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Singhal R, Hingane S, Bhalla M, Sharma A, Ferdosh S, Tiwari A, Jayaswal P, Yadav RN, Arora J, Dewan RK, Sharma S. Evaluation of AAICare®-TB sequence analysis tool for accurate diagnosis of drug-resistant tuberculosis: A comparative study with TB-Profiler and Mykrobe. Tuberculosis (Edinb) 2024; 147:102515. [PMID: 38744006 DOI: 10.1016/j.tube.2024.102515] [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: 11/10/2023] [Revised: 04/27/2024] [Accepted: 05/07/2024] [Indexed: 05/16/2024]
Abstract
A rapid and comprehensive drug susceptibility test is essential for eliminating drug resistant tuberculosis. Next generation sequencing (NGS) based susceptibility testing is being explored as a potential substitute for the conventional phenotypic and genotypic testing methods. However, the adoption of NGS based genotypic susceptibility testing depends on the availability of simple, accurate and efficient analysis tools. This preliminary study aimed to evaluate the performance of a Mycobacterium tuberculosis (Mtb) genome analysis pipeline, AAICare®-TB, for susceptibility prediction, in comparison to two widely used gDST prediction tools, TB-Profiler and Mykrobe. This study was performed in a National Reference Laboratory in India on presumptive drug-resistant tuberculosis (DR-TB) isolates. Whole genome sequences of the 120 cultured isolates were obtained through Illumina sequencing on a MiSeq platform. Raw sequences were simultaneously analysed using the three tools. Susceptibility prediction reports thus generated, were compared to estimate the total concordance and discordance. WHO mutation catalogue (1st edition, 2021) was used as the reference standard for categorizing the mutations. In this study, AAICare®-TB was able to predict drug resistance status for First Line (Streptomycin, Isoniazid, Rifampicin, Ethambutol and Pyrazinamide) and Second Line drugs (Fluoroquinolones, Second Line Injectables and Ethionamide) in 93 samples along with lineage and hetero-resistance as per the WHO guidelines.
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Affiliation(s)
- Ritu Singhal
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, 110030, India.
| | - Smita Hingane
- AarogyaAI® Innovations Pvt. Ltd., No. 677, 1st Floor, Suite 918, 13th Cross, Sector 1, HSR Layout, Bangalore, 560102, Karnataka, India
| | - Manpreet Bhalla
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, 110030, India
| | - Aniruddh Sharma
- AarogyaAI® Innovations Pvt. Ltd., No. 677, 1st Floor, Suite 918, 13th Cross, Sector 1, HSR Layout, Bangalore, 560102, Karnataka, India
| | - Sehnaz Ferdosh
- AarogyaAI® Innovations Pvt. Ltd., No. 677, 1st Floor, Suite 918, 13th Cross, Sector 1, HSR Layout, Bangalore, 560102, Karnataka, India
| | - Avlokita Tiwari
- AarogyaAI® Innovations Pvt. Ltd., No. 677, 1st Floor, Suite 918, 13th Cross, Sector 1, HSR Layout, Bangalore, 560102, Karnataka, India
| | - Praapti Jayaswal
- AarogyaAI® Innovations Pvt. Ltd., No. 677, 1st Floor, Suite 918, 13th Cross, Sector 1, HSR Layout, Bangalore, 560102, Karnataka, India
| | - Raj Narayan Yadav
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, 110030, India
| | - Jyoti Arora
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, 110030, India
| | - Ravindra Kumar Dewan
- National Institute of Tuberculosis and Respiratory Diseases, New Delhi, 110030, India
| | - Sangeeta Sharma
- National Institute of Tuberculosis and Respiratory Diseases, New Delhi, 110030, India
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Wulandari DA, Hartati YW, Ibrahim AU, Pitaloka DAE, Irkham. Multidrug-resistant tuberculosis. Clin Chim Acta 2024; 559:119701. [PMID: 38697459 DOI: 10.1016/j.cca.2024.119701] [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: 03/31/2024] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/05/2024]
Abstract
One of predominant contributors to global mortality is tuberculosis (TB), an infection caused by Mycobacterium tuberculosis (MTB). Inappropriate and ineffectual treatment can lead to the development of drug-resistant TB. One of the most common forms of drug-resistant TB is multidrug-resistant tuberculosis (MDR-TB), caused by mutations in the rpoB and katG genes that lead to resistance to anti-TB drugs, rifampicin (RIF) and isoniazid (INH), respectively. Although culturing remains the gold standard, it is not rapid thereby delaying potential treatment and potentially increasing the incidence of MDR-TB. In contrast, molecular techniques provide a highly sensitive and specific alternative. This review discusses the classification of biomarkers used to detect MDR-TB, some of the commonly used anti-TB drugs, and DNA mutations in MTB that lead to anti-TB resistance. The objective of this review is to increase awareness of the need for rapid and precise detection of MDR-TB cases to decrease morbidity and mortality of this infectious disease worldwide.
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Affiliation(s)
- Dika Apriliana Wulandari
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang Km 21, 45363, Indonesia
| | - Yeni Wahyuni Hartati
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang Km 21, 45363, Indonesia
| | - Abdullahi Umar Ibrahim
- Department of Biomedical Engineering, Near East University, Mersin 10, Nicosia 99010, Turkey; Research Center for Science, Technology and Engineering (BILTEM), Near East University, 99138 Nicosia, TRNC, Mersin 10, Turkey
| | - Dian Ayu Eka Pitaloka
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Bandung, Indonesia
| | - Irkham
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang Km 21, 45363, Indonesia.
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Sanchini A, Lanni A, Giannoni F, Mustazzolu A. Exploring diagnostic methods for drug-resistant tuberculosis: A comprehensive overview. Tuberculosis (Edinb) 2024; 148:102522. [PMID: 38850839 DOI: 10.1016/j.tube.2024.102522] [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: 03/19/2024] [Revised: 05/14/2024] [Accepted: 05/30/2024] [Indexed: 06/10/2024]
Abstract
Despite available global efforts and funding, Tuberculosis (TB) continues to affect a considerable number of patients worldwide. Policy makers and stakeholders set clear goals to reduce TB incidence and mortality, but the emergence of multidrug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB) complicate the reach of these goals. Drug-resistance TB needs to be diagnosed rapidly and accurately to effectively treat patients, prevent the transmission of MDR-TB, minimise mortality, reduce treatment costs and avoid unnecessary hospitalisations. In this narrative review, we provide a comprehensive overview of laboratory methods for detecting drug resistance in MTB, focusing on phenotypic, molecular and other drug susceptibility testing (DST) techniques. We found a large variety of methods used, with the BACTEC MGIT 960 being the most common phenotypic DST and the Xpert MTB/RIF being the most common molecular DST. We emphasise the importance of integrating phenotypic and molecular DST to address issues like resistance to new drugs, heteroresistance, mixed infections and low-level resistance mutations. Notably, most of the analysed studies adhered to the outdated definition of XDR-TB and did not consider the pre-XDR definition, thus posing challenges in aligning diagnostic methods with the current landscape of TB resistance.
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Affiliation(s)
| | - Alessio Lanni
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy.
| | - Federico Giannoni
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy.
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Rupasinghe P, Ashraf A, Barreda N, Parveen S, Zubair M, Calderon R, Asif S, Hirani N, Chingisova L, Bulane A, Hang PT, Ha DT, Ardizzoni E, Kursheed N, De Rijk WB, Rigouts L, Guglielmetti L, Mitnick C, de Jong BC. Reduced critical concentration might not have improved MGIT-based DST's sensitivity to rifampicin. Antimicrob Agents Chemother 2024; 68:e0170123. [PMID: 38534101 PMCID: PMC11064607 DOI: 10.1128/aac.01701-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024] Open
Affiliation(s)
- Praharshinie Rupasinghe
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Azka Ashraf
- The Indus Hospital laboratory, Karachi, Pakistan
| | | | | | | | | | - Sunil Asif
- The Indus Hospital laboratory, Karachi, Pakistan
| | - Nilma Hirani
- Department of Microbiology, Sir JJ Hospital, Mumbai, India
| | | | - Atang Bulane
- Center for Tuberculosis, National Institute of Communicable Diseases, Mohakhali, South Africa
| | - Pham Thu Hang
- Regional Tuberculosis Reference Lab, Ho Chi Minh, Vietnam
| | - Doan Thu Ha
- National Tuberculosis Reference Lab, Hanoi, Vietnam
| | - Elisa Ardizzoni
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
| | | | | | - Leen Rigouts
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Lorenzo Guglielmetti
- Medical Department, MSF, Paris, France
- Sorbonne University, Centre d’Immunologie et des Maladies Infectieuses (Cimi-Paris), Paris, France
- AP-HP, Bactériologie-Hygiène, Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries, Paris, France
| | - Carol Mitnick
- Brigham and Women's Hospital, Boston, Massachusetts, USA
- Partners In Health, Boston, Massachusetts, USA
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Bouke C. de Jong
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
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Svensson E, Ketelsen H, Andres S, Folkvardsen DB, Hillemann D, Conteh O, Norman A, Niemann S, Lillebaek T, Kuhns M. Dual-centre evaluation of the FluoroType MTBDR version 2 assay for detection of Mycobacterium tuberculosis complex and resistance-conferring mutations in pulmonary and extrapulmonary samples from Denmark, Germany and Sierra Leone. Clin Microbiol Infect 2024:S1198-743X(24)00192-7. [PMID: 38621623 DOI: 10.1016/j.cmi.2024.04.006] [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: 11/06/2023] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/17/2024]
Abstract
OBJECTIVES We evaluated the ability of FluoroType MTBDR version 2 (FTv2; Hain Lifescience), a second-step real-time PCR assay, to simultaneously detect Mycobacterium tuberculosis complex (MTBC) DNA and mutations conferring resistance to rifampicin (RIF) and isoniazid (INH), in pulmonary and extrapulmonary samples from patients and compared them with corresponding cultures. METHODS FTv2 MTBC was evaluated on 1815 and 432 samples from Denmark (DK) and Germany (DE), respectively. RIF and INH resistance mutations were assessed in the German samples and 110 samples from Sierra Leone and subsequently compared to phenotypic antimicrobial susceptibility testing and a composite reference DNA (CRD) based on the GenoType MTBDR line-probe assay and Sanger sequencing or whole-genome sequencing. RESULTS Of the 584 (557 smear-negative) Danish and 277 (85 smear-negative) German sputum samples, 42 (16) and 246 (54) were culture positive, and 44 (18) and 222 (35) were FTv2 positive, providing an FTv2 sensitivity and specificity of 0.86 (0.63) and 0.98 (DK), 0.90 (0.65) and 1.00 (DE), respectively. The count, sensitivities, and specificities for all pulmonary samples were 1434, 0.79, and 0.99 (DK) and 347, 0.86, and 1.00 (DE), respectively; for extrapulmonary samples, 381, 0.33, 0.99 (DK) and 83, 0.50, and 1.00 (DE). The valid count, sensitivity, and specificity compared with CRD for detecting resistance mutations were RIF 355, 0.99, 0.96, and INH 340, 1.00, and 0.98, respectively. DISCUSSION FTv2 reliably detects MTBC DNA in pulmonary and extrapulmonary samples and detects resistance mutations for INH and RIF resistance in inhA promoter, katG, and rpoB genes.
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Affiliation(s)
- Erik Svensson
- Statens Serum Institut, International Reference Laboratory of Mycobacteriology, WHO Supranational Reference Laboratory, Copenhagen, Denmark.
| | - Hannah Ketelsen
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Sönke Andres
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Dorte Bek Folkvardsen
- Statens Serum Institut, International Reference Laboratory of Mycobacteriology, WHO Supranational Reference Laboratory, Copenhagen, Denmark
| | - Doris Hillemann
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Ousman Conteh
- National Tuberculosis Reference Laboratory, Lakka Government Hospital, Freetown, Sierra Leone
| | - Anders Norman
- Statens Serum Institut, International Reference Laboratory of Mycobacteriology, WHO Supranational Reference Laboratory, Copenhagen, Denmark
| | - Stefan Niemann
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany; Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Troels Lillebaek
- Statens Serum Institut, International Reference Laboratory of Mycobacteriology, WHO Supranational Reference Laboratory, Copenhagen, Denmark; Department of Public Health, University of Copenhagen, Denmark
| | - Martin Kuhns
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
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Liu A, Liu S, Lv K, Zhu Q, Wen J, Li J, Liang C, Huang X, Gong C, Sun Q, Gu H. Rapid detection of multidrug resistance in tuberculosis using nanopore-based targeted next-generation sequencing: a multicenter, double-blind study. Front Microbiol 2024; 15:1349715. [PMID: 38495513 PMCID: PMC10940340 DOI: 10.3389/fmicb.2024.1349715] [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: 12/05/2023] [Accepted: 02/13/2024] [Indexed: 03/19/2024] Open
Abstract
Background Resistance to anti-tuberculous drugs is a major challenge in the treatment of tuberculosis (TB). We aimed to evaluate the clinical availability of nanopore-based targeted next-generation sequencing (NanoTNGS) for the diagnosis of drug-resistant tuberculosis (DR-TB). Methods This study enrolled 253 patients with suspected DR-TB from six hospitals. The diagnostic efficacy of NanoTNGS for detecting Mycobacterium tuberculosis and its susceptibility or resistance to first- and second-line anti-tuberculosis drugs was assessed by comparing conventional phenotypic drug susceptibility testing (pDST) and Xpert MTB/RIF assays. NanoTNGS can be performed within 12 hours from DNA extraction to the result delivery. Results NanoTNGS showed a remarkable concordance rate of 99.44% (179/180) with the culture assay for identifying the Mycobacterium tuberculosis complex. The sensitivity of NanoTNGS for detecting drug resistance was 93.53% for rifampicin, 89.72% for isoniazid, 85.45% for ethambutol, 74.00% for streptomycin, and 88.89% for fluoroquinolones. Specificities ranged from 83.33% to 100% for all drugs tested. Sensitivity for rifampicin-resistant tuberculosis using NanoTNGS increased by 9.73% compared to Xpert MTB/RIF. The most common mutations were S531L (codon in E. coli) in the rpoB gene, S315T in the katG gene, and M306V in the embB gene, conferring resistance to rifampicin, isoniazid, and ethambutol, respectively. In addition, mutations in the pncA gene, potentially contributing to pyrazinamide resistance, were detected in 32 patients. Other prevalent variants, including D94G in the gyrA gene and K43R in the rpsL gene, conferred resistance to fluoroquinolones and streptomycin, respectively. Furthermore, the rv0678 R94Q mutation was detected in one sample, indicating potential resistance to bedaquiline. Conclusion NanoTNGS rapidly and accurately identifies resistance or susceptibility to anti-TB drugs, outperforming traditional methods. Clinical implementation of the technique can recognize DR-TB in time and provide guidance for choosing appropriate antituberculosis agents.
