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Ghazvini K, Khoshbakht R, Tadayon K, Mosavari N, BahramiTaghanaki HR, Mohammadi GR, Rashti Baf M, Nourian K, Samiei A, Ghavidel M. Genotyping of Mycobacterium tuberculosis complex isolated from humans and animals in northeastern Iran. Sci Rep 2023; 13:6746. [PMID: 37185604 PMCID: PMC10127167 DOI: 10.1038/s41598-023-33740-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
The objective of this study was to genotype Mycobacterium tuberculosis complex isolated from humans and cattle in northern Iran. Over the course of one year, a total of 120 human and 21 cattle isolates were tested using region of difference (RD)-based polymerase chain reaction (PCR) and mycobacterial interspersed repetitive unites-variable number tandem repeats (MIRU-VNTR). In M. tuberculosis, out of 120 isolates investigated, the most common genotype detected was NEW-1 (53.3%), followed by CAS/ Delhi (24.1%), Haarlem (5%), Beijing (4.16%), Uganda I (4.16%), S (3.3%), Ural (0.83%), TUR (0.83%), Uganda II (0.83%), Lam (0.83%) and Cameroon (0.83%). The HGDI rate was 0.9981 and the clustering rate was 10.83. Of the isolates, QUB26 had the highest allele diversity (h: 0.76), while the loci Mtub29 and MIRU24 had the lowest (h: 0). In M. Bovis, out of 123 collected tissue samples, 21 (17%) grew on culture media. The HGDI rate was 0.71 and clustering rate was 85.7%. The locus ETRC had the highest allele diversity (h: 0.45). The findings of this study suggest that there is high genetic diversity among M. tuberculosis isolates in Khorasan Razavi Province, which is consistent with similar results from other studies in other provinces in Iran and neighboring countries. This indicates that the prevalent genotypes in this study are spreading in the Middle East region. Furthermore, considering that M. Bovis isolates were identified in two clusters, it seems that all of them have a common origin and are circulating among the livestock farms in the province.
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Affiliation(s)
- Kiarash Ghazvini
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Reza Khoshbakht
- Department of Laboratory Sciences, School of Paramedical Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Keyvan Tadayon
- Department of Microbiology, Razi Vaccine and Serum Research Institute (RVSRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Nader Mosavari
- PPD Tuberculin Department, Razi Vaccine and Serum Research Institute, (RVSRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | | | - Gholam Reza Mohammadi
- Department of Clinical Sciences, School of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammad Rashti Baf
- Deputy of Veterinary Administration of Khorasan Razavi Province, Mashhad, Iran
| | - Kimiya Nourian
- Department of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Amin Samiei
- Tuberculosis and Leprosy Coordinator at Health Chancellor, Health Center of Khorasan State, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahdis Ghavidel
- Shahid Hasheminejad Hospital, Mashhad University of Medical Sciences, Mashhad, Iran.
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Maghradze N, Jugheli L, Borrell S, Tukvadze N, Kempker RR, Blumberg HM, Gagneux S. Developing customized stepwise MIRU-VNTR typing for tuberculosis surveillance in Georgia. PLoS One 2022; 17:e0264472. [PMID: 35231041 PMCID: PMC8887741 DOI: 10.1371/journal.pone.0264472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 02/10/2022] [Indexed: 11/19/2022] Open
Abstract
Introduction
Mycobacterial Interspersed Repetitive Units–Variable Tandem Repeats (MIRU-VNTR) typing has been widely used for molecular epidemiological studies of tuberculosis (TB). However, genotyping tools for Mycobacterium tuberculosis (Mtb) may be limiting in some settings due to high cost and workload. In this study developed a customized stepwise MIRU-VNTR typing that prioritizes high discriminatory loci and validated this method using penitentiary system cohort in the country of Georgia.
Methods
We used a previously generated MIRU-VNTR dataset from recurrent TB cases (32 cases) in Georgia and a new dataset of TB cases from the penitentiary system (102 cases) recruited from 2014 to 2015. A Hunter-Gaston Discriminatory Index (HGDI) was calculated utilizing a 24 standard loci panel, to select high discriminatory power loci, subsequently defined as the customized Georgia-specific set of loci for initial typing. The remaining loci were scored and hierarchically grouped for second and third step typing of the cohort. We then compared the processing time and costs of the customized stepwise method to the standard 24-loci method.
Results
For the customized Georgia-specific set that was used for initial typing, 10 loci were selected with a minimum value of 0.32 to the highest HGDI score locus. Customized 10 loci (step 1) typing of 102 Mtb patient isolates revealed 35.7% clustered cases. This proportion was reduced to 19.5% after hierarchical application of 2nd and 3rd step typing with the corresponding groups of loci. Our customized stepwise MIRU-VNTR genotyping approach reduced the quantity of samples to be typed and therefore overall processing time and costs by 42.6% each.
Conclusion
Our study shows that our customized stepwise MIRU-VNTR typing approach is a valid alternative of standard MIRI-VNTR typing panels for molecular epidemiological investigation in Georgia that saves time, workload and costs. Similar approaches could be developed for other settings.
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Affiliation(s)
- Nino Maghradze
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- National Center for Tuberculosis and Lung Diseases (NCTLD), Tbilisi, Georgia
| | - Levan Jugheli
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- National Center for Tuberculosis and Lung Diseases (NCTLD), Tbilisi, Georgia
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Nestani Tukvadze
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- National Center for Tuberculosis and Lung Diseases (NCTLD), Tbilisi, Georgia
| | - Russell R. Kempker
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, United States of America
| | - Henry M. Blumberg
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, United States of America
- Departments of Epidemiology and Global Health, Rollins School of Public Health of Emory University, Atlanta, GA, United States of America
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- * E-mail:
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Mudliar SKR, Kulsum U, Rufai SB, Umpo M, Nyori M, Singh S. Snapshot of Mycobacterium tuberculosis Phylogenetics from an Indian State of Arunachal Pradesh Bordering China. Genes (Basel) 2022. [DOI: https://doi.org/10.3390/genes13020263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Uncontrolled transmission of Mycobacterium tuberculosis (M. tuberculosis, MTB) drug resistant strains is a challenge to control efforts of the global tuberculosis program. Due to increasing multi-drug resistant (MDR) cases in Arunachal Pradesh, a northeastern state of India, the tracking and tracing of these resistant MTB strains is crucial for infection control and spread of drug resistance. This study aims to correlate the phenotypic DST, genomic DST (gDST) and phylogenetic analysis of MDR-MTB strains in the region. Of the total 200 samples 22 (11%) patients suspected of MDR-TB and 160 (80%) previously treated MDR-TB cases, 125 (62.5%) were identified as MTB. MGIT-960 SIRE DST detected 71/125 (56.8%) isolates as MDR/RR-MTB of which 22 (30.9%) were detected resistant to second-line drugs. Whole-genome sequencing of 65 isolates and their gDST found Ser315Thr mutation in katG (35/45; 77.8%) and Ser531Leu mutation in rpoB (21/41; 51.2%) associated with drug resistance. SNP barcoding categorized the dataset with Lineage2 (41; 63.1%) being predominant followed by Lineage3 (10; 15.4%), Lineage1 (8; 12.3%) and Lineage4 (6; 9.2%) respectively. Phylogenetic assignment by cgMLST gave insights of two Beijing sub-lineages viz; 2.2.1 (SNP difference < 19) and 2.2.1.2 (SNP difference < 9) associated with recent ongoing transmission in Arunachal Pradesh. This study provides insights in identifying two virulent Beijing sub-lineages (sub-lineage 2.2.1 and 2.2.1.2) with ongoing transmission of TB drug resistance in Arunachal Pradesh.
