centre c/T.M.H. Annexe, Parel, Mumbai-400012, India
| | | | - Kristin Kremer
- Mycobacteria reference unit, Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | - Milan Kubin
- Municipal Institute of Hygiene, Prague, Czech Republic
| | - Savita P Kulkarni
- Laboratory Nuclear Medicine Section, Isotope group, Bhabha Atomic Research Centre c/T.M.H. Annexe, Parel, Mumbai-400012, India
| | - Benjamin Liens
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
| | - Troels Lillebaek
- Statens Serum Institute, Int. Ref. lab. for Mycobacteriology, Copenhagen Denmark
| | - Ho Minh Ly
- Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | - Christian Martin
- Laboratoire de Bactério-virologie-hygiène, CHU Dupuytren, Limoges, France
| | - Igor Mokrousov
- Institut Pasteur de Saint-Petersbourg, Saint Petersbourg, Russia
| | - Olga Narvskaïa
- Institut Pasteur de Saint-Petersbourg, Saint Petersbourg, Russia
| | - Yun Fong Ngeow
- Dept of Medical Microbiology and Pathology, faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia, School of Public Health
| | - Ludmilla Naumann
- Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
| | - Stefan Niemann
- Forschungszentrum, National Reference Center for Mycobacteria, Borstel, Germany
| | - Ida Parwati
- Dept of Clinical Pathology, Padjadjaran University, Dr. Hasan Sadikin Hospital, Bandung, Indonesia
| | - Zeaur Rahim
- Tuberculosis Laboratory, International Centre for Diarrhoeal Research, Dhaka, Bangladesh
| | | | | | | | - Sabine Rüsch-Gerdes
- Forschungszentrum, National Reference Center for Mycobacteria, Borstel, Germany
| | - Anna Sajduda
- Dept of Genetics of Microorganisms, University of Lódz, Lodz, Poland
| | - Sofia Samper
- Servicio Microbiología, Hospital Universitario Miguel Servet, Zaragoza, Spain
| | - Igor G Shemyakin
- State Research Center for Applied Microbiology, Obolensk, Russian Federation
| | | | - Akos Somoskovi
- Dept. of Respiratory Medicine School of Medicine Semmelweis University, Budapest, Hungary
| | - Robin A Skuce
- Veterinary Sciences Division, Department of agriculture for Northern Ireland, Belfast, UK
| | - Dick van Soolingen
- Mycobacteria reference unit, Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | - Elisabeth M Streicher
- MRC Centre for Molecular and Cellular Biology, Dept of medical Biochemistry, University of Stellenbosch, Tygerberg, South Africa
| | - Philip N Suffys
- Laboratory of Molecular Biology applied to Mycobacteria, Dept. Mycobacteriosis, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | - Enrico Tortoli
- Centro regionale di Riferimento per i Micobatteri, Laboratorio de Microbiologia e Virologia, Ospedale Careggi, Firenze, Italy
| | | | - Véronique Vincent
- Centre National de Référence des Mycobactéries, Institut Pasteur, Paris, France
| | - Tommie C Victor
- MRC Centre for Molecular and Cellular Biology, Dept of medical Biochemistry, University of Stellenbosch, Tygerberg, South Africa
| | - Robin M Warren
- MRC Centre for Molecular and Cellular Biology, Dept of medical Biochemistry, University of Stellenbosch, Tygerberg, South Africa
| | - Sook Fan Yap
- Dept of Medical Microbiology and Pathology, faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia, School of Public Health
| | - Khadiza Zaman
- Tuberculosis Laboratory, International Centre for Diarrhoeal Research, Dhaka, Bangladesh
| | - Françoise Portaels
- Mycobacteriology Unit, Prince Leopold Institute of Tropical Medicine, Antwerp, Belgium
| | - Nalin Rastogi
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
| | - Christophe Sola
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
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Nicol MP, Sola C, February B, Rastogi N, Steyn L, Wilkinson RJ. Distribution of strain families of Mycobacterium tuberculosis causing pulmonary and extrapulmonary disease in hospitalized children in Cape Town, South Africa. J Clin Microbiol 2005; 43:5779-81. [PMID: 16272518 PMCID: PMC1287833 DOI: 10.1128/jcm.43.11.5779-5781.2005] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We studied the association between strain family and extrapulmonary tuberculosis among 285 children presenting to a pediatric hospital. Extrapulmonary disease occurred in 56% of children without known human immunodeficiency virus infection, with meningitis accounting for 22% of the cases. Two strain families, LAM3/F11 and W-Beijing, predominated; but there was no overall association with extrapulmonary disease.
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Affiliation(s)
- Mark P Nicol
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa.
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