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Al-Mutairi NM, Ahmad S, Mokaddas E, Al-Hajoj S. First insights into the phylogenetic diversity of Mycobacterium tuberculosis in Kuwait and evaluation of REBA MTB-MDR assay for rapid detection of MDR-TB. PLoS One 2022; 17:e0276487. [PMID: 36264939 PMCID: PMC9584360 DOI: 10.1371/journal.pone.0276487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
Early detection of Mycobacterium tuberculosis (Mtb) in clinical specimens, its susceptibility to anti-TB drugs and disruption of infection transmission to new hosts are essential components for global tuberculosis (TB) control efforts. This study investigated major Mtb genotypes circulating in Kuwait and evaluated the performance of REBA MTB-MDR (REBA) test in comparison to GenoType MTBDRplus (gMTBDR+) assay for rapid detection of resistance of Mtb to isoniazid and rifampicin (MDR-TB). M. tuberculosis isolates (n = 256) originating predominantly from expatriate patients during a 6-month period were tested by spoligotyping and a dendrogram was created by UPGMA using MIRU-VNTRplus software. Phenotypic drug susceptibility testing (DST) was performed by MGIT 960 system. Genotypic DST for isoniazid and rifampicin was done by REBA and gMTBDR+ assays. Spoligotyping assigned 188 (73.4%) isolates to specific spoligotype international type (SIT) while 68 isolates exhibited orphan patterns. All major M. tuberculosis lineages were detected and EAI, CAS and Beijing families were predominant. Phylogenetic tree showed 131 patterns with 105 isolates exhibiting a unique pattern while 151 isolates clustered in 26 patterns. Fifteen isolates were resistant to one/more drugs. REBA and gMTBDR+ detected isoniazid resistance in 11/12 and 10/12 and rifampicin resistance in 4/5 and 4/5 resistant isolates, respectively. The diversity of SIT patterns are highly suggestive of infection of most expatriate patients with unique Mtb strains, likely acquired in their native countries before their arrival in Kuwait. Both, REBA and gMTBDR+ assays performed similarly for detection of resistance of Mtb to isoniazid and rifampicin for rapid detection of MDR-TB.
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Affiliation(s)
- Noura M. Al-Mutairi
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
- * E-mail: ,
| | - Eiman Mokaddas
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
- Kuwait National TB Control Laboratory, Shuwaikh, Kuwait
| | - Sahal Al-Hajoj
- Department of Infection and Immunity, Mycobacteriology Research Section, King Faisal Special Hospital and Research Center (KFSH & RC), Riyadh, Saudi Arabia
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Bakhtiyariniya P, Khosravi AD, Hashemzadeh M, Savari M. Genetic diversity of drug-resistant Mycobacterium tuberculosis clinical isolates from Khuzestan province, Iran. AMB Express 2022; 12:85. [PMID: 35789443 PMCID: PMC9253214 DOI: 10.1186/s13568-022-01425-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 06/21/2022] [Indexed: 11/10/2022] Open
Abstract
The emergence of drug-resistant strains of the Mycobacterium tuberculosis (MTB) has challenged tuberculosis control programs. So far, few studies using the 24-locus mycobacterial interspersed repetitive unit variable number tandem repeats (MIRU-VNTR) have investigated the genetic diversity of MTB in Iran. This study aimed to determine the genetic diversity of MTB isolates resistant to first-line anti-tuberculosis drugs using 24-locus MIRU-VNTR in southwestern Iran. Out of 6620 MTB clinical isolates, 29 resistant isolates to one or more isoniazid, rifampin, and ethambutol were detected using drug susceptibility testing by the proportional method. The manual 24-locus MIRU-VNTR was used to determine the MTB resistant isolates’ phylogenetic relationship. MIRU-VNTRplus web application tools were applied to analyze the associated data. Using 24-locus MIRU-VNTR, 13.8% of isolates (n = 4) were distributed in two clusters, and the remaining 86.2% (n = 25) showed a unique pattern. Four clonal complexes were observed in the minimum spanning tree based on the double-locus variant. Most isolates belonged to Delhi/CAS (34.5%, 10/29) and NEW-1 (24.1%, 7/29) sub-lineages, followed by EAI and LAM with a frequency of 6.9% (2/29) and 3.5% (1/29), respectively. Eight isolates (27.6%) did not match any genotype in the database. The 24-locus MIRU-VNTR showed a high discriminatory power; however, the 15-locus and 12-locus set analyses were more discriminative. Our study revealed a high degree of genetic diversity among drug-resistant MTB isolates, which could be interpreted as the low rate of person-to-person transmission in this region. The 15-locus MIRU-VNTR would be recommended for preliminary genotyping of drug-resistant MTB.
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Affiliation(s)
- Pejman Bakhtiyariniya
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Azar Dokht Khosravi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran. .,Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran. .,Iranian Study Group on Microbial Drug Resistance, Tehran, Iran.
| | - Mohammad Hashemzadeh
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Savari
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Asgharzadeh M, Rashedi J, Poor BM, Kafil HS, Zadeh HM, Ahmadpour E. How Molecular Epidemiology Can Affect Tuberculosis Control in the Middle East Countries: A Systematic Review and Meta-Analysis. Infect Disord Drug Targets 2021; 21:28-37. [PMID: 31903887 DOI: 10.2174/1871526520666200106123619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/13/2019] [Accepted: 12/24/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Nowadays, due to the incidence of specific strains of Mycobacterium tuberculosis and also an increase in the rate of drug resistant-TB, the mortality rate has been increased by this disease. The identification of common strains in the region, as well as the sources of transmission, is essential to control the disease, which is possible by using molecular epidemiology. OBJECTIVES In this survey, the studies utilizing the spoligotyping method in Muslim Middle East countries are reviewed to determine their role in the control of TB. METHODS All studies conducted from 2005 to June 2016 were considered systematically in three electronic databases out of which 23 studies were finally selected. RESULTS The average rate of clustering was 84% and the rate of recent transmission varied from 21.7% to 92.4%. The incidence of Beijing strains has been found to be rising in the abovementioned countries. In Iran and Saudi Arabia known as immigration and labour-hosting countries, respectively, rapid transmittable and drug-resistant Beijing strains were higher than those in other Muslim Middle East countries. CONCLUSION Considering the incidence of highly virulent strains, due to the increase in immigration and people infected with HIV, tuberculosis, especially drug-resistant form, careful monitoring is needed.
