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Schön T, Chryssanthou E. Minimum inhibitory concentration distributions for Mycobacterium avium complex—towards evidence-based susceptibility breakpoints. Int J Infect Dis 2017; 55:122-124. [DOI: 10.1016/j.ijid.2016.12.027] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/21/2016] [Accepted: 12/23/2016] [Indexed: 11/28/2022] Open
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Schön T, Miotto P, Köser CU, Viveiros M, Böttger E, Cambau E. Mycobacterium tuberculosis drug-resistance testing: challenges, recent developments and perspectives. Clin Microbiol Infect 2016; 23:154-160. [PMID: 27810467 DOI: 10.1016/j.cmi.2016.10.022] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/21/2016] [Accepted: 10/22/2016] [Indexed: 11/16/2022]
Abstract
Drug-resistance testing, or antimicrobial susceptibility testing (AST), is mandatory for Mycobacterium tuberculosis in cases of failure on standard therapy. We reviewed the different methods and techniques of phenotypic and genotypic approaches. Although multiresistant and extensively drug-resistant (MDR/XDR) tuberculosis is present worldwide, AST for M. tuberculosis (AST-MTB) is still mainly performed according to the resources available rather than the drug-resistance rates. Phenotypic methods, i.e. culture-based AST, are commonly used in high-income countries to confirm susceptibility of new cases of tuberculosis. They are also used to detect resistance in tuberculosis cases with risk factors, in combination with genotypic tests. In low-income countries, genotypic methods screening hot-spot mutations known to confer resistance were found to be easier to perform because they avoid the culture and biosafety constraint. Given that genotypic tests can rapidly detect the prominent mechanisms of resistance, such as the rpoB mutation for rifampicin resistance, we are facing new challenges with the observation of false-resistance (mutations not conferring resistance) and false-susceptibility (mutations different from the common mechanism) results. Phenotypic and genotypic approaches are therefore complementary for obtaining a high sensitivity and specificity for detecting drug resistances and susceptibilities to accurately predict MDR/XDR cure and to gather relevant data for resistance surveillance. Although AST-MTB was established in the 1960s, there is no consensus reference method for MIC determination against which the numerous AST-MTB techniques can be compared. This information is necessary for assessing in vitro activity and setting breakpoints for future anti-tuberculosis agents.
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Affiliation(s)
- T Schön
- Department of Clinical Microbiology and Infectious Diseases, Kalmar County Hospital, Kalmar, Sweden; Division of Medical Microbiology, Department of Clinical and Experimental Medicine, Linköping University, Sweden; European Society for Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Mycobacterial Infections (ESGMYC), ESCMID, Basel, Switzerland
| | - P Miotto
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - C U Köser
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - M Viveiros
- European Society for Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Mycobacterial Infections (ESGMYC), ESCMID, Basel, Switzerland; Unidade de Microbiologia Médica, Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Lisboa, Portugal
| | - E Böttger
- European Society for Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Mycobacterial Infections (ESGMYC), ESCMID, Basel, Switzerland; Institut für Medizinische Mikrobiologie, Nationales Zentrum für Mykobakterien, Universität Zürich, Zürich, Switzerland
| | - E Cambau
- European Society for Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Mycobacterial Infections (ESGMYC), ESCMID, Basel, Switzerland; National Reference Center for Mycobacteria and Antimycobacterial Resistance, Paris, France; APHP, Hôpital Lariboisière, Laboratory of Bacteriology, Paris, France; University Paris Diderot, INSERM IAME UMR1137, Sorbonne Paris Cité, Paris, France.
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Gilpin C, Korobitsyn A, Weyer K. Current tools available for the diagnosis of drug-resistant tuberculosis. Ther Adv Infect Dis 2016; 3:145-151. [PMID: 28386407 DOI: 10.1177/2049936116673553] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Drug-resistant tuberculosis (DR-TB) poses a major threat to control of tuberculosis worldwide. Diagnosis and treatment of DR-TB are considerably more difficult than for drug-susceptible tuberculosis (TB) and require higher level infrastructure and proficiency from laboratory specialists and clinicians. The World Health Organization (WHO) End TB Strategy calls for early diagnosis and initiation of appropriate treatment of all persons of all ages with any form of drug-susceptible TB or DR-TB. This requires ensuring access to WHO-recommended rapid diagnostics and universal drug susceptibility testing (DST) for all persons with signs and symptoms of TB. There are a number of laboratory tools available for diagnosis of DR-TB, including phenotypic culture-based DST as well as molecular methods. Optimal and complementary use of the available diagnostic tools at the different levels of the tiered network of TB laboratories, as well as correct interpretation of the diagnostic results provided by them is critical for accurate and timely diagnosis of DR-TB thus enabling effective treatment and care of patients.
