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Torokaa PR, Majigo MV, Kileo H, Urio L, Mbwana MR, Monah MC, Ntibabara SS, Kimambo J, Seleman P, Franklin C, Balama R, Kisonga RM, Joachim A. The pattern of rpoB gene mutation of Mycobacterium tuberculosis and predictors of rifampicin resistance detected by GeneXpert MTB/RIF assay in Tanzania. PLoS One 2024; 19:e0296563. [PMID: 39186753 PMCID: PMC11346956 DOI: 10.1371/journal.pone.0296563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 08/12/2024] [Indexed: 08/28/2024] Open
Abstract
INTRODUCTION Antimicrobial resistance in Mycobacterium tuberculosis (MTB) poses a significant challenge to tuberculosis (TB) management worldwide. Rifampicin resistance (RR) has been associated with the rpoB gene mutation. No study was conducted in Tanzania to determine the commonest mutation. The inconsistent findings from various studies support the need to determine whether reported mutation patterns are applicable in our setting. We determined the frequency of rpoB gene mutation and factors associated with RR, which were detected using GeneXpert MTB/RIF assay. METHODS We conducted a retrospective cross-sectional study involving data from the National Tuberculosis and Leprosy Program database from 2020 to 2022 for cases investigated using GeneXpert MTB/RIF assay. Descriptive analysis was performed to determine the frequency of categorical variables. The chi-square test and logistic regression analysis assessed the relationship between the independent variables and outcome. The 95% confidence interval and a significance level of p<0.05 were used to assess the strength of association. RESULTS A total of 56,004 participants had a status of MTB and RR, where 38,705/56,004 (69.11%) were males. Probe E mutation (codon 529-533), 89/219 (40.64%) was predominant. Human immunodeficiency virus (HIV)-positive patients had a higher gene mutation, 134/10601 (1.26%) than HIV-negative, 306/45016 (0.68%) (p<0.001). Patients with both pulmonary and extra-pulmonary TB had about four times greater odds of developing rifampicin resistance (AOR 3.88, 95%CI: 1.80-8.32). RR was nearly nine times higher in previously treated patients than new patients (AOR 8.66, 95% CI: 6.97-10.76). HIV-positive individuals had nearly twice the odds of developing RR than HIV-negative individuals (AOR 1.91, 95%CI: 1.51-2.42). CONCLUSION The rate of RR was lower compared to other studies in Tanzania, with probe E mutations the most prevalent. Patients with disseminated TB, HIV co-infection and those with prior exposure to anti-TB had more risk of RR. The findings highlight the need to strengthen surveillance of multidrug-resistant TB among high risk patients.
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Affiliation(s)
- Peter Richard Torokaa
- Muhimbili University of Health and Allied Sciences, School of Public Health and Social Sciences, Dar es Salaam, Tanzania
- Tanzania Field Epidemiology and Laboratory Training Program, Dar es Salaam, Tanzania
| | - Mtebe V. Majigo
- Muhimbili University of Health and Allied Sciences, School of Diagnostic Medicine, Dar es Salaam, Tanzania
| | - Heledy Kileo
- Muhimbili University of Health and Allied Sciences, School of Diagnostic Medicine, Dar es Salaam, Tanzania
| | - Loveness Urio
- Tanzania Field Epidemiology and Laboratory Training Program, Dar es Salaam, Tanzania
| | - Mariam R. Mbwana
- Muhimbili University of Health and Allied Sciences, School of Public Health and Social Sciences, Dar es Salaam, Tanzania
- Tanzania Field Epidemiology and Laboratory Training Program, Dar es Salaam, Tanzania
| | - Mariam C. Monah
- Muhimbili University of Health and Allied Sciences, School of Public Health and Social Sciences, Dar es Salaam, Tanzania
- Tanzania Field Epidemiology and Laboratory Training Program, Dar es Salaam, Tanzania
| | - Sephord Saul Ntibabara
- Muhimbili University of Health and Allied Sciences, School of Public Health and Social Sciences, Dar es Salaam, Tanzania
- Tanzania Field Epidemiology and Laboratory Training Program, Dar es Salaam, Tanzania
| | - Jasper Kimambo
- Muhimbili University of Health and Allied Sciences, School of Public Health and Social Sciences, Dar es Salaam, Tanzania
- Tanzania Field Epidemiology and Laboratory Training Program, Dar es Salaam, Tanzania
| | - Paschal Seleman
- Ministry of Health, National TB and Leprosy Programme, Dodoma, Tanzania
| | - Collins Franklin
- Ministry of Health, National TB and Leprosy Programme, Dodoma, Tanzania
| | - Robert Balama
- Ministry of Health, National TB and Leprosy Programme, Dodoma, Tanzania
| | - Riziki M. Kisonga
- Ministry of Health, National TB and Leprosy Programme, Dodoma, Tanzania
| | - Agricola Joachim
- Muhimbili University of Health and Allied Sciences, School of Diagnostic Medicine, Dar es Salaam, Tanzania
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Wu G, Wang J, Xu X, Wei H, Cai L, Liu L. Factors influencing false-positive results of rifampicin resistance detected by Xpert MTB/RIF: A retrospective study in Zhejiang, China. Heliyon 2024; 10:e31680. [PMID: 38841482 PMCID: PMC11152942 DOI: 10.1016/j.heliyon.2024.e31680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 05/20/2024] [Accepted: 05/20/2024] [Indexed: 06/07/2024] Open
Abstract
Objective This study aimed to explore the factors influencing false-positive results for rifampicin resistance (RIF-R) detected using Xpert MTB/RIF (Xpert). Methods This retrospective analysis included the clinical data of patients from September 2019 to February 2023. The chi-square and rank sum tests were used to compare differences in patient characteristics between the true-positive and false-positive groups. Logistic regression was used to analyze the factors influencing false positives in the detection of RIF-R by Xpert. Results A total of 384 patients were included. Logistic regression analysis revealed that, with mutation of probe E as the reference, mutations on probe A or C (OR = 72.68, P < 0.001), probe D (OR = 6.44, P < 0.001), and multiple probes (OR = 5.94, P = 0.002) were associated with false-positive results in Xpert detection of RIF-R. Taking probe delay ΔCt <4 as the reference, ΔCt (4-5.9) (OR = 13.54, P < 0.001), ΔCt (6-7.9) (OR = 48.08, P < 0.001) probe delays were associated with false positives in Xpert detection of RIF-R. When very low quantification is accompanied by a probe delay, the probability of false-positive RIF-R detection can reach 80 %. Conclusions Clinicians should consider factors such as probe mutation type, probe delay, and very low quantification accompanied by probe delay when interpreting Xpert results, which can reduce the misdiagnosis of tuberculosis drug resistance.