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Affiliation(s)
- Mohammad Asgharzadeh
- Biotechnology Research Center, Faculty of Paramedicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jalil Rashedi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behroz Mahdavi Poor
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Moharram Zadeh
- Women's Reproduction Health Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ehsan Ahmadpour
- Department of Medical Parasitology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Devi KR, Pradhan J, Bhutia R, Dadul P, Sarkar A, Gohain N, Narain K. Molecular diversity of Mycobacterium tuberculosis complex in Sikkim, India and prediction of dominant spoligotypes using artificial intelligence. Sci Rep 2021; 11:7365. [PMID: 33795751 PMCID: PMC8016865 DOI: 10.1038/s41598-021-86626-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 03/12/2021] [Indexed: 02/06/2023] Open
Abstract
In India, tuberculosis is an enormous public health problem. This study provides the first description of molecular diversity of the Mycobacterium tuberculosis complex (MTBC) from Sikkim, India. A total of 399 Acid Fast Bacilli sputum positive samples were cultured on Lőwenstein-Jensen media and genetic characterisation was done by spoligotyping and 24-loci MIRU-VNTR typing. Spoligotyping revealed the occurrence of 58 different spoligotypes. Beijing spoligotype was the most dominant type constituting 62.41% of the total isolates and was associated with Multiple Drug Resistance. Minimum Spanning tree analysis of 249 Beijing strains based on 24-loci MIRU-VNTR analysis identified 12 clonal complexes (Single Locus Variants). The principal component analysis was used to visualise possible grouping of MTBC isolates from Sikkim belonging to major spoligotypes using 24-MIRU VNTR profiles. Artificial intelligence-based machine learning (ML) methods such as Random Forests (RF), Support Vector Machines (SVM) and Artificial Neural Networks (ANN) were used to predict dominant spoligotypes of MTBC using MIRU-VNTR data. K-fold cross-validation and validation using unseen testing data set revealed high accuracy of ANN, RF, and SVM for predicting Beijing, CAS1_Delhi, and T1 Spoligotypes (93-99%). However, prediction using the external new validation data set revealed that the RF model was more accurate than SVM and ANN.
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Affiliation(s)
- Kangjam Rekha Devi
- grid.420069.90000 0004 1803 0080N.E. Region, Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Post Box #105, Dibrugarh, Assam 786 001 India
| | - Jagat Pradhan
- National Tuberculosis Elimination Programme (NTEP), Gangtok, Sikkim India
| | - Rinchenla Bhutia
- National Tuberculosis Elimination Programme (NTEP), Gangtok, Sikkim India
| | - Peggy Dadul
- Department of Health Care, Human Services and Family Welfare, State Tuberculosis Control Society, Gangtok, Sikkim India
| | - Atanu Sarkar
- grid.420069.90000 0004 1803 0080N.E. Region, Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Post Box #105, Dibrugarh, Assam 786 001 India
| | - Nitumoni Gohain
- grid.420069.90000 0004 1803 0080N.E. Region, Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Post Box #105, Dibrugarh, Assam 786 001 India
| | - Kanwar Narain
- grid.420069.90000 0004 1803 0080N.E. Region, Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Post Box #105, Dibrugarh, Assam 786 001 India
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Sivakumar S, Chandramohan Y, Kathamuthu GR, Sekar G, Kandhasamy D, Padmanaban V, Hissar S, Tripathy SP, Bethunaickan R, Dhanaraj B, Babu S, Ranganathan UD. The recent trend in mycobacterial strain diversity among extra pulmonary lymph node tuberculosis and their association with drug resistance and the host immunological response in South India. BMC Infect Dis 2020; 20:894. [PMID: 33243148 PMCID: PMC7690019 DOI: 10.1186/s12879-020-05597-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/08/2020] [Indexed: 11/11/2022] Open
Abstract
Background Tuberculosis (TB) though primarily affects the lungs it may also affect the other parts of the body and referred as extra pulmonary (EPTB). This study is focused on understanding the genetic diversity and molecular epidemiology of Mycobacterium tuberculosis (M.tb) among tuberculous lymphadenitis (TBL), a form of EPTB patients identified in Chennai, Tamil Nadu. Methods The genetic diversity was identified by performing spoligotyping on the M.tb clinical isolates that were recovered from lymph node samples. A total of 71 M.tb isolates were recovered from extra pulmonary lymph node samples and subjected to Drug susceptibility testing and spoligotyping was carried out. In addition, immunological characterization from blood of same individuals from whom M.tb was isolated was carried out between the two major lineages groups East African Indian 3 (EAI3) and non-EAI3 strains by ELISA. The results of spoligotyping patterns were compared with the world Spoligotyping Database of Institute Pasteur de Guadeloupe (SpolDB4). Results We found 41 spoligotype patterns and their associated lineages. Out of 41 spoligotype pattern, only 22 patterns are available in the spoldB4 database with Spoligotype international Type (SIT) number and remaining patterns were orphan strains without SIT number. The most predominant spoligotype lineage that was found in lymph node sample in this region of India was EAI (36), followed by central Asian strain (CAS) (6), T1 (5), Beijing (3), Latin American & Mediterranean (LAM) (2), U (1), X2 (1) and orphan (22). In addition to EAI, CAS and Beijing, our study identified the presence of orphan and unique spoligotyping patterns in Chennai region. We observed six drug resistant isolates. Out of six drug resistant isolates, four were resistant to isoniazid drug and associated with EAI family. Moreover, we observed increased levels of type 2 and type 17 cytokine profiles between EAI3 and non-EAI family, infected individuals. Conclusions The study confirms that EAI lineage to be the most predominant lineages in EPTB patients with lymphadenitis and were found to have increased type 1 and type 17 proinflammatory cytokine profiles. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-020-05597-0.
