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Zhang H, Tang M, Li D, Xu M, Ao Y, Lin L. Applications and advances in molecular diagnostics: revolutionizing non-tuberculous mycobacteria species and subspecies identification. Front Public Health 2024; 12:1410672. [PMID: 38962772 PMCID: PMC11220129 DOI: 10.3389/fpubh.2024.1410672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 06/10/2024] [Indexed: 07/05/2024] Open
Abstract
Non-tuberculous mycobacteria (NTM) infections pose a significant public health challenge worldwide, affecting individuals across a wide spectrum of immune statuses. Recent epidemiological studies indicate rising incidence rates in both immunocompromised and immunocompetent populations, underscoring the need for enhanced diagnostic and therapeutic approaches. NTM infections often present with symptoms similar to those of tuberculosis, yet with less specificity, increasing the risk of misdiagnosis and potentially adverse outcomes for patients. Consequently, rapid and accurate identification of the pathogen is crucial for precise diagnosis and treatment. Traditional detection methods, notably microbiological culture, are hampered by lengthy incubation periods and a limited capacity to differentiate closely related NTM subtypes, thereby delaying diagnosis and the initiation of targeted therapies. Emerging diagnostic technologies offer new possibilities for the swift detection and accurate identification of NTM infections, playing a critical role in early diagnosis and providing more accurate and comprehensive information. This review delineates the current molecular methodologies for NTM species and subspecies identification. We critically assess the limitations and challenges inherent in these technologies for diagnosing NTM and explore potential future directions for their advancement. It aims to provide valuable insights into advancing the application of molecular diagnostic techniques in NTM infection identification.
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Affiliation(s)
- Haiyang Zhang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Maoting Tang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Deyuan Li
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Min Xu
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Yusen Ao
- Department of Pediatrics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Liangkang Lin
- Department of Pediatrics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
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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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Hadifar S, Kargarpour Kamakoli M, Eybpoosh S, Nakhaeizadeh M, Kargarpour Kamakoli MA, Ebrahimifard N, Fateh A, Siadat SD, Vaziri F. The shortcut of mycobacterial interspersed repetitive unit-variable number tandem repeat typing for Mycobacterium tuberculosis differentiation. Front Microbiol 2022; 13:978355. [PMID: 36160200 PMCID: PMC9493315 DOI: 10.3389/fmicb.2022.978355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
The 24-loci mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) genotyping has been used as an international standard method for Mycobacterium tuberculosis (Mtb) genotyping. However, different optimized VNTR loci sets for improving the discrimination of specific Mtb genotypes have been proposed. In this regard, we investigated the efficacy of accumulation of the percentage differences (APDs) compared with the least absolute shrinkage and selection operator (LASSO) regression strategy to identify a customized genotype-specific VNTR loci set which provides a resolution comparable to 24-loci MIRU-VNTR in divergent Mtb populations. We utilized Spoligotyping and 24-loci MIRU-VNTR typing for genotyping 306 Mtb isolates. The APD and LASSO regression approaches were used to identify a customized VNTR set in our studied isolates. Besides, the Hunter-Gaston discriminatory index (HGDI), sensitivity, and specificity of each selected loci set were calculated based on both strategies. The selected loci based on LASSO regression compared with APD-based loci showed a better discriminatory power for identifying all studied genotypes except for T genotype, which APD-based loci showed promising discriminative power. Our findings suggested the LASSO regression rather than the APD approach is more effective in the determination of possible discriminative VNTR loci set to precise discrimination of our studied Mtb population and may be beneficial to be used in finding reduced number loci sets in other Mtb genotypes or sublineages. Moreover, we proposed customized genotype-specific MIRU-VNTR loci sets based on the LASSO regression and APD approaches for precise Mtb strains identification. As the proposed VNTR sets offered a comparable discriminatory power to the standard 24 MIRU-VNTR loci set could be promising alternatives to the standard genotyping for using in resource-limited settings.
