1
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Tram TTB, Trieu LPT, Nhat LTH, Thu DDA, Quang NL, Bang ND, Chau TTH, Thwaites GE, Walker TM, Ha VTN, Thuong NTT. Targeted sequencing from cerebrospinal fluid for rapid identification of drug-resistant tuberculous meningitis. J Clin Microbiol 2024; 62:e0128723. [PMID: 38466092 PMCID: PMC11005362 DOI: 10.1128/jcm.01287-23] [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: 10/02/2023] [Accepted: 02/03/2024] [Indexed: 03/12/2024] Open
Abstract
Mortality from tuberculous meningitis (TBM) remains around 30%, with most deaths occurring within 2 months of starting treatment. Mortality from drug-resistant strains is higher still, making early detection of drug resistance (DR) essential. Targeted next-generation sequencing (tNGS) produces high read depths, allowing the detection of DR-associated alleles with low frequencies. We applied Deeplex Myc-TB-a tNGS assay-to cerebrospinal fluid (CSF) samples from 72 adults with microbiologically confirmed TBM and compared its genomic drug susceptibility predictions to a composite reference standard of phenotypic susceptibility testing (pDST) and whole genome sequencing, as well as to clinical outcomes. Deeplex detected Mycobacterium tuberculosis complex DNA in 24/72 (33.3%) CSF samples and generated full DR reports for 22/24 (91.7%). The read depth generated by Deeplex correlated with semi-quantitative results from MTB/RIF Xpert. Alleles with <20% frequency were seen at canonical loci associated with first-line DR. Disregarding these low-frequency alleles, Deeplex had 100% concordance with the composite reference standard for all drugs except pyrazinamide and streptomycin. Three patients had positive CSF cultures after 30 days of treatment; reference tests and Deeplex identified isoniazid resistance in two, and Deeplex alone identified low-frequency rifampin resistance alleles in one. Five patients died, of whom one had pDST-identified pyrazinamide resistance. tNGS on CSF can rapidly and accurately detect drug-resistant TBM, but its application is limited to those with higher bacterial loads. In those with lower bacterial burdens, alternative approaches need to be developed for both diagnosis and resistance detection.
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Affiliation(s)
| | | | | | - Do Dang Anh Thu
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Le Quang
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Duc Bang
- Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, Vietnam
| | | | - Guy E. Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Timothy M. Walker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Vu Thi Ngoc Ha
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Thuy Thuong Thuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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2
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Dheda K, Mirzayev F, Cirillo DM, Udwadia Z, Dooley KE, Chang KC, Omar SV, Reuter A, Perumal T, Horsburgh CR, Murray M, Lange C. Multidrug-resistant tuberculosis. Nat Rev Dis Primers 2024; 10:22. [PMID: 38523140 DOI: 10.1038/s41572-024-00504-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/16/2024] [Indexed: 03/26/2024]
Abstract
Tuberculosis (TB) remains the foremost cause of death by an infectious disease globally. Multidrug-resistant or rifampicin-resistant TB (MDR/RR-TB; resistance to rifampicin and isoniazid, or rifampicin alone) is a burgeoning public health challenge in several parts of the world, and especially Eastern Europe, Russia, Asia and sub-Saharan Africa. Pre-extensively drug-resistant TB (pre-XDR-TB) refers to MDR/RR-TB that is also resistant to a fluoroquinolone, and extensively drug-resistant TB (XDR-TB) isolates are additionally resistant to other key drugs such as bedaquiline and/or linezolid. Collectively, these subgroups are referred to as drug-resistant TB (DR-TB). All forms of DR-TB can be as transmissible as rifampicin-susceptible TB; however, it is more difficult to diagnose, is associated with higher mortality and morbidity, and higher rates of post-TB lung damage. The various forms of DR-TB often consume >50% of national TB budgets despite comprising <5-10% of the total TB case-load. The past decade has seen a dramatic change in the DR-TB treatment landscape with the introduction of new diagnostics and therapeutic agents. However, there is limited guidance on understanding and managing various aspects of this complex entity, including the pathogenesis, transmission, diagnosis, management and prevention of MDR-TB and XDR-TB, especially at the primary care physician level.
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Affiliation(s)
- 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 and Tropical Medicine, London, UK.
| | - Fuad Mirzayev
- Global Tuberculosis Programme, WHO, Geneva, Switzerland
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute Milan, Milan, Italy
| | - Zarir Udwadia
- Department of Pulmonology, Hinduja Hospital & Research Center, Mumbai, India
| | - Kelly E Dooley
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kwok-Chiu Chang
- Tuberculosis and Chest Service, Centre for Health Protection, Department of Health, Hong Kong, SAR, China
| | - Shaheed Vally Omar
- Centre for Tuberculosis, National & WHO Supranational TB Reference Laboratory, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Molecular Medicine & Haematology, School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Anja Reuter
- Sentinel Project on Paediatric Drug-Resistant Tuberculosis, Boston, MA, USA
| | - Tahlia Perumal
- 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 and Tropical Medicine, London, UK
| | - C Robert Horsburgh
- Department of Epidemiology, Boston University Schools of Public Health and Medicine, Boston, MA, USA
| | - Megan Murray
- Department of Epidemiology, Harvard Medical School, Boston, MA, USA
| | - Christoph Lange
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), TTU-TB, Borstel, Germany
- Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
- Department of Paediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
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3
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Zhang X, Lam C, Martinez E, Sim E, Crighton T, Marais BJ, Sintchenko V. Genomic markers of drug resistance in Mycobacterium tuberculosis populations with minority variants. J Clin Microbiol 2023; 61:e0048523. [PMID: 37750734 PMCID: PMC10595065 DOI: 10.1128/jcm.00485-23] [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: 04/18/2023] [Accepted: 07/17/2023] [Indexed: 09/27/2023] Open
Abstract
Minority variants of Mycobacterium tuberculosis harboring mutations conferring resistance can become dominant populations during tuberculosis (TB) treatment, leading to treatment failure. Our understanding of drug-resistant within-host subpopulations and the frequency of resistance-conferring mutations in minority variants remains limited. M. tuberculosis sequences recovered from liquid cultures of culture-confirmed TB cases notified between January 2017 and December 2021 in New South Wales, Australia were examined. Potential drug resistance-conferring minority variants were identified using LoFreq, and mixed populations of different M. tuberculosis strains (≥100 SNPs apart) were examined using QuantTB. A total of 1831 routinely sequenced M. tuberculosis strains were included in the analysis. Drug resistance-conferring minority variants were detected in 3.5% (65/1831) of sequenced cultures; 84.6% (55/65) had majority strains that were drug susceptible and 15.4% (10/65) had majority strains that were drug resistant. Minority variants with high-confidence drug resistance-conferring mutations were 1.5 times more common when the majority strains were drug resistant. Mixed M. tuberculosis strain populations were documented in 10.0% (183/1831) of specimens. Minority variants with high-confidence drug resistance-conferring mutations were more frequently detected in mixed M. tuberculosis strain populations (2.7%, 5/183) than in single strain populations (0.6%, 10/1648; P = 0.01). Drug-resistant minority variants require monitoring in settings that implement routine M. tuberculosis sequencing. The frequency with which drug-resistant minority variants are detected is likely influenced by pre-culture requirement. Culture-independent sequencing methods should provide a more accurate reflection of drug-resistant subpopulations.
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Affiliation(s)
- Xiaomei Zhang
- Centre for Research Excellence in Tuberculosis (TB-CRE), Centenary Institute, Sydney, New South Wales, Australia
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, New South Wales, Australia
| | - Connie Lam
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, New South Wales, Australia
| | - Elena Martinez
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, 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, Sydney, New South Wales, Australia
| | - Eby Sim
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, New South Wales, Australia
| | - Taryn Crighton
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, 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, Sydney, New South Wales, Australia
| | - Ben J. Marais
- Centre for Research Excellence in Tuberculosis (TB-CRE), Centenary Institute, Sydney, New South Wales, Australia
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Research Excellence in Tuberculosis (TB-CRE), Centenary Institute, Sydney, New South Wales, Australia
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, 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, Sydney, New South Wales, Australia
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4
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Zhang S, Chen X, Lin Z, Tan Y, Liang B, Pan Y, Huang M, Su B, Hu X, Xu Y, Li Q. Quantification of Isoniazid-Heteroresistant Mycobacterium tuberculosis Using Droplet Digital PCR. J Clin Microbiol 2023; 61:e0188422. [PMID: 37195177 PMCID: PMC10281145 DOI: 10.1128/jcm.01884-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/04/2023] [Indexed: 05/18/2023] Open
Abstract
The quantitative detection of drug-resistance mutations in Mycobacterium tuberculosis (MTB) is critical for determining the drug resistance status of a sample. We developed a drop-off droplet digital PCR (ddPCR) assay targeting all major isoniazid (INH)-resistant mutations. The ddPCR assay consisted of three reactions: reaction A detects mutations at katG S315; reaction B detects inhA promoter mutations; and reaction C detects ahpC promoter mutations. All reactions could quantify 1%-50% of mutants in the presence of the wild-type, ranging from 100 to 50,000 copies/reaction. Clinical evaluation with 338 clinical isolates yielded clinical sensitivity of 94.5% (95% confidence interval [CI] = 89.1%-97.3%) and clinical specificity of 97.6% (95% CI = 94.6%-99.0%) compared with the traditional drug susceptibility testing (DST). Further clinical evaluation using 194 nucleic acid-positive MTB sputum samples revealed clinical sensitivity of 87.8% (95% CI = 75.8%-94.3%) and clinical specificity of 96.5% (95% CI = 92.2%-98.5%) in comparison with DST. All the mutant and heteroresistant samples detected by the ddPCR assay but susceptible by DST were confirmed by combined molecular assays, including Sanger sequencing, mutant-enriched Sanger sequencing and a commercial melting curve analysis-based assay. Finally, the ddPCR assay was used to monitor longitudinally the INH-resistance status and the bacterial load in nine patients undergoing treatment. Overall, the developed ddPCR assay could be an indispensable tool for quantification of INH-resistant mutations in MTB and bacterial loads in patients.