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Affiliation(s)
- Aimei Liu
- Department of Tuberculosis, Guangxi Zhuang Autonomous Region Chest Hospital, Liuzhou, Guangxi, China
| | - Sang Liu
- Department of Tuberculosis, Guangxi Zhuang Autonomous Region Chest Hospital, Liuzhou, Guangxi, China
| | - Kangyan Lv
- Department of Tuberculosis, Guangxi Zhuang Autonomous Region Chest Hospital, Liuzhou, Guangxi, China
| | - Qingdong Zhu
- Department of Tuberculosis, The Fourth People's Hospital of Nanning, Nanning, Guangxi, China
| | - Jun Wen
- Department of Pulmonary Medicine, The Third People's Hospital of Guilin, Guilin, Guangxi, China
| | - Jianpeng Li
- Department of Pulmonary Medicine, The Third People's Hospital of Wuzhou, Wuzhou, Guangxi, China
| | - Chengyuan Liang
- Department of Infectious Diseases, The People's Hospital of Baise, Baise, Guangxi, China
| | - Xuegang Huang
- Department of Infectious Diseases, The First People's Hospital of Fangchenggang, Fangchenggang, Guangxi, China
| | - Chunming Gong
- Department of Tuberculosis, Guangxi Zhuang Autonomous Region Chest Hospital, Liuzhou, Guangxi, China
| | - Qingfeng Sun
- Department of Tuberculosis, Guangxi Zhuang Autonomous Region Chest Hospital, Liuzhou, Guangxi, China
| | - Hongcang Gu
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China
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Batisti Biffignandi G, Chindelevitch L, Corbella M, Feil EJ, Sassera D, Lees JA. Optimising machine learning prediction of minimum inhibitory concentrations in Klebsiella pneumoniae. Microb Genom 2024; 10:001222. [PMID: 38529944 PMCID: PMC10995625 DOI: 10.1099/mgen.0.001222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/07/2024] [Indexed: 03/27/2024] Open
Abstract
Minimum Inhibitory Concentrations (MICs) are the gold standard for quantitatively measuring antibiotic resistance. However, lab-based MIC determination can be time-consuming and suffers from low reproducibility, and interpretation as sensitive or resistant relies on guidelines which change over time. Genome sequencing and machine learning promise to allow in silico MIC prediction as an alternative approach which overcomes some of these difficulties, albeit the interpretation of MIC is still needed. Nevertheless, precisely how we should handle MIC data when dealing with predictive models remains unclear, since they are measured semi-quantitatively, with varying resolution, and are typically also left- and right-censored within varying ranges. We therefore investigated genome-based prediction of MICs in the pathogen Klebsiella pneumoniae using 4367 genomes with both simulated semi-quantitative traits and real MICs. As we were focused on clinical interpretation, we used interpretable rather than black-box machine learning models, namely, Elastic Net, Random Forests, and linear mixed models. Simulated traits were generated accounting for oligogenic, polygenic, and homoplastic genetic effects with different levels of heritability. Then we assessed how model prediction accuracy was affected when MICs were framed as regression and classification. Our results showed that treating the MICs differently depending on the number of concentration levels of antibiotic available was the most promising learning strategy. Specifically, to optimise both prediction accuracy and inference of the correct causal variants, we recommend considering the MICs as continuous and framing the learning problem as a regression when the number of observed antibiotic concentration levels is large, whereas with a smaller number of concentration levels they should be treated as a categorical variable and the learning problem should be framed as a classification. Our findings also underline how predictive models can be improved when prior biological knowledge is taken into account, due to the varying genetic architecture of each antibiotic resistance trait. Finally, we emphasise that incrementing the population database is pivotal for the future clinical implementation of these models to support routine machine-learning based diagnostics.
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Affiliation(s)
- Gherard Batisti Biffignandi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
- MRC Centre for Global Infectious Disease Analysis, Imperial College, London, England, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Leonid Chindelevitch
- MRC Centre for Global Infectious Disease Analysis, Imperial College, London, England, UK
| | - Marta Corbella
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Edward J. Feil
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
| | - Davide Sassera
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
- Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - John A. Lees
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
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Maitre T, Baulard A, Aubry A, Veziris N. Optimizing the use of current antituberculosis drugs to overcome drug resistance in Mycobacterium tuberculosis. Infect Dis Now 2024; 54:104807. [PMID: 37839674 DOI: 10.1016/j.idnow.2023.104807] [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: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 10/17/2023]
Abstract
Antibiotic-resistant tuberculosis continues to be one of the major threats to global tuberculosis control. After a hiatus of over 40 years in antituberculosis drug development, the last decade has seen a resurgence of research, yielding a number of promising compounds in the tuberculosis drug pipeline, with some that are now game changers in the treatment of MDRTB. Despite this progress, there are still obstacles restricting the use of these molecules as first-line drugs. The quick appearance of bacteria resistant to these new treatments highlights a continuing need to fuel the discovery and development of new molecules. With this in mind, alternative strategies aimed at optimizing the utilization of existing antituberculosis agents are currently under evaluation. They are focused on enhancing the efficacy of antibiotics against their bacterial targets, primarily by augmenting the quantity of antibiotic that engages with these targets. This objective can be achieved through two primary approaches: (1) Provided that toxicity concerns are not a limiting factor, increased dosing is a viable avenue, as demonstrated by rifampicin, isoniazid, and fluoroquinolones, for which escalated dosing has been effective; and (2) Employing enhancers such as drug activator boosters (ethionamide), efflux pump inhibitors, or hydrolytic enzyme inhibitors (kanamycin) can elevate the concentration of antibiotics in bacterial cells. These strategies offer the potential to mitigate antibiotic obsolescence and complement the discovery of new antibiotics.
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Affiliation(s)
- Thomas Maitre
- Sorbonne Université, Centre d'Immunologie et des Maladies Infectieuses (Cimi-Paris), UMR 1135, Paris, France; Service de Pneumologie et d'Oncologie Thoracique, Centre constitutif maladies rares, Hôpital Tenon, AP-HP, Sorbonne-Université, Paris, France.
| | - Alain Baulard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Alexandra Aubry
- Sorbonne Université, Centre d'Immunologie et des Maladies Infectieuses (Cimi-Paris), UMR 1135, Paris, France; AP-HP, Sorbonne-Universite, Hôpital Pitié Salpêtrière, Laboratoire de Bactériologie-Hygiene, Centre National de Référence des Mycobactéries, Paris France
| | - Nicolas Veziris
- Sorbonne Université, Centre d'Immunologie et des Maladies Infectieuses (Cimi-Paris), UMR 1135, Paris, France; AP-HP, Sorbonne-Université, Hôpital Saint-Antoine, Département de Bactériologie, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Hôpital Pitié-Salpêtrière, Paris, France
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9
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Qadir M, Faryal R, Khan MT, Khan SA, Zhang S, Li W, Wei DQ, Tahseen S, McHugh TD. Phenotype versus genotype discordant rifampicin susceptibility testing in tuberculosis: implications for a diagnostic accuracy. Microbiol Spectr 2024; 12:e0163123. [PMID: 37982632 PMCID: PMC10783056 DOI: 10.1128/spectrum.01631-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/10/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE An accurate diagnosis of drug resistance in clinical isolates is an important step for better treatment outcomes. The current study observed a higher discordance rate of rifampicin resistance on Mycobacteria Growth Indicator Tube (MGIT) drug susceptibility testing (DST) than Lowenstein-Jenson (LJ) DST when compared with the rpoB sequencing. We detected a few novel mutations and their combination in rifampicin resistance isolates that were missed by MGIT DST and may be useful for the better management of tuberculosis (TB) treatment outcomes. Few novel deletions in clinical isolates necessitate the importance of rpoB sequencing in large data sets in geographic-specific locations, especially high-burden countries. We explored the discordance rate on MGIT and LJ, which is important for the clinical management of rifampicin resistance to avoid the mistreatment of drug-resistant TB. Furthermore, MGIT-sensitive isolates may be subjected to molecular methods of diagnosis for further confirmation and treatment options.
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Affiliation(s)
- Mehmood Qadir
- National TB Control Program, National TB Reference Laboratory, Islamabad, Pakistan
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Rani Faryal
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Tahir Khan
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nanyang, Henan, China
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, Lahore, Pakistan
| | - Sajjad Ahmed Khan
- National TB Control Program, National TB Reference Laboratory, Islamabad, Pakistan
| | - Shulin Zhang
- School of Medicine, Department of Immunology and Microbiology, Shanghai Jiao Tong University, Shanghai, China
| | - Weimin Li
- National Tuberculosis Clinical Lab of China, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Dong Qing Wei
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nanyang, Henan, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Peng Cheng Laboratory, Shenzhen, Guangdong, China
| | - Sabira Tahseen
- National TB Control Program, National TB Reference Laboratory, Islamabad, Pakistan
| | - Timothy D. McHugh
- Centre for Clinical Microbiology, University College London, London, United Kingdom
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10
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Li K, Hu Q, Liu J, Liu S, He Y. Effects of sputum bacillary load and age on GeneXpert and traditional methods in pulmonary tuberculosis: a 4-year retrospective comparative study. BMC Infect Dis 2023; 23:831. [PMID: 38012541 PMCID: PMC10680317 DOI: 10.1186/s12879-023-08832-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 11/18/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND The purpose of this study was to evaluate the diagnostic value of the GeneXpert® MTB/RIF (Xpert®), Auramine O staining method, and Lowenstein-Jensen medium for bacteriologically confirmed pulmonary tuberculosis and explore the effects of the sputum bacillary load (SBL) and qRT‒PCR threshold cycle (Ct) value on the detection methods. METHODS We retrospectively analysed the results in the Department of Infectious Disease for 49 months. The χ2 test was used to compare the performances of each method, receiver operating characteristic curve analysis was used to determine the optimal cut-off values, and the factors associated with a false-negative result from Xpert® were analysed by logistic regression. RESULTS Simultaneous analysis of 980 sputum specimens showed that the positive detection rate of Xpert® did not increase with increasing SBL, and there were differences between the three when SBL ≤ 1 + (all P < 0.05). There was a good negative correlation between the Ct value and the SBL (P < 0.0001). Age was an independent risk factor for false-negative Xpert® results (P = 0.029), and when Ct < 16, the diagnostic sensitivity and specificity were both 100.00%. The optimal cut-off Ct values for resegmentation based on the drug resistance classification were < 18.6, 18.6-34.1, and > 34.1 cycles. CONCLUSIONS Xpert® was not affected by SBL but it was by age, and it is more advantageous when SBL ≤ 1 + . The results regarding rifampicin resistance were reliable, and the novel Ct segmentation was a practical and more clinically meaningful classification method for diagnosing rifampicin resistance. These findings will help improve physicians' ability to accurately diagnose TB.
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Affiliation(s)
- Kui Li
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West YantaRoad, Xi'an, Shaanxi Province, 710061, China
- Department of Infectious Diseases, Ankang Central Hospital, 85 South Jinzhou Road, Ankang, Shaanxi Province, 725000, China
| | - Qianqian Hu
- Laboratory of Molecular Pathology and Tuberculosis Diseases, Ankang Central Hospital, 85 South Jinzhou Road, Ankang, Shaanxi Province, 725000, China
| | - Jun Liu
- Laboratory of Molecular Pathology and Tuberculosis Diseases, Ankang Central Hospital, 85 South Jinzhou Road, Ankang, Shaanxi Province, 725000, China
| | - Siyi Liu
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West YantaRoad, Xi'an, Shaanxi Province, 710061, China
| | - Yingli He
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West YantaRoad, Xi'an, Shaanxi Province, 710061, China.
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11
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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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12
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Rao M, Wollenberg K, Harris M, Kulavalli S, Thomas L, Chawla K, Shenoy VP, Varma M, Saravu K, Hande HM, Shanthigrama Vasudeva CS, Jeffrey B, Gabrielian A, Rosenthal A. Lineage classification and antitubercular drug resistance surveillance of Mycobacterium tuberculosis by whole-genome sequencing in Southern India. Microbiol Spectr 2023; 11:e0453122. [PMID: 37671895 PMCID: PMC10580826 DOI: 10.1128/spectrum.04531-22] [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: 11/13/2022] [Accepted: 07/03/2023] [Indexed: 09/07/2023] Open
Abstract
Whole-genome sequencing has created a revolution in tuberculosis management by providing a comprehensive picture of the various genetic polymorphisms with unprecedented accuracy. Studies mapping genomic heterogeneity in clinical isolates of Mycobacterium tuberculosis using a whole-genome sequencing approach from high tuberculosis burden countries are underrepresented. We report whole-genome sequencing results of 242 clinical isolates of culture-confirmed M. tuberculosis isolates from tuberculosis patients referred to a tertiary care hospital in Southern India. Phylogenetic analysis revealed that the isolates in our study belonged to five different lineages, with Indo-Oceanic (lineage 1, n = 122) and East-African Indian (lineage 3, n = 80) being the most prevalent. We report several mutations in genes conferring resistance to first and second line antitubercular drugs including the genes rpoB, katG, ahpC, inhA, fabG1, embB, pncA, rpsL, rrs, and gyrA. The majority of these mutations were identified in relatively high proportions in lineage 1. Our study highlights the utility of whole-genome sequencing as a potential supplemental tool to the existing genotypic and phenotypic methods, in providing expedited comprehensive surveillance of mutations that may be associated with antitubercular drug resistance as well as lineage characterization of M. tuberculosis isolates. Further larger-scale whole-genome datasets with linked minimum inhibition concentration testing are imperative for resolving the discrepancies between whole-genome sequencing and phenotypic drug sensitivity testing results and quantifying the level of the resistance associated with the mutations for optimization of antitubercular drug and precise dose selection in clinics. IMPORTANCE Studies mapping genetic heterogeneity of clinical isolates of M. tuberculosis for determining their strain lineage and drug resistance by whole-genome sequencing are limited in high tuberculosis burden settings. We carried out whole-genome sequencing of 242 M. tuberculosis isolates from drug-sensitive and drug-resistant tuberculosis patients, identified and collected as part of the TB Portals Program, to have a comprehensive insight into the genetic diversity of M. tuberculosis in Southern India. We report several genetic variations in M. tuberculosis that may confer resistance to antitubercular drugs. Further wide-scale efforts are required to fully characterize M. tuberculosis genetic diversity at a population level in high tuberculosis burden settings for providing precise tuberculosis treatment.