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Affiliation(s)
- Shanmugam Sivakumar
- Department of Bacteriology, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600 031, India
| | - Yuvaraj Chandramohan
- Department of Immunology, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600 031, India
| | - Gokul Raj Kathamuthu
- National Institute of Health -International Center for Excellence in Research - National Institute for Research in Tuberculosis, Chennai, India
| | - Gomathi Sekar
- Department of Bacteriology, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600 031, India
| | - Devika Kandhasamy
- Department of Bacteriology, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600 031, India
| | - Venkatesan Padmanaban
- Department of Immunology, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600 031, India
| | - Syed Hissar
- Department of Clinical Health Research, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600 031, India
| | - Srikanth P Tripathy
- National Institute for Research in Tuberculosis, Chetpet, Chennai, 600 031, India
| | - Ramalingam Bethunaickan
- Department of Immunology, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600 031, India
| | - Baskaran Dhanaraj
- Department of Clinical Health Research, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600 031, India
| | - Subash Babu
- National Institute of Health -International Center for Excellence in Research - National Institute for Research in Tuberculosis, Chennai, India
| | - Uma Devi Ranganathan
- Department of Immunology, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600 031, India.
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An ancestral genomic locus in Mycobacterium tuberculosis clinical isolates from India hints the genetic link with Mycobacterium canettii. Int Microbiol 2020; 23:397-404. [PMID: 31898033 DOI: 10.1007/s10123-019-00113-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/06/2019] [Accepted: 12/05/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND Tuberculosis remains a worldwide public health emergency. To better understand M. tuberculosis and to identify genomic variations characteristic to the Indian clinical isolates by a low-cost method, a genomic subtractive hybridization between M. tuberculosis H37Rv and a clinical isolate from South India was performed. RESULTS This revealed a novel 0.4-kb subtractive fragment which was used as a handle to pull out a 4.5-kb genomic region characteristic to the clinical isolate and was absent in H37Rv. On further studies, this 4.5-kb region was found to be present in 91% of the M. tuberculosis clinical isolates screened from Kerala, a state in South India. Interestingly, this novel region has 99% identity (with 100% query coverage) with genomic regions of M. canettii. DISCUSSION The present study hypothesizes that this locus was present in the recent common environmental ancestor of mycobacteria, retained to the maximum extent in M. canettii and ancestral isolates of M. tuberculosis, and later deleted in other modern lineages of M. tuberculosis. Thus, this region may serve as one of the links between the pathogenic mycobacteria and the environmental species. We also propose that the Indian isolates of M. tuberculosis might be closely related to the putative progenitor M. prototuberculosis with respect to this locus. More studies on other genomic loci from different strains of M. tuberculosis are required to establish more links in this direction.
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Poonawala H, Kumar N, Peacock SJ. A review of published spoligotype data indicates the diversity of Mycobacterium tuberculosis from India is under-represented in global databases. INFECTION GENETICS AND EVOLUTION 2019; 78:104072. [PMID: 31618692 DOI: 10.1016/j.meegid.2019.104072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 10/07/2019] [Accepted: 10/11/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Mycobacterium tuberculosis (MTBC) lineages differ in clinical presentation, virulence, transmission, drug resistance and immunological responses. Despite having the largest burden of tuberculosis (TB) in the world, strains from India are underrepresented in international databases. We reviewed published spoligotype data to determine the distribution and diversity of MTBC lineages in India. METHODS A Pubmed/MEDLINE search identified 34 M. tuberculosis spoligotyping studies from India. Spoligotype patterns were extracted and the Spoligotype International Type (SIT) number, sub-lineage and lineage determined. Minimum Spanning Trees were used to determine relationships between patterns. RESULTS We identified 1528 spoligotype patterns distributed across 8300 isolates; 6733 isolates belonged to 472 SITs, with 53% of all isolates belonging to 12 SITs with at least 100 isolates each. Lineage 1 and Lineage 3 made up 67% of all isolates, although a lineage could not be assigned for 16% of isolates. Lineage 1 isolates were most common in Southern, Western and Eastern India, and Lineage 3 was most common in Northern and Central India. The RULE, CBN and KBBN lineage prediction algorithms from the TB-lineage tools performed variably, with the correct lineage predicted correctly for only 64% of patterns with known lineage. Using a consensus definition, 64% of the 1359 isolates with unknown lineage were assigned to Lineage 1, and 14% each were assigned to Lineages 3 and 4. With these lineage assignments, 80% of all isolates belonged to either Lineage 1 or Lineage 3. CONCLUSION Our findings indicate significant M. tuberculosis diversity in India. The documentation of 1056 orphan and unreported patterns indicate that this diversity is under-represented in global databases.
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Affiliation(s)
- Husain Poonawala
- National Institute for Research in Tuberculosis, Chetpet, Chennai 600031, India; Institute of Public Health, Banashankari, Bangalore 560070, India.
| | - Narender Kumar
- Department of Medicine, University of Cambridge, Hills Rd, Cambridge CB2 0QQ, United Kingdom
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Hills Rd, Cambridge CB2 0QQ, United Kingdom.
