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Seid A, Kassa M, Girma Y, Dereb E, Nureddin S, Abebe A, Berhane N. Molecular characterization of genetic mutations with fitness loss in pulmonary tuberculosis patients associated with HIV co-infection in Northwest Amhara, Ethiopia. SAGE Open Med 2023; 11:20503121231208266. [PMID: 37933292 PMCID: PMC10625730 DOI: 10.1177/20503121231208266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 09/29/2023] [Indexed: 11/08/2023] Open
Abstract
Objectives Molecular approaches to identifying resistance-conferring mutations suggest a revolution in the field of tuberculosis. The aim of the study was to determine the association between resistance-conferring mutations with fitness loss in Mycobacterium tuberculosis clinical isolates and HIV co-infection in the Amhara region of Ethiopia. Methods A laboratory-based cross-sectional study was conducted between September 2022 and June 2023. A line probe assay was performed on 146 culture-positive clinical isolates. Logistic regression analysis was used to measure the strength of the association between the drug-resistance-conferring mutations with fitness loss in M. tuberculosis isolates and tuberculosis/HIV co-infection. A p-value ⩽ 0.05 was considered statistically significant. Results A total of 11 distinct mutations at four genetic loci among 19 resistant isolates were detected. The frequency of rifampicin, isoniazid, and fluoroquinolones resistance-conferring mutations was identified in 12 (8.2%), 17 (11.6%), and 2 (1.4%) of the isolates, respectively. The most prominent specific mutations were S450L (5/9, 55.6%), S315T (11/11, 100%), C-15T (4/4, 100%), and D94G (1/1, 100%). Double mutations were observed in 10 (52.6%) multidrug-resistant tuberculosis isolates; the most common were detected in both the rpoB and katG genes (8/10, 80.0%). The HIV-co-infected tuberculosis patients carried a higher proportion of low fitness of non-rpoB S450L variants than those tuberculosis patients without HIV (80.0% vs 14.3%) and showed a significant association (cOR = 0.042, 95% CI: 0.002-0.877, p = 0.041), but not with the low fitness of non-katG S315T variants (cOR = 3.00, 95% CI: 0.348-25.870, p = 0.318). Conclusion This study provides valuable information on the genetic variants with fitness loss associated with HIV co-infection, but requires further whole-genome-based mutation analysis.
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Affiliation(s)
- Aynias Seid
- Department of Biology, College of Natural and Computational Science, Debre-Tabor University, Debre-Tabor, Ethiopia
- Department of Medical Biotechnology, Institute of Biotechnology, University of Gondar, Gondar, Ethiopia
| | - Meseret Kassa
- TB Culture Laboratory, University of Gondar Comprehensive Specialized Hospital, Gondar, Ethiopia
| | - Yilak Girma
- TB Culture Laboratory, University of Gondar Comprehensive Specialized Hospital, Gondar, Ethiopia
| | - Eseye Dereb
- TB Culture Laboratory, University of Gondar Comprehensive Specialized Hospital, Gondar, Ethiopia
| | - Semira Nureddin
- Department of Biology, College of Natural and Computational Science, Woldia University, Woldia, Ethiopia
| | - Ayenesh Abebe
- TB Culture Laboratory, University of Gondar Comprehensive Specialized Hospital, Gondar, Ethiopia
| | - Nega Berhane
- Department of Medical Biotechnology, Institute of Biotechnology, University of Gondar, Gondar, Ethiopia
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Assefa G, Desta K, Araya S, Girma S, Hailu E, Mihret A, Hailu T, Tilahun M, Diriba G, Dagne B, Atnafu A, Endalafer N, Abera A, Bekele S, Mengistu Y, Bobosha K, Aseffa A. Drug Resistance in Tuberculous Lymphadenitis: Molecular Characterization. Tuberc Res Treat 2023; 2023:3291538. [PMID: 37032734 PMCID: PMC10076118 DOI: 10.1155/2023/3291538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 02/27/2023] [Accepted: 03/11/2023] [Indexed: 03/31/2023] Open
Abstract
Background Drug-resistant tuberculosis (TB) epidemic in high-TB-incidence countries, particularly Ethiopia, remains a significant challenge. As a result, we investigated the drug resistance, common gene mutation, and molecular characterization of mycobacterial isolates from patients with suspected tuberculous lymphadenitis (TBLN). Methodology. A cross-sectional study of 218 FNA samples from TBLN patients inoculated on Lowenstein-Jensen media was carried out. The culture isolates were identified as MTB by polymerase chain reaction (PCR) and the difference-9 (RD9) test region. In addition, the GenoType MTBDRplus assay tested the first and second-line MTB drugs, and the spoligotyping strain-dependent polymorphism test was determined. Results Among the 50 culture-positive isolates, 14% (7/50) had drug resistance caused by a gene mutation. Out of these, 4 (8%) isolates were mono-resistant to isoniazid drug, which is caused by a gene mutation in katG in the region of interrogated at codon 315 in the amino acid sequence of S315T1, and 3 (6%) isolates were resistant to both rifampicin and isoniazid drugs. The mutation was observed for katG (at codon 315 with a change in the sequence of amino acid S315T) and rpoB (at codon 530-533 with a change in the sequence of amino acid S531L (S450L)) genes. The most prevalent spoligotypes were orphan and SIT53 strains. Conclusion The predominance of INH mono-resistance poses a critical risk for the potential development of MDR-TB, as INH mono-resistance is a typical pathway to the occurrence of MDR-TB. The orphan and SIT53 (T) strains were the most common in the study area, and a drug-resistant strain caused by a common gene mutation could indicate the transmission of clonal-resistant strains in the community.