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Affiliation(s)
- Mahadev Rao
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Kurt Wollenberg
- Department of Health and Human Services, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael Harris
- Department of Health and Human Services, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Shrivathsa Kulavalli
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Levin Thomas
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Kiran Chawla
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Vishnu Prasad Shenoy
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Muralidhar Varma
- Department of Infectious Diseases, Kasturba Medical College, Manipal, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Kavitha Saravu
- Department of Infectious Diseases, Kasturba Medical College, Manipal, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - H. Manjunatha Hande
- Department of Medicine, Kasturba Medical College, Manipal, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | | | - Brendan Jeffrey
- Department of Health and Human Services, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrei Gabrielian
- Department of Health and Human Services, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Alex Rosenthal
- Department of Health and Human Services, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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13
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Lempens P, Van Deun A, Aung KJM, Hossain MA, Behruznia M, Decroo T, Rigouts L, de Jong BC, Meehan CJ. Borderline rpoB mutations transmit at the same rate as common rpoB mutations in a tuberculosis cohort in Bangladesh. Microb Genom 2023; 9:001109. [PMID: 37750750 PMCID: PMC10569737 DOI: 10.1099/mgen.0.001109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023] Open
Abstract
The spread of multidrug-resistant tuberculosis (MDR-TB) is a growing problem in many countries worldwide. Resistance to one of the primary first-line drugs, rifampicin, is caused by mutations in the Mycobacterium tuberculosis rpoB gene. So-called borderline rpoB mutations confer low-level resistance, in contrast to more common rpoB mutations which confer high-level resistance. While some borderline mutations show lower fitness in vitro than common mutations, their in vivo fitness is currently unknown. We used a dataset of 394 whole genome sequenced MDR-TB isolates from Bangladesh, representing around 44 % of notified MDR-TB cases over 6 years, to look at differences in transmission clustering between isolates with borderline rpoB mutations and those with common rpoB mutations. We found a relatively low percentage of transmission clustering in the dataset (34.8 %) but no difference in clustering between different types of rpoB mutations. Compensatory mutations in rpoA, rpoB, and rpoC were associated with higher levels of transmission clustering as were lineages two, three, and four relative to lineage one. Young people as well as patients with high sputum smear positive TB were more likely to be in a transmission cluster. Our findings show that although borderline rpoB mutations have lower in vitro growth potential this does not translate into lower transmission potential or in vivo fitness. Proper detection of these mutations is crucial to ensure they do not go unnoticed and spread MDR-TB within communities.
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Affiliation(s)
- Pauline Lempens
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | | | | | | | - Tom Decroo
- Unit of HIV and TB, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Leen Rigouts
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Bouke C. de Jong
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Conor J. Meehan
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biosciences, Nottingham Trent University, Nottingham, UK
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14
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Rigouts L, Keysers J, Rabab R, Fissette K, van Deun A, de Jong BC. GeneXpert MTB/RIF Ultra performance to detect uncommon rpoB mutations in Mycobacterium tuberculosis. BMC Res Notes 2023; 16:146. [PMID: 37452349 PMCID: PMC10347863 DOI: 10.1186/s13104-023-06394-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 06/18/2023] [Indexed: 07/18/2023] Open
Abstract
OBJECTIVE To investigate the performance of GeneXpert MTB/RIF Ultra to accurately detect rifampicin resistance for less common rpoB mutations that potentially confer phenotypic resistance, we tested 28 such Mycobacterium tuberculosis cultures with Xpert Ultra. RESULTS They represented 22 different (combinations of) rpoB mutations. Of 28 isolates tested, one was reported by Xpert Ultra as "No rifampicin resistance detected", 8 yielded a "Rifampicin indeterminate" result, and 19 were identified as rifampicin resistant. Overall, our results corroborate previous observations on the "Indeterminate" results for mutations at codon 432, while we add Lys446Gln as additional "Indeterminate" result and Pro439Leu as a false rifampicin-susceptible result. Furthermore, we document other uncommon point mutations and indels across the rpoB gene that are mostly correctly identified as rifampicin resistant by Xpert ultra (V3). Taken together, "Indeterminate" results in Xpert Ultra may indicate underlying rpoB mutations within the rifampicin-resistance determining region and thus increase the post-test probability of rifampicin resistance, albeit to an unknown extent.
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Affiliation(s)
- Leen Rigouts
- Institute of Tropical Medicine, Mycobacteriology Unit, Nationalestraat 155, Antwerp, Belgium
| | - Jelle Keysers
- Institute of Tropical Medicine, Mycobacteriology Unit, Nationalestraat 155, Antwerp, Belgium
| | - Reenaers Rabab
- Institute of Tropical Medicine, Mycobacteriology Unit, Nationalestraat 155, Antwerp, Belgium
| | - Kristina Fissette
- Institute of Tropical Medicine, Mycobacteriology Unit, Nationalestraat 155, Antwerp, Belgium
| | | | - Bouke Catherine de Jong
- Institute of Tropical Medicine, Mycobacteriology Unit, Nationalestraat 155, Antwerp, Belgium
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15
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Domínguez J, Boeree MJ, Cambau E, Chesov D, Conradie F, Cox V, Dheda K, Dudnyk A, Farhat MR, Gagneux S, Grobusch MP, Gröschel MI, Guglielmetti L, Kontsevaya I, Lange B, van Leth F, Lienhardt C, Mandalakas AM, Maurer FP, Merker M, Miotto P, Molina-Moya B, Morel F, Niemann S, Veziris N, Whitelaw A, Horsburgh CR, Lange C. Clinical implications of molecular drug resistance testing for Mycobacterium tuberculosis: a 2023 TBnet/RESIST-TB consensus statement. THE LANCET. INFECTIOUS DISEASES 2023; 23:e122-e137. [PMID: 36868253 DOI: 10.1016/s1473-3099(22)00875-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 03/05/2023]
Abstract
Drug-resistant tuberculosis is a substantial health-care concern worldwide. Despite culture-based methods being considered the gold standard for drug susceptibility testing, molecular methods provide rapid information about the Mycobacterium tuberculosis mutations associated with resistance to anti-tuberculosis drugs. This consensus document was developed on the basis of a comprehensive literature search, by the TBnet and RESIST-TB networks, about reporting standards for the clinical use of molecular drug susceptibility testing. Review and the search for evidence included hand-searching journals and searching electronic databases. The panel identified studies that linked mutations in genomic regions of M tuberculosis with treatment outcome data. Implementation of molecular testing for the prediction of drug resistance in M tuberculosis is key. Detection of mutations in clinical isolates has implications for the clinical management of patients with multidrug-resistant or rifampicin-resistant tuberculosis, especially in situations when phenotypic drug susceptibility testing is not available. A multidisciplinary team including clinicians, microbiologists, and laboratory scientists reached a consensus on key questions relevant to molecular prediction of drug susceptibility or resistance to M tuberculosis, and their implications for clinical practice. This consensus document should help clinicians in the management of patients with tuberculosis, providing guidance for the design of treatment regimens and optimising outcomes.
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Affiliation(s)
- José Domínguez
- Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, CIBER Enfermedades Respiratorias, INNOVA4TB Consortium, Barcelona, Spain.
| | - Martin J Boeree
- Department of Lung Diseases, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Emmanuelle Cambau
- Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France, APHP-Hôpital Bichat, Mycobacteriology Laboratory, INSERM, University Paris Cite, IAME UMR1137, Paris, France
| | - Dumitru Chesov
- Department of Pneumology and Allergology, Nicolae Testemițanu State University of Medicine and Pharmacy, Chisinau, Moldova; Division of Clinical Infectious Diseases, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany; Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Francesca Conradie
- Department of Clinical Medicine, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Vivian Cox
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Keertan Dheda
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa; Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, UK
| | - Andrii Dudnyk
- Department of Tuberculosis, Clinical Immunology and Allergy, National Pirogov Memorial Medical University, Vinnytsia, Ukraine; Public Health Center, Ministry of Health of Ukraine, Kyiv, Ukraine
| | - Maha R Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland
| | - Martin P Grobusch
- Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Amsterdam University Medical Centers, Amsterdam Infection & Immunity, Amsterdam Public Health, University of Amsterdam, Amsterdam, Netherlands
| | - Matthias I Gröschel
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Lorenzo Guglielmetti
- Sorbonne Université, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, (Cimi-Paris), APHP Sorbonne Université, Department of Bacteriology Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France
| | - Irina Kontsevaya
- Division of Clinical Infectious Diseases, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany; Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany; Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Berit Lange
- Department for Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany; German Centre for Infection Research, TI BBD, Braunschweig, Germany
| | - Frank van Leth
- Department of Health Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands; Amsterdam Public Health Research Institute, Amsterdam, Netherlands
| | - Christian Lienhardt
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK; UMI 233 IRD-U1175 INSERM - Université de Montpellier, Institut de Recherche pour le Développement, Montpellier, France
| | - Anna M Mandalakas
- Division of Clinical Infectious Diseases, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany; Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany; Global TB Program, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Florian P Maurer
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany; Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Matthias Merker
- Division of Evolution of the Resistome, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany
| | - Paolo Miotto
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Barbara Molina-Moya
- Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, CIBER Enfermedades Respiratorias, INNOVA4TB Consortium, Barcelona, Spain
| | - Florence Morel
- Sorbonne Université, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, (Cimi-Paris), APHP Sorbonne Université, Department of Bacteriology Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France
| | - Stefan Niemann
- Division of Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany; Department of Human, Biological and Translational Medical Sciences, School of Medicine, University of Namibia, Windhoek, Namibia
| | - Nicolas Veziris
- Sorbonne Université, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, (Cimi-Paris), APHP Sorbonne Université, Department of Bacteriology Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France
| | - Andrew Whitelaw
- Division of Medical Microbiology, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa; National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Charles R Horsburgh
- Departments of Epidemiology, Biostatistics, Global Health and Medicine, Boston University Schools of Public Health and Medicine, Boston, MA, USA
| | - Christoph Lange
- Division of Clinical Infectious Diseases, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany; Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany; Global TB Program, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
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16
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Performance Evaluation of the BACTEC MGIT 960 System for Rifampin Drug-Susceptibility Testing of Mycobacterium tuberculosis Using the Current WHO Critical Concentration. J Clin Microbiol 2023; 61:e0108622. [PMID: 36602360 PMCID: PMC9879093 DOI: 10.1128/jcm.01086-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The World Health Organization recently lowered the rifampin (RIF) critical concentration (CC) for drug-susceptibility testing (DST) of Mycobacterium tuberculosis complex (MTBC) using the mycobacterial growth indicator tube (MGIT) 960 system. Here, we evaluated the diagnostic performance of the MGIT system with the revised CC for determining MTBC RIF resistance with 303 clinical MTBC isolates, including 122 isolates with rpoB mutations, of which 32 had single borderline-resistance mutations, and 181 wild-type rpoB isolates. The phenotypic RIF resistance was determined via the absolute concentration method (AC) and via MGIT using both previous (1 mg/L) and revised (0.5 mg/L) CCs for the latter method. The diagnostic accuracy of each phenotypic DST (pDST) was assessed based on rpoB genotyping as the reference standard. The overall sensitivity of the AC was 95.1% (95% confidence interval [CI], 89.6 to 98.2%), while the MGIT results with previous and revised CCs were 82.0% (95% CI 74.0 to 88.3%) and 83.6% (95% CI 75.8 to 89.7%), respectively. The 32 MTBC isolates with single borderline-resistance mutations showed a wide range of MICs, and sensitivity was not significantly increased by reducing the MGIT CC. All 181 wild-type rpoB isolates were RIF-susceptible in the AC and with MGIT using the previous CC, whereas 1 isolate was misclassified as RIF-resistant with the revised CC. Our results demonstrate that the overall diagnostic performances of the MGIT DST with the revised RIF CC and previous CC were comparable. A further large-scale study is required to demonstrate the optimal RIF CC for MGIT.
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First Detection of Mycobacterium tuberculosis Clinical Isolates Harboring I491F Borderline Resistance rpoB Mutation in Myanmar. Antimicrob Agents Chemother 2022; 66:e0092522. [PMID: 36342155 PMCID: PMC9765286 DOI: 10.1128/aac.00925-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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18
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Schaberg T, Brinkmann F, Feiterna-Sperling C, Geerdes-Fenge H, Hartmann P, Häcker B, Hauer B, Haas W, Heyckendorf J, Lange C, Maurer FP, Nienhaus A, Otto-Knapp R, Priwitzer M, Richter E, Salzer HJ, Schoch O, Schönfeld N, Stahlmann R, Bauer T. Tuberkulose im Erwachsenenalter. Pneumologie 2022; 76:727-819. [DOI: 10.1055/a-1934-8303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
ZusammenfassungDie Tuberkulose ist in Deutschland eine seltene, überwiegend gut behandelbare Erkrankung. Weltweit ist sie eine der häufigsten Infektionserkrankungen mit ca. 10 Millionen Neuerkrankungen/Jahr. Auch bei einer niedrigen Inzidenz in Deutschland bleibt Tuberkulose insbesondere aufgrund der internationalen Entwicklungen und Migrationsbewegungen eine wichtige Differenzialdiagnose. In Deutschland besteht, aufgrund der niedrigen Prävalenz der Erkrankung und der damit verbundenen abnehmenden klinischen Erfahrung, ein Informationsbedarf zu allen Aspekten der Tuberkulose und ihrer Kontrolle. Diese Leitlinie umfasst die mikrobiologische Diagnostik, die Grundprinzipien der Standardtherapie, die Behandlung verschiedener Organmanifestationen, den Umgang mit typischen unerwünschten Arzneimittelwirkungen, die Besonderheiten in der Diagnostik und Therapie resistenter Tuberkulose sowie die Behandlung bei TB-HIV-Koinfektion. Sie geht darüber hinaus auf Versorgungsaspekte und gesetzliche Regelungen wie auch auf die Diagnosestellung und präventive Therapie einer latenten tuberkulösen Infektion ein. Es wird ausgeführt, wann es der Behandlung durch spezialisierte Zentren bedarf.Die Aktualisierung der S2k-Leitlinie „Tuberkulose im Erwachsenenalter“ soll allen in der Tuberkuloseversorgung Tätigen als Richtschnur für die Prävention, die Diagnose und die Therapie der Tuberkulose dienen und helfen, den heutigen Herausforderungen im Umgang mit Tuberkulose in Deutschland gewachsen zu sein.
