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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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Ramachandran G, Chandrasekaran P, Gaikwad S, Agibothu Kupparam HK, Thiruvengadam K, Gupte N, Paradkar M, Dhanasekaran K, Sivaramakrishnan GN, Kagal A, Thomas B, Pradhan N, Kadam D, Hanna LE, Balasubramanian U, Kulkarni V, Murali L, Golub J, Gupte A, Shivakumar SVBY, Swaminathan S, Dooley KE, Gupta A, Mave V. Subtherapeutic Rifampicin Concentration Is Associated With Unfavorable Tuberculosis Treatment Outcomes. Clin Infect Dis 2021; 70:1463-1470. [PMID: 31075166 DOI: 10.1093/cid/ciz380] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/09/2019] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The relationships between first-line drug concentrations and clinically important outcomes among patients with tuberculosis (TB) remain poorly understood. METHODS We enrolled a prospective cohort of patients with new pulmonary TB receiving thrice-weekly treatment in India. The maximum plasma concentration of each drug was determined at months 1 and 5 using blood samples drawn 2 hours postdose. Subtherapeutic cutoffs were: rifampicin <8 µg/mL, isoniazid <3 µg/mL, and pyrazinamide <20 µg/mL. Factors associated with lower log-transformed drug concentrations, unfavorable outcomes (composite of treatment failure, all-cause mortality, and recurrence), and individual outcomes were examined using Poisson regression models. RESULTS Among 404 participants, rifampicin, isoniazid, and pyrazinamide concentrations were subtherapeutic in 85%, 29%, and 13%, respectively, at month 1 (with similar results for rifampicin and isoniazid at month 5). Rifampicin concentrations were lower with human immunodeficiency virus coinfection (median, 1.6 vs 4.6 µg/mL; P = .015). Unfavorable outcome was observed in 19%; a 1-μg/mL decrease in rifampicin concentration was independently associated with unfavorable outcome (adjusted incidence rate ratio [aIRR], 1.21 [95% confidence interval {CI}, 1.01-1.47]) and treatment failure (aIRR, 1.16 [95% CI, 1.05-1.28]). A 1-μg/mL decrease in pyrazinamide concentration was associated with recurrence (aIRR, 1.05 [95% CI, 1.01-1.11]). CONCLUSIONS Rifampicin concentrations were subtherapeutic in most Indian patients taking a thrice-weekly TB regimen, and low rifampicin and pyrazinamide concentrations were associated with poor outcomes. Higher or more frequent dosing is needed to improve TB treatment outcomes in India.
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Affiliation(s)
| | | | - Sanjay Gaikwad
- Byramjee Jeejeebhoy Government Medical College, Pune, India
| | | | | | - Nikhil Gupte
- Johns Hopkins School of Medicine, Baltimore, Maryland.,Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune
| | - Mandar Paradkar
- Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune
| | | | | | - Anju Kagal
- Byramjee Jeejeebhoy Government Medical College, Pune, India
| | - Beena Thomas
- National Institute for Research in Tuberculosis, Chennai
| | - Neeta Pradhan
- Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune
| | - Dileep Kadam
- Byramjee Jeejeebhoy Government Medical College, Pune, India
| | | | - Usha Balasubramanian
- Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune
| | - Vandana Kulkarni
- Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune
| | | | - Jonathan Golub
- Johns Hopkins School of Medicine, Baltimore, Maryland.,Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Akshay Gupte
- Johns Hopkins School of Medicine, Baltimore, Maryland
| | | | | | | | - Amita Gupta
- Johns Hopkins School of Medicine, Baltimore, Maryland.,Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune.,Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Vidya Mave
- Johns Hopkins School of Medicine, Baltimore, Maryland.,Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune
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Mansoori N, Vaziri F, Amini S, Khanipour S, Pourazar Dizaji S, Douraghi M. Spoligotype and Drug Susceptibility Profiles of Mycobacterium tuberculosis Complex Isolates in Golestan Province, North Iran. Infect Drug Resist 2020; 13:2073-2081. [PMID: 32669860 PMCID: PMC7335844 DOI: 10.2147/idr.s255889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 06/18/2020] [Indexed: 11/23/2022] Open
Abstract
Introduction Despite the moderate incidence of tuberculosis (TB) in many parts of Iran, Golestan province had a permanently higher TB incidence rate than the national average. Moreover, Golestan province receives immigrants, mainly from TB-endemic areas of Iran and neighbor countries. Here, we aimed to characterize the circulating Mycobacterium tuberculosis complex (MTBC) isolates in terms of the spoligotype and drug resistance patterns, across Golestan province. Materials and Methods A set of 166 MTBC isolates was collected during July 2014 to July 2015 and subjected to drug susceptibility testing for first- and second-line anti-TB drugs and spoligotyping. Results Of 166 MTBC isolates, 139 (83.7%) isolates were assigned to 28 spoligotype international types (SITs). The