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Shamebo T, Gumi B, Zewude A, Gashaw F, Mohammed T, Girma M, Zerihun B, Getu M, Mekasha S, Getahun M, Wondale B, Petros B, Ameni G. Molecular epidemiology and drug sensitivity of Mycobacterium tuberculosis in homeless individuals in the Addis Ababa city, Ethiopia. Sci Rep 2023; 13:21370. [PMID: 38049519 PMCID: PMC10695943 DOI: 10.1038/s41598-023-48407-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 11/26/2023] [Indexed: 12/06/2023] Open
Abstract
Although homeless segment of the society could be the hotspots for tuberculosis (TB) transmission, there is little data on TB in homeless individuals in Ethiopia. The objective of this study was to investigate the molecular epidemiology and drug sensitivity of Mycobacterium tuberculosis (M. tuberculosis) isolated from homeless individuals in Addis Ababa, Ethiopia. The study was conducted on 59 M. tuberculosis isolates, which were recovered by the clinical screening of 5600 homeless individuals and bacteriological examination of 641 individuals with symptoms of pulmonary tuberculosis (PTB). Region of difference-9 (RD9) based polymerase-chain reaction (PCR), Spoligotyping and 24-loci Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeat (MIRU-VNTR) typing were used for genotyping of the isolates. In addition, drug sensitivity test was performed on the isolates using BD Bactec Mycobacterial Growth Inhibition Tube (MGIT) 960. Fifty-eight of the 59 isolates were positive by spoligotyping and spoligotyping International type (SIT) 53, SIT 37, and SIT 149 were the dominant spoligotypes; each consisting of 19%, 15.5%, and10.3% of the isolates, respectively. The majority of the isolates (89.7%) were members of the Euro-American (EA) major lineage. MIRU-VNTR identified Ethiopia_3, Delhi/CAS, Ethiopia_2, TUR, X-type, Ethiopia_H37Rv-like strain, Haarlem and Latin-American Mediterranean (LAM) sub lineages. The proportion of clustering was 77.6% (45/58) in spoligotyping while it was 39.7% (23/58) in 24-loci MIRU-VNTR typing. Furthermore, the proportion of clustering was significantly lowered to 10.3% (6/58) when a combination of spoligotyping and 24-loci MIRU-VNTRplus was used. The recent transmission index (RTI) recorded by spoligotyping, 24-loci MIRU-VNTR typing, and a combination of the two genotyping methods were 58.6%, 27.6% and 5.2%, respectively. Young age and living in groups were significantly associated with strain clustering (P < 0.05). The drug sensitivity test (DST) result showed 8.9% (4/58) of the isolates were resistant to one or more first line ant-TB drugs; but multidrug resistant isolate was not detected. Clustering and RTI could suggest the transmission of TB in the homeless individuals, which could suggest a similar pattern of transmission between homeless individuals and the general population. Hence, the TB control program should consider homeless individuals during the implementation of TB control program.
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Affiliation(s)
- Tsegaye Shamebo
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, PO. Box 1176, Addis Ababa, Ethiopia
| | - Balako Gumi
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Po. Box 1176, Addis Ababa, Ethiopia
| | - Aboma Zewude
- Ethiopian National Tuberculosis Reference Laboratory, Ethipian Public Health Institute, PO. Box 1242 or 5654, Addis Ababa, Ethiopia
- Arba Minch University, Araba Minch, Ethiopia
| | - Fikru Gashaw
- Kotebe University of Education, Addis Ababa, Ethiopia
| | - Temesgen Mohammed
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, PO Box 15551, Al Ain, United Arab Emirates
- Arba Minch University, Araba Minch, Ethiopia
| | - Muse Girma
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Po. Box 1176, Addis Ababa, Ethiopia
| | - Betselot Zerihun
- Ethiopian National Tuberculosis Reference Laboratory, Ethipian Public Health Institute, PO. Box 1242 or 5654, Addis Ababa, Ethiopia
| | - Melak Getu
- Ethiopian National Tuberculosis Reference Laboratory, Ethipian Public Health Institute, PO. Box 1242 or 5654, Addis Ababa, Ethiopia
| | - Sindew Mekasha
- Ethiopian National Tuberculosis Reference Laboratory, Ethipian Public Health Institute, PO. Box 1242 or 5654, Addis Ababa, Ethiopia
| | - Muluwork Getahun
- Ethiopian National Tuberculosis Reference Laboratory, Ethipian Public Health Institute, PO. Box 1242 or 5654, Addis Ababa, Ethiopia
| | | | - Beyene Petros
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, PO. Box 1176, Addis Ababa, Ethiopia
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Po. Box 1176, Addis Ababa, Ethiopia.
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, PO Box 15551, Al Ain, United Arab Emirates.
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Dlamini TC, Mkhize BT, Sydney C, Maningi NE, Malinga LA. Molecular investigations of Mycobacterium tuberculosis genotypes among baseline and follow-up strains circulating in four regions of Eswatini. BMC Infect Dis 2023; 23:566. [PMID: 37644382 PMCID: PMC10466871 DOI: 10.1186/s12879-023-08546-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 08/18/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND The tuberculosis (TB) epidemic remains a major global health problem and Eswatini is not excluded. Our study investigated the circulating genotypes in Eswatini and compared them at baseline (start of treatment) and follow-up during TB treatment. METHODS Three hundred and ninety (n = 390) participants were prospectively enrolled from referral clinics and patients who met the inclusion criteria, were included in the study. A total of 103 participants provided specimens at baseline and follow-up within six months. Mycobacterium tuberculosis (M.tb) strains were detected by GeneXpert® MTB/RIF assay (Cephied, USA) and Ziehl -Neelsen (ZN) microscopy respectively at baseline and follow-up time-points respectively. The 206 collected specimens were decontaminated and cultured on BACTEC™ MGIT™ 960 Mycobacteria Culture System (Becton Dickinson, USA). Drug sensitivity testing was performed at both baseline and follow-up time points. Spoligotyping was performed on both baseline and follow-up strains after DNA extraction. RESULTS Resistance to at least one first line drug was detected higher at baseline compared to follow-up specimens with most of them developing into multidrug-resistant (MDR)-TB. A total of four lineages and twenty genotypes were detected. The distribution of the lineages varied among the different regions in Eswatini. The Euro-American lineage was the most prevalent with 46.12% (95/206) followed by the East Asian with 24.27% (50/206); Indo-Oceanic at 9.71% (20/206) and Central Asian at 1.94% (4/206). Furthermore, a high proportion of the Beijing genotype at 24.27% (50/206) and S genotype at 16.50% (34/206) were detected. The Beijing genotype was predominant in follow-up specimens collected from the Manzini region with 48.9% (23/47) (p = 0.001). A significant proportion of follow-up specimens developed MDR-TB (p = 0.001) with Beijing being the major genotype in most follow-up specimens (p < 0.000). CONCLUSION Eswatini has a high M.tb genotypic diversity. A significant proportion of the TB infected participants had the Beijing genotype associated with MDR-TB in follow-up specimens and thus indicate community wide transmission.
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Affiliation(s)
- Talent C Dlamini
- Department of Medical Laboratory Sciences, Southern Africa Nazarene University, Manzini, Eswatini.