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Affiliation(s)
- Tom Schaberg
- Deutsches Zentralkomitee zur Bekämpfung der Tuberkulose e. V. (DZK), Berlin
| | - Folke Brinkmann
- Abteilung für pädiatrische Pneumologie/CF-Zentrum, Universitätskinderklinik der Ruhr-Universität Bochum, Bochum
| | - Cornelia Feiterna-Sperling
- Klinik für Pädiatrie mit Schwerpunkt Pneumologie, Immunologie und Intensivmedizin, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin und Humboldt-Universität zu Berlin, Berlin
| | | | - Pia Hartmann
- Labor Dr. Wisplinghoff Köln, Klinische Infektiologie, Köln
- Department für Klinische Infektiologie, St. Vinzenz-Hospital, Köln
| | - Brit Häcker
- Deutsches Zentralkomitee zur Bekämpfung der Tuberkulose e. V. (DZK), Berlin
| | | | | | - Jan Heyckendorf
- Klinik für Innere Medizin I, Universitätsklinikum Schleswig-Holstein, Campus Kiel
| | - Christoph Lange
- Klinische Infektiologie, Forschungszentrum Borstel
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hamburg-Lübeck-Borstel-Riems
- Respiratory Medicine and International Health, Universität zu Lübeck, Lübeck
- Baylor College of Medicine and Texas Childrenʼs Hospital, Global TB Program, Houston, TX, USA
| | - Florian P. Maurer
- Nationales Referenzzentrum für Mykobakterien, Forschungszentrum Borstel, Borstel
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg
| | - Albert Nienhaus
- Institut für Versorgungsforschung in der Dermatologie und bei Pflegeberufen (IVDP), Universitätsklinikum Hamburg Eppendorf (UKE), Hamburg
| | - Ralf Otto-Knapp
- Deutsches Zentralkomitee zur Bekämpfung der Tuberkulose e. V. (DZK), Berlin
| | | | | | | | | | | | - Ralf Stahlmann
- Institut für klinische Pharmakologie und Toxikologie, Charité Universitätsmedizin, Berlin
| | - Torsten Bauer
- Deutsches Zentralkomitee zur Bekämpfung der Tuberkulose e. V. (DZK), Berlin
- Lungenklinik Heckeshorn, Helios Klinikum Emil von Behring, Berlin
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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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20
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Akki M, Reddy DS, Katagi KS, Kumar A, Devarajegowda HC, M SK, Babagond V, Mane S, Joshi SD. Synthesis of coumarin-thioether conjugates as potential anti-tubercular agents: Their molecular docking and X-ray crystal studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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21
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Mvelase NR, Singh R, Swe Swe-Han K, Mlisana KP. Pyrazinamide resistance in rifampicin discordant tuberculosis. PLoS One 2022; 17:e0274688. [PMID: 36129921 PMCID: PMC9491533 DOI: 10.1371/journal.pone.0274688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/01/2022] [Indexed: 11/22/2022] Open
Abstract
Introduction Mycobacterium tuberculosis strains with phenotypically susceptible rpoB mutations (rifampicin discordant) have emerged following implementation of rapid molecular drug resistance testing for tuberculosis. Whilst rifampicin resistance is known to be associated with resistance to other rifamycins (rifapentine and rifabutin) as well as isoniazid and pyrazinamide, rifampicin discordant strains have shown high rates of susceptibility to isoniazid and rifabutin. However, pyrazinamide susceptibly testing results have not been reported. Materials and methods We evaluated pyrazinamide resistance in 80 rifampicin discordant and 25 rifampicin and isoniazid susceptible isolates from KwaZulu-Natal in South Africa using Mycobacteria Growth Indicator Tube method and sequencing of the pncA. We also compared susceptibility of pyrazinamide with that of isoniazid. Results Pyrazinamide resistance was found in 6/80 (7.5%) rifampicin discordant isolates. All pyrazinamide resistant isolates were also resistant to isoniazid and pyrazinamide resistance was found to be associated with isoniazid resistance. No pyrazinamide resistance was found among the isoniazid susceptible isolates. Conclusion Given the low prevalence of pyrazinamide resistance in rifampicin discordant TB, this anti-TB drug still has a significant role in the treatment of these patients. Performing pyrazinamide susceptibility testing remains a challenge, our findings show that isoniazid susceptible isolates are unlikely to be resistant to pyrazinamide among the discordant TB isolates.
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Affiliation(s)
- Nomonde Ritta Mvelase
- Department of Medical Microbiology, National Health Laboratory Service, Inkosi Albert Luthuli Hospital, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, Department of Medical Microbiology, University of KwaZulu-Natal, College of Health Sciences, Durban, South Africa
- * E-mail:
| | - Ravesh Singh
- Department of Medical Microbiology, National Health Laboratory Service, Inkosi Albert Luthuli Hospital, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, Department of Medical Microbiology, University of KwaZulu-Natal, College of Health Sciences, Durban, South Africa
| | - Khine Swe Swe-Han
- Department of Medical Microbiology, National Health Laboratory Service, Inkosi Albert Luthuli Hospital, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, Department of Medical Microbiology, University of KwaZulu-Natal, College of Health Sciences, Durban, South Africa
| | - Koleka Patience Mlisana
- Department of Medical Microbiology, National Health Laboratory Service, Inkosi Albert Luthuli Hospital, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, Department of Medical Microbiology, University of KwaZulu-Natal, College of Health Sciences, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, Durban, South Africa
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22
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Che Y, Lin Y, Yang T, Chen T, Sang G, Chen Q, He T. Evaluation of whole-genome sequence to predict drug resistance of nine anti- tuberculosis drugs and characterize resistance genes in clinical rifampicin-resistant Mycobacterium tuberculosis isolates from Ningbo, China. Front Public Health 2022; 10:956171. [PMID: 36062095 PMCID: PMC9433565 DOI: 10.3389/fpubh.2022.956171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/28/2022] [Indexed: 01/24/2023] Open
Abstract
Setting Controlling drug-resistant tuberculosis in Ningbo, China. Objective Whole-genome sequencing (WGS) has not been employed to comprehensively study Mycobacterium tuberculosis isolates, especially rifampicin-resistant tuberculosis, in Ningbo, China. Here, we aim to characterize genes involved in drug resistance in RR-TB and create a prognostic tool for successfully predicting drug resistance in patients with TB. Design Drug resistance was predicted by WGS in a "TB-Profiler" web service after phenotypic drug susceptibility tests (DSTs) against nine anti-TB drugs among 59 clinical isolates. A comparison of consistency, sensitivity, specificity, and positive and negative predictive values between WGS and DST were carried out for each drug. Results The sensitivities and specificities for WGS were 95.92 and 90% for isoniazid (INH), 100 and 64.1% for ethambutol (EMB), 97.37 and 100% for streptomycin (SM), 75 and 100% for amikacin (AM), 80 and 96.3%for capreomycin (CAP), 100 and 97.22% for levofloxacin (LFX), 93.33 and 90.91% for prothionamide (PTO), and 70 and 97.96% for para-aminosalicylic acid (PAS). Around 53 (89.83%) and 6 (10.17%) of the isolates belonged to lineage two (East-Asian) and lineage four (Euro-American), respectively. Conclusion Whole-genome sequencing is a reliable method for predicting resistance to INH, RIF, EMB, SM, AM, CAP, LFX, PTO, and PAS with high consistency, sensitivity, and specificity. There was no transmission that occurred among the patients with RR-TB in Ningbo, China.
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Affiliation(s)
- Yang Che
- Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Yi Lin
- Center for Health Economics, Faculty of Humanities and Social Sciences, University of Nottingham, Ningbo, China
| | - Tianchi Yang
- Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Tong Chen
- Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Guoxin Sang
- Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Qin Chen
- Department of Disease Prevention and Health Promotion, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China,*Correspondence: Qin Chen
| | - Tianfeng He
- Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China,Tianfeng He
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Yusoof KA, García JI, Schami A, Garcia-Vilanova A, Kelley HV, Wang SH, Rendon A, Restrepo BI, Yotebieng M, Torrelles JB. Tuberculosis Phenotypic and Genotypic Drug Susceptibility Testing and Immunodiagnostics: A Review. Front Immunol 2022; 13:870768. [PMID: 35874762 PMCID: PMC9301132 DOI: 10.3389/fimmu.2022.870768] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/06/2022] [Indexed: 12/24/2022] Open
Abstract
Tuberculosis (TB), considered an ancient disease, is still killing one person every 21 seconds. Diagnosis of Mycobacterium tuberculosis (M.tb) still has many challenges, especially in low and middle-income countries with high burden disease rates. Over the last two decades, the amount of drug-resistant (DR)-TB cases has been increasing, from mono-resistant (mainly for isoniazid or rifampicin resistance) to extremely drug resistant TB. DR-TB is problematic to diagnose and treat, and thus, needs more resources to manage it. Together with+ TB clinical symptoms, phenotypic and genotypic diagnosis of TB includes a series of tests that can be used on different specimens to determine if a person has TB, as well as if the M.tb strain+ causing the disease is drug susceptible or resistant. Here, we review and discuss advantages and disadvantages of phenotypic vs. genotypic drug susceptibility testing for DR-TB, advances in TB immunodiagnostics, and propose a call to improve deployable and low-cost TB diagnostic tests to control the DR-TB burden, especially in light of the increase of the global burden of bacterial antimicrobial resistance, and the potentially long term impact of the coronavirus disease 2019 (COVID-19) disruption on TB programs.
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Affiliation(s)
- Kizil A. Yusoof
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX, United States
| | - Juan Ignacio García
- Population Health Program, Tuberculosis Group, Texas Biomedical Research Institute, San Antonio, TX, United States
- *Correspondence: Juan Ignacio García, ; Blanca I. Restrepo, ; Marcel Yotebieng, ; Jordi B. Torrelles,
| | - Alyssa Schami
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX, United States
- Population Health Program, Tuberculosis Group, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Andreu Garcia-Vilanova
- Population Health Program, Tuberculosis Group, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Holden V. Kelley
- Population Health Program, Tuberculosis Group, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Shu-Hua Wang
- Department of Internal Medicine, Division of Infectious Diseases, College of Medicine and Global One Health Initiative, The Ohio State University, Columbus, OH, United States
| | - Adrian Rendon
- Centro de Investigación, Prevención y Tratamiento de Infecciones Respiratorias (CIPTIR), Hospital Universitario de Monterrey Universidad Autónoma de Nuevo León (UANL), Monterrey, Mexico
| | - Blanca I. Restrepo
- School of Public Health, University of Texas Health Science Center at Houston, Brownsville, TX, United States
- School of Medicine, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Edinburg, TX, United States
- *Correspondence: Juan Ignacio García, ; Blanca I. Restrepo, ; Marcel Yotebieng, ; Jordi B. Torrelles,
| | - Marcel Yotebieng
- Division of General Internal Medicine, Department of Medicine, Albert Einstein College of Medicine, New York City, NY, United States
- *Correspondence: Juan Ignacio García, ; Blanca I. Restrepo, ; Marcel Yotebieng, ; Jordi B. Torrelles,
| | - Jordi B. Torrelles
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX, United States
- Population Health Program, Tuberculosis Group, Texas Biomedical Research Institute, San Antonio, TX, United States
- *Correspondence: Juan Ignacio García, ; Blanca I. Restrepo, ; Marcel Yotebieng, ; Jordi B. Torrelles,
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Hunt M, Letcher B, Malone KM, Nguyen G, Hall MB, Colquhoun RM, Lima L, Schatz MC, Ramakrishnan S, Iqbal Z. Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes. Genome Biol 2022; 23:147. [PMID: 35791022 PMCID: PMC9254434 DOI: 10.1186/s13059-022-02714-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 06/20/2022] [Indexed: 12/30/2022] Open
Abstract
There are many short-read variant-calling tools, with different strengths and weaknesses. We present a tool, Minos, which combines outputs from arbitrary variant callers, increasing recall without loss of precision. We benchmark on 62 samples from three bacterial species and an outbreak of 385 Mycobacterium tuberculosis samples. Minos also enables joint genotyping; we demonstrate on a large (N=13k) M. tuberculosis cohort, building a map of non-synonymous SNPs and indels in a region where all such variants are assumed to cause rifampicin resistance. We quantify the correlation with phenotypic resistance and then replicate in a second cohort (N=10k).