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Mudliar SKR, Kulsum U, Rufai SB, Umpo M, Nyori M, Singh S. Snapshot of Mycobacterium tuberculosis Phylogenetics from an Indian State of Arunachal Pradesh Bordering China. Genes (Basel) 2022. [DOI: https:/doi.org/10.3390/genes13020263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Uncontrolled transmission of Mycobacterium tuberculosis (M. tuberculosis, MTB) drug resistant strains is a challenge to control efforts of the global tuberculosis program. Due to increasing multi-drug resistant (MDR) cases in Arunachal Pradesh, a northeastern state of India, the tracking and tracing of these resistant MTB strains is crucial for infection control and spread of drug resistance. This study aims to correlate the phenotypic DST, genomic DST (gDST) and phylogenetic analysis of MDR-MTB strains in the region. Of the total 200 samples 22 (11%) patients suspected of MDR-TB and 160 (80%) previously treated MDR-TB cases, 125 (62.5%) were identified as MTB. MGIT-960 SIRE DST detected 71/125 (56.8%) isolates as MDR/RR-MTB of which 22 (30.9%) were detected resistant to second-line drugs. Whole-genome sequencing of 65 isolates and their gDST found Ser315Thr mutation in katG (35/45; 77.8%) and Ser531Leu mutation in rpoB (21/41; 51.2%) associated with drug resistance. SNP barcoding categorized the dataset with Lineage2 (41; 63.1%) being predominant followed by Lineage3 (10; 15.4%), Lineage1 (8; 12.3%) and Lineage4 (6; 9.2%) respectively. Phylogenetic assignment by cgMLST gave insights of two Beijing sub-lineages viz; 2.2.1 (SNP difference < 19) and 2.2.1.2 (SNP difference < 9) associated with recent ongoing transmission in Arunachal Pradesh. This study provides insights in identifying two virulent Beijing sub-lineages (sub-lineage 2.2.1 and 2.2.1.2) with ongoing transmission of TB drug resistance in Arunachal Pradesh.
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Mudliar SKR, Kulsum U, Rufai SB, Umpo M, Nyori M, Singh S. Snapshot of Mycobacterium tuberculosis Phylogenetics from an Indian State of Arunachal Pradesh Bordering China. Genes (Basel) 2022; 13:genes13020263. [PMID: 35205308 PMCID: PMC8872330 DOI: 10.3390/genes13020263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 02/07/2023] Open
Abstract
Uncontrolled transmission of Mycobacterium tuberculosis (M. tuberculosis, MTB) drug resistant strains is a challenge to control efforts of the global tuberculosis program. Due to increasing multi-drug resistant (MDR) cases in Arunachal Pradesh, a northeastern state of India, the tracking and tracing of these resistant MTB strains is crucial for infection control and spread of drug resistance. This study aims to correlate the phenotypic DST, genomic DST (gDST) and phylogenetic analysis of MDR-MTB strains in the region. Of the total 200 samples 22 (11%) patients suspected of MDR-TB and 160 (80%) previously treated MDR-TB cases, 125 (62.5%) were identified as MTB. MGIT-960 SIRE DST detected 71/125 (56.8%) isolates as MDR/RR-MTB of which 22 (30.9%) were detected resistant to second-line drugs. Whole-genome sequencing of 65 isolates and their gDST found Ser315Thr mutation in katG (35/45; 77.8%) and Ser531Leu mutation in rpoB (21/41; 51.2%) associated with drug resistance. SNP barcoding categorized the dataset with Lineage2 (41; 63.1%) being predominant followed by Lineage3 (10; 15.4%), Lineage1 (8; 12.3%) and Lineage4 (6; 9.2%) respectively. Phylogenetic assignment by cgMLST gave insights of two Beijing sub-lineages viz; 2.2.1 (SNP difference < 19) and 2.2.1.2 (SNP difference < 9) associated with recent ongoing transmission in Arunachal Pradesh. This study provides insights in identifying two virulent Beijing sub-lineages (sub-lineage 2.2.1 and 2.2.1.2) with ongoing transmission of TB drug resistance in Arunachal Pradesh.
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Affiliation(s)
- Shiv kumar Rashmi Mudliar
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, Madhya Pradesh, India; (S.k.R.M.); (U.K.)
| | - Umay Kulsum
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, Madhya Pradesh, India; (S.k.R.M.); (U.K.)
| | - Syed Beenish Rufai
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Center, Montreal, QC H4A 3J1, Canada;
- McGill International TB Center, Montreal, QC H4A 3J1, Canada
| | - Mika Umpo
- Tomo Riba Institute of Health & Medical Sciences, Naharlagun 791110, Arunachal Pradesh, India;
| | - Moi Nyori
- State TB Cell, Naharlagun 791110, Arunachal Pradesh, India;
| | - Sarman Singh
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, Madhya Pradesh, India; (S.k.R.M.); (U.K.)
- Correspondence: ; Tel.: +91-9810813435
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Singh J, Singh N, Suresh G, Srivastava R, Aggarwal U, Behera D, Munisamy M, Malhotra AG, Singh S. A comparative analysis of molecular genotypes of Mycobacterium tuberculosis isolates from HIV-positive and HIV-negative patients. Front Cell Infect Microbiol 2022; 12:953443. [PMID: 36310875 PMCID: PMC9597297 DOI: 10.3389/fcimb.2022.953443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/30/2022] [Indexed: 02/05/2023] Open
Abstract
SETTING Tuberculosis Research Laboratory, Division of Clinical Microbiology and Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences, and the National Institute of Tuberculosis and Respiratory Diseases (NITRD), both situated in New Delhi. OBJECTIVES We aimed to identify the distribution of various genotypes of M. tuberculosis among HIV-positive and HIV-negative patients suspected of having Tuberculosis, seen at the National Institute of Tuberculosis and Respiratory Diseases, New Delhi, which is a tertiary care dedicated TB hospital. PATIENTS AND METHODS Genotyping by Spoligotyping and 24 loci MIRU-VNTR was performed and analyzed using SITVITWEB and MIRU-VNTRplus. Drug susceptibility patterns were also analyzed. RESULTS A total of 503 subjects who were PTB/EPTB suspected were recruited and 287 were culture positive. Among them, 276 had growth of Mycobacterium tuberculosis (MTB) and in 11 patients non-tuberculous mycobacteria (NTM) were grown. The isolation rate of NTM was predominantly from HIV positive [10 of 130 (7.6%)] patients. Of the total isolates of MTB, 156 (56.5%) were from HIV negative patients and 120 (43.5%) were from HIV positive patients. All 276 M. tuberculosis isolates were genotyped and tested for drug susceptibility patterns. The CAS genotype was most predominant [153 (55.4%)], followed by Beijing lineage [44 (15.9%)], East African India [25 (9.1%)] and others [54 (19.6%)]. Beijing genotype was significantly more common in HIV positive patients (22.5%) than in HIV negative patients (10.9%). In MIRU-VNTR analysis, clustering was found to be more frequent in CAS strains irrespective of HIV status. In the HIV positive group, spoligotyping could differentiate various genotypes in 90% of isolates and MIRU-VNTR analysis in 84.2% of isolates. The clustering of various MTB strains was more associated with drug resistance. CONCLUSION The Beijing lineage was predominant in HIV-TB coinfected cases, even though the Central Asian Strain (CAS) was overall more predominant in the region.