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Affiliation(s)
- Siqi Zhang
- Engineering Research Centre of Molecular Diagnostics of Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiaohong Chen
- The Pulmonary Hospital of Fuzhou in Fujian Province, Fuzhou, Fujian, China
| | - Zhonghui Lin
- The Pulmonary Hospital of Fuzhou in Fujian Province, Fuzhou, Fujian, China
| | - Yaoju Tan
- Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou, China
| | - Bin Liang
- Engineering Research Centre of Molecular Diagnostics of Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yuying Pan
- Engineering Research Centre of Molecular Diagnostics of Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Mingxiang Huang
- The Pulmonary Hospital of Fuzhou in Fujian Province, Fuzhou, Fujian, China
| | - Biyi Su
- Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou, China
| | - Xiaoman Hu
- Engineering Research Centre of Molecular Diagnostics of Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Ye Xu
- Engineering Research Centre of Molecular Diagnostics of Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Qingge Li
- Engineering Research Centre of Molecular Diagnostics of Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
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5
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Hu Y, Chi Y, Feng X, Yu F, Li H, Shang Y, Pan J, Pang Y. Comparison of the Diagnostic Performance of MeltPro and Next-Generation Sequencing in Determining Fluoroquinolone Resistance in Multidrug-Resistant Tuberculosis Isolates. J Mol Diagn 2023; 25:342-351. [PMID: 37208048 DOI: 10.1016/j.jmoldx.2023.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 12/20/2022] [Accepted: 02/09/2023] [Indexed: 05/21/2023] Open
Abstract
This study systematically investigated the performance of MeltPro and next-generation sequencing in the diagnosis of fluoroquinolone (FQ) resistance among multidrug-resistant tuberculosis patients and explored the relationship between nucleotide alteration and the level of phenotypic susceptibility to FQs. From March 2019 to June 2020, a feasibility and validation study with both MeltPro and next-generation sequencing was performed in 126 patients with multidrug-resistant tuberculosis. Using phenotypic drug susceptibility testing as the gold standard, 95.3% (82 of 86) of ofloxacin-resistant isolates were identified correctly by MeltPro. In addition, whole-genome sequencing was able to detect 83 phenotypically ofloxacin-resistant isolates. The isolates with an individual gyrB mutation outside the quinolone resistance-determining region (QRDR) had minimum inhibitory concentrations (MICs) of ≤2 μg/mL. Despite showing low MICs close to the breakpoint for isolates carrying only gyrA_Ala90Val, the combined mutation gyrB_Asp461Asn caused the ofloxacin MIC to be eight higher than that obtained in Mycobacterium tuberculosis (MTB) isolates with the Ala90Val mutation alone (median, 32 μg/mL; P = 0.038). Heteroresistance was observed in 12 of 88 isolates harboring mutations in the QRDRs. In conclusion, our data show that MeltPro and the whole-genome sequencing assay correctly can identify FQ resistance caused by mutations in the gyrA QRDR. The combined gyrB_Asp461Asn mutation may significantly decrease in vitro FQ susceptibility of MTB isolates with low-level-resistance-associated gyrA mutations.
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Affiliation(s)
- Yan Hu
- Tuberculosis Reference Laboratory, Chongqing Municipal Institute of Tuberculosis, Chongqing, China
| | - Yuqing Chi
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Xin Feng
- Tuberculosis Reference Laboratory, Chongqing Municipal Institute of Tuberculosis, Chongqing, China
| | - Fengping Yu
- Tuberculosis Reference Laboratory, Chongqing Municipal Institute of Tuberculosis, Chongqing, China
| | - Haoran Li
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Yuanyuan Shang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Junhua Pan
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China.
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China.
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6
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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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7
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Yan M, Zhao Z, Wu T, Liu T, Xu G, Xu H, Ying B. Highly Sensitive Detection of Complicated Mutations of Drug Resistance in Mycobacterium tuberculosis Using a Simple, Accurate, Rapid, and Low-Cost Tailored-Design Competitive Wild-Type Blocking Assay. SMALL METHODS 2023; 7:e2201322. [PMID: 36683186 DOI: 10.1002/smtd.202201322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Establishing simple, rapid, and highly sensitive molecular assays is crucial for timely diagnosis and effective treatment of drug-resistant tuberculosis. However, current genotypic drug susceptibility testing (DST) still encounters enormous challenges including lower sensitivity than phenotypic DST and insufficient accuracy. Herein, a simple, low-cost, multiplex real-time polymerase chain reaction-based assay is established to achieve highly sensitive detection of low-abundant mutants through competitive wild-type blocking (COWTB). Analytical performance of the COWTB assay can achieve 1% or even 0.1% mutants under background of 10 000 wild-type genomes/test. Furthermore, clinical practice feasibility is evaluated to identify resistance to rifampicin (RIF), isoniazid (INH), and streptomycin (SM) on 92 actual clinical samples, its sensitivity is 93.8% for RIF and 100% for INH and SM, and specificity is 100% each for RIF, INH, and SM when using DNA sequencing as the reference standard. In comparison, the sensitivity of reverse dot blotting assay commonly used in clinics is 93.8%, 90.0%, and 84.6%, and the specificity is 96.1%, 98.6%, and 100% for RIF, INH, and SM, respectively. Importantly, the COWTB assay can also be applicable for other drug-resistant mutations and pave a promising detection strategy to fill the gap between phenotypic and genotypic DST for detecting low-abundant drug-resistant M. tuberculosis.
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Affiliation(s)
- Mengqiu Yan
- School of Biomedical Engineering/Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Zhenzhen Zhao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, P. R. China
| | - Tao Wu
- Department of Clinical Laboratory Medicine, People's Hospital of Ningxia Hui Autonomous Region (First Affiliated Hospital of Northwest Minzu University), Yinchuan, 750002, P. R. China
| | - Tangyuheng Liu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, P. R. China
| | - Gaolian Xu
- School of Biomedical Engineering/Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Hong Xu
- School of Biomedical Engineering/Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, P. R. China
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8
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Desikan P, Panwalkar N, Punde RP, Khan Z, Pauranik A, Mirza SB, Chourey M, Anand S, Sachdeva K. Heteroresistance to rifampicin & isoniazid in clinical samples of patients with presumptive drug-resistant tuberculosis in Central India. Indian J Med Res 2023; 157:174-182. [PMID: 37202936 PMCID: PMC10319389 DOI: 10.4103/ijmr.ijmr_607_22] [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: 03/09/2022] [Indexed: 04/28/2023] Open
Abstract
Background & objectives A combination of resistant and susceptible Mycobacterium tuberculosis (MTB) isolated from clinical specimens is referred to as heteroresistance. Heteroresistance leads to difficulties in drug resistance testing and may adversely affect treatment outcomes. The present study estimated the proportion of heteroresistance among MTB in clinical samples of presumptive drug-resistant tuberculosis (TB) patients in Central India. Methods A retrospective analysis of data generated from line probe assay (LPA) at a tertiary care hospital in Central India between January 2013 and December 2018 was carried out. A heteroresistant MTB in a sample was indicated by the presence of both wild-type and mutant-type patterns on an LPA strip. Results Data analysis was carried out on interpretable 11,788 LPA results. Heteroresistance in MTB was detected in 637 (5.4%) samples. Of these, heteroresistance in MTB was detected in 413 (64.8%), 163 (25.5%) and 61 (9.5%) samples with respect to rpoB, katG and inhA genes, respectively. Interpretation & conclusions Heteroresistance is considered a preliminary step in the development of drug resistance. Delayed or suboptimal anti-tubercular therapy in patients with heteroresistance of MTB may elicit full clinical resistance and negatively impact the National TB Elimination Programme. Further studies are, however, needed to determine the impact of heteroresistance on treatment outcomes in individual patients.
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Affiliation(s)
- Prabha Desikan
- ICMR-Bhopal Memorial Hospital & Research Centre, Bhopal, Madhya Pradesh, India
| | | | | | - Zeba Khan
- Department of Microbiology, Bhopal, Madhya Pradesh, India
| | - Ankur Pauranik
- Department of Microbiology, Bhopal, Madhya Pradesh, India
| | | | - Manju Chourey
- Department of Microbiology, Bhopal, Madhya Pradesh, India
| | - Sridhar Anand
- World Health Organization, Ministry of Health & Family Welfare, New Delhi, India
| | - K.S. Sachdeva
- Central TB Division, Ministry of Health & Family Welfare, New Delhi, India
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Ludi Z, Sule AA, Samy RP, Putera I, Schrijver B, Hutchinson PE, Gunaratne J, Verma I, Singhal A, Nora RLD, van Hagen PM, Dik WA, Gupta V, Agrawal R. Diagnosis and biomarkers for ocular tuberculosis: From the present into the future. Theranostics 2023; 13:2088-2113. [PMID: 37153734 PMCID: PMC10157737 DOI: 10.7150/thno.81488] [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: 12/02/2022] [Accepted: 03/19/2023] [Indexed: 05/10/2023] Open
Abstract
Tuberculosis is an airborne disease caused by Mycobacterium tuberculosis (Mtb) and can manifest both pulmonary and extrapulmonary disease, including ocular tuberculosis (OTB). Accurate diagnosis and swift optimal treatment initiation for OTB is faced by many challenges combined with the lack of standardized treatment regimens this results in uncertain OTB outcomes. The purpose of this study is to summarize existing diagnostic approaches and recently discovered biomarkers that may contribute to establishing OTB diagnosis, choice of anti-tubercular therapy (ATT) regimen, and treatment monitoring. The keywords ocular tuberculosis, tuberculosis, Mycobacterium, biomarkers, molecular diagnosis, multi-omics, proteomics, genomics, transcriptomics, metabolomics, T-lymphocytes profiling were searched on PubMed and MEDLINE databases. Articles and books published with at least one of the keywords were included and screened for relevance. There was no time limit for study inclusion. More emphasis was placed on recent publications that contributed new information about the pathogenesis, diagnosis, or treatment of OTB. We excluded abstracts and articles that were not written in the English language. References cited within the identified articles were used to further supplement the search. We found 10 studies evaluating the sensitivity and specificity of interferon-gamma release assay (IGRA), and 6 studies evaluating that of tuberculin skin test (TST) in OTB patients. IGRA (Sp = 71-100%, Se = 36-100%) achieves overall better sensitivity and specificity than TST (Sp = 51.1-85.7%; Se = 70.9-98.5%). For nuclear acid amplification tests (NAAT), we found 7 studies on uniplex polymerase chain reaction (PCR) with different Mtb targets, 7 studies on DNA-based multiplex PCR, 1 study on mRNA-based multiplex PCR, 4 studies on loop-mediated isothermal amplification (LAMP) assay with different Mtb targets, 3 studies on GeneXpert assay, 1 study on GeneXpert Ultra assay and 1 study for MTBDRplus assay for OTB. Specificity is overall improved but sensitivity is highly variable for NAATs (excluding uniplex PCR, Sp = 50-100%; Se = 10.5-98%) as compared to IGRA. We also found 3 transcriptomic studies, 6 proteomic studies, 2 studies on stimulation assays, 1 study on intraocular protein analysis and 1 study on T-lymphocyte profiling in OTB patients. All except 1 study evaluated novel, previously undiscovered biomarkers. Only 1 study has been externally validated by a large independent cohort. Future theranostic marker discovery by a multi-omics approach is essential to deepen pathophysiological understanding of OTB. Combined these might result in swift, optimal and personalized treatment regimens to modulate the heterogeneous mechanisms of OTB. Eventually, these studies could improve the current cumbersome diagnosis and management of OTB.