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Affiliation(s)
- Martin Hunt
- EMBL-EBI, Cambridge, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | | | | | - Rachel M Colquhoun
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | | | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
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25
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Diriba G, Kebede A, Tola HH, Alemu A, Yenew B, Moga S, Addise D, Mohammed Z, Getahun M, Fantahun M, Tadesse M, Dagne B, Amare M, Assefa G, Abera D, Desta K. Utility of line probe assay in detecting drug resistance and the associated mutations in patients with extrapulmonary tuberculosis in Addis Ababa, Ethiopia. SAGE Open Med 2022; 10:20503121221098241. [PMID: 35646363 PMCID: PMC9130810 DOI: 10.1177/20503121221098241] [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: 12/01/2021] [Accepted: 04/14/2022] [Indexed: 11/29/2022] Open
Abstract
Introduction Molecular tests allow rapid detection of Mycobacterium tuberculosis and drug resistance in a few days. Identifying the mutations in genes associated with drug resistance may contribute to the development of appropriate interventions to improve tuberculosis control. So far, there is little information in Ethiopia about the diagnostic performance of line probe assay (LPA) and the M. tuberculosis common gene mutations associated with drug resistance in extrapulmonary tuberculosis. Thus, this study aimed to assess the frequency of drug resistance-associated mutations in patients with extrapulmonary tuberculosis (EPTB) and to compare the agreement and determine the utility of the genotypic in the detection of drug resistance in Addis Ababa, Ethiopia. Methods A cross-sectional study was conducted on stored M. tuberculosis isolates. The genotypic and phenotypic drug susceptibility tests were performed using LPA and BACTEC-MGIT-960, respectively. The common mutations were noted, and the agreement and the utility of the LPA were determined using the BACTEC-MGIT-960 as a gold standard. Results Of the 151 isolates, the sensitivity and specificity of MTBDRplus in detecting isoniazid resistance were 90.9% and 100%, respectively. While for rifampicin, it was 100% and 99.3% for sensitivity and specificity, respectively. The katG S315Tl was the most common mutation observed in 85.7% of the isoniazid-resistant isolates. In the case of rifampicin, the most common mutation (61.9%) was observed at position rpoB S531L. Mutations in the gyrA promoter region were strongly associated with Levofloxacin and Moxifloxacin resistance. Conclusion Line probe assay has high test performance in detecting resistance to anti-TB drugs in EPTB isolates. The MTBDRplus test was slightly less sensitive for the detection of isoniazid resistance as compared to the detection of rifampicin. The most prevalent mutations associated with isoniazid and rifampicin resistance were observed at katG S315Tl and rpoB S531L respectively. Besides, all the fluoroquinolone-resistant cases were associated with gyrA gene. Finally, a validation study with DNA sequencing is recommended.
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Affiliation(s)
- Getu Diriba
- Ethiopian Public Health Institute,
Addis Ababa, Ethiopia
- Department of Medical Laboratory
Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa,
Ethiopia
| | - Abebaw Kebede
- Ethiopian Public Health Institute,
Addis Ababa, Ethiopia
- Department of Microbial, Cellular and
Molecular Biology, College of Natural and Computational Sciences, Addis Ababa
University, Addis Ababa, Ethiopia
| | | | - Ayinalem Alemu
- Ethiopian Public Health Institute,
Addis Ababa, Ethiopia
- Aklilu Lemma Institute of Pathobiology,
Addis Ababa University, Addis Ababa, Ethiopia
| | - Bazezew Yenew
- Ethiopian Public Health Institute,
Addis Ababa, Ethiopia
| | - Shewki Moga
- Ethiopian Public Health Institute,
Addis Ababa, Ethiopia
| | | | | | | | - Mengistu Fantahun
- St. Paul’s Hospital Millennium Medical
College, Addis Ababa, Ethiopia
| | | | - Biniyam Dagne
- Ethiopian Public Health Institute,
Addis Ababa, Ethiopia
| | - Misikir Amare
- Ethiopian Public Health Institute,
Addis Ababa, Ethiopia
| | | | - Dessie Abera
- 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
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26
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Rapid molecular diagnostics of tuberculosis resistance by targeted stool sequencing. Genome Med 2022; 14:52. [PMID: 35585607 PMCID: PMC9118838 DOI: 10.1186/s13073-022-01054-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/05/2022] [Indexed: 11/29/2022] Open
Abstract
Background Stool is an important diagnostic specimen for tuberculosis in populations who struggle to provide sputum, such as children or people living with HIV. However, the culture of Mycobacterium tuberculosis (M. tuberculosis) complex strains from stool perform poorly. This limits the opportunity for phenotypic drug resistance testing with this specimen. Therefore, reliable molecular methods are urgently needed for comprehensive drug resistance testing on stool specimens. Methods We evaluated the performance of targeted next-generation sequencing (tNGS, Deeplex® Myc-TB) for the detection of mutations associated with M. tuberculosis complex drug resistance on DNA isolated from stool specimens provided by participants from a prospective cohort of patients treated for tuberculosis in Eswatini (n = 66; 56 with and 10 participants without M. tuberculosis complex DNA detected in stool by real-time quantitative PCR), and an independent German validation cohort of participants with culture-confirmed tuberculosis (n = 21). Results The tNGS assay detected M. tuberculosis complex DNA in 38 of 56 (68%) samples; for 28 of 38 (74%) samples, a full M. tuberculosis complex drug resistance prediction report was obtained. There was a high degree of concordance with sputum phenotypic drug susceptibility results (κ = 0.82). The ability to predict resistance was concentration-dependent and successful in 7/10 (70%), 18/25 (72%), and 3/21 (14%) of samples with stool PCR concentration thresholds of > 100 femtogram per microliter (fg/μl), 1 to 100 fg/μl, and < 1 fg/μl, respectively (p = 0.0004). The German cohort confirmed these results and demonstrated a similarly high concordance between stool tNGS and sputum phenotypic drug susceptibility results (κ = 0.84). Conclusions tNGS can identify drug resistance from stool provided by tuberculosis patients. This affords the opportunity to obtain critical diagnostic information for tuberculosis patients who struggle to provide respiratory specimens. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01054-6.
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Georghiou SB, Rodwell TC, Korobitsyn A, Abbadi SH, Ajbani K, Alffenaar JW, Alland D, Alvarez N, Andres S, Ardizzoni E, Aubry A, Baldan R, Ballif M, Barilar I, Böttger EC, Chakravorty S, Claxton PM, Cirillo DM, Comas I, Coulter C, Denkinger CM, Derendinger B, Desmond EP, de Steenwinkel JE, Dheda K, Diacon AH, Dolinger DL, Dooley KE, Egger M, Ehsani S, Farhat MR, Fattorini L, Finci I, Le Ray LF, Furió V, Groenheit R, Gumbo T, Heysell SK, Hillemann D, Hoffmann H, Hsueh PR, Hu Y, Huang H, Hussain A, Ismail F, Izumi K, Jagielski T, Johnson JL, Kambli P, Kaniga K, Eranga Karunaratne G, Sharma MK, Keller PM, Kelly EC, Kholina M, Kohli M, Kranzer K, Laurenson IF, Limberis J, Grace Lin SY, Liu Y, López-Gavín A, Lyander A, Machado D, Martinez E, Masood F, Mitarai S, Mvelase NR, Niemann S, Nikolayevskyy V, Maurer FP, Merker M, Miotto P, Omar SV, Otto-Knapp R, Palaci M, Palacios Gutiérrez JJ, Peacock SJ, Peloquin CA, Perera J, Pierre-Audigier C, Pholwat S, Posey JE, Prammananan T, Rigouts L, Robledo J, Rockwood N, Rodrigues C, Salfinger M, Schechter MC, Seifert M, Sengstake S, Shinnick T, Shubladze N, Sintchenko V, Sirgel F, Somasundaram S, Sterling TR, Spitaleri A, Streicher E, Supply P, Svensson E, Tagliani E, Tahseen S, Takaki A, Theron G, Torrea G, Van Deun A, van Ingen J, Van Rie A, van Soolingen D, Vargas Jr R, Venter A, Veziris N, Villellas C, Viveiros M, Warren R, Wen S, Werngren J, Wilkinson RJ, Yang C, Yılmaz FF, Zhang T, Zimenkov D, Ismail N, Köser CU, Schön T. Updating the approaches to define susceptibility and resistance to anti-tuberculosis agents: implications for diagnosis and treatment. Eur Respir J 2022; 59:2200166. [PMID: 35422426 PMCID: PMC9059840 DOI: 10.1183/13993003.00166-2022] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/05/2022] [Indexed: 11/07/2022]
Abstract
Approximately 85 000 deaths globally in 2019 were due to drug-resistant tuberculosis (TB), which corresponds to 7% of global deaths attributable to bacterial antimicrobial resistance [1]. Yet concerns have been mounting that drug-resistant TB was being underestimated because the approaches to define susceptibility and resistance to anti-TB agents had not kept up with those used for other major bacterial pathogens [2–9]. Here, we outline the recent, evidence-based initiatives spearheaded by the World Health Organization (WHO) and others to update breakpoints (traditionally referred to as critical concentrations (CCs)) that are used for phenotypic antimicrobial susceptibility testing (AST), also called drug susceptibility testing in the TB literature. Inappropriately high breakpoints have resulted in systematic false-susceptible AST results to anti-TB drugs. MIC, PK/PD and clinical outcome data should be combined when setting breakpoints to minimise the emergence and spread of antimicrobial resistance. https://bit.ly/3i43wb6
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Aono A, Murase Y, Minegishi M, Ohtawa S, Yano M, Chikamatsu K, Shimomura Y, Hosoya M, Igarashi Y, Morishige Y, Yamada H, Takaki A, Togashi K, Hiura M, Mitarai S. Clinical evaluation of the cobas® MTB-RIF/INH reagent and the cobas® 6800 for the detection of isoniazid and rifampicin resistance. Tuberculosis (Edinb) 2022; 134:102199. [DOI: 10.1016/j.tube.2022.102199] [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: 03/09/2022] [Accepted: 03/15/2022] [Indexed: 11/24/2022]
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Xia H, Song Y, Zheng Y, Wang S, Zhao B, He W, Liu D, Ou X, Zhou Y, Zhao Y. Detection of Mycobacterium tuberculosis Rifampicin Resistance Conferred by Borderline rpoB Mutations: Xpert MTB/RIF is Superior to Phenotypic Drug Susceptibility Testing. Infect Drug Resist 2022; 15:1345-1352. [PMID: 35378895 PMCID: PMC8976515 DOI: 10.2147/idr.s358301] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/12/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Hui Xia
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yuanyuan Song
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yang Zheng
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Shengfen Wang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Bing Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Wencong He
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Dongxin Liu
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, Shenzhen, People’s Republic of China
| | - Xichao Ou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yang Zhou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- Correspondence: Yanlin Zhao, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, People’s Republic of China, Tel +86 10-58900517, Email
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Van Deun A, Bola V, Lebeke R, Kaswa M, Hossain MA, Gumusboga M, Torrea G, De Jong BC, Rigouts L, Decroo T. OUP accepted manuscript. JAC Antimicrob Resist 2022; 4:dlac037. [PMID: 35415609 PMCID: PMC8994197 DOI: 10.1093/jacamr/dlac037] [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: 02/08/2022] [Accepted: 03/13/2022] [Indexed: 11/14/2022] Open
Abstract
Background Objectives Methods Results Conclusions
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Affiliation(s)
| | - Valentin Bola
- Programme National de Lutte contre la Tuberculose, Direction Provinciale de Kinshasa, Kinshasa, République Démocratique du Congo
| | - Rossin Lebeke
- Programme National de Lutte contre la Tuberculose, Direction Provinciale de Kinshasa, Kinshasa, République Démocratique du Congo
| | - Michel Kaswa
- Programme National de Lutte contre la Tuberculose, Direction Nationale, Kinshasa, République Démocratique du Congo
| | | | - Mourad Gumusboga
- Institute of Tropical Medicine, Unit of Mycobacteriology, Department of Biomedical Sciences, 2000 Antwerp, Belgium
| | - Gabriela Torrea
- Institute of Tropical Medicine, Unit of Mycobacteriology, Department of Biomedical Sciences, 2000 Antwerp, Belgium
| | - Bouke Catharine De Jong
- Institute of Tropical Medicine, Unit of Mycobacteriology, Department of Biomedical Sciences, 2000 Antwerp, Belgium
| | - Leen Rigouts
- Institute of Tropical Medicine, Unit of Mycobacteriology, Department of Biomedical Sciences, 2000 Antwerp, Belgium
| | - Tom Decroo
- Institute of Tropical Medicine, Unit of HIV and TB, Department of Clinical Sciences, 2000 Antwerp, Belgium
- Corresponding author. E-mail:
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Welekidan LN, Yimer SA, Skjerve E, Dejene TA, Homberset H, Tønjum T, Brynildsrud O. Whole Genome Sequencing of Drug Resistant and Drug Susceptible Mycobacterium tuberculosis Isolates From Tigray Region, Ethiopia. Front Microbiol 2021; 12:743198. [PMID: 34938276 PMCID: PMC8685502 DOI: 10.3389/fmicb.2021.743198] [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: 07/17/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Tuberculosis, mainly caused by Mycobacterium tuberculosis (Mtb), is an ancient human disease that gravely affects millions of people annually. We wanted to explore the genetic diversity and lineage-specific association of Mtb with drug resistance among pulmonary tuberculosis patients. Methods: Sputum samples were collected from pulmonary tuberculosis patients at six different healthcare institutions in Tigray, Ethiopia, between July 2018 and August 2019. DNA was extracted from 74 Mtb complex isolates for whole-genome sequencing (WGS). All genomes were typed and screened for mutations with known associations with antimicrobial resistance using in silico methods, and results were cross-verified with wet lab methods. Results: Lineage (L) 4 (55.8%) was predominant, followed by L3 (41.2%); L1 (1.5%) and L2 (1.5%) occurred rarely. The most frequently detected sublineage was CAS (38.2%), followed by Ural (29.4%), and Haarlem (11.8%). The recent transmission index (RTI) was relatively low. L4 and Ural strains were more resistant than the other strains to any anti-TB drug (P < 0.05). The most frequent mutations to RIF, INH, EMB, SM, PZA, ETH, FLQs, and 2nd-line injectable drugs occurred at rpoB S450L, katG S315T, embB M306I/V, rpsL K43R, pncA V139A, ethA M1R, gyrA D94G, and rrs A1401G, respectively. Disputed rpoB mutations were also shown in four (16%) of RIF-resistant isolates. Conclusion: Our WGS analysis revealed the presence of diverse Mtb genotypes. The presence of a significant proportion of disputed rpoB mutations highlighted the need to establish a WGS facility at the regional level to monitor drug-resistant mutations. This will help control the transmission of DR-TB and ultimately contribute to the attainment of 100% DST coverage for TB patients as per the End TB strategy.