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Affiliation(s)
- Jitendra Singh
- Division of Clinical Microbiology and Molecular Medicine, All India Institute of Medical Sciences, New Delhi, India
- Translational Medicine Centre, All India Institute of Medical Sciences, Bhopal, India
| | - Niti Singh
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases (NITRD), New Delhi, India
| | - Gayatri Suresh
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases (NITRD), New Delhi, India
| | - Rahul Srivastava
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases (NITRD), New Delhi, India
| | - Upasna Aggarwal
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases (NITRD), New Delhi, India
| | - Digamber Behera
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases (NITRD), New Delhi, India
- Department of Pulmonary Medicine, PGIMER, Chandigarh, India
| | - Murali Munisamy
- Translational Medicine Centre, All India Institute of Medical Sciences, Bhopal, India
| | | | - Sarman Singh
- Division of Clinical Microbiology and Molecular Medicine, All India Institute of Medical Sciences, New Delhi, India
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal, India
- Medical Science and Engineering Research Centre, Indian Institute of Science Education and Research, Bhopal, India
- *Correspondence: Sarman Singh, ;
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Taye H, Alemu K, Mihret A, Wood JLN, Shkedy Z, Berg S, Aseffa A. Global prevalence of Mycobacterium bovis infections among human tuberculosis cases: Systematic review and meta-analysis. Zoonoses Public Health 2021; 68:704-718. [PMID: 34169644 PMCID: PMC8487997 DOI: 10.1111/zph.12868] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 03/12/2021] [Accepted: 05/23/2021] [Indexed: 12/30/2022]
Abstract
Tuberculosis (TB) is a chronic communicable bacterial disease caused by Mycobacterium tuberculosis complex (MTBC) species. M. tuberculosis is the main causative agent of human TB, and cattle are the primary host of Mycobacterium bovis; due to close interaction between cattle and humans, M. bovis poses a zoonotic risk. This review summarizes and estimates the prevalence of M. bovis infection among human cases. Studies reporting TB prevalence data that were published in English during 10 years from 20 April 2009 to 17 April 2019 were identified through search of PubMed and other sources. Quality of studies and risk of bias were assessed using standard tools for prevalence study reports. Characteristics of included studies and their main findings were summarized in tables and discussed with narrative syntheses. Meta-analysis was performed on 19 included studies, with a total of 7,185 MTBC isolates identified; 702 (9.7%) of them were characterized as of subspecies M. bovis, but there was a large prevalence difference between the studies, ranging from 0.4% to 76.7%. The genotyping-based studies reported significantly lower prevalence of zoonotic TB than did the studies based on older techniques. The overall pooled prevalence of M. bovis aggregated from all included studies was 12.1% of the total MTBC isolates, while the corresponding pooled figure from the 14 genotyping-based studies was only 1.4%. Generally, human M. bovis cases reported from different countries of the world suggest that the impact of zoonotic TB is still important in all regions. However, it was difficult to understand the true picture of the disease prevalence because of methodological differences. Future investigations on zoonotic TB should carefully consider these differences when evaluating prevalence results.
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Affiliation(s)
- Hawult Taye
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
- Department of Epidemiology and Biostatistics, University of Gondar, Gondar, Ethiopia
| | - Kassahun Alemu
- Department of Epidemiology and Biostatistics, University of Gondar, Gondar, Ethiopia
| | - Adane Mihret
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - James L. N. Wood
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Ziv Shkedy
- Department of Epidemiology and Biostatistics, University of Gondar, Gondar, Ethiopia
- Biostatistics and bioinformatics, University of Hasselt, Hasselt, Belgium
| | - Stefan Berg
- Bacteriology Department, Animal and Plant Health Agency, Weybridge, UK
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
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Dusthackeer A, Kumar A, Mohanvel SK, Mahizhaveni B, Shivakumar S, Raghavi S, Azhagendran S, Vetrivel S, Rao VG, Yadav R, Paluru V, Purthy AJ, Hussain T, Kashyap V, Devi KR, Krishnan AKI, Anand P, Das P, Bansal AK, Das M, Kaur H, Raghunath D, Mondal R, Thomas BE. Mycobacterium tuberculosis strain lineage in mixed tribal population across India and Andaman Nicobar Island. World J Microbiol Biotechnol 2021; 37:192. [PMID: 34637049 DOI: 10.1007/s11274-021-03164-6] [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: 06/28/2021] [Accepted: 10/04/2021] [Indexed: 10/20/2022]
Abstract
In India, the tribal population constitutes almost 8.6% of the nation's total population. Despite their large presence, there are only a few reports available on Mycobacterium tuberculosis (M. tb) strain prevalence in Indian tribal communities considering the mobile nature of this population and also the influence of the mainstream populations they coexist within many areas for their livelihood. This study attempts to provide critical information pertaining to the TB strain diversity, its public health implications, and distribution among the tribal population in eleven Indian states and Andaman & Nicobar (A&N) Island. The study employed a population-based molecular approach. Clinical isolates were received from 66 villages (10 states and Island) and these villages were selected by implying situation analysis. A total of 78 M. tb clinical isolates were received from 10 different states and A&N Island. Among these, 16 different strains were observed by spoligotyping technique. The major M. tb strains spoligotype belong to the Beijing, CAS1_DELHI, and EAI5 family of M. tb strains followed by EAI1_SOM, EAI6_BGD1, LAM3, LAM6, LAM9, T1, T2, U strains. Drug-susceptibility testing (DST) results showed almost 15.4% of clinical isolates found to be resistant to isoniazid (INH) or rifampicin (RMP) + INH. Predominant multidrug-resistant (MDR-TB) isolates seem to be Beijing strain. Beijing, CAS1_DELHI, EAI3_IND, and EAI5 were the principal strains infecting mixed tribal populations across India. Despite the small sample size, this study has demonstrated higher diversity among the TB strains with significant MDR-TB findings. Prevalence of Beijing MDR-TB strains in Central, Southern, Eastern India and A&N Island indicates the transmission of the TB strains.
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Affiliation(s)
- Azger Dusthackeer
- Department of Bacteriology, Indian Council of Medical Research-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, 600031, India.
| | - Ashok Kumar
- Department of Bacteriology, Indian Council of Medical Research-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, 600031, India
| | | | - B Mahizhaveni
- Department of Bacteriology, Indian Council of Medical Research-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, 600031, India
| | - S Shivakumar
- Department of Bacteriology, Indian Council of Medical Research-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, 600031, India
| | - S Raghavi
- Department of Social and Behavioural Research, Indian Council of Medical Research-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, 600031, India
| | - S Azhagendran
- Department of Social and Behavioural Research, Indian Council of Medical Research-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, 600031, India
| | - S Vetrivel
- Department of Social and Behavioural Research, Indian Council of Medical Research-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, 600031, India
| | - Vikas Gangadhar Rao
- Division of Communicable Diseases, Indian Council of Medical Research-National Institute for Research in Tribal Health, Jabalpur, Madhya Pradesh, 482003, India
| | - Rajiv Yadav
- Division of Communicable Diseases, Indian Council of Medical Research-National Institute for Research in Tribal Health, Jabalpur, Madhya Pradesh, 482003, India
| | - Vijayachari Paluru
- Clinical Microbiology, Indian Council of Medical Research-Regional Medical Research Centre, Port Blair, Andaman and Nicobar Island, 744101, India
| | - Anil Jacob Purthy
- Department of Community Medicine, Pondicherry Institute of Medical Sciences, Puducherry, 605014, India
| | - Tahziba Hussain
- Department of Immunology, Indian Council of Medical Research-Regional Medical Research Centre, Bhubaneshwar, Odisha, 721023, India
| | - Vivek Kashyap
- Department of Preventive and Social Medicine, Rajendra Institute of Medical Sciences, Ranchi, Jharkhand, 834009, India
| | - K Rekha Devi
- ICMR - Regional Medical Research Centre, N. E. Region, Diburgah, Assam, 786 001, India
| | - Anil Kumar Indira Krishnan
- School of Public Health, SRM Medical College Research Centre, Kancheepuram (Dt), Kattankulathur, Tamil Nadu, 603203, India
| | - Praveen Anand
- Desert Medicine Research Centre (ICMR), New Pali Road, Jodhpur, Rajasthan, 342005, India
| | - Pradeep Das
- ICMR - Rajendra Memorial Research of Medical Science (RMRIMS), Agamkuan, Patna, Bihar, 800007, India
| | - Avi Kumar Bansal
- Department of Epidemiology/Public Health, ICMR-National JALMA Institute of Leprosy and Other Mycobacterial Diseases, Dr. M. Miyazaki Marg, Tajganj, Agra, 282001, India
| | - Madhuchhanda Das
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, 110016, India
| | - Harpreet Kaur
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, 110016, India
| | - D Raghunath
- Tribal TB ICMR Task Force, Indian Council of Medical Research, New Delhi, 110016, India
| | - Rajesh Mondal
- ICMR - Bhopal Memorial Hospital & Research Centre, Bhopal, India.
