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Faye LM, Hosu MC, Oostvogels S, Dippenaar A, Warren RM, Sineke N, Vasaikar S, Apalata T. The Detection of Mutations and Genotyping of Drug-Resistant Mycobacterium tuberculosis Strains Isolated from Patients in the Rural Eastern Cape Province. Infect Dis Rep 2023; 15:403-416. [PMID: 37489395 PMCID: PMC10366782 DOI: 10.3390/idr15040041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/01/2023] [Accepted: 07/06/2023] [Indexed: 07/26/2023] Open
Abstract
Drug-resistant tuberculosis (DR-TB) is still a major public health concern in South Africa. Mutations in M. tuberculosis can cause varying levels of phenotypic resistance to anti-TB medications. There have been no prior studies on gene mutations and the genotyping of DR-TB in the rural Eastern Cape Province; hence, we aimed to identify DR-TB mutations, genetic diversity, and allocated lineages among patients in this area. Using Xpert® MTB/RIF, we assessed the rifampin resistance of sputum samples collected from 1157 patients suspected of having tuberculosis. GenoType MTBDR plus VER 2.0 was used for the detection of mutations causing resistance to anti-TB medications. The next step was to spoligotype 441 isolates. The most prevalent rifampin resistance-conferring mutations were in rpoB codon S531L in INH-resistant strains; the katG gene at codon S315TB and the inhA gene at codon C-15TB had the most mutations; 54.5% and 24.7%, respectively. In addition, 24.6% of strains showed mutations in both the rpoB and inhA genes, while 69.9% of strains showed mutations in both the katG and rpoB genes. Heteroresistance was seen in 17.9% of all cases in the study. According to spoligotyping analysis, Beijing families predominated. Investigation of the evolutionary lineages of M. tuberculosis isolates can be carried out using the information provided by the study's diversity of mutations. In locations wherein these mutations have been discovered, decision-making regarding the standardization of treatment regimens or individualized treatment may be aided by the detection frequency of rpoB, katG, and inhA mutations in various study areas.
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Affiliation(s)
- Lindiwe M Faye
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
| | - Mojisola C Hosu
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
| | - Selien Oostvogels
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, BE-2000 Antwerp, Belgium
| | - Anzaan Dippenaar
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, BE-2000 Antwerp, Belgium
| | - Robin M Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council, Parowvallei, Cape Town 7505, South Africa
- Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Ncomeka Sineke
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
| | - Sandeep Vasaikar
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
| | - Teke Apalata
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
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Bokop C, Faye LM, Apalata T. Analysis of Discordance between Genotypic and Phenotypic Assays for Rifampicin-Resistant Mycobacterium tuberculosis Isolated from Healthcare Facilities in Mthatha. Pathogens 2023; 12:909. [PMID: 37513756 PMCID: PMC10384316 DOI: 10.3390/pathogens12070909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/05/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
The study sought to determine the rate of discordant results between genotypic and phenotypic tests for the diagnosis of drug-resistant tuberculosis (DR-TB). Sputum samples and cultured isolates from suspected DR-TB patients were, respectively, analyzed for Mycobacterium tuberculosis by Xpert® MTB/RIF (Cepheid, Sunnyvale, CA, USA) and line probe assays (LPA) (Hain, Nehren, Germany). Discrepant rifampicin (RMP)-resistant results were confirmed using BACTEC MGIT960 (BD, New York, NY, USA). Of the 224 RMP-resistant results obtained by Xpert MTB/RIF, 5.4% were susceptible to RMP by LPA. MGIT960 showed a 75% agreement with LPA. The discrepancy was attributed to either heteroresistance or DNA contamination during LPA testing in 58.3% of cases. In 25% of the samples showing agreement in RMP resistance between Xpert MTB/RIF and MGIT960, the discrepancy was attributed to laboratory errors causing false RMP susceptible results with LPA. In 16.7% of the cases, the discrepancy was attributed to false RMP susceptible results with Xpert MTB/RIF. Out of the 224 isolates, susceptibility to isoniazid (INH) by LPA was performed in 73.7% RMP-resistant isolates, of which, 80.6% were resistant. All RMP-resistant isolates by Xpert MTB/RIF were confirmed in 98.5% by LPA if TB isolates were resistant to INH, but were only confirmed in 81.3% if TB isolates were susceptible to INH (p < 0.001). In conclusion, laboratory errors should be considered when investigating discordant results.