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Affiliation(s)
- Zhang Ludi
- Lee Kong Chian School of Medicine, Nanyang Technological University of Singapore, Singapore
| | - Ashita Ashish Sule
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ramar Perumal Samy
- National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore, Singapore
| | - Ikhwanuliman Putera
- Department of Ophthalmology, Faculty of Medicine Universitas Indonesia - CiptoMangunkusmoKirana Eye Hospital, Jakarta, Indonesia
- Laboratory Medical Immunology, Department of Immunology, ErasmusMC, UniversityMedical Centre, Rotterdam, the Netherlands
- Department of Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Department of Ophthalmology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Benjamin Schrijver
- Laboratory Medical Immunology, Department of Immunology, ErasmusMC, UniversityMedical Centre, Rotterdam, the Netherlands
| | - Paul Edward Hutchinson
- Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Jayantha Gunaratne
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Indu Verma
- Department of Biochemistry, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Amit Singhal
- Lee Kong Chian School of Medicine, Nanyang Technological University of Singapore, Singapore
- A*SATR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Rina La Distia Nora
- Department of Ophthalmology, Faculty of Medicine Universitas Indonesia - CiptoMangunkusmoKirana Eye Hospital, Jakarta, Indonesia
- Laboratory Medical Immunology, Department of Immunology, ErasmusMC, UniversityMedical Centre, Rotterdam, the Netherlands
- University of Indonesia Hospital (RSUI), Depok, West Java, Indonesia
| | - P. Martin van Hagen
- Laboratory Medical Immunology, Department of Immunology, ErasmusMC, UniversityMedical Centre, Rotterdam, the Netherlands
- Department of Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Willem A Dik
- Laboratory Medical Immunology, Department of Immunology, ErasmusMC, UniversityMedical Centre, Rotterdam, the Netherlands
| | - Vishali Gupta
- Advanced Eye Centre, Post-Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Rupesh Agrawal
- Lee Kong Chian School of Medicine, Nanyang Technological University of Singapore, Singapore
- National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore, Singapore
- Duke NUS Medical School, Singapore, Singapore
- Singapore Eye Research Institute, Singapore, Singapore
- National Institute for Health Research Biomedical Research Centre, Moorfields Eye Hospital, London, UK
- School of Pharmacy, Nantong University, Nantong, P. R. China
- Department of Mechanical Engineering, University College London, London, United Kingdom
- ✉ Corresponding author: A/Prof (Dr) Rupesh Agrawal, Senior Consultant, National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore 308433,
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10
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Mvelase NR, Cele LP, Singh R, Naidoo Y, Giandhari J, Wilkinson E, de Oliveira T, Swe-Han KS, Mlisana KP. Consequences of rpoB mutations missed by the GenoType MTBDR plus assay in a programmatic setting in South Africa. Afr J Lab Med 2023; 12:1975. [PMID: 36873290 PMCID: PMC9982466 DOI: 10.4102/ajlm.v12i1.1975] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/24/2022] [Indexed: 02/05/2023] Open
Abstract
Background Rifampicin resistance missed by commercial rapid molecular assays but detected by phenotypic assays may lead to discordant susceptibility results and affect patient management. Objective This study was conducted to evaluate the causes of rifampicin resistance missed by the GenoType MTBDRplus and its impact on the programmatic management of tuberculosis in KwaZulu-Natal, South Africa. Methods We analysed routine tuberculosis programme data from January 2014 to December 2014 on isolates showing rifampicin susceptibility on the GenoType MTBDRplus assay but resistance on the phenotypic agar proportion method. Whole-genome sequencing was performed on a subset of these isolates. Results Out of 505 patients with isoniazid mono-resistant tuberculosis on the MTBDRplus, 145 (28.7%) isolates showed both isoniazid and rifampicin resistance on the phenotypic assay. The mean time from MTBDRplus results to initiation of drug-resistant tuberculosis therapy was 93.7 days. 65.7% of the patients had received previous tuberculosis treatment. The most common mutations detected in the 36 sequenced isolates were I491F (16; 44.4%) and L452P (12; 33.3%). Among the 36 isolates, resistance to other anti-tuberculosis drugs was 69.4% for pyrazinamide, 83.3% for ethambutol, 69.4% for streptomycin, and 50% for ethionamide. Conclusion Missed rifampicin resistance was mostly due to the I491F mutation located outside the MTBDRplus detection area and the L452P mutation, which was not included in the initial version 2 of the MTBDRplus. This led to substantial delays in the initiation of appropriate therapy. The previous tuberculosis treatment history and the high level of resistance to other anti-tuberculosis drugs suggest an accumulation of resistance.
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Affiliation(s)
- Nomonde R Mvelase
- Department of Medical Microbiology, KwaZulu-Natal Academic Complex, National Health Laboratory Service, Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Lindiwe P Cele
- Department of Public Health, Epidemiology and Biostatistics Unit, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Ravesh Singh
- Department of Medical Microbiology, KwaZulu-Natal Academic Complex, National Health Laboratory Service, Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Yeshnee Naidoo
- KwaZulu-Natal Research Innovation and Sequencing Platform, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.,Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
| | - Khine Swe Swe-Han
- Department of Medical Microbiology, KwaZulu-Natal Academic Complex, National Health Laboratory Service, Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Koleka P Mlisana
- Department of Medical Microbiology, KwaZulu-Natal Academic Complex, National Health Laboratory Service, Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
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11
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Wu SH, Xiao YX, Hsiao HC, Jou R. Development and Assessment of a Novel Whole-Gene-Based Targeted Next-Generation Sequencing Assay for Detecting the Susceptibility of Mycobacterium tuberculosis to 14 Drugs. Microbiol Spectr 2022; 10:e0260522. [PMID: 36255328 PMCID: PMC9769975 DOI: 10.1128/spectrum.02605-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/23/2022] [Indexed: 01/07/2023] Open
Abstract
Targeted next-generation sequencing (tNGS) has emerged as an alternative method for detecting drug-resistant tuberculosis (DR-TB). To provide comprehensive drug susceptibility information and to address mutations missed by available commercial molecular diagnostics, we developed and evaluated a tNGS panel with 22 whole-gene targets using the Ion Torrent platform to predict drug resistance to 14 drugs, namely, rifampicin (RIF), isoniazid (INH), ethambutol (EMB), pyrazinamide (PZA), moxifloxacin (MFX), levofloxacin (LFX), amikacin (AMK), capreomycin (CM), kanamycin (KM), streptomycin (SM), bedaquiline (BDQ), clofazimine (CFZ), linezolid (LZD), and delamanid (DLM). We selected 50 and 35 Mycobacterium tuberculosis isolates with various DR profiles as the training set and the challenge set, respectively. Comparative variant analyses of the DR genes were performed using Sanger sequencing and whole-genome sequencing (WGS). Phenotypic drug susceptibility testing (pDST) results were used as gold standards. Regarding the limit of detection, the tNGS assay detected 2.9 to 3.8% minority variants in 4% mutant mixtures. The sensitivity and specificity of tNGS were 97.0% (95% confidence interval [CI] = 93.1 to 98.7%) and 99.1% (95% CI = 97.7 to 99.7%), respectively. The concordance of tNGS with pDST was 98.5% (95% CI = 97.2 to 99.2%), which was comparable to that of WGS (98.7%, 95% CI = 97.4 to 99.3%) and better than that of Sanger sequencing (96.9%, 95% CI = 95.3 to 98.0%). The agreement between tNGS and pDST was almost perfect for RIF, INH, EMB, MFX, LFX, AMK, CM, KM, SM, BDQ, and LZD (kappa value = 0.807 to 1.000) and substantial for PZA (kappa value = 0.791). Our customized novel whole-gene-based tNGS panel is highly consistent with pDST and WGS for comprehensive and accurate prediction of drug resistance in a strengthened and streamlined DR-TB laboratory program. IMPORTANCE We developed and validated a tNGS assay that was the first to target 22 whole genes instead of regions of drug resistance genes and comprehensively detected susceptibility to 14 anti-TB drugs, with great flexibility to include new or repurposed drugs. Notably, we demonstrated that our custom-designed Ion AmpliSeq TB research panel platform had high concordance with pDST and could significantly reduce turnaround time (by approximately 70%) to meet a clinically actionable time frame. Our tNGS assay is a promising DST solution for providing needed clinical information for precision medicine-guided therapies for DR-TB and allows the rollout of active pharmacovigilance.