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Affiliation(s)
- Letemichael Negash Welekidan
- Department of Production Animal Medicine, Norwegian University of Life Sciences, Oslo, Norway.,Division of Biomedical Sciences, Department of Medical Microbiology and Immunology, College of Health Sciences, Mekelle University, Mekelle, Ethiopia
| | - Solomon Abebe Yimer
- Coalition for Epidemic Preparedness Innovations, Oslo, Norway.,Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway
| | - Eystein Skjerve
- Department of Production Animal Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Tsehaye Asmelash Dejene
- Division of Biomedical Sciences, Department of Medical Microbiology and Immunology, College of Health Sciences, Mekelle University, Mekelle, Ethiopia
| | - Håvard Homberset
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway
| | - Tone Tønjum
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway.,Unit for Genome Dynamics, Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Ola Brynildsrud
- Department of Production Animal Medicine, Norwegian University of Life Sciences, Oslo, Norway.,Norwegian Institute of Public Health, Oslo, Norway
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Bonnet I, Enouf V, Morel F, Ok V, Jaffré J, Jarlier V, Aubry A, Robert J, Sougakoff W. A Comprehensive Evaluation of GeneLEAD VIII DNA Platform Combined to Deeplex Myc-TB ® Assay to Detect in 8 Days Drug Resistance to 13 Antituberculous Drugs and Transmission of Mycobacterium tuberculosis Complex Directly From Clinical Samples. Front Cell Infect Microbiol 2021; 11:707244. [PMID: 34778100 PMCID: PMC8586210 DOI: 10.3389/fcimb.2021.707244] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/04/2021] [Indexed: 11/21/2022] Open
Abstract
The GeneLEAD VIII (Diagenode, Belgium) is a new, fully automated, sample-to-result precision instrument for the extraction of DNA and PCR detection of Mycobacterium tuberculosis complex (MTBC) directly from clinical samples. The Deeplex Myc-TB® assay (Genoscreen, France) is a diagnostic kit based on the deep sequencing of a 24-plexed amplicon mix allowing simultaneously the detection of resistance to 13 antituberculous (antiTB) drugs and the determination of spoligotype. We evaluated the performance of a strategy combining the both mentioned tools to detect directly from clinical samples, in 8 days, MTBC and its resistance to 13 antiTB drugs, and identify potential transmission of strains from patient-to-patient. Using this approach, we screened 112 clinical samples (65 smear-negative) and 94 MTBC cultured strains. The sensitivity and the specificity of the GeneLEAD/Deeplex Myc-TB approach for MTBC detection were 79.3% and 100%, respectively. One hundred forty successful Deeplex Myc-TB results were obtained for 46 clinical samples and 94 strains, a total of 85.4% of which had a Deeplex Myc-TB susceptibility and resistance prediction consistent with phenotypic drug susceptibility testing (DST). Importantly, the Deeplex Myc-TB assay was able to detect 100% of the multidrug-resistant (MDR) MTBC tested. The lowest concordance rates were for pyrazinamide, ethambutol, streptomycin, and ethionamide (84.5%, 81.5%, 73%, and 55%, respectively) for which the determination of susceptibility or resistance is generally difficult with current tools. One of the main difficulties of Deeplex Myc-TB is to interpret the non-synonymous uncharacterized variants that can represent up to 30% of the detected single nucleotide variants. We observed a good level of concordance between Deeplex Myc-TB-spoligotyping and MIRU-VNTR despite a lower discriminatory power for spoligotyping. The median time to obtain complete results from clinical samples was 8 days (IQR 7–13) provided a high-throughput NGS sequencing platform was available. Our results highlight that the GeneLEAD/Deeplex Myc-TB approach could be a breakthrough in rapid diagnosis of MDR TB in routine practice.
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Affiliation(s)
- Isabelle Bonnet
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
| | - Vincent Enouf
- Plateforme de Microbiologie Mutualisée (P2M), Pasteur International Bioresources network (PIBnet), Institut Pasteur, Paris, France
| | - Florence Morel
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
| | - Vichita Ok
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
| | - Jérémy Jaffré
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
| | - Vincent Jarlier
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France
| | - Alexandra Aubry
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
| | - Jérôme Robert
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
| | - Wladimir Sougakoff
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
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Rando-Segura A, Aznar ML, Moreno MM, Espasa Soley M, Sulleiro Igual E, Bocanegra Garcia C, Gil Olivas E, Nindia Eugénio A, Escartin Huesca C, Zacarias A, Vegue Collado J, Katimba D, Vivas Cano MC, Gabriel E, López García MT, Pumarola Suñe T, Molina Romero I, Tórtola Fernández MT. Molecular characterization of rpoB gene mutations in isolates from tuberculosis patients in Cubal, Republic of Angola. BMC Infect Dis 2021; 21:1056. [PMID: 34641802 PMCID: PMC8507306 DOI: 10.1186/s12879-021-06763-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 09/17/2021] [Indexed: 11/30/2022] Open
Abstract
Background The importance of Mycobacterium tuberculosis strains with disputed rpoB mutations remains to be defined. This study aimed to assess the frequency and types of rpoB mutations in M. tuberculosis isolates from Cubal, Angola, a country with a high incidence of tuberculosis. Methods All isolates included (n = 308) were analyzed using phenotypic drug susceptibility testing and GenoType MTBDRplus assay. DNA sequencing of the rpoB gene and determination of rifampicin MIC by macrodilution method were additionally performed on isolates yielding discordant results (n = 12) and those in which the mutation detected was not characterized (n = 8). Results In total, 85.1% (74/87) of rifampicin-resistant strains had undisputed rpoB mutations -S450L (49), D435V (15), H445D (3), H445Y (2), Q432ins (1), L449M plus S450F (1), S450F (1), S450W (1) and S450Y (1)-; 10.3% (9/87) had disputed rpoB mutations—L430P plus S493L (1), N437del (1), H445L (3), D435Y (2), L452P (2)-, 2.3% (2.3%) showed no rpoB mutations and 2.3% (2/87) showed heteroresistance—D435Y plus L452P and L430P plus S493L-. Conclusion Disputed rpoB mutations were common, occurring in 10.3% of rifampicin resistant isolates. Current phenotyping techniques may be unable to detect this resistance pattern. To increase their sensitivity, a lower concentration of RIF could be used in these tests or alternatively, rpoB mutations could be screened and characterized in all M. tuberculosis strains.
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Affiliation(s)
- Ariadna Rando-Segura
- Microbiology Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119 - 129, 08035, Barcelona, Spain.
| | - María Luisa Aznar
- Infectious Disease Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Barcelona, Spain.,Hospital Nossa Senhora da Paz, Cubal, Angola
| | | | - Mateu Espasa Soley
- Microbiology Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119 - 129, 08035, Barcelona, Spain
| | - Elena Sulleiro Igual
- Microbiology Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119 - 129, 08035, Barcelona, Spain
| | - Cristina Bocanegra Garcia
- Infectious Disease Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Barcelona, Spain.,Hospital Nossa Senhora da Paz, Cubal, Angola
| | - Eva Gil Olivas
- Infectious Disease Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Barcelona, Spain.,Hospital Nossa Senhora da Paz, Cubal, Angola
| | | | - Carlos Escartin Huesca
- Microbiology Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119 - 129, 08035, Barcelona, Spain
| | | | - Josep Vegue Collado
- Microbiology Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119 - 129, 08035, Barcelona, Spain
| | | | - Maria Carmen Vivas Cano
- Microbiology Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119 - 129, 08035, Barcelona, Spain
| | | | | | - Tomas Pumarola Suñe
- Microbiology Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119 - 129, 08035, Barcelona, Spain
| | - Israel Molina Romero
- Infectious Disease Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - María Teresa Tórtola Fernández
- Microbiology Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119 - 129, 08035, Barcelona, Spain
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Disputed rpoB Mutations in Mycobacterium tuberculosis and Tuberculosis Treatment Outcomes. Antimicrob Agents Chemother 2021; 65:e0157320. [PMID: 33846134 DOI: 10.1128/aac.01573-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Discordant results between genotypic drug susceptibility testing (gDST) and phenotypic DST (pDST) for Mycobacterium tuberculosis isolates with disputed (discordance between gDST and pDST results) mutations affect rifampin (RIF)-resistant (RR) and multidrug-resistant (MDR) tuberculosis (TB) treatments due to a lack of practical clinical guidelines. To investigate the role of disputed rpoB mutations in M. tuberculosis and TB treatment outcomes, initial isolates of 837 clinical RR- or MDR-TB cases confirmed during 2014 to 2018 were retested using agar-based RIF pDST and rpoB gene sequencing. MICs were determined for isolates with disputed rpoB mutations. Disputed rpoB mutations were identified in 77 (9.2%) M. tuberculosis isolates, including 50 (64.9%) and 14 (18.2%) phenotypically RIF- and rifabutin (RFB)-resistant isolates, respectively. The predominant single mutations were those encoding L533P (a change of L to P at position 533) (44.2%) and L511P (20.8%). Most of the isolates harboring mutations encoding L511P (87.5%), H526N (100%), D516Y (70.0%), and L533P (63.6%) had MICs of ≤1 mg/liter, whereas isolates harboring the mutation encoding H526L (75%) had a MIC of >1 mg/liter. Of the 63 cases with treatment outcomes available, 11 (17.5%) cases died, 1 (1.6%) case transferred out, and 51 (81%) cases had favorable outcomes, including 8 and 20 cases treated with standard-dose RIF- and RFB-containing regimens, respectively. Excluding cases that transferred out or received no or 1-day treatment, we observed statistically significant differences between the outcomes using active and inactive fluoroquinolones (FQs) (P = 0.008, odds ratio = 0.05 [95% confidence interval, 0.01 to 0.38]) in 57 cases (where active means a case susceptible to the drug and inactive means a case resistant to the drug or drug not used). We concluded that disputed rpoB mutations are not rare. Depending on the resources available, sequencing and/or MIC testing is recommended for better management of RR- and MDR-TB cases.
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Ssengooba W, de Dieu Iragena J, Komakech K, Okello I, Nalunjogi J, Katagira W, Kimuli I, Adakun S, Joloba ML, Torrea G, Kirenga BJ. Discordance of the Repeat GeneXpert MTB/RIF Test for Rifampicin Resistance Detection Among Patients Initiating MDR-TB Treatment in Uganda. Open Forum Infect Dis 2021; 8:ofab173. [PMID: 34189166 PMCID: PMC8223903 DOI: 10.1093/ofid/ofab173] [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: 01/25/2021] [Accepted: 03/31/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The Global Laboratory Initiative (GLI) guidelines recommend repeat for GeneXpertMTB/RIF (XpertMTB/RIF) in patients with a low pretest probability of rifampicin resistance (RR). METHODS This was a cross-sectional study using results of sputum specimens collected from participants screened for the STREAM 2 trial. We recruited all patients with XpertMTB/RIF RR-TB detected who were referred for RR/multidrug-resistant (MDR) TB treatment initiation at Mulago National Referral Hospital, Kampala, between September 2017 and October 2019. At baseline, smear microscopy, repeat XpertMTB/RIF, Xpert Ultra, and MTBDRplus assays were done on sputum specimens. Culture-based drug susceptibility testing (DST) was performed on discordant specimens. We analyzed the prevalence and factors associated with discordance between initial and repeat XpertMTB/RIF RR and false XpertMTB/RIF RR. False XpertMTB/RIF RR was defined as no RR detected by any of Xpert Ultra, LPA, or culture DST (reference comparator). RESULTS A total of 126/130 patients had repeat XpertMTB/RIF results, of whom 97 (77.0%) had M. tuberculosis detected, 81 (83.5%) had RR detected, and 1 (1.0%) had RR indeterminate. The prevalence of discordant XpertMTB/RIF RR was 15/96 (15.6%), whereas false XpertMTB/RIF RR prevalence was 10/96 (10.4%).Low-bacillary load sputum specimens were more likely to have discordant XpertMTB/RIF RR and false XpertMTB/RIF RR results (adjusted odds ratio [aOR], 0.04; 95% CI, 0.00-0.37; P = .01; aOR, 0.02; 95% CI, 0.01-0.35; P = .01, respectively). CONCLUSIONS Our findings show a high false-positive rifampicin resistance rate in low-TB burden patients, which calls for repeat testing in order to prevent unnecessary prescription of anti-MDR-TB therapy.
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Affiliation(s)
- Willy Ssengooba
- College of Health Sciences, Makerere University Lung Institute, Kampala, Uganda
- Mycobacteriology (BSL-3) Laboratory, Department of Medical Microbiology, Makerere University, Kampala, Uganda
| | - Jean de Dieu Iragena
- Communicable Diseases Cluster, HIV/TB and Hepatitis Programme, World Health Organization Regional Office for Africa, Brazzaville, Congo
| | - Kevin Komakech
- Mycobacteriology (BSL-3) Laboratory, Department of Medical Microbiology, Makerere University, Kampala, Uganda
| | - Iginitius Okello
- College of Health Sciences, Makerere University Lung Institute, Kampala, Uganda
| | - Joanitah Nalunjogi
- College of Health Sciences, Makerere University Lung Institute, Kampala, Uganda
| | - Winceslaus Katagira
- College of Health Sciences, Makerere University Lung Institute, Kampala, Uganda
| | - Ivan Kimuli
- College of Health Sciences, Makerere University Lung Institute, Kampala, Uganda
| | - Susan Adakun
- College of Health Sciences, Makerere University Lung Institute, Kampala, Uganda
- National Tuberculosis Treatment Unit, Mulago Hospital, Kampala, Uganda
| | - Moses L Joloba
- College of Health Sciences, Makerere University Lung Institute, Kampala, Uganda
- Mycobacteriology (BSL-3) Laboratory, Department of Medical Microbiology, Makerere University, Kampala, Uganda
| | - Gabriela Torrea
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Bruce J Kirenga
- College of Health Sciences, Makerere University Lung Institute, Kampala, Uganda
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36
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Thin-Layer-Agar-Based Direct Phenotypic Drug Susceptibility Testing on Sputum in Eswatini Rapidly Detects Mycobacterium tuberculosis Growth and Rifampicin Resistance Otherwise Missed by WHO-Endorsed Diagnostic Tests. Antimicrob Agents Chemother 2021; 65:AAC.02263-20. [PMID: 33722892 PMCID: PMC8315964 DOI: 10.1128/aac.02263-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 03/02/2021] [Indexed: 11/20/2022] Open
Abstract
Xpert MTB/RIF rapidly detects resistance to rifampicin (RR); however, this test misses I491F-RR conferring rpoB mutation, common in southern Africa. In addition, Xpert MTB/RIF does not distinguish between viable and dead Mycobacterium tuberculosis (MTB). We aimed to investigate the ability of thin-layer agar (TLA) direct drug-susceptibility testing (DST) to detect MTB and its drug-resistance profiles in field conditions in Eswatini. Consecutive samples were tested in parallel with Xpert MTB/RIF and TLA for rifampicin (1.0 μg/ml) and ofloxacin (2.0 μg/ml). TLA results were compared at the Reference Laboratory in Antwerp with indirect-DST on Löwenstein-Jensen or 7H11 solid media and additional phenotypic and genotypic testing to resolve discordance. TLA showed a positivity rate for MTB detection of 7.1% versus 10.0% for Xpert MTB/RIF. Of a total of 4,547 samples included in the study, 200 isolates were available for comparison to the composite reference. Within a median of 18.4 days, TLA detected RR with 93.0% sensitivity (95% confidence interval [CI], 77.4 to 98.0) and 99.4% specificity (95% CI, 96.7 to 99.9) versus 62.5% (95% CI, 42.7 to 78.8) and 99.3% (95% CI, 96.2 to 99.9) for Xpert MTB/RIF. Eight isolates, 28.6% of all RR-confirmed isolates, carried the I491F mutation, all detected by TLA. TLA also correctly identified 183 of the 184 ofloxacin-susceptible isolates (99.5% specificity; 95% CI, 97.0 to 99.9). In field conditions, TLA rapidly detects RR, and in this specific setting, it contributed to detection of additional RR patients over Xpert MTB/RIF, mainly but not exclusively due to I491F. TLA also accurately excluded fluoroquinolone resistance.