| | - Beena E Thomas
- Department of Social and Behavioural Research, Indian Council of Medical Research-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, 600031, India
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Singh AV, Singh S, Yadav A, Kushwah S, Yadav R, Sai DK, Chauhan DS. Genetic variability in multidrug-resistant Mycobacterium tuberculosis isolates from patients with pulmonary tuberculosis in North India. BMC Microbiol 2021; 21:123. [PMID: 33879047 PMCID: PMC8059304 DOI: 10.1186/s12866-021-02174-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 03/25/2021] [Indexed: 11/28/2022] Open
Abstract
Background Information on the genetic variability of drug resistant isolates of Mycobacterium tuberculosis is of paramount importance to understand transmission dynamics of disease and to improve TB control strategies. Despite of largest number of multidrug-resistant (MDR) tuberculosis cases (1, 30,000; 27% of the global burden), strains responsible for the expansion or development of drug-resistant Mycobacterium tuberculosis infections have been poorly characterized in India. Present study was aimed to investigate the genetic diversity in MDR isolates of Mycobacterium tuberculosis in North India. Results Spacer oligonucleotide typing (spoligotyping) was performed on 293 clinical MDR isolates of Mycobacterium tuberculosis recovered from cases of pulmonary tuberculosis from North India. Spoligotyping identified 74 distinct spoligotype patterns. Comparison with an international spoligotype database (spoldb4 database) showed that 240 (81.91%) and 32 (10.92%) strains displayed known and shared type patterns, while 21 (7.16%) strains displayed unique spoligotype patterns. Among the phylogeographic lineages, lineage 3 (East African-Indian) was found most predominant lineage (n = 159, 66.25%), followed by lineage 2 (East Asian; n = 34, 14.16%), lineage 1 (Indo-Oceanic; n = 30, 12.50%) and lineage 4 (Euro American; n = 17, 7.08%). Overall, CAS1_DEL (60.41%; SITs 2585, 26, 2694, 309, 381, 428, 1401, 141, 25, 1327) was found most pre-dominant spoligotype pattern followed by Beijing (14.16%; SITs255, 260, 1941, 269) and EAI3_IND (5.00%; SITs 298, 338, 11). The demographic and clinical characteristics were not found significantly associated with genotypic lineages of MDR-M.tuberculosis isolates recovered from pulmonary TB patients of North India. Conclusions Present study reveals high genetic diversity among the Mycobacterium tuberculosis isolates and highlights that SIT141/CAS1_Del followed by SIT26/ Beijing lineage is the most common spoligotype responsible for the development and transmission of MDR-TB in North India. The high presence of shared type and unique spoligotype patterns of MDR strains indicates epidemiological significance of locally evolved strains in ongoing transmission of MDR-TB within this community which needs to be further monitored using robust molecular tools with high discriminatory power.
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Affiliation(s)
- Ajay Vir Singh
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar Pradesh, 282004, India.
| | - Suman Singh
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar Pradesh, 282004, India
| | - Anjali Yadav
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar Pradesh, 282004, India
| | - Shweta Kushwah
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar Pradesh, 282004, India
| | - Rajbala Yadav
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar Pradesh, 282004, India
| | - Davuluri Kushma Sai
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar Pradesh, 282004, India
| | - Devendra Singh Chauhan
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar Pradesh, 282004, India
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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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11
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Gupta SR, Gupta E, Ohri A, Shrivastava SK, Kachhwaha S, Sharma V, Mishra RK, Niraj RRK. Comparative Proteome Analysis of Mycobacterium Tuberculosis Strains - H37Ra, H37Rv, CCDC5180, and CAS/NITR204: A Step Forward to Identify Novel Drug Targets. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180817999200531165148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background:
Mycobacterium tuberculosis is a causative agent of tuberculosis. It is a
non-motile, acid-fast, obligatory aerobic bacterium. Finding novel drug targets in Mycobacterium
tuberculosis has become extremely important as the bacterium is evolving into a more dangerous
multi-drug resistant pathogen. The predominant strains in India belong to the Central-Asian, East-
African Indian, and Beijing clad. For the same reason, the whole proteomes of a non-virulent strain
(H37Ra), a virulent (H37Rv) and two clinical strains, a Central-Asian clad (CAS/NITR204) and a
Beijing clad (CCDC5180) have been selected for comparative study. Selecting a phylogenetically
close and majorly studied non-virulent strain is helpful in removing the common and undesired proteins
from the study.
Objective:
The study compares the whole proteome of non-virulent strain with the other three virulent
strains to find a unique protein responsible for virulence in virulent strains. It is expected that
the drugs developed against identified targets will be specific to the virulent strains. Additionally, to
assure minimal toxicity to the host, we also screened the human proteome.
Methods:
Comparative proteome analysis was used for target identification and in silico validation
of identified target protein Rv2466c, identification of the respective ligand of the identified target
protein and binding interaction study using Molecular docking and Molecular Dynamic Simulation
study were used in this study.
Results and Discussion:
Finally, eleven proteins were found to be unique in virulent strain only and
out of which, Rv2466c (PDB-ID: 4ZIL) was found to be an essential protein and identified as a putative
drug target protein for further study. The compound glutathione was found to be a suitable
inhibitor for Rv2466c. In this study, we used a comparative proteomics approach to identify novel
target proteins.
Conclusion:
This study is unique as we are assured that the study will move forward the research in
a new direction to cure the deadly disease (tuberculosis) caused by Mycobacterium tuberculosis.
Rv2466c was identified as a novel drug target and glutathione as a respective ligand of Rv2466c.
Discovery of the novel drug target as well as the drug will provide a solution to drug resistance as
well as the infection caused by Mycobacterium tuberculosis.
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Affiliation(s)
| | - Ekta Gupta
- Dr B. Lal Institute of Biotechnology Jaipur, Jaipur, India
| | - Avnam Ohri
- Dr B. Lal Institute of Biotechnology Jaipur, Jaipur, India
| | | | | | - Vinay Sharma
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
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Spoligotype Diversity of Mycobacterium tuberculosis over Two Decades from Tiruvallur, South India. Int J Microbiol 2020; 2020:8841512. [PMID: 33110429 PMCID: PMC7582057 DOI: 10.1155/2020/8841512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/30/2020] [Indexed: 11/17/2022] Open
Abstract
Geographically, most tuberculosis (TB) cases in 2018 were reported from India. This TB burden is compounded by MDR-TB and XDR-TB. The strategies for the management and control of TB in the community depend on an understanding of the mode of spread of the different strains of TB isolates in the community. To determine the distribution and trends of M. tb strains over the time period in the community due to treatment, we carried out the present study on changes over two decades. Design/Methods. A total of 1218 M. tb isolates (year: 2001-2018) from Tiruvallur, India, were genotyped by spoligotyping after DNA extraction and subjected to anti-TB drug susceptibility testing for the first-line anti-TB drugs. Results. On analysis with the SpolDB4 database, majority (2001-2003: 53.32% and 2015-2018: 46.3%) of the isolates belonged to East African Indian (EAI) lineage, and the orphans designated in comparison to SpolDB4 stood 33% among 2001-2003 strain collection and 46.3% among 2015-2018 strain collection. 10.2% (2001-2003) and 9.26% (2015 to 2018) of isolates were monoresistant to isoniazid (H). MDR strains were less common among EAI strains (3.2%) compared to non-EAI strains (10.32%). Conclusions. EAI is the most predominant lineage in Tiruvallur, despite the presence of highly transmissible lineages like Beijing for the last two decades. The prevalence of MDR-TB is below the national average of 2-3% among the new TB cases in the last two decades. The reason can be attributed to the well-established nature of the locally circulating strains in this region which are not associated with drug resistance.