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Affiliation(s)
- Guihua Wu
- Centre of Laboratory Medicine, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang, China
| | - Jing Wang
- Centre of Laboratory Medicine, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang, China
| | - Xiaoqun Xu
- Centre of Laboratory Medicine, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang, China
| | - Hui Wei
- Centre of Laboratory Medicine, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang, China
| | - Long Cai
- Centre of Laboratory Medicine, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang, China
| | - Libin Liu
- Centre of Laboratory Medicine, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang, China
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Nie Q, Sun D, Zhu M, Tu S, Chen N, Chen H, Zhou Y, Yao G, Zhang X, Zhang T, Yang C, Tao L. Phenotypic drug susceptibility characterization and clinical outcomes of tuberculosis strains with A-probe mutation by GeneXpert MTB/RIF. BMC Infect Dis 2023; 23:832. [PMID: 38012619 PMCID: PMC10680243 DOI: 10.1186/s12879-023-08509-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 08/03/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND GeneXpert MTB/RIF (Xpert) assay was applied widely to detect Mycobacterium tuberculosis (MTB) and rifampicin resistance. METHODS Retrospectively investigated the association among treatment histories, phenotypic drug susceptibility testing (pDST) results, and clinical outcomes of patients infected with probe A absent mutation isolate confirmed by Xpert. RESULTS 63 patients with only probe A absent mutation and 40 with additional pDST results were analyzed. 24 (60.0%) patients had molecular-phenotypic discordant rifampicin (RIF) susceptibility testing results, including 12 (12/13, 92.3%) new tuberculosis (TB) patients and 12 (12/27, 44.4%) retreated ones. 28 (28/39, 71.8%) retreated patients received first-line treatment regime within two years with failed outcomes. New patients had better treatment outcomes than retreated ones (successful: 83.3% VS. 53.8%; P value = 0.02). The clinical results of RIF-susceptible TB confirmed by pDST were not better than RIF-resistant TB (successful: 62.5% VS. 50.0%; P value = 0.43). INH-resistant TB and INH-susceptible TB had similar treatment outcomes too (successful: 61.5% VS. 50.0%; P value = 0.48). 11 (11/12, 91.7%) new patients treated with the short treatment regimen (STR) had successful outcomes. CONCLUSIONS More than half of mono probe A absent isolates had RIF molecular-phenotypic discordance results, especially in new patients. Probe A mutations were significantly associated with unsuccessful clinical outcomes, whether the pDST results were RIF susceptible or not. STR was the best choice for new patients. TRIAL REGISTRATION retrospectively registered in Wuhan Jinyintan Hospital (No. 2021-KY-16).
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Affiliation(s)
- Qi Nie
- College of Life Sciences and Health, Wuhan University of Science and Technology, Hubei, China
- Department of MDR/RR-TB, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong, Wuhan Research Center for Communicable Disease Diagnosis and Treatment, University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Chinese Academy of Medical Sciences, Hubei, China
| | - Dan Sun
- Department of Interventional therapy, Wuhan Pulmonary Hospital, Hubei, China
| | - Muxin Zhu
- Department of MDR/RR-TB, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong, Wuhan Research Center for Communicable Disease Diagnosis and Treatment, University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Chinese Academy of Medical Sciences, Hubei, China
| | - Shengjin Tu
- Department of MDR/RR-TB, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong, Wuhan Research Center for Communicable Disease Diagnosis and Treatment, University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Chinese Academy of Medical Sciences, Hubei, China
| | - Nanshan Chen
- Department of MDR/RR-TB, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong, Wuhan Research Center for Communicable Disease Diagnosis and Treatment, University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Chinese Academy of Medical Sciences, Hubei, China
| | - Hua Chen
- Department of MDR/RR-TB, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong, Wuhan Research Center for Communicable Disease Diagnosis and Treatment, University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Chinese Academy of Medical Sciences, Hubei, China
| | - Yong Zhou
- Department of MDR/RR-TB, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong, Wuhan Research Center for Communicable Disease Diagnosis and Treatment, University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Chinese Academy of Medical Sciences, Hubei, China
| | - Ge Yao
- Department of MDR/RR-TB, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong, Wuhan Research Center for Communicable Disease Diagnosis and Treatment, University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Chinese Academy of Medical Sciences, Hubei, China
| | - Xiaoqing Zhang
- Department of MDR/RR-TB, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong, Wuhan Research Center for Communicable Disease Diagnosis and Treatment, University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Chinese Academy of Medical Sciences, Hubei, China
| | - Tongcun Zhang
- College of Life Sciences and Health, Wuhan University of Science and Technology, Hubei, China.