- Biomedical and Clinical Technology, Department, Durban University of Technology, Durban, South Africa.
| | - Brenda T Mkhize
- Biomedical and Clinical Technology, Department, Durban University of Technology, Durban, South Africa
| | - Clive Sydney
- Biomedical and Clinical Technology, Department, Durban University of Technology, Durban, South Africa
| | | | - Lesibana A Malinga
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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Gaballah A, Ghazal A, Almiry R, Hussein S, Emad R, El-Sherbini E. Fingerprinting of Mycobacterium tuberculosis isolates by MIRU-VNTR genotyping and detection of isoniazid resistance by real-time PCR. J Med Microbiol 2022; 71. [DOI: 10.1099/jmm.0.001603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Tuberculosis (TB) is a great public health problem in developing countries such as Egypt. Genotyping of
Mycobacterium tuberculosis
isolates has a prominent role in the field of TB prevention.
Aim. This study aimed to evaluate real-time PCR using Minor Groove Binder (MGB) probes and to identify circulating lineages/sub-lineages of
M. tuberculosis
and their transmission patterns.
Hypothesis. We hypothesize that MIRU-VNTR technique is efficient in identifying circulating
M. tuberculosis
lineages in Egypt.
Methodology. Fifty sputum specimens positive for acid-fast bacilli were included. Isoniazid (INH) resistance was detected using the 1 % proportion method. Real-time PCR using MGB-probes was used for simultaneous detection of TB infection and INH resistance. Partial sequencing of the katG gene was used to confirm INH resistance results. A standard 15 Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (15-MIRU-VNTR) approach was used for genotyping through the MIRU-VNTRplus online platform.
Results. Only seven specimens showed phenotypic resistance to INH.
M. tuberculosis
was detected in all samples, while a mutation in the katG gene codon 315 was detected only in five samples, which were also phenotypically INH-resistant. Sequencing of the katG gene showed codon 315 mutation genotypically and phenotypically in the five INH-resistant isolates. Molecular genotyping of
M. tuberculosis
isolates revealed that the majority of isolates (26/50, 52 %) belonged to the S family of lineage_4. A low clustering rate (2 %) was observed among our isolates. According to the Hunter-Gaston Discriminatory Index (HGDI), 11 MIRU-VNTR loci were highly or moderately discriminative, while four loci were less polymorphic.
Conclusion. MIRU-VNTR genotyping revealed a low clustering rate with a low recent transmission rate of
M. tuberculosis
strains in Alexandria, Egypt.
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Affiliation(s)
- Ahmed Gaballah
- Department of Microbiology, Medical Research Institute, Alexandria University, Egypt
| | - Abeer Ghazal
- Department of Microbiology, Medical Research Institute, Alexandria University, Egypt
| | - Reda Almiry
- Department of Clinical Pathology, Alexandria Armed Forces Hospital, Alexandria, Egypt
| | - Somaya Hussein
- Elmamoura Chest Hospital, Egyptian Ministry of Health, Alexandria, Egypt
| | - Rasha Emad
- Alexandria Main University Hospital, Alexandria University, Alexandria, Egypt
| | - Eglal El-Sherbini
- Department of Microbiology, Medical Research Institute, Alexandria University, Egypt
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Ismail S, Al Amry K, Aggor G, El Naggar H, Selim S. Spoligotyping with pncA sequencing strategy conferring the transmission of multidrug-resistant tuberculosis in Egypt. Int J Mycobacteriol 2020; 8:211-217. [PMID: 31512595 DOI: 10.4103/ijmy.ijmy_111_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background This study explored the genetic diversity of Mycobacterium tuberculosis isolates in Egypt by spoligotyping in combination with pncA gene sequencing, spoNC. Methods First, isolates were selected from 400 isolates positive for M. tuberculosis that referred to Central Labs Ministry of Health and then were subjected to the study analyses. Results Twenty one isolates were found to be multidrug resistant (MDR) and 29 isolates were sensitive for isonizide (INH) and rifampicine (RIF) after testing by phenotypic drug susceptibility testing (DST) and Mycobacteria Growth Indicator Tube (MGIT). Spoligotyping yielded 45 patterns belonging to seven families that previously reported in neighboring countries such as Iraq, Syria, Iran, and Turkey. While four isolates were orphans. Conclusion Application of spoNC on obtained spoligotype patterns enhances to reduce the clustering rate. Bejing family the predominant (34%) were subdivided by pncA sequence into three sensitive DST pncA wild type, three MDR-DST isolates showing cys14Arg mutation in pncA, two sensitive DST isolates with pncA Gly97Asp mutation, and three sensitive DST pncAVal128Gly mutation. The next most common CASI_DELHI family (16%) were subdivided by pncA sequencing into CASI_DELHI (st 381, MDR) including two pncA silent mutation ser65ser (tcc > tct) and CASI_DELHI (st26, sensitive) which included six pncA (wild-type) results, and Latin-American-Mediterranean 6 family (6%) all had PncA Gly97Asp mutation. We concluded that spoNC provides good snap shot for MDR surveillance and its country origin and performs early identification of outbreaks in Egypt.
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Affiliation(s)
- Suzan Ismail
- Department of Biotechnology, Animal Health Research Institute, Giza, Egypt
| | - Khaled Al Amry
- Department of Microbiology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Galal Aggor
- Department of Biotechnology, Animal Health Research Institute, Giza, Egypt
| | - Hoida El Naggar
- Mycobacteriology Unit, Central Labs of Ministry of Health and Population, Cairo, Egypt
| | - Salah Selim
- Department of Microbiology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
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Bhembe NL, Nwodo UU, Okoh AI, Obi CL, Mabinya LV, Green E. Clonality and genetic profiles of drug-resistant Mycobacterium tuberculosis in the Eastern Cape Province, South Africa. Microbiologyopen 2019; 8:e00449. [PMID: 30801981 PMCID: PMC6436438 DOI: 10.1002/mbo3.449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/15/2016] [Accepted: 12/20/2016] [Indexed: 01/05/2023] Open
Abstract
In this study, we investigated the diversity of drug-resistant Mycobacterium tuberculosis isolates from families who own cattle in the Eastern Cape Province of South Africa using spoligotyping and mycobacterial interspersed repetitive-unit-variable number tandem repeat (MIRU-VNTR) typing. The Mycobacterium tuberculosis was investigated using MIRU-VNTR and the Mycobacterium tuberculosis families were evaluated using spoligotyping. Spoligotyping grouped 91% of the isolates into seven clusters, while 9% of the deoxyribonucleic acid (DNA) from TB isolates were unclustered from a total of 154 DNA used. Previously described shared types were observed in 89.6% of the isolates, with the Beijing family, SIT1, the principal genotype in the province, while the families T, SIT53 and X1, SIT1329 were the least detected genotypes. MIRU-VNTR grouped 81% of the isolates in 23 clusters while 19% were unclustered. A combination of the VNTR and spoligotyping grouped 79% of the isolates into 23 clusters with 21% unclustered. The low level of diversity and the clonal spread of drug-resistant Mycobacterium tuberculosis isolates advocate that the spread of TB in this study may be instigated by the clonal spread of Beijing genotype. The results from this study provide vital information about the lack of TB control and distribution of Mycobacterium tuberculosis complex strain types in the Eastern Cape Province of South Africa.