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Affiliation(s)
- Christopher Gilpin
- The Global TB Programme, World Health Organization (WHO), 20, avenue Appia, 1211, Geneva 27, Switzerland
| | - A Korobitsyn
- The Global TB Programme, World Health Organization (WHO), 20, avenue Appia, 1211, Geneva 27, Switzerland
| | - K Weyer
- The Global TB Programme, World Health Organization (WHO), 20, avenue Appia, 1211, Geneva 27, Switzerland
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A Multilaboratory, Multicountry Study To Determine MIC Quality Control Ranges for Phenotypic Drug Susceptibility Testing of Selected First-Line Antituberculosis Drugs, Second-Line Injectables, Fluoroquinolones, Clofazimine, and Linezolid. J Clin Microbiol 2016; 54:2963-2968. [PMID: 27654338 DOI: 10.1128/jcm.01138-16] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 09/19/2016] [Indexed: 11/20/2022] Open
Abstract
Our objective was to establish reference MIC quality control (QC) ranges for drug susceptibility testing of antimycobacterials, including first-line agents, second-line injectables, fluoroquinolones, and World Health Organization category 5 drugs for multidrug-resistant tuberculosis using a 7H9 broth microdilution MIC method. A tier-2 reproducibility study was conducted in eight participating laboratories using Clinical Laboratory and Standards Institute (CLSI) guidelines. Three lots of custom-made frozen 96-well polystyrene microtiter plates were used and prepared with 2× prediluted drugs in 7H9 broth-oleic acid albumin dextrose catalase. The QC reference strain was Mycobacterium tuberculosis H37Rv. MIC frequency, mode, and geometric mean were calculated for each drug. QC ranges were derived based on predefined, strict CLSI criteria. Any data lying outside CLSI criteria resulted in exclusion of the entire laboratory data set. Data from one laboratory were excluded due to higher MIC values than other laboratories. QC ranges were established for 11 drugs: isoniazid (0.03 to 0.12 μg/ml), rifampin (0.03 to 0.25 μg/ml), ethambutol (0.25 to 2 μg/ml), levofloxacin (0.12 to 1 μg/ml), moxifloxacin (0.06 to 0.5 μg/ml), ofloxacin (0.25 to 2 μg/ml), amikacin (0.25 to 2 μg/ml), kanamycin (0.25 to 2 μg/ml), capreomycin (0.5 to 4 μg/ml), linezolid (0.25 to 2 μg/ml), and clofazimine (0.03 to 0.25 μg/ml). QC ranges could not be established for nicotinamide (pyrazinamide surrogate), prothionamide, or ethionamide, which were assay nonperformers. Using strict CLSI criteria, QC ranges against the M. tuberculosis H37Rv reference strain were established for the majority of commonly used antituberculosis drugs, with a convenient 7H9 broth microdilution MIC method suitable for use in resource-limited settings.