| | - Chengfeng Yang
- Hubei Provincial Center for Disease Control and Prevention, Hubei, China.
| | - Lixuan Tao
- Emergency Department, Puren Hospital, Wuhan University of science and technology, Hubei, China.
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Scott LE, Shapiro AN, Da Silva MP, Tsoka J, Jacobson KR, Emch M, Moultrie H, Jenkins HE, Moore D, Van Rie A, Stevens WS. Integrating Molecular Diagnostics and GIS Mapping: A Multidisciplinary Approach to Understanding Tuberculosis Disease Dynamics in South Africa Using Xpert MTB/RIF. Diagnostics (Basel) 2023; 13:3163. [PMID: 37891984 PMCID: PMC10606157 DOI: 10.3390/diagnostics13203163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/30/2023] [Accepted: 09/14/2023] [Indexed: 10/29/2023] Open
Abstract
An investigation was carried out to examine the use of national Xpert MTB/RIF data (2013-2017) and GIS technology for MTB/RIF surveillance in South Africa. The aim was to exhibit the potential of using molecular diagnostics for TB surveillance across the country. The variables analysed include Mycobacterium tuberculosis (Mtb) positivity, the mycobacterial proportion of rifampicin-resistant Mtb (RIF), and probe frequency. The summary statistics of these variables were generated and aggregated at the facility and municipal level. The spatial distribution patterns of the indicators across municipalities were determined using the Moran's I and Getis Ord (Gi) statistics. A case-control study was conducted to investigate factors associated with a high mycobacterial load. Logistic regression was used to analyse this study's results. There was striking spatial heterogeneity in the distribution of Mtb and RIF across South Africa. The median patient age, urban setting classification, and number of health care workers were found to be associated with the mycobacterial load. This study illustrates the potential of using data generated from molecular diagnostics in combination with GIS technology for Mtb surveillance in South Africa. Spatially targeted interventions can be implemented in areas where high-burden Mtb persists.
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Affiliation(s)
- Lesley Erica Scott
- Wits Diagnostic Innovation Hub, Faculty of Health Science, University of the Witwatersrand, Johannesburg 2093, South Africa; (M.P.D.S.); (J.T.); (W.S.S.)
| | - Anne Nicole Shapiro
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA; (A.N.S.); (H.E.J.)
| | - Manuel Pedro Da Silva
- Wits Diagnostic Innovation Hub, Faculty of Health Science, University of the Witwatersrand, Johannesburg 2093, South Africa; (M.P.D.S.); (J.T.); (W.S.S.)
- National Priority Program of the National Health Laboratory Services (NHLS), Johannesburg 2131, South Africa
| | - Jonathan Tsoka
- Wits Diagnostic Innovation Hub, Faculty of Health Science, University of the Witwatersrand, Johannesburg 2093, South Africa; (M.P.D.S.); (J.T.); (W.S.S.)
| | - Karen Rita Jacobson
- Division of Infectious Diseases, Boston Medical Center, Boston, MA 02118, USA;
| | - Michael Emch
- Department of Epidemiology, University of North Carolina School, Chapel Hill, NC 27127, USA;
- Department of Geography and Environment, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Harry Moultrie
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2192, South Africa;
| | - Helen Elizabeth Jenkins
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA; (A.N.S.); (H.E.J.)
| | - David Moore
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK;
| | - Annelies Van Rie
- Faculty of Medicine and Health Sciences, University of Antwerp, 2000 Antwerpen, Belgium;
| | - Wendy Susan Stevens
- Wits Diagnostic Innovation Hub, Faculty of Health Science, University of the Witwatersrand, Johannesburg 2093, South Africa; (M.P.D.S.); (J.T.); (W.S.S.)