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Affiliation(s)
- Sheng-Han Wu
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Yu-Xin Xiao
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Hseuh-Chien Hsiao
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Ruwen Jou
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
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12
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Narang A, Marras SAE, Kurepina N, Chauhan V, Shashkina E, Kreiswirth B, Varma-Basil M, Vinnard C, Subbian S. Ultrasensitive Detection of Multidrug-Resistant Mycobacterium tuberculosis Using SuperSelective Primer-Based Real-Time PCR Assays. Int J Mol Sci 2022; 23:ijms232415752. [PMID: 36555395 PMCID: PMC9779475 DOI: 10.3390/ijms232415752] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/02/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
The emergence of drug-resistant tuberculosis is a significant global health issue. The presence of heteroresistant Mycobacterium tuberculosis is critical to developing fully drug-resistant tuberculosis cases. The currently available molecular techniques may detect one copy of mutant bacterial genomic DNA in the presence of about 1-1000 copies of wild-type M. tuberculosis DNA. To improve the limit of heteroresistance detection, we developed SuperSelective primer-based real-time PCR assays, which, by their unique assay design, enable selective and exponential amplification of selected point mutations in the presence of abundant wild-type DNA. We designed SuperSelective primers to detect genetic mutations associated with M. tuberculosis resistance to the anti-tuberculosis drugs isoniazid and rifampin. We evaluated the efficiency of our assay in detecting heteroresistant M. tuberculosis strains using genomic DNA isolated from laboratory strains and clinical isolates from the sputum of tuberculosis patients. Results show that our assays detected heteroresistant mutations with a specificity of 100% in a background of up to 104 copies of wild-type M. tuberculosis genomic DNA, corresponding to a detection limit of 0.01%. Therefore, the SuperSelective primer-based RT-PCR assay is an ultrasensitive tool that can efficiently diagnose heteroresistant tuberculosis in clinical specimens and contributes to understanding the drug resistance mechanisms. This approach can improve the management of antimicrobial resistance in tuberculosis and other infectious diseases.
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Affiliation(s)
- Anshika Narang
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Salvatore A. E. Marras
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
- Correspondence: (S.A.E.M.); (S.S.)
| | | | - Varsha Chauhan
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 110021, India
| | | | | | - Mandira Varma-Basil
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 110021, India
| | | | - Selvakumar Subbian
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
- Correspondence: (S.A.E.M.); (S.S.)
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13
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Rapid Identification of Drug Resistance and Phylogeny in M. tuberculosis, Directly from Sputum Samples. Microbiol Spectr 2022; 10:e0125222. [PMID: 36102651 PMCID: PMC9602270 DOI: 10.1128/spectrum.01252-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Tuberculosis (TB) remains one of the most important infectious diseases globally. Establishing a resistance profile from the initial TB diagnosis is a priority. Rapid molecular tests evaluate only the most common genetic variants responsible for resistance to certain drugs, and Whole Genome Sequencing (WGS) needs culture prior to next-generation sequencing (NGS), limiting their clinical value. Targeted sequencing (TS) from clinical samples avoids these drawbacks, providing a signature of genetic markers that can be associated with drug resistance and phylogeny. In this study, a proof-of-concept protocol was developed for detecting genomic variants associated with drug resistance and for the phylogenetic classification of Mycobacterium Tuberculosis (Mtb) in sputum samples. Initially, a set of Mtb reference strains from the WHO were sequenced (WGS and TS). The results from the protocol agreed >95% with WHO reported data and phenotypic drug susceptibility testing (pDST). Lineage genetics results were 100% concordant with those derived from WGS. After that, the TS protocol was applied to sputum samples from TB patients to detect resistance to first- and second-line drugs and derive phylogeny. The accuracy was >90% for all evaluated drugs, except Eto/Pto (77.8%), and 100% were phylogenetically classified. The results indicate that the described protocol, which affords the complete drug resistance profile and phylogeny of Mtb from sputum, could be useful in the clinical area, advancing toward more personalized and more effective treatments in the near future. IMPORTANCE The COVID-19 pandemic negatively affected the progress in accessing essential Tuberculosis (TB) services and reducing the burden of TB disease, resulting in a decreased detection of new cases and increased deaths. Generating molecular diagnostic tests with faster results without losing reliability is considered a priority. Specifically, developing an antimicrobial resistance profile from the initial stages of TB diagnosis is essential to ensure appropriate treatment. Currently available rapid molecular tests evaluate only the most common genetic variants responsible for resistance to certain drugs, limiting their clinical value. In this work, targeted sequencing on sputum samples from TB patients was used to identify Mycobacterium tuberculosis mutations in genes associated with drug resistance and to derive a phylogeny of the infecting strain. This protocol constitutes a proof-of-concept toward the goal of helping clinicians select a timely and appropriate treatment by providing them with actionable information beyond current molecular approaches.
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14
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Nimmo C, Millard J, Faulkner V, Monteserin J, Pugh H, Johnson EO. Evolution of Mycobacterium tuberculosis drug resistance in the genomic era. Front Cell Infect Microbiol 2022; 12:954074. [PMID: 36275027 PMCID: PMC9585206 DOI: 10.3389/fcimb.2022.954074] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/20/2022] [Indexed: 12/02/2022] Open
Abstract
Mycobacterium tuberculosis has acquired drug resistance to all drugs that have been used against it, including those only recently introduced into clinical practice. Compared to other bacteria, it has a well conserved genome due to its role as an obligate human pathogen that has adapted to a niche over five to ten thousand years. These features facilitate reconstruction and dating of M. tuberculosis phylogenies, giving key insights into how resistance has been acquired and spread globally. Resistance to each new drug has occurred within five to ten years of clinical use and has occurred even more rapidly with recently introduced drugs. In most cases, resistance-conferring mutations come with a fitness cost, but this can be overcome by compensatory mutations which restore fitness to that of wild-type bacteria. It is likely that M. tuberculosis acquires drug resistance while maintaining limited genomic variability due the generation of low frequency within-host variation, combined with ongoing purifying selection causing loss of variants without a clear fitness advantage. However, variants that do confer an advantage, such as drug resistance, can increase in prevalence amongst all bacteria within a host and become the dominant clone. These resistant strains can then be transmitted leading to primary drug resistant infection in a new host. As many countries move towards genomic methods for diagnosis of M. tuberculosis infection and drug resistance, it is important to be aware of the implications for the evolution of resistance. Currently, understanding of resistance-conferring mutations is incomplete, and some targeted genetic diagnostics create their own selective pressures. We discuss an example where a rifampicin resistance-conferring mutation which was not routinely covered by standard testing became dominant. Finally, resistance to new drugs such as bedaquiline and delamanid is caused by individually rare mutations occurring across a large mutational genomic target that have been detected over a short time, and do not provide statistical power for genotype-phenotype correlation – in contrast to longer-established drugs that form the backbone of drug-sensitive antituberculosis therapy. Therefore, we need a different approach to identify resistance-conferring mutations of new drugs before their resistance becomes widespread, abrogating their usefulness.
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Affiliation(s)
- Camus Nimmo
- Systems Chemical Biology of Infection and Resistance Laboratory, Francis Crick Institute, London, United Kingdom
- *Correspondence: Camus Nimmo,
| | - James Millard
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Valwynne Faulkner
- Systems Chemical Biology of Infection and Resistance Laboratory, Francis Crick Institute, London, United Kingdom
| | - Johana Monteserin
- Systems Chemical Biology of Infection and Resistance Laboratory, Francis Crick Institute, London, United Kingdom
| | - Hannah Pugh
- Systems Chemical Biology of Infection and Resistance Laboratory, Francis Crick Institute, London, United Kingdom
| | - Eachan Oliver Johnson
- Systems Chemical Biology of Infection and Resistance Laboratory, Francis Crick Institute, London, United Kingdom
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15
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Lozano N, Lanza VF, Suárez-González J, Herranz M, Sola-Campoy PJ, Rodríguez-Grande C, Buenestado-Serrano S, Ruiz-Serrano MJ, Tudó G, Alcaide F, Muñoz P, García de Viedma D, Pérez-Lago L. Detection of Minority Variants and Mixed Infections in Mycobacterium tuberculosis by Direct Whole-Genome Sequencing on Noncultured Specimens Using a Specific-DNA Capture Strategy. mSphere 2021; 6:e0074421. [PMID: 34908457 PMCID: PMC8673255 DOI: 10.1128/msphere.00744-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/24/2021] [Indexed: 12/01/2022] Open
Abstract
Detection of mixed Mycobacterium tuberculosis (MTB) infections is essential, particularly when resistance mutations are present in minority bacterial populations that may affect patients' disease evolution and treatment. Whole-genome sequencing (WGS) has extended the amount of key information available for the diagnosis of MTB infection, including the identification of mixed infections. Having genomic information at diagnosis for early intervention requires carrying out WGS directly on the clinical samples. However, few studies have been successful with this approach due to the low representation of MTB DNA in sputa. In this study, we evaluated the ability of a strategy based on specific MTB DNA enrichment by using a newly designed capture platform (MycoCap) to detect minority variants and mixed infections by WGS on controlled mixtures of MTB DNAs in a simulated sputum genetic background. A pilot study was carried out with 12 samples containing 98% of a DNA pool from sputa of patients without MTB infection and 2% of MTB DNA mixtures at different proportions. Our strategy allowed us to generate sequences with a quality equivalent to those obtained from culture: 62.5× depth coverage and 95% breadth coverage (for at least 20× reads). Assessment of minority variant detection was carried out by manual analysis and allowed us to identify heterozygous positions up to a 95:5 ratio. The strategy also automatically distinguished mixed infections up to a 90:10 proportion. Our strategy efficiently captures MTB DNA in a nonspecific genetic background, allows detection of minority variants and mixed infections, and is a promising tool for performing WGS directly on clinical samples. IMPORTANCE We present a new strategy to identify mixed infections and minority variants in Mycobacterium tuberculosis by whole-genome sequencing. The objective of the strategy is the direct detection in patient sputum; in this way, minority populations of resistant strains can be identified at the time of diagnosis, facilitating identification of the most appropriate treatment for the patient from the first moment. For this, a platform for capturing M. tuberculosis-specific DNA was designed to enrich the clinical sample and obtain quality sequences.