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Theron G, Peter J, Richardson M, Warren R, Dheda K, Steingart KR. GenoType ® MTBDRsl assay for resistance to second-line anti-tuberculosis drugs. Cochrane Database Syst Rev 2016; 9:CD010705. [PMID: 27605387 PMCID: PMC5034505 DOI: 10.1002/14651858.cd010705.pub3] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Genotype® MTBDRsl (MTBDRsl) is a rapid DNA-based test for detecting specific mutations associated with resistance to fluoroquinolones and second-line injectable drugs (SLIDs) in Mycobacterium tuberculosis complex. MTBDRsl version 2.0 (released in 2015) identifies the mutations detected by version 1.0, as well as additional mutations. The test may be performed on a culture isolate or a patient specimen, which eliminates delays associated with culture. Version 1.0 requires a smear-positive specimen, while version 2.0 may use a smear-positive or -negative specimen. We performed this updated review as part of a World Health Organization process to develop updated guidelines for using MTBDRsl. OBJECTIVES To assess and compare the diagnostic accuracy of MTBDRsl for: 1. fluoroquinolone resistance, 2. SLID resistance, and 3. extensively drug-resistant tuberculosis, indirectly on a M. tuberculosis isolate grown from culture or directly on a patient specimen. Participants were people with rifampicin-resistant or multidrug-resistant tuberculosis. The role of MTBDRsl would be as the initial test, replacing culture-based drug susceptibility testing (DST), for detecting second-line drug resistance. SEARCH METHODS We searched the following databases without language restrictions up to 21 September 2015: the Cochrane Infectious Diseases Group Specialized Register; MEDLINE; Embase OVID; Science Citation Index Expanded, Conference Proceedings Citation Index-Science, and BIOSIS Previews (all three from Web of Science); LILACS; and SCOPUS; registers for ongoing trials; and ProQuest Dissertations & Theses A&I. We reviewed references from included studies and contacted specialists in the field. SELECTION CRITERIA We included cross-sectional and case-control studies that determined MTBDRsl accuracy against a defined reference standard (culture-based DST, genetic sequencing, or both). DATA COLLECTION AND ANALYSIS Two review authors independently extracted data and assessed quality using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. We synthesized data for versions 1.0 and 2.0 separately. We estimated MTBDRsl sensitivity and specificity for fluoroquinolone resistance, SLID resistance, and extensively drug-resistant tuberculosis when the test was performed indirectly or directly (smear-positive specimen for version 1.0, smear-positive or -negative specimen for version 2.0). We explored the influence on accuracy estimates of individual drugs within a drug class and of different reference standards. We performed most analyses using a bivariate random-effects model with culture-based DST as reference standard. MAIN RESULTS We included 27 studies. Twenty-six studies evaluated version 1.0, and one study version 2.0. Of 26 studies stating specimen country origin, 15 studies (58%) evaluated patients from low- or middle-income countries. Overall, we considered the studies to be of high methodological quality. However, only three studies (11%) had low risk of bias for the reference standard; these studies used World Health Organization (WHO)-recommended critical concentrations for all drugs in the culture-based DST reference standard. MTBDRsl version 1.0 Fluoroquinolone resistance: indirect testing, MTBDRsl pooled sensitivity and specificity (95% confidence interval (CI)) were 85.6% (79.2% to 90.4%) and 98.5% (95.7% to 99.5%), (19 studies, 2223 participants); direct testing (smear-positive specimen), pooled sensitivity and specificity were 86.2% (74.6% to 93.0%) and 98.6% (96.9% to 99.4%), (nine studies, 1771 participants, moderate quality evidence). SLID resistance: indirect testing, MTBDRsl pooled sensitivity and specificity were 76.5% (63.3% to 86.0%) and 99.1% (97.3% to 99.7%), (16 studies, 1921 participants); direct testing (smear-positive specimen), pooled sensitivity and specificity were 87.0% (38.1% to 98.6%) and 99.5% (93.6% to 100.0%), (eight studies, 1639 participants, low quality evidence). Extensively drug-resistant tuberculosis: indirect testing, MTBDRsl pooled sensitivity and specificity were 70.9% (42.9% to 88.8%) and 98.8% (96.1% to 99.6%), (eight studies, 880 participants); direct testing (smear-positive specimen), pooled sensitivity and specificity were 69.4% (38.8% to 89.0%) and 99.4% (95.0% to 99.3%), (six studies, 1420 participants, low quality evidence).Similar to the original Cochrane review, we found no evidence of a significant difference in MTBDRsl version 1.0 accuracy between indirect and direct testing for fluoroquinolone resistance, SLID resistance, and extensively drug-resistant tuberculosis. MTBDRsl version 2.0 Fluoroquinolone resistance: direct testing, MTBDRsl sensitivity and specificity were 97% (83% to 100%) and 98% (93% to 100%), smear-positive specimen; 80% (28% to 99%) and 100% (40% to 100%), smear-negative specimen. SLID resistance: direct testing, MTBDRsl sensitivity and specificity were 89% (72% to 98%) and 90% (84% to 95%), smear-positive specimen; 80% (28% to 99%) and 100% (40% to 100%), smear-negative specimen. Extensively drug-resistant tuberculosis: direct testing, MTBDRsl sensitivity and specificity were 79% (49% to 95%) and 97% (93% to 99%), smear-positive specimen; 50% (1% to 99%) and 100% (59% to 100%), smear-negative specimen.We had insufficient data to estimate summary sensitivity and specificity of version 2.0 (smear-positive and -negative specimens) or to compare accuracy of the two versions.A limitation was that most included studies did not consistently use the World Health Organization (WHO)-recommended concentrations for drugs in the culture-based DST reference standard. AUTHORS' CONCLUSIONS In people with rifampicin-resistant or multidrug-resistant tuberculosis, MTBDRsl performed on a culture isolate or smear-positive specimen may be useful in detecting second-line drug resistance. MTBDRsl (smear-positive specimen) correctly classified around six in seven people as having fluoroquinolone or SLID resistance, although the sensitivity estimates for SLID resistance varied. The test rarely gave a positive result for people without drug resistance. However, when second-line drug resistance is not detected (MTBDRsl result is negative), conventional DST can still be used to evaluate patients for resistance to the fluoroquinolones or SLIDs.We recommend that future work evaluate MTBDRsl version 2.0, in particular on smear-negative specimens and in different settings to account for different resistance-causing mutations that may vary by strain. Researchers should also consider incorporating WHO-recommended critical concentrations into their culture-based reference standards.
