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Sangu KG, Azger Dusthackeer VN, Singh VK, Maykalwar S, Krishna EV, Angayarkanni B, Maitra R, Chopra S, Misra S, Rode HB. 3,5-disubstituted pyridines with potent activity against drug-resistant Mycobacterium tuberculosis clinical isolates. Future Med Chem 2024:1-19. [PMID: 39363626 DOI: 10.1080/17568919.2024.2403963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 09/09/2024] [Indexed: 10/05/2024] Open
Abstract
Aim: We designed and synthesized a series of compounds with a 3,5-disubstituted pyridine moiety and evaluated them against Mycobacterium tuberculosis (Mtb) and drug-resistant Mtb clinical isolates.Methodology: A library of 3,5-disubstituted pyridine was synthesized. The compounds were screened for activity against M. tuberculosis H37Rv. The optimal substitutions needed for the activity were identified through structure-activity relationship (SAR) studies.Results: From the screening studies, compounds 24 and 26 were identified as potent members of this series with Minimum Inhibitory Concentration (MIC) of 1.56 μg/ml against M. tuberculosis H37Rv. These compounds did not show any inhibition against a panel of ESKAPE pathogens at >50 μg/ml indicating their selective killing of M. tuberculosis H37Rv. Importantly, compound 24 showed a selectivity index of 54.64 against CHO-K1 and 78.26 against VERO cell lines, while compound 26 showed a selectivity index of 108.5 against CHO-K1 and 63.2 against VERO cell lines, respectively. Compound 24 formed a stable complex with the target protein DprE1 with predicted binding energy -8.73 kcal/mol and inhibited multidrug-resistant clinical isolate of M. tuberculosis at 6.25 μg/ml.Conclusion: This study identified the 3,5-disubstituted pyridine derivative 24 with potent antituberculosis activity and can be taken forward to generate new preclinical candidate.
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Affiliation(s)
- Komal G Sangu
- Department of Natural Products & Medicinal Chemistry, CSIR - Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500 007, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201 002, India
| | | | - Vishal K Singh
- Department of Natural Products & Medicinal Chemistry, CSIR - Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500 007, India
| | - Shivani Maykalwar
- Department of Natural Products & Medicinal Chemistry, CSIR - Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500 007, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201 002, India
| | - Eruva Vamshi Krishna
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201 002, India
- Department of Applied Biology, CSIR - Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500 007, India
| | | | - Rahul Maitra
- Department of Molecular Microbiology & Immunology, CSIR - Central Drug Research Institute, Sitapur Road, Janakipuram Extension, Lucknow, Uttar Pradesh, 226 031, India
| | - Sidharth Chopra
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201 002, India
- Department of Molecular Microbiology & Immunology, CSIR - Central Drug Research Institute, Sitapur Road, Janakipuram Extension, Lucknow, Uttar Pradesh, 226 031, India
| | - Sunil Misra
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201 002, India
- Department of Applied Biology, CSIR - Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500 007, India
| | - Haridas B Rode
- Department of Natural Products & Medicinal Chemistry, CSIR - Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500 007, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201 002, India
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Pei S, Song Z, Yang W, He W, Ou X, Zhao B, He P, Zhou Y, Xia H, Wang S, Jia Z, Walker TM, Zhao Y. The catalogue of Mycobacterium tuberculosis mutations associated with drug resistance to 12 drugs in China from a nationwide survey: a genomic analysis. THE LANCET. MICROBE 2024:100899. [PMID: 39353459 DOI: 10.1016/s2666-5247(24)00131-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/05/2024] [Accepted: 05/10/2024] [Indexed: 10/04/2024]
Abstract
BACKGROUND WHO issued the first edition catalogue of Mycobacterium tuberculosis complex (MTBC) mutations associated with drug resistance in 2021. However, country-specific issues might lead to arising complex and additional drug-resistant mutations. We aimed to fully reflect the characteristics of drug resistance mutations in China. METHODS We analysed MTBC isolates from the nationwide drug-resistant tuberculosis surveillance with 70 counties in 31 provinces, municipalities, and autonomous regions in China. Three types of MYCOTB plates were used to perform drug susceptibility testing for 12 antibiotics (rifampicin, isoniazid, ethambutol, levofloxacin, moxifloxacin, amikacin, kanamycin, ethionamide, clofazimine, linezolid, delamanid, and bedaquiline). Mutations were divided into five groups according to their odds ratios, positive predictive values, false discovery rate-corrected p values, and 95% CIs: (1) associated with resistance; (2) associated with resistance-interim; (3) uncertain significance; (4) not associated with resistance-interim; and (5) not associated with resistance. The Wilcoxon rank-sum and Kruskal-Wallis tests were used to quantify the association between mutations and minimum inhibitory concentrations (MICs). Our dataset was compared with the first edition of the WHO catalogue. FINDINGS We analysed 10 146 MTBC isolates, of which 9071 (89·4%) isolates were included in the final analysis. 744 (8·2%) isolates were resistant to rifampicin and 1339 (14·8%) to isoniazid. 208 (1·9%) of 11 065 mutations were classified as associated with resistance or associated with resistance-interim. 33 (97·1%) of 34 mutations in group 1 and 92 (52·9%) of 174 in group 2 also appeared in groups 1 or 2 of the WHO catalogue. Of 81 indel mutations in group 2, 15 (18·5%) were in the WHO catalogue. The newly discovered mutation gyrA_Ala288Asp was associated with levofloxacin resistance. MIC values for rifampicin, isoniazid, moxifloxacin, and levofloxacin corresponding to resistance mutations in group 1 were significantly different (p<0·0001), and 12 high-level resistance mutations were detected. 61 mutations in group 3 occurred as solo in at least five phenotypically susceptible isolates, but with MIC values moderately higher than other susceptible isolates. Among 945 phenotypically resistant but genotypically susceptible isolates, 433 (45·8%) were mutated for at least one efflux pump gene. INTERPRETATION Our analysis reflects the complexity of drug resistance mutations in China and suggests that indel mutations, efflux pump genes, protein structure, and MICs should be fully considered in the WHO catalogue, especially in countries with a high tuberculosis burden. FUNDING National Key Research and Development Program of China and the Science and Technology Major Project of Tibetan Autonomous Region of China.
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Affiliation(s)
- Shaojun Pei
- Department of Global Health, School of Public Health, Peking University, Beijing, China; National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zexuan Song
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wei Yang
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Shenzhen, China
| | - Wencong He
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xichao Ou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Bing Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ping He
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yang Zhou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hui Xia
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shengfen Wang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhongwei Jia
- Department of Global Health, School of Public Health, Peking University, Beijing, China.
| | - Timothy M Walker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK.
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China; National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Shenzhen, China.
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Sanchini A, Lanni A, Giannoni F, Mustazzolu A. Exploring diagnostic methods for drug-resistant tuberculosis: A comprehensive overview. Tuberculosis (Edinb) 2024; 148:102522. [PMID: 38850839 DOI: 10.1016/j.tube.2024.102522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/14/2024] [Accepted: 05/30/2024] [Indexed: 06/10/2024]
Abstract
Despite available global efforts and funding, Tuberculosis (TB) continues to affect a considerable number of patients worldwide. Policy makers and stakeholders set clear goals to reduce TB incidence and mortality, but the emergence of multidrug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB) complicate the reach of these goals. Drug-resistance TB needs to be diagnosed rapidly and accurately to effectively treat patients, prevent the transmission of MDR-TB, minimise mortality, reduce treatment costs and avoid unnecessary hospitalisations. In this narrative review, we provide a comprehensive overview of laboratory methods for detecting drug resistance in MTB, focusing on phenotypic, molecular and other drug susceptibility testing (DST) techniques. We found a large variety of methods used, with the BACTEC MGIT 960 being the most common phenotypic DST and the Xpert MTB/RIF being the most common molecular DST. We emphasise the importance of integrating phenotypic and molecular DST to address issues like resistance to new drugs, heteroresistance, mixed infections and low-level resistance mutations. Notably, most of the analysed studies adhered to the outdated definition of XDR-TB and did not consider the pre-XDR definition, thus posing challenges in aligning diagnostic methods with the current landscape of TB resistance.
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Affiliation(s)
| | - Alessio Lanni
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy.
| | - Federico Giannoni
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy.
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Vasiliauskaitė L, Bakuła Z, Vasiliauskienė E, Bakonytė D, Decewicz P, Dziurzyński M, Proboszcz M, Davidavičienė EV, Nakčerienė B, Krenke R, Kačergius T, Stakėnas P, Jagielski T. Detection of multidrug-resistance in Mycobacterium tuberculosis by phenotype- and molecular-based assays. Ann Clin Microbiol Antimicrob 2024; 23:81. [PMID: 39198827 PMCID: PMC11360294 DOI: 10.1186/s12941-024-00741-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 08/16/2024] [Indexed: 09/01/2024] Open
Abstract
BACKGROUND The whole-genome sequencing (WGS) is becoming an increasingly effective tool for rapid and accurate detection of drug resistance in Mycobacterium tuberculosis complex (MTBC). This approach, however, has still been poorly evaluated on strains from Central and Eastern European countries. The purpose of this study was to assess the performance of WGS against conventional drug susceptibility testing (DST) for the detection of multi-drug resistant (MDR) phenotypes among MTBC clinical strains from Poland and Lithuania. METHODS The study included 208 MTBC strains (130 MDR; 78 drug susceptible), recovered from as many tuberculosis patients in Lithuania and Poland between 2018 and 2021. Resistance to rifampicin (RIF) and isoniazid (INH) was assessed by Critical Concentration (CC) and Minimum Inhibitory Concentration (MIC) DST as well as molecular-based techniques, including line-probe assay (LPA) and WGS. The analysis of WGS results was performed using bioinformatic pipeline- and software-based tools. RESULTS The results obtained with the CC DST were more congruent with those by LPA compared to pipeline-based WGS. Software-based tools showed excellent concordance with pipeline-based analysis in prediction of RIF/INH resistance. The RIF-resistant strains demonstrated a relatively homogenous MIC distribution with the mode at the highest tested MIC value. The most frequent RIF-resistance conferring mutation was rpoB S450L. The mode MIC for INH was two-fold higher among double katG and inhA mutants than among single katG mutants. The overall rate of discordant results between all methods was calculated at 5.3%. Three strains had discordant results by both genotypic methods (LPA and pipeline-based WGS), one strain by LPA only, three strains by MIC DST, two strains by both MIC DST and pipeline-based WGS, and the remaining two strains showed discordant results with all three methods, compared to CC DST. CONCLUSIONS Considering MIC DST results, current CCs of the first-line anti-TB drugs might be inappropriately high and may need to be revised. Both molecular methods demonstrated 100% specificity, while pipeline-based WGS had slightly lower sensitivity for RIF and INH than LPA, compared to CC DST.
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Affiliation(s)
- Laima Vasiliauskaitė
- Department of Physiology, Biochemistry, Microbiology and Laboratory Medicine, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Centre of Laboratory Medicine, Laboratory of Infectious Diseases and Tuberculosis, Vilnius University Hospital Santaros klinikos, Vilnius, Lithuania
| | - Zofia Bakuła
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Edita Vasiliauskienė
- Department of Physiology, Biochemistry, Microbiology and Laboratory Medicine, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Centre of Laboratory Medicine, Laboratory of Infectious Diseases and Tuberculosis, Vilnius University Hospital Santaros klinikos, Vilnius, Lithuania
| | - Daiva Bakonytė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Przemysław Decewicz
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | | | - Małgorzata Proboszcz
- Department of Internal Medicine, Pulmonology, and Allergology, Warsaw Medical University, Warsaw, Poland
| | - Edita Valerija Davidavičienė
- Department of Programs and State Tuberculosis Information System, Vilnius University Hospital Santaros klinikos, Vilnius, Lithuania
| | - Birutė Nakčerienė
- Department of Programs and State Tuberculosis Information System, Vilnius University Hospital Santaros klinikos, Vilnius, Lithuania
| | - Rafał Krenke
- Department of Internal Medicine, Pulmonology, and Allergology, Warsaw Medical University, Warsaw, Poland
| | - Tomas Kačergius
- Department of Physiology, Biochemistry, Microbiology and Laboratory Medicine, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Petras Stakėnas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Tomasz Jagielski
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
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Hiebert M, Sharma MK, Rabb M, Karlowsky L, Bergman K, Soualhine H. Mutations in embB406 Are Associated with Low-Level Ethambutol Resistance in Canadian Mycobacterium tuberculosis Isolates. Antibiotics (Basel) 2024; 13:624. [PMID: 39061306 PMCID: PMC11273804 DOI: 10.3390/antibiotics13070624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/28/2024] [Accepted: 06/30/2024] [Indexed: 07/28/2024] Open
Abstract
In Mycobacterium tuberculosis, molecular predictions of ethambutol resistance rely primarily on the detection of mutations within embB. However, discordance between embB406 mutations and gold standard phenotypic drug sensitivity testing (DST) questions the significance of embB406 mutations used in molecular DST. This study tabulates embB mutations found in Canadian M. tuberculosis isolates and evaluates the impact of specific mutations on ethambutol resistance. The National Reference Centre for Mycobacteriology culture collection (n = 2796) was screened for isolates with embB mutations. Phenotypic DST was performed on the BACTEC™ MGIT™ 960 at ethambutol concentrations of 2-5 μg/mL. Whole genome sequencing was used for drug resistance predictions, phylogenomics and single nucleotide polymorphism analysis. Detection of resistance-associated embB mutations corresponded to a positive predictive value of 64.3%, negative predictive value of 99.2%, 98.7% specificity, and 73.3% sensitivity compared to phenotypic DST. Two embB406 mutation subtypes (Gly406Asp, Gly406Ala) were found among 16 isolates, of which 12 were sensitive at 5 µg/mL ethambutol with variable resistance between 2-4 µg/mL. A novel frameshift mutation in regulator embR (Gln258fs) was found in nine isolates. Mutations in embB406 were associated with low-level ethambutol resistance undetectable at the recommended critical concentration (5 μg/mL). These novel mutations may exacerbate variability in ethambutol resistance.
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Affiliation(s)
- Morgan Hiebert
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.H.); (M.K.S.); (M.R.); (L.K.); (K.B.)
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Meenu K. Sharma
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.H.); (M.K.S.); (M.R.); (L.K.); (K.B.)
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Melissa Rabb
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.H.); (M.K.S.); (M.R.); (L.K.); (K.B.)
| | - Lisa Karlowsky
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.H.); (M.K.S.); (M.R.); (L.K.); (K.B.)
| | - Kiana Bergman
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.H.); (M.K.S.); (M.R.); (L.K.); (K.B.)
| | - Hafid Soualhine
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.H.); (M.K.S.); (M.R.); (L.K.); (K.B.)
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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Solanki P, Elton L, Honeyborne I, Park M, Satta G, McHugh TD. Improving the diagnosis of tuberculosis: old and new laboratory tools. Expert Rev Mol Diagn 2024; 24:487-496. [PMID: 38832527 DOI: 10.1080/14737159.2024.2362165] [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: 12/22/2023] [Accepted: 05/28/2024] [Indexed: 06/05/2024]
Abstract
INTRODUCTION Despite recent advances in diagnostic technologies and new drugs becoming available, tuberculosis (TB) remains a major global health burden. If detected early, screened for drug resistance, and fully treated, TB could be easily controlled. AREAS COVERED Here the authors discuss M. tuberculosis culture methods which are considered the definitive confirmation of M. tuberculosis infection, and limited advances made to build on these core elements of TB laboratory diagnosis. Literature searches showed that molecular techniques provide enhanced speed of turnaround, sensitivity, and richness of data. Sequencing of the whole genome, is becoming well established for identification and inference of drug resistance. PubMed® literature searches were conducted (November 2022-March 2024). EXPERT OPINION This section highlights future advances in diagnosis and infection control. Prevention of prolonged hospital admissions and rapid TAT are of the most benefit to the overall patient experience. Host transcriptional blood markers have been used in treatment monitoring studies and, with appropriate evaluation, could be rolled out in a diagnostic setting. Additionally, the MBLA is being incorporated into latest clinical trial designs. Whole genome sequencing has enhanced epidemiological evidence. Artificial intelligence, along with machine learning, have the ability to revolutionize TB diagnosis and susceptibility testing within the next decade.
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Affiliation(s)
- Priya Solanki
- UCL-TB and Centre for Clinical Microbiology, Division of Infection & Immunity, Royal Free Campus, London, UK
| | - Linzy Elton
- UCL-TB and Centre for Clinical Microbiology, Division of Infection & Immunity, Royal Free Campus, London, UK
| | - Isobella Honeyborne
- UCL-TB and Centre for Clinical Microbiology, Division of Infection & Immunity, Royal Free Campus, London, UK
| | - Mirae Park
- Respiratory Medicine, Imperial Healthcare NHS Trust, London, UK
| | - Giovanni Satta
- UCL-TB and Centre for Clinical Microbiology, Division of Infection & Immunity, Royal Free Campus, London, UK
| | - Timothy D McHugh
- UCL-TB and Centre for Clinical Microbiology, Division of Infection & Immunity, Royal Free Campus, London, UK
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Xia H, Song Y, Zheng Y, Zhou Y, Ou X, Wang S, Zhao B, Zhao Y. Proficiency testing for drug susceptibility testing of Mycobacterium tuberculosis complex using commercial broth microdilution plate in China in 2021. J Glob Antimicrob Resist 2024; 36:230-236. [PMID: 38072239 DOI: 10.1016/j.jgar.2023.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 07/31/2023] [Accepted: 11/28/2023] [Indexed: 02/02/2024] Open
Abstract
OBJECTIVES The characteristic and performance of Broth microdilution (BMD) plates for drug susceptibility of Mycobacterium tuberculosis have not been systematically evaluated in China. This study was designed to review the key information and assess the performance of BMD plates by analysis of proficiency testing results. METHODS We retrospectively analysed the proficiency testing results of phenotypic drug susceptibility testing (PT-DST) of 45 laboratories using BMD plates in China in 2021. Critical information, such as drug layout, concentration range of each drug, plate storage conditions and duration, operating procedures, and interpretation criteria for binary results were compared. The performance was also analysed. RESULTS Eight types of BMD plates produced by four manufactures were reported. The drug layout, number of drugs on plates, and concentration range varied a lot between different plates. The total sensitivity and specificity of BMD plates for drug susceptibility of Mycobacterium tuberculosis to ten drugs (isoniazid (INH), rifampin (RIF), kanamycin (KAM), amikacin (AM), levofloxacin (LFX), moxifloxacin (MFX), bedaquiline (BDQ), linezolid (LZD), clofazimine (CFZ), and delamanid (DLM)) were 93.9% (95% CI 92.-94.9) and 99.1% (95% CI 98.8-99.3), respectively. The lowest sensitivity was 84.8% (95% CI 80.3-88.4) for LFX and 86.4% (95% CI 82.5-89.6) for MFX, or 87.5% (95% CI 84.2-90.2) for Y1 plate and 87.9% (95% CI 83.5-91.1) for T plate. The lowest specificity was 94.4% (95% CI 91.4-96.4) for DLM, or 97.9% (95% CI 96.8-98.7) for B3 plate. CONCLUSION Commercial BMD plates in China showed varied drug layouts and operational procedures, indicating the urgency of standardization. The lower performance for some drugs showed the low quality of the plates utilized or lack of proficiency of lab staffs in operating and interpreting results.