- National Priority Program of the National Health Laboratory Services (NHLS), Johannesburg 2131, South Africa
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Dahiya B, Mehta N, Soni A, Mehta PK. Diagnosis of extrapulmonary tuberculosis by GeneXpert MTB/RIF Ultra assay. Expert Rev Mol Diagn 2023; 23:561-582. [PMID: 37318829 DOI: 10.1080/14737159.2023.2223980] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 06/06/2023] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Diagnosis of extrapulmonary tuberculosis (EPTB) is an arduous task owing to different anatomical locations, unusual clinical presentations, and sparse bacillary load in clinical specimens. Although GeneXpert® MTB/RIF is a windfall in TB diagnostics including EPTB, it yields low sensitivities but high specificities in many EPTB specimens. To further improve the sensitivity of GeneXpert®, GeneXpert® Ultra, a fully nested real-time PCR targeting IS6110, IS1081 and rpoB (Rv0664) has been endorsed by the WHO (2017), wherein melt curve analysis is utilized to detect rifampicin-resistance (RIF-R). AREA COVERED We described the assay chemistry/work design of Xpert Ultra and evaluated its performance in several EPTB types, that is, TB lymphadenitis, TB pleuritis, TB meningitis, and so on, against the microbiological reference standard or composite reference standard. Notably, Xpert Ultra exhibited better sensitivities than Xpert, but mostly at the compensation of specificity values. Moreover, Xpert Ultra exhibited low false-negative and false-positive RIF-R results, compared with Xpert. We also detailed other molecular tests, that is, Truenat MTBTM/TruPlus, commercial real-time PCR, line probe assay, and so on, for EPTB diagnosis. EXPERT OPINION A combination of clinical features, imaging, histopathological findings, and Xpert Ultra are adequate for definite EPTB diagnosis so as to initiate an early anti-tubercular therapy.
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Affiliation(s)
- Bhawna Dahiya
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
| | - Neeru Mehta
- Department of Medical Electronics, Ambedkar Delhi Skill & Entrepreneurship University, Shakarpur, New Delhi, India
| | - Aishwarya Soni
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
- Department of Biotechnology, Deenbandhu Chhotu Ram University of Science and Technology, Murthal, Sonipat, India
| | - Promod K Mehta
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
- Microbiology Department, Faculty of Allied Health Sciences, SGT University, Budhera, Gurgaon, India
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Nielsen MC, Clarner P, Paroha R, Lee S, Thwe PM, Ren P. Comparison of Analytical Sensitivity (Limit of Detection) of Xpert MTB/RIF and Xpert MTB/RIF Ultra for Non-Sputum Specimens. Pathogens 2023; 12:pathogens12020157. [PMID: 36839429 PMCID: PMC9962446 DOI: 10.3390/pathogens12020157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/15/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023] Open
Abstract
Tuberculosis (TB) is a significant public health threat and has remained a leading cause of death in many parts of the world. Rapid and accurate testing and timely diagnosis can improve treatment efficacy and reduce new exposures. The Cepheid Xpert® MTB/RIF tests have two marketed products (US-IVD and Ultra) that are widely accepted for diagnosis of TB but have not yet been approved for non-sputum specimens. Despite numerous studies in the literature, no data for the analytical sensitivity of these two products on the non-sputum samples are available to date. This is the first study that systematically determined the analytical sensitivities of both US-IVD and Ultra tests on cerebrospinal fluid (CSF), tissue, and bronchoalveolar lavage (BAL). The limits of detection (LoDs) on the US-IVD test for both Mycobacterium tuberculosis and rifampin resistance in CFU/mL, respectively, were as follows: CSF (3.3 and 4.6), tissue (15 and 23), and bronchoalveolar lavage (BAL) (45 and 60), and on the Ultra test: CSF (0.16 and 2.7), tissue (0.11 and 12), and BAL (0.65, and 7.5). Overall, the analytical sensitivities of the Ultra test were substantially better than US-IVD for all sample types tested. This study provided a foundation for using either the US-IVD or Ultra test for the early detection of both pulmonary and extrapulmonary (EP) TB. Furthermore, using Ultra could result in higher TB case detection rates in subjects with paucibacillary TB and EP TB, positively impacting WHO goals to eradicate TB.
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Affiliation(s)
- Marisa C. Nielsen
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Paula Clarner
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Ruchi Paroha
- Department of Immunology and Microbiology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Sunhee Lee
- Department of Immunology and Microbiology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Phyu M. Thwe
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Pathology, Infectious Disease Testing, Montefiore Medical Center, Bronx, NY 10467, USA
- Correspondence: (P.M.T.); (P.R.)
| | - Ping Ren
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Correspondence: (P.M.T.); (P.R.)