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Affiliation(s)
- Shima Hadifar
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mansour Kargarpour Kamakoli
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Sana Eybpoosh
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Mehran Nakhaeizadeh
- Modeling in Health Research Center, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
- Department of Biostatistics and Epidemiology, School of Public Health, Kerman University of Medical Sciences, Kerman, Iran
| | | | - Nasim Ebrahimifard
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
- *Correspondence: Farzam Vaziri, ,
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Farnad MS, Momtaz H, Mosavari N, Khosravi Y, Tadayon K. Insight into population structure of Mycobacterium tuberculosis isolates in the multiethnic province of Alborz, Iran. IRANIAN JOURNAL OF MICROBIOLOGY 2021; 13:58-64. [PMID: 33889363 PMCID: PMC8043826 DOI: 10.18502/ijm.v13i1.5493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background and Objectives: Genetic diversity of Mycobacterium tuberculosis clinical isolates from tuberculosis patients in the multiethnic province of Alborz, Iran was assessed. Materials and Methods: A total of 17 isolates in the period of 2012–2013 were collected and subjected to a Multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) consisted of 6 variable numbers of tandem repeats (VNTRs) including ETR-A, ETR-B, ETR-C, ElTR-D, ETR-E, ETR-F, 5 Mycobacterial Interspersed Repetitive Units including MIRU10, MIRU16, MIRU26, MIRU39, MIRU40, and 1 Queen University of Belfast locus, QUB11. Results: This classified all isolates into 17 distinct MIRU-VNTR types, a reflection of a highly heterogenic population. Within the 12 used VNTR loci, ten proved highly or moderately discriminant according to the calculated HGDI scores. No cluster of isolates was identified in the study panel, giving a clustering rate of 0%, several events of SVL (N=5) and DVL (N=4) and TVL (N=3) were detected. Conclusion: The greater heterogeneity observed here by MLVA-VNTR analysis is most likely due to limited background data in the study region rather than a genuine more heterogeneous population compared to other provinces of the country.
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Affiliation(s)
- Morassa Sadat Farnad
- Department of Microbiology, Shahrekord Branch, Islamic Azad University, Sharekord, Iran
| | - Hassan Momtaz
- Department of Microbiology, Shahrekord Branch, Islamic Azad University, Sharekord, Iran
| | - Nader Mosavari
- Department of Tuberculin & Mallein, Razi Vaccine & Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Yahya Khosravi
- Department of Occupational Health and Safety Engineering, Non-communicable Diseases, Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Keyvan Tadayon
- Department of Microbiology, Shahrekord Branch, Islamic Azad University, Sharekord, Iran.,Department of Tuberculin & Mallein, Razi Vaccine & Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
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5
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Hadifar S, Fateh A, Pourbarkhordar V, Siadat SD, Mostafaei S, Vaziri F. Variation in Mycobacterium tuberculosis population structure in Iran: a systemic review and meta-analysis. BMC Infect Dis 2021; 21:2. [PMID: 33397308 PMCID: PMC7784266 DOI: 10.1186/s12879-020-05639-7] [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: 07/03/2020] [Accepted: 11/19/2020] [Indexed: 01/30/2023] Open
Abstract
Background Acquiring comprehensive insight into the dynamics of Mycobacterium tuberculosis (Mtb) population structure is an essential step to adopt effective tuberculosis (TB) control strategies and improve therapeutic methods and vaccines. Accordingly, we performed this systematic review and meta-analysis to determine the overall prevalence of Mtb genotypes/ sublineages in Iran. Methods We carried out a comprehensive literature search using the international databases of MEDLINE and Scopus as well as Iranian databases. Articles published until April 2020 were selected based on the PRISMA flow diagram. The overall prevalence of the Mtb genotypes/sublineage in Iran was determined using the random effects or fixed effect model. The metafor R package and MedCalc software were employed for performing this meta-analysis. Results We identified 34 studies for inclusion in this study, containing 8329 clinical samples. Based on the pooled prevalence of the Mtb genotypes, NEW1 (21.94, 95% CI: 16.41–28.05%), CAS (19.21, 95% CI: 14.95–23.86%), EAI (12.95, 95% CI: 7.58–19.47%), and T (12.16, 95% CI: 9.18–15.50%) were characterized as the dominant circulating genotypes in Iran. West African (L 5/6), Cameroon, TUR and H37Rv were identified as genotypes with the lowest prevalence in Iran (< 2%). The highest pooled prevalence rates of multidrug-resistant strains were related to Beijing (2.52, 95% CI) and CAS (1.21, 95% CI). Conclusions This systematic review showed that Mtb populations are genetically diverse in Iran, and further studies are needed to gain a better insight into the national diversity of Mtb populations and their drug resistance pattern.