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Affiliation(s)
- Hui Xia
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuanyuan Song
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yang Zheng
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yang Zhou
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xichao Ou
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shengfen Wang
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Bing Zhao
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
| | - Yanlin Zhao
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
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Sun Q, Zou Y, Feng Q, Gong Z, Song M, Li M, Chen Z. The acetylation of pknH is linked to the ethambutol resistance of Mycobacterium tuberculosis. Arch Microbiol 2023; 205:337. [PMID: 37740776 DOI: 10.1007/s00203-023-03676-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/04/2023] [Accepted: 09/04/2023] [Indexed: 09/25/2023]
Abstract
EmbR, a substrate of pknH in Mycobacterium tuberculosis (Mtb), is related to the ethambutol (EMB) resistance. This study aimed to investigate the relationship between acetylation of pknH and the resistance of EMB mono-resistant Mtb. The EMB mono-resistant Mtb strain was constructed based on the MYCOTB and the Löwenstein-Jensen (LJ) proportion method. The growth kinetics was used to evaluate the bacterial growth. Escherichia coli, as the host of Mtb, was used for cloning and protein purification. Moreover, the immunoprecipitation was performed along with western blot to evaluate the EmbR phosphorylation and pknH acetylation. Each independent experiment was conducted in triplicate. EMB mono-resistant Mtb strain was successfully constructed according to the results of MIC values of 14 anti-Mtb drugs. The EMB resistant (ER) Mtb strain showed faster growth than the wild-type (WT) Mtb strain, and the difference was statistically significant. Moreover, pknH robustly phosphorylates EmbR, and pknH and acetylated pknH protein levels were downregulated in ER strain. The acetylation of pknH may reduce the phosphorylation of EmbR to inhibit the growth of Mtb strain. Enhancing the acetylation of pknH may be a promising method to inhibit the EMB resistance against Mtb.
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Affiliation(s)
- Qing Sun
- Department of Medicine, Hunan Traditional Chinese Medical College, No.136, Lusong Road, Lusong District, Zhuzhou, 412000, Hunan Province, China.
| | - Yan Zou
- Department of Medicine, Hunan Traditional Chinese Medical College, No.136, Lusong Road, Lusong District, Zhuzhou, 412000, Hunan Province, China
| | - Qian Feng
- Department of Medicine, Hunan Traditional Chinese Medical College, No.136, Lusong Road, Lusong District, Zhuzhou, 412000, Hunan Province, China
| | - Zongyue Gong
- Department of Medicine, Hunan Traditional Chinese Medical College, No.136, Lusong Road, Lusong District, Zhuzhou, 412000, Hunan Province, China
| | - Manlin Song
- Hunan Traditional Chinese Medical College, Zhuzhou, China
| | - Machao Li
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Zhuang Chen
- Department of Medicine, Hunan Traditional Chinese Medical College, No.136, Lusong Road, Lusong District, Zhuzhou, 412000, Hunan Province, China
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Jeon SM, Park S, Lim NR, Lee N, Jung J, Sung N, Kim S. Molecular Analysis of Anti-Tuberculosis Drug Resistance of Mycobacterium tuberculosis Isolated in the Republic of Korea. Antibiotics (Basel) 2023; 12:1324. [PMID: 37627744 PMCID: PMC10451913 DOI: 10.3390/antibiotics12081324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/03/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Rapid and accurate detection of tuberculosis (TB) drug resistance is critical for the successful treatment and control of TB. Here, we investigated resistance to anti-TB drugs and genetic variations in 215 drug-resistant Mycobacterium tuberculosis isolates in Korea. Genetic variations were observed in rpoB Ser531Leu, katG Ser315Thr, and gyrA Asp94Gly; however, the minimum inhibitory concentrations varied, which can be attributed to other resistance mechanisms. Examination of genetic relatedness among drug-resistant isolates revealed that the cluster size of resistant bacteria was less than six strains, suggesting no evidence of a large-scale epidemic caused by a specific strain. However, rpoC mutants of the rifampicin-resistant isolates were composed of five types of clusters, suggesting that these compensatory mutations advance propagation. In the present study, more than 90% of the resistance mechanisms to major anti-TB drugs were identified, and the effect of each mutation on drug resistance was estimated. With the clinical application of recent next-generation sequencing-based susceptibility testing, the present study is expected to improve the clinical utilization of genotype-based drug susceptibility testing for the diagnosis and treatment of patients with drug-resistant TB.
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Affiliation(s)
- Se-Mi Jeon
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
| | - Sanghee Park
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
| | - Na-Ra Lim
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
| | - Noori Lee
- Clinical Research Center, Masan National Tuberculosis Hospital, Changwon-si 51755, Republic of Korea; (N.L.); (J.J.); (N.S.)
| | - Jihee Jung
- Clinical Research Center, Masan National Tuberculosis Hospital, Changwon-si 51755, Republic of Korea; (N.L.); (J.J.); (N.S.)
| | - Nackmoon Sung
- Clinical Research Center, Masan National Tuberculosis Hospital, Changwon-si 51755, Republic of Korea; (N.L.); (J.J.); (N.S.)
| | - Seonghan Kim
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
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10
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Ke H, Gui X, Sun W, Zhang S, Yang Y, Zhang Z, Fan L. The Safety and Efficacy of Prolonged Use of Bedaquiline for the Treatment of Patients with Pulmonary Multi-Drug Resistant/Rifampin-Resistant Tuberculosis: A Prospective, Cohort Study in China. Infect Drug Resist 2023; 16:5055-5064. [PMID: 37576523 PMCID: PMC10417604 DOI: 10.2147/idr.s419996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/20/2023] [Indexed: 08/15/2023] Open
Abstract
Objective To evaluate the safety, tolerability, and efficacy of prolonged bedaquiline (Bdq) treatment in patients with multi-drug/rifampin-resistant tuberculosis (MDR/RR-TB). Methods This prospective cohort study was performed from August 2018 to August 2021. Patients diagnosed with MDR/RR-TB who met the inclusion criteria were prospectively included. Patients were treated with individual regimens of 18-20 months containing Bdq for six months or a prolonged course of nine or 12 months according to treatment demands, and the efficacy and safety with a different course of Bdq-containing regimens were compared and evaluated. Results A total of 159 MDR/RR-TB patients were included in the study, including 96 cases with six months of Bdq, 50 cases with nine months of Bdq, and 13 patients with 12 months of Bdq. The treatment success rates were 89.6%, 90%, and 84.6% in Bdq at six months, nine months, and 12 months, respectively, which were not statistically different (P = 0.85). The main adverse events (AEs) were anemia, thrombocytopenia, and liver dysfunction in all patients, with no significant difference among the three groups. Patients who had fewer drugs chosen, disseminated lesions or lesions that were slowly absorbed, and severe cavities were the common reasons for prolonged use of Bdq. Conclusion Prolonged course use of Bdq from six months to 12 months clinically proved to be safe and efficient, and patients with severe or disseminated lesions had the chance to prolong the use of Bdq for more than six months to achieve optimal treatment outcomes.
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Affiliation(s)
- Hui Ke
- Department of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai Clinic and Research Center of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai, People’s Republic of China
| | - Xuwei Gui
- Department of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai Clinic and Research Center of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai, People’s Republic of China
| | - Wenwen Sun
- Department of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai Clinic and Research Center of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai, People’s Republic of China
| | - Shaojun Zhang
- Department of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai Clinic and Research Center of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai, People’s Republic of China
| | - Yan Yang
- Department of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai Clinic and Research Center of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai, People’s Republic of China
| | - Zhemin Zhang
- Department of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai Clinic and Research Center of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai, People’s Republic of China
| | - Lin Fan
- Department of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai Clinic and Research Center of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai, People’s Republic of China
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11
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Green AG, Vargas R, Marin MG, Freschi L, Xie J, Farhat MR. Analysis of Genome-Wide Mutational Dependence in Naturally Evolving Mycobacterium tuberculosis Populations. Mol Biol Evol 2023; 40:msad131. [PMID: 37352142 PMCID: PMC10292908 DOI: 10.1093/molbev/msad131] [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: 07/29/2022] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 06/25/2023] Open
Abstract
Pathogenic microorganisms are in a perpetual struggle for survival in changing host environments, where host pressures necessitate changes in pathogen virulence, antibiotic resistance, or transmissibility. The genetic basis of phenotypic adaptation by pathogens is difficult to study in vivo. In this work, we develop a phylogenetic method to detect genetic dependencies that promote pathogen adaptation using 31,428 in vivo sampled Mycobacterium tuberculosis genomes, a globally prevalent bacterial pathogen with increasing levels of antibiotic resistance. We find that dependencies between mutations are enriched in antigenic and antibiotic resistance functions and discover 23 mutations that potentiate the development of antibiotic resistance. Between 11% and 92% of resistant strains harbor a dependent mutation acquired after a resistance-conferring variant. We demonstrate the pervasiveness of genetic dependency in adaptation of naturally evolving populations and the utility of the proposed computational approach.
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Affiliation(s)
- Anna G Green
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Roger Vargas
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Computational Biomedicine, Harvard Medical School, Boston, MA, USA
| | - Maximillian G Marin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Luca Freschi
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Jiaqi Xie
- Department of Genetics, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - 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
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12
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Epidemiological cut-off values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of M. tuberculosis. Eur Respir J 2022; 60:2200239. [PMID: 35301246 PMCID: PMC9556810 DOI: 10.1183/13993003.00239-2022] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/22/2022] [Indexed: 12/15/2022]
Abstract
Drug susceptibility testing of M. tuberculosis is rooted in a binary susceptible/resistant paradigm. While there are considerable advantages in measuring the minimum inhibitory concentrations (MICs) of a panel of drugs for an isolate, it is necessary to measure the epidemiological cut-off values (ECOFF/ECVs) to permit comparison with qualitative data. Here we present ECOFF/ECVs for 13 anti-tuberculosis compounds, including bedaquiline and delamanid, derived from 20 637 clinical isolates collected by 14 laboratories based in 11 countries on five continents. Each isolate was incubated for 14 days on a dry 96-well broth microdilution plate and then read. Resistance to most of the drugs due to prior exposure is expected and the MIC distributions for many of the compounds are complex, and therefore a phenotypically wild-type population could not be defined. Since a majority of samples also underwent genetic sequencing, we defined a genotypically wild-type population and measured the MIC of the 99th percentile by direct measurement and via fitting a Gaussian using interval regression. The proposed ECOFF/ECVs were then validated by comparing with the MIC distributions of high-confidence genetic variants that confer resistance and with qualitative drug susceptibility tests obtained via the Mycobacterial Growth Indicator Tube (MGIT) system or Microscopic-Observation Drug Susceptibility (MODS) assay. These ECOFF/ECVs will inform and encourage the more widespread adoption of broth microdilution: this is a cheap culture-based method that tests the susceptibility of 12-14 antibiotics on a single 96-well plate and so could help personalise the treatment of tuberculosis.
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Affiliation(s)
- The CRyPTIC Consortium
- For a list of all members of the CRyPTIC Consortium and their affiliations, please see the section at the end of this article
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13
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Tang Q, Ke H, Sun WW, Zhang SJ, Fan L. The Correlations of Minimal Inhibitory Concentration Values of Anti-TB Drugs with Treatment Outcomes and Clinical Profiles in Patients with Multidrug-Resistant Tuberculosis (MDR-TB) in China. Infect Drug Resist 2022; 15:5275-5287. [PMID: 36106053 PMCID: PMC9464630 DOI: 10.2147/idr.s374687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/20/2022] [Indexed: 11/23/2022] Open
Abstract
Objective It is a challenge to obtain satisfactory treatment outcomes for patients with multidrug-resistant/rifampicin-resistant tuberculosis (MDR/RR-TB); the study aims to correlate the Minimum Inhibitory Concentration (MIC) value of drugs with the outcome of patients with MDR/RR-TB to obtain an understanding for better regimens and optimal outcomes. Methods The patients diagnosed with MDR/RR-TB were retrospectively enrolled from January 1, 2018 to December 31, 2019, recorded clinical characteristics, MIC DST (Drug Susceptibility Test) results, and followed the treatment outcome. The data were analyzed on the correlations of MIC DST values with outcomes and clinical characteristics. Results A total of 276 patients with MDR/RR-TB were included, containing 98 cases (35.5%) with newly treated patients and 178 cases (64.5%) with re-treated patients. A total of 220 cases recorded treatment success (79.7%) and 49 cases recorded treatment failure or died. MIC values of isoniazid (H), moxifloxacin (Mfx), and ethionamide (Eto) in newly treated patients were lower than those in retreated patients, and resistance levels of Mfx and H were closely associated with the treatment outcome (P < 0.05) while those of other drugs had no close association with treatment outcome. Conclusions MIC values of some anti-TB drugs, such as fluoroquinolones (FQs) and H, can reflect the treatment outcome for patients with MDR/RR-TB, which can contribute to making regimens for better treatment outcomes.
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Affiliation(s)
- Qin Tang
- Department of Tuberculosis, Shanghai Clinical Research Center for Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai Clinical Research Center for Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai, 200433, People's Republic of China
| | - Hui Ke
- Department of Tuberculosis, Shanghai Clinical Research Center for Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai Clinical Research Center for Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai, 200433, People's Republic of China
| | - Wen-Wen Sun
- Department of Tuberculosis, Shanghai Clinical Research Center for Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai Clinical Research Center for Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai, 200433, People's Republic of China
| | - Shao-Jun Zhang
- Department of Tuberculosis, Shanghai Clinical Research Center for Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai Clinical Research Center for Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai, 200433, People's Republic of China
| | - Lin Fan
- Department of Tuberculosis, Shanghai Clinical Research Center for Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai Clinical Research Center for Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai, 200433, People's Republic of China
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14
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Getahun M, Blumberg HM, Ameni G, Beyene D, Kempker RR. Minimum inhibitory concentrations of rifampin and isoniazid among multidrug and isoniazid resistant Mycobacterium tuberculosis in Ethiopia. PLoS One 2022; 17:e0274426. [PMID: 36099255 PMCID: PMC9469996 DOI: 10.1371/journal.pone.0274426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 08/30/2022] [Indexed: 11/30/2022] Open
Abstract
Introduction Traditionally, single critical concentrations of drugs are utilized for Mycobacterium tuberculosis (Mtb) drug susceptibility testing (DST); however, the level of drug resistance can impact treatment choices and outcomes. Mutations at the katG gene are the major genetic mutations in multidrug resistant (MDR) Mtb and usually associated with high level resistance. We assessed the minimum inhibitory concentrations (MICs) of MDR or rifampin resistant (RR) and isoniazid (INH) resistant Mtb isolates to determine the quantification of drug resistance among key anti-tuberculosis drugs. Methods The study was conducted on stored Mtb isolates collected as part of a national drug resistance survey in Ethiopia. MIC values were determined using Sensititre™ MYCOTB plates. A line probe assay (MTBDRplus) was also performed to identify genetic determinants of resistance for all isolates. Results MIC testing was performed on 74 Mtb isolates including 46 MDR, 2 RR and 26 INH phenotypically resistant isolates as determined by the Löwenstein Jensen (LJ) method. Four (15%) INH resistant Mtb isolates were detected as borderline rifampin resistance (MIC = 1 μg/ml) using MYCOTB MIC plates and no rifampin resistance mutations were detected by LPA. Among the 48 MDR/RR TB cases, 9 (19%) were rifabutin susceptible (MIC was between ≤0.25 and 0.5μg/ml). Additionally, the MIC for isoniazid was between 2–4 μg/ml (moderate resistance) for 58% of MDR TB isolates and 95.6% (n = 25) of the isolates had mutations at the katG gene. Conclusion Our findings suggest a role for rifabutin treatment in a subset of RR TB patients, thus potentially preserving an important drug class. The high proportion of moderate level INH resistant among MDR Mtb isolates indicates the potential benefit of high dose isoniazid treatment in a high proportion of katG gene harboring MDR Mtb isolates.