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Akalu GT, Tessema B, Petros B. High proportion of RR-TB and mutations conferring RR outside of the RRDR of the rpoB gene detected in GeneXpert MTB/RIF assay positive pulmonary tuberculosis cases, in Addis Ababa, Ethiopia. PLoS One 2022; 17:e0277145. [PMID: 36584037 PMCID: PMC9803184 DOI: 10.1371/journal.pone.0277145] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/13/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Globally, TB is the leading cause of infectious disease morbidity and mortality with many diagnostic uncertainties. Access to affordable and rapid diagnostics remained a major challenge for many developing countries which bear the greatest burden of TB delaying the initiation time to treatment. OBJECTIVE This study aimed to assess the GeneXpert MTBRIF assay probe utility for the detection of pulmonary TB and Rifampicin-resistant TB cases in Addis Ababa, Ethiopia. MATERIALS AND METHODS A cross-sectional study was performed from October 2019 to July 2020 in Saint Peter TB Specialized Hospital in Addis Ababa metropolitan area, Ethiopia. This study enrolled 216 clinically suspected new presumptive pulmonary TB cases confirmed by GeneXpert MTB/RIF Assay. Sociodemographic and clinical characteristics were captured using a structured tool. Data were entered in Microsoft Excel 2019, checked for inconsistency, cleaned promptly, and exported to IBM SPSS Statistics for Windows, Version 26.0. Armonk, N.Y: IBM Corp, the USA for analysis. Descriptive analysis and binary and multivariate logistics regression were performed and all statistical significance was determined at a 95% confidence level. RESULTS The majority of the study participants, 55.1% [119/216] were males aged 6-80 years. The prevalence of RR MTB was 11.11% [24/216]. A higher proportion of RR TB was found in female patients [54.2%, 13/24], in patients in the age group of 30-50 years [45.8%, 11/24], in married individuals [62.5%, 15/24], in persons whose residence is urban [79.2%, 19/24], in persons who had a previous history of TB symptoms [100%, 24/24], in persons who had a history of contact with active and LTBI [33.3%, 8/24], and in persons who had a history of HIV and IDUs [41.7%, 10/24]. Occupation (AOR 22.868, 95% CI 1.655-316.022, p = 0.019), history of previous PTB+ (AOR 4.222, 95% CI 1.020-17.47, p = 0.047), and history of HIV and IDUs (AOR 4.733, 95% CI 1.416-15.819, p = 0.012) were independent predictors associated with RR-TB emergence. The commonest mutation 62.5% [15/24] was found in probe E (codons 529-533) region. There was no mutation associated with probe A (codons 507-511), probe B (codons 511-518), and probe C (codons 518-523) regions, as well as no combination of missed probes, was revealed. However, 12.5% [3/24] of RR TB patients were found without unidentified missed probe types detected outside of the RRDR. The delta Ct max was >4.0 and the highest proportion of 35.6% [77/216] RR TB was detected in samples of medium DNA load. CONCLUSION The proportion of RR-TB we observed in this study was high. Similarly, a higher proportion of RR TB was detected outside of the RRDR. Moreover, a significant number of the GeneXpert MTB/RIF Assay probes were identified as unhybridized and this critical observation would mean that most of the probes had no or minimal utility in this geographical region. This calls for further studies to uncover mutation in the rpoB gene conferring RR and reshape TB triage and definite diagnostic algorithm in Ethiopia.
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Affiliation(s)
- Gizachew Taddesse Akalu
- Department of Microbial, Cellular, and Molecular Biology, Faculty of Life Sciences, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Microbiology, Immunology, and Parasitology, St. Paul’s Hospital Millennium Medical College, Addis Ababa, Ethiopia
- * E-mail:
| | - Belay Tessema
- Department of Medical Microbiology, School of Biomedical and Laboratory Medicine, University of Gondar, Gondar, Ethiopia
| | - Beyene Petros
- Department of Microbial, Cellular, and Molecular Biology, Faculty of Life Sciences, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
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Muacevic A, Adler JR, V. Bhesania Hodiwala A, Wagh S, Patil MS. Evaluation of Rpoβ Gene and Its Various Mutants in Multidrug-Resistant Tuberculosis Cases by GeneXpert Method. Cureus 2022; 14:e31249. [PMID: 36514629 PMCID: PMC9733785 DOI: 10.7759/cureus.31249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 11/08/2022] [Indexed: 11/11/2022] Open
Abstract
INTRODUCTION India is one of the countries in the world which contribute to the global burden of multidrug-resistant tuberculosis (MDR-TB). GeneXpert is a method recommended by the World Health Organization (WHO) that uses five overlapping probes (Probe A to E) to detect mutation in the beta subunit of ribonucleic acid (RNA) polymerase gene (Rpoβ) responsible for rifampicin resistance in Mycobacterium tuberculosis (MTB). METHOD All the pulmonary and extrapulmonary samples received in tuberculosis (TB) laboratory for testing of MTB from January 2018 to December 2020 were analyzed for bacillary load and rifampicin resistance was identified by analyzing the number of missing probes. RESULTS During the study period, a total of 10,021 samples were tested for MDR-TB. Out of those samples, 2674 samples were positive for MTB of which 2321 were pulmonary samples and 353 were extra-pulmonary samples. Rifampicin resistance was detected in 385 pulmonary samples and 63 extrapulmonary samples. These samples were further differentiated according to the bacillary load. The highest number of mutations was observed in Probe E followed by Probe B, Probe A, and Probe D, and the lowest was observed in Probe C. Also, mutations were associated when all probes were present or a few combinations of probes were missing. CONCLUSION GeneXpert assay is a rapid molecular method that detected MTB and rifampicin resistance with a two-hour turnaround. It uses molecular beacons to detect mutation in the Rpoβ gene. This study can be useful in analyzing the prevalence and epidemiology of MTB in a particular demographic area and also the addition of a few more probes can enhance the identification of the mutation in other codons and therefore better therapeutic interventions can be developed accordingly.