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Affiliation(s)
- Gebeyehu Assefa
- Armauer Hansen Research Institute, AHRI, Addis Ababa, Ethiopia
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Kassu Desta
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Shambel Araya
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Selfu Girma
- Armauer Hansen Research Institute, AHRI, Addis Ababa, Ethiopia
| | - Elena Hailu
- Armauer Hansen Research Institute, AHRI, Addis Ababa, Ethiopia
| | - Adane Mihret
- Armauer Hansen Research Institute, AHRI, Addis Ababa, Ethiopia
| | - Tsegaye Hailu
- Armauer Hansen Research Institute, AHRI, Addis Ababa, Ethiopia
| | - Melaku Tilahun
- Armauer Hansen Research Institute, AHRI, Addis Ababa, Ethiopia
| | - Getu Diriba
- Ethiopian Public Health Institute, EPHI, Addis Ababa, Ethiopia
| | - Biniyam Dagne
- Ethiopian Public Health Institute, EPHI, Addis Ababa, Ethiopia
| | - Abay Atnafu
- Armauer Hansen Research Institute, AHRI, Addis Ababa, Ethiopia
| | | | - Adugna Abera
- Ethiopian Public Health Institute, EPHI, Addis Ababa, Ethiopia
| | - Shiferaw Bekele
- Armauer Hansen Research Institute, AHRI, Addis Ababa, Ethiopia
| | | | - Kidist Bobosha
- Armauer Hansen Research Institute, AHRI, Addis Ababa, Ethiopia
| | - Abraham Aseffa
- Armauer Hansen Research Institute, AHRI, Addis Ababa, Ethiopia
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Agonafir M, Belay G, Feleke A, Maningi N, Girmachew F, Reta M, Fourie PB. Profile and Frequency of Mutations Conferring Drug-Resistant Tuberculosis in the Central, Southeastern and Eastern Ethiopia. Infect Drug Resist 2023; 16:2953-2961. [PMID: 37201127 PMCID: PMC10187580 DOI: 10.2147/idr.s408567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/05/2023] [Indexed: 05/20/2023] Open
Abstract
Purpose Advances in molecular tools that assess genes harboring drug resistance mutations have greatly improved the detection and treatment of drug-resistant tuberculosis (DR-TB). This study was conducted to determine the frequency and type of mutations that are responsible for resistance to rifampicin (RIF), isoniazid (INH), fluoroquinolones (FLQs) and second-line injectable drugs (SLIDs) in Mycobacterium tuberculosis (MTB) isolates obtained from culture-positive pulmonary tuberculosis (TB) patients in the central, southeastern and eastern Ethiopia. Patients and Methods In total, 224 stored culture-positive MTB isolates from pulmonary TB patients referred to Adama and Harar regional TB laboratories between August 2018 and January 2019 were assessed for mutations conferring RIF, INH, FLQs and SLIDs resistance using GenoType®MTBDRplus (MTBDRplus) and GenoType®MTBDRsl (MTBDRsl). Results RIF, INH, FLQs and SLIDs resistance-conferring mutations were identified in 88/224 (39.3%), 85/224 (38.0%), 7/77 (9.1%), and 3/77% (3.9%) of MTB isolates, respectively. Mutation codons rpoB S531L (59.1%) for RIF, katG S315T (96.5%) for INH, gyrA A90V (42.1%) for FLQs and WT1 rrs (100%) for SLIDs were observed in the majority of the isolates tested. Over a 10th of rpoB mutations detected in the current study were unknown. Conclusion In this study, the most common mutations conferring drug resistance to RIF, INH, FLQs were identified. However, a significant proportion of RIF-resistant isolates manifested unknown rpoB mutations. Similarly, although few in number, all SLID-resistant isolates had unknown rrs mutations. To further elucidate the entire spectrum of mutations, tool such as whole-genome sequencing is imperative. Furthermore, the expansion of molecular drug susceptibility testing services is critical for tailoring patient treatment and preventing disease transmission.