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Affiliation(s)
- Muluwork Getahun
- TB and HIV Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
- * E-mail:
| | - Henry M. Blumberg
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Dereje Beyene
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Russell R. Kempker
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
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15
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Puyén ZM, Santos-Lázaro D, Vigo AN, Coronel J, Alarcón MJ, Cotrina VV, Moore DAJ. Evaluation of the broth microdilution plate methodology for susceptibility testing of Mycobacterium tuberculosis in Peru. BMC Infect Dis 2022; 22:705. [PMID: 36002805 PMCID: PMC9399989 DOI: 10.1186/s12879-022-07677-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is a communicable, preventable and curable disease caused by the bacterium Mycobacterium tuberculosis (MTB). Peru is amongst the 30 countries with the highest burden of multidrug-resistant tuberculosis (MDR-TB) worldwide. In the fight against drug-resistant tuberculosis, the UKMYC6 microdilution plate was developed and validated by the CRyPTIC project. The objective of the study was to evaluate the use of the broth microdilution (BMD) plate methodology for susceptibility testing of drug-resistant MTB strains in Peru. METHODS MTB strains isolated between 2015 and 2018 in Peru were used. 496 nationally-representative strains determined as drug-resistant by the routine 7H10 Agar Proportion Method (APM) were included in the present study. The Minimum Inhibitory Concentration (MIC) of 13 antituberculosis drugs were determined for each strain using the UKMYC6 microdilution plates. Diagnostic agreement between APM and BMD plate methodology was determined for rifampicin, isoniazid, ethambutol, ethionamide, kanamycin and levofloxacin. Phenotypes were set using binary (or ternary) classification based on Epidemiological cut-off values (ECOFF/ECV) proposed by the CRyPTIC project. Whole Genome Sequencing (WGS) was performed on strains with discrepant results between both methods. RESULTS MIC distributions were determined for 13 first- and second-line anti-TB drugs, including new (bedaquiline, delamanid) and repurposed (clofazimine, linezolid) agents. MIC results were available for 80% (397/496) of the strains at 14 days and the remainder at 21 days. The comparative analysis determined a good agreement (0.64 ≤ k ≤ 0.79) for the drugs rifampicin, ethambutol, ethionamide and kanamycin, and the best agreement (k > 0.8) for isoniazid and levofloxacin. Overall, 12% of MIC values were above the UKMYC6 plate dilution ranges, most notably for the drugs rifampicin and rifabutin. No strain presented MICs higher than the ECOFF/ECV values for the new or repurposed drugs. Discrepant analysis using genotypic susceptibility testing by WGS supported half of the results obtained by APM (52%, 93/179) and half of those obtained by BMD plate methodology (48%, 86/179). CONCLUSIONS The BMD methodology using the UKMYC6 plate allows the complete susceptibility characterization, through the determination of MICs, of drug-resistant MTB strains in Peru. This methodology shows good diagnostic performances for rifampicin, isoniazid, ethambutol, ethionamide, kanamycin and levofloxacin. It also allows for the characterization of MICs for other drugs used in previous years against tuberculosis, as well as for new and repurposed drugs recently introduced worldwide.
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Affiliation(s)
- Zully M Puyén
- Instituto Nacional de Salud, Lima, Perú.
- Escuela de Medicina, Universidad Peruana de Ciencias Aplicadas, Lima, Perú.
| | | | | | | | | | | | - David A J Moore
- Universidad Peruana Cayetano Heredia, Lima, Perú
- London School of Hygiene & Tropical Medicine, London, UK
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16
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Heysell SK, Mpagama SG, Ogarkov OB, Conaway M, Ahmed S, Zhdanova S, Pholwat S, Alshaer MH, Chongolo AM, Mujaga B, Sariko M, Saba S, Rahman SMM, Uddin MKM, Suzdalnitsky A, Moiseeva E, Zorkaltseva E, Koshcheyev M, Vitko S, Mmbaga BT, Kibiki GS, Pasipanodya JG, Peloquin CA, Banu S, Houpt ER. Pharmacokinetic-Pharmacodynamic Determinants of Clinical Outcomes for Rifampin-Resistant Tuberculosis: A Multisite Prospective Cohort Study. Clin Infect Dis 2022; 76:497-505. [PMID: 35731948 PMCID: PMC9907514 DOI: 10.1093/cid/ciac511] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/13/2022] [Accepted: 06/17/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Rifampin-resistant and/or multidrug-resistant tuberculosis (RR/MDR-TB) treatment requires multiple drugs, and outcomes remain suboptimal. Some drugs are associated with improved outcome. It is unknown whether particular pharmacokinetic-pharmacodynamic relationships predict outcome. METHODS Adults with pulmonary RR/MDR-TB in Tanzania, Bangladesh, and the Russian Federation receiving local regimens were enrolled from June 2016 to July 2018. Serum was collected after 2, 4, and 8 weeks for each drug's area under the concentration-time curve over 24 hours (AUC0-24). Quantitative susceptibility of the M. tuberculosis isolate was measured by minimum inhibitory concentrations (MICs). Individual drug AUC0-24/MIC targets were assessed by adjusted odds ratios (ORs) for favorable treatment outcome, and hazard ratios (HRs) for time to sputum culture conversion. K-means clustering algorithm separated the cohort of the most common multidrug regimen into 4 clusters by AUC0-24/MIC exposures. RESULTS Among 290 patients, 62 (21%) experienced treatment failure, including 30 deaths. Moxifloxacin AUC0-24/MIC target of 58 was associated with favorable treatment outcome (OR, 3.75; 95% confidence interval, 1.21-11.56; P = .022); levofloxacin AUC0-24/MIC of 118.3, clofazimine AUC0-24/MIC of 50.5, and pyrazinamide AUC0-24 of 379 mg × h/L were associated with faster culture conversion (HR >1.0, P < .05). Other individual drug exposures were not predictive. Clustering by AUC0-24/MIC revealed that those with the lowest multidrug exposures had the slowest culture conversion. CONCLUSIONS Amidst multidrug regimens for RR/MDR-TB, serum pharmacokinetics and M. tuberculosis MICs were variable, yet defined parameters to certain drugs-fluoroquinolones, pyrazinamide, clofazimine-were predictive and should be optimized to improve clinical outcome. CLINICAL TRIALS REGISTRATION NCT03559582.
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Affiliation(s)
- Scott K Heysell
- Correspondence: Scott K. Heysell, 345 Crispell Drive, MR-6; Charlottesville, VA 29908, USA ()
| | | | - Oleg B Ogarkov
- Department of Epidemiology and Microbiology, Scientific Centre for Family Health and Human Reproduction Problems, Irkutsk, Russian Federation
| | - Mark Conaway
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, USA
| | - Shahriar Ahmed
- International Center for Diarrheal Diseases Research, Bangladesh, Dhaka, Bangladesh
| | - Svetlana Zhdanova
- Department of Epidemiology and Microbiology, Scientific Centre for Family Health and Human Reproduction Problems, Irkutsk, Russian Federation
| | - Suporn Pholwat
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Mohammad H Alshaer
- Infectious Disease Pharmacokinetics Lab, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Anna M Chongolo
- Kibong’oto Infectious Diseases Hospital, Sanya Juu, Tanzania
| | - Buliga Mujaga
- Kilimanjaro Clinical Research Institute and Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Margaretha Sariko
- Kilimanjaro Clinical Research Institute and Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Sabrina Saba
- International Center for Diarrheal Diseases Research, Bangladesh, Dhaka, Bangladesh
| | - S M Mazidur Rahman
- International Center for Diarrheal Diseases Research, Bangladesh, Dhaka, Bangladesh
| | | | - Alexey Suzdalnitsky
- Irkutsk Regional Tuberculosis Referral Hospital, Irkutsk, Russian Federation
| | - Elena Moiseeva
- Irkutsk Regional Tuberculosis Referral Hospital, Irkutsk, Russian Federation
| | - Elena Zorkaltseva
- Irkutsk State Medical Academy of Postgraduate Education–Branch of Russian Medical Academy of Continuing Professional Education, Irkutsk, Russian Federation
| | - Mikhail Koshcheyev
- Irkutsk Regional Tuberculosis Referral Hospital, Irkutsk, Russian Federation
| | - Serhiy Vitko
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Blandina T Mmbaga
- Kilimanjaro Clinical Research Institute and Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Gibson S Kibiki
- Kilimanjaro Clinical Research Institute and Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Jotam G Pasipanodya
- Quantitative Preclinical & Clinical Sciences Department, Praedicare Inc, Dallas, Texas, USA
| | - Charles A Peloquin
- Infectious Disease Pharmacokinetics Lab, College of Pharmacy, University of Florida, Gainesville, Florida, USA
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Prediction of drug resistance profile of multidrug-resistant Mycobacterium tuberculosis (MDR-MTB) isolates from newly diagnosed case by whole genome sequencing (WGS): a study from a high tuberculosis burden country. BMC Infect Dis 2022; 22:499. [PMID: 35624432 PMCID: PMC9137048 DOI: 10.1186/s12879-022-07482-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/17/2022] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES Our aim was to assess the ability of the Whole-genome sequencing (WGS) in predicting drug resistance profile of multidrug-resistant mycobacterium tuberculosis (MDR-MTB) from newly diagnosed cases in China. METHODS We validated the Phenotypic drug Sensitivity Test (pDST) for 12 anti-tuberculosis drugs using the Bactec MGIT 960 system. We described the characteristics of the isolates enrolled and compared the pDST results with resistance profiles predicted by WGS. RESULTS The pDST showed that of the 43 isolates enrolled, 25.6% were sensitive to rifabutin (RFB); 97.7%、97.7%、93.0% and 93.0% were sensitive to cycloserine (Cs), amikacin/kanamycin (Ak/Km), para-aminosalicylic acid (Pas) and ethionamide Eto), respectively; 18.6% were resistant to fluoroquinolones (FQs) or second-line injections. Genotype DST determined by WGS of Ak/Km、Eto and RFP reached high consistency to 97.7% compared with pDST, followed by moxifloxacin (Mfx) 95.3%, levofloxaci (Lfx) and Pas 93%, streptomycin (Sm) 90.3%. The genotype DST of RFB and EMB showed low consistency with the pDST of 67.2 and 79.1%. WGS also detected 27.9% isolates of pyrazinamide(PZA)-related drug-resistant mutation. No mutations associated with linezolid (Lzd), bedaquiline (Bdq) and clofazimine (Cfz) were detectd. CONCLUSIONS WGS has the potential to infer resistance profiles without time-consuming phenotypic methods, which could be provide a basis to formulate reasonable treatment in high TB burden areas.
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Getahun M, Ameni G, Mollalign H, Diriba G, Beyene D. Genotypic and phenotypic drug-resistance detection and prevalence of heteroresistance in patients with isoniazid- and multidrug-resistant tuberculosis in Ethiopia. IJID REGIONS 2022; 2:149-153. [PMID: 35757078 PMCID: PMC9216396 DOI: 10.1016/j.ijregi.2021.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/28/2021] [Accepted: 12/19/2021] [Indexed: 11/25/2022]
Abstract
Objective To assess the agreement between genotypic and phenotypic methods for detecting drug resistance, and examine the prevalence of heteroresistance among isoniazid (INH)- and multidrug/rifampicin-resistant (MDR/RR) TB. Method In total, 127 Mycobacterium tuberculosis (Mtb) isolates, including 65 MDR/RR and 62 INH resistant, were used. First-line drug susceptibility testing (DST) was performed using the LJ method to determine the percentage of resistant bacteria. All drug-resistant isolates underwent testing with LPA. Heteroresistance was defined as simultaneous detection of wild-type and resistance-conferring mutations using LPA. Result The sensitivity of LPA (compared with LJ DST) was 96% for any INH-resistant TB and 94% for any RR TB. The prevalence of heteroresistance among the 123. Mtb isolates was 9.8%. The percentage of resistant bacteria ranged from 1% to 10% for heteroresistant TB. Rifampicin heteroresistance was detected in 1.6% of MDR TB patients. INH heteroresistance was detected in 1.6% and 16.7% of MDR and INH-resistant TB patients, respectively. The proportion of INH heteroresistance was significantly higher (p = 0.030) in persons living with HIV. Conclusion Some phenotypic drug resistances were not captured by LPA. The prevalence and percentage of resistant bacteria among heteroresistant TB highlight the importance of LPA for early detection of heteroresistant TB.
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Affiliation(s)
- Muluwork Getahun
- Ethiopian Public Health Institute
- Addis Ababa University, Department of Microbial, Cellular, and Molecular Biology
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, PO Box 1176, Addis Ababa, Ethiopia
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, PO Box 15551, Al Ain, United Arab Emirates University
| | | | | | - Dereje Beyene
- Addis Ababa University, Department of Microbial, Cellular, and Molecular Biology
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19
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Mbelele PM, Utpatel C, Sauli E, Mpolya EA, Mutayoba BK, Barilar I, Dreyer V, Merker M, Sariko ML, Swema BM, Mmbaga BT, Gratz J, Addo KK, Pletschette M, Niemann S, Houpt ER, Mpagama SG, Heysell SK. OUP accepted manuscript. JAC Antimicrob Resist 2022; 4:dlac042. [PMID: 35465240 PMCID: PMC9021016 DOI: 10.1093/jacamr/dlac042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/25/2022] [Indexed: 12/02/2022] Open
Abstract
Background Rifampicin- or multidrug-resistant (RR/MDR) Mycobacterium tuberculosis complex (MTBC) strains account for considerable morbidity and mortality globally. WGS-based prediction of drug resistance may guide clinical decisions, especially for the design of RR/MDR-TB therapies. Methods We compared WGS-based drug resistance-predictive mutations for 42 MTBC isolates from MDR-TB patients in Tanzania with the MICs of 14 antibiotics measured in the Sensititre™ MycoTB assay. An isolate was phenotypically categorized as resistant if it had an MIC above the epidemiological-cut-off (ECOFF) value, or as susceptible if it had an MIC below or equal to the ECOFF. Results Overall, genotypically non-wild-type MTBC isolates with high-level resistance mutations (gNWT-R) correlated with isolates with MIC values above the ECOFF. For instance, the median MIC value (mg/L) for rifampicin-gNWT-R strains was >4.0 (IQR 4.0–4.0) compared with 0.5 (IQR 0.38–0.50) in genotypically wild-type (gWT-S, P < 0.001); isoniazid-gNWT-R >4.0 (IQR 2.0–4.0) compared with 0.25 (IQR 0.12–1.00) among gWT-S (P = 0.001); ethionamide-gNWT-R 15.0 (IQR 10.0–20.0) compared with 2.50 (IQR; 2.50–5.00) among gWT-S (P < 0.001). WGS correctly predicted resistance in 95% (36/38) and 100% (38/38) of the rifampicin-resistant isolates with ECOFFs >0.5 and >0.125 mg/L, respectively. No known resistance-conferring mutations were present in genes associated with resistance to fluoroquinolones, aminoglycosides, capreomycin, bedaquiline, delamanid, linezolid, clofazimine, cycloserine, or p-amino salicylic acid. Conclusions WGS-based drug resistance prediction worked well to rule-in phenotypic drug resistance and the absence of second-line drug resistance-mediating mutations has the potential to guide the design of RR/MDR-TB regimens in the future.
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Affiliation(s)
- Peter M. Mbelele
- Kibong’oto Infectious Diseases Hospital (KIDH), Siha, Kilimanjaro, Tanzania
- Department of Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
- Corresponding author. E-mail:
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany
| | - Elingarami Sauli
- Department of Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
| | - Emmanuel A. Mpolya
- Department of Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
| | - Beatrice K. Mutayoba
- Ministry of Health, National AIDS Control Program, Department of Preventive Services, Dodoma, Tanzania
- CIHLMU Center for International Health, University Hospital, LMU Munich, Germany
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany
| | - Viola Dreyer
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- Evolution of the Resistome, Research Center Borstel, Borstel, Germany
| | | | | | - Blandina T. Mmbaga
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Jean Gratz
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Kennedy K. Addo
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Michel Pletschette
- CIHLMU Center for International Health, University Hospital, LMU Munich, Germany
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Munich, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany
| | - Eric R. Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Stellah G. Mpagama
- Kibong’oto Infectious Diseases Hospital (KIDH), Siha, Kilimanjaro, Tanzania
- Department of Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Scott K. Heysell
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
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Wang R, Zhao X, Wan K. Deterioration of Cycloserine in Drug Susceptibility Testing of Mycobacterium. Infect Drug Resist 2022; 15:135-140. [PMID: 35046677 PMCID: PMC8763265 DOI: 10.2147/idr.s348428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/23/2021] [Indexed: 11/26/2022] Open
Abstract
Purpose Cycloserine is an effective group C anti-tuberculosis drug. But the reliability and reproducibility of drug susceptibility tests (DST) for this drug cannot be guaranteed and provide poor clinical predictive values. However, DST of cycloserine in practice provides rough estimate of the drug resistance of Mycobacterium strains, there is practical need to clarify the problem of cycloserine in in vitro DST, and to explore solutions to overcome these limitations. Methods The effectiveness of serial cycloserine solutions incubated at 37°C for 1 to 29 days was tested using the Alamar Blue assay, and cycloserine in culture medium was analyzed by UPLC-MS. Results The data revealed that cycloserine itself continuously degraded in culture medium. This amount of degradation was sufficient to alter the minimum inhibitory concentration (MIC) value of Mycobacterium strains and therefore could not be ignored, although it was more stable than in phosphoric acid buffer. Conclusion The different test times and the degradation of cycloserine were responsible for the lack of agreements between the cycloserine DST methods and the low reliability of this in vitro test. By adjusting with the incubation time depended degradation ratio of cycloserine, more accurate MIC values may be obtained allowing for improved coincidence between in vitro experiment and clinic use. Furthermore, it can guide clinicians to carry out this anti-tuberculosis treatment more effectively and reliably.