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Affiliation(s)
- Shima Hadifar
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Centre (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Centre (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Vahid Pourbarkhordar
- Department of Pharmacology and Toxicology, School of Pharmacy and Pharmaceutical Science, Isfahan University of Medical Science, Isfahan, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Centre (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Shayan Mostafaei
- Department of Biostatistics, School of Health, Kermanshah University of Medical Sciences, Kermanshah, Iran. .,Epidemiology and Biostatistics Unit, Rheumatology Research Centre, Tehran University of Medical Sciences, Tehran, Iran.
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran. .,Microbiology Research Centre (MRC), Pasteur Institute of Iran, Tehran, Iran.
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6
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Mousavi S, Amini S, Mirsaeidi M, Dabiri H, Hamzehloo G, Goudarzi H, Nasiri M. Genotyping and drug susceptibility testing of Mycobacterium tuberculosis in Iran: a multi-centre study. New Microbes New Infect 2020; 37:100729. [PMID: 32774869 PMCID: PMC7404542 DOI: 10.1016/j.nmni.2020.100729] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 02/24/2020] [Accepted: 07/09/2020] [Indexed: 01/20/2023] Open
Abstract
Tuberculosis (TB) is a deadly infection and caused 1.4 million deaths in 2018. Assessing the geographic distribution of major lineages of Mycobacterium tuberculosis can contribute greatly to TB control. Mycobacterial interspersed repetitive unit variable number tandem repeat (MIRU-VNTR) typing is commonly used to differentiate various lineages of M. tuberculosis. A total of 2747 clinical specimens were collected consecutively from October 2018 through June 2019. Clinical isolates were identified as M. tuberculosis using standard biochemical tests. The standard 15-locus MIRU-VNTR typing was used for the genotyping of clinical isolates. Drug susceptibility testing was performed using the conventional proportion method. From the collected specimens, 100 were culture positive for M. tuberculosis. Using MIRU-VNTR, 99 different patterns were detected among the 100 isolates. They were distributed in one cluster comprising two strains and 98 unique patterns. Most of our isolates were similar to New-1 and Delhi/CAS strains. Of the M. tuberculosis isolates, 83 (83.0%) were pan-susceptible and 17 (17.0%) were resistant to at least one drug. Our study showed that MIRU-VNTR is a useful method for studying the genetic diversity of M. tuberculosis isolates in different regional settings and will help the health authorities to construct a preventive programme for TB.