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Affiliation(s)
- Mulualem Agonafir
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Correspondence: Mulualem Agonafir, Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, P.O. Box 34738, Addis Ababa, Ethiopia, Tel +251911446959, Email
| | - Gurja Belay
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Adey Feleke
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Nontuthuko Maningi
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | | | - Melese Reta
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- Department of Medical Laboratory Sciences, College of Health Sciences, Woldia University, Woldia, Ethiopia
| | - P Bernard Fourie
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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Frequency of rpoB, katG, and inhA Gene Polymorphisms Associated with Multidrug-Resistant Mycobacterium tuberculosis Complex Isolates among Ethiopian TB Patients: A Systematic Review. Interdiscip Perspect Infect Dis 2022; 2022:1967675. [PMID: 35757683 PMCID: PMC9225881 DOI: 10.1155/2022/1967675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/05/2022] [Accepted: 05/26/2022] [Indexed: 11/18/2022] Open
Abstract
Tuberculosis (TB) is one of the top 10 causes of mortality and the first killer among infectious diseases of poverty (IDoPs) worldwide. It disproportionately affects on-third of the world's low-income countries including Ethiopia. One of the factors driving the TB epidemic is the global rise of MDR/XDR-TB and their low detection affect the global TB control progress. Recently, the resistance-associated genetic mutations in MTBC known to confer drug resistance have been detected by rapid molecular diagnostic tests and sequencing methods. In this article, the published literature searched by PubMed database from 2010 to 2021 and English language were considered. The aim of this systematic review was to assess the prevalence of the most common rpoB, katG, and inhA gene mutations associated with multidrug resistance in MTBC clinical strains among TB patients in Ethiopia. Though 22 studies met our eligibility criteria, only 6 studies were included in the final analysis. Using the molecular GenoType MTBDRplus and MTBDRsl line probe assay and sequencing procedures, a total of 932 culture-positive MTBC isolates were examined to determine RIF, INH, and MDR-TB resistance patterns along with rpoB, katG, and inhA gene mutation analysis. As a result, among the genotypically tested MTBC isolates, 119 (12.77%), 83 (8.91%), and 73 (7.32%) isolates were INH, RIF, and MDR-TB resistant, respectively. In any RIF-resistant MTBC strains, the most common single point mutations were in codon 531 (S531L) followed by codon 526 (H526Y) of the rpoB gene. Besides, the most common mutations in any INH-resistant MTBC were strains observed at codon 315 (S315T) and WT probe in the katG gene and at codon C15T and WT1 probe in the inhA promoter region. Detection of resistance allele in rpoB, KatG, and inhA genes for RIF and INH could serve as a marker for MDR-TB strains. Tracking the most common S531L, S315T, and C15T mutations in rpoB, katG, and inhA genes among RIF- and INH-resistant isolates would be valuable in TB diagnostics and treatment regimens, and could reduce the development and risk of MDR/XDR-TB drug-resistance patterns.
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Ye M, Yuan W, Molaeipour L, Azizian K, Ahmadi A, Kouhsari E. Antibiotic heteroresistance in Mycobacterium tuberculosis isolates: a systematic review and meta-analysis. Ann Clin Microbiol Antimicrob 2021; 20:73. [PMID: 34645463 PMCID: PMC8513340 DOI: 10.1186/s12941-021-00478-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 10/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycobacterium tuberculosis (MTB) is responsible for tuberculosis; that continues to be a public health threat across the globe. Furthermore, increasing heteroresistance (HR)-the presence of resistant and susceptible isolates among MTB strains- has been reported from around the world. This phenomenon can lead to full resistance development and treatment failure. METHODS We systematically searched the relevant studies in PubMed, Scopus, and Embase (Until October 21, 2020). The study outcomes revealed the weighted pooled prevalence of antibiotic HR in MTB isolates with subgroup analysis by year, quality of study, and heteroresistance detection method. RESULTS A total of 38 studies which had investigated MTB isolates were included in the meta-analysis. Geographically, the highest number of studies were reported from Asia (n = 24), followed by Africa (n = 5). Nineteen studies reported HR to isoniazid, with a weighted pooled prevalence of 5% (95% CI 0-12) among 11,761 MTB isolates. Also, there is no important trend for the subgroup analysis by the study period (2001-2014 vs 2015-2017 vs 2018-2020). HR to rifampin was reported in 17 studies, with a weighted pooled prevalence of 7% (95% CI 2-14) among 3782 MTB isolates. HR to fluoroquinolone and ethambutol were reported in 12 and 4 studies, respectively, with weighted pooled prevalence of 10% and 1% among 2153 and 1509 MTB isolates, correspondingly. CONCLUSION Based on our analysis, HR in MTB isolates with different frequency rate is present worldwide. Thus, the selection of appropriate and reliable methods for HR detection is crucial for TB eradication.