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Affiliation(s)
- Ruibai Wang
- State Key Laboratory for Infectious Diseases Prevention and Control, Tuberculosis Department, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- Correspondence: Ruibai Wang State Key Laboratory for Infectious Diseases Prevention and Control, Tuberculosis Department, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changbai Road 155, Changping, Beijing, 102206, People’s Republic of ChinaTel +86-10-58900779 Email
| | - Xiuqin Zhao
- State Key Laboratory for Infectious Diseases Prevention and Control, Tuberculosis Department, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Kanglin Wan
- State Key Laboratory for Infectious Diseases Prevention and Control, Tuberculosis Department, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
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21
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Strong Increase in Moxifloxacin Resistance Rate among Multidrug-Resistant Mycobacterium tuberculosis Isolates in China, 2007 to 2013. Microbiol Spectr 2021; 9:e0040921. [PMID: 34851179 PMCID: PMC8635133 DOI: 10.1128/spectrum.00409-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We designed this study to determine the trend of moxifloxacin resistance among multidrug-resistant tuberculosis (MDR-TB) patients from 2007 to 2013 in China to inform the composition of multidrug-resistant/rifampicin-resistant tuberculosis (MDR/RR-TB) treatment regimens. We assessed moxifloxacin resistance among MDR-TB isolates collected in national drug resistance surveys in 2007 and 2013 that included 3,634 smear-positive and 7,206 culture-positive pulmonary tuberculosis patients, respectively. Moxifloxacin susceptibility was examined by a Mycobacterium growth indicator tube (MGIT) 960 for the 2007 isolates, and by the minimum inhibitory concentration (MIC) method for the 2013 isolates, at both breakpoints 0.5 and 2.0 μg/mL. Risk factors were explored through multivariable log-binominal regression analysis. Mutations in gyrA and gyrB for part of the isolates were also studied through sequencing. Of 401 MDR strains isolated in 2007, moxifiloxacin resistance could be determined for 319 (79.6%): 41 (12.9%) and 10 (3.1%) were resistant at 0.5 and 2.0 μg/mL, respectively. Of 365 MDR strains isolated in 2013, 338 (92.6%) could be analyzed: 140 (41.4%) and 79 (23.4%) were resistant at 0.5 and 2.0 μg/mL. For patients in 2007, no characteristics were significantly associated with moxifloxacin resistance. For patients in 2013, patients aged ≥60 years (adjusted prevalence ratio [aPR], 1.46; 95% confidence interval [CI], 1.10 to 1.93) were more likely to have resistance at 0.5 μg/mL, whereas those residing in eastern China compared to those in central China had an increased risk of resistance at both 0.5 (aPR, 1.85; 95% CI, 1.38 to 2.48) and 2.0 μg/mL (aPR, 2.14; 95% CI, 1.35 to 3.40). Sequencing results were obtained for 245 and 266 MDR-TB isolates in 2007 and 2013, respectively. In total, 34 of 38 (89.5%) and 89 of 104 (85.6%) of 2007 and 2013 moxifloxacin-resistant (0.5 μg/mL) MDR-TB strains had mutations in the gyrA and gyrB gene, respectively. Asp94Gly was the most common mutation among 2007 (11 of 38, 28.9%) and 2013 isolates (24 of 104, 23.1%) and conferred high-level moxifloxacin resistance. Moxifloxacin resistance among MDR-TB patients in China increased from modest to high from 2007 to 2013. Moxifloxacin should be used carefully as a potentially effective drug for composing MDR/RR-TB regimens especially for elderly patients in China. Individual susceptibility testing especially rapid molecular-based assays should be conducted to confirm the susceptibility to moxifloxacin. IMPORTANCE China is one of the high-burden countries for multidrug-resistant/rifampicin-resistant tuberculosis (MDR/RR-TB). Moxifloxacin is one of the critical antituberculosis drugs for MDR/RR-TB treatment. Susceptibility to moxifloxacin is therefore very important to compose effective regimens and to provide protection against development of resistance of companion drugs such as bedaquiline and linezolid. There are, however, no nationally representative data on moxifloxacin resistance among MDR/RR-TB cases in China. Therefore, we assessed the resistance prevalence for moxifloxacin among MDR-TB strains isolated in national drug resistance surveys in 2007 and 2013 that covered 72 sites around the country. We demonstrate that the prevalence of moxifloxacin resistance in MDR-TB isolates increased from modest to high, which should prompt the national tuberculosis program to use moxifloxacin cautiously in second-line regimens to treat MDR/RR-TB unless susceptibility can be laboratory-confirmed.
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22
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Garcia Carvalho NF, Pedace CS, Barbosa de Almeida AR, Dos Santos Simeão FC, Chimara E. Evaluation of drug susceptibility in nontuberculous mycobacteria using the SLOMYCO and RAPMYCO sensititre plates. Int J Mycobacteriol 2021; 10:379-387. [PMID: 34916455 DOI: 10.4103/ijmy.ijmy_219_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background Non-tuberculous Mycobacteria (NTM) cause different forms of diseases. According to recent guideline by ATS/ERS/ESCMID/IDSA, drug susceptibility test (DST) is an important requirement to choose adequate treatment. The minimum inhibitory concentration (MIC) test is the recommended method. Sensititre SLOMYCO and RAPMYCO commercial panels were developed to perform mycobacteria DST easier. However, there are only two comparative studies between SLOMYCO and the MIC method and none for the RAPMYCO panel. The present study aimed to evaluate the Sensititre SLOMYCO and RAPMYCO plates in determining drug susceptibility compared to the gold standard method (MIC). Methods The tests were carried out with clinical isolates received in the diagnostic routine of the Tuberculosis Laboratory at Institute Adolfo Lutz from the most frequent species in the state of São Paulo, Brazil. Reference strains were tested for repeatability and reproducibility analyses. MIC and Sensititre plates readings were compared with and without resazurin stain. Agreement between results was defined as MIC within the same dilution or dilution variation resulting the same category in both tests. Results were classified by categorical errors. Results The RAPMYCO panel had 100% agreement for the drugs amikacin, doxycycline, ciprofloxacin and trimethoprim/sulfamethoxazole, 83.3% for clarithromycin and moxifloxacin and 60% for cefoxitin. The SLOMYCO panel had 80% agreement for amikacin and moxifloxacin and 60% for clarithromycin, rifabutin, rifampicin and ciprofloxacin. The repeatability and reproducibility with RAPMYCO and SLOMYCO plates showed a high level of agreement for the drugs tested, being higher with the use of resazurin. However, an evaluation on routine condition is needed. Conclusions The present study found that the fewer steps in the tests with Sensititre plates and reading with resazurin allow its use with greater safety and efficiency in the laboratory routine. The results presented here will facilitate the execution of a validation for complete incorporation of Sensititre plates into a diagnostic routine.
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Affiliation(s)
| | | | | | | | - Erica Chimara
- Tuberculosis and Mycobacteriosis Laboratory, Institute Adolfo Lutz, São Paulo, Brazil
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23
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Liu D, Huang F, Zhang G, He W, Ou X, He P, Zhao B, Zhu B, Liu F, Li Z, Liu C, Xia H, Wang S, Zhou Y, Walker TM, Liu L, Crook DW, Zhao Y. Whole-genome sequencing for surveillance of tuberculosis drug resistance and determination of resistance level in China. Clin Microbiol Infect 2021; 28:731.e9-731.e15. [PMID: 34600118 DOI: 10.1016/j.cmi.2021.09.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 09/09/2021] [Accepted: 09/11/2021] [Indexed: 01/07/2023]
Abstract
OBJECTIVES Phenotypic drug susceptibility testing for prediction of tuberculosis (TB) drug resistance is slow and unreliable, limiting individualized therapy and monitoring of national TB data. Our study evaluated whole-genome sequencing (WGS) for its predictive accuracy, use in TB drug-resistance surveillance and ability to quantify the effects of resistance-associated mutations on MICs of anti-TB drugs. METHODS We used WGS to measure the susceptibility of 4880 isolates to ten anti-TB drugs; for pyrazinamide, we used BACTEC MGIT 960. We determined the accuracy of WGS by comparing the prevalence of drug resistance, measured by WGS, with the true prevalence, determined by phenotypic susceptibility testing. We used the Student-Newman-Keuls test to confirm MIC differences of mutations. RESULTS Resistance to isoniazid, rifampin and ethambutol was highly accurately predicted with at least 92.92% (95% confidence interval [CI], 88.19-97.65) sensitivity, resistance to pyrazinamide with 50.52% (95% CI, 40.57-60.47) sensitivity, and resistance to six second-line drugs with 85.05% (95% CI, 80.27-89.83) to 96.01% (95% CI, 93.89-98.13) sensitivity. The rpoB S450L, katG S315T and gyrA D94G mutations always confer high-level resistance, while rpoB L430P, rpoB L452P, fabG1 C-15T and embB G406S often confer low-level resistance or sub-epidemiological cutoff (ECOFF) MIC elevation. CONCLUSION WGS can predict phenotypic susceptibility with high accuracy and could be a valuable tool for drug-resistance surveillance and allow the detection of drug-resistance level; It can be an important approach in TB drug-resistance surveillance and for determining therapeutic schemes.
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Affiliation(s)
- Dongxin Liu
- Chinese Centre for Disease Control and Prevention, Beijing, China; National Clinical Research Centre for Infectious Diseases, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Fei Huang
- Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Guoliang Zhang
- National Clinical Research Centre for Infectious Diseases, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Wencong He
- Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Xichao Ou
- Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Ping He
- Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Bing Zhao
- Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Baoli Zhu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Fei Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhiyuan Li
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Chunfa Liu
- Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Hui Xia
- Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Shengfen Wang
- Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Yang Zhou
- Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Timothy M Walker
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Lei Liu
- National Clinical Research Centre for Infectious Diseases, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Derrick W Crook
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Yanlin Zhao
- Chinese Centre for Disease Control and Prevention, Beijing, China.
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24
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Grobbel HP, Merker M, Köhler N, Andres S, Hoffmann H, Heyckendorf J, Reimann M, Barilar I, Dreyer V, Hillemann D, Kalsdorf B, Kohl TA, Sanchez-Carballo P, Schaub D, Todt K, Utpatel C, Maurer FP, Lange C, Niemann S. Design of multidrug-resistant tuberculosis treatment regimens based on DNA sequencing. Clin Infect Dis 2021; 73:1194-1202. [PMID: 33900387 DOI: 10.1093/cid/ciab359] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Comprehensive and reliable drug susceptibility testing (DST) is urgently needed to provide adequate treatment regimens for patients with multidrug-resistant/rifampicin-resistant tuberculosis (MDR/RR-TB). We investigated if next generation sequencing (NGS) analysis of Mycobacterium tuberculosis complex isolates and genes implicated in drug resistance can guide the design of effective MDR/RR-TB treatment regimens. METHODS NGS-based genomic DST predictions of M. tuberculosis complex isolates from MDR/RR-TB patients admitted to a TB reference center in Germany between 01/01/2015 and 04/30/2019 were compared with phenotypic DST results of Mycobacteria growth indicator tubes (MGIT). Standardized treatment algorithms were applied to design individualized therapies based on either genomic or phenotypic DST results, and discrepancies were further evaluated by determination of minimum inhibitory drug concentrations (MIC) using Sensititre MYCOTBI and UKMYC microtiter plates. RESULTS In 70 patients with MDR/RR-TB, agreement among 1048 pairwise comparisons of genomic and phenotypic DST was 86.3%; 76 (7.2%) results were discordant, and 68 (6.5%) could not be evaluated due to presence of polymorphisms with yet unknown implications for drug resistance. Importantly, 549/561 (97.9%) predictions of drug susceptibility were phenotypically confirmed in MGIT, and 27/64 (42.2%) false positive results were linked to previously described mutations mediating a low or moderate MIC increase. Virtually all drugs (99.0%) used in combination therapies that were inferred from genomic DST, were confirmed to be susceptible by pDST. CONCLUSIONS NGS-based genomic DST can reliably guide the design of effective MDR/RR-TB treatment regimens.
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Affiliation(s)
- Hans-Peter Grobbel
- Research Center Borstel, Clinical Infectious Diseases, Borstel, Germany.,German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Matthias Merker
- German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Niklas Köhler
- Research Center Borstel, Clinical Infectious Diseases, Borstel, Germany.,German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Sönke Andres
- National and WHO Supranational Reference Laboratory for Tuberculosis, Research Center Borstel, Borstel, Germany
| | - Harald Hoffmann
- Institute of Microbiology and Laboratory Medicine, WHO Supranational Reference Laboratory of TB, IML red GmbH, Gauting, Bavaria, Germany.,SYNLAB Gauting, SYNLAB MVZ of Human Genetics Munich, Bavaria, Germany
| | - Jan Heyckendorf
- Research Center Borstel, Clinical Infectious Diseases, Borstel, Germany.,German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Maja Reimann
- Research Center Borstel, Clinical Infectious Diseases, Borstel, Germany.,German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Viola Dreyer
- Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Doris Hillemann
- National and WHO Supranational Reference Laboratory for Tuberculosis, Research Center Borstel, Borstel, Germany
| | - Barbara Kalsdorf
- Research Center Borstel, Clinical Infectious Diseases, Borstel, Germany.,German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Patricia Sanchez-Carballo
- Research Center Borstel, Clinical Infectious Diseases, Borstel, Germany.,German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Dagmar Schaub
- Research Center Borstel, Clinical Infectious Diseases, Borstel, Germany.,German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Katharina Todt
- Institute of Microbiology and Laboratory Medicine, WHO Supranational Reference Laboratory of TB, IML red GmbH, Gauting, Bavaria, Germany.,SYNLAB Gauting, SYNLAB MVZ of Human Genetics Munich, Bavaria, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Florian P Maurer
- National and WHO Supranational Reference Laboratory for Tuberculosis, Research Center Borstel, Borstel, Germany.,Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christoph Lange
- Research Center Borstel, Clinical Infectious Diseases, Borstel, Germany.,German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany.,Global TB Program, Baylor College of Medicine, Houston, TX, USA
| | - Stefan Niemann
- German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany.,National and WHO Supranational Reference Laboratory for Tuberculosis, Research Center Borstel, Borstel, Germany
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25
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Kempker RR, Mikiashvili L, Zhao Y, Benkeser D, Barbakadze K, Bablishvili N, Avaliani Z, Peloquin CA, Blumberg HM, Kipiani M. Clinical Outcomes Among Patients With Drug-resistant Tuberculosis Receiving Bedaquiline- or Delamanid-Containing Regimens. Clin Infect Dis 2020; 71:2336-2344. [PMID: 31712809 PMCID: PMC7713674 DOI: 10.1093/cid/ciz1107] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/08/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Bedaquiline and delamanid are newly available drugs for treating multidrug-resistant tuberculosis (MDR-TB); however, there are limited data guiding their use and no comparison studies. METHODS We conducted a prospective, observational study among patients with MDR-TB in Georgia who were receiving a bedaquiline- or delamanid-based treatment regimen. Monthly sputum cultures, minimal inhibitory concentration testing, and adverse event monitoring were performed. Primary outcomes were culture conversion rates and clinical outcomes. Targeted maximum likelihood estimation and super learning were utilized to produce a covariate-adjusted proportion of outcomes for each regimen. RESULTS Among 156 patients with MDR-TB, 100 were enrolled and 95 were receiving a bedaquiline-based (n = 64) or delamanid-based (n = 31) regimen. Most were male (82%) and the median age was 38 years. Rates of previous treatment (56%) and cavitary disease (61%) were high. The most common companion drugs included linezolid, clofazimine, cycloserine, and a fluoroquinolone. The median numbers of effective drugs received among patients on bedaquiline-based (4; interquartile range [IQR], 4-4) and delamanid-based (4; IQR, 3.5-5) regimens were similar. Rates of acquired drug resistance were significantly higher among patients receiving delamanid versus bedaquiline (36% vs 10%, respectively; P < .01). Adjusted rates of sputum culture conversion at 2 months (67% vs 47%, respectively; P = .10) and 6 months (95% vs 74%, respectively; P < .01), as well as more favorable clinical outcomes (96% vs 72%, respectively; P < .01), were higher among patients receiving bedaquiline versus delamanid. CONCLUSIONS Among patients with MDR-TB, bedaquiline-based regimens were associated with higher rates of sputum culture conversion, more favorable outcomes, and a lower rate of acquired drug resistance versus delamanid-based regimens.
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Affiliation(s)
- R R Kempker
- Department of Medicine, Division of Infectious Disease, Emory University School of Medicine, Atlanta, Georgia, USA
| | - L Mikiashvili
- National Center for Tuberculosis and Lung Disease, Tbilisi, Georgia
| | - Y Zhao
- Department of Biostatistics and Bioinformatics, Emory Rollins School of Public Health, Atlanta, Georgia, USA
| | - D Benkeser
- Department of Biostatistics and Bioinformatics, Emory Rollins School of Public Health, Atlanta, Georgia, USA
| | - K Barbakadze
- National Center for Tuberculosis and Lung Disease, Tbilisi, Georgia
| | - N Bablishvili
- National Center for Tuberculosis and Lung Disease, Tbilisi, Georgia
| | - Z Avaliani
- National Center for Tuberculosis and Lung Disease, Tbilisi, Georgia
| | - C A Peloquin
- Department of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - H M Blumberg
- Department of Medicine, Division of Infectious Disease, Emory University School of Medicine, Atlanta, Georgia, USA
- Departments of Epidemiology and Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - M Kipiani
- National Center for Tuberculosis and Lung Disease, Tbilisi, Georgia
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26
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Nanoluciferase Reporter Mycobacteriophage for Sensitive and Rapid Detection of Mycobacterium tuberculosis Drug Susceptibility. J Bacteriol 2020; 202:JB.00411-20. [PMID: 32900827 PMCID: PMC7585058 DOI: 10.1128/jb.00411-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/01/2020] [Indexed: 01/02/2023] Open
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis disease, remains a public health crisis on a global scale, and development of new interventions and identification of drug resistance are pillars in the World Health Organization End TB Strategy. Leveraging the tractability of the TM4 mycobacteriophage and the sensitivity of the nanoluciferase reporter enzyme, the present work describes an evolution of phage-mediated detection and drug susceptibility testing of M. tuberculosis, adding a valuable tool in drug discovery and basic biology research. With additional validation, this system may play a role as a quantitative phenotypic reference method and complement to genotypic methods for diagnosis and antibiotic susceptibility testing. Phenotypic testing for drug susceptibility of Mycobacterium tuberculosis is critical to basic research and managing the evolving problem of antimicrobial resistance in tuberculosis management, but it remains a specialized technique to which access is severely limited. Here, we report on the development and validation of an improved phage-mediated detection system for M. tuberculosis. We incorporated a nanoluciferase (Nluc) reporter gene cassette into the TM4 mycobacteriophage genome to create phage TM4-nluc. We assessed the performance of this reporter phage in the context of cellular limit of detection and drug susceptibility testing using multiple biosafety level 2 drug-sensitive and -resistant auxotrophs as well as virulent M. tuberculosis strains. For both limit of detection and drug susceptibility testing, we developed a standardized method consisting of a 96-hour cell preculture followed by a 72-hour experimental window for M. tuberculosis detection with or without antibiotic exposure. The cellular limit of detection of M. tuberculosis in a 96-well plate batch culture was ≤102 CFU. Consistent with other phenotypic methods for drug susceptibility testing, we found TM4-nluc to be compatible with antibiotics representing multiple classes and mechanisms of action, including inhibition of core central dogma functions, cell wall homeostasis, metabolic inhibitors, compounds currently in clinical trials (SQ109 and Q203), and susceptibility testing for bedaquiline, pretomanid, and linezolid (components of the BPaL regimen for the treatment of multi- and extensively drug-resistant tuberculosis). Using the same method, we accurately identified rifampin-resistant and multidrug-resistant M. tuberculosis strains. IMPORTANCEMycobacterium tuberculosis, the causative agent of tuberculosis disease, remains a public health crisis on a global scale, and development of new interventions and identification of drug resistance are pillars in the World Health Organization End TB Strategy. Leveraging the tractability of the TM4 mycobacteriophage and the sensitivity of the nanoluciferase reporter enzyme, the present work describes an evolution of phage-mediated detection and drug susceptibility testing of M. tuberculosis, adding a valuable tool in drug discovery and basic biology research. With additional validation, this system may play a role as a quantitative phenotypic reference method and complement to genotypic methods for diagnosis and antibiotic susceptibility testing.