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Affiliation(s)
- S.M.J. Mousavi
- Department of Microbiology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - S. Amini
- Regional Tuberculosis Reference Laboratory, Tehran University of Medical Science, Tehran, Iran
| | - M. Mirsaeidi
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - H. Dabiri
- Department of Microbiology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - G. Hamzehloo
- Regional Tuberculosis Reference Laboratory, Tehran University of Medical Science, Tehran, Iran
| | - H. Goudarzi
- Department of Microbiology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - M.J. Nasiri
- Department of Microbiology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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7
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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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Keikha M. There is significant relationship between Beijing genotype family strains and resistance to the first-line anti-tuberculosis drugs in the Iranian population. J Clin Tuberc Other Mycobact Dis 2020; 19:100161. [PMID: 32368621 PMCID: PMC7186555 DOI: 10.1016/j.jctube.2020.100161] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Masoud Keikha
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
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Kargarpour Kamakoli M, Farmanfarmaei G, Masoumi M, Khanipour S, Gharibzadeh S, Sola C, Fateh A, Siadat SD, Refregier G, Vaziri F. Prediction of the hidden genotype of mixed infection strains in Iranian tuberculosis patients. Int J Infect Dis 2020; 95:22-27. [PMID: 32251801 DOI: 10.1016/j.ijid.2020.03.056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 03/19/2020] [Accepted: 03/24/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Patients with mixed-strain Mycobacterium tuberculosis infections may be at a high risk of poor treatment outcomes. However, the mechanisms through which mixed infections affect the clinical manifestations are not well recognized. Evidence suggests that failure to detect the pathogen diversity within the host can influence the clinical results. We aimed to investigate the effects of different genotypes in mixed infections and determine their relationship with heteroresistance in the treatment of Iranian tuberculosis patients. METHODS One of the genotypes was identified in the culture and another genotype pattern in the mixed infection was predicted by comparing the pattern of MIRU-VNTR between the clinical specimens and their respective cultures in each patient. For all patients, the drug susceptibility testing was carried out on three single colonies from each clinical sample. The follow-up of patients was carried out during six months of treatment. RESULTS Based on MIRU-VNTR profiles of clinical samples, we showed that 55.6% (25/45) of the Iranian patients included in the study had mixed infections. Patients with mixed infections had a higher rate of treatment failure, compared to others (P=0.03). By comparing clinical sample profiles to profiles obtained after culture, we were able to distinguish between major and hidden genotypes. Among hidden genotypes, Haarlem (L4.1.2) and Beijing (L2) were associated to treatment failure (6/8 patients). CONCLUSIONS To conclude, we propose a procedure using the MIRU-VNTR method to identify the different genotypes in mixed infections. The present findings suggest that genotypes with potentially higher pathogenicity may not be detected when performing experimental culture in patients with mixed infections.
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Affiliation(s)
- Mansour Kargarpour Kamakoli
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Ghazaleh Farmanfarmaei
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Morteza Masoumi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, 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
| | - Safoora Gharibzadeh
- Department of Epidemiology and Biostatistics, Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Christophe Sola
- Institut for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Guislaine Refregier
- Institut for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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10
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Hadifar S, Kamakoli MK, Fateh A, Siadat SD, Vaziri F. Enhancing the differentiation of specific genotypes in Mycobacterium tuberculosis population. Sci Rep 2019; 9:17946. [PMID: 31784605 PMCID: PMC6884525 DOI: 10.1038/s41598-019-54393-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 11/14/2019] [Indexed: 12/18/2022] Open
Abstract
Today, significant attention is directed towards the global lineages and sublineages of Mycobacterium tuberculosis (Mtb). NEW-1 (SIT 127) and CAS1-Delhi (SIT 26) strains are recognized as growing and circulating Mtb genotypes, especially in Asian countries. It is crucial to develop or enhance Mtb genotyping methods for a more accurate and simple differentiation of these families. We used 24-loci mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing for genotyping 217 Mtb isolates. To select the optimal MIRU-VNTR loci, we calculated the Hunter-Gaston discriminatory index (HGDI), allelic diversity, and accumulation of percentage differences (APDs) between the strains among different groups of genotypes (NEW-1 and non-NEW-1; CAS1-Delhi and non-CAS). Finally, the minimum spanning tree was constructed for clustering analysis. In the NEW-1 population, loci with APD > 60% were found to have a high discriminatory power. VNTR loci with APD > 50% showed high discrimination power for the CAS population. Our findings suggest that APDs, which are valuable for the selection of VNTR loci sets, may improve the discriminatory power of MIRU-VNTR typing for identification of Mtb genotypes in specific regions.
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Affiliation(s)
- Shima Hadifar
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Mansour Kargarpour Kamakoli
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, 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.