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Affiliation(s)
- Nolwazi L Bhembe
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa.,Molecular Pathogenesis and Molecular Epidemiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
| | - Uchechukwu U Nwodo
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa.,Molecular Pathogenesis and Molecular Epidemiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
| | - Anthony I Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa.,Molecular Pathogenesis and Molecular Epidemiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
| | - Chikwelu L Obi
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa.,Academic and Research Division, University of Fort Hare, Alice, South Africa
| | - Leonard V Mabinya
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa.,Molecular Pathogenesis and Molecular Epidemiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
| | - Ezekiel Green
- Department of Biotechnology and Food Science, Faculty of Science, University of Johannesburg, Doornfontein, South Africa
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Khalid FA, Gasmelseed N, Hailu E, Eldirdery MM, Abebe M, Berg S, Aseffa A. Molecular identification of Mycobacterium tuberculosis causing Pulmonary Tuberculosis in Sudan. EUROPEAN ACADEMIC RESEARCH 2016; 4:7842-7855. [PMID: 29805964 PMCID: PMC5966043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
BACKGROUND Tuberculosis (TB) is a major public health problem in Sudan. However, the strains responsible for the epidemic of TB have been poorly characterized. The aim of this study was to characterize the causative agent of TB isolates circulating in Kassala and Gezira States during 2011-2012. METHOD Ninety two Mycobacterium tuberculosis complex (MTBC) strains were isolated from sputum samples of pulmonary TB patients, attending the Teaching Hospitals in Kassala and Gezira states. Molecular identification was performed using region of difference 9 (RD9) deletion and spoligotyping methods. Spoligotype patterns were compared with those listed in the international SITVIT2 spoligotyping database. RESULTS The results determined the circulation of Euro-American, Central Asian, and Indo-Oceanic Lineages. They were clustered in the following clades: Manu2 (64.8%), CAS (22.7%), EAI (4.5), LAM2 (2.3%), H3 (1.1%), T (1.1%), T3-ETH (1.1%), T5-RUS1 (1.1%). Comparison with the international multi-marker database SITVIT2, 76.1% of isolates matched the database, while 23.9% of the isolates were not represented in SITVIT2 (orphans). SIT54 (Manu2) was the most common strain circulating in the two states. CONCLUSION The study showed that a large variety of Mycobacterium tuberculosis (MTB) genotypes were circulating in the two states. Further studies on identification and molecular characterization of mycobacterial are needed to understand the biodiversity, rate of transmission and the associated risk factors of MTB in Sudan.
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Affiliation(s)
| | - Nagla Gasmelseed
- Department of Molecular Biology, National Cancer Institute, Sudan
- Department of Biology, Faculty of Science University of Hafr Al Batin, Saudi Arabia
| | - Elena Hailu
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | | | - Markos Abebe
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Stefan Berg
- Animal and Plant Health Agency, New Haw, Surrey, UK
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
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Mbugi EV, Katale BZ, Streicher EM, Keyyu JD, Kendall SL, Dockrell HM, Michel AL, Rweyemamu MM, Warren RM, Matee MI, van Helden PD, Couvin D, Rastogi N. Mapping of Mycobacterium tuberculosis Complex Genetic Diversity Profiles in Tanzania and Other African Countries. PLoS One 2016; 11:e0154571. [PMID: 27149626 PMCID: PMC4858144 DOI: 10.1371/journal.pone.0154571] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/15/2016] [Indexed: 11/23/2022] Open
Abstract
The aim of this study was to assess and characterize Mycobacterium tuberculosis complex (MTBC) genotypic diversity in Tanzania, as well as in neighbouring East and other several African countries. We used spoligotyping to identify a total of 293 M. tuberculosis clinical isolates (one isolate per patient) collected in the Bunda, Dar es Salaam, Ngorongoro and Serengeti areas in Tanzania. The results were compared with results in the SITVIT2 international database of the Pasteur Institute of Guadeloupe. Genotyping and phylogeographical analyses highlighted the predominance of the CAS, T, EAI, and LAM MTBC lineages in Tanzania. The three most frequent Spoligotype International Types (SITs) were: SIT21/CAS1-Kili (n = 76; 25.94%), SIT59/LAM11-ZWE (n = 22; 7.51%), and SIT126/EAI5 tentatively reclassified as EAI3-TZA (n = 18; 6.14%). Furthermore, three SITs were newly created in this study (SIT4056/EAI5 n = 2, SIT4057/T1 n = 1, and SIT4058/EAI5 n = 1). We noted that the East-African-Indian (EAI) lineage was more predominant in Bunda, the Manu lineage was more common among strains isolated in Ngorongoro, and the Central-Asian (CAS) lineage was more predominant in Dar es Salaam (p-value<0.0001). No statistically significant differences were noted when comparing HIV status of patients vs. major lineages (p-value = 0.103). However, when grouping lineages as Principal Genetic Groups (PGG), we noticed that PGG2/3 group (Haarlem, LAM, S, T, and X) was more associated with HIV-positive patients as compared to PGG1 group (Beijing, CAS, EAI, and Manu) (p-value = 0.03). This study provided mapping of MTBC genetic diversity in Tanzania (containing information on isolates from different cities) and neighbouring East African and other several African countries highlighting differences as regards to MTBC genotypic distribution between Tanzania and other African countries. This work also allowed underlining of spoligotyping patterns tentatively grouped within the newly designated EAI3-TZA lineage (remarkable by absence of spacers 2 and 3, and represented by SIT126) which seems to be specific to Tanzania. However, further genotyping information would be needed to confirm this specificity.
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Affiliation(s)
- Erasto V. Mbugi
- Department of Biochemistry, Muhimbili University of Health and Allied Sciences, P. O. Box 65001, Dar es Salaam, Tanzania
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania
| | - Bugwesa Z. Katale
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania
- Tanzania Wildlife Research Institute (TAWIRI), P.O. Box 661, Arusha, Tanzania
| | - Elizabeth M. Streicher
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ South African Medical Research Council (MRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa
| | - Julius D. Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), P.O. Box 661, Arusha, Tanzania
| | - Sharon L. Kendall
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
| | - Hazel M. Dockrell
- The Royal Veterinary College, Royal College Street, London, NW1 0TU, United Kingdom
| | - Anita L. Michel
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Mark M. Rweyemamu
- Southern African Centre for Infectious Disease Surveillance, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Robin M. Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ South African Medical Research Council (MRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa
| | - Mecky I. Matee
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania
| | - Paul D. van Helden
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ South African Medical Research Council (MRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa
| | - David Couvin
- WHO Supranational TB Reference Laboratory, Tuberculosis & Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Morne Joliviere, BP 484, 97183, Abymes, Guadeloupe
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Tuberculosis & Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Morne Joliviere, BP 484, 97183, Abymes, Guadeloupe
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Diab HM, Nakajima C, Kotb SA, Mokhtar A, Khder NFM, Abdelaal ASA, Hegazy A, Poudel A, Shah Y, Suzuki Y. First insight into the genetic population structure of Mycobacterium tuberculosis isolated from pulmonary tuberculosis patients in Egypt. Tuberculosis (Edinb) 2015; 96:13-20. [PMID: 26786649 DOI: 10.1016/j.tube.2015.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 10/31/2015] [Accepted: 11/08/2015] [Indexed: 11/19/2022]
Abstract
The present study aimed to assess the population structure of Mycobacterium tuberculosis (MTB) isolates from Egypt. A total of 230 MTB isolates were analysed using spoligotyping, large sequence polymorphism (LSPs), mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing and multi-locus sequence typing (MLST). The majority of isolates (93.0%) belonged to lineage 4, including 44.3, 13.4 and 10.8% of the ill-defined T clade, LAM and Haarlem families, respectively, and lineage 3 was identified in 7.0% of the isolates. MIRU-VNTRs typing allowed efficient discrimination of the spoligotype-defined clusters, including spoligo-international types (SIT) 53, 34, and 4, into 56 patterns, including 13 clusters and 43 unique patterns. A new SNP at position 311614 was identified in all six isolates to form the biggest MIRU-VNTR cluster, which suggested a recent clonal expansion. This SNP could possibly be used as a genetic marker for robust discriminations of Egyptian MTB isolates belonging to SIT53. The combination of spoligotyping, 12 MIRU-VNTRs loci and MLST provided insight into the genetic diversity and transmission dynamics of the Egyptian MTB genotypes and could be a key to implementation of effective control measures by public health authorities.