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27
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Theron G, Limberis J, Venter R, Smith L, Pietersen E, Esmail A, Calligaro G, Te Riele J, de Kock M, van Helden P, Gumbo T, Clark TG, Fennelly K, Warren R, Dheda K. Bacterial and host determinants of cough aerosol culture positivity in patients with drug-resistant versus drug-susceptible tuberculosis. Nat Med 2020; 26:1435-1443. [PMID: 32601338 PMCID: PMC8353872 DOI: 10.1038/s41591-020-0940-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 05/13/2020] [Indexed: 12/27/2022]
Abstract
A burgeoning epidemic of drug-resistant tuberculosis (TB) threatens to derail global control efforts. Although the mechanisms remain poorly clarified, drug-resistant strains are widely believed to be less infectious than drug-susceptible strains. Consequently, we hypothesized that lower proportions of patients with drug-resistant TB would have culturable Mycobacterium tuberculosis from respirable, cough-generated aerosols compared to patients with drug-susceptible TB, and that multiple factors, including mycobacterial genomic variation, would predict culturable cough aerosol production. We enumerated the colony forming units in aerosols (≤10 µm) from 452 patients with TB (227 with drug resistance), compared clinical characteristics, and performed mycobacterial whole-genome sequencing, dormancy phenotyping and drug-susceptibility analyses on M. tuberculosis from sputum. After considering treatment duration, we found that almost half of the patients with drug-resistant TB were cough aerosol culture-positive. Surprisingly, neither mycobacterial genomic variants, lineage, nor dormancy status predicted cough aerosol culture positivity. However, mycobacterial sputum bacillary load and clinical characteristics, including a lower symptom score and stronger cough, were strongly predictive, thereby supporting targeted transmission-limiting interventions. Effective treatment largely abrogated cough aerosol culture positivity; however, this was not always rapid. These data question current paradigms, inform public health strategies and suggest the need to redirect TB transmission-associated research efforts toward host-pathogen interactions.
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Affiliation(s)
- Grant Theron
- 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
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research and South African Medical Research Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Jason Limberis
- 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
| | - Rouxjeane Venter
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research and South African Medical Research Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Liezel Smith
- 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
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research and South African Medical Research Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Elize Pietersen
- 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
| | - Aliasgar Esmail
- 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
| | - Greg Calligaro
- 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
| | | | - Marianna de Kock
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research and South African Medical Research Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Paul van Helden
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research and South African Medical Research Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Tawanda Gumbo
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor University Medical Center, Dallas, TX, USA
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Faculty of Epidemiology and Public Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Kevin Fennelly
- Pulmonary Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Robin Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research and South African Medical Research Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, 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, London School of Hygiene & Tropical Medicine, London, UK.
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28
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Evidence for Expanding the Role of Streptomycin in the Management of Drug-Resistant Mycobacterium tuberculosis. Antimicrob Agents Chemother 2020; 64:AAC.00860-20. [PMID: 32540971 DOI: 10.1128/aac.00860-20] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 06/06/2020] [Indexed: 01/09/2023] Open
Abstract
In 2019, the WHO tuberculosis (TB) treatment guidelines were updated to recommend only limited use of streptomycin, in favor of newer agents or amikacin as the preferred aminoglycoside for drug-resistant Mycobacterium tuberculosis However, the emergence of resistance to newer drugs, such as bedaquiline, has prompted a reanalysis of antitubercular drugs in search of untapped potential. Using 211 clinical isolates of M. tuberculosis from South Africa, we performed phenotypic drug susceptibility testing (DST) to aminoglycosides by both critical concentration and MIC determination in parallel with whole-genome sequencing to identify known genotypic resistance elements. Isolates with low-level streptomycin resistance mediated by gidB were frequently misclassified with respect to streptomycin resistance when using the WHO-recommended critical concentration of 2 μg/ml. We identified 29 M. tuberculosis isolates from South Africa with low-level streptomycin resistance concomitant with high-level amikacin resistance, conferred by gidB and rrs 1400, respectively. Using a large global data set of M. tuberculosis genomes, we observed 95 examples of this corresponding resistance genotype (gidB-rrs 1400), including identification in 81/257 (31.5%) of extensively drug resistant (XDR) isolates. In a phylogenetic analysis, we observed repeated evolution of low-level streptomycin and high-level amikacin resistance in multiple countries. Our findings suggest that current critical concentration methods and the design of molecular diagnostics need to be revisited to provide more accurate assessments of streptomycin resistance for gidB-containing isolates. For patients harboring isolates of M. tuberculosis with high-level amikacin resistance conferred by rrs 1400, and for whom newer agents are not available, treatment with streptomycin may still prove useful, even in the face of low-level resistance conferred by gidB.
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29
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Dusthackeer A, Saadhali SA, Thangam M, Hassan S, Balasubramanian M, Balasubramanian A, Ramachandran G, Kumar AKH, Thiruvenkadam K, Shanmugam G, Nirmal CR, Rajadas SE, Mohanvel SK, Mondal R. Wild-Type MIC Distribution for Re-evaluating the Critical Concentration of Anti-TB Drugs and Pharmacodynamics Among Tuberculosis Patients From South India. Front Microbiol 2020; 11:1182. [PMID: 32695072 PMCID: PMC7338667 DOI: 10.3389/fmicb.2020.01182] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 05/08/2020] [Indexed: 11/13/2022] Open
Abstract
The World Health Organization (WHO) has developed specific guidelines for critical concentrations (CCs) of antibiotics used for tuberculosis (TB) treatment, which is universally followed for drug susceptibility testing (DST) of clinical specimens. However, the CC of drugs can differ significantly among the mycobacterial species based on the population, geographic location, and the prevalence of the infecting strain in a particular area. The association between CC and the minimal inhibitory concentration (MIC) of anti-TB drugs is poorly understood. In this study, we assessed the MICs of anti-TB drugs, including isoniazid (INH), rifampicin (RMP), moxifloxacin (MXF), ethambutol (ETH), and p-aminosalicylic acid (PAS) on drug-sensitive Mtb isolates from pulmonary TB patients in South India. The MIC assays performed using solid- and liquid-growth media showed changes in the CC of a few of the tested antibiotics compared with the WHO-recommended levels. Our observation suggests that the WHO guidelines could potentially lead to overdiagnosis of drug-resistant cases, which can result in inappropriate therapeutic decisions. To evaluate the correlation between drug-resistance and CC, we performed the whole-genome sequencing for 16 mycobacterial isolates, including two wild-type and 14 resistant isolates. Our results showed that two of the isolates belonged to the W-Beijing lineage, while the rest were of the East-African-Indian type. We identified a total of 74 mutations, including five novel mutations, which are known to be associated with resistance to anti-TB drugs in these isolates. In our previous study, we determined the serum levels of INH and RMP among the same patients recruited in the current study and estimated the MICs of the corresponding infected isolates in these cases. Using these data and the CCs for INH and RMP from the present study, we performed pharmacodynamics (PD) evaluation. The results show that the PD of RMP was subtherapeutic. Together, these observations emphasize the need for optimizing the drug dosage based on the PD of large-scale studies conducted in different geographical settings.
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Affiliation(s)
- Azger Dusthackeer
- Department of Bacteriology, National Institute for Research in Tuberculosis, Chennai, India
| | - Shainaba A Saadhali
- Department of Bacteriology, National Institute for Research in Tuberculosis, Chennai, India
| | | | - Sameer Hassan
- Division of Neurogeriatrics, Karolinska Institutet, Solna, Sweden
| | | | | | - Geetha Ramachandran
- Department of Biochemistry, National Institute for Research in Tuberculosis, Chennai, India
| | - A K Hemanth Kumar
- Department of Biochemistry, National Institute for Research in Tuberculosis, Chennai, India
| | - Kannan Thiruvenkadam
- Department of Epidemiology, National Institute for Research in Tuberculosis, Chennai, India
| | - Govindarajan Shanmugam
- Department of Bacteriology, National Institute for Research in Tuberculosis, Chennai, India
| | | | - Sam Ebenezer Rajadas
- Department of Bacteriology, National Institute for Research in Tuberculosis, Chennai, India
| | | | - Rajesh Mondal
- Department of Bacteriology, National Institute for Research in Tuberculosis, Chennai, India
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30
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Ismail NA, Ismail F, Joseph L, Govender N, Blows L, Kaniga K, Omar SV. Epidemiological cut-offs for Sensititre susceptibility testing of Mycobacterium tuberculosis: interpretive criteria cross validated with whole genome sequencing. Sci Rep 2020; 10:1013. [PMID: 31974497 PMCID: PMC6978314 DOI: 10.1038/s41598-020-57992-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 01/08/2020] [Indexed: 11/20/2022] Open
Abstract
Universal drug susceptibility testing (DST) is an important requirement of the End TB Strategy. The Sensititre broth micro-dilution assay (BMD) tests multiple drugs quantitatively. We defined interpretive criteria for this assay and analysed genotypic-phenotypic relationships. 385 Mycobacterium tuberculosis clinical isolates were processed for BMD and whole genome sequencing. The epidemiological cut-off value 99% (ECV99) amongst genotypically wild type (gWT) strains defined susceptibility. Minimum inhibitory concentration distributions of the resistance-associated variants (RAVs) for each drug were analysed. Susceptibility (µg/mL) criteria were determined as follows: rifampicin (≤0.125), isoniazid (≤0.25), ethambutol (≤2.0), moxifloxacin (≤0.5), levofloxacin (≤1.0), amikacin (≤2.0), kanamycin (≤8.0), capreomycin (≤4.0), clofazimine (≤0.25) and linezolid (≤2.0). Most drugs showed clear separation between gWT and RAV. Isoniazid showed a tri-modal pattern with 14/17 strains at ECV99 harbouring a fabG1 c. -15C > T RAV. Ethambutol RAVs at embB codons 306, 405 and 497 were responsible for resistance and showed differential distributions. Moxifloxacin RAVs (gyrA codon 90) were a dilution or two higher than the ECV99 while gyrB RAVs were uncommon and showed drug specific resistance propensity. Interpretive criteria established were robust facilitating progress towards universal DST and individualised precision medicine. This study demonstrates the value of quantitative DST to accurately interpret mutation data.
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Affiliation(s)
- Nazir A Ismail
- National Institute for Communicable Diseases, Centre for Tuberculosis, Johannesburg, South Africa.
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.
- Department of Internal Medicine, University of Witwatersrand, Johannesburg, South Africa.
| | - Farzana Ismail
- National Institute for Communicable Diseases, Centre for Tuberculosis, Johannesburg, South Africa
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - Lavania Joseph
- National Institute for Communicable Diseases, Centre for Tuberculosis, Johannesburg, South Africa
| | - Netricia Govender
- National Institute for Communicable Diseases, Centre for Tuberculosis, Johannesburg, South Africa
| | - Linsay Blows
- National Institute for Communicable Diseases, Centre for Tuberculosis, Johannesburg, South Africa
| | - Koné Kaniga
- Janssen Research & Development, Titusville, NJ, United States of America
| | - Shaheed V Omar
- National Institute for Communicable Diseases, Centre for Tuberculosis, Johannesburg, South Africa
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31
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Jaglal P, Pillay M, Mlisana K. Resazurin microtitre plate assay and Sensititre® MycoTB for detection of Mycobacterium tuberculosis resistance in a high tuberculosis resistance setting. Afr J Lab Med 2019; 8:840. [PMID: 31956551 PMCID: PMC6956686 DOI: 10.4102/ajlm.v8i1.840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 03/13/2019] [Indexed: 11/04/2022] Open
Abstract
Background Rapid diagnosis of drug-resistant Mycobacterium tuberculosis is a challenge in low-income countries. Phenotypic drug susceptibility testing using Sensititre® MycoTB assay and the resazurin microtitre plate assay (REMA) are relatively new innovative methods to determine drug susceptibility. Objectives This study aimed to determine the performance of the Sensititre and REMA for M. tuberculosis drug susceptibility testing in a high-volume tuberculosis reference laboratory. Methods A laboratory-based study was performed at the Inkosi Albert Luthuli Central Hospital Tuberculosis Laboratory from January 2014 to June 2015. The Sensititre® MycoTB plate and REMA were compared to the gold standard agar proportion method (APM) using 134 stored isolates. Results Agreement between the Sensititre® MycoTB plate and APM was observed with 98% sensitivity, 82% specificity, 94% positive and 93% negative predictive values of the Sensititre® MycoTB assay for the detection of rifampicin resistance and 97%, 96%, 99% and 88% for isoniazid resistance. Good categorical agreement between the REMA and the APM was observed among isolates with 89% sensitivity, 68% specificity, 89% positive and 68% negative predictive value for the detection of rifampicin resistance and 95%, 96%, 99% and 81% for isoniazid resistance. Results for the second-line drugs showed elevated minimum inhibitory concentrations for multidrug-resistant and extensively drug-resistant tuberculosis isolates. Conclusion The REMA and Sensititre® MycoTB plate are attractive alternatives to the gold standard APM for the phenotypic detection of M. tuberculosis drug resistance.
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Affiliation(s)
- Prenika Jaglal
- Department of Medical Microbiology, National Health Laboratory Services, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Melendhran Pillay
- Department of Medical Microbiology/Virology, National Health Laboratory Service, Durban, South Africa
| | - Koleka Mlisana
- Department of Medical Microbiology, National Health Laboratory Services, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
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32
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Wu X, Yang J, Tan G, Liu H, Liu Y, Guo Y, Gao R, Wan B, Yu F. Drug Resistance Characteristics of Mycobacterium tuberculosis Isolates From Patients With Tuberculosis to 12 Antituberculous Drugs in China. Front Cell Infect Microbiol 2019; 9:345. [PMID: 31828045 PMCID: PMC6849330 DOI: 10.3389/fcimb.2019.00345] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 09/25/2019] [Indexed: 11/29/2022] Open
Abstract
Objective: To investigate the drug resistance characteristics of Mycobacterium tuberculosis (MTB) isolates from patients with tuberculosis to 12 antituberculous drugs in China. Methods: All clinical isolates of MTB were isolated from patients with tuberculosis in Shanghai Pulmonary Hospital (SPH) during the period from January 1st to December 31th, 2018. Drug susceptibility testing (DST) was performed in micro plates with 12 antituberculous drugs in accordance with relevant guideline. Demographic information, including sex, age, and treatment history was recorded. Results: A total of 1,950 MTB isolates were included in this retrospective study which were isolated from 1,950 patients from 29 regions in China. One thousand six hundred and forty-four were initial treated and 306 were re-treated in the hospital. Two hundred and eight (10.67%, 208/1,950) cases were diagnosed as multidrug-resistant tuberculosis (MDR-TB), from which 74 (4.50%, 74/1,644) cases were initial treated, and the remaining (43.79%, 134/306) were re-treated cases. Besides, the percentage of extensively drug-resistant tuberculosis (XDR-TB) varied in such 3 different groups: 1.64% (32/1,950) in total cases, 0.30% (5/1,644) in initial treated cases and 8.82% (27/306) in re-treated cases. The total resistance rates were as follows: isoniazid (361, 18.51%), streptomycin (302, 15.49%), rifampin (241, 12.36%), ofloxacin (239, 12.26%), moxifloxacin (232, 11.90%), rifabutin (195, 10.00%), ethambutol (100, 5.13%), cycloserine (55, 2.82%), kanamycin (48, 2.46%), ethionamide (40, 2.05%), amikacin (39, 2.00%), and aminosalicylic acid (21, 1.08%). Rates of resistance to any drug in re-treated cases were significantly higher than in initial treated cases. The drug resistance rates of the 12 drugs were higher in males than in females. Patients older than 60 years had significantly lower percentages of MDR/XDR-TB (7.11 and 0.65%) than in younger age groups. The proportion of re-treated cases in Shanghai (11.38%, 88/773) was lower than that in other regions. Meanwhile, the percentages of MDR/XDR-TB in Shanghai (4.79 and 0.65%) were significantly lower than in other regions. Conclusions: In this study, we found higher proportion of MDR/XDR-TB among re-treated cases than initial treated cases in China and the drug resistance rate of tuberculosis varied with age, sex, and region, indicating that standardized anti-tuberculosis treatment can reduce the incidence of drug-resistant tuberculosis and the recurrence of tuberculosis.