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Sailo CV, Lalremruata R, Sanga Z, Fela V, Kharkongor F, Chhakchhuak Z, Chhakchhuak L, Nemi L, Zothanzama J, Kumar NS. Distribution and frequency of common mutations in rpoB gene of Mycobacterium tuberculosis detected by Xpert MTB/RIF and identification of residential areas of Rifampicin Resistant-TB cases: A first retrospective study from Mizoram, Northeast India. J Clin Tuberc Other Mycobact Dis 2022; 29:100342. [DOI: 10.1016/j.jctube.2022.100342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Worku G, Gumi B, Girma M, Mohammedbirhan B, Diriba G, Seid G, Getu M, Amare M, Sinshaw W, Ashagre W, Tschopp R, Carruth L, Ameni G. Drug sensitivity of clinical isolates of Mycobacterium tuberculosis and its association with bacterial genotype in the Somali region, Eastern Ethiopia. Front Public Health 2022; 10:942618. [PMID: 36062084 PMCID: PMC9428271 DOI: 10.3389/fpubh.2022.942618] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/25/2022] [Indexed: 01/21/2023] Open
Abstract
Background Drug resistance is becoming a major bottleneck for tuberculosis (TB) control programs in countries with high TB burdens. Although several studies were conducted on the drug sensitivity of Mycobacterium tuberculosis (M. tuberculosis) in central Ethiopia, there is a lack of data on the drug sensitivity of M. tuberculosis in the peripheral regions of the country including in the Somali region. Therefore, the objective of this study was to evaluate the drug sensitivity of M. tuberculosis and its association with bacterial genotype and evaluate the performance of Xpert MTB/RIF (Xpert) in detecting resistance to rifampicin (RIF). Methods A total of 302 M. tuberculosis were tested using the BD BACTEC-Mycobacteria Growth Indicator Tube 960 (MGIT 960) system for their drug sensitivity to the first-line anti-TB drugs. Besides, the drug sensitivity of 10 multidrug-resistant (MDR) M. tuberculosis isolates was evaluated for the second-line anti-TB drugs. Additionally, 177 of the 302 isolates were tested for genotypic drug resistance using Xpert. Chi-square and Fisher's exact tests were used for the evaluation of the association between variables and drug sensitivity. Results The overall prevalence of resistance to at least one drug was 11.6% (95% CI: 7.9-15.2%), while the prevalence of MDR was 3.3% (95% CI: 1.3-5.3%). Two of the 10 MDR isolates were resistant to capreomycin. The spoligotype Shared International Type (SIT) 149 was significantly associated with either monoresistance or MDR (p < 0.05). Of the 177 isolates tested by Xpert, 6.2% (11/177) were RIF-resistant. Discordant between Xpert and MGIT 960 was observed in one isolate and linked with probe-binding delay (ΔCT max = 5.8). The sensitivity and specificity of the Xpert assay were 100 and 99.4%, respectively, while its positive and negative predictive values were 90.9 and 100%, respectively. Conclusion The magnitude of MDR M. tuberculosis in the Somali region of Ethiopia was higher than the national prevalence of MDR-TB warranting the strengthening of the TB control program in the Somali region. Besides, drug resistance was associated with SIT 149 spoligotype (genotype). The Xpert assay was observed to have high sensitivity and specificity in detecting RIF-resistant M. tuberculosis, which is encouraging for its application widely.
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Affiliation(s)
- Getnet Worku
- College of Medicine and Health Sciences, Jigjiga University, Jigjiga, Ethiopia,Animal Health and Zoonotic Unit, Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Balako Gumi
- Animal Health and Zoonotic Unit, Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Musse Girma
- Animal Health and Zoonotic Unit, Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Getu Diriba
- Ethiopian Public Health Institute, National Tuberculosis Reference Laboratory, Addis Ababa, Ethiopia
| | - Getachew Seid
- Ethiopian Public Health Institute, National Tuberculosis Reference Laboratory, Addis Ababa, Ethiopia
| | - Melak Getu
- Ethiopian Public Health Institute, National Tuberculosis Reference Laboratory, Addis Ababa, Ethiopia
| | - Misikir Amare
- Ethiopian Public Health Institute, National Tuberculosis Reference Laboratory, Addis Ababa, Ethiopia
| | - Waganeh Sinshaw
- Ethiopian Public Health Institute, National Tuberculosis Reference Laboratory, Addis Ababa, Ethiopia
| | - Wondimu Ashagre
- One-Health Unit, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Rea Tschopp
- One-Health Unit, Armauer Hansen Research Institute, Addis Ababa, Ethiopia,Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Lauren Carruth
- School of International Service, American University, Washington DC, DC, United States
| | - Gobena Ameni
- Animal Health and Zoonotic Unit, Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia,Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, United Arab Emirates,*Correspondence: Gobena Ameni ;
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WITHDRAWN: Analysis of the application value of molecular diagnostic technology of mycobacterium tuberculosis. J Clin Tuberc Other Mycobact Dis 2022. [DOI: 10.1016/j.jctube.2022.100330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Peñata A, Pérez C, Castaño T, Bustamante J, Ospina S. Distribución y frecuencia de potenciales mutaciones asociadas con la resistencia a rifampicina en el gen rpoB de Mycobacterium tuberculosis detectadas mediante un método molecular automatizado. REVISTA DE LA FACULTAD DE MEDICINA 2022. [DOI: 10.15446/revfacmed.v71n1.98079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Introducción. La tuberculosis continúa siendo un problema de salud pública agravado por la resistencia de Mycobacterium tuberculosis a los fármacos. Más del 95% de cepas de M. tuberculosis resistentes a rifampicina (RIF) poseen mutaciones en una región del gen rpoB. Xpert® MTB/RIF es un sistema de biología molecular que, mediante 5 sondas (A, B, C, D, E) que conforman las secuencias del gen rpoB, permite identificar mutaciones en la región determinante de resistencia a la RIF de este gen.