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Affiliation(s)
- Hassan Mahmoud Diab
- Department of Animal Hygiene, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt; Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Hokkaido University, The Global Station for Zoonosis Control, Sapporo, Japan
| | - Saber A Kotb
- Department of Animal Hygiene, Faculty of Veterinary Medicine, Assiut University, Egypt
| | - Alaa Mokhtar
- National Tuberculosis Control Program, Ministry of Health and Population, Egypt
| | - Nagwa F M Khder
- TB Supranational Reference Laboratory, Central Public Health Laboratories, Clinical Microbiology Department, Ministry of Health and Population, Egypt
| | - Ahmed S A Abdelaal
- TB Supranational Reference Laboratory, Central Public Health Laboratories, Clinical Microbiology Department, Ministry of Health and Population, Egypt
| | - Azza Hegazy
- TB Supranational Reference Laboratory, Central Public Health Laboratories, Clinical Microbiology Department, Ministry of Health and Population, Egypt
| | - Ajay Poudel
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Yogendra Shah
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Hokkaido University, The Global Station for Zoonosis Control, Sapporo, Japan.
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Sun Z, Xu Y, Sun Y, Liu Y, Zhang X, Huang H, Li C. Ofloxacin resistance in Mycobacterium tuberculosis is associated with efflux pump activity independent of resistance pattern and genotype. Microb Drug Resist 2015; 20:525-32. [PMID: 24940805 DOI: 10.1089/mdr.2013.0171] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Drug-resistance to ofloxacin (OFX) in Mycobacterium tuberculosis is due to missense mutations in gyrA and other factors, such as alterations in the activity of drug efflux pumps. In this study, we identified 8 extensively drug resistant tuberculosis (XDR-TB), 40 multidrug resistant TB (MDR-TB), 38 polydrug resistant TB (PDR-TB), and 16 single OFX-resistant TB from 102 clinical isolates. We tested the effect of three efflux inhibitors, reserpine, verapamil, and carbonyl cyanide m-chlorophenyl hydrazone (CCCP), on changes in the OFX minimum inhibitory concentration (MIC) using Resazurin microtitre assay. These three inhibitors changed the MICs from 2- to 32-fold, with CCCP having the strongest effect. A total of 55%, 74%, and 83% of the tested isolates had changes in MIC of more than two-fold by reserpine, verapamil, and CCCP, respectively. The inhibitors led to similar fold-changes of OFX MICs in the XDR, MDR, PDR, and single OFX-resistant isolates. For each inhibitor, a higher resistance to OFX was associated with the greater efflux pump activity. There were no significant differences in the effect of efflux pump inhibitors upon Beijing and non-Beijing M. tuberculosis genotypes. Taken together, these results indicate that the efflux pump activity was greater in the isolates higher resistant to OFX and had similar effects on isolates with different drug resistant pattern, and had similar effects on Beijing and non-Beijing genotypes.
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Affiliation(s)
- Zhaogang Sun
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University , Beijing, People's Republic of China
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Osman DA, Phelippeau M, Drancourt M, Musso D. Diversity of Mycobacterium tuberculosis lineages in French Polynesia. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2015; 50:199-206. [PMID: 26271142 DOI: 10.1016/j.jmii.2015.05.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 05/01/2015] [Accepted: 05/28/2015] [Indexed: 11/19/2022]
Abstract
BACKGROUND/PURPOSE French Polynesia is an overseas territory located in the South Pacific. The incidence of tuberculosis in French Polynesia has been stable since 2000 with an average of 20 cases/y/100,000 inhabitants. Molecular epidemiology of Mycobacterium tuberculosis in French Polynesia is unknown because M. tuberculosis isolates have not been routinely genotyped. METHODS From 2009 to 2012, 34 isolates collected from 32 French Polynesian patients were identified as M. tuberculosis by probe hybridization. These isolates were genotyped using spoligotyping and 24-loci mycobacterial interspersed repetitive units (MIRUs)-variable number of tandem repeat (VNTR). Spoligotype patterns obtained using commercial kits were compared with the online international database SITVIT. MIRU-VNTR genotyping was performed using an in-house protocol based on capillary electrophoresis sizing for 24-loci MIRU-VNTR genotyping. RESULTS The results of the spoligotyping method revealed that 25 isolates grouped into six previously described spoligotypes [H1, H3, U likely (S), T1, Manu, and Beijing] and nine isolates grouped into six new spoligotypes. Comparison with the international database MIRU-VNTRplus distributed 30 isolates into five lineages (Haarlem, Latin American Mediterranean, S, X, and Beijing) and four as unassigned isolates. CONCLUSION Genotyping identified four phylogenetic lineages belonging to the modern Euro-American subgroup, one Beijing genotype responsible for worldwide pandemics, including remote islands in the South Pacific, and one Manu genotype of the ancestral lineage of M. tuberculosis.
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Affiliation(s)
- Djaltou Aboubaker Osman
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UMR CNRS 7278, IRD 198, INSERM 1095, Faculté de Médecine, Marseille, France; Institut de Recherche Médicinale (IRM), Centre d'études et de Recherche de Djibouti (CERD), Djibouti
| | - Michael Phelippeau
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UMR CNRS 7278, IRD 198, INSERM 1095, Faculté de Médecine, Marseille, France
| | - Michel Drancourt
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UMR CNRS 7278, IRD 198, INSERM 1095, Faculté de Médecine, Marseille, France.
| | - Didier Musso
- Pôle de recherche et de veille sur les maladies infectieuses émergente, Institut Louis Malardé, Tahiti, French Polynesia.
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Discrepancies in Drug Susceptibility Test for Tuberculosis Patients Resulted from the Mixed Infection and the Testing System. BIOMED RESEARCH INTERNATIONAL 2015; 2015:651980. [PMID: 26064938 PMCID: PMC4433640 DOI: 10.1155/2015/651980] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 10/29/2014] [Accepted: 11/03/2014] [Indexed: 11/17/2022]
Abstract
To find the potential reasons for the discrepancies in the drug susceptibility test (DST) of M. tuberculosis isolates, twenty paired isolates with disputed drug susceptibilities to isoniazid (INH) were selected according to the MGIT960 testing and Löwenstein-Jensen (L-J) proportion methods. Their MICs were confirmed again by broth microdilution method and by L-J proportion method. The spoligotyping results showed that, of all the 20 paired strains, 11 paired isolates belonged to the Beijing genotype and 6 paired isolates belonged to SIT1634, and that each of the remaining 3 paired isolates had two genotypes, namely, SIT1 and SIT1634. Those 3 paired isolates with different intrapair spoligotypes were further confirmed as mixed infection by the results that those three pairs of isolates with different 12 locus MIRU intrapair types and one pair carried different base pair at codon 315 (AGC versus AAC). Totally mutations in the katG gene were identified in 13 paired isolates. No mutations were found in the regulatory sequences and open reading frames (ORF) of the inhA and ahpC genes in any of the tested isolates. Those results showed that the different test systems and the mixed infection with particular genotypes of M. tuberculosis strains contributed to the drug susceptibility discrepancies.