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Affiliation(s)
- Xiaocui Wu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jinghui Yang
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Guangkun Tan
- Department of Clinical Laboratory, Shanghai University of Traditional Chinese Medical Attached Shuguang Hospital, Shanghai, China
| | - Haican Liu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yin Liu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yinjuan Guo
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Rongliang Gao
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Baoshan Wan
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Fangyou Yu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
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Torrea G, Ng KCS, Van Deun A, André E, Kaisergruber J, Ssengooba W, Desmaretz C, Gabriels S, Driesen M, Diels M, Asnong S, Fissette K, Gumusboga M, Rigouts L, Affolabi D, Joloba M, De Jong BC. Variable ability of rapid tests to detect Mycobacterium tuberculosis rpoB mutations conferring phenotypically occult rifampicin resistance. Sci Rep 2019; 9:11826. [PMID: 31413308 PMCID: PMC6694172 DOI: 10.1038/s41598-019-48401-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 08/01/2019] [Indexed: 01/15/2023] Open
Abstract
We compared the ability of commercial and non-commercial, phenotypic and genotypic rapid drug susceptibility tests (DSTs) to detect rifampicin resistance (RR)-conferring ‘disputed’ mutations frequently missed by Mycobacterium Growth Indicator Tube (MGIT), namely L430P, D435Y, L452P, and I491F. Strains with mutation S450L served as positive control while wild-types were used as negative control. Of the 38 mutant strains, 5.7% were classified as RR by MGIT, 16.2% by Trek Sensititre MYCOTB MIC plate, 19.4% by resazurin microtiter plate assay (REMA), 50.0% by nitrate reductase assay (NRA), and 62.2% by microscopic observation direct susceptibility testing (MODS). Reducing MGIT rifampicin concentration to 0.5 µg/ml, and/or increasing incubation time, enhanced detection of disputed mutations from 5.7% to at least 65.7%, particularly for mutation I491F (from 0.0 to 75.0%). Compared with MGIT at standard pre-set time with 0.25 µg/ml ECOFF as breakpoint, we found a statistically significant increase in the ability of MGIT to resolve disputed mutants and WT strains at extended incubation period of 15 and 21 days, with 0.5 µg/ml and 1 µg/ml ECOFF respectively. MODS detected 75.0% of the I491F strains and NRA 62.5%, while it was predictably missed by all molecular assays. Xpert MTB/RIF, Xpert Ultra, and GenoscholarTB-NTM + MDRTB detected all mutations within the 81 bp RR determining region. Only GenoType MTBDRplus version 2 missed mutation L430P in 2 of 11 strains. Phenotypic and genotypic DSTs varied greatly in detecting occult rifampicin resistance. None of these methods detected all disputed mutations without misclassifying wild-type strains.
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Affiliation(s)
- Gabriela Torrea
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
| | - Kamela C S Ng
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Armand Van Deun
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Emmanuel André
- Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | | | - Willy Ssengooba
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda
| | - Christel Desmaretz
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Siemon Gabriels
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Michèle Driesen
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Maren Diels
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Sylvie Asnong
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Kristina Fissette
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Mourad Gumusboga
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Leen Rigouts
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Moses Joloba
- Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda
| | - Bouke C De Jong
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
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Rockwood N, Cerrone M, Barber M, Hill AM, Pozniak AL. Global access of rifabutin for the treatment of tuberculosis - why should we prioritize this? J Int AIDS Soc 2019; 22:e25333. [PMID: 31318176 PMCID: PMC6637439 DOI: 10.1002/jia2.25333] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 06/05/2019] [Indexed: 12/24/2022] Open
Abstract
INTRODUCTION Rifabutin, a rifamycin of equivalent potency to rifampicin, has several advantages in its pharmacokinetic and toxicity profile, particularly in HIV co-infected patients on combined antiretroviral therapy (cART). In this commentary, we evaluate evidence supporting increased global use of rifabutin and highlight key recommendations for action. DISCUSSION Although extrapolation of data from HIV uninfected patients would suggest non-inferiority, there has been no randomized controlled study comparing rifabutin versus rifampicin in the outcomes of relapse-free cure, in drug susceptible tuberculosis (TB), in HIV co-infected patients on currently utilized cART regimens or in paediatric populations. An important advantage of rifabutin is that compared to the dose adjustments required with rifampicin, it can be co-administered with the integrase strand transfer inhibitors raltegravir or dolutegravir without the need for dose adjustments. This strategy would be easier to implement in a programmatic setting and would save costs. We have assessed cost incentives to utilize rifabutin and have estimated generic costs for a range of rifabutin dosage scenarios. Where facilities are present for drug re-challenge and monitoring for drug toxicity and cross-reactivity, rifabutin offers a switch alternative for adverse drug reactions (ADR)s attributed to rifampicin. This would negate the need to prolong treatment in the absence of a rifamycin as part of short-course multidrug therapy. There is evidence of incomplete cross-resistance to rifampicin and rifabutin. Rifabutin may be useful in rifampicin-resistant TB, in an estimated 20% of cases, based on phenotypic or genotypic rifabutin susceptibility testing. CONCLUSIONS Rifabutin should be available globally as a first-line rifamycin in HIV co-infected individuals and as a switch option in cases of rifampicin associated ADRs. Further studies are needed to ascertain the utility of rifabutin in rifampicin-resistant rifabutin-susceptible TB.
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Affiliation(s)
- Neesha Rockwood
- Department of MedicineImperial College LondonLondonUK
- Department of HIV MedicineChelsea and Westminster HospitalLondonUK
| | - Maddalena Cerrone
- Department of MedicineImperial College LondonLondonUK
- Department of HIV MedicineChelsea and Westminster HospitalLondonUK
| | - Melissa Barber
- Department of Global Health and PopulationHarvard TH Chan School of Public HealthBostonMAUSA
| | - Andrew M Hill
- Department of Pharmacology and TherapeuticsLiverpool UniversityLiverpoolUK
| | - Anton L Pozniak
- Department of HIV MedicineChelsea and Westminster HospitalLondonUK
- Department of Clinical ResearchLondon School of Tropical Medicine and HygieneLondonUK
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Jajou R, van der Laan T, de Zwaan R, Kamst M, Mulder A, de Neeling A, Anthony R, van Soolingen D. WGS more accurately predicts susceptibility of Mycobacterium tuberculosis to first-line drugs than phenotypic testing. J Antimicrob Chemother 2019; 74:2605-2616. [DOI: 10.1093/jac/dkz215] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/12/2019] [Accepted: 04/22/2019] [Indexed: 01/13/2023] Open
Abstract
Abstract
Background
Drug-susceptibility testing (DST) of Mycobacterium tuberculosis complex (MTBC) isolates by the Mycobacteria Growth Indicator Tube (MGIT) approach is the most widely applied reference standard. However, the use of WGS is increasing in many developed countries to detect resistance and predict susceptibility. We investigated the reliability of WGS in predicting drug susceptibility, and analysed the discrepancies between WGS and MGIT against the first-line drugs rifampicin, isoniazid, ethambutol and pyrazinamide.
Methods
DST by MGIT and WGS was performed on MTBC isolates received in 2016/2017. Nine genes and/or their promotor regions were investigated for resistance-associated mutations: rpoB, katG, fabG1, ahpC, inhA, embA, embB, pncA and rpsA. Isolates that were discrepant in their MGIT/WGS results and a control group with concordant results were retested in the MGIT, at the critical concentration and a lower concentration, and incubated for up to 45 days after the control tube became positive in the MGIT.
Results
In total, 1136 isolates were included, of which 1121 were routine MTBC isolates from the Netherlands. The negative predictive value of WGS was ≥99.3% for all four first-line antibiotics. The majority of discrepancies for isoniazid and ethambutol were explained by growth at the lower concentrations, and for rifampicin by prolonged incubation in the MGIT, both indicating low-level resistance.
Conclusions
Applying WGS in a country like the Netherlands, with a low TB incidence and low prevalence of resistance, can reduce the need for phenotypic DST for ∼90% of isolates and accurately detect mutations associated with low-level resistance, often missed in conventional DST.
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Affiliation(s)
- Rana Jajou
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Tridia van der Laan
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Rina de Zwaan
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Miranda Kamst
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Arnout Mulder
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Albert de Neeling
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Richard Anthony
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Dick van Soolingen
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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Lee S, Chu D, Choi YM, Jo E, Kim S, Kim H, Kim HJ, Chang J, Sung H, Kang G, Jin B, Kim EG, Kwon S, Kim MN. Clinical Validation of the QMAC-DST System for Testing the Drug Susceptibility of Mycobacterium tuberculosis to First- and Second-Line Drugs. Front Microbiol 2019; 10:706. [PMID: 31057494 PMCID: PMC6477073 DOI: 10.3389/fmicb.2019.00706] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/20/2019] [Indexed: 01/18/2023] Open
Abstract
There is a high demand for novel approaches to counter the various challenges of conventional drug susceptibility testing (DST) for tuberculosis, the most prevalent infectious disease with significant global mortality. The QMAC-DST system was recently developed for rapid DST using image technology to track the growth of single cells of Mycobacterium tuberculosis (MTB). The purpose of this study was to clinically validate the QMAC-DST system compared to conventional DST. In total, 178 MTB isolates recovered from clinical specimens in Asan Medical Center in 2016 were tested by both QMAC-DST and absolute concentration methods using Lowenstein-Jensen media (LJ-DST). Among the isolates, 156 were subjected to DST using BACTEC MGIT 960 SIRE kits (BD, Sparks, MD, United States) (MGIT-DST). The susceptibility/resistance results obtained by QMAC-DST were read against 13 drugs after 7 days of incubation and compared with those of LJ-DST. Based on the gold standard LJ-DST, the agreement rates of QMAC-DST for all drugs were 97.8%, 97.9%, and 97.8% among susceptible, resistant, and total isolates, respectively, while the overall agreement of MGIT-DST tested for 156 isolates against first-line drugs was 95.5%. QMAC-DST showed the highest major error of 6.4% for rifampin, however, it could be corrected by a revised threshold of growth since false-resistant isolates showed grew only half than the true-resistant isolates. The rapid and accurate performance of QMAC-DST warrants ideal phenotypic DST for a wide range of first-line and second-line drugs.
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Affiliation(s)
| | - Daehyun Chu
- Department of Laboratory Medicine University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea
| | - Youn Mi Choi
- Veterans Health Service Medical Center, Seoul, South Korea
| | - EunJi Jo
- QuantaMatrix Inc., Seoul, South Korea
| | | | - Haeun Kim
- QuantaMatrix Inc., Seoul, South Korea
| | | | - Jeonghyun Chang
- Department of Laboratory Medicine University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea
| | - Heungsup Sung
- Department of Laboratory Medicine University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea
| | | | | | | | - Sunghoon Kwon
- QuantaMatrix Inc., Seoul, South Korea.,Department of Electrical Engineering and Computer Science, Seoul National University, Seoul, South Korea
| | - Mi-Na Kim
- Department of Laboratory Medicine University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea
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Whole-Genome Sequencing for Drug Resistance Profile Prediction in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2019; 63:AAC.02175-18. [PMID: 30718257 PMCID: PMC6496161 DOI: 10.1128/aac.02175-18] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/25/2019] [Indexed: 01/10/2023] Open
Abstract
Whole-genome sequencing allows rapid detection of drug-resistant Mycobacterium tuberculosis isolates. However, the availability of high-quality data linking quantitative phenotypic drug susceptibility testing (DST) and genomic data have thus far been limited. We determined drug resistance profiles of 176 genetically diverse clinical M. tuberculosis isolates from the Democratic Republic of the Congo, Ivory Coast, Peru, Thailand, and Switzerland by quantitative phenotypic DST for 11 antituberculous drugs using the BD Bactec MGIT 960 system and 7H10 agar dilution to generate a cross-validated phenotypic DST readout. We compared DST results with predicted drug resistance profiles inferred by whole-genome sequencing. Classification of strains by the two phenotypic DST methods into resistotype/wild-type populations was concordant in 73 to 99% of cases, depending on the drug. Our data suggest that the established critical concentration (5 mg/liter) for ethambutol resistance (MGIT 960 system) is too high and misclassifies strains as susceptible, unlike 7H10 agar dilution. Increased minimal inhibitory concentrations were explained by mutations identified by whole-genome sequencing. Using whole-genome sequences, we were able to predict quantitative drug resistance levels for the majority of drug resistance mutations. Predicting quantitative levels of drug resistance by whole-genome sequencing was partially limited due to incompletely understood drug resistance mechanisms. The overall sensitivity and specificity of whole-genome-based DST were 86.8% and 94.5%, respectively. Despite some limitations, whole-genome sequencing has the potential to infer resistance profiles without the need for time-consuming phenotypic methods.
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Novel 1,3,4-oxadiazoles as antitubercular agents with limited activity against drug-resistant tuberculosis. Future Med Chem 2019; 11:499-510. [PMID: 30892944 DOI: 10.4155/fmc-2018-0378] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
AIM In recent times, heterocyclic chemotypes are being explored for the development of new antimycobacterials that target the drug-resistant tuberculosis. Here, we are disclosing the 5-substitued 2-mercapto-1,3,4-oxadiazoles as potent antitubercular agents. METHODOLOGY A small library of 2-mercapto-1,3,4-oxadiazoles was synthesized using various acids. The compounds were evaluated for antituberculosis activity against M. tuberculosis H37Rv. RESULTS Compound 8j was identified as antitubercular lead with MIC of 0.6 μg/ml against M. tuberculosis H37Rv. This compound was nontoxic to CHO-K1 cells and showed selectivity index of 39. Of note, 8j showed antitubercular activity against pre-extensively drug-resistant clinical isolate of Mycobacterium with MIC of 2 μg/ml. CONCLUSION This study provides potent antitubercular agent which can be further optimized to discover novel antibiotics.
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39
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Synthesis and evaluation of α-aminoacyl amides as antitubercular agents effective on drug resistant tuberculosis. Eur J Med Chem 2019; 164:665-677. [DOI: 10.1016/j.ejmech.2019.01.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/30/2018] [Accepted: 01/01/2019] [Indexed: 11/20/2022]
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40
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Tagliani E, Nikolayevskyy V, Tortoli E, Cirillo DM. Laboratory diagnosis of tuberculosis. Tuberculosis (Edinb) 2018. [DOI: 10.1183/2312508x.10021318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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41
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Deshpande D, Alffenaar JWC, Köser CU, Dheda K, Chapagain ML, Simbar N, Schön T, Sturkenboom MGG, McIlleron H, Lee PS, Koeuth T, Mpagama SG, Banu S, Foongladda S, Ogarkov O, Pholwat S, Houpt ER, Heysell SK, Gumbo T. d-Cycloserine Pharmacokinetics/Pharmacodynamics, Susceptibility, and Dosing Implications in Multidrug-resistant Tuberculosis: A Faustian Deal. Clin Infect Dis 2018; 67:S308-S316. [PMID: 30496460 PMCID: PMC6260153 DOI: 10.1093/cid/ciy624] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background d-cycloserine is used to treat multidrug-resistant tuberculosis. Its efficacy, contribution in combination therapy, and best clinical dose are unclear, also data on the d-cycloserine minimum inhibitory concentration (MIC) distributions is scant. Methods We performed a systematic search to identify pharmacokinetic and pharmacodynamic studies performed with d-cycloserine. We then performed a combined exposure-effect and dose fractionation study of d-cycloserine in the hollow fiber system model of tuberculosis (HFS-TB). In parallel, we identified d-cycloserine MICs in 415 clinical Mycobacterium tuberculosis (Mtb) isolates from patients. We utilized these results, including intracavitary concentrations, to identify the clinical dose that would be able to achieve or exceed target exposures in 10000 patients using Monte Carlo experiments (MCEs). Results There were no published d-cycloserine pharmacokinetics/pharmacodynamics studies identified. Therefore, we performed new HFS-TB experiments. Cyloserine killed 6.3 log10 colony-forming units (CFU)/mL extracellular bacilli over 28 days. Efficacy was driven by the percentage of time concentration persisted above MIC (%TMIC), with 1.0 log10 CFU/mL kill achieved by %TMIC = 30% (target exposure). The tentative epidemiological cutoff value with the Sensititre MYCOTB assay was 64 mg/L. In MCEs, 750 mg twice daily achieved target exposure in lung cavities of 92% of patients whereas 500 mg twice daily achieved target exposure in 85% of patients with meningitis. The proposed MCE-derived clinical susceptibility breakpoint at the proposed doses was 64 mg/L. Conclusions Cycloserine is cidal against Mtb. The susceptibility breakpoint is 64 mg/L. However, the doses likely to achieve the cidality in patients are high, and could be neurotoxic.
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Affiliation(s)
- Devyani Deshpande
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Jan-Willem C Alffenaar
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Claudio U Köser
- Department of Genetics, University of Cambridge, United Kingdom
| | - Keertan Dheda
- Lung Immunity Unit, Division of Pulmonology, Department of Medicine, University of Cape Town, Observatory, South Africa
| | - Moti L Chapagain
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Noviana Simbar
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Thomas Schön
- Department of Infectious Diseases and Clinical Microbiology, Kalmar County Hospital
- Department of Clinical and Experimental Medicine, Division of Medical Microbiology, Linköping University, Sweden
| | - Marieke G G Sturkenboom
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Helen McIlleron
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory, South Africa
| | - Pooi S Lee
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Thearith Koeuth
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | | | - Sayera Banu
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka
| | | | - Oleg Ogarkov
- Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russian Federation
| | - Suporn Pholwat
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville
| | - Eric R Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville
| | - Scott K Heysell
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville
| | - Tawanda Gumbo
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
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Davies Forsman L, Niward K, Hu Y, Zheng R, Zheng X, Ke R, Cai W, Hong C, Li Y, Gao Y, Werngren J, Paues J, Kuhlin J, Simonsson USH, Eliasson E, Alffenaar JW, Mansjö M, Hoffner S, Xu B, Schön T, Bruchfeld J. Plasma concentrations of second-line antituberculosis drugs in relation to minimum inhibitory concentrations in multidrug-resistant tuberculosis patients in China: a study protocol of a prospective observational cohort study. BMJ Open 2018; 8:e023899. [PMID: 30287613 PMCID: PMC6173237 DOI: 10.1136/bmjopen-2018-023899] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 06/21/2018] [Accepted: 08/06/2018] [Indexed: 12/16/2022] Open
Abstract
INTRODUCTION Individualised treatment through therapeutic drug monitoring (TDM) may improve tuberculosis (TB) treatment outcomes but is not routinely implemented. Prospective clinical studies of drug exposure and minimum inhibitory concentrations (MICs) in multidrug-resistant TB (MDR-TB) are scarce. This translational study aims to characterise the area under the concentration-time curve of individual MDR-TB drugs, divided by the MIC for Mycobacterium tuberculosis isolates, to explore associations with markers of treatment progress and to develop useful strategies for clinical implementation of TDM in MDR-TB. METHODS AND ANALYSIS Adult patients with pulmonary MDR-TB treated in Xiamen, China, are included. Plasma samples for measure of drug exposure are obtained at 0, 1, 2, 4, 6, 8 and 10 hours after drug intake at week 2 and at 0, 4 and 6 hours during weeks 4 and 8. Sputum samples for evaluating time to culture positivity and MIC determination are collected at days 0, 2 and 7 and at weeks 2, 4, 8 and 12 after treatment initiation. Disease severity are assessed with a clinical scoring tool (TBscore II) and quality of life evaluated using EQ-5D-5L. Drug concentrations of pyrazinamide, ethambutol, levofloxacin, moxifloxacin, cycloserine, prothionamide and para-aminosalicylate are measured by liquid chromatography tandem-mass spectrometry and the levels of amikacin measured by immunoassay. Dried blood spot on filter paper, to facilitate blood sampling for analysis of drug concentrations, is also evaluated. The MICs of the drugs listed above are determined using custom-made broth microdilution plates and MYCOTB plates with Middlebrook 7H9 media. MIC determination of pyrazinamide is performed in BACTEC MGIT 960. ETHICS AND DISSEMINATION This study has been approved by the ethical review boards of Karolinska Institutet, Sweden and Fudan University, China. Informed written consent is given by participants. The study results will be submitted to a peer-reviewed journal. TRIAL REGISTRATION NUMBER NCT02816931; Pre-results.