Objetivo. Describir la distribución y frecuencia de potenciales mutaciones asociadas con la resistencia a RIF en el gen rpoB de M. tuberculosis detectadas en muestras pulmonares y extrapulmonares usando el método Xpert® MTB/RIF.
Materiales y métodos. Estudio retrospectivo. Se analizaron 66 muestras positivas para M. tuberculosis resistente a RIF procesadas por el sistema GeneXpert MTB/RIF entre enero de 2011 y julio de 2019 en un hospital universitario de Medellín, Colombia. De acuerdo con el software Dx System del instrumento GenXpert, se determinó que había una potencial mutación y resistencia a RIF, si la sondas no se unían a su secuencia complementaria natural o si se presentaba un atraso en la unión (delta CT >4) en relación con las otras sondas por presencia de una secuencia anormal. Los datos se analizaron mediante estadística descriptiva.
Resultados. De las 66 muestras (48 pulmonares y 18 extrapulmonares), el 63.64% eran de hombres y la edad media de los participantes fue 39.60 ± 17.69 años. La frecuencia y distribución de mutaciones fue la siguiente: sonda E: 38 mutaciones (57.58%); B: 16 (24.24%), D: 8 (12.12%); A: 3 (4.54%) y D&E: 1 (1.52%). No se detectó ninguna mutación en la sonda C.
Conclusiones. Las mutaciones asociadas a la resistencia a RIF en el gen rpoB de M. tuberculosis detectadas por el método Xpert® MTB/RIF se encontraron principalmente en la sonda E (codones 529–533). Por el contrario, en la sonda C no se no se detectó ninguna mutación.
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Rajendran P, Kumar MP, Thiruvengadam K, Sreenivasan P, Veeraraghavan T, Ramalingam R, Hasini S, Dhanaraju T, Kuppamuthu R, Shanmugam S, Frederick A, Padmapriyadarsini C. Characterization of probes associated with rifampicin resistance in M.tuberculosis detected by GenXpert from a national reference laboratory at Chennai. Tuberculosis (Edinb) 2022; 133:102182. [DOI: 10.1016/j.tube.2022.102182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/29/2022] [Accepted: 02/06/2022] [Indexed: 11/29/2022]
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Gupta NK, Ish P. Tuberculosis with discordant drug resistance patterns- A diagnostic dilemma. Indian J Tuberc 2022; 69:8-11. [PMID: 35074156 DOI: 10.1016/j.ijtb.2021.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 05/22/2021] [Indexed: 06/14/2023]
Abstract
Programmatic management of drug-resistant tuberculosis (PMDT) guidelines in India specify the use of cartridge based nucleic acid amplification test (CBNAAT) and Line probe assay (LPA) for early diagnosis of drug-resistant Tuberculosis. However, discrepancy among these genotypic tests (CBNAAT and LPA) or with the phenotypic DST in real practice poses a clinical dilemma. The usual solutions are to rely on methods with short turnaround times like CBNAAT and LPA to start an initial regimen. The culture and DST results, that are typically available after at least a few weeks, are used to modify the regimen if required. This practice is based on the fact that culture and DST based sensitivity patterns are considered the gold standard for diagnosing and drug resistance. DNA sequencing by pyrosequencing, Sanger sequencing and next generation sequencing (NGS) are being evaluated; their future availability may help in early clarifications in discordant drug resistance patterns. Such tests are costly and have limited availability, however, in view of immense benefit to detect TB Drug-resistant phenotypes, national guidelines plan to scale up their use in national and well-performing intermediate TB reference laboratories.
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Affiliation(s)
- Neeraj Kumar Gupta
- Department of Pulmonary, Critical Care and Sleep Medicine and Nodal Officer for DOTS, VMMC and Safdarjung Hospital, New Delhi, India
| | - Pranav Ish
- Department of Pulmonary, Critical Care and Sleep Medicine, VMMC and Safdarjung Hospital, New Delhi, India.
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Abdullah SF. Sociodemographic profile of mono rifampicin-resistant (RR) cases among pulmonary tuberculosis patients, Erbil, Iraq, 2015–2020. MEDICAL JOURNAL OF BABYLON 2022. [DOI: 10.4103/mjbl.mjbl_75_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Baikunje N, Hosmane GB, Y. SK. Endobronchial Ultrasound in Evaluating Mediastinal Lymphadenopathy. JOURNAL OF HEALTH AND ALLIED SCIENCES NU 2021. [DOI: 10.1055/s-0041-1725241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractTuberculosis can involve most of the body parts, and tubercular lymphadenitis is common. But isolated involvement of mediastinal lymph nodes without lung parenchymal involvement is rare in adults. A 45-year-old lady presented with subcarinal lymph node enlargement. A conventional transbronchial needle aspiration done at a local hospital was inconclusive. Endobronchial ultrasound-guided transbronchial needle aspiration was done. Cytology showed epithelioid histiocytes and caseous necrosis. Stain for acid-fast bacilli and cartridge-based nucleic acid amplification test for tuberculosis were positive. Endobronchial ultrasound-guided transbronchial needle aspiration is a minimally invasive bronchoscopic technique to visualize and sample mediastinal lymph nodes. However, its availability is limited to specific centers and expertise is required to interpret images and take diagnostic samples.