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Weerasekera D, Magana-Arachchi D, Madegedara D, Dissanayake N, Thevanesam V. Genetic diversity of Mycobacterium tuberculosis isolates obtained from three distinct population groups in the Central Province, Sri Lanka. ASIAN PACIFIC JOURNAL OF TROPICAL DISEASE 2015. [DOI: 10.1016/s2222-1808(14)60802-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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13
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Strain diversity of Mycobacterium tuberculosis isolates from pulmonary tuberculosis patients in Afar pastoral region of Ethiopia. BIOMED RESEARCH INTERNATIONAL 2014; 2014:238532. [PMID: 24734230 PMCID: PMC3966356 DOI: 10.1155/2014/238532] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 01/22/2014] [Indexed: 12/02/2022]
Abstract
Data on genotypic diversity of Mycobacterium tuberculosis complex (MTBC) is important to understand its epidemiology, human adaptation, clinical phenotypes, and drug resistance.
This study aimed to characterize MTBC clinical isolates circulating in a predominantly pastoralist area in Ethiopia, a country where tuberculosis is the second leading cause of mortality.
Culture of sputum samples collected from a total of 325 pulmonary TB suspects was done to isolate MTBC. Spoligotyping was used to characterize 105 isolates from culture positive
slopes and the result was compared with an international database. Forty-four spoligotype patterns were observed to correspond to 35 shared-types (SITs) containing 96 isolates and
9 orphan patterns; 27 SITs containing 83 isolates matched a preexisting shared-type in the database, whereas 8 SITs (n = 13 isolates) were newly created. A total of 19 SITs containing
80 isolates were clustered within this study (overall clustering of 76.19%). Three dominant lineages (T, CAS, and Manu) accounted for 76.19% of the isolates. SIT149/T3-ETH was one
of the two most dominant sublineages. Unlike previous reports, we show that Manu lineage strains not only constitute a dominant lineage, but are also associated with HIV infection in
Afar region of Ethiopia. The high level of clustering suggests the presence of recent transmission that should be further studied using additional genotyping markers.
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14
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Molecular epidemiology and genotyping of Mycobacterium tuberculosis isolated in Baghdad. BIOMED RESEARCH INTERNATIONAL 2014; 2014:580981. [PMID: 24719873 PMCID: PMC3955663 DOI: 10.1155/2014/580981] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 01/17/2014] [Accepted: 01/18/2014] [Indexed: 12/17/2022]
Abstract
Tuberculosis (TB) remains a major health problem in Iraq but the strains responsible for the epidemic have been poorly characterized. Our aim was to characterize the TB strains circulating in Bagdad (Iraq). A total of 270 Mycobacterium tuberculosis complex (MTBC) strains isolated between 2010 and 2011 from TB patients attending the Center of Chest and Respiratory diseases in Baghdad were analyzed by Spoligotyping. The analysis indicated that 94.1% of the isolates belong to known genotype clades: CAS 39.6%, ill-defined T clade 29.6%, Manu 7.4%, Haarlem 7%, Ural 4.1%, LAM 3.3%, X 0.7%, LAM7-TUR 0.7%, EAI 0.7%, S 0.7%, and unknown 5.9%. Comparison with the international multimarker database SITVIT2 showed that SIT 309 (CAS1-Delhi) and SIT1144 (T1) were the most common types. In addition, 44 strains were included in SITVIT2 database under 16 new Spoligotype International Types (SITs); of these, 6 SITs (SIT3346, SIT3497, SIT3708, SIT3790, SIT3791, and SIT3800) (n = 32 strains) were created within the present study and 10 were created after a match with an orphan in the database. By using 24-loci MIRU-VNTR-typing on a subset of 110 samples we found a high recent transmission index (RTI) of 33.6%. In conclusion, we present the first unifying framework for both epidemiology and evolutionary analysis of M. tuberculosis in Iraq.
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Joseph BV, Soman S, Radhakrishnan I, Hill V, Dhanasooraj D, Ajay Kumar R, Rastogi N, Mundayoor S. Molecular epidemiology of Mycobacterium tuberculosis isolates from Kerala, India using IS6110-RFLP, spoligotyping and MIRU-VNTRs. INFECTION GENETICS AND EVOLUTION 2013; 16:157-64. [DOI: 10.1016/j.meegid.2013.01.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 01/05/2013] [Accepted: 01/11/2013] [Indexed: 11/28/2022]
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16
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Arega SM, Conraths FJ, Ameni G. Prevalence of tuberculosis in pigs slaughtered at two abattoirs in Ethiopia and molecular characterization of Mycobacterium tuberculosis isolated from tuberculous-like lesions in pigs. BMC Vet Res 2013; 9:97. [PMID: 23647845 PMCID: PMC3661388 DOI: 10.1186/1746-6148-9-97] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 04/24/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is an infectious, granulomatous disease caused by acid-fast bacilli of the genus Mycobacterium. The disease affects practically all species of vertebrates. Although mammalian tuberculosis has been nearly controlled in many developed countries, it is still a serious problem in humans and domestic animals including pigs in developing countries. In Ethiopia, the prevalence of TB in pigs is not known. Therefore, this study was designed to estimate the prevalence of TB in pigs in central Ethiopia and to characterize the causative agents using molecular techniques. RESULTS The estimated prevalence of TB was 5.8% (49/841). Age and origin of pigs were significantly associated (P<0.001) with the prevalence. In contrast, an association of sex, floor type and water source with the prevalence could not be shown. Culture positivity was confirmed in 30.6% (15/49) of the tuberculous-like lesions. Of the 15 isolates, 12 were acid fast positive while five of the latter were confirmed by multiplex PCR as members of the M. tuberculosis complex. Speciation of the five isolates further confirmed that they were M. tuberculosis, belonging to SIT1088 (two isolates) and SIT1195 (one isolate). The remaining two isolates belong to an identical spoligotype, the pattern of which was not found in the spoligotype database (SpolDB4). CONCLUSIONS The isolation of M. tuberculosis from pigs suggests a possible risk of transmission between humans and pigs. Hence, establishing feasible control methods is required.
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Affiliation(s)
- Sintayehu Mulugeta Arega
- Department of Veterinary Clinical Medicine, Faculty of Veterinary Medicine, University of Gondar, PO Box 196, Gondar, Ethiopia.