most frequent SITs were SIT127/Ural-2 (n=25, 15.1%), followed by SIT1/Beijing (n=21, 12.7%) and SIT3427/Ural-2 (n=18, 10.8%). The set of 18 isolates (10.8%) showed resistance to at least one drug, which mainly belonged to SIT1/Beijing (n=7, 38.9%), orphan patterns (n=4, 22.2%) and SIT357/CAS1-Delhi (n=3, 16.7%). In addition, four isolates (2.4%) were resistant to pyrazinamide. The analysis of mutation corresponded to resistance to rifampin and isoniazid showed that two isolates had Ser531Leu substitution in rpoB, four isolates had Ser315Thr substitution in katG and one isolate had [C(−15)T] in inhA locus. Conclusion High diversity in spoligotypes of the MTBC isolates and lack of dominant genotype might be due to residence of immigrants in this region and consequent reactivation of latent infection. In addition, due to the presence of extensively drug-resistant (XDR) isolates in Golestan province, it is important to conduct future studies to determine transmission pattern of drug-resistant isolates in this region.
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Affiliation(s)
- Noormohamad Mansoori
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Sirus Amini
- Regional Tuberculosis Reference Laboratory, Tehran University of Medical Sciences, Tehran, Iran
| | - Sharareh Khanipour
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Shahin Pourazar Dizaji
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Masoumeh Douraghi
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Food Microbiology Research Center, Tehran University of Medical Sciences, Tehran, Iran
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The arms race between man and Mycobacterium tuberculosis: Time to regroup. INFECTION GENETICS AND EVOLUTION 2018; 66:361-375. [DOI: 10.1016/j.meegid.2017.08.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 12/12/2022]
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Sinkov V, Ogarkov O, Mokrousov I, Bukin Y, Zhdanova S, Heysell SK. New epidemic cluster of pre-extensively drug resistant isolates of Mycobacterium tuberculosis Ural family emerging in Eastern Europe. BMC Genomics 2018; 19:762. [PMID: 30348088 PMCID: PMC6198502 DOI: 10.1186/s12864-018-5162-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/11/2018] [Indexed: 01/08/2023] Open
Abstract
Background Ural genetic family is a part of the Euro-American lineage of Mycobacterium tuberculosis and is endemic in Northern Eurasia (former Soviet Union [FSU]). These strains were long described as drug susceptible and of low virulence, but recent studies reported an increasing circulation of the multidrug-resistant (MDR) and extensively drug-resistant (XDR) Ural strains. Here, we analyzed all publicly available whole genome sequence data of Ural genotype isolates, in order to elucidate their phylogenomic diversity with a special focus on MDR and potentially epidemic clones. Results A total of 149 M. tuberculosis genomes of Ural isolates from FSU countries were mined from the GMTV database and TB-ARC project. We identified 6002 variable amino acid positions that were assessed for functional significance and used to build ML, NJ trees and for Bayesian TMRCA estimation. Three robust monophyletic clades were identified: Clade A (31 isolates from Russia, Belarus, Moldova), Clade B (52 isolates from Russia), and Clade C (37 isolates from Moldova, 2 from Belarus). Clade C was significantly associated with XDR or pre-XDR status compared to the pooled Clades A and B (33/39 versus 5/83, P < 0.0001). Time of origin was estimated for Clade A at 77.7–137 years ago and for Clade B at 56.3–99.2 years ago compared to the significantly more recent origin for Clade C. in silico spoligotyping identified signatures specific of the Clade A (spoligotype SIT35), and Clades B and C (both SIT262). Conclusions A genetically compact and evolutionarily young Ural Clade C, likely originated after collapse of the Soviet Union, and reached epidemic proportions in Moldova in the last 20 years. This epidemic pre-XDR clone (mostly rifampin, isoniazid and kanamycin resistant) is characterized by a specific combination of mutations: KatG Ser315Thr, fabG1 -15C > T, RpoB Ser450Leu, RpsL Lys88Arg, eis -12G > A and EmbB Ser297Ala/T > G. Its further dissemination may occur towards both Russia and European Union and should be taken into consideration by health authorities. The identified spoligotyping signatures can serve for rapid preliminary detection and surveillance of the more hazardous pre-XDR associated strains of the Ural family, both in populations from countries of their endemic circulation and migrant communities. Electronic supplementary material The online version of this article (10.1186/s12864-018-5162-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Viacheslav Sinkov
- Department Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, 16 Timiriazeva street, Irkutsk, 664003, Russia
| | - Oleg Ogarkov
- Department Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, 16 Timiriazeva street, Irkutsk, 664003, Russia. .,Irkutsk State Medical Academy of Continuing Education, Irkutsk, 664049, Russia.
| | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, 14 Mira street, St. Petersburg, 197101, Russia.
| | - Yuri Bukin
- Limnological Institute SB RAS, Irkutsk, 664033, Russia.,Irkutsk National Research Technical University, Irkutsk, 664074, Russia
| | - Svetlana Zhdanova
- Department Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, 16 Timiriazeva street, Irkutsk, 664003, Russia
| | - Scott K Heysell
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, 22908, USA
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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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Gurjav U, Erkhembayar B, Burneebaatar B, Narmandakh E, Tumenbayar O, Hill-Cawthorne GA, Marais BJ, Sintchenko V. Transmission of multi-drug resistant tuberculosis in Mongolia is driven by Beijing strains of Mycobacterium tuberculosis resistant to all first-line drugs. Tuberculosis (Edinb) 2016; 101:49-53. [PMID: 27865397 DOI: 10.1016/j.tube.2016.07.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/17/2016] [Accepted: 07/19/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND Mongolia has high and rising rates of multi-drug resistant tuberculosis (MDR-TB). Spatio-temporal and programmatic evidence suggests a major contribution from MDR-TB transmission, but genotypic evidence has not been assessed. METHODS All MDR-TB cases identified during 2012 were examined. Demographic and bacteriological data were obtained from the National Tuberculosis Reference Laboratory. Isolates of Mycobacterium tuberculosis from culture-confirmed category 1 treatment failures were genotyped using 24-loci mycobacterium interspersed repetitive unit (MIRU-24) analysis. RESULTS Of the 210 MDR-TB cases identified, 115 (54.8%) were treatment failures (34.8% category 1; 20.0% category 2). Streptomycin resistance was present in 156 (74.3%) cases; including 55/73 (75.3%) category 1 treatment failures who had never been exposed to streptomycin. Among category 1 treatment failures, Beijing lineage strains predominated (88.0%; 59/67 of genotyped isolates). MIRU-24 clustering was documented in 62.7% (42/67) of strains; 55.2% (37/67) remained clustered when drug susceptibility test results were considered. In total 59.5% (25/42) of clustered strains were Beijing lineage and demonstrated in-vitro resistance to all first-line drugs tested. CONCLUSION The MDR-TB epidemic in Mongolia appears to be driven by primary transmission of Beijing lineage strains resistant to all first-line drugs. Enhanced infection control strategies together with early MDR-TB case detection and appropriate treatment are necessary to limit escalation of the MDR-TB epidemic.
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Affiliation(s)
- Ulziijargal Gurjav
- Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Sydney, Australia.
| | - Baasansuren Erkhembayar
- National Tuberculosis Reference Laboratory, National Center for Communicable Diseases, Ulaanbaatar, Mongolia
| | - Buyankhishig Burneebaatar
- National Tuberculosis Reference Laboratory, National Center for Communicable Diseases, Ulaanbaatar, Mongolia
| | - Erdenegerel Narmandakh
- National Tuberculosis Reference Laboratory, National Center for Communicable Diseases, Ulaanbaatar, Mongolia
| | - Oyuntuya Tumenbayar
- National Tuberculosis Reference Laboratory, National Center for Communicable Diseases, Ulaanbaatar, Mongolia
| | - Grant A Hill-Cawthorne
- Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia; Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia
| | - Ben J Marais
- Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
| | - Vitali Sintchenko
- Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Sydney, Australia
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