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Mahghani GA, Kargar M, Kafilzadeh F, Davoodi H, Ghaemi EA. Comparison of two molecular diagnostic methods for identifying Beijing genotype of Mycobacterium tuberculosis. IRANIAN JOURNAL OF MICROBIOLOGY 2020; 12:209-215. [PMID: 32685117 PMCID: PMC7340603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND AND OBJECTIVES The Beijing family of Mycobacterium tuberculosis has been identified as a severe pathogen among this species and found in many clinical isolates during the last decade. Early identification of such genotype is important for better prevention and treatment of tuberculosis. The present study performed to compare the efficiency of Real-Time PCR and IS6110-Based Inverse PCR methods to identify the Beijing family. MATERIALS AND METHODS This study was carried out on 173 clinical isolates of Mycobacterium tuberculosis complex in Golestan Province, northern Iran. DNA extraction performed by boiling and determining the Beijing and non-Beijing strains carried out using Real-Time PCR and IS6110-Based Inverse PCR. RESULTS In both Real-Time PCR and IS6110-Based Inverse PCR method, 24 specimens (13.9%) of the Beijing family were identified and the result of the IS6110-Based Inverse PCR method showed that all the Beijing strains in this region belonged to the Ancient Beijing sub-lineage. CONCLUSION Although the efficacy of the two methods in the diagnosis of the Beijing family is similar, the IS6110-Based Inverse PCR is more applicable to the ability to detect new and old Beijing family.
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Affiliation(s)
- Ghorban Ali Mahghani
- Department of Microbiology, Jahrom Branch, Islamic Azad University, Jahrom, Iran
| | - Mohammad Kargar
- Department of Microbiology, Jahrom Branch, Islamic Azad University, Jahrom, Iran
| | - Farshid Kafilzadeh
- Department of Microbiology, Jahrom Branch, Islamic Azad University, Jahrom, Iran
| | - Homa Davoodi
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ezzat Allah Ghaemi
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, Iran,Corresponding author: Ezzat Allah Ghaemi, PhD, Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, Iran. Tel: +98-9113711770, Fax: +98-1732235452,
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14
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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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15
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Ghavidel M, Tadayon K, Mosavari N, Nourian K, BahramiTaghanaki HR, Mohammadi GR, Rashtibaf M, Ghazvini K. Introducing the Best Six Loci in Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat (MIRU-VNTR) Typing for Mycobacterium Tuberculosis Genotyping. Rep Biochem Mol Biol 2019; 8:335-346. [PMID: 32274406 PMCID: PMC7103078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 06/30/2019] [Indexed: 06/11/2023]
Abstract
BACKGROUND Tuberculosis (TB) still remains endemic worldwide making epidemiological studies essential to mitigating efforts implicated in identifying its source, controlling, and preventing the spread of dangerous strains amongst humans such as Mycobacterium tuberculosis (Mtb). METHODS In this study, we sought to determine the 6 Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat (MIRU-VNTR) loci with high discriminatory powers for Mtb genotyping as well as the loci with the highest and the lowest discriminatory powers for MIRU-VNTR. To conduct our search, we used several databases such as science direct, Embase (Elsevier), Web of Science, Scopus and Medline via PubMed. Searches were performed using key words including: Mycobacterium tuberculosis, MIRU-VNTR, Allele diversity, Genetic diversity and human patient. Finally, 56 articles were selected after filtering out titles, abstracts and full texts. RESULTS Loci with high discriminatory powers included MIRU10 and MIRU26, while MIRU2, MIRU20, MIRU24 and ETRD had poor discriminatory powers. According to previous data in the literature, the loci MIRU10, MIRU26, MIRU40, QUB 26, QUB 11b and Mtub21 have high discriminatory powers. CONCLUSION Therefore, these loci recommended for genotyping Mtb to save time and cost and to ensure the production of reliable results.
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Affiliation(s)
- Mahdis Ghavidel
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Microbiology and Virology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Keyvan Tadayon
- Department of Microbiology, Razi Vaccine and Serum Research Institute (RVSRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
| | - Nader Mosavari
- PPD Tuberculin Department, Razi Vaccine and Serum Research Institute, (RVSRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
| | - Kimiya Nourian
- Doctor of Veterinary Medicine, Graduate Student of School of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran.
| | | | - Gholam Reza Mohammadi
- Department of Clinical Sciences, School of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad – Iran.
| | - Mohammad Rashtibaf
- Deputy of Veterinary administration of Khorasan Razavi Province, Mashhad,Iran.
| | - Kiarash Ghazvini
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Microbiology and Virology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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16
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Bakuła Z, Javed H, Pleń M, Jamil N, Tahir Z, Jagielski T. Genetic diversity of multidrug-resistant Mycobacterium tuberculosis isolates in Punjab, Pakistan. INFECTION GENETICS AND EVOLUTION 2019; 72:16-24. [DOI: 10.1016/j.meegid.2019.02.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 02/13/2019] [Accepted: 02/25/2019] [Indexed: 10/27/2022]
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Couvin D, Reynaud Y, Rastogi N. Two tales: Worldwide distribution of Central Asian (CAS) versus ancestral East-African Indian (EAI) lineages of Mycobacterium tuberculosis underlines a remarkable cleavage for phylogeographical, epidemiological and demographical characteristics. PLoS One 2019; 14:e0219706. [PMID: 31299060 PMCID: PMC6625721 DOI: 10.1371/journal.pone.0219706] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/29/2019] [Indexed: 11/18/2022] Open
Abstract
The East African Indian (EAI) and Central Asian (CAS) lineages of Mycobacterium tuberculosis complex (MTBC) mainly infect tuberculosis (TB) patients in the eastern hemisphere which contains many of the 22 high TB burden countries including China and India. We investigated if phylogeographical, epidemiological and demographical characteristics for these 2 lineages differed in SITVIT2 database. Genotyping results and associated data (age, sex, HIV serology, drug resistance) on EAI and CAS lineages (n = 10,974 strains) were extracted. Phylogenetic and Bayesian, and other statistical analyses were used to compare isolates. The male/female sex ratio was 907/433 (2.09) for the EAI group vs. 881/544 (1.62) for CAS (p-value<0.002). The proportion of younger patients aged 0-20 yrs. with CAS lineage was significantly higher than for EAI lineage (18.07% vs. 10.85%, p-value<0.0001). The proportion of multidrug resistant and extensively drug resistant TB among CAS group (30.63% and 1.03%, respectively) was significantly higher than in the EAI group (12.14% and 0.29%, respectively; p-value<0.0001). Lastly, the proportion of HIV+ patients was 20.34% among the EAI group vs. 3.46% in the CAS group (p-value<0.0001). This remarkable split observed between various parameters for these 2 lineages was further corroborated by their geographic distribution profile (EAI being predominantly found in Eastern-Coast of Africa, South-India and Southeast Asia, while CAS was predominantly found in Afghanistan, Pakistan, North India, Nepal, Middle-east, Libya, Sudan, Ethiopia, Kenya and Tanzania). Some geo-specificities were highlighted. This study demonstrated a remarkable cleavage for aforementioned characteristics of EAI and CAS lineages, showing a North-South divide along the tropic of cancer in Eastern hemisphere-mainly in Asia, and partly prolonged along the horn of Africa. Such studies would be helpful to better comprehend prevailing TB epidemic in context of its historical spread and evolutionary features, and provide clues to better treatment and patient-care in countries and regions concerned by these lineages.
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Affiliation(s)
- David Couvin
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
- * E-mail: (DC); (NR)
| | - Yann Reynaud
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
- * E-mail: (DC); (NR)
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Oliveira-de-Souza D, Vinhaes CL, Arriaga MB, Kumar NP, Cubillos-Angulo JM, Shi R, Wei W, Yuan X, Zhang G, Cai Y, Barry CE, Via LE, Sher A, Babu S, Mayer-Barber KD, Nakaya HI, Fukutani KF, Andrade BB. Molecular degree of perturbation of plasma inflammatory markers associated with tuberculosis reveals distinct disease profiles between Indian and Chinese populations. Sci Rep 2019; 9:8002. [PMID: 31142816 PMCID: PMC6541651 DOI: 10.1038/s41598-019-44513-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/17/2019] [Indexed: 12/14/2022] Open
Abstract
Tuberculosis (TB) is a chronic inflammatory disease caused by Mycobacterium tuberculosis infection which causes tremendous morbidity and mortality worldwide. Clinical presentation of TB patients is very diverse and disease heterogeneity is associated with changes in biomarker signatures. Here, we compared at the molecular level the extent of individual inflammatory perturbation of plasma protein and lipid mediators associated with TB in patients in China versus India. We performed a cross-sectional study analyzing the overall degree of inflammatory perturbation in treatment-naïve pulmonary TB patients and uninfected individuals from India (TB: n = 97, healthy: n = 20) and China (TB: n = 100, healthy: n = 11). We employed the molecular degree of perturbation (MDP) adapted to plasma biomarkers to examine the overall changes in inflammation between these countries. M. tuberculosis infection caused a significant degree of molecular perturbation in patients from both countries, with higher perturbation detected in India. Interestingly, there were differences in biomarker perturbation patterns and the overall degree of inflammation. Patients with severe TB exhibited increased MDP values and Indian patients with this condition exhibited even higher degree of perturbation compared to Chinese patients. Network analyses identified IFN-α, IFN-β, IL-1RI and TNF-α as combined biomarkers that account for the overall molecular perturbation in the entire study population. Our results delineate the magnitude of the systemic inflammatory perturbation in pulmonary TB and reveal qualitative changes in inflammatory profiles between two countries with high disease prevalence.