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Blouin Y, Hauck Y, Soler C, Fabre M, Vong R, Dehan C, Cazajous G, Massoure PL, Kraemer P, Jenkins A, Garnotel E, Pourcel C, Vergnaud G. Significance of the identification in the Horn of Africa of an exceptionally deep branching Mycobacterium tuberculosis clade. PLoS One 2012; 7:e52841. [PMID: 23300794 PMCID: PMC3531362 DOI: 10.1371/journal.pone.0052841] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 11/21/2012] [Indexed: 02/02/2023] Open
Abstract
Molecular and phylogeographic studies have led to the definition within the Mycobacterium tuberculosis complex (MTBC) of a number of geotypes and ecotypes showing a preferential geographic location or host preference. The MTBC is thought to have emerged in Africa, most likely the Horn of Africa, and to have spread worldwide with human migrations. Under this assumption, there is a possibility that unknown deep branching lineages are present in this region. We genotyped by spoligotyping and multiple locus variable number of tandem repeats (VNTR) analysis (MLVA) 435 MTBC isolates recovered from patients. Four hundred and eleven isolates were collected in the Republic of Djibouti over a 12 year period, with the other 24 isolates originating from neighbouring countries. All major M. tuberculosis lineages were identified, with only two M. africanum and one M. bovis isolates. Upon comparison with typing data of worldwide origin we observed that several isolates showed clustering characteristics compatible with new deep branching. Whole genome sequencing (WGS) of seven isolates and comparison with available WGS data from 38 genomes distributed in the different lineages confirms the identification of ancestral nodes for several clades and most importantly of one new lineage, here referred to as lineage 7. Investigation of specific deletions confirms the novelty of this lineage, and analysis of its precise phylogenetic position indicates that the other three superlineages constituting the MTBC emerged independently but within a relatively short timeframe from the Horn of Africa. The availability of such strains compared to the predominant lineages and sharing very ancient ancestry will open new avenues for identifying some of the genetic factors responsible for the success of the modern lineages. Additional deep branching lineages may be readily and efficiently identified by large-scale MLVA screening of isolates from sub-Saharan African countries followed by WGS analysis of a few selected isolates.
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Affiliation(s)
- Yann Blouin
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
| | - Yolande Hauck
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
| | - Charles Soler
- Laboratoire de biologie clinique, hôpital d'instruction des armées Percy, Clamart, France
| | - Michel Fabre
- Laboratoire de biologie clinique, hôpital d'instruction des armées Percy, Clamart, France
| | - Rithy Vong
- Laboratoire de biologie clinique, hôpital d'instruction des armées Percy, Clamart, France
| | | | | | | | - Philippe Kraemer
- Hôpital d'instruction des armées Alphonse Laveran, Marseille, France
| | - Akinbowale Jenkins
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, Pretoria, South Africa
| | - Eric Garnotel
- Hôpital d'instruction des armées Alphonse Laveran, Marseille, France
| | - Christine Pourcel
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
| | - Gilles Vergnaud
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
- DGA/MRIS- Mission pour la Recherche et l'Innovation Scientifique, Bagneux, France
- * E-mail:
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18
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Spoligotypes of Mycobacterium tuberculosis complex isolates from patients residents of 11 states of Brazil. INFECTION GENETICS AND EVOLUTION 2012; 12:649-56. [DOI: 10.1016/j.meegid.2011.08.027] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 08/26/2011] [Accepted: 08/28/2011] [Indexed: 11/23/2022]
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19
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Mycobacterium tuberculosis spoligotypes that may derive from mixed strain infections are revealed by a novel computational approach. INFECTION GENETICS AND EVOLUTION 2012; 12:798-806. [DOI: 10.1016/j.meegid.2011.08.028] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 08/23/2011] [Accepted: 08/24/2011] [Indexed: 10/17/2022]
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20
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Varma-Basil M, Kumar S, Arora J, Angrup A, Zozio T, Banavaliker JN, Singh UB, Rastogi N, Bose M. Comparison of spoligotyping, mycobacterial interspersed repetitive units typing and IS6110-RFLP in a study of genotypic diversity of Mycobacterium tuberculosis in Delhi, North India. Mem Inst Oswaldo Cruz 2012; 106:524-35. [PMID: 21894371 DOI: 10.1590/s0074-02762011000500002] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 06/06/2011] [Indexed: 11/22/2022] Open
Abstract
The aim of the present study was to compare polymerase chain reaction (PCR)-based methods--spoligotyping and mycobacterial interspersed repetitive units (MIRU) typing--with the gold-standard IS6110 restriction fragment length polymorphism (RFLP) analysis in 101 isolates of Mycobacterium tuberculosis to determine the genetic diversity of M. tuberculosis clinical isolates from Delhi, North India. Spoligotyping resulted in 49 patterns (14 clusters); the largest cluster was composed of Spoligotype International Types (SITs)26 [Central-Asian (CAS)1-Delhi lineage], followed by SIT11 [East-African-Indian (EAI) 3-Indian lineage]. A large number of isolates (75%) belonged to genotypic lineages, such as CAS, EAI and Manu, with a high specificity for the Indian subcontinent, emphasising the complex diversity of the phylogenetically coherent M. tuberculosis in North India. MIRU typing, using 11 discriminatory loci, was able to distinguish between all but two strains based on individual patterns. IS6110-RFLP analysis (n = 80 strains) resulted in 67 unique isolates and four clusters containing 13 strains. MIRUs discriminated all 13 strains, whereas spoligotyping discriminated 11 strains. Our results validate the use of PCR-based molecular typing of M. tuberculosis using repetitive elements in Indian isolates and demonstrate the usefulness of MIRUs for discriminating low-IS6110-copy isolates, which accounted for more than one-fifth of the strains in the present study.
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Affiliation(s)
- Mandira Varma-Basil
- Deptartment of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
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Thomas SK, Iravatham CC, Moni BH, Kumar A, Archana BV, Majid M, Priyadarshini Y, Rani PS, Valluri V, Hasnain SE, Ahmed N. Modern and ancestral genotypes of Mycobacterium tuberculosis from Andhra Pradesh, India. PLoS One 2011; 6:e27584. [PMID: 22114678 PMCID: PMC3219672 DOI: 10.1371/journal.pone.0027584] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 10/19/2011] [Indexed: 02/06/2023] Open
Abstract
Traditionally, the distribution of the Mycobacterium tuberculosis genotypes in India has been characterized by widespread prevalence of ancestral lineages (TbD1+ strains and variants) in the south and the modern forms (TbD1− CAS and variants) predominating in the north of India. The pattern was, however, not clearly known in the south-central region such as Hyderabad and the rest of the state of Andhra Pradesh where the prevalence of both tuberculosis (TB) and human immunodeficiency virus (HIV) infection is one of the highest in the country; this area has been the hotspot of TB vaccine trials. Spoligotyping of 101 clinical isolates obtained from Hyderabad and rural Andhra Pradesh confirmed the occurrence of major genogroups such as the ancestral (or the TbD1+ type or the East African Indian (EAI) type), the Central Asian (CAS) or Delhi type and the Beijing lineage in Andhra Pradesh. Sixty five different spoligotype patterns were observed for the isolates included in this study; these were further analyzed based on specific genetic signatures/mutations. It was found that the major genogroups, CAS and “ancestral,” were almost equally prevalent in our collection but followed a north-south compartmentalization as was also reported previously. However, we observed a significant presence of MANU lineage in south Andhra Pradesh, which was earlier reported to be overwhelmingly present in Mumbai. This study portrays genotypic diversity of M. tuberculosis from the Indian state of Andhra Pradesh and provides a much needed snapshot of the strain diversity that will be helpful in devising effective TB control programs in this part of the world.