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Affiliation(s)
- Grant Theron
- Stellenbosch UniversityDST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health SciencesTygerbergSouth Africa
| | - Jonny Peter
- University of Cape TownDivision of Clinical Immunology and Allergology, Department of MedicineCape TownSouth Africa
| | - Marty Richardson
- Liverpool School of Tropical MedicineCochrane Infectious Diseases GroupPembroke PlaceLiverpoolUKL3 5QA
| | - Rob Warren
- Stellenbosch UniversityDST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health SciencesMatielandSouth Africa
| | - Keertan Dheda
- University of Cape TownLung Infection and Immunity Unit, Department of MedicineCape TownSouth Africa
| | - Karen R Steingart
- Liverpool School of Tropical MedicineCochrane Infectious Diseases GroupPembroke PlaceLiverpoolUKL3 5QA
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Shah NS, Grace Lin SY, Barry PM, Cheng YN, Schecter G, Desmond E. Clinical Impact on Tuberculosis Treatment Outcomes of Discordance Between Molecular and Growth-Based Assays for Rifampin Resistance, California 2003-2013. Open Forum Infect Dis 2016; 3:ofw150. [PMID: 27704008 PMCID: PMC5047429 DOI: 10.1093/ofid/ofw150] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/11/2016] [Indexed: 11/23/2022] Open
Abstract
Background. Data from international settings suggest that isolates of Mycobacterium tuberculosis with rpoB mutations testing phenotypically susceptible to rifampin (RIF) may have clinical significance. We analyzed treatment outcomes of California patients with discordant molecular-phenotypic RIF results. Methods. We included tuberculosis (TB) patients, during 2003-2013, whose specimens tested RIF susceptible phenotypically but had a rpoB mutation determined by pyrosequencing. Demographic data were abstracted from the California TB registry. Phenotypic drug-susceptibility testing, medical history, treatment, and outcomes were abstracted from medical records. Results. Of 3330 isolates tested, 413 specimens had a rpoB mutation (12.4%). Of these, 16 (3.9%) had molecular-phenotypic discordant RIF results. Seven mutations were identified: 511Pro, 516Phe, 526Asn, 526Ser (AGC and TCC), 526Cys, and 533Pro. Fourteen (88%) had isoniazid (INH) resistance, 6 of whom were also phenotypically resistant to ethambutol (EMB) and/or pyrazinamide (PZA). Five patients (25%), 1 with 511Pro and 4 with 526Asn, relapsed or failed treatment. The initial regimen for 3 patients was RIF, PZA, and EMB; 1 patient received RIF, PZA, EMB, and a fluoroquinolone (FQN); and 1 patient received RIF, EMB, FQN, and some second-line medications. Upon retreatment with an expanded regimen, 3 (75%) patients completed treatment, 1 patient moved before treatment completion, and 1 patient continues on treatment. The remaining 11 patients had a successful outcome with 9 having received a FQN and/or a rifamycin. Conclusions. Rifampin molecular-phenotypic discordance was rare, and most isolates had INH resistance. Patients who did not receive an expanded regimen had poor outcomes. These mutations may have clinical importance, and expanded treatment regimens should be considered.