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Affiliation(s)
- Deivide Oliveira-de-Souza
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, 40296-710, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Fundação José Silveira, Salvador, 40210-320, Brazil
- Curso de Medicina, Faculdade de Tecnologia e Ciências (FTC), Salvador, 40290-150, Brazil
| | - Caian L Vinhaes
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, 40296-710, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Fundação José Silveira, Salvador, 40210-320, Brazil
- Curso de Medicina, Faculdade de Tecnologia e Ciências (FTC), Salvador, 40290-150, Brazil
| | - Maria B Arriaga
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, 40296-710, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Fundação José Silveira, Salvador, 40210-320, Brazil
| | - Nathella Pavan Kumar
- National Institutes of Health- National Institute for Research in Tuberculosis, International Center for Excellence in Research, Chennai, 600031, India
| | - Juan M Cubillos-Angulo
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, 40296-710, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Fundação José Silveira, Salvador, 40210-320, Brazil
| | - Ruiru Shi
- Henan Chest Hospital, Zhengzhou, 450000, China
| | - Wang Wei
- Henan Chest Hospital, Zhengzhou, 450000, China
| | - Xing Yuan
- Henan Chest Hospital, Zhengzhou, 450000, China
| | - Guolong Zhang
- Sino-US International Research Center for Tuberculosis, and Henan Public Health Center, Zhengzhou, 450000, China
| | - Ying Cai
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, 20892, USA
| | - Clifton E Barry
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, 20892, USA
| | - Laura E Via
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, 20892, USA
| | - Alan Sher
- Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, 20892, USA
| | - Subash Babu
- National Institutes of Health- National Institute for Research in Tuberculosis, International Center for Excellence in Research, Chennai, 600031, India
| | - Katrin D Mayer-Barber
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, 20892, USA
| | - Helder I Nakaya
- Department of Pathophysiology and Toxicology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, 05508, Brazil
| | - Kiyoshi F Fukutani
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, 40296-710, Brazil
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Fundação José Silveira, Salvador, 40210-320, Brazil
- Curso de Medicina, Faculdade de Tecnologia e Ciências (FTC), Salvador, 40290-150, Brazil
| | - Bruno B Andrade
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, 40296-710, Brazil.
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Fundação José Silveira, Salvador, 40210-320, Brazil.
- Curso de Medicina, Faculdade de Tecnologia e Ciências (FTC), Salvador, 40290-150, Brazil.
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.
- Universidade Salvador (UNIFACS), Laureate Universities, Salvador, 41720-200, Brazil.
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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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20
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Spoligotyping, phenotypic and genotypic characterization of katG, rpoB gene of M. tuberculosis isolates from Sahariya tribe of Madhya Pradesh India. J Infect Public Health 2019; 12:395-402. [PMID: 30611735 DOI: 10.1016/j.jiph.2018.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/14/2018] [Accepted: 12/17/2018] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Sahariya, a primitive tribal group, residing in Gwalior and Sheopur districts of Madhya Pradesh, India, show high incidence and prevalence of pulmonary tuberculosis (PTB). The study was designed to understand the genetic diversity and phenotype - genotype association of drug resistant M. tuberculosis strains, infecting Sahariya tribe. MATERIALS AND METHODS A total of 103 pulmonary tuberculosis patients from Sahariya tribe were recruited from Gwalior and Sheopur districts. Sputum samples were collected and cultured on LJ slants and drug sensitivity tests were carried out. Genomic DNA was extracted, followed by spoligotyping and genotyping of drug target genes, katG and rpoB, using MAS-PCR, PCR-RFLP and DNA sequencing. RESULT Seventeen different spoligotypes were identified, in which, EAI3_IND/ST11 M. tuberculosis strain appeared predominant, followed by CAS1_Delhi/ST26. Results of our phenotypic drug susceptibility test identified high incidence (12.6%) of isoniazid-resistant tuberculosis, while 4.85% isolates were multi drug resistant (MDR). Further genotyping of drug target genes identified 8.7% of isoniazid-R isolates to have a mutation at katG codon 463, while 3.8% isolates showed mutations at two sites, katG codons 315 and 463. In case of MDR-TB isolates, all from CAS lineage, 3.85% had mutations on katG and rpoB genes, at codon 463 and codon 526, respectively, while 0.97% isolates were harbouring mutations at codons 315, 463 and 531. CONCLUSION Our findings have revealed that EAI3_IND strain is the predominant strain infecting Sahariya. The incidence of isoniazid-R M. tuberculosis strain infection is high, with an increased propensity to evolve into MDR-TB. Therefore, the TB centres should also consider isoniazid-R status of the isolates along with CBNAAT before deciding the drug regimen for the patients.
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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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Maharjan B, Nakajima C, Isoda N, Thapa J, Poudel A, Shah Y, Yamaguchi T, Shrestha B, Hoffmann H, Avsar K, Shrestha A, Gordon SV, Suzuki Y. Genetic diversity and distribution dynamics of multidrug-resistant Mycobacterium tuberculosis isolates in Nepal. Sci Rep 2018; 8:16634. [PMID: 30413747 PMCID: PMC6226479 DOI: 10.1038/s41598-018-34306-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 10/11/2018] [Indexed: 01/06/2023] Open
Abstract
Multidrug-resistant tuberculosis (MDR-TB) is an emerging public health problem in Nepal. Despite the implementation of a successful TB control program in Nepal, notifications of MDR-TB are increasing, yet the reasons are unknown. The objective of this study was to understand the genetic diversity and epidemiological characteristics of MDR-Mycobacterium tuberculosis (MTB) isolates in Nepal. We isolated and genotyped 498 MDR-MTB isolates collected from April 2009 to March 2013 and analyzed the patients' background information. Our results showed that the lineage 2 (Beijing family) was the most predominant lineage (n = 241; 48.4%), followed by lineage 3 (n = 153, 30.7%). Lineage 4 was the third most prevalent (n = 73, 14.5%) followed by lineage 1 (n = 32, 6.4%). The lineages were significantly associated with geographic region, ethnic group, age and sex of patients. The Beijing genotype was found to have an important role in transmitting MDR-TB in Nepal and was significantly associated with the eastern region, mongoloid ethnic group and younger age group. We conclude that early diagnosis and treatment including molecular-epidemiological surveillance of MDR-TB cases will help to control transmission of MDR-TB in Nepal.
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Affiliation(s)
- Bhagwan Maharjan
- German Nepal TB Project (GENETUP/NATA), Kathmandu, Nepal.,Division of Bioresources, Hokkaido University, Research Center for Zoonosis Control, Hokkaido, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University, Research Center for Zoonosis Control, Hokkaido, Japan.,Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Hokkaido, Japan
| | - Norikazu Isoda
- Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Hokkaido, Japan.,Unit of Risk Analysis and Management, Research Center for Zoonosis Control, Hokkaido, Japan
| | - Jeewan Thapa
- Division of Bioresources, Hokkaido University, Research Center for Zoonosis Control, Hokkaido, Japan
| | - Ajay Poudel
- Department of Microbiology, Chitwan Medical College Teaching Hospital, Chitwan, Nepal
| | - Yogendra Shah
- Division of Bioresources, Hokkaido University, Research Center for Zoonosis Control, Hokkaido, Japan
| | - Tomoyuki Yamaguchi
- Division of Bioresources, Hokkaido University, Research Center for Zoonosis Control, Hokkaido, Japan
| | | | - Harald Hoffmann
- WHO-Supranational Reference Laboratory of Tuberculosis, Munich, Gauting, Germany.,KuratoriumTuberkulose in der Welt e.V, München-Gauting, Germany
| | - Korkut Avsar
- KuratoriumTuberkulose in der Welt e.V, München-Gauting, Germany.,Asklepios Klinik, Gauting, Germany
| | - Ashish Shrestha
- National Tuberculosis Center, Thimi, Bhaktapur, Nepal.,World Health Organization, Kathmandu, Nepal
| | - Stephen V Gordon
- Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Hokkaido, Japan.,UCD School of Veterinary Medicine, University College Dublin, Dublin, D04 W6F6, Ireland
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University, Research Center for Zoonosis Control, Hokkaido, Japan. .,Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Hokkaido, Japan.