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Affiliation(s)
- Lina Davies Forsman
- Division of Infectious Diseases, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Disease, Karolinska University Hospital, Stockholm, Sweden
| | - Katarina Niward
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Department of Infectious Diseases, Linköping University, Linkoping, Sweden
| | - Yi Hu
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety, Fudan University, Shanghai, China
| | - Rongrong Zheng
- Department of Tuberculosis and AIDS prevention, Xiamen City Centre for Disease Control, Xiamen, China
| | - Xubin Zheng
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety, Fudan University, Shanghai, China
| | - Ran Ke
- Department of Tuberculosis and AIDS prevention, Xiamen City Centre for Disease Control, Xiamen, China
| | - Weiping Cai
- Department of Tuberculosis and AIDS prevention, Xiamen City Centre for Disease Control, Xiamen, China
| | - Chao Hong
- Department of Tuberculosis and AIDS prevention, Xiamen City Centre for Disease Control, Xiamen, China
| | - Yang Li
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety, Fudan University, Shanghai, China
| | - Yazhou Gao
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety, Fudan University, Shanghai, China
| | - Jim Werngren
- Department of Microbiology, The Public Health Agency of Sweden, Stockholm, Sweden
| | - Jakob Paues
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Department of Infectious Diseases, Linköping University, Linkoping, Sweden
| | - Johanna Kuhlin
- Division of Infectious Diseases, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Disease, Karolinska University Hospital, Stockholm, Sweden
| | | | - Erik Eliasson
- Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Jan-Willem Alffenaar
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Mikael Mansjö
- Department of Microbiology, The Public Health Agency of Sweden, Stockholm, Sweden
| | - Sven Hoffner
- Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Biao Xu
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety, Fudan University, Shanghai, China
| | - Thomas Schön
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Department of Clinical Microbiology and Infectious Diseases, Kalmar County Hospital, Kalmar, Sweden
| | - Judith Bruchfeld
- Division of Infectious Diseases, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Disease, Karolinska University Hospital, Stockholm, Sweden
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Koch A, Cox H, Mizrahi V. Drug-resistant tuberculosis: challenges and opportunities for diagnosis and treatment. Curr Opin Pharmacol 2018; 42:7-15. [PMID: 29885623 PMCID: PMC6219890 DOI: 10.1016/j.coph.2018.05.013] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 05/11/2018] [Accepted: 05/21/2018] [Indexed: 01/01/2023]
Abstract
With an estimated incidence of 490000 cases in 2016, multidrug resistant tuberculosis (TB), against which key first-line anti-tuberculars are less efficacious, presents major challenges for global health. Poor treatment outcomes coupled with a yawning treatment gap between those in need of second-line therapy and those who receive it, underscore the urgent need for new approaches to tackle the scourge of drug-resistant TB. Against this background, significant progress has been made in understanding the complex biology of TB drug resistance and disease pathogenesis, and in establishing a pipeline for delivering new drugs and drug combinations. In this review, we highlight the challenges of drug-resistant TB and the ways in which new advances could be harnessed to improve treatment outcomes.
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Affiliation(s)
- Anastasia Koch
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research and Wellcome Centre for Clinical Infectious Diseases Research in Africa, University of Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine and Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Helen Cox
- Institute of Infectious Disease and Molecular Medicine and Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Valerie Mizrahi
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research and Wellcome Centre for Clinical Infectious Diseases Research in Africa, University of Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine and Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa.
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Litvinov V, Makarova M, Galkina K, Khachaturiants E, Krasnova M, Guntupova L, Safonova S. Drug susceptibility testing of slowly growing non-tuberculous mycobacteria using slomyco test-system. PLoS One 2018; 13:e0203108. [PMID: 30222736 PMCID: PMC6141080 DOI: 10.1371/journal.pone.0203108] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 08/15/2018] [Indexed: 11/18/2022] Open
Abstract
Objective The objective of the research was to assess the susceptibility of the slowly growing nontuberculous mycobacteria strains to the antimicrobial drugs used for mycobaterioses treatment using SLOMYCO test system. Materials and methods We assessed 363 NTM strains: 177 MAC (161 M. avium, 16 M. intracellulare), 112 M. kansasii and 74 M. xenopi collected from the respiratory material of the patients were under the treatment or under diagnostic procedures at our Center, affiliates and the diagnostic department in 2010–2016. Drug sucseptibility for NTM was tested using the Sensititre SLOWMYCO system (TREK DIAGNOSTIC Systems Ltd., UK). MICs were established by microdilutions in Mueller-Hinton broth on polystyrene 96-well plates. The statistical analysis was done using the StatGraphics Plus 5.0 software. The data were compared pairwise using Pearson χ2 test with Yates correction. 95% confidence interval (CI) were calculated. Statistically significant differences were considered for p <0.05. Log-rank test and Kaplan-Meier curves were used to assess the concentration-dependent surveillance probability. Results The statistically significant differences were revealed in sensitivity/resistance isolates of M. avium and M. intracellulare: M. avium strains were resistant to higher concentrations of amikacin, clarithromycin, linezolid and streptomycin (p <0.01); M. intracellulare strains were resistant to higher concentrations of ethionamide (p <0.05). The isolates of M. avium were significantly more resistant than M. kansasii to amikacin, doxycycline, isoniazid, clarithromycin, linezolid, moxifloxacin, rifabutin, rifampicin, streptomycin, trimethoprim/sulfamethoxazole, ciprofloxacin, ethambutol, ethionamide (visible growth of M. avium were inhibited by higher drug concentrations, p <0.01). The isolates of M. avium showed significantly higher resistance than M. xenopi to amikacin, doxycycline, isoniazid, clarithromycin, linezolid, moxifloxacin, rifampicin, streptomycin, trimethoprim/sulfamethoxazole, ciprofloxacin, ethambutol, and ethionamide (visible growth of M. avium were inhibited by higher drug concentrations, p <0.01). Statistically significant differences in the dynamics of the response to the antibacterial effects of isoniazid, linezolid, moxifloxacin, rifampicin, trimethoprim/sulfamethoxazole, ethambutol, and ethionamide were found for M. intracellulare and M. xenopi (complete inhibition of the visible growth of M. intracellulare required higher drugs concentrations, p <0, 05). Comparison of the Kaplan-Meyer curves revealed statistically significant differences in survialence probability of M. kansasii and M. xenopi for amikacin, doxycycline, rifampicin, trimethoprim/sulfamethoxazole, ciprofloxacin, ethambutol, and ethionamide (a higher number of isolates of M. xenopi were inhibited by low drugs concentrations, p <0.05). Conclusions Our data show that M. avium and M. intracellulare were more resistant to the majority of the studied drugs than M. kansasii and M. xenopi.
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Affiliation(s)
- Vitalii Litvinov
- Department of problems of laboratory diagnostics of tuberculosis and pathomorphology, Scientific and Clinical Antituberculosis Center of Moscow Government Health Department, Moscow, Russian Federation
| | - Marina Makarova
- Department of problems of laboratory diagnostics of tuberculosis and pathomorphology, Scientific and Clinical Antituberculosis Center of Moscow Government Health Department, Moscow, Russian Federation
- * E-mail:
| | - Ksenia Galkina
- Department of problems of laboratory diagnostics of tuberculosis and pathomorphology, Scientific and Clinical Antituberculosis Center of Moscow Government Health Department, Moscow, Russian Federation
| | - Elena Khachaturiants
- Department of problems of laboratory diagnostics of tuberculosis and pathomorphology, Scientific and Clinical Antituberculosis Center of Moscow Government Health Department, Moscow, Russian Federation
| | - Maria Krasnova
- Department of problems of laboratory diagnostics of tuberculosis and pathomorphology, Scientific and Clinical Antituberculosis Center of Moscow Government Health Department, Moscow, Russian Federation
| | - Lidia Guntupova
- City consultation diagnostic center, Scientific and Clinical Antituberculosis Center of Moscow Government Health Department, Moscow, Russian Federation
| | - Svetlana Safonova
- Department of problems of laboratory diagnostics of tuberculosis and pathomorphology, Scientific and Clinical Antituberculosis Center of Moscow Government Health Department, Moscow, Russian Federation
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Miotto P, Zhang Y, Cirillo DM, Yam WC. Drug resistance mechanisms and drug susceptibility testing for tuberculosis. Respirology 2018; 23:1098-1113. [PMID: 30189463 DOI: 10.1111/resp.13393] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/03/2018] [Accepted: 08/12/2018] [Indexed: 12/12/2022]
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (MTB) is the deadliest infectious disease and the associated global threat has worsened with the emergence of drug resistance, in particular multidrug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB). Although the World Health Organization (WHO) End-TB Strategy advocates for universal access to antimicrobial susceptibility testing, this is not widely available and/or it is still underused. The majority of drug resistance in clinical MTB strains is attributed to chromosomal mutations. Resistance-related mutations could also exert certain fitness cost to the drug-resistant MTB strains and growth fitness could be restored by the presence of compensatory mutations. Understanding these underlying mechanisms could provide an important insight into TB pathogenesis and predict the future trend of MDR-TB global pandemic. This review covers the mechanisms of resistance in MTB and provides a comprehensive overview of current phenotypic and molecular approaches for drug susceptibility testing, with particular attention to the methods endorsed and recommended by the WHO.
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Affiliation(s)
- Paolo Miotto
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Ying Zhang
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Wing Cheong Yam
- Department of Microbiology, Queen Mary Hospital Compound, The University of Hong Kong, Hong Kong, China
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Rancoita PMV, Cugnata F, Gibertoni Cruz AL, Borroni E, Hoosdally SJ, Walker TM, Grazian C, Davies TJ, Peto TEA, Crook DW, Fowler PW, Cirillo DM. Validating a 14-Drug Microtiter Plate Containing Bedaquiline and Delamanid for Large-Scale Research Susceptibility Testing of Mycobacterium tuberculosis. Antimicrob Agents Chemother 2018; 62:e00344-18. [PMID: 29941636 PMCID: PMC6125532 DOI: 10.1128/aac.00344-18] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 06/12/2018] [Indexed: 12/19/2022] Open
Abstract
The UKMYC5 plate is a 96-well microtiter plate designed by the CRyPTIC Consortium (Comprehensive Resistance Prediction for Tuberculosis: an International Consortium) to enable the measurement of MICs of 14 different antituberculosis (anti-TB) compounds for >30,000 clinical Mycobacterium tuberculosis isolates. Unlike the MYCOTB plate, on which the UKMYC5 plate is based, the UKMYC5 plate includes two new (bedaquiline and delamanid) and two repurposed (clofazimine and linezolid) compounds. UKMYC5 plates were tested by seven laboratories on four continents by use of a panel of 19 external quality assessment (EQA) strains, including H37Rv. To assess the optimal combination of reading method and incubation time, MICs were measured from each plate by two readers, using three methods (mirrored box, microscope, and Vizion digital viewing system), after 7, 10, 14, and 21 days of incubation. In addition, all EQA strains were subjected to whole-genome sequencing and phenotypically characterized by the 7H10/7H11 agar proportion method (APM) and by use of MGIT960 mycobacterial growth indicator tubes. We concluded that the UKMYC5 plate is optimally read using the Vizion system after 14 days of incubation, achieving an interreader agreement of 97.9% and intra- and interlaboratory reproducibility rates of 95.6% and 93.1%, respectively. The mirrored box had a similar reproducibility. Strains classified as resistant by APM, MGIT960, or the presence of mutations known to confer resistance consistently showed elevated MICs compared to those for strains classified as susceptible. Finally, the UKMYC5 plate records intermediate MICs for one strain for which the APM measured MICs close to the applied critical concentration, providing early evidence that the UKMYC5 plate can quantitatively measure the magnitude of resistance to anti-TB compounds that is due to specific genetic variation.
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Affiliation(s)
- Paola M V Rancoita
- University Centre of Statistics in the Biomedical Sciences, Vita-Salute San Raffaele University, Milan, Italy
| | - Federica Cugnata
- University Centre of Statistics in the Biomedical Sciences, Vita-Salute San Raffaele University, Milan, Italy
| | - Ana Luíza Gibertoni Cruz
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford, United Kingdom
| | - Emanuele Borroni
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sarah J Hoosdally
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford, United Kingdom
| | - Timothy M Walker
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford, United Kingdom
| | - Clara Grazian
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford, United Kingdom
| | - Timothy J Davies
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford, United Kingdom
| | - Timothy E A Peto
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford, United Kingdom
| | - Derrick W Crook
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford, United Kingdom
| | - Philip W Fowler
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford, United Kingdom
| | - Daniela M Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
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Colangeli R, Jedrey H, Kim S, Connell R, Ma S, Chippada Venkata UD, Chakravorty S, Gupta A, Sizemore EE, Diem L, Sherman DR, Okwera A, Dietze R, Boom WH, Johnson JL, Mac Kenzie WR, Alland D. Bacterial Factors That Predict Relapse after Tuberculosis Therapy. N Engl J Med 2018; 379:823-833. [PMID: 30157391 PMCID: PMC6317071 DOI: 10.1056/nejmoa1715849] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
BACKGROUND Approximately 5% of patients with drug-susceptible tuberculosis have a relapse after 6 months of first-line therapy, as do approximately 20% of patients after 4 months of short-course therapy. We postulated that by analyzing pretreatment isolates of Mycobacterium tuberculosis obtained from patients who subsequently had a relapse or were cured, we could determine any correlations between the minimum inhibitory concentration (MIC) of a drug below the standard resistance breakpoint and the relapse risk after treatment. METHODS Using data from the Tuberculosis Trials Consortium Study 22 (development cohort), we assessed relapse and cure isolates to determine the MIC values of isoniazid and rifampin that were below the standard resistance breakpoint (0.1 μg per milliliter for isoniazid and 1.0 μg per milliliter for rifampin). We combined this analysis with clinical, radiologic, and laboratory data to generate predictive relapse models, which we validated by analyzing data from the DMID 01-009 study (validation cohort). RESULTS In the development cohort, the mean (±SD) MIC of isoniazid below the breakpoint was 0.0334±0.0085 μg per milliliter in the relapse group and 0.0286±0.0092 μg per milliliter in the cure group, which represented a higher value in the relapse group by a factor of 1.17 (P=0.02). The corresponding MIC values of rifampin were 0.0695±0.0276 and 0.0453±0.0223 μg per milliliter, respectively, which represented a higher value in the relapse group by a factor of 1.53 (P<0.001). Higher MIC values remained associated with relapse in a multivariable analysis that included other significant between-group differences. In an analysis of receiver-operating-characteristic curves of relapse based on these MIC values, the area under the curve (AUC) was 0.779. In the development cohort, the AUC in a multivariable model that included MIC values was 0.875. In the validation cohort, the MIC values either alone or combined with other patient characteristics were also predictive of relapse, with AUC values of 0.964 and 0.929, respectively. The use of a model score for the MIC values of isoniazid and rifampin to achieve 75.0% sensitivity in cross-validation analysis predicted relapse with a specificity of 76.5% in the development cohort and a sensitivity of 70.0% and a specificity of 100% in the validation cohort. CONCLUSIONS In pretreatment isolates of M. tuberculosis with decrements of MIC values of isoniazid or rifampin below standard resistance breakpoints, higher MIC values were associated with a greater risk of relapse than lower MIC values. (Funded by the National Institute of Allergy and Infectious Diseases.).