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Affiliation(s)
- Shirly K. Thomas
- Institute of Life Sciences, University of Hyderabad Campus, Hyderabad, India
| | | | - Bottu Heleena Moni
- Pathogen Biology Laboratory, Department of Biotechnology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Ashutosh Kumar
- Pathogen Biology Laboratory, Department of Biotechnology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Bandaru V. Archana
- Institute of Life Sciences, University of Hyderabad Campus, Hyderabad, India
| | - Mohammad Majid
- Pathogen Biology Laboratory, Department of Biotechnology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Yerra Priyadarshini
- Pathogen Biology Laboratory, Department of Biotechnology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Pittu Sandhya Rani
- Pathogen Biology Laboratory, Department of Biotechnology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Vijayalakshmi Valluri
- Bhagwan Mahavir Hospital and Research Centre, AC Guards, Hyderabad, India
- Blue Peter Research Centre – Lepra India, Cherlapally, Hyderabad, India
| | - Seyed E. Hasnain
- Institute of Life Sciences, University of Hyderabad Campus, Hyderabad, India
- School of Biological Sciences, Indian Institute of Technology, New Delhi, India
| | - Niyaz Ahmed
- Institute of Life Sciences, University of Hyderabad Campus, Hyderabad, India
- Pathogen Biology Laboratory, Department of Biotechnology, School of Life Sciences, University of Hyderabad, Hyderabad, India
- Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail:
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Mokrousov I. The quiet and controversial: Ural family of Mycobacterium tuberculosis. INFECTION GENETICS AND EVOLUTION 2011; 12:619-29. [PMID: 22036706 DOI: 10.1016/j.meegid.2011.09.026] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 09/29/2011] [Accepted: 09/30/2011] [Indexed: 12/15/2022]
Abstract
The absence of lateral gene exchange is a characteristic feature defining the genome evolution and clonal population structure of Mycobacterium tuberculosis. Certain of its lineages have justly attracted more attention due to their global dissemination and/or remarkable pathogenic properties. In this critical review, I discuss the population structure and genetic geography of the less 'popular' but in some aspects no less noteworthy M. tuberculosis lineage, Ural family. Its specific signature was initially defined by single copy in MIRU26, and large (>6) copy number in MIRU10 loci, and by 43-spoligotyping as absence of signals 29-31 and 33-36. Here, I suggest to subdivide Ural strains with present and absent spoligosignal 2 into primary Ural-1 and secondary Ural-2 sublineages, respectively, while 1 copy in MIRU26 is specific of Ural-1. Furthermore, three copies were recently described in MIRU10 in Ural-1 strains which highlights a high diversity of this locus in Ural genotype. The data on the two Ural sublineages were extracted from SpolDB4 database and original publications in order to trace their distribution at global and within-country levels. Importantly, the rigorous reanalysis suggested the true rate of the Ural genotype in the Ural area in Russia to be only 7%. In contrast, the frequencies of the Ural sublineages peak elsewhere: in South Ukraine and Georgia/Abkhazia (Ural-1, up to 14-19%), and in southwestern Iran (Ural-2, up to 26%). However, as this name is used since 2005, it seems most parsimonious to continue its use even if misleading. The forest graph was built on the available spoligoprofiles of Ural family strains from Eurasia. It helped to suggest routes of their primary dispersal that are discussed in the context of the known human migrations also influenced by natural barriers. The north/east Pontic area may have been an area of origin and primary dispersal of the Ural (Ural-1) genotype in Eurasia, whereas political and natural borders may have influenced its subsequent dissemination throughout Central Asia. Studies of phenotypic properties in different models, comparison with host genetics give evidence that the Ural family strains are not associated with increased capacity to acquire drug resistance, pathogenicity or transmissibility. Instead since Ural family is rather moderately widespread in Eurasia beyond the hypothesized areas of origin, this situation may be a result of its low contagiosity as a consequence of long-term co-adaptation with human host. Future research should be focused on whole-genome sequencing in order to identify Ural-specific SNP and/or deletion, to resolve its phylogenetic and phylogeographic uncertainty and to elucidate biological features underlying its circulation and co-evolution with the human species.
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Affiliation(s)
- Igor Mokrousov
- Laboratory of Molecular Microbiology, St. Petersburg Pasteur Institute, St. Petersburg, Russia.
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Mycobacterium tuberculosis Complex Genotype Diversity and Drug Resistance Profiles in a Pediatric Population in Mexico. Tuberc Res Treat 2011; 2011:239042. [PMID: 22567263 PMCID: PMC3335619 DOI: 10.1155/2011/239042] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 05/22/2011] [Indexed: 11/25/2022] Open
Abstract
The aim of this study was to determine the frequency of drug resistance and the clonality of genotype patterns in M. tuberculosis clinical isolates from pediatric patients in Mexico (n = 90 patients from 19 states; time period—January 2002 to December 2003). Pulmonary disease was the most frequent clinical manifestation (71%). Children with systemic tuberculosis (TB) were significantly younger compared to patients with localized TB infections (mean 7.7 ± 6.2
years versus 15 ± 3.4
years P = 0.001). Resistance to any anti-TB drug was detected in 24/90 (26.7%) of the isolates; 21/90 (23.3%) and 10/90 (11.1%) were resistant to Isoniazid and Rifampicin, respectively, and 10/90 (11.1%) strains were multidrug-resistant (MDR). Spoligotyping produced a total of 55 different patterns; 12/55 corresponded to clustered isolates (n = 47, clustering rate of 52.2%), and 43/55 to unclustered isolates (19 patterns were designated as orphan by the SITVIT2 database). Database comparison led to designation of 36 shared types (SITs); 32 SITs (n = 65
isolates) matched a preexisting shared type in SITVIT2, whereas 4 SITs (n = 6
isolates) were newly created. Lineage classification based on principal genetic groups (PGG) revealed that 10% of the strains belonged to PGG1 (Bovis and Manu lineages). Among PGG2/3 group, the most predominant clade was the Latin-American and Mediterranean (LAM) in 27.8% of isolates, followed by Haarlem and T lineages. The number of single drug-resistant (DR) and multidrug-resistant (MDR-TB) isolates in this study was similar to previously reported in studies from adult population with risk factors. No association between the spoligotype, age, region, or resistance pattern was observed. However, contrary to a study on M. tuberculosis spoligotyping in Acapulco city that characterized a single cluster of SIT19 corresponding to the EAI2-Manila lineage in 70 (26%) of patients, not a single SIT19 isolate was found in our pediatric patient population. Neither did we find any shared type belonging to the EAI family which represents ancestral PGG1 strains within the M. tuberculosis complex. We conclude that the population structure of pediatric TB in our setting is different from the one prevailing in adult TB patient population of Guerrero.