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Affiliation(s)
- Nuria Lozano
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Val F. Lanza
- Bioinformatics Unit IRYCIS, University Hospital Ramón y Cajal, Madrid, Spain
- CIBER Enfermedades Infecciosas, Madrid, Spain
| | - Julia Suárez-González
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Unidad de Genómica, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Marta Herranz
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias, CIBERES, Madrid, Spain
| | - Pedro J. Sola-Campoy
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Cristina Rodríguez-Grande
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Sergio Buenestado-Serrano
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - María Jesús Ruiz-Serrano
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Griselda Tudó
- Servei de Microbiologia, Hospital Clinic-CDB, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
| | - Fernando Alcaide
- Servicio de Microbiología, Hospital Universitario de Bellvitge-IDIBELL, L’Hospitalet de Llobregat, Barcelona, Spain
- Department of Pathology and Experimental Therapy, University of Barcelona, L’Hospitalet de Llobregat, Barcelona, Spain
| | - Patricia Muñoz
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias, CIBERES, Madrid, Spain
- Departmento de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Darío García de Viedma
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias, CIBERES, Madrid, Spain
| | - Laura Pérez-Lago
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
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16
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Ssengooba W, Komakech K, Namiiro S, Byabajungu H, Nalunjogi J, Katagira W, Kimuli I, Joloba ML, Adakun S, Nakiyingi L, Torrea G, Kirenga BJ. Rifampicin susceptibility discordance between Xpert MTB/RIF G4 and Xpert Ultra before MDRT-TB treatment initiation: A case report from Uganda. J Clin Tuberc Other Mycobact Dis 2021; 25:100286. [PMID: 34816021 PMCID: PMC8592849 DOI: 10.1016/j.jctube.2021.100286] [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] [Indexed: 12/02/2022] Open
Abstract
Tuberculosis (TB) resistance to rifampicin, the most powerful drug leads to increase in mortality. Globally, half a million new patients develop such resistant TB each year, coupled with both inappropriate diagnosis and treatment initiation. We report a case of rifampicin resistant Mycobacterium tuberculosis whose rifampicin resistance was missed by Xpert MTB/RIF Assay G4 but detected by the Xpert MTB/RIF Ultra assay at different time points leading to increased delays for MDR-TB treatment initiation at Mulago Hospital, Kampala, Uganda. Our case report compels greater urgency in accelerating the transition to the newer assay, Ultra, to benefit from higher sensitivity of rifampicin resistance detection.
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Affiliation(s)
- Willy Ssengooba
- Makerere University Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
- Makerere University, Department of Medical Microbiology, Mycobacteriology (BSL-3) Laboratory, P.O.BOX 7072, Kampala, Uganda
| | - Kevin Komakech
- Makerere University, Department of Medical Microbiology, Mycobacteriology (BSL-3) Laboratory, P.O.BOX 7072, Kampala, Uganda
| | - Sharon Namiiro
- Makerere University Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Henry Byabajungu
- National TB Reference Laboratory, Ministry of Health, Kampala, Uganda
| | - Joanitah Nalunjogi
- Makerere University Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Winceslaus Katagira
- Makerere University Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Ivan Kimuli
- Makerere University Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Moses L Joloba
- Makerere University Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
- Makerere University, Department of Medical Microbiology, Mycobacteriology (BSL-3) Laboratory, P.O.BOX 7072, Kampala, Uganda
| | - Susan Adakun
- Makerere University Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
- National Tuberculosis Treatment Unit, Mulago Hospital, Kampala, Uganda
| | - Lydia Nakiyingi
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Gabriela Torrea
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Bruce J Kirenga
- Makerere University Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
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17
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Ye M, Yuan W, Molaeipour L, Azizian K, Ahmadi A, Kouhsari E. Antibiotic heteroresistance in Mycobacterium tuberculosis isolates: a systematic review and meta-analysis. Ann Clin Microbiol Antimicrob 2021; 20:73. [PMID: 34645463 PMCID: PMC8513340 DOI: 10.1186/s12941-021-00478-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 10/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycobacterium tuberculosis (MTB) is responsible for tuberculosis; that continues to be a public health threat across the globe. Furthermore, increasing heteroresistance (HR)-the presence of resistant and susceptible isolates among MTB strains- has been reported from around the world. This phenomenon can lead to full resistance development and treatment failure. METHODS We systematically searched the relevant studies in PubMed, Scopus, and Embase (Until October 21, 2020). The study outcomes revealed the weighted pooled prevalence of antibiotic HR in MTB isolates with subgroup analysis by year, quality of study, and heteroresistance detection method. RESULTS A total of 38 studies which had investigated MTB isolates were included in the meta-analysis. Geographically, the highest number of studies were reported from Asia (n = 24), followed by Africa (n = 5). Nineteen studies reported HR to isoniazid, with a weighted pooled prevalence of 5% (95% CI 0-12) among 11,761 MTB isolates. Also, there is no important trend for the subgroup analysis by the study period (2001-2014 vs 2015-2017 vs 2018-2020). HR to rifampin was reported in 17 studies, with a weighted pooled prevalence of 7% (95% CI 2-14) among 3782 MTB isolates. HR to fluoroquinolone and ethambutol were reported in 12 and 4 studies, respectively, with weighted pooled prevalence of 10% and 1% among 2153 and 1509 MTB isolates, correspondingly. CONCLUSION Based on our analysis, HR in MTB isolates with different frequency rate is present worldwide. Thus, the selection of appropriate and reliable methods for HR detection is crucial for TB eradication.
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Affiliation(s)
- Mao Ye
- Department of Pharmacy, Clinical Pharmaceutics Room, Sichuan Science City Hospital, Mianyang, 621000, China
| | - Wen Yuan
- Sichuan College of Traditional Chinese Medicine, Mianyang, 621000, China
| | - Leila Molaeipour
- Department of Epidemiology, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Khalil Azizian
- Department of Clinical Microbiology, Sirjan School of Medical Sciences, P.O. Box 78169-16338, Sirjan, Iran.
| | - Alireza Ahmadi
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
- Department of Laboratory Sciences, Faculty of Paramedicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ebrahim Kouhsari
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran.
- Department of Laboratory Sciences, Faculty of Paramedicine, Golestan University of Medical Sciences, Gorgan, Iran.
- Laboratory Sciences Research Center, Faculty of Paramedical Sciences, Golestan University of Medical Sciences, Negative Floor 1, Gorgan-Sari Road, P.O. Box: 4918936316, Gorgan, Golestan Province, Iran.
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18
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Rapid Molecular Diagnosis of Tuberculosis and Its Resistance to Rifampicin and Isoniazid with Automated MDR/MTB ELITe MGB ® Assay. Antibiotics (Basel) 2021; 10:antibiotics10070797. [PMID: 34208899 PMCID: PMC8300793 DOI: 10.3390/antibiotics10070797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 11/22/2022] Open
Abstract
The MDR/MTB ELITe MGB® kit (ELITech) carried on the ELITe InGenius® platform is a new real-time PCR assay allowing automated extraction and detection of DNA of the Mycobacterium tuberculosis complex (MTB) and mutations in the rpoB and katG genes and inhA promoter region (pro-inhA) associated to resistance to rifampicin and isoniazid, the two markers of multidrug-resistant TB (MDR). We assessed the performances of the test on a collection of strains (n = 54) and a set of clinical samples (n = 242) from routine practice, comparatively to TB diagnosis and genotypic drug susceptibility testing (gDST) as references. Regarding the 242 clinical samples, the sensitivity and specificity of MTB detection by ELITe were 90.9% and 97.5%, respectively. For the detection of resistance-conferring mutations on positive clinical samples, we observed perfect agreement with gDST for katG and pro-inhA (κ = 1.0) and two discordant results for rpoB (κ = 0.82). Considering the 54 cultured strains, very good agreement with gDST was observed for the detection of the 25 distinct mutations in rpoB, katG, and pro-inhA, (κ = 0.95, 0.88, and 0.95, respectively). In conclusion, the automated MDR/MTB ELITe MGB® assay shows great promise and appears to be a valuable tool for rapid detection of pre-MDR- and MDR-TB directly from clinical specimens.
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19
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Genestet C, Hodille E, Barbry A, Berland JL, Hoffmann J, Westeel E, Bastian F, Guichardant M, Venner S, Lina G, Ginevra C, Ader F, Goutelle S, Dumitrescu O. Rifampicin exposure reveals within-host Mycobacterium tuberculosis diversity in patients with delayed culture conversion. PLoS Pathog 2021; 17:e1009643. [PMID: 34166469 PMCID: PMC8224949 DOI: 10.1371/journal.ppat.1009643] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/13/2021] [Indexed: 12/21/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) genetic micro-diversity in clinical isolates may underline mycobacterial adaptation to tuberculosis (TB) infection and provide insights to anti-TB treatment response and emergence of resistance. Herein we followed within-host evolution of Mtb clinical isolates in two cohorts of TB patients, either with delayed Mtb culture conversion (> 2 months), or with fast culture conversion (< 2 months). We captured the genetic diversity of Mtb isolates obtained in each patient, by focusing on minor variants detected as unfixed single nucleotide polymorphisms (SNPs). To unmask antibiotic tolerant sub-populations, we exposed these isolates to rifampicin (RIF) prior to whole genome sequencing (WGS) analysis. Thanks to WGS, we detected at least 1 unfixed SNP within the Mtb isolates for 9/15 patients with delayed culture conversion, and non-synonymous (ns) SNPs for 8/15 patients. Furthermore, RIF exposure revealed 9 additional unfixed nsSNP from 6/15 isolates unlinked to drug resistance. By contrast, in the fast culture conversion cohort, RIF exposure only revealed 2 unfixed nsSNP from 2/20 patients. To better understand the dynamics of Mtb micro-diversity, we investigated the variant composition of a persistent Mtb clinical isolate before and after controlled stress experiments mimicking the course of TB disease. A minor variant, featuring a particular mycocerosates profile, became enriched during both RIF exposure and macrophage infection. The variant was associated with drug tolerance and intracellular persistence, consistent with the pharmacological modeling predicting increased risk of treatment failure. A thorough study of such variants not necessarily linked to canonical drug-resistance, but which are prone to promote anti-TB drug tolerance, may be crucial to prevent the subsequent emergence of resistance. Taken together, the present findings support the further exploration of Mtb micro-diversity as a promising tool to detect patients at risk of poorly responding to anti-TB treatment, ultimately allowing improved and personalized TB management. Tuberculosis (TB) is caused by Mycobacterium tuberculosis (Mtb), bacteria that are able to persist inside the patient for many months or years, thus requiring long antibiotic treatments. Here we focused on TB patients with delayed response to treatment and we performed genetic characterization of Mtb isolates to search for sub-populations that may tolerate anti-TB drugs. We found that Mtb cultured from 9/15 patients contained different sub-populations, and in vitro drug exposure revealed Mtb sub-populations in 6/15 isolates, none related to known drug-resistance mechanisms. By contrast, drug exposure revealed Mtb sup-populations in 2/20 isolates in the control cohort of patients with fast culture conversion. Furthermore, we characterized a Mtb variant isolated from a sub-population growing in the presence of rifampicin (RIF), a major anti-TB drug. We found that this variant featured a modified lipidic envelope, and that it was able to develop in the presence of RIF and inside human macrophage cells. We performed pharmacological modelling and found that this kind of variant may be related to a poor response to treatment. In conclusion, searching for particular Mtb sub-populations may help to detect patients at risk of treatment failure and provide additional guidance for TB management.