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11
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Konstantynovska O, Rekrotchuk M, Hrek I, Rohozhyn A, Rudova N, Poteiko P, Gerilovych A, Bortz E, Solodiankin O. Severe Clinical Outcomes of Tuberculosis in Kharkiv Region, Ukraine, Are Associated with Beijing Strains of Mycobacterium tuberculosis. Pathogens 2019; 8:pathogens8020075. [PMID: 31185670 PMCID: PMC6631893 DOI: 10.3390/pathogens8020075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/02/2019] [Accepted: 06/06/2019] [Indexed: 11/16/2022] Open
Abstract
Genotypic variation in Beijing lineages of Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis (TB), has been associated with hyper virulence and the spread of extensively and multiple drug (X/MDR) resistant MTB strains in Eastern Europe, Central Asia, and East Asia. The clinical outcomes of 215 new cases of TB among the population of the Kharkiv region of Eastern Ukraine were analyzed to uncover factors associated with severe infection. Infecting MTB strains were profiled by 5 locus exact tandem repeats (ETRs) and 15 locus mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) genotyping. Among diverse MTB genotypes discovered in Ukraine, the Beijing genotype (MIRU-VNTR 42425) was significantly associated with risk factors for severe outcomes of disease in the study population, including TB/HIV co-infection and treatment failure. Strain replacement (superinfection) was observed in 10 patients, suggesting repeated exposure to novel MTB strains in hospital or community settings. Inclusion of MTB genotyping data may identify at-risk patients and improve treatment adherence to prevent X/MDR development for effective public health response against tuberculosis in Ukraine.
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Affiliation(s)
| | - Mariia Rekrotchuk
- National Scientific Center Institute of Experimental and Clinical Veterinary Medicine (NSC IECVM), 61023 Kharkiv, Ukraine.
| | - Ivan Hrek
- Kharkiv Medical Academy of Postgraduate Education, 61176 Kharkiv, Ukraine.
| | - Anton Rohozhyn
- Kharkiv Medical Academy of Postgraduate Education, 61176 Kharkiv, Ukraine.
| | - Nataliia Rudova
- National Scientific Center Institute of Experimental and Clinical Veterinary Medicine (NSC IECVM), 61023 Kharkiv, Ukraine.
| | - Petro Poteiko
- Kharkiv Medical Academy of Postgraduate Education, 61176 Kharkiv, Ukraine.
| | - Anton Gerilovych
- National Scientific Center Institute of Experimental and Clinical Veterinary Medicine (NSC IECVM), 61023 Kharkiv, Ukraine.
| | - Eric Bortz
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK 99508, USA.
| | - Oleksii Solodiankin
- National Scientific Center Institute of Experimental and Clinical Veterinary Medicine (NSC IECVM), 61023 Kharkiv, Ukraine.
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12
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Genetic diversity of Mycobacterium tuberculosis isolates causing pulmonary and extrapulmonary tuberculosis in the capital of Iran. Mol Phylogenet Evol 2018; 132:46-52. [PMID: 30513341 DOI: 10.1016/j.ympev.2018.11.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 11/24/2018] [Accepted: 11/26/2018] [Indexed: 01/12/2023]
Abstract
OBJECTIVES Evaluation of the genetic diversity of Mycobacterium tuberculosis (M.tb) and determining if the association between a specific genotype and the site of infection is crucial. Accordingly, the current study aimed at comparing predominant M.tb genotypes in pulmonary (PTB) and extrapulmonary tuberculosis (EPTB) isolates circulating in the capital of Iran. METHODS The genetic diversity of culture-confirmed PTB and EPTB isolates were evaluated by Spoligotyping and MIRU-VNTR (mycobacterial interspersed repetitive-unit-variable-number tandem-repeat) typing methods. Genotyping data were analyzed with SITVIT, MIRU-VNTRplus, and TBminer databases. To assess adjusted associations, chi-square/the Fisher exact test and multiple logistic regression model were applied. RESULTS URAL2 (NEW-1) (28/88; 31.8%) and CAS1-DELHI (25/84; 29.8%) genotypes were predominant in EPTB and PTB strains, respectively. Based on MIRU-VNTR typing, 158 different MIRU-VNTR patterns were identified. Clustering rate and minimum estimate of the proportion of TB caused by recent transmission was 4.1% and 8.1%, respectively. CONCLUSIONS The current study provided new insight into circulating genotypes of M.tb in PTB and EPTB patients in Tehran, Iran. This low percentage of TB transmission rate, demonstrated that mode of TB transmission was mainly associated with reactivation of latent TB rather than recently transmitted infection in this region. There was no significant difference in the association between the genotypes of M.tb strains and the site of the disease.
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