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Genetic diversity of Mycobacterium tuberculosis complex isolates circulating in an area with high tuberculosis incidence: Using 24-locus MIRU-VNTR method. Tuberculosis (Edinb) 2018; 112:89-97. [PMID: 30205974 DOI: 10.1016/j.tube.2018.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 07/15/2018] [Accepted: 08/02/2018] [Indexed: 01/24/2023]
Abstract
We aimed to determine the genetic diversity, phylogenetic relationship and transmission dynamics of Mycobacterium tuberculosis complex (MTBC) genotypes in an area with high tuberculosis (TB) incidence. A set of 164 MTBC isolates from new TB patients of Golestan province, Iran, were subjected to genotyping using the standard 24-locus MIRU-VNTR method. Recent TB transmission was evaluated and phylogenetic relationships were analysed by minimum spanning tree and cluster-graph methods. Among the 164 isolates, 132 distinct patterns were detected. The 48 clustered isolates (29.3%) were distributed into 16 clusters ranging in size from 2 to 12 isolates. The most frequent genotype was Central Asian Strain/Delhi (CAS/Delhi) (n = 67, 40.8%), followed by NEW-1 (n = 53, 32.3%) and Beijing (n = 19, 11.6%) genotypes. Thirty five (72.9%) of NEW-1 isolates were recovered from immigrant patients and 84.2% (n = 16) of Beijing genotypes recovered from native cases. Statistically significant association was found between clustering and smoking (p = 0.047), drug addiction (p = 0.01) and prison history (p = 0.003). The estimated proportion of recent transmission was 19.5%. Presence of highly diverse MTBC isolates circulating in this province without a dominant genotype might be a consequence of importation of various genotypes in this area.
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Molecular characterization and drug susceptibility profile of Mycobacterium tuberculosis isolates from Northeast Bangladesh. INFECTION GENETICS AND EVOLUTION 2018; 65:136-143. [PMID: 30048809 DOI: 10.1016/j.meegid.2018.07.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/24/2018] [Accepted: 07/22/2018] [Indexed: 12/14/2022]
Abstract
Tuberculosis (TB) remains a major public health problem worldwide including in Bangladesh. Molecular epidemiological tools provide genotyping profiles of Mycobacterium tuberculosis (M. tuberculosis) strains that can give insight into the transmission of TB in a specific region. The objective of the study was to identify the genetic diversity and drug susceptibility profile of M. tuberculosis strains circulating in the northeast Bangladesh. A total of 244 smear-positive sputum specimens were collected from two referral hospitals in Mymensingh and Netrakona districts. The isolated strains were genotyped by deletion analysis, spoligotyping, and MIRU-VNTR typing. We also analyzed the distributions of drug susceptibility pattern and demographic data among different genotypes. All isolates were identified as M. tuberculosis and among them 167 strains (68.44%) were 'ancestral' and the remaining 77 (31.56%) were 'modern' type. Spoligotyping analysis yielded 119 distinct patterns, among them, 86 isolates had unique patterns and the remaining 158 were grouped into 33 distinct clusters containing 2 to 18 isolates. The predominant spoligotypes belong to the EAI lineage strains, comprising 66 (27.04%) isolates followed by Beijing (7.38%), T1 (6.15%), CAS1-Delhi (5.33), LAM9 (3.28%), MANU-2 and X2. MIRU-VNTR analysis revealed 167 isolates (68%) had unique patterns, whereas 77 (32%) were grouped into 26 clusters and the rate of recent transmission was 20.9%, suggesting that the majority of TB cases in this region are caused by the reactivation of previous TB infections rather than recent transmission. About 136 (55.7%) isolates were sensitive to four anti-TB drugs, 69 (28.3%) were resistant to one or more (except rifampicin and isoniazid combination) drugs and 39 (15.9%) were MDR. In conclusion, our study provides a first insight into molecular characterization and drug resistance profile of M. tuberculosis strains in northeast Bangladesh which will ultimately contribute to the national TB control program.
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Chae H, Shin SJ. Importance of differential identification of Mycobacterium tuberculosis strains for understanding differences in their prevalence, treatment efficacy, and vaccine development. J Microbiol 2018; 56:300-311. [PMID: 29721826 DOI: 10.1007/s12275-018-8041-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 02/14/2018] [Accepted: 02/14/2018] [Indexed: 01/28/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a serious global health problem in the 21st century because of its high mortality. Mtb is an extremely successful human-adapted pathogen that displays a multifactorial ability to control the host immune response and to evade killing by drugs, resulting in the breakdown of BCG vaccine-conferred anti-TB immunity and development of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mtb. Although genetic components of the genomes of the Mtb complex strains are highly conserved, showing over 99% similarity to other bacterial genera, recently accumulated evidence suggests that the genetic diversity of the Mtb complex strains has implications for treatment outcomes, development of MDR/XDR Mtb, BCG vaccine efficacy, transmissibility, and epidemiological outbreaks. Thus, new insights into the pathophysiological features of the Mtb complex strains are required for development of novel vaccines and for control of MDR/XDR Mtb infection, eventually leading to refinement of treatment regimens and the health care system. Many studies have focused on the differential identification of Mtb complex strains belonging to different lineages because of differences in their virulence and geographical dominance. In this review, we discuss the impact of differing genetic characteristics among Mtb complex strains on vaccine efficacy, treatment outcome, development of MDR/XDR Mtb strains, and epidemiological outbreaks by focusing on the best-adapted human Mtb lineages. We further explore the rationale for differential identification of Mtb strains for more effective control of TB in clinical and laboratory settings by scrutinizing current diagnostic methods.