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Affiliation(s)
- Carine Bokop
- Division of Medical Microbiology, Department of Laboratory Medicine and Pathology, Faculty of Health Sciences, Walter Sisulu University, Mthatha 5099, Eastern Cape, South Africa
| | - Lindiwe M Faye
- Department of Laboratory Medicine and Pathology, Faculty of Health Sciences and National Health Laboratory Services (NHLS), Walter Sisulu University, Mthatha 5099, Eastern Cape, South Africa
| | - Teke Apalata
- Department of Laboratory Medicine and Pathology, Faculty of Health Sciences and National Health Laboratory Services (NHLS), Walter Sisulu University, Mthatha 5099, Eastern Cape, South Africa
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Faye LM, Hosu MC, Iruedo J, Vasaikar S, Nokoyo KA, Tsuro U, Apalata T. Treatment Outcomes and Associated Factors among Tuberculosis Patients from Selected Rural Eastern Cape Hospitals: An Ambidirectional Study. Trop Med Infect Dis 2023; 8:315. [PMID: 37368733 DOI: 10.3390/tropicalmed8060315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/27/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
An essential metric for determining the efficacy of tuberculosis (TB) control programs is the evaluation of TB treatment outcomes; this study was conducted to investigate treatment outcomes and associated factors among tuberculosis patients in rural areas of Eastern Cape, South Africa. Assessing treatment outcomes is fundamental to facilitating the End TB Strategy's set target. Clinic records from 457 patients with DR-TB were examined for data collection while 101 patients were followed up prospectively. Data were analyzed using Stata version 17.0. The odds ratio and 95% confidence interval were calculated to check the association between variables. p ≤ 0.05 was considered statistically significant. Of the 427 participants, 65.8% had successful treatment whilst 34.2% had unsuccessful TB treatment. A total of 61.2% and 39% of the HIV-positive and HIV-negative participants had a successful TB treatment whilst 66% and 34% of both HIV-negative and positive participants had unsuccessful TB treatment. From the 101 patients that were followed up, smokers took longer to have treatment outcomes compared to non-smokers. In the study with HIV/TB co-infection, men predominated. HIV and tuberculosis co-infection made therapy difficult with unfavorable effects on TB management. The treatment success rate (65.8%) was lower than the WHO threshold standard with a high proportion of patients being lost to the follow up. The co-infection of tuberculosis and HIV resulted in undesirable treatment outcomes. Strengthening TB surveillance and control is recommended.
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Affiliation(s)
- Lindiwe M Faye
- Department of Laboratory Medicine and Pathology, Walter Sisulu University and National Health Laboratory Services (NHLS), Private Bag X5117, Mthatha 5099, South Africa
| | - Mojisola C Hosu
- Department of Laboratory Medicine and Pathology, Walter Sisulu University and National Health Laboratory Services (NHLS), Private Bag X5117, Mthatha 5099, South Africa
| | - Joshua Iruedo
- Department of Family Medicine, Walter Sisulu University, Private Bag X5117, Mthatha 5099, South Africa
| | - Sandeep Vasaikar
- Department of Laboratory Medicine and Pathology, Walter Sisulu University and National Health Laboratory Services (NHLS), Private Bag X5117, Mthatha 5099, South Africa
| | - Kolisa A Nokoyo
- Wits School of Public Health, 27 St Andrew Road, Parktown, Johannesburg 2193, South Africa
| | - Urgent Tsuro
- Department of Public Health, Walter Sisulu University, Private Bag X5117, Mthatha 5099, South Africa
| | - Teke Apalata
- Department of Laboratory Medicine and Pathology, Walter Sisulu University and National Health Laboratory Services (NHLS), Private Bag X5117, Mthatha 5099, South Africa
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Faye LM, Hosu MC, Vasaikar S, Dippenaar A, Oostvogels S, Warren RM, Apalata T. Spatial Distribution of Drug-Resistant Mycobacterium tuberculosis Infections in Rural Eastern Cape Province of South Africa. Pathogens 2023; 12:pathogens12030475. [PMID: 36986397 PMCID: PMC10059723 DOI: 10.3390/pathogens12030475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/05/2023] [Accepted: 03/08/2023] [Indexed: 03/30/2023] Open
Abstract
Tuberculosis (TB), an infectious airborne disease caused by Mycobacterium tuberculosis (Mtb), is a serious public health threat reported as the leading cause of morbidity and mortality worldwide. South Africa is a high-TB-burden country with TB being the highest infectious disease killer. This study investigated the distribution of Mtb mutations and spoligotypes in rural Eastern Cape Province. The Mtb isolates included were 1157 from DR-TB patients and analysed by LPA followed by spoligotyping of 441 isolates. The distribution of mutations and spoligotypes was done by spatial analysis. The rpoB gene had the highest number of mutations. The distribution of rpoB and katG mutations was more prevalent in four healthcare facilities, inhA mutations were more prevalent in three healthcare facilities, and heteroresistant isolates were more prevalent in five healthcare facilities. The Mtb was genetically diverse with Beijing more prevalent and largely distributed. Spatial analysis and mapping of gene mutations and spoligotypes revealed a better picture of distribution.
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Affiliation(s)
- Lindiwe M Faye
- Department of Laboratory Medicine and Pathology, Walter Sisulu University and National Health Laboratory Services (NHLS), Private Bag X5117, Mthatha 5099, South Africa
| | - Mojisola C Hosu
- Department of Laboratory Medicine and Pathology, Walter Sisulu University and National Health Laboratory Services (NHLS), Private Bag X5117, Mthatha 5099, South Africa
| | - Sandeep Vasaikar
- Department of Laboratory Medicine and Pathology, Walter Sisulu University and National Health Laboratory Services (NHLS), Private Bag X5117, Mthatha 5099, South Africa
| | - Anzaan Dippenaar
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, BE-2000 Antwerp, Belgium
| | - Selien Oostvogels
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, BE-2000 Antwerp, Belgium
| | - Rob M Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Teke Apalata
- Department of Laboratory Medicine and Pathology, Walter Sisulu University and National Health Laboratory Services (NHLS), Private Bag X5117, Mthatha 5099, South Africa
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