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Groenheit R, Ghebremichael S, Svensson J, Rabna P, Colombatti R, Riccardi F, Couvin D, Hill V, Rastogi N, Koivula T, Källenius G. The Guinea-Bissau family of Mycobacterium tuberculosis complex revisited. PLoS One 2011; 6:e18601. [PMID: 21533101 PMCID: PMC3080393 DOI: 10.1371/journal.pone.0018601] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2010] [Accepted: 03/07/2011] [Indexed: 11/19/2022] Open
Abstract
The Guinea-Bissau family of strains is a unique group of the Mycobacterium tuberculosis complex that, although genotypically closely related, phenotypically demonstrates considerable heterogeneity. We have investigated 414 M. tuberculosis complex strains collected in Guinea-Bissau between 1989 and 2008 in order to further characterize the Guinea-Bissau family of strains. To determine the strain lineages present in the study sample, binary outcomes of spoligotyping were compared with spoligotypes existing in the international database SITVIT2. The major circulating M. tuberculosis clades ranked in the following order: AFRI (n = 195, 47.10%), Latin-American-Mediterranean (LAM) (n = 75, 18.12%), ill-defined T clade (n = 53, 12.8%), Haarlem (n = 37, 8.85%), East-African-Indian (EAI) (n = 25, 6.04%), Unknown (n = 12, 2.87%), Beijing (n = 7, 1.68%), X clade (n = 4, 0.96%), Manu (n = 4, 0.97%), CAS (n = 2, 0.48%). Two strains of the LAM clade isolated in 2007 belonged to the Cameroon family (SIT61). All AFRI isolates except one belonged to the Guinea-Bissau family, i.e. they have an AFRI_1 spoligotype pattern, they have a distinct RFLP pattern with low numbers of IS6110 insertions, and they lack the regions of difference RD7, RD8, RD9 and RD10, RD701 and RD702. This profile classifies the Guinea-Bissau family, irrespective of phenotypic biovar, as part of the M. africanum West African 2 lineage, or the AFRI_1 sublineage according to the spoligtyping nomenclature. Guinea-Bissau family strains display a variation of biochemical traits classically used to differentiate M. tuberculosis from M. bovis. Yet, the differential expression of these biochemical traits was not related to any genes so far investigated (narGHJI and pncA). Guinea-Bissau has the highest prevalence of M. africanum recorded in the African continent, and the Guinea-Bissau family shows a high phylogeographical specificity for Western Africa, with Guinea-Bissau being the epicenter. Trends over time however indicate that this family of strains is waning in most parts of Western Africa, including Guinea-Bissau (p = 0.048).
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Affiliation(s)
- Ramona Groenheit
- Department of Preparedness, Swedish Institute for Infectious Disease Control, Solna, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Solomon Ghebremichael
- Department of Preparedness, Swedish Institute for Infectious Disease Control, Solna, Sweden
| | - Jenny Svensson
- Department of Preparedness, Swedish Institute for Infectious Disease Control, Solna, Sweden
| | - Paulo Rabna
- Laboratório Nacional de Saúde Pública, Bissau, Guinea-Bissau
- Bandim Health Project, Indepth Network, Bissau, Guinea-Bissau
| | - Raffaella Colombatti
- Hospital “Raoul Follereau”, Bissau, Guinea-Bissau
- Department of Pediatrics, Azienda Ospedaliera-Università di Padova, Padova, Italy
| | - Fabio Riccardi
- Department of Public Health, University of “Tor Vergata”, Rome, Italy
| | - David Couvin
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Guadeloupe, France
| | - Véronique Hill
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Guadeloupe, France
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Guadeloupe, France
| | - Tuija Koivula
- Department of Preparedness, Swedish Institute for Infectious Disease Control, Solna, Sweden
- Department of Clinical Science and Education, Karolinska Institutet, Stockholm, Sweden
| | - Gunilla Källenius
- Department of Clinical Science and Education, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
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Zhang J, Heng S, Le Moullec S, Refregier G, Gicquel B, Sola C, Guillard B. A first assessment of the genetic diversity of Mycobacterium tuberculosis complex in Cambodia. BMC Infect Dis 2011; 11:42. [PMID: 21299851 PMCID: PMC3062598 DOI: 10.1186/1471-2334-11-42] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 02/07/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cambodia is among the 22 high-burden TB countries, and has one of the highest rates of TB in South-East Asia. This study aimed to describe the genetic diversity among clinical Mycobacterium tuberculosis complex (MTC) isolates collected in Cambodia and to relate these findings to genetic diversity data from neighboring countries. METHODS We characterized by 24 VNTR loci genotyping and spoligotyping 105 Mycobacterium tuberculosis clinical isolates collected between 2007 and 2008 in the region of Phnom-Penh, Cambodia, enriched in multidrug-resistant (MDR) isolates (n = 33). RESULTS Classical spoligotyping confirmed that the East-African Indian (EAI) lineage is highly prevalent in this area (60%-68% respectively in whole sample and among non-MDR isolates). Beijing lineage is also largely represented (30% in whole sample, 21% among non-MDR isolates, OR = 4.51, CI 95% [1.77, 11.51]) whereas CAS lineage was absent. The 24 loci MIRU-VNTR typing scheme distinguished 90 patterns with only 13 multi-isolates clusters covering 28 isolates. The clustering of EAI strains could be achieved with only 8 VNTR combined with spoligotyping, which could serve as a performing, easy and cheap genotyping standard for this family. Extended spoligotyping suggested relatedness of some unclassified "T1 ancestors" or "Manu" isolates with modern strains and provided finer resolution. CONCLUSIONS The genetic diversity of MTC in Cambodia is driven by the EAI and the Beijing families. We validate the usefulness of the extended spoligotyping format in combination with 8 VNTR for EAI isolates in this region.
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Affiliation(s)
- Jian Zhang
- Institut de Génétique et Microbiologie, UMR8621 CNRS-Université Paris-Sud 11, UniverSud, Infection Genetics Emerging Pathogens Evolution (IGEPE) Team, Bât, 400, F-91405 Orsay-Cedex, France
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Spoligotype profile of Mycobacterium tuberculosis complex strains from HIV-positive and -negative patients in Nigeria: a comparative analysis. J Clin Microbiol 2010; 49:220-6. [PMID: 21048016 DOI: 10.1128/jcm.01241-10] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We ran a comparative analysis of all patients for whom a positive culture of Mycobacterium tuberculosis complex was available between April 2004 and October 2005 and whose HIV serology results were known, with spoligotyping results (n = 163) split into 49 HIV-positive patients and 114 HIV-negative patients. Spoligotype international type 373 (SIT373) (T1 lineage), which was highly prevalent among the HIV(+) patients, was totally absent from the HIV(-) population, suggesting that we had a specific clone affecting nearly 1/3 of all HIV-tuberculosis (TB)-coinfected patients. Among the LAM10-CAM sublineage strains, we had only a single strain of SIT403 among HIV(-) patients (0.88%), as opposed to 12.25% of the HIV(+) population (χ(2) = 10.77; P < 0.01), indicating a strong association between the strain and the HIV(+) population. The LAM10-CAM lineage spoligotype SIT61 was prevalent among the 2 subsets (37.72% in HIV(-) versus 12.24% in HIV(+) populations), though, with a significant difference between the 2 groups (χ(2) = 10.53; P < 0.01). However, there was no significant difference for SIT53 (T1 lineage) in the 2 subsets: 6.14 versus 8.2% (χ(2) = 0.22; P > 0.05). A total of 7/49, or 14.3%, other SITs among HIV(+) patients were not found among the HIV(-) patients. When added to the most prevalent SIT among HIV(+) patients (SIT373; n = 16), 23/49, or 47%, isolates among HIV-TB-coinfected patients were unique. We conclude that further studies should be carried out to investigate the evolution of these genotypes and others in the emergence of multidrug resistance and control of tuberculosis in Nigeria.
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Abadia E, Zhang J, Vultos TD, Ritacco V, Kremer K, Aktas E, Matsumoto T, Refregier G, Soolingen DV, Gicquel B, Sola C. Resolving lineage assignation on Mycobacterium tuberculosis clinical isolates classified by spoligotyping with a new high-throughput 3R SNPs based method. INFECTION GENETICS AND EVOLUTION 2010; 10:1066-74. [DOI: 10.1016/j.meegid.2010.07.006] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 07/01/2010] [Accepted: 07/02/2010] [Indexed: 11/16/2022]
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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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