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Affiliation(s)
- Neha S Shah
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia; California Department of Health, Tuberculosis Control Branch, Richmond
| | - S Y Grace Lin
- California Department of Health , Tuberculosis Control Branch , Richmond
| | - Pennan M Barry
- California Department of Health , Tuberculosis Control Branch , Richmond
| | - Yi-Ning Cheng
- San Diego Health and Human Services Agency , California
| | - Gisela Schecter
- California Department of Health, Tuberculosis Control Branch, Richmond; University of California San Francisco
| | - Ed Desmond
- California Department of Health , Tuberculosis Control Branch , Richmond
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Wild-Type and Non-Wild-Type Mycobacterium tuberculosis MIC Distributions for the Novel Fluoroquinolone Antofloxacin Compared with Those for Ofloxacin, Levofloxacin, and Moxifloxacin. Antimicrob Agents Chemother 2016; 60:5232-7. [PMID: 27324769 PMCID: PMC4997829 DOI: 10.1128/aac.00393-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/10/2016] [Indexed: 12/16/2022] Open
Abstract
Antofloxacin (AFX) is a novel fluoroquinolone that has been approved in China for the treatment of infections caused by a variety of bacterial species. We investigated whether it could be repurposed for the treatment of tuberculosis by studying its in vitro activity. We determined the wild-type and non-wild-type MIC ranges for AFX as well as ofloxacin (OFX), levofloxacin (LFX), and moxifloxacin (MFX), using the microplate alamarBlue assay, of 126 clinical Mycobacterium tuberculosis strains from Beijing, China, of which 48 were OFX resistant on the basis of drug susceptibility testing on Löwenstein-Jensen medium. The MIC distributions were correlated with mutations in the quinolone resistance-determining regions of gyrA (Rv0006) and gyrB (Rv0005). Pharmacokinetic/pharmacodynamic (PK/PD) data for AFX were retrieved from the literature. AFX showed lower MIC levels than OFX but higher MIC levels than LFX and MFX on the basis of the tentative epidemiological cutoff values (ECOFFs) determined in this study. All strains with non-wild-type MICs for AFX harbored known resistance mutations that also resulted in non-wild-type MICs for LFX and MFX. Moreover, our data suggested that the current critical concentration of OFX for Löwenstein-Jensen medium that was recently revised by the World Health Organization might be too high, resulting in the misclassification of phenotypically non-wild-type strains with known resistance mutations as wild type. On the basis of our exploratory PK/PD calculations, the current dose of AFX is unlikely to be optimal for the treatment of tuberculosis, but higher doses could be effective.
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Ghimire S, van't Boveneind-Vrubleuskaya N, Akkerman OW, de Lange WCM, van Soolingen D, Kosterink JGW, van der Werf TS, Wilffert B, Touw DJ, Alffenaar JWC. Pharmacokinetic/pharmacodynamic-based optimization of levofloxacin administration in the treatment of MDR-TB. J Antimicrob Chemother 2016; 71:2691-703. [DOI: 10.1093/jac/dkw164] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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Desjardins CA, Cohen KA, Munsamy V, Abeel T, Maharaj K, Walker BJ, Shea TP, Almeida DV, Manson AL, Salazar A, Padayatchi N, O'Donnell MR, Mlisana KP, Wortman J, Birren BW, Grosset J, Earl AM, Pym AS. Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance. Nat Genet 2016; 48:544-51. [PMID: 27064254 PMCID: PMC4848111 DOI: 10.1038/ng.3548] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 03/18/2016] [Indexed: 12/19/2022]
Abstract
A more complete understanding of the genetic basis of drug resistance in Mycobacterium tuberculosis is critical for prompt diagnosis and optimal treatment, particularly for toxic second-line drugs such as D-cycloserine. Here we used the whole-genome sequences from 498 strains of M. tuberculosis to identify new resistance-conferring genotypes. By combining association and correlated evolution tests with strategies for amplifying signal from rare variants, we found that loss-of-function mutations in ald (Rv2780), encoding L-alanine dehydrogenase, were associated with unexplained drug resistance. Convergent evolution of this loss of function was observed exclusively among multidrug-resistant strains. Drug susceptibility testing established that ald loss of function conferred resistance to D-cycloserine, and susceptibility to the drug was partially restored by complementation of ald. Clinical strains with mutations in ald and alr exhibited increased resistance to D-cycloserine when cultured in vitro. Incorporation of D-cycloserine resistance in novel molecular diagnostics could allow for targeted use of this toxic drug among patients with susceptible infections.