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Affiliation(s)
- Charlotte Genestet
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
- * E-mail:
| | - Elisabeth Hodille
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
| | - Alexia Barbry
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
| | - Jean-Luc Berland
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Fondation Mérieux, Emerging Pathogens Laboratory, Lyon, France
| | - Jonathan Hoffmann
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Fondation Mérieux, Emerging Pathogens Laboratory, Lyon, France
| | - Emilie Westeel
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Fondation Mérieux, Emerging Pathogens Laboratory, Lyon, France
| | - Fabiola Bastian
- Plateforme DTAMB, CNRS, Université Lyon 1, Villeurbanne, France
| | - Michel Guichardant
- CarMeN laboratory, INSA Lyon, INSERM U1060, INRA U1397, Université Lyon 1, Villeurbanne, France
| | - Samuel Venner
- Laboratoire de Biométrie et Biologie Évolutive, CNRS UMR 5558, Université Lyon 1, Villeurbanne, France
| | - Gérard Lina
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
- Université Lyon 1, Facultés de Médecine et de Pharmacie de Lyon, Lyon, France
| | - Christophe Ginevra
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
| | - Florence Ader
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Service des Maladies infectieuses et tropicales, Lyon, France
| | - Sylvain Goutelle
- Laboratoire de Biométrie et Biologie Évolutive, CNRS UMR 5558, Université Lyon 1, Villeurbanne, France
- Université Lyon 1, Facultés de Médecine et de Pharmacie de Lyon, Lyon, France
- Hospices Civils de Lyon, Groupement Hospitalier Nord, Service pharmaceutique, Lyon, France
| | - Oana Dumitrescu
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
- Université Lyon 1, Facultés de Médecine et de Pharmacie de Lyon, Lyon, France
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20
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Sonnenkalb L, Strohe G, Dreyer V, Andres S, Hillemann D, Maurer FP, Niemann S, Merker M. Microevolution of Mycobacterium tuberculosis Subpopulations and Heteroresistance in a Patient Receiving 27 Years of Tuberculosis Treatment in Germany. Antimicrob Agents Chemother 2021; 65:e0252020. [PMID: 33903103 PMCID: PMC8218629 DOI: 10.1128/aac.02520-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 04/16/2021] [Indexed: 12/13/2022] Open
Abstract
Preexisting and newly emerging resistant pathogen subpopulations (heteroresistance) are potential risk factors for treatment failure of multi/extensively drug resistant (MDR/XDR) tuberculosis (TB). Intrapatient evolutionary dynamics of Mycobacterium tuberculosis complex (Mtbc) strains and their implications on treatment outcomes are still not completely understood. To elucidate how Mtbc strains escape therapy, we analyzed 13 serial isolates from a German patient by whole-genome sequencing. Sequencing data were compared with phenotypic drug susceptibility profiles and the patient's collective 27-year treatment history to further elucidate factors fostering intrapatient resistance evolution. The patient endured five distinct TB episodes, ending in resistance to 16 drugs and a nearly untreatable XDR-TB infection. The first isolate obtained, during the patient's 5th TB episode, presented fixed resistance mutations to 7 anti-TB drugs, including isoniazid, rifampin, streptomycin, pyrazinamide, prothionamide, para-aminosalicylic acid, and cycloserine-terizidone. Over the next 13 years, a dynamic evolution with coexisting, heterogeneous subpopulations was observed in 6 out of 13 sequential bacterial isolates. The emergence of drug-resistant subpopulations coincided with frequent changes in treatment regimens, which often included two or fewer active compounds. This evolutionary arms race between competing subpopulations ultimately resulted in the fixation of a single XDR variant. Our data demonstrate the complex intrapatient microevolution of Mtbc subpopulations during failing MDR/XDR-TB treatment. Designing effective treatment regimens based on rapid detection of (hetero) resistance is key to avoid resistance development and treatment failure.
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Affiliation(s)
- Lindsay Sonnenkalb
- Molecular and Experimental Mycobacteriology, Research Centre Borstel, Borstel, Germany
| | - Gerald Strohe
- Landratsamt Karlsruhe, Gesundheitsamt, Karlsruhe, Germany
| | - Viola Dreyer
- Molecular and Experimental Mycobacteriology, Research Centre Borstel, Borstel, Germany
| | - Sönke Andres
- National and Supranational Reference Centre for Mycobacteria, Research Centre Borstel, Borstel, Germany
| | - Doris Hillemann
- National and Supranational Reference Centre for Mycobacteria, Research Centre Borstel, Borstel, Germany
| | - Florian P. Maurer
- National and Supranational Reference Centre for Mycobacteria, Research Centre Borstel, Borstel, Germany
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Centre Borstel, Borstel, Germany
- German Centre for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel, Borstel, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Centre Borstel, Borstel, Germany
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21
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Kontsevaya I, Lange C, Comella-Del-Barrio P, Coarfa C, DiNardo AR, Gillespie SH, Hauptmann M, Leschczyk C, Mandalakas AM, Martinecz A, Merker M, Niemann S, Reimann M, Rzhepishevska O, Schaible UE, Scheu KM, Schurr E, Abel Zur Wiesch P, Heyckendorf J. Perspectives for systems biology in the management of tuberculosis. Eur Respir Rev 2021; 30:30/160/200377. [PMID: 34039674 DOI: 10.1183/16000617.0377-2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/28/2021] [Indexed: 12/18/2022] Open
Abstract
Standardised management of tuberculosis may soon be replaced by individualised, precision medicine-guided therapies informed with knowledge provided by the field of systems biology. Systems biology is a rapidly expanding field of computational and mathematical analysis and modelling of complex biological systems that can provide insights into mechanisms underlying tuberculosis, identify novel biomarkers, and help to optimise prevention, diagnosis and treatment of disease. These advances are critically important in the context of the evolving epidemic of drug-resistant tuberculosis. Here, we review the available evidence on the role of systems biology approaches - human and mycobacterial genomics and transcriptomics, proteomics, lipidomics/metabolomics, immunophenotyping, systems pharmacology and gut microbiomes - in the management of tuberculosis including prediction of risk for disease progression, severity of mycobacterial virulence and drug resistance, adverse events, comorbidities, response to therapy and treatment outcomes. Application of the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach demonstrated that at present most of the studies provide "very low" certainty of evidence for answering clinically relevant questions. Further studies in large prospective cohorts of patients, including randomised clinical trials, are necessary to assess the applicability of the findings in tuberculosis prevention and more efficient clinical management of patients.
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Affiliation(s)
- Irina Kontsevaya
- Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.,International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - Christoph Lange
- Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.,International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - Patricia Comella-Del-Barrio
- Research Institute Germans Trias i Pujol, CIBER Respiratory Diseases, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Cristian Coarfa
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.,Molecular and Cellular Biology, Center for Precision Environmental health, Baylor College of Medicine, Houston, TX, USA
| | - Andrew R DiNardo
- The Global Tuberculosis Program, Texas Children's Hospital, Dept of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | | | - Matthias Hauptmann
- Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Christoph Leschczyk
- Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Anna M Mandalakas
- The Global Tuberculosis Program, Texas Children's Hospital, Dept of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Antal Martinecz
- Dept of Biology, Pennsylvania State University, University Park, PA, USA.,Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.,Dept of Pharmacy, Faculty of Health Sciences, UiT, Arctic University of Norway, Tromsø, Norway
| | - Matthias Merker
- Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Stefan Niemann
- Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Maja Reimann
- Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.,International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - Olena Rzhepishevska
- Dept of Chemistry, Umeå University, Umeå, Sweden.,Dept of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Ulrich E Schaible
- Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | | | - Erwin Schurr
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
| | - Pia Abel Zur Wiesch
- Dept of Biology, Pennsylvania State University, University Park, PA, USA.,Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Jan Heyckendorf
- Research Center Borstel, Borstel, Germany .,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.,International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
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22
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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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23
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Ndambuki J, Nzomo J, Muregi L, Mutuku C, Makokha F, Nthusi J, Ambale C, Lynen L, Decroo T. Comparison of first-line tuberculosis treatment outcomes between previously treated and new patients: a retrospective study in Machakos subcounty, Kenya. Int Health 2021; 13:272-280. [PMID: 32860045 PMCID: PMC8079320 DOI: 10.1093/inthealth/ihaa051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/24/2020] [Accepted: 08/10/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Since 2016, patients with rifampicin-susceptible tuberculosis (TB) have been treated with the 6-month first-line regimen, regardless of treatment history. We assessed treatment outcomes of previously treated and new patients in Machakos subcounty, Kenya. METHODS We performed a retrospective cohort study in patients started on first-line treatment between 2016 and 2017. Firth's logistic regression was used to estimate the effect of previous treatment on having a programmatic adverse outcome (either lost to follow-up, death, failure) and treatment failure vs treatment success (either cure or completion). RESULTS Of 1024 new and 79 previously treated patients, 88.1% and 74.7% were treated successfully, 6.5% and 7.6% died, 4.2% and 10.1% were lost to follow-up and 1.2% and 7.6% had treatment failure, respectively. Previous treatment predicted having a programmatic adverse outcome (adjusted odds ratio [aOR] 2.4 [95% confidence interval {CI} 1.4 to 4.2]) and treatment failure (aOR 7.3 [95% CI 2.6 to 20.4]) but not mortality. Similar correlations were found in 334 new and previously treated patients with confirmed baseline rifampicin susceptibility. CONCLUSION Previously treated patients were more at risk of experiencing a poor treatment outcome, mainly lost to follow-up and treatment failure. Adherence support may reduce lost to follow-up. Rifampicin drug susceptibility testing coverage should increase. More robust retreatment regimens may reduce treatment failure.