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Mendis C, Thevanesam V, Kumara A, Wickramasinghe S, Madegedara D, Gamage C, Gordon SV, Suzuki Y, Ratnatunga C, Nakajima C. Insight into genetic diversity of Mycobacterium tuberculosis in Kandy, Sri Lanka reveals predominance of the Euro-American lineage. Int J Infect Dis 2019; 87:84-91. [PMID: 31299365 DOI: 10.1016/j.ijid.2019.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/24/2019] [Accepted: 07/01/2019] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE Sri Lanka is a country where the molecular epidemiology of Mycobacterium tuberculosis (MTB) is poorly explored. Therefore, this study was performed to identify circulating lineages/sub-lineages of MTB and their transmission patterns. METHODS DNA was extracted from 89 isolates of MTB collected during 2012 and 2013 from new pulmonary tuberculosis patients in Kandy, Sri Lanka and analyzed by spoligotyping, large sequence polymorphism (LSP), mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing, and drug resistance-associated gene sequencing. RESULTS The predominant lineage was lineage 4 (Euro-American, 45.9%), followed by lineage 1 (Indo-Oceanic, 29.4%), lineage 2 (East-Asian, 23.5%), and lineage 3 (Central-Asian, 1.2%). Among 26 spoligotype patterns, eight were undesignated or new types and seven of these belonged to lineage 4. Undesignated lineage 4/SIT124 (n=2/8) and SIT3234 (n=8/8) clustered together based on 24-locus MIRU-VNTR typing. The dominant sub-lineage was Beijing/SIT1 (n=19), with the isoniazid resistance katG G944C mutation (Ser315Thr) detected in two of them. CONCLUSIONS The population structure of MTB in Kandy, Sri Lanka was different from that in the South Asian region. The clonal expansion of locally evolved lineage 4/SIT3234 and detection of the pre-multidrug resistant Beijing isolates from new tuberculosis patients is alarming and will require continuous monitoring.
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Affiliation(s)
- Charitha Mendis
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Department of Medical Laboratory Science, Faculty of Allied Health Sciences, University of Peradeniya, Sri Lanka
| | - Vasanthi Thevanesam
- Department of Microbiology, Faculty of Medicine, University of Peradeniya, Sri Lanka
| | - Athula Kumara
- Department of Microbiology, Faculty of Medicine, University of Peradeniya, Sri Lanka
| | - Susiji Wickramasinghe
- Department of Parasitology, Faculty of Medicine, University of Peradeniya, Sri Lanka
| | | | - Chandika Gamage
- Department of Microbiology, Faculty of Medicine, University of Peradeniya, Sri Lanka
| | - Stephen V Gordon
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland; Global Station for Zoonosis Control, Hokkaido University Global Institute for Collaborative Research and Education, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Global Station for Zoonosis Control, Hokkaido University Global Institute for Collaborative Research and Education, Sapporo, Japan
| | - Champa Ratnatunga
- Department of Microbiology, Faculty of Medicine, University of Peradeniya, Sri Lanka.
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Global Station for Zoonosis Control, Hokkaido University Global Institute for Collaborative Research and Education, Sapporo, Japan.
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Prakash R, Gupta R, Sharma P, Jain S, Chauhan DS, Katoch VM, Tiwari PK. Genotypic diversity of Mycobacterium tuberculosis isolates from North-Central Indian population. Pathog Glob Health 2019; 113:39-48. [PMID: 30821646 DOI: 10.1080/20477724.2019.1583881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
BACKGROUND Different strains of Mycobacterium tuberculosis (MTB) are known to have different epidemiological and clinical characteristics. Some of them are widely distributed and associated with drug resistance, whereas others are locally predominated. Molecular epidemiological investigations have always been beneficial in identifying new strains and studying their transmission dynamics. Sahariya a primitive tribe of North Madhya Pradesh, India, has already been reported to have high prevalence of tuberculosis (TB) than their non-tribal neighbours. However, the information about MTB genotypes prevalent in Sahariya tribe and their non-tribal neighbours is not available. METHODS A total of 214 clinical isolates representing Sahariya tribe and non-tribes were analyzed by spoligotyping and MIRU-VNTR typing. RESULTS The EAI3_IND/SIT11 genotype was observed as major genotype in Sahariya tribe followed by CAS1_Delhi/SIT26 genotype. A 3.04 fold higher risk of getting TB with EAI3_IND/SIT11 genotype was observed in Sahariya as compared to the non-tribal population. The EAI_IND/SIT11 genotype also found to have more number of MDR-TB cases in Sahariya as well as true and possible transmission links. In Sahariya tribe, 3 clusters (6 isolates) reflected true transmission links, whereas 8 clusters consisted of 26 isolates revealed possible transmission links within the same geographical location or nearby houses. CONCLUSION The present study highlighted the predominance of EAI3_IND/SIT11 genotype in Sahariya tribe followed by CAS1_Delhi/SIT26 genotype. Combined approach of MIRU-VNTR typing and spoligotyping was observed more favourable in discrimination of MTB genotypes. Further, longitudinal studies using whole genome sequencing can provide more insights into genetic diversity, drug resistance and transmission dynamics of these prevalent genotypes.
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Affiliation(s)
- Ravi Prakash
- a Centre for Genomics, Molecular and Human Genetics , Jiwaji University , Gwalior , India.,b Department of Microbiology and Molecular Biology , National JALMA Institute for Leprosy and other Mycobacterial Diseases , Agra , India.,c Key Laboratory of Medical Molecular Virology , Fudan University , Shanghai , China
| | - Rahul Gupta
- a Centre for Genomics, Molecular and Human Genetics , Jiwaji University , Gwalior , India
| | - Pragya Sharma
- b Department of Microbiology and Molecular Biology , National JALMA Institute for Leprosy and other Mycobacterial Diseases , Agra , India
| | - Sanjay Jain
- d Revised National Tuberculosis Control Programme , District Hospital , Sheopur , India
| | - Devendra Singh Chauhan
- b Department of Microbiology and Molecular Biology , National JALMA Institute for Leprosy and other Mycobacterial Diseases , Agra , India
| | - Vishwa Mohan Katoch
- e Former Secretary, Department of Health Research, Govt. of India and Former Director General , Indian Council of Medical Research , Ansari Nagar , New Delhi , India.,f Rajasthan University of Health Sciences , Jaipur , India
| | - Pramod Kumar Tiwari
- a Centre for Genomics, Molecular and Human Genetics , Jiwaji University , Gwalior , India
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Chawla K, Kumar A, Shenoy VP, Chauhan DS, Sharma P. Genetic diversity of Mycobacterium tuberculosis in south coastal Karnataka, India, using spoligotyping. Indian J Med Res 2018; 147:278-286. [PMID: 29923517 PMCID: PMC6022373 DOI: 10.4103/ijmr.ijmr_2026_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Background & objectives: Despite high occurrence of tuberculosis in India very little information is available about the genetic diversity of Mycobacterium tuberculosis isolates prevailing in coastal Karnataka, India. Thus, the present study was undertaken to explore the genetic biodiversity of M. tuberculosis isolates prevailing in south coastal region of Karnataka (Udupi District), India. Methods: A total of 111 Mycobacterial isolates were cultured in Lowenstein Jensen (LJ) medium and after obtaining growth, DNA was extracted and spoligotyping was performed. SITVIT WEB database was used to locate families of spoligotypes. Results: On analyzing the hybridization results of all 111 isolates on SITVIT WEB database 57 (51.35%) isolates were clustered into 11 Spoligotype International Types (SIT). The largest cluster of 14 (12.61%) isolates was SIT-48 (EAI1-SOM), followed by SIT-1942 (CAS1-Delhi) with 11 isolates (9.9%) and SIT-11 with seven (6.30%). Moreover, 23 isolates (20.72%) had unique spoligotypes and 31 (27.92%) were orphans. Spotclust analysis revealed that majority (67%) of orphan isolates were variants of CAS (37%) and EAI-5 (34%). Interpretation & conclusions: The present study revealed high biodiversity among the circulating isolates of M. tuberculosis in this region with the presence of mixed genotypes earlier reported from north and south India along with certain new genotypes with unique SITs. The study highlights the need for further longitudinal studies to explore the genetic diversity and to understand the transmission dynamics of prevailing isolates.