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Affiliation(s)
- Roberto Colangeli
- From the Department of Medicine, Rutgers-New Jersey Medical School (R. Colangeli, H.J., U.D.C.V., S.C., A.G., D.A.), and the Department of Biostatistics, Rutgers School of Public Health (S.K., R. Connell), Newark; the Center for Infectious Disease Research, Seattle (S.M., D.R.S.); the Centers for Disease Control and Prevention, Atlanta (E.E.S., L.D., W.R.M.K.); Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda (A.O.); Nucleo de Doencas Infecciosas, Centro de Ciencias da Saude, Universidade Federal do Espirito Santo, Vitoria, Brazil (R.D.); and the Tuberculosis Research Unit, Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland (W.H.B., J.L.J.)
| | - Hannah Jedrey
- From the Department of Medicine, Rutgers-New Jersey Medical School (R. Colangeli, H.J., U.D.C.V., S.C., A.G., D.A.), and the Department of Biostatistics, Rutgers School of Public Health (S.K., R. Connell), Newark; the Center for Infectious Disease Research, Seattle (S.M., D.R.S.); the Centers for Disease Control and Prevention, Atlanta (E.E.S., L.D., W.R.M.K.); Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda (A.O.); Nucleo de Doencas Infecciosas, Centro de Ciencias da Saude, Universidade Federal do Espirito Santo, Vitoria, Brazil (R.D.); and the Tuberculosis Research Unit, Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland (W.H.B., J.L.J.)
| | - Soyeon Kim
- From the Department of Medicine, Rutgers-New Jersey Medical School (R. Colangeli, H.J., U.D.C.V., S.C., A.G., D.A.), and the Department of Biostatistics, Rutgers School of Public Health (S.K., R. Connell), Newark; the Center for Infectious Disease Research, Seattle (S.M., D.R.S.); the Centers for Disease Control and Prevention, Atlanta (E.E.S., L.D., W.R.M.K.); Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda (A.O.); Nucleo de Doencas Infecciosas, Centro de Ciencias da Saude, Universidade Federal do Espirito Santo, Vitoria, Brazil (R.D.); and the Tuberculosis Research Unit, Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland (W.H.B., J.L.J.)
| | - Roy Connell
- From the Department of Medicine, Rutgers-New Jersey Medical School (R. Colangeli, H.J., U.D.C.V., S.C., A.G., D.A.), and the Department of Biostatistics, Rutgers School of Public Health (S.K., R. Connell), Newark; the Center for Infectious Disease Research, Seattle (S.M., D.R.S.); the Centers for Disease Control and Prevention, Atlanta (E.E.S., L.D., W.R.M.K.); Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda (A.O.); Nucleo de Doencas Infecciosas, Centro de Ciencias da Saude, Universidade Federal do Espirito Santo, Vitoria, Brazil (R.D.); and the Tuberculosis Research Unit, Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland (W.H.B., J.L.J.)
| | - Shuyi Ma
- From the Department of Medicine, Rutgers-New Jersey Medical School (R. Colangeli, H.J., U.D.C.V., S.C., A.G., D.A.), and the Department of Biostatistics, Rutgers School of Public Health (S.K., R. Connell), Newark; the Center for Infectious Disease Research, Seattle (S.M., D.R.S.); the Centers for Disease Control and Prevention, Atlanta (E.E.S., L.D., W.R.M.K.); Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda (A.O.); Nucleo de Doencas Infecciosas, Centro de Ciencias da Saude, Universidade Federal do Espirito Santo, Vitoria, Brazil (R.D.); and the Tuberculosis Research Unit, Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland (W.H.B., J.L.J.)
| | - Uma D Chippada Venkata
- From the Department of Medicine, Rutgers-New Jersey Medical School (R. Colangeli, H.J., U.D.C.V., S.C., A.G., D.A.), and the Department of Biostatistics, Rutgers School of Public Health (S.K., R. Connell), Newark; the Center for Infectious Disease Research, Seattle (S.M., D.R.S.); the Centers for Disease Control and Prevention, Atlanta (E.E.S., L.D., W.R.M.K.); Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda (A.O.); Nucleo de Doencas Infecciosas, Centro de Ciencias da Saude, Universidade Federal do Espirito Santo, Vitoria, Brazil (R.D.); and the Tuberculosis Research Unit, Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland (W.H.B., J.L.J.)
| | - Soumitesh Chakravorty
- From the Department of Medicine, Rutgers-New Jersey Medical School (R. Colangeli, H.J., U.D.C.V., S.C., A.G., D.A.), and the Department of Biostatistics, Rutgers School of Public Health (S.K., R. Connell), Newark; the Center for Infectious Disease Research, Seattle (S.M., D.R.S.); the Centers for Disease Control and Prevention, Atlanta (E.E.S., L.D., W.R.M.K.); Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda (A.O.); Nucleo de Doencas Infecciosas, Centro de Ciencias da Saude, Universidade Federal do Espirito Santo, Vitoria, Brazil (R.D.); and the Tuberculosis Research Unit, Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland (W.H.B., J.L.J.)
| | - Aditi Gupta
- From the Department of Medicine, Rutgers-New Jersey Medical School (R. Colangeli, H.J., U.D.C.V., S.C., A.G., D.A.), and the Department of Biostatistics, Rutgers School of Public Health (S.K., R. Connell), Newark; the Center for Infectious Disease Research, Seattle (S.M., D.R.S.); the Centers for Disease Control and Prevention, Atlanta (E.E.S., L.D., W.R.M.K.); Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda (A.O.); Nucleo de Doencas Infecciosas, Centro de Ciencias da Saude, Universidade Federal do Espirito Santo, Vitoria, Brazil (R.D.); and the Tuberculosis Research Unit, Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland (W.H.B., J.L.J.)
| | - Erin E Sizemore
- From the Department of Medicine, Rutgers-New Jersey Medical School (R. Colangeli, H.J., U.D.C.V., S.C., A.G., D.A.), and the Department of Biostatistics, Rutgers School of Public Health (S.K., R. Connell), Newark; the Center for Infectious Disease Research, Seattle (S.M., D.R.S.); the Centers for Disease Control and Prevention, Atlanta (E.E.S., L.D., W.R.M.K.); Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda (A.O.); Nucleo de Doencas Infecciosas, Centro de Ciencias da Saude, Universidade Federal do Espirito Santo, Vitoria, Brazil (R.D.); and the Tuberculosis Research Unit, Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland (W.H.B., J.L.J.)
| | - Lois Diem
- From the Department of Medicine, Rutgers-New Jersey Medical School (R. Colangeli, H.J., U.D.C.V., S.C., A.G., D.A.), and the Department of Biostatistics, Rutgers School of Public Health (S.K., R. Connell), Newark; the Center for Infectious Disease Research, Seattle (S.M., D.R.S.); the Centers for Disease Control and Prevention, Atlanta (E.E.S., L.D., W.R.M.K.); Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda (A.O.); Nucleo de Doencas Infecciosas, Centro de Ciencias da Saude, Universidade Federal do Espirito Santo, Vitoria, Brazil (R.D.); and the Tuberculosis Research Unit, Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland (W.H.B., J.L.J.)
| | - David R Sherman
- From the Department of Medicine, Rutgers-New Jersey Medical School (R. Colangeli, H.J., U.D.C.V., S.C., A.G., D.A.), and the Department of Biostatistics, Rutgers School of Public Health (S.K., R. Connell), Newark; the Center for Infectious Disease Research, Seattle (S.M., D.R.S.); the Centers for Disease Control and Prevention, Atlanta (E.E.S., L.D., W.R.M.K.); Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda (A.O.); Nucleo de Doencas Infecciosas, Centro de Ciencias da Saude, Universidade Federal do Espirito Santo, Vitoria, Brazil (R.D.); and the Tuberculosis Research Unit, Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland (W.H.B., J.L.J.)
| | - Alphonse Okwera
- From the Department of Medicine, Rutgers-New Jersey Medical School (R. Colangeli, H.J., U.D.C.V., S.C., A.G., D.A.), and the Department of Biostatistics, Rutgers School of Public Health (S.K., R. Connell), Newark; the Center for Infectious Disease Research, Seattle (S.M., D.R.S.); the Centers for Disease Control and Prevention, Atlanta (E.E.S., L.D., W.R.M.K.); Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda (A.O.); Nucleo de Doencas Infecciosas, Centro de Ciencias da Saude, Universidade Federal do Espirito Santo, Vitoria, Brazil (R.D.); and the Tuberculosis Research Unit, Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland (W.H.B., J.L.J.)
| | - Reynaldo Dietze
- From the Department of Medicine, Rutgers-New Jersey Medical School (R. Colangeli, H.J., U.D.C.V., S.C., A.G., D.A.), and the Department of Biostatistics, Rutgers School of Public Health (S.K., R. Connell), Newark; the Center for Infectious Disease Research, Seattle (S.M., D.R.S.); the Centers for Disease Control and Prevention, Atlanta (E.E.S., L.D., W.R.M.K.); Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda (A.O.); Nucleo de Doencas Infecciosas, Centro de Ciencias da Saude, Universidade Federal do Espirito Santo, Vitoria, Brazil (R.D.); and the Tuberculosis Research Unit, Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland (W.H.B., J.L.J.)
| | - W Henry Boom
- From the Department of Medicine, Rutgers-New Jersey Medical School (R. Colangeli, H.J., U.D.C.V., S.C., A.G., D.A.), and the Department of Biostatistics, Rutgers School of Public Health (S.K., R. Connell), Newark; the Center for Infectious Disease Research, Seattle (S.M., D.R.S.); the Centers for Disease Control and Prevention, Atlanta (E.E.S., L.D., W.R.M.K.); Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda (A.O.); Nucleo de Doencas Infecciosas, Centro de Ciencias da Saude, Universidade Federal do Espirito Santo, Vitoria, Brazil (R.D.); and the Tuberculosis Research Unit, Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland (W.H.B., J.L.J.)
| | - John L Johnson
- From the Department of Medicine, Rutgers-New Jersey Medical School (R. Colangeli, H.J., U.D.C.V., S.C., A.G., D.A.), and the Department of Biostatistics, Rutgers School of Public Health (S.K., R. Connell), Newark; the Center for Infectious Disease Research, Seattle (S.M., D.R.S.); the Centers for Disease Control and Prevention, Atlanta (E.E.S., L.D., W.R.M.K.); Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda (A.O.); Nucleo de Doencas Infecciosas, Centro de Ciencias da Saude, Universidade Federal do Espirito Santo, Vitoria, Brazil (R.D.); and the Tuberculosis Research Unit, Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland (W.H.B., J.L.J.)
| | - William R Mac Kenzie
- From the Department of Medicine, Rutgers-New Jersey Medical School (R. Colangeli, H.J., U.D.C.V., S.C., A.G., D.A.), and the Department of Biostatistics, Rutgers School of Public Health (S.K., R. Connell), Newark; the Center for Infectious Disease Research, Seattle (S.M., D.R.S.); the Centers for Disease Control and Prevention, Atlanta (E.E.S., L.D., W.R.M.K.); Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda (A.O.); Nucleo de Doencas Infecciosas, Centro de Ciencias da Saude, Universidade Federal do Espirito Santo, Vitoria, Brazil (R.D.); and the Tuberculosis Research Unit, Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland (W.H.B., J.L.J.)
| | - David Alland
- From the Department of Medicine, Rutgers-New Jersey Medical School (R. Colangeli, H.J., U.D.C.V., S.C., A.G., D.A.), and the Department of Biostatistics, Rutgers School of Public Health (S.K., R. Connell), Newark; the Center for Infectious Disease Research, Seattle (S.M., D.R.S.); the Centers for Disease Control and Prevention, Atlanta (E.E.S., L.D., W.R.M.K.); Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda (A.O.); Nucleo de Doencas Infecciosas, Centro de Ciencias da Saude, Universidade Federal do Espirito Santo, Vitoria, Brazil (R.D.); and the Tuberculosis Research Unit, Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland (W.H.B., J.L.J.)
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Ssengooba W, Nakayita G, Namaganda CC, Joloba ML. Agreement of Middle brook 7H10 with Lowenstein Jensen and accuracy of the Sensititre MYCOTB plate using either method as a reference standard for Mycobacterium tuberculosis first line drug susceptibility testing. PLoS One 2018; 13:e0199638. [PMID: 29953491 PMCID: PMC6023171 DOI: 10.1371/journal.pone.0199638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/11/2018] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Although Sensititre Mycobacterium tuberculosis (MYCOTB) plate offers both drug susceptibility testing (DST) and minimum inhibitory concentration (MIC) results, it has not been evaluated against both Lowenstein Jensen (LJ) and Middlebrook 7H10 (MB7H10) DST methods at standard critical concentrations. MATERIALS AND METHODS We analyzed 76 M. tuberculosis isolates consisting of 54 isolates from the Uganda National TB drug resistance survey done December 2009-February 2011 and 22 isolates from the World Health Organization External Quality Assessment panel for the year 2011. All isolates were tested for LJ, MB7H10 and MYCOTB plate based DSTs for streptomycin, isoniazid, rifampicin and ethambutol anti-tuberculosis drugs. The agreement of MB7H10 with LJ and accuracy of MYCOTB plate using either LJ-DST or MB7H10 as a reference standard were determined. RESULTS The agreement (kappa) of MB7H10 with LJ was; 0.687 for rifampicin, 0.498 for isoniazid, 0.275 for streptomycin and 0.082 for ethambutol which as almost similar when compared with MYCOTB plate. The sensitivity (95% confidence interval; CI) of MYCOTB plate when LJ was used as a reference standard was higher for streptomycin 87.5% (81.6-98.4) followed by isoniazid 75.9% (65.1-95.6) and rifampicin 73.1% (52.2-88.4). When MB7H10 was used as reference standard, the sensitivity of MYCOTB plate improved significantly; isoniazid 96.2% (80.3-99.9), rifampicin 94.0 (83.4-98.7) and 93.8% (69.7-99.8). There was good agreement between MYCOTB plate and MB7H10; 1.00 for ethambutol, 0.959 for streptomycin, 0.915 for rifampicin and 0.778 for isoniazid. CONCLUSIONS The performance of the two culture-based reference standards for phenotypic first-line drug susceptibility testing methods, LJ and MB7H10, varied much even with acceptable MYCOTB plate MICs. There was acceptable agreement and accuracy of MYCOTB plate for drug susceptibility testing when MB7H10 was used as reference standard than with LJ-DST. Results from MIC information makes the MYCOTB plate more suitable for guiding clinicians on the choice of the most appropriate TB treatment regimen as well as limits of detection for TB drug resistance.
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Affiliation(s)
- Willy Ssengooba
- Makerere University, Department of Medical Microbiology, Mycobacteriology (BSL-3) Laboratory, Kampala, Uganda
| | - Germine Nakayita
- Makerere University, Department of Medical Microbiology, Mycobacteriology (BSL-3) Laboratory, Kampala, Uganda
| | - Carolyn C. Namaganda
- Makerere University, Department of Medical Microbiology, Mycobacteriology (BSL-3) Laboratory, Kampala, Uganda
| | - Moses L. Joloba
- Makerere University, Department of Medical Microbiology, Mycobacteriology (BSL-3) Laboratory, Kampala, Uganda
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Ruesen C, Riza AL, Florescu A, Chaidir L, Editoiu C, Aalders N, Nicolosu D, Grecu V, Ioana M, van Crevel R, van Ingen J. Linking minimum inhibitory concentrations to whole genome sequence-predicted drug resistance in Mycobacterium tuberculosis strains from Romania. Sci Rep 2018; 8:9676. [PMID: 29946139 PMCID: PMC6018741 DOI: 10.1038/s41598-018-27962-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 06/01/2018] [Indexed: 11/23/2022] Open
Abstract
Mycobacterium tuberculosis drug resistance poses a major threat to tuberculosis control. Current phenotypic tests for drug susceptibility are time-consuming, technically complex, and expensive. Whole genome sequencing is a promising alternative, though the impact of different drug resistance mutations on the minimum inhibitory concentration (MIC) remains to be investigated. We examined the genomes of 72 phenotypically drug-resistant Mycobacterium tuberculosis isolates from 72 Romanian patients for drug resistance mutations. MICs for first- and second-line drugs were determined using the MycoTB microdilution method. These MICs were compared to macrodilution critical concentration testing by the Mycobacterium Growth Indicator Tube (MGIT) platform and correlated to drug resistance mutations. Sixty-three (87.5%) isolates harboured drug resistance mutations; 48 (66.7%) were genotypically multidrug-resistant. Different drug resistance mutations were associated with different MIC ranges; katG S315T for isoniazid, and rpoB S450L for rifampicin were associated with high MICs. However, several mutations such as in rpoB, rrs and rpsL, or embB were associated with MIC ranges including the critical concentration for rifampicin, aminoglycosides or ethambutol, respectively. Different resistance mutations lead to distinct MICs, some of which may still be overcome by increased dosing. Whole genome sequencing can aid in the timely diagnosis of Mycobacterium tuberculosis drug resistance and guide clinical decision-making.
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Affiliation(s)
- Carolien Ruesen
- Department of Internal Medicine, Radboud university medical center, Nijmegen, The Netherlands
| | - Anca Lelia Riza
- Department of Internal Medicine, Radboud university medical center, Nijmegen, The Netherlands
- Human Genomics Laboratory, University of Medicine and Pharmacy of Craiova, Craiova, Romania
| | - Adriana Florescu
- "Victor Babes" Infectious Diseases and Pneumophtisiology Hospital Craiova, Dolj County, Romania
| | - Lidya Chaidir
- Health Research Unit, Faculty of Medicine, Padjadjaran University/Hasan Sadikin Hospital, Bandung, Indonesia
| | - Cornelia Editoiu
- "Victor Babes" Infectious Diseases and Pneumophtisiology Hospital Craiova, Dolj County, Romania
| | - Nicole Aalders
- Department of Medical Microbiology, Radboud university medical center, Nijmegen, The Netherlands
| | - Dragos Nicolosu
- "Victor Babes" Infectious Diseases and Pneumophtisiology Hospital Craiova, Dolj County, Romania
| | - Victor Grecu
- "Victor Babes" Infectious Diseases and Pneumophtisiology Hospital Craiova, Dolj County, Romania
| | - Mihai Ioana
- Human Genomics Laboratory, University of Medicine and Pharmacy of Craiova, Craiova, Romania
| | - Reinout van Crevel
- Department of Internal Medicine, Radboud university medical center, Nijmegen, The Netherlands
| | - Jakko van Ingen
- Department of Medical Microbiology, Radboud university medical center, Nijmegen, The Netherlands.
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Sharan R, Yang HJ, Sule P, Cirillo JD. Imaging Mycobacterium tuberculosis in Mice with Reporter Enzyme Fluorescence. J Vis Exp 2018:56801. [PMID: 29553533 PMCID: PMC5931367 DOI: 10.3791/56801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Reporter enzyme fluorescence (REF) utilizes substrates that are specific for enzymes present in target organisms of interest for imaging or detection by fluorescence or bioluminescence. We utilize BlaC, an enzyme expressed constitutively by all M. tuberculosis strains. REF allows rapid quantification of bacteria in lungs of infected mice. The same group of mice can be imaged at many time points, greatly reducing costs, enumerating bacteria more quickly, allowing novel observations in host-pathogen interactions, and increasing statistical power, since more animals per group are readily maintained. REF is extremely sensitive due to the catalytic nature of the BlaC enzymatic reporter and specific due to the custom flourescence resonance energy transfer (FRET) or fluorogenic substrates used. REF does not require recombinant strains, ensuring normal host-pathogen interactions. We describe the imaging of M. tuberculosis infection using a FRET substrate with maximal emission at 800 nm. The wavelength of the substrate allows sensitive deep tissue imaging in mammals. We will outline aerosol infection of mice with M. tuberculosis, anesthesia of mice, administration of the REF substrate, and optical imaging. This method has been successfully applied to evaluating host-pathogen interactions and efficacy of antibiotics targeting M. tuberculosis.
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Affiliation(s)
- Riti Sharan
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center
| | - Hee-Jeong Yang
- Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health
| | - Preeti Sule
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center
| | - Jeffrey D Cirillo
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center;
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