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Affiliation(s)
| | - Joseph Nzomo
- Department of Health and Emergency Services, Machakos County, Kenya
| | - Lucy Muregi
- Department of Health and Emergency Services, Machakos County, Kenya
| | - Chris Mutuku
- Department of Health and Emergency Services, Machakos County, Kenya
| | - Francis Makokha
- Directorate of Research and Innovation, Mount Kenya University, Box 342-01000, Thika, Kenya
| | - Jonathan Nthusi
- Department of Health and Emergency Services, Machakos County, Kenya
| | - Clarice Ambale
- Department of Health and Emergency Services, Machakos County, Kenya
| | - Lutgarde Lynen
- Institute of Tropical Medicine-Antwerp, Nationalestraat 155-B-2000, Belgium
| | - Tom Decroo
- Institute of Tropical Medicine-Antwerp, Nationalestraat 155-B-2000, Belgium.,Research Foundation Flanders, Brussels, 1000 Brussels, Belgium
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24
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Jouet A, Gaudin C, Badalato N, Allix-Béguec C, Duthoy S, Ferré A, Diels M, Laurent Y, Contreras S, Feuerriegel S, Niemann S, André E, Kaswa MK, Tagliani E, Cabibbe A, Mathys V, Cirillo D, de Jong BC, Rigouts L, Supply P. Deep amplicon sequencing for culture-free prediction of susceptibility or resistance to 13 anti-tuberculous drugs. Eur Respir J 2021; 57:13993003.02338-2020. [PMID: 32943401 PMCID: PMC8174722 DOI: 10.1183/13993003.02338-2020] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/03/2020] [Indexed: 02/06/2023]
Abstract
Conventional molecular tests for detecting Mycobacterium tuberculosis complex (MTBC) drug resistance on clinical samples cover a limited set of mutations. Whole-genome sequencing (WGS) typically requires culture. Here, we evaluated the Deeplex Myc-TB targeted deep-sequencing assay for prediction of resistance to 13 anti-tuberculous drugs/drug classes, directly applicable on sputum. With MTBC DNA tests, the limit of detection was 100–1000 genome copies for fixed resistance mutations. Deeplex Myc-TB captured in silico 97.1–99.3% of resistance phenotypes correctly predicted by WGS from 3651 MTBC genomes. On 429 isolates, the assay predicted 92.2% of 2369 first- and second-line phenotypes, with a sensitivity of 95.3% and a specificity of 97.4%. 56 out of 69 (81.2%) residual discrepancies with phenotypic results involved pyrazinamide, ethambutol and ethionamide, and low-level rifampicin or isoniazid resistance mutations, all notoriously prone to phenotypic testing variability. Only two out of 91 (2.2%) resistance phenotypes undetected by Deeplex Myc-TB had known resistance-associated mutations by WGS analysis outside Deeplex Myc-TB targets. Phenotype predictions from Deeplex Myc-TB analysis directly on 109 sputa from a Djibouti survey matched those of MTBSeq/PhyResSE/Mykrobe, fed with WGS data from subsequent cultures, with a sensitivity of 93.5/98.5/93.1% and a specificity of 98.5/97.2/95.3%, respectively. Most residual discordances involved gene deletions/indels and 3–12% heteroresistant calls undetected by WGS analysis or natural pyrazinamide resistance of globally rare “Mycobacterium canettii” strains then unreported by Deeplex Myc-TB. On 1494 arduous sputa from a Democratic Republic of the Congo survey, 14 902 out of 19 422 (76.7%) possible susceptible or resistance phenotypes could be predicted culture-free. Deeplex Myc-TB may enable fast, tailored tuberculosis treatment. The novel Deeplex Myc-TB molecular assay shows a high degree of accuracy for extensive prediction of susceptibility and resistance to 13 anti-tuberculous drugs, directly achievable without culture, which may enable fast, tailored tuberculosis treatmenthttps://bit.ly/3bAvcAt
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Affiliation(s)
- Agathe Jouet
- GenoScreen, Lille, France.,These authors contributed equally to this work
| | - Cyril Gaudin
- GenoScreen, Lille, France.,These authors contributed equally to this work
| | | | | | | | | | - Maren Diels
- BCCM/ITM, Mycobacteria Collection, Institute of Tropical Medicine, Antwerp, Belgium
| | | | | | - Silke Feuerriegel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel, Borstel, Germany
| | - Emmanuel André
- Laboratory of Clinical Bacteriology and Mycology, Dept of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Michel K Kaswa
- National Tuberculosis Program, Kinshasa, Democratic Republic of the Congo
| | - Elisa Tagliani
- Emerging Bacterial Pathogens, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Cabibbe
- Emerging Bacterial Pathogens, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Vanessa Mathys
- Unit Bacterial Diseases Service, Infectious Diseases in Humans, Sciensano, Brussels, Belgium
| | - Daniela Cirillo
- Emerging Bacterial Pathogens, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Bouke C de Jong
- Mycobacteriology Unit, Dept of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Leen Rigouts
- Mycobacteriology Unit, Dept of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Dept of Biomedical Sciences, Antwerp University, Antwerp, Belgium
| | - Philip Supply
- Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL (Center for Infection and Immunity of Lille), Lille, France
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25
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Li G, Guo Q, Liu H, Wan L, Jiang Y, Li M, Zhao LL, Zhao X, Liu Z, Wan K. Detection of Resistance to Fluoroquinolones and Second-Line Injectable Drugs Among Mycobacterium tuberculosis by a Reverse Dot Blot Hybridization Assay. Infect Drug Resist 2020; 13:4091-4104. [PMID: 33204126 PMCID: PMC7666996 DOI: 10.2147/idr.s270209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/07/2020] [Indexed: 01/23/2023] Open
Abstract
Background Reliable and timely determination of second-line drug resistance is essential for early initiation effective anti-tubercular treatment among multi-drug resistant (MDR) patients and blocking the spread of MDR and extensively drug-resistant tuberculosis. Molecular methods have the potency to provide accurate and rapid drug susceptibility results. We aimed to establish and evaluate the accuracy of a reverse dot blot hybridization (RDBH) assay to simultaneously detect the resistance of fluoroquinolones (FQs), kanamycin (KN), amikacin (AMK), capreomycin (CPM) and second-line injectable drugs (SLIDs) in Mycobacterium tuberculosis. Methods We established and evaluated the accuracy of the RDBH assay by comparing to the phenotypic drug susceptibility testing (DST) and sequencing in 170 M. tuberculosis, of which 94 and 27 were respectively resistant to ofloxacin (OFX) and SLIDs. Results The results show that, compared to phenotypic DST, the sensitivity and specificity of the RDBH assay for resistance detection were 63.8% and 100.0% for OFX, 60.0% and 100.0% for KN, 61.5% and 98.1% for AMK, 50.0% and 99.3% for CPM, and 55.6% and 100% for SLIDs, respectively; compared to sequencing, the sensitivity and specificity of the RDBH assay were 95.2% and 100.0% for OFX, 93.8% and 100.0% for SLIDs or KN (both based on mutations in rrs 1400 region and eis promoter), and 91.6% and 100.0% for AMK or CPM (both based on mutations in rrs 1400 region), respectively. The turnaround time of the RDBH assay was 7 h for testing 42 samples. Conclusion Our data suggested that compared to sequencing, the RDBH assay could serve as a rapid and reliable method for testing the resistance of M. tuberculosis against OFX and SLIDs, enabling early administration of appropriate treatment regimens among MDR tuberculosis patients.
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Affiliation(s)
- Guilian Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Qian Guo
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China.,Department of Molecular Biology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, People's Republic of China
| | - Haican Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Li Wan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Yi Jiang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Machao Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Li-Li Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Xiuqin Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Zhiguang Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Kanglin Wan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
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26
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Lange C, Aarnoutse R, Chesov D, van Crevel R, Gillespie SH, Grobbel HP, Kalsdorf B, Kontsevaya I, van Laarhoven A, Nishiguchi T, Mandalakas A, Merker M, Niemann S, Köhler N, Heyckendorf J, Reimann M, Ruhwald M, Sanchez-Carballo P, Schwudke D, Waldow F, DiNardo AR. Perspective for Precision Medicine for Tuberculosis. Front Immunol 2020; 11:566608. [PMID: 33117351 PMCID: PMC7578248 DOI: 10.3389/fimmu.2020.566608] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/02/2020] [Indexed: 12/28/2022] Open
Abstract
Tuberculosis is a bacterial infectious disease that is mainly transmitted from human to human via infectious aerosols. Currently, tuberculosis is the leading cause of death by an infectious disease world-wide. In the past decade, the number of patients affected by tuberculosis has increased by ~20 percent and the emergence of drug-resistant strains of Mycobacterium tuberculosis challenges the goal of elimination of tuberculosis in the near future. For the last 50 years, management of patients with tuberculosis has followed a standardized management approach. This standardization neglects the variation in human susceptibility to infection, immune response, the pharmacokinetics of drugs, and the individual duration of treatment needed to achieve relapse-free cure. Here we propose a package of precision medicine-guided therapies that has the prospect to drive clinical management decisions, based on both host immunity and M. tuberculosis strains genetics. Recently, important scientific discoveries and technological advances have been achieved that provide a perspective for individualized rather than standardized management of patients with tuberculosis. For the individual selection of best medicines and host-directed therapies, personalized drug dosing, and treatment durations, physicians treating patients with tuberculosis will be able to rely on these advances in systems biology and to apply them at the bedside.