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Affiliation(s)
- Nandakishore Baikunje
- Department of Pulmonary Medicine, K.S. Hegde Medical Academy, Nitte (Deemed to be) University, Nityananda Nagara, Deralakatte, Mangaluru, Karnataka, India
| | - Giridhar Belur Hosmane
- Department of Pulmonary Medicine, K.S. Hegde Medical Academy, Nitte (Deemed to be) University, Nityananda Nagara, Deralakatte, Mangaluru, Karnataka, India
| | - Sunil Kumar Y.
- Department of Pathology, K.S. Hegde Medical Academy, Nitte (Deemed to be) University, Nityananda Nagara, Deralakatte, Mangaluru, Karnataka, India
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Seifert M, Aung HT, Besler N, Harris V, Mar TT, Colman RE, Rodwell TC, Aung ST. Age and sex distribution of Mycobacterium tuberculosis infection and rifampicin resistance in Myanmar as detected by Xpert MTB/RIF. BMC Infect Dis 2021; 21:781. [PMID: 34372793 PMCID: PMC8351356 DOI: 10.1186/s12879-021-06296-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/31/2021] [Indexed: 11/28/2022] Open
Abstract
Background Detection of tuberculosis disease (TB) and timely identification of Mycobacterium tuberculosis (Mtb) strains that are resistant to treatment are key to halting tuberculosis transmission, improving treatment outcomes, and reducing mortality. Methods We used 332,657 Xpert MTB/RIF assay results, captured as part of the Myanmar Data Utilization Project, to characterize Mtb test positivity and rifampicin resistance by both age and sex, and to evaluate risk factors associated with rifampicin resistance. Results Overall, 70% of individuals diagnosed with TB were males. Test positivity was higher among males (47%) compared to females (39%). The highest positivity by age occurred among individuals aged 16–20, with test positivity for females (65%) higher than for males (57%). Although a greater absolute number of males were rifampicin resistant, a greater proportion of females (11.4%) were rifampicin resistant as compared to males (9.3%). In the multivariate model, history of previous treatment, age less than 30, testing in the Yangon region, and female sex were significantly positively associated with rifampicin resistance after adjusting for HIV status and year test was performed. Conclusions Our results indicate that young adults were more likely to test positive for TB and be identified as rifampicin resistant compared to older adults.
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Affiliation(s)
- Marva Seifert
- University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA.
| | | | - Nicole Besler
- University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Victoria Harris
- FIND, the global alliance for diagnostics, Campus Biotech, 9 Chemin des Mines -, 1202, Geneva, Switzerland
| | - Tin Tin Mar
- Ministry of Health and Sports, Office No. 4, Naypyitaw, Myanmar
| | - Rebecca E Colman
- University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Timothy C Rodwell
- University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Si Thu Aung
- Ministry of Health and Sports, Office No. 4, Naypyitaw, Myanmar
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Laniado-Laborín R. Clinical Interpretation of Drug Susceptibility Tests in Tuberculosis. CURRENT RESPIRATORY MEDICINE REVIEWS 2021. [DOI: 10.2174/1573398x16999201007164411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
:
Prompt and accurate diagnosis of drug resistance is essential for optimal treatment of
drug-resistant tuberculosis. However, only 20% of the more than half a million patients eligible for
the treatment of MDR-TB/RR-TB receive an appropriate drug regimen. Drug-resistant TB regimens
must include a sufficient number of effective medications, a significant challenge for clinicians
worldwide, as most are forced to make therapeutic decisions without any, or very little information
on drug susceptibility testing. Although phenotypic DST is still commonly regarded as the
gold standard for determining M. tuberculosis susceptibility to antituberculosis drugs, it has several
limitations, mainly its prolonged turnaround time. Molecular methods based on M. tuberculosis genomic
DNA sequencing have been developed during the past two decades, to identify the most
common mutations involved in drug resistance. The Xpert
®
MTB/RIF is a real-time polymerase
chain reaction that offers results in less than two hours and has an overall sensitivity for rifampin resistance
of 96% and 98% specificity. Line probe assays (LPAs) are commercial DNA strip-based
tests for detecting the most frequent mutations responsible for resistance to rifampin, isoniazid, fluoroquinolones,
and second-line injectable drugs.
:
Discrepancies between phenotypic and genotyping methods are a problem that the clinician will
face in everyday practice. However, any resistance result (with any type of test) in a person with
risk factors for harboring resistant microorganisms should be considered appropriate while the results
of complementary tests are available.
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Affiliation(s)
- Rafael Laniado-Laborín
- Clinica y Laboratorio de Tuberculosis, Hospital General Tijuana, ISESALUD, Mexicali, Mexico
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