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Affiliation(s)
- Kiran Chawla
- Department of Microbiology, Kasturba Medical College, MAHE, Manipal, India
| | - Ajay Kumar
- Department of Microbiology, Kasturba Medical College, MAHE, Manipal, India
| | | | - Devendra Singh Chauhan
- Department of Microbiology & Molecular Biology, ICMR-National JALMA Institute for Leprosy & other Mycobacterial Diseases, Agra, India
| | - Pragya Sharma
- Department of Microbiology & Molecular Biology, ICMR-National JALMA Institute for Leprosy & other Mycobacterial Diseases, Agra, India
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11
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The clinical course of chemoresistant pulmonary tuberculosis in the dynamics of treatment depending on the genotypes of M. tuberculosis. Fam Med 2018. [DOI: 10.30841/2307-5112.3.2018.147190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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The Epidemiological Significance and Temporal Stability of Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats-Based Method Applied to Mycobacterium tuberculosis in China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15040782. [PMID: 29673235 PMCID: PMC5923824 DOI: 10.3390/ijerph15040782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/11/2018] [Accepted: 04/11/2018] [Indexed: 11/17/2022]
Abstract
This study aimed to validate the epidemiological significance and temporal stability of Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) typing in a genetically and geographically diverse set of clinical isolates from patients diagnosed with pulmonary tuberculosis in China. Between 2010 and 2013, a total of 982 Mycobacterium tuberculosis isolates were collected from four population-based investigations in China. Apart from the currently applied 24-locus MIRU-VNTR, six additional hypervariable loci were analyzed in order to validate the MIRU-VNTR combinations in terms of their epidemiological links, clustering time span, and paired geographic distance. In vitro temporal stability was analyzed for both individual MIRU-VNTR loci, and for several combinations of loci. In the present study, four MIRU-VNTR combinations, including the hypervariable loci 3820, 3232, 2163a, and 4120, were evaluated. All of these combinations obtained a Hunter-Gaston discriminatory index (HGDI) value over 0.9900 with a reduced clustering proportion (from 32.0% to 25.6%). By comparing epidemiological links, clustering time span, and paired geographic distance, we found that the performances of the four MIRU-VNTR combinations were comparable to the insertion sequence 6110 restriction fragment length polymorphism (IS6110-RFLP), and significantly better than that of 24-locus MIRU-VNTR genotyping alone. The proportion of temporally stable loci ranged from 90.5% to 92.5% within the combined MIRU-VNTR genotyping, which is higher than IS6110-RFLP (85.4%). By adding four hypervariable loci to the standard 24-locus MIRU-VNTR genotyping, we obtained a high discriminatory power, stability and epidemiological significance. This algorithm could therefore be used to improve tuberculosis transmission surveillance and outbreak investigation in China.
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Augusto CJ, Carvalho WDS, Almeida IND, Figueiredo LJDA, Dantas NGT, Suffys PN, Miranda SSD. Comparative study of RFLP-IS6110 and MIRU-VNTR from Mycobacterium tuberculosis isolated in the state of Minas Gerais, Brazil. Braz J Microbiol 2017; 49:641-646. [PMID: 29249565 PMCID: PMC6112052 DOI: 10.1016/j.bjm.2017.04.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 02/08/2017] [Accepted: 04/06/2017] [Indexed: 11/16/2022] Open
Abstract
DNA genotyping of Mycobacterium tuberculosis has been widely applied in the understanding of disease transmission in many countries. The purpose of this study was to genotype the strains of M. tuberculosis isolated in patients with new tuberculosis (TB) cases in Minas Gerais, as well as to compare the similarity, discriminatory power, and agreement of the clusters between the IS6110 Restriction Fragment Length Polymorfism (RFLP) and 12 loci Variable Number Tandem Repeat – Mycobacterial Interspersed Repetitive Units (MIRU-VNTR) techniques. It was observed that 32% (66/204) of the isolated strains in the RFLP-IS6110 and 50.9% (104/204) of the isolated strains in the MIRU-VNTR presented a similarity of equal to or above 85%. The RFLP-IS6110 and MIRU-VNTR proved to contain a high discriminatory power. The similarity index resulting from the RFLP showed no recent transmission. Good agreement was observed between the techniques when clusters were detected; however, the best epidemiological relationship was found when using the RFLP-IS6110.