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Should treatment of low-level rifampicin mono-resistant tuberculosis be different? J Clin Tuberc Other Mycobact Dis 2021; 23:100240. [PMID: 34095546 PMCID: PMC8167426 DOI: 10.1016/j.jctube.2021.100240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Shah M, Paradis S, Betz J, Beylis N, Bharadwaj R, Caceres T, Gotuzzo E, Joloba M, Mave V, Nakiyingi L, Nicol MP, Pradhan N, King B, Armstrong D, Knecht D, Maus CE, Cooper CK, Dorman SE, Manabe YC. Multicenter Study of the Accuracy of the BD MAX Multidrug-resistant Tuberculosis Assay for Detection of Mycobacterium tuberculosis Complex and Mutations Associated With Resistance to Rifampin and Isoniazid. Clin Infect Dis 2021; 71:1161-1167. [PMID: 31560049 PMCID: PMC7442848 DOI: 10.1093/cid/ciz932] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 10/08/2019] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Tuberculosis (TB) control is hindered by absence of rapid tests to identify Mycobacterium tuberculosis (MTB) and detect isoniazid (INH) and rifampin (RIF) resistance. We evaluated the accuracy of the BD MAX multidrug-resistant (MDR)-TB assay (BD MAX) in South Africa, Uganda, India, and Peru. METHODS Outpatient adults with signs/symptoms of pulmonary TB were prospectively enrolled. Sputum smear microscopy and BD MAX were performed on a single raw sputum, which was then processed for culture and phenotypic drug susceptibility testing (DST), BD MAX, and Xpert MTB/RIF (Xpert). RESULTS 1053 participants with presumptive TB were enrolled (47% female; 32% with human immunodeficiency virus). In patients with confirmed TB, BD MAX sensitivity was 93% (262/282 [95% CI, 89-95%]); specificity was 97% (593/610 [96-98%]) among participants with negative cultures on raw sputa. BD MAX sensitivity was 100% (175/175 [98-100%]) for smear-positive samples (fluorescence microscopy), and 81% (87/107 [73-88%]) in smear-negative samples. Among participants with both BD MAX and Xpert, sensitivity was 91% (249/274 [87-94%]) for BD MAX and 90% (246/274 [86-93%]) for Xpert on processed sputa. Sensitivity and specificity for RIF resistance compared with phenotypic DST were 90% (9/10 [60-98%]) and 95% (211/222 [91-97%]), respectively. Sensitivity and specificity for detection of INH resistance were 82% (22/27 [63-92%]) and 100% (205/205 [98-100%]), respectively. CONCLUSIONS The BD MAX MDR-TB assay had high sensitivity and specificity for detection of MTB and RIF and INH drug resistance and may be an important tool for rapid detection of TB and MDR-TB globally.
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Affiliation(s)
- Maunank Shah
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sonia Paradis
- Becton, Dickinson and Company, Sparks, Maryland, USA
| | - Joshua Betz
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Natalie Beylis
- Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa.,Medical Microbiology Laboratory National Health Laboratory Services Groote Schuur Hospital, Cape Town, South Africa
| | - Renu Bharadwaj
- Byramjee Jeejeebhoy Government Medical College, Johns Hopkins University Clinical Research Site, Pune, Maharashtra, India
| | - Tatiana Caceres
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Eduardo Gotuzzo
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Moses Joloba
- Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Vidya Mave
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Byramjee Jeejeebhoy Government Medical College, Johns Hopkins University Clinical Research Site, Pune, Maharashtra, India
| | - Lydia Nakiyingi
- Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Mark P Nicol
- Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa.,Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Neeta Pradhan
- Byramjee Jeejeebhoy Government Medical College, Johns Hopkins University Clinical Research Site, Pune, Maharashtra, India
| | - Bonnie King
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Derek Armstrong
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | | | - Susan E Dorman
- Medical University of South Carolina, Charleston, South Carolina, USA
| | - Yukari C Manabe
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda
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Che Y, Yang T, Lin L, Xiao Y, Jiang F, Chen Y, Chen T, Zhou J. Comparative Utility of Genetic Determinants of Drug Resistance and Phenotypic Drug Susceptibility Profiling in Predicting Clinical Outcomes in Patients With Multidrug-Resistant Mycobacterium tuberculosis. Front Public Health 2021; 9:663974. [PMID: 33968888 PMCID: PMC8100237 DOI: 10.3389/fpubh.2021.663974] [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: 02/04/2021] [Accepted: 02/26/2021] [Indexed: 11/13/2022] Open
Abstract
Setting: Programmatic management of drug-resistant tuberculosis in Ningbo, China. Objective: To assess whether data-driven genetic determinants of drug resistance patterns could outperform phenotypic drug susceptibility testing in predicting clinical meaningful outcomes among patients with multidrug-resistant tuberculosis (MDR-TB). Design: We conducted a prospective cohort study of 104 MDR-TB patients. All MDR-TB isolates underwent drug susceptibility testing and genotyping for mutations that could cause drug resistance. Study outcomes were time to sputum smear conversion and probability of treatment success, as well as time to culture conversion within 6 months. Data were analyzed using latent class analysis, Kaplan–Meier curves, and Cox regression models. Results: We report that latent class analysis of data identified two latent classes that predicted sputum smear conversion with P = 0.001 and area under receiver-operating characteristic curve of 0.73. The predicted latent class memberships were associated with superior capability in predicting sputum culture conversion at 6 months and overall treatment success compared to phenotypic drug susceptibility profiling using boosted logistic regression models. Conclusion: These results suggest that genetic determinants of drug resistance in combination with phenotypic drug-resistant tests could serve as useful biomarkers in predicting treatment prognosis in MDR-TB.
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Affiliation(s)
- Yang Che
- Ningbo Municipal Center for Disease Control and Prevention, Institute of Tuberculosis Prevention and Control, Ningbo, China
| | - Tianchi Yang
- Ningbo Municipal Center for Disease Control and Prevention, Institute of Tuberculosis Prevention and Control, Ningbo, China
| | - Lv Lin
- Ningbo Municipal Center for Disease Control and Prevention, Institute of Tuberculosis Prevention and Control, Ningbo, China
| | - Yue Xiao
- School of International Pharmaceutical Business, China Pharmaceutical University, Nanjing, China
| | - Feng Jiang
- School of International Pharmaceutical Business, China Pharmaceutical University, Nanjing, China
| | - Yanfei Chen
- School of International Pharmaceutical Business, China Pharmaceutical University, Nanjing, China
| | - Tong Chen
- Ningbo Municipal Center for Disease Control and Prevention, Institute of Tuberculosis Prevention and Control, Ningbo, China
| | - Jifang Zhou
- School of International Pharmaceutical Business, China Pharmaceutical University, Nanjing, China
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Al-Mutairi NM, Ahmad S, Mokaddas E. Increasing prevalence of resistance to second-line drugs among multidrug-resistant Mycobacterium tuberculosis isolates in Kuwait. Sci Rep 2021; 11:7765. [PMID: 33833390 PMCID: PMC8032671 DOI: 10.1038/s41598-021-87516-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/30/2021] [Indexed: 11/13/2022] Open
Abstract
Molecular methods detect genetic mutations associated with drug resistance. This study detected resistance-conferring mutations in gyrA/gyrB for fluoroquinolones and rrs/eis genes for second-line injectable drugs (SLIDs) among multidrug-resistant Mycobacterium tuberculosis (MDR-TB) isolates in Kuwait. Fifty pansusceptible M. tuberculosis and 102 MDR-TB strains were tested. Phenotypic susceptibility testing was performed by MGIT 960 system using SIRE drug kit. GenoType MTBDRsl version 1 (gMTBDRslv1) and GenoType MTBDRsl version 2 (gMTBDRslv2) tests were used for mutation detection. Results were validated by PCR-sequencing of respective genes. Fingerprinting was performed by spoligotyping. No mutations were detected in pansusceptible isolates. gMTBDRslv1 detected gyrA mutations in 12 and rrs mutations in 8 MDR-TB isolates. gMTBDRsl2 additionally detected gyrB mutations in 2 and eis mutation in 1 isolate. Mutations in both gyrA/gyrB and rrs/eis were not detected. gMTBDRslv1 also detected ethambutol resistance-conferring embB mutations in 59 isolates. Although XDR-TB was not detected, frequency of resistance-conferring mutations for fluoroquinolones or SLIDs was significantly higher among isolates collected during 2013–2019 versus 2006–2012. Application of both tests is warranted for proper management of MDR-TB patients in Kuwait as gMTBDRslv2 detected resistance to fluoroquinolones and/or SLIDs in 3 additional isolates while gMTBDRslv1 additionally detected resistance to ethambutol in 58% of MDR-TB isolates.
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Affiliation(s)
- Noura M Al-Mutairi
- Department of Microbiology, Faculty of Medicine, Health Sciences Centre, Kuwait University, P. O. Box 24923, 13110, Safat, Kuwait
| | - Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Health Sciences Centre, Kuwait University, P. O. Box 24923, 13110, Safat, Kuwait.
| | - Eiman Mokaddas
- Department of Microbiology, Faculty of Medicine, Health Sciences Centre, Kuwait University, P. O. Box 24923, 13110, Safat, Kuwait.,Kuwait National TB Control Laboratory, Shuwaikh, Kuwait
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Lam C, Martinez E, Crighton T, Furlong C, Donnan E, Marais BJ, Sintchenko V. Value of routine whole genome sequencing for Mycobacterium tuberculosis drug resistance detection. Int J Infect Dis 2021; 113 Suppl 1:S48-S54. [PMID: 33753222 DOI: 10.1016/j.ijid.2021.03.033] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/02/2021] [Accepted: 03/10/2021] [Indexed: 10/21/2022] Open
Abstract
Routine whole genome sequencing (WGS) of pathogens is becoming more feasible as sequencing costs decrease and access to benchtop sequencing equipment and bioinformatics pipelines increases. This study examined the added value gained from implementing routine WGS of all Mycobacterium tuberculosis isolates in New South Wales, Australia. Drug resistance markers inferred from WGS data were compared to commercial genotypic drug susceptibility testing (DST) assays and conventional phenotypic DST in all isolates sequenced between 2016 and 2019. Of the 1107 clinical M. tuberculosis isolates sequenced, 29 (2.6%) were multi-drug resistant (MDR); most belonged to Beijing (336; 30.4%) or East-African Indian (332; 30%) lineages. Compared with conventional phenotypic DST, WGS identified an additional 1% of isolates which were likely drug resistant, explained by mutations previously associated with treatment failure and mixed bacterial populations. However, WGS provided a 20% increase in drug resistance detection in comparison with commercial genotypic assays by identifying mutations outside of the classic resistance determining regions in rpoB, inhA, katG, pncA and embB genes. Gains in drug resistance detection were significant (p = 0.0137, paired t-test), but varied substantially for different phylogenetic lineages. In low incidence settings, routine WGS of M. tuberculosis provides better guidance for person-centered management of drug resistant tuberculosis than commercial genotypic assays.
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Affiliation(s)
- Connie Lam
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia.
| | - Elena Martinez
- NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology - Western, Sydney, New South Wales, Australia
| | - Taryn Crighton
- NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology - Western, Sydney, New South Wales, Australia
| | - Catriona Furlong
- New South Wales Tuberculosis Program, Health Protection NSW, Sydney, New South Wales, Australia
| | - Ellen Donnan
- New South Wales Tuberculosis Program, Health Protection NSW, Sydney, New South Wales, Australia
| | - Ben J Marais
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Centre for Research Excellence in Tuberculosis (TB-CRE), The University of Sydney, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia; NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology - Western, Sydney, New South Wales, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity and Centre for Research Excellence in Tuberculosis (TB-CRE), The University of Sydney, Sydney, New South Wales, Australia
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Low-Level Rifampin Resistance and rpoB Mutations in Mycobacterium tuberculosis: an Analysis of Whole-Genome Sequencing and Drug Susceptibility Test Data in New York. J Clin Microbiol 2021; 59:JCM.01885-20. [PMID: 32999007 DOI: 10.1128/jcm.01885-20] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/05/2020] [Indexed: 01/02/2023] Open
Abstract
Rapid and reliable detection of rifampin (RIF) resistance is critical for the diagnosis and treatment of drug-resistant and multidrug-resistant (MDR) tuberculosis. Discordant RIF phenotype/genotype susceptibility results remain a challenge due to the presence of rpoB mutations that do not confer high levels of RIF resistance, as have been exhibited in strains with mutations such as Ser450Leu. These strains, termed low-level RIF resistant, exhibit elevated RIF MICs compared to fully susceptible strains but remain phenotypically susceptible by mycobacterial growth indicator tube (MGIT) testing and have been associated with poor patient outcomes. Here, we assess RIF resistance prediction by whole-genome sequencing (WGS) among a set of 1,779 prospectively tested strains by both prevalence of rpoB gene mutation and phenotype as part of routine clinical testing during a 2.5-year period. During this time, 139 strains were found to have nonsynonymous rpoB mutations, 53 of which were associated with RIF resistance, including both low-level and high-level resistance. Resistance to RIF (1.0 μg/ml in MGIT) was identified in 43 (81.1%) isolates. The remaining 10 (18.9%) strains were susceptible by MGIT but were confirmed to be low-level RIF resistant by MIC testing. Full rpoB gene sequencing overcame the limitations of critical concentration phenotyping, probe-based genotyping, and partial gene sequencing methods. Universal clinical WGS with concurrent phenotypic testing provided a more complete understanding of the prevalence and type of rpoB mutations and their association with RIF resistance in New York.