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Affiliation(s)
- Hansong Chae
- Department of Microbiology, Institute for Immunology and Immunological Diseases, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Diseases, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
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Blanco-Guillot F, Delgado-Sánchez G, Mongua-Rodríguez N, Cruz-Hervert P, Ferreyra-Reyes L, Ferreira-Guerrero E, Yanes-Lane M, Montero-Campos R, Bobadilla-del-Valle M, Torres-González P, Ponce-de-León A, Sifuentes-Osornio J, Garcia-Garcia L. Molecular clustering of patients with diabetes and pulmonary tuberculosis: A systematic review and meta-analysis. PLoS One 2017; 12:e0184675. [PMID: 28902922 PMCID: PMC5597214 DOI: 10.1371/journal.pone.0184675] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/24/2017] [Indexed: 11/18/2022] Open
Abstract
Introduction Many studies have explored the relationship between diabetes mellitus (DM) and tuberculosis (TB) demonstrating increased risk of TB among patients with DM and poor prognosis of patients suffering from the association of DM/TB. Owing to a paucity of studies addressing this question, it remains unclear whether patients with DM and TB are more likely than TB patients without DM to be grouped into molecular clusters defined according to the genotype of the infecting Mycobacterium tuberculosis bacillus. That is, whether there is convincing molecular epidemiological evidence for TB transmission among DM patients. Objective: We performed a systematic review and meta-analysis to quantitatively evaluate the propensity for patients with DM and pulmonary TB (PTB) to cluster according to the genotype of the infecting M. tuberculosis bacillus. Materials and methods We conducted a systematic search in MEDLINE and LILACS from 1990 to June, 2016 with the following combinations of key words “tuberculosis AND transmission” OR “tuberculosis diabetes mellitus” OR “Mycobacterium tuberculosis molecular epidemiology” OR “RFLP-IS6110” OR “Spoligotyping” OR “MIRU-VNTR”. Studies were included if they met the following criteria: (i) studies based on populations from defined geographical areas; (ii) use of genotyping by IS6110- restriction fragment length polymorphism (RFLP) analysis and spoligotyping or mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR) or other amplification methods to identify molecular clustering; (iii) genotyping and analysis of 50 or more cases of PTB; (iv) study duration of 11 months or more; (v) identification of quantitative risk factors for molecular clustering including DM; (vi) > 60% coverage of the study population; and (vii) patients with PTB confirmed bacteriologically. The exclusion criteria were: (i) Extrapulmonary TB; (ii) TB caused by nontuberculous mycobacteria; (iii) patients with PTB and HIV; (iv) pediatric PTB patients; (v) TB in closed environments (e.g. prisons, elderly homes, etc.); (vi) diabetes insipidus and (vii) outbreak reports. Hartung-Knapp-Sidik-Jonkman method was used to estimate the odds ratio (OR) of the association between DM with molecular clustering of cases with TB. In order to evaluate the degree of heterogeneity a statistical Q test was done. The publication bias was examined with Begg and Egger tests. Review Manager 5.3.5 CMA v.3 and Biostat and Software package R were used. Results Selection criteria were met by six articles which included 4076 patients with PTB of which 13% had DM. Twenty seven percent of the cases were clustered. The majority of cases (48%) were reported in a study in China with 31% clustering. The highest incidence of TB occurred in two studies from China. The global OR for molecular clustering was 0.84 (IC 95% 0.40–1.72). The heterogeneity between studies was moderate (I2 = 55%, p = 0.05), although there was no publication bias (Beggs test p = 0.353 and Eggers p = 0.429). Conclusion There were very few studies meeting our selection criteria. The wide confidence interval indicates that there is not enough evidence to draw conclusions about the association. Clustering of patients with DM in TB transmission chains should be investigated in areas where both diseases are prevalent and focus on specific contexts.
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Affiliation(s)
- Francles Blanco-Guillot
- Doctorado en Ciencias en Enfermedades Infecciosas, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Guadalupe Delgado-Sánchez
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Norma Mongua-Rodríguez
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
- Maestría en Ciencias Médicas con énfasis en Epidemiología, Facultad de Medicina, Universidad Nacional Autónoma de México, Distrito Federal, México
| | - Pablo Cruz-Hervert
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Leticia Ferreyra-Reyes
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Elizabeth Ferreira-Guerrero
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Mercedes Yanes-Lane
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
- Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, San Luis Potosí, México
| | - Rogelio Montero-Campos
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Miriam Bobadilla-del-Valle
- Laboratorio de Microbiología, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, México, Distrito Federal, México
| | - Pedro Torres-González
- Laboratorio de Microbiología, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, México, Distrito Federal, México
| | - Alfredo Ponce-de-León
- Laboratorio de Microbiología, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, México, Distrito Federal, México
| | - José Sifuentes-Osornio
- Dirección Médica, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, México, Distrito Federal, México
| | - Lourdes Garcia-Garcia
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
- * E-mail:
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Comparative study of genotypes of Mycobacterium tuberculosis from a Northern Indian setting with strains reported from other parts of India and neighboring countries. Tuberculosis (Edinb) 2017; 105:60-72. [DOI: 10.1016/j.tube.2017.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 04/03/2017] [Accepted: 04/08/2017] [Indexed: 01/11/2023]
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Development of a One-Step Multiplex PCR Assay for Differential Detection of Major Mycobacterium Species. J Clin Microbiol 2017; 55:2736-2751. [PMID: 28659320 DOI: 10.1128/jcm.00549-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/20/2017] [Indexed: 12/17/2022] Open
Abstract
The prevalence of tuberculosis continues to be high, and nontuberculous mycobacterial (NTM) infection has also emerged worldwide. Moreover, differential and accurate identification of mycobacteria to the species or subspecies level is an unmet clinical need. Here, we developed a one-step multiplex PCR assay using whole-genome analysis and bioinformatics to identify novel molecular targets. The aims of this assay were to (i) discriminate between the Mycobacterium tuberculosis complex (MTBC) and NTM using rv0577 or RD750, (ii) differentiate M. tuberculosis (M. tuberculosis) from MTBC using RD9, (iii) selectively identify the widespread M. tuberculosis Beijing genotype by targeting mtbk_20680, and (iv) simultaneously detect five clinically important NTM (M. avium, M. intracellulare, M. abscessus, M. massiliense, and M. kansasii) by targeting IS1311, DT1, mass_3210, and mkan_rs12360 An initial evaluation of the multiplex PCR assay using reference strains demonstrated 100% specificity for the targeted Mycobacterium species. Analytical sensitivity ranged from 1 to 10 pg for extracted DNA and was 103 and 104 CFU for pure cultures and nonhomogenized artificial sputum cultures, respectively, of the targeted species. The accuracy of the multiplex PCR assay was further evaluated using 55 reference strains and 94 mycobacterial clinical isolates. Spoligotyping, multilocus sequence analysis, and a commercial real-time PCR assay were employed as standard assays to evaluate the multiplex PCR assay with clinical M. tuberculosis and NTM isolates. The PCR assay displayed 100% identification agreement with the standard assays. Our multiplex PCR assay is a simple, convenient, and reliable technique for differential identification of MTBC, M. tuberculosis, M. tuberculosis Beijing genotype, and major NTM species.
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Teeter LD, Kammerer JS, Ghosh S, Nguyen DTM, Vempaty P, Tapia J, Miramontes R, Cronin WA, Graviss EA. Evaluation of 24-locus MIRU-VNTR genotyping in Mycobacterium tuberculosis cluster investigations in four jurisdictions in the United States, 2006-2010. Tuberculosis (Edinb) 2017; 106:9-15. [PMID: 28802410 DOI: 10.1016/j.tube.2017.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 05/09/2017] [Accepted: 05/24/2017] [Indexed: 12/15/2022]
Abstract
The U.S. Centers for Disease Control and Prevention (CDC) uses a combination of spacer oligonucleotide typing (spoligotyping) and mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) analyses as part of the National TB Genotyping Service (NTGS). The NTGS expansion from 12-locus MIRU-VNTR (MIRU12) to 24-locus MIRU-VNTR (MIRU24) in 2009 enhanced the ability to discriminate Mycobacterium tuberculosis strains. In the current study, we investigated the MIRU24 concordance among epidemiologic-linked tuberculosis (TB) patients in four U.S. health jurisdictions. We also evaluated the programmatic benefits of combining MIRU24 and spoligotyping with epidemiologic evidence in identifying potential recent TB transmission. We examined 342 TB patients in 42 spoligotype/MIRU12 (PCRType) clusters (equivalent to 46 spoligotype/MIRU24 [GENType] clusters) to identify epidemiologic links among cases. GENType clusters, when compared to PCRType clusters, had 12 times higher odds of epidemiologic links being identified if patients were younger than 25 years and 3 times higher odds if patients resided in the same zip code, or had HIV infection. Sixty (18%) fewer PCRType-clustered patients would need investigations if clusters are defined using GENType instead of PCRType. An important advantage of defining clusters by MIRU24 is resource savings related to the reduced number of clustered cases needing investigation.
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Affiliation(s)
- Larry D Teeter
- Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX 77030, USA.
| | - J Steven Kammerer
- Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA 30333, USA.
| | - Smita Ghosh
- Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA 30333, USA.
| | - Duc T M Nguyen
- Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX 77030, USA.
| | - Padmaja Vempaty
- Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA 30333, USA.
| | - Jane Tapia
- Emory University School of Medicine, 1648 Pierce Dr NE, Atlanta, GA 30307, USA.
| | - Roque Miramontes
- Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA 30333, USA.
| | - Wendy A Cronin
- Maryland Department of Health and Mental Hygiene, 201 W Preston St, Baltimore, MD 21201, USA.
| | - Edward A Graviss
- Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX 77030, USA.
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