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Affiliation(s)
- Christoph Lange
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
- Cluster of Excellence Precision Medicine in Chronic Inflammation, Kiel, Germany
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Rob Aarnoutse
- Department of Internal Medicine, Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands
| | - Dumitru Chesov
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
- Department of Pulmonology and Allergology, Nicolae Testemitanu University of Medicine and Pharmacy, Chisinau, Moldova
| | - Reinout van Crevel
- Department of Internal Medicine, Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Hans-Peter Grobbel
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
| | - Barbara Kalsdorf
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
- Cluster of Excellence Precision Medicine in Chronic Inflammation, Kiel, Germany
| | - Irina Kontsevaya
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
| | - Arjan van Laarhoven
- Department of Internal Medicine, Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands
| | - Tomoki Nishiguchi
- The Global Tuberculosis Program, Texas Children's Hospital, Immigrant and Global Health, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Anna Mandalakas
- The Global Tuberculosis Program, Texas Children's Hospital, Immigrant and Global Health, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Matthias Merker
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Cluster of Excellence Precision Medicine in Chronic Inflammation, Kiel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Stefan Niemann
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Cluster of Excellence Precision Medicine in Chronic Inflammation, Kiel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Niklas Köhler
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
| | - Jan Heyckendorf
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
| | - Maja Reimann
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
| | - Morten Ruhwald
- Foundation of Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Patricia Sanchez-Carballo
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
| | - Dominik Schwudke
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Bioanalytical Chemistry, Priority Area Infection, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- Airway Research Center North, German Center for Lung Research (DZL), Borstel, Germany
| | - Franziska Waldow
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Bioanalytical Chemistry, Priority Area Infection, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Andrew R. DiNardo
- The Global Tuberculosis Program, Texas Children's Hospital, Immigrant and Global Health, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
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27
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Huo F, Ma Y, Li S, Xue Y, Shang Y, Dong L, Li Y, Pang Y. Specific gyrA Gene Mutations Correlate with High Prevalence of Discordant Levofloxacin Resistance in Mycobacterium tuberculosis Isolates from Beijing, China. J Mol Diagn 2020; 22:1199-1204. [DOI: 10.1016/j.jmoldx.2020.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 05/25/2020] [Accepted: 06/18/2020] [Indexed: 11/26/2022] Open
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28
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Ng KCS, Rigouts L, de Jong BC, Lynen L. False Rifampicin Resistance in Xpert Ultra Applied to Lymph Node Aspirate: A Case Report. Open Forum Infect Dis 2020; 7:ofaa204. [PMID: 32607388 PMCID: PMC7307434 DOI: 10.1093/ofid/ofaa204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/29/2020] [Indexed: 02/06/2023] Open
Abstract
A 36-year-old male patient was diagnosed with tuberculosis in Antwerp, Belgium, in May 2018. His lymph node aspirate initially tested rifampicin resistant in Xpert MTB/RIF Ultra, but tested susceptible in all other tests including targeted deep sequencing due to a rare matrix effect in the Xpert MTB/RIF Ultra reaction tube.
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Affiliation(s)
- Kamela C S Ng
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States
| | - Leen Rigouts
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Bouke C de Jong
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Lutgarde Lynen
- HIV/TB Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
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29
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Van Deun A, Decroo T, Kya Jai Maug A, Hossain MA, Gumusboga M, Mulders W, Ortuño-Gutiérrez N, Lynen L, de Jong BC, Rieder HL. The perceived impact of isoniazid resistance on outcome of first-line rifampicin-throughout regimens is largely due to missed rifampicin resistance. PLoS One 2020; 15:e0233500. [PMID: 32421749 PMCID: PMC7233532 DOI: 10.1371/journal.pone.0233500] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 05/06/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Meta-analyses on impact of isoniazid-resistant tuberculosis informed the World Health Organization recommendation of a levofloxacin-strengthened rifampicin-based regimen. We estimated the effect of initial rifampicin resistance (Rr) and/or isoniazid resistance (Hr) on treatment failure or relapse. We also determined the frequency of missed initial and acquired Rr to estimate the impact of true Hr. METHODS Retrospective analysis of 7291 treatment episodes with known initial isoniazid and rifampicin status obtained from individual patient databases maintained by the Damien Foundation Bangladesh over 20 years. Drug susceptibility test results were confirmed by the programme's designated supra-national tuberculosis laboratory. To detect missed Rr among isolates routinely classified as Hr, rpoB gene sequencing was done randomly and on a sample selected for suspected missed Rr. RESULTS Initial Hr caused a large recurrence excess after the 8-month regimen for new cases (rifampicin for two months), but had little impact on rifampicin-throughout regimens: (6 months, new cases; 3.8%; OR 0.8, 95%CI:0.3,2.8; 8 months, retreatment cases: 7.3%, OR 1.8; 95%CI:1.3,2.6). Rr was missed in 7.6% of randomly selected "Hr" strains. Acquired Rr was frequent among recurrences on rifampicin-throughout regimens, particularly after the retreatment regimen (31.9%). It was higher in mono-Hr (29.3%; aOR 3.5, 95%CI:1.5,8.5) and poly-Hr (53.3%; aOR 10.2, 95%CI 4.4,23.7) than in susceptible tuberculosis, but virtually absent after the 8-month new case regimen. Comparing Bangladesh (low Rr prevalence) with a high Rr prevalence setting,true Hr corrected for missed Rr caused only 2-3 treatment failures per 1000 TB cases (of whom 27% were retreatments) in both. CONCLUSIONS Our analysis reveals a non-negligible extent of misclassifying as isoniazid resistance of what is actually missed multidrug-resistant tuberculosis. Recommending for such cases a "strengthened" regimen containing a fluoroquinolone provokes a direct route to extensive resistance while offering little benefit against the minor role of true Hr tuberculosis in rifampicin-throughout first-line regimen.
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Affiliation(s)
- Armand Van Deun
- Biomedical Department, Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Tom Decroo
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Research Foundation Flanders, Brussels, Belgium
| | | | | | - Murid Gumusboga
- Biomedical Department, Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Wim Mulders
- Biomedical Department, Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Lutgarde Lynen
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Bouke C. de Jong
- Biomedical Department, Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Hans L. Rieder
- Tuberculosis Consultant Services, Kirchlindach, Switzerland
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30
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Nimmo C, Brien K, Millard J, Grant AD, Padayatchi N, Pym AS, O'Donnell M, Goldstein R, Breuer J, Balloux F. Dynamics of within-host Mycobacterium tuberculosis diversity and heteroresistance during treatment. EBioMedicine 2020; 55:102747. [PMID: 32361247 PMCID: PMC7195533 DOI: 10.1016/j.ebiom.2020.102747] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/02/2020] [Accepted: 03/19/2020] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Studying within-host genetic diversity of Mycobacterium tuberculosis (Mtb) in patients during treatment may identify adaptations to antibiotic and immune pressure. Understanding the significance of genetic heteroresistance, and more specifically heterozygous resistance-associated variants (RAVs), is clinically important given increasing use of rapid molecular tests and whole genome sequencing (WGS). METHODS We analyse data from six studies in KwaZulu-Natal, South Africa. Most patients (>75%) had baseline rifampicin resistance. Sputum was collected for culture at baseline and at between two and nine intervals until month six. Positive cultures underwent WGS. Mixed infections and reinfections were excluded from analysis. FINDINGS Baseline Mtb overall genetic diversity (at treatment initiation or major change to regimen) was associated with cavitary disease, not taking antiretroviral therapy if HIV infected, infection with lineage 2 strains and absence of second-line drug resistance on univariate analyses. Baseline genetic diversity was not associated with six-month outcome. Genetic diversity increased from baseline to weeks one and two before returning to previous levels. Baseline genetic heteroresistance was most common for bedaquiline (6/10 [60%] of isolates with RAVs) and fluoroquinolones (9/62 [13%]). Most patients with heterozygous RAVs on WGS with sequential isolates available demonstrated RAV persistence or fixation (17/20, 85%). New RAVs emerged in 9/286 (3%) patients during treatment. We could detect low-frequency RAVs preceding emergent resistance in only one case, although validation of deep sequencing to detect rare variants is required. INTERPRETATION In this study of single-strain Mtb infections, baseline within-host bacterial genetic diversity did not predict outcome but may reveal adaptations to host and drug pressures. Predicting emergent resistance from low-frequency RAVs requires further work to separate transient from consequential mutations. FUNDING Wellcome Trust, NIH/NIAID.
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MESH Headings
- Adult
- Antitubercular Agents/therapeutic use
- Cohort Studies
- Diarylquinolines/therapeutic use
- Drug Resistance, Multiple, Bacterial/genetics
- Female
- Fluoroquinolones/therapeutic use
- Gene Expression Regulation, Bacterial
- Genes, Bacterial
- Genetic Variation
- Host-Pathogen Interactions/genetics
- Humans
- Male
- Metabolic Networks and Pathways/genetics
- Microbial Sensitivity Tests
- Middle Aged
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/metabolism
- Rifampin/therapeutic use
- South Africa
- Sputum/microbiology
- Tuberculosis, Multidrug-Resistant/drug therapy
- Tuberculosis, Multidrug-Resistant/microbiology
- Tuberculosis, Multidrug-Resistant/pathology
- Tuberculosis, Pulmonary/drug therapy
- Tuberculosis, Pulmonary/microbiology
- Tuberculosis, Pulmonary/pathology
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Affiliation(s)
- Camus Nimmo
- Division of Infection and Immunity, University College London, London, UK; UCL Genetics Institute, University College London, London, UK; Africa Health Research Institute, Durban, South Africa.
| | - Kayleen Brien
- Africa Health Research Institute, Durban, South Africa
| | - James Millard
- Africa Health Research Institute, Durban, South Africa; Wellcome Trust Liverpool Glasgow Centre for Global Health Research, Liverpool, UK; Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Alison D Grant
- Africa Health Research Institute, Durban, South Africa; London School of Hygiene & Tropical Medicine, London, UK
| | - Nesri Padayatchi
- CAPRISA MRC-HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | | | - Max O'Donnell
- CAPRISA MRC-HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa; Department of Medicine & Epidemiology, Columbia University Medical Center, New York, NY, USA
| | - Richard Goldstein
- Division of Infection and Immunity, University College London, London, UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
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31
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Whole-genome sequencing in drug susceptibility testing of Mycobacterium tuberculosis in routine practice in Lyon, France. Int J Antimicrob Agents 2020; 55:105912. [DOI: 10.1016/j.ijantimicag.2020.105912] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/08/2020] [Accepted: 01/18/2020] [Indexed: 11/23/2022]
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