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Affiliation(s)
- Cláudio José Augusto
- Fundação Ezequiel Dias, Belo Horizonte, MG, Brazil; Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | | | | | | | | | - Philip Noel Suffys
- Fundação Oswaldo Cruz Foundation (FIOCRUZ), Instituto Oswaldo Cruz, Laboratório de Biologia Molecular Aplicada a Micobactérias, Rio de Janeiro, RJ, Brazil
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Khosravi AD, Shahraki AH, Dezfuli SK, Hashemzadeh M, Goodarzi H, Mohajeri P. Genetic diversity of multidrug-resistant Mycobacterium tuberculosis strains isolated from tuberculosis patients in Iran using MIRU-VNTR technique. Kaohsiung J Med Sci 2017; 33:550-557. [PMID: 29050672 DOI: 10.1016/j.kjms.2017.06.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 06/13/2017] [Accepted: 06/20/2017] [Indexed: 12/15/2022] Open
Abstract
Tuberculosis (TB) is considered as one of the most important infectious diseases in the world, and recent rise and spread of multidrug-resistant (MDR) Mycobacterium tuberculosis (MTB) strains, have made the matter worsened. Due to the importance of TB prevalence in Iran, this study was designed to investigate the genetic diversity among MDR strains of MTB by MIRU-VNTR typing scheme. A total of 88 drug resistant M. tuberculosis isolates belong to pulmonary TB cases were collected from several TB reference centers of Iran. Drug susceptibility testing for Isoniazid and Rifampin was performed using the agar proportion method and MDR isolates were underwent genotyping by using 12-locus- based MIRU-VNTR typing. On performing proportion method, 22 isolates were identified as MDR. By typing of MDR isolates using 12-loci MIRU-VNTR technique, high diversity were demonstrated in MDR strains and these were classified into 20 distinct MIRU-VNTR genotypes. MIRU loci 10 and 26 were the most discriminatory loci with 8 and 7 alleles respectively; while MIRU loci 2, 20, 24 and 39 were found to be the least discriminatory with 1-2 alleles each. We noticed a mixed infection in isolate 53, as this isolate comprised simultaneous two alleles in MIRU loci 40, 10, 16 and 39. In conclusion, this result represents MIRU-VNTR typing as a useful tool for studying genetic diversity of MDR-MTB in regional settings, and will help the health sectors to construct a preventive program for MDR-TB. Additionally, it can detect mixed infection which can facilitate management of treatment.
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Affiliation(s)
- Azar Dokht Khosravi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran; Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Soolmaz Khandan Dezfuli
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Mohammad Hashemzadeh
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Hamed Goodarzi
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Parviz Mohajeri
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
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15
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Desikan P, Chauhan DS, Sharma P, Panwalkar N, Chourey M, Patidar ML, Yadav P, Chandrasekaran V, Ohri BS. Genetic diversity of Mycobacterium tuberculosis isolates from central India. Indian J Med Res 2017; 143:481-6. [PMID: 27377505 PMCID: PMC4928555 DOI: 10.4103/0971-5916.184287] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Background & objectives: There is a paucity of data available on genetic biodiversity of Mycobacterium tuberculosis isolates from central India. The present study was carried out on isolates of M. tuberculosis cultured from diagnostic clinical samples of patients from Bhopal, central India, using spoligotyping as a method of molecular typing. Methods: DNA was extracted from 340 isolates of M. tuberculosis from culture, confirmed as M. tuberculosis by molecular and biochemical methods and subjected to spoligotyping. The results were compared with the international SITVIT2 database. Results: Sixty five different spoligo international type (SIT) patterns were observed. A total of 239 (70.3%) isolates could be clustered into 25 SITs. The Central Asian (CAS) and East African Indian (EAI) families were found to be the two major circulating families in this region. SIT26/CAS1_DEL was identified as the most predominant type, followed by SIT11/EAI3_IND and SIT288/CAS2. Forty (11.8%) unique (non-clustered) and 61 (17.9%) orphan isolates were identified in the study. There was no significant association of clustering with clinical and demographic characteristics of patients. Interpretation & conclusions: Well established SITs were found to be predominant in our study. SIT26/CAS1_DEL was the most predominant type. However, the occurrence of a substantial number of orphan isolates may indicate the presence of active spatial and temporal evolutionary dynamics within the isolates of M. tuberculosis.
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Affiliation(s)
- Prabha Desikan
- Bhopal Memorial Hospital & Research Centre (ICMR), Bhopal, Madhya Pradesh, India
| | - D S Chauhan
- National JALMA Institute of Leprosy & Other Mycobacterial Diseases (ICMR), Agra, India
| | - Pragya Sharma
- National JALMA Institute of Leprosy & Other Mycobacterial Diseases (ICMR), Agra, India
| | - Nikita Panwalkar
- Bhopal Memorial Hospital & Research Centre (ICMR), Bhopal, Madhya Pradesh, India
| | - Manju Chourey
- Bhopal Memorial Hospital & Research Centre (ICMR), Bhopal, Madhya Pradesh, India
| | - Mohan Lal Patidar
- Bhopal Memorial Hospital & Research Centre (ICMR), Bhopal, Madhya Pradesh, India
| | - Priyanka Yadav
- National JALMA Institute of Leprosy & Other Mycobacterial Diseases (ICMR), Agra, India
| | - V Chandrasekaran
- National Institute for Research in Tuberculosis (ICMR), Chennai, India
| | - B S Ohri
- State TB Office, Directorate of Health Services, Bhopal, Madhya Pradesh, India
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Singhal P, Dixit P, Singh P, Jaiswal I, Singh M, Jain A. A study on pre-XDR & XDR tuberculosis & their prevalent genotypes in clinical isolates of Mycobacterium tuberculosis in north India. Indian J Med Res 2017; 143:341-7. [PMID: 27241648 PMCID: PMC4892081 DOI: 10.4103/0971-5916.182625] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Background & objectives: Pre-extensively drug resistant (pre-XDR) and extensively drug resistant tuberculosis (XDR-TB) have been areas of growing concern, and are posing threat to global efforts of TB control. The present study was planned to study the presence of pre-XDR and XDR Mycobacterium tuberculosis and their genotypes in clinical isolates obtained from previously treated cases of pulmonary TB. Methods: A total of 219 isolates obtained from previously treated cases of pulmonary TB were subjected to first-line (streptomycin, isoniazid, rifampicin and ethambutol) and second-line (ofloxacin, kanamycin, capreomycin and amikacin) drug susceptibility testing on solid Lowenstein-Jensen medium by proportion method. Genotyping was done for pre-XDR and XDR-TB isolates using 12 loci Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats (MIRU-VNTR). Results: Multi-drug resistance was observed in 39.7 per cent (87/219) isolates. Pre-XDR and XDR M. tuberculosis isolates amongst 87 multi-drug resistant (MDR) TB isolates were 43 (49.4%) and 10 (11.4%), respectively. Two most dominant genotypes among pre-XDR and XDR M. tuberculosis isolates were Beijing and Delhi/CAS types. Interpretation & conclusions: Resistance to second-line anti-tubercular drugs should be routinely assessed in areas endemic for TB. Similar genotype patterns were seen in pre-XDR and XDR-TB isolates. Beijing and Delhi/CAS were predominant genotypes.