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Affiliation(s)
- Mao Ye
- Department of Pharmacy, Clinical Pharmaceutics Room, Sichuan Science City Hospital, Mianyang, 621000, China
| | - Wen Yuan
- Sichuan College of Traditional Chinese Medicine, Mianyang, 621000, China
| | - Leila Molaeipour
- Department of Epidemiology, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Khalil Azizian
- Department of Clinical Microbiology, Sirjan School of Medical Sciences, P.O. Box 78169-16338, Sirjan, Iran.
| | - Alireza Ahmadi
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
- Department of Laboratory Sciences, Faculty of Paramedicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ebrahim Kouhsari
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran.
- Department of Laboratory Sciences, Faculty of Paramedicine, Golestan University of Medical Sciences, Gorgan, Iran.
- Laboratory Sciences Research Center, Faculty of Paramedical Sciences, Golestan University of Medical Sciences, Negative Floor 1, Gorgan-Sari Road, P.O. Box: 4918936316, Gorgan, Golestan Province, Iran.
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Ayalew S, Wegayehu T, Taye H, Wassie L, Girma S, Berg S, Mihret A. Drug Resistance Conferring Mutation and Genetic Diversity of Mycobacterium tuberculosis Isolates in Tuberculosis Lymphadenitis Patients; Ethiopia. Infect Drug Resist 2021; 14:575-584. [PMID: 33623398 PMCID: PMC7894881 DOI: 10.2147/idr.s298683] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 01/31/2021] [Indexed: 12/16/2022] Open
Abstract
Background Tuberculosis lymphadenitis (TBLN) is a growing public health concern in Ethiopia. However, there is limited information available on gene mutations conferring drug resistance and genetic diversity of M. tuberculosis isolates from TBLN patients. Methods Drug resistance and genetic diversity analysis were done on 91 M. tuberculosis isolates from culture positive TBLN patients collected between 2016 and 2017. Detection of mutations conferring resistance was carried out using GenoType MTBDRplus VER 2.0. Thereafter, isolates were typed using spoligotyping. Results Out of the 91 strains, mutations conferring resistance to rifampicin (RIF) and isoniazid (INH) were observed in two (2.2%) and six (6.6%) isolates, respectively. The two RIF resistant isolates displayed a mutation at codon 531 in the rpoB gene with amino acid change of S531L. Among the six INH resistant strains, four isolates had shown mutation at the KatG gene at codon 315 with amino acid change of S315T, one isolate had a mutation at the inhA gene at codon 15 with amino acid change of C15T and one isolate had a mutation at the inhA gene with unknown amino acid change. All drug resistant isolates were from treatment naive TBLN patients. The dominantly identified Spoligo International Types (SITs) were SIT25, SIT149, and SIT53, respectively; these accounted for 43% of the total number of strains. The isolates were grouped into four main lineages; Lineage 1 (2, 2.2%), Lineage 3 (38, 41.7%), Lineage 4 (49, 53.8%) and Lineage 7 (2, 2.2%). Four out of six (66.7%) isolates with drug resistance conferring mutations belonged to clustered strains (strains with shared SIT). Conclusion The detection of drug resistant conferring mutation in treatment naïve TBLN patients together with detection of drug resistant isolates among clustered strains might suggest resistant strains' transmission in the community. This needs to be carefully considered to prevent the spread of drug resistant clones in the country.
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Affiliation(s)
- Sosina Ayalew
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia.,Department of Biology, College of Natural Sciences, Arba Minch University (AMU), Arba Minch, Ethiopia
| | - Teklu Wegayehu
- Department of Biology, College of Natural Sciences, Arba Minch University (AMU), Arba Minch, Ethiopia
| | - Hawult Taye
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Liya Wassie
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Selfu Girma
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Stefan Berg
- Bacteriology Department, Animal and Plant Health Agency, Weybridge, UK
| | - Adane Mihret
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
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