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Abstract
We present a case of a 59-year-old man, who on being evaluated for abdominal pain and headache, was found to have a pancreatic head mass and inflammatory hypophysitis. Xpert MTB/Rif of the pancreatic mass biopsy showed the presence of tuberculosis (TB) with a very low load, and rifampicin resistance was detected with absence of probes A and B. Pyrosequencing (a novel genotypic test for TB) of the Xpert MTB/Rif isolate detected a single, rare, high-confidence mutation (S512T) in the rpoB region (rifampicin resistance determining region in the MTB genome). The TB mycobacteria growth indicator tube (TBMGIT) phenotypic drug susceptibility test (DST), however, showed rifampicin susceptibility. Incidentally, he was unable to tolerate rifampicin and responded well to a non-rifampicin-based regimen. We discuss a possible hypothesis of the Xpert-DST discordance in accordance with a recent literature review on phenotypic DST methods. We also discuss the utility of pyrosequencing in clinical practice for the diagnosis of TB and its resistance patterns.
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Affiliation(s)
- Umang Agrawal
- Department of Infectious Diseases, PD Hinduja National Hospital and Medical Research Centre, Mumbai, Maharashtra, India
| | - Krutarth Kanjiya
- Department of Infectious Diseases, PD Hinduja National Hospital and Medical Research Centre, Mumbai, Maharashtra, India
| | - Camilla Rodrigues
- Department of Microbiology, PD Hinduja National Hospital and Medical Research Centre, Mumbai, Maharashtra, India
| | - Ayesha Sunavala
- Department of Infectious Diseases, PD Hinduja National Hospital and Medical Research Centre, Mumbai, Maharashtra, India
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Shi J, Tao B, Li Z, Song H, Wu J, Qiu B, Wang J. Diagnostic Performance of GeneChip for the Rapid Detection of Drug-Resistant Tuberculosis in Different Subgroups of Patients. Infect Drug Resist 2021; 14:597-608. [PMID: 33633456 PMCID: PMC7900445 DOI: 10.2147/idr.s297725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 01/27/2021] [Indexed: 11/25/2022] Open
Abstract
Objective Drug-resistant tuberculosis (DR-TB) is a growing problem worldwide. The rapid drug susceptibility test (DST) of DR-TB enables the timely administration of a chemotherapy regimen that effectively treats DR-TB. GeneChip has been reported as a novel molecular diagnostic tool for rapid diagnosis but has limited data on the performance of subgroup patients with DR-TB. This study aims to assess the diagnostic value of GeneChip in patients with different sexes, ages, treatment histories, treatment outcomes, and places of residence. Methods We recruited newly registered sputum smear-positive pulmonary TB patients from January 2011 to September 2020 in Lianyungang City, Jiangsu Province, China. We applied both GeneChip and DST to measure drug resistance to rifampin (RIF) and isoniazid (INH). The kappa value, sensitivity, specificity, and agreement rate (AR) were calculated. We also applied a Classification and Regression Tree to explore factors related to the performance of GeneChip. Results We observed that sex, age, treatment history, treatment outcomes, and drug resistance type were significantly associated with the performance of GeneChip. For RIF resistance, there was significant accordance in young patients (kappa: 0.79) and cases with the treatment failure outcome (kappa: 0.92). For multidrug resistance (MDR), there was significant accordance in young cases (kappa: 0.77). Compared with previously treated patients, the newly treated patients had a significantly higher AR in detecting RIF resistance (0.97 vs 0.92), INH resistance (0.95 vs 0.89), and MDR (0.98 vs 0.92). The overall sensitivity, specificity, AR and kappa value for the diagnosis of MDR-TB were 0.70 (95% CI: 0.63–0.70), 0.99 (95% CI: 0.98–0.99), 0.98 (95% CI: 0.97–0.98), and 0.72 (95% CI: 0.67–0.78), respectively. Conclusion We observed a high concordance between GeneChip and DST among TB patients with different characteristics, indicating that GeneChip can be a potential alternative tool for rapid MDR-TB detection.
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Affiliation(s)
- Jinyan Shi
- Department of Clinical Laboratory, The Fourth People's Hospital of Lianyungang, Lianyungang, Jiangsu, People's Republic of China
| | - Bilin Tao
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Zhongqi Li
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Huan Song
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Jizhou Wu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Beibei Qiu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Jianming Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
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Gonzaga LDM, Gils T, Decroo T, Jacobs BKM, Lynen L. Case Report: Therapeutic Threshold for Rifampicin-Resistant Tuberculosis in a Patient from Maputo, Mozambique. Am J Trop Med Hyg 2021; 104:1317-1320. [PMID: 33556043 PMCID: PMC8045612 DOI: 10.4269/ajtmh.20-0959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 12/10/2020] [Indexed: 11/07/2022] Open
Abstract
We present a case of a patient in Mozambique, who initiated treatment for rifampicin-resistant tuberculosis (RR-TB) without proof of resistance. For this patient, we estimated the probability of RR-TB using likelihood ratios of clinical arguments. The probability of RR-TB in Mozambique, positive HIV status, and treatment failure after a first treatment and after retreatment were included as confirming arguments, and a rapid molecular test showing rifampicin susceptibility as excluding argument. The therapeutic threshold to start treatment for RR-TB is unknown, but probably lower than 47% and should be calculated to guide clinical decisions.
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Affiliation(s)
| | - Tinne Gils
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Tom Decroo
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Research Foundation Flanders, Brussels, Belgium
| | - Bart K. M. Jacobs
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Lutgarde Lynen
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
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Ngabonziza JCS, Decroo T, Maniliho R, Habimana YM, Van Deun A, de Jong BC. Low Cycle Threshold Value in Xpert MTB/RIF Assay May Herald False Detection of Tuberculosis and Rifampicin Resistance: A Study of Two Cases. Open Forum Infect Dis 2021; 8:ofab034. [PMID: 33614819 PMCID: PMC7885858 DOI: 10.1093/ofid/ofab034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 01/19/2021] [Indexed: 11/15/2022] Open
Abstract
We report 2 cases for whom Xpert MTB/RIF falsely signaled rifampicin-resistant tuberculosis, based on unusually low cycle threshold and 3 of 5 probes missing. Other mycobacterial tests were negative. Further optimization of the Xpert MTB/RIF algorithm is warranted.
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Affiliation(s)
- Jean Claude S Ngabonziza
- National Reference Laboratory Division, Department of Biomedical Services, Rwanda Biomedical Centre, Kigali, Rwanda
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Tom Decroo
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Research Foundation Flanders, Brussels, Belgium
| | | | - Yves M Habimana
- Tuberculosis and Other Respiratory Diseases Division, Institute of HIV/AIDS Disease Prevention and Control, Rwanda Biomedical Center, Kigali, Rwanda
| | | | - Bouke C de Jong
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
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Gopie F, Commiesie E, Baldi S, Kamst M, Kaur D, de Lange W, Pinas P, Stijnberg D, Wongsokarijo M, Zijlmans C, de Zwaan R, van Soolingen D, Vreden S, de Vries G. Should treatment of low-level rifampicin mono-resistant tuberculosis be different? J Clin Tuberc Other Mycobact Dis 2021; 23:100222. [PMID: 33598570 PMCID: PMC7869001 DOI: 10.1016/j.jctube.2021.100222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background Rifampicin resistant tuberculosis (RR-TB) was frequently detected in Suriname after the introduction of Xpert MTB/RIF in 2012. Subsequent phenotypic drug-susceptibility testing (DST) was not conclusive at that moment, while RR-TB patients treated with first-line tuberculostatics had good treatment outcome. In our study, we analysed this interesting observation. Methods We collected demographic and clinical characteristics and treatment outcome of TB patients from May 2012-December 2018 and performed a univariate and multivariate analysis to assess possible associations with resistance to rifampicin. Secondly, we conducted whole genome sequencing on all available Mycobacterium tuberculosis isolates that had a rifampicin resistance in the Xpert MTB/RIF test and performed phenotypic DST on selected isolates. Findings RR-TB was detected in 59 (9.6%) patients confirmed by Xpert. These patients were treated with rifampicin-containing regimens in most (88%) of the cases. In all 32 samples examined, a D435Y mutation in the rpoB gene was identified; only one isolate revealed an additional isoniazid mutation. Phenotypic DST indicated low-level rifampicin resistance. In multivariate analysis, the Creole ethnicity was a factor associated with rifampicin resistance (aOR 3.5; 95%CI 1.9–6.4). The treatment success rate for patients with RR-TB (78.0%) was comparable to the treatment outcome in non-RR-TB patients 77.8%. Interpretation This study confirms a low-level rifampicin mono-resistance in TB patients of Suriname. These patients could benefit from a first-line regimen with high dose rifampicin (or rifabutin), rather than from the lengthy treatment regimens for rifampicin-resistant and multi-drug resistant TB, a concept of stratified medicine also advocated for the treatment of TB. Funding None.
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Affiliation(s)
- F.A. Gopie
- Academic Hospital Paramaribo, Paramaribo, Suriname
- Faculty of Medical Sciences, Anton de Kom University of Suriname, Paramaribo, Suriname
- Corresponding author at: Academic Hospital Paramaribo, Paramaribo, Suriname.
| | - E. Commiesie
- National Tuberculosis Program, Paramaribo, Suriname
| | - S. Baldi
- Central Laboratory, Paramaribo, Suriname
| | - M. Kamst
- National Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - D. Kaur
- Massachusetts Supranational TB Reference Laboratory, University of Massachusetts Medical School, Jamaica Plane, MA, USA
| | - W.C.M. de Lange
- Department Pulmonary Diseases and Tuberculosis, University Medical Center Groningen, the Netherlands
| | - P.S. Pinas
- Central Laboratory, Paramaribo, Suriname
| | - D. Stijnberg
- National Tuberculosis Program, Paramaribo, Suriname
| | | | - C.W.R. Zijlmans
- Faculty of Medical Sciences, Anton de Kom University of Suriname, Paramaribo, Suriname
| | - R. de Zwaan
- National Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - D. van Soolingen
- National Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | | | - G. de Vries
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
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Guo Y, Cao X, Yang J, Wu X, Liu Y, Wan B, Hu L, Wang H, Yu F. Rifampin-resistance-associated mutations in the rifampin-resistance-determining region of the rpoB gene of Mycobacterium tuberculosis clinical isolates in Shanghai, PR China. J Med Microbiol 2021; 70. [PMID: 33507146 DOI: 10.1099/jmm.0.001317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Resistance to rifampin (RIF) in Mycobacterium tuberculosis infection is associated with mutations in the rpoB gene coding for the β-subunit of RNA polymerase. The contribution of various rpoB mutations to the development and level of RIF resistance remains elusive.Hypothesis/Gap Statement. Various rpoB mutations may be associated with differential levels of RIF resistance.Aim. This study aimed to investigate the relationship between specific rpoB mutations and the MICs of RIF and rifabutin (RFB) against M. tuberculosis.Methodology. Of the 195 clinical isolates, 105 and 90 isolates were randomly selected from isolates resistant to RIF and sensitive to RIF, respectively. The MICs of 12 agents for M. tuberculosis isolates were determined using commercial Sensititre M. tuberculosis MIC plates and the broth microdilution method. Strains were screened for rpoB mutations by DNA extraction, rpoB gene amplification and DNA sequence analysis.Results. One hundred isolates (95.24 %) were found to have mutations in the RIF-resistance-determining region (RRDR) of the rpoB gene. Three rpoB mutations were identified in 90 RIF-susceptible isolates. Out of 105 isolates, 86 (81.90 %) were cross-resistant to both RIF and RFB. The most frequent mutation occurred at codons 450 and 445. We also found a novel nine-nucleotide (ATCATGCAT) deletion (between positions 1543 and 1551) in the rpoB gene in two strains (1.90 %) with resistance to RIF, but susceptibility to RFB. In addition, the mutation frequency at codon 450 was significantly higher in RIF-resistant/RFB-resistant (RIFR/RFBR) strains than in RIFR/RFBS strains (75.58 % versus 21.05 %, P<0.01), whereas the mutation frequency at codon 435 was significantly lower in RIFR/RFBR strains than in RIFR/RFBS strains (1.16 % versus 26.32 %, P<0.01).Conclusion. Our data support previous findings, which reported that various rpoB mutations are associated with differential levels of RIF resistance. The specific mutations in the rpoB gene in RIFR/RFBR isolates differed from those in the RIFR/RFBS isolates. A novel deletion mutation in the RRDR might be associated with resistance to RIF, but not to RFB. Further clinical studies are required to investigate the efficacy of RFB in the treatment of infections caused by M. tuberculosis strains harbouring these mutations.
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Affiliation(s)
- Yinjuan Guo
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, PR China.,Department of Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, PR China
| | - Xingwei Cao
- Jiangxi Provincial Key laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, 330000, PR China
| | - Jinghui Yang
- Department of Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, PR China
| | - Xiaocui Wu
- Department of Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, PR China
| | - Yin Liu
- Department of Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, PR China
| | - Baoshan Wan
- Department of Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, PR China
| | - Longhua Hu
- Jiangxi Provincial Key laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, 330000, PR China
| | - Hongxiu Wang
- Department of Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, PR China
| | - Fangyou Yu
- Department of Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, PR China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, PR China
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49
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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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50
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Banaei N, Musser KA, Salfinger M, Somoskovi A, Zelazny AM. Novel Assays/Applications for Patients Suspected of Mycobacterial Diseases. Clin Lab Med 2020; 40:535-552. [DOI: 10.1016/j.cll.2020.08.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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