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Affiliation(s)
- Parul Singhal
- Department of Microbiology, King George's Medical University, Lucknow, India
| | - Pratima Dixit
- Department of Microbiology, King George's Medical University, Lucknow, India
| | - Pooja Singh
- Department of Microbiology, King George's Medical University, Lucknow, India
| | - Indu Jaiswal
- Department of Microbiology, King George's Medical University, Lucknow, India
| | - Mastan Singh
- Department of Microbiology, King George's Medical University, Lucknow, India
| | - Amita Jain
- Department of Microbiology, King George's Medical University, Lucknow, India
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17
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Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria. Clin Microbiol Rev 2016; 29:239-90. [PMID: 26912567 DOI: 10.1128/cmr.00055-15] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Molecular typing has revolutionized epidemiological studies of infectious diseases, including those of a mycobacterial etiology. With the advent of fingerprinting techniques, many traditional concepts regarding transmission, infectivity, or pathogenicity of mycobacterial bacilli have been revisited, and their conventional interpretations have been challenged. Since the mid-1990s, when the first typing methods were introduced, a plethora of other modalities have been proposed. So-called molecular epidemiology has become an essential subdiscipline of modern mycobacteriology. It serves as a resource for understanding the key issues in the epidemiology of tuberculosis and other mycobacterial diseases. Among these issues are disclosing sources of infection, quantifying recent transmission, identifying transmission links, discerning reinfection from relapse, tracking the geographic distribution and clonal expansion of specific strains, and exploring the genetic mechanisms underlying specific phenotypic traits, including virulence, organ tropism, transmissibility, or drug resistance. Since genotyping continues to unravel the biology of mycobacteria, it offers enormous promise in the fight against and prevention of the diseases caused by these pathogens. In this review, molecular typing methods for Mycobacterium tuberculosis and nontuberculous mycobacteria elaborated over the last 2 decades are summarized. The relevance of these methods to the epidemiological investigation, diagnosis, evolution, and control of mycobacterial diseases is discussed.
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18
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Devi KR, Bhutia R, Bhowmick S, Mukherjee K, Mahanta J, Narain K. Genetic Diversity of Mycobacterium tuberculosis Isolates from Assam, India: Dominance of Beijing Family and Discovery of Two New Clades Related to CAS1_Delhi and EAI Family Based on Spoligotyping and MIRU-VNTR Typing. PLoS One 2015; 10:e0145860. [PMID: 26701129 PMCID: PMC4689458 DOI: 10.1371/journal.pone.0145860] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 12/09/2015] [Indexed: 11/24/2022] Open
Abstract
Tuberculosis (TB) is one of the major public health concerns in Assam, a remote state located in the northeastern (NE) region of India. The present study was undertaken to explore the circulating genotypes of Mycobacterium tuberculosis complex (MTBC) in this region. A total of 189 MTBC strains were collected from smear positive pulmonary tuberculosis cases from different designated microscopy centres (DMC) from various localities of Assam. All MTBC isolates were cultured on Lowenstein-Jensen (LJ) media and subsequently genotyped using spoligotyping and 24-loci mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) typing. Spoligotyping of MTBC isolates revealed 89 distinct spoligo patterns. The most dominant MTBC strain belonged to Beijing lineage and was represented by 35.45% (n = 67) of total isolates, followed by MTBC strains belonging to Central Asian-Delhi (CAS/Delhi) lineage and East African Indian (EAI5) lineage. In addition, in the present study 43 unknown spoligo patterns were detected. The discriminatory power of spoligotyping was found to be 0.8637 based on Hunter Gaston Discriminatory Index (HGDI). On the other hand, 24-loci MIRU-VNTR typing revealed that out of total 189 MTBC isolates from Assam 185 (97.9%) isolates had unique MIRU-VNTR profiles and 4 isolates grouped into 2 clusters. Phylogenetic analysis of 67 Beijing isolates based on 24-loci MIRU-VNTR typing revealed that Beijing isolates from Assam represent two major groups, each comprising of several subgroups. Neighbour-Joining (NJ) phylogenetic tree analysis based on combined spoligotyping and 24-loci MIRU-VNTR data of 78 Non-Beijing isolates was carried out for strain lineage identification as implemented by MIRU-VNTRplus database. The important lineages of MTBC identified were CAS/CAS1_Delhi (41.02%, n = 78) and East-African-Indian (EAI, 33.33%). Interestingly, phylogenetic analysis of orphan (23.28%) MTBC spoligotypes revealed that majority of these orphan isolates from Assam represent two new sub-clades Assam/EAI and Assam/CAS. The prevalence of multidrug resistance (MDR) in Beijing and Non-Beijing strains was found to be 10.44% and 9.01% respectively. In conclusion, the present study has shown the predominance of Beijing isolates in Assam which is a matter of great concern because Beijing strains are considered to be ecologically more fit enabling wider dissemination of M. tuberculosis. Other interesting finding of the present study is the discovery of two new clades of MTBC isolates circulating in Assam. More elaborate longitudinal studies are required to be undertaken in this region to understand the transmission dynamics of MTBC.
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Affiliation(s)
- Kangjam Rekha Devi
- Regional Medical Research Centre, N.E. Region (Indian Council of Medical Research), Post Box #105, Dibrugarh 786 001, Assam, India
| | - Rinchenla Bhutia
- Regional Medical Research Centre, N.E. Region (Indian Council of Medical Research), Post Box #105, Dibrugarh 786 001, Assam, India
| | - Shovonlal Bhowmick
- Regional Medical Research Centre, N.E. Region (Indian Council of Medical Research), Post Box #105, Dibrugarh 786 001, Assam, India
| | - Kaustab Mukherjee
- Regional Medical Research Centre, N.E. Region (Indian Council of Medical Research), Post Box #105, Dibrugarh 786 001, Assam, India
| | - Jagadish Mahanta
- Regional Medical Research Centre, N.E. Region (Indian Council of Medical Research), Post Box #105, Dibrugarh 786 001, Assam, India
| | - Kanwar Narain
- Regional Medical Research Centre, N.E. Region (Indian Council of Medical Research), Post Box #105, Dibrugarh 786 001, Assam, India
- * E-mail:
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Kandhakumari G, Stephen S, Sivakumar S, Narayanan S. Spoligotype patterns of Mycobacterium tuberculosis isolated from extra pulmonary tuberculosis patients in Puducherry, India. Indian J Med Microbiol 2015; 33:267-70. [PMID: 25865980 DOI: 10.4103/0255-0857.154871] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
PURPOSE Genotyping studies like spoligotyping are valuable tools in understanding the genetic diversity and epidemiology of Mycobacterium tuberculosis. Though there are reports of spoligotyping of M. tuberculosis isolates from pulmonary specimens from different parts of India, spoligotyping of extra pulmonary tuberculosis isolates are very few. Puducherry has not yet recorded spoligopatterns of M. tuberculosis from either pulmonary or extra pulmonary (EPTB) specimens. The aim of this study is to analyze the spoligotype patterns of EPTB strains circulating in Puducherry and neighboring districts of Tamil Nadu. MATERIALS AND METHODS During June 2011 to December 2013, 570 EPTB specimens were processed by culturing on to Lowenstein Jensen (LJ) medium and automated Mycobacterium Growth Indicator Tube system (MGIT960). Identification of M. tuberculosis was carried out as per standard procedures, and MPT 64 antigen positivity in a commercial immunochromatography kit. Spoligotyping was carried out at National Institute of Research in Tuberculosis (ICMR), Chennai. RESULTS M. tuberculosis was isolated from 67 single EPTB specimens (11.8%) like pus/cold abscess (34), TB spine (10), pleural fluid (10), urine (5), tissue bit (2), lymph nodes (2), ascitic fluid (2), synovial fluid (1) and endometrial curetting (1). Among 67 isolates with 41 spoligopatterns, EAI lineage with 28 isolates (41.8%) predominated followed by 18 orphans (26.9%), 10 Beijing (14.9%) and 8 U (11.9%). BOVIS1_BCG (ST482), T1-T2 (ST78) and H3 (ST50) were represented by one strain each (1.5%). C onclusions: Spoligotyping plays a significant role in the epidemiology of tuberculosis. Three spoligotypes, T1-T2 (ST78), EAI6 (ST292) and U (ST1429) are reported for the first time in India.
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Affiliation(s)
| | - S Stephen
- Department of Microbiology, Mahatma Gandhi Medical College and Research Institute, Pondicherry, Tamil Nadu, India
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Chen YY, Chang JR, Huang WF, Hsu CH, Cheng HY, Sun JR, Kuo SC, Su IJ, Lin MS, Chen W, Dou HY. Genetic diversity of the Mycobacterium tuberculosis East African-Indian family in three tropical Asian countries. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2015; 50:886-892. [PMID: 26922173 DOI: 10.1016/j.jmii.2015.10.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/29/2015] [Accepted: 10/22/2015] [Indexed: 10/22/2022]
Abstract
BACKGROUND The Beijing lineage of Mycobacterium tuberculosis (MTB) is the most predominant MTB strain in Asian countries and is spreading worldwide, however, the East African-Indian (EAI) lineage is also particularly prevalent in many tropical Asian countries. The evolutionary relationships among MTB EAI isolates from Taiwan and those of tropical Asian countries remain unknown. METHODS The EAI strains collected from patients in Taiwan were analyzed using spacer oligonucleotide typing and mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR) typing, and compared with published profiles from Cambodia and Singapore to investigate potential epidemiological linkages. RESULTS Among the three countries, the EAI lineage was most prevalent in Cambodia (60%; Singapore, 25.62%; and Taiwan, 21.85%), having also the highest rates of multidrug resistance and lowest rates of clustering of MTB isolates. We describe a convenient method using seven selected MIRU-VNTR loci for first-line typing to discriminate Beijing and EAI lineages. A potential epidemiological linkage in these tropical Asian countries is also discussed based on a minimum-spanning tree constructed using 24 MIRU-VNTR loci of MTB EAI strains. CONCLUSION This study identified evolutionary relationships among MTB EAI isolates from Taiwan and those of two other tropical Asian countries, Cambodia and Singapore.
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Affiliation(s)
- Yih-Yuan Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan, ROC; Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan, ROC.
| | - Jia-Ru Chang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan, ROC
| | - Wei-Feng Huang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan, ROC
| | - Chih-Hao Hsu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan, ROC
| | - Han-Yin Cheng
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan, ROC
| | - Jun-Ren Sun
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital and National Defense Medical Center, Taipei, Taiwan, ROC
| | - Shu-Chen Kuo
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan, ROC
| | - Ih-Jen Su
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan, ROC
| | - Ming-Shian Lin
- Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan, ROC
| | - Wei Chen
- Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan, ROC
| | - Horng-Yunn Dou
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan, ROC.
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Sekati E, Molepo J, Nchabeleng M. Molecular characterisation and associated drug susceptibility patterns of Mycobacterium tuberculosis isolates from South African children. S Afr J Infect Dis 2015. [DOI: 10.1080/23120053.2015.1103955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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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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