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Affiliation(s)
| | - Keira A Cohen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa
| | - Vanisha Munsamy
- KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa
| | - Thomas Abeel
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Delft Bioinformatics Laboratory, Delft University of Technology, Delft, the Netherlands
| | - Kashmeel Maharaj
- KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa
| | - Bruce J Walker
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Terrance P Shea
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Deepak V Almeida
- KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa
- Center for Tuberculosis Research, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Abigail L Manson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Alex Salazar
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Delft Bioinformatics Laboratory, Delft University of Technology, Delft, the Netherlands
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Max R O'Donnell
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University College of Physicians and Surgeons, New York, New York, USA
- Department of Epidemiology, Columbia Mailman School of Public Health, New York, New York, USA
| | - Koleka P Mlisana
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- National Health Laboratory Service, Durban, South Africa
| | - Jennifer Wortman
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Bruce W Birren
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jacques Grosset
- KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa
- Center for Tuberculosis Research, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Ashlee M Earl
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Alexander S Pym
- KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa
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Zuur MA, Bolhuis MS, Anthony R, den Hertog A, van der Laan T, Wilffert B, de Lange W, van Soolingen D, Alffenaar JWC. Current status and opportunities for therapeutic drug monitoring in the treatment of tuberculosis. Expert Opin Drug Metab Toxicol 2016; 12:509-21. [DOI: 10.1517/17425255.2016.1162785] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Marlanka A. Zuur
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Mathieu S. Bolhuis
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Richard Anthony
- Royal Tropical Institute (KIT), KIT Biomedical Research, Amsterdam, The Netherlands
| | - Alice den Hertog
- Royal Tropical Institute (KIT), KIT Biomedical Research, Amsterdam, The Netherlands
| | - Tridia van der Laan
- National Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Bob Wilffert
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Pharmacy, section Pharmacotherapy and Pharmaceutical Care, University of Groningen, Groningen, The Netherlands
| | - Wiel de Lange
- University of Groningen, University Medical Center Groningen, Tuberculosis Centre Beatrixoord, Haren, The Netherlands
- Department of Pulmonary Diseases and Tuberculosis, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Dick van Soolingen
- National Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Departments of Pulmonary Diseases and Medical Microbiology, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Jan-Willem C. Alffenaar
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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Georghiou SB, Ajbani K, Rodrigues C, Rodwell TC. Performance of a pyrosequencing platform in diagnosing drug-resistant extra-pulmonary tuberculosis in India. Int J Tuberc Lung Dis 2016; 20:160-5. [PMID: 26792466 DOI: 10.5588/ijtld.15.0459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
SETTING Pyrosequencing diagnostic assays have shown great utility in identifying and characterizing pulmonary drug-resistant tuberculosis (TB) infections. However, the method has yet to be evaluated for the diagnosis of drug-resistant extra-pulmonary TB (EPTB). OBJECTIVE To evaluate the performance of a pyrosequencing platform in establishing molecular drug resistance profiles for 79 clinical EPTB specimens at a referral center for drug-resistant TB in India. DESIGN Genotypic drug resistance profiles were established for all 79 non-pulmonary, culture-positive TB clinical specimens. Acid-fast bacilli smear microscopy, MGIT™ 960™ culture and drug susceptibility testing were performed on all specimens for reference. RESULTS In comparison to MGIT 960, the sensitivity and specificity of pyrosequencing in detecting drug resistance among specimens was found to be respectively 100% and 100%, 67% and 98%, and 100% and 100% for isoniazid, rifampicin, and the fluoroquinolones. No EPTB specimens were phenotypically resistant to any of the injectables, but the specificity of the assay was determined to be 100%, 98%, and 98% for amikacin, kanamycin, and capreomycin. CONCLUSIONS Pyrosequencing is a rapid, appropriate technology for the diagnosis of isoniazid-, fluoroquinolone-, and potentially injectable drug-resistant EPTB clinical specimens, and should be considered as an alternative to conventional growth-based diagnostic methods for EPTB when resistance to these drugs is suspected.
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Affiliation(s)
- S B Georghiou
- Division of Global Public Health, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - K Ajbani
- Section Microbiology, Department of Laboratory Medicine, P D Hinduja National Hospital and Medical Research Centre, Mumbai, India
| | - C Rodrigues
- Section Microbiology, Department of Laboratory Medicine, P D Hinduja National Hospital and Medical Research Centre, Mumbai, India
| | - T C Rodwell
- Division of Global Public Health, School of Medicine, University of California San Diego, La Jolla, California, USA
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Niward K, Ängeby K, Chryssanthou E, Paues J, Bruchfeld J, Jureen P, Giske CG, Kahlmeter G, Schön T. Susceptibility testing breakpoints for Mycobacterium tuberculosis categorize isolates with resistance mutations in gyrA as susceptible to fluoroquinolones: implications for MDR-TB treatment and the definition of XDR-TB. J Antimicrob Chemother 2015; 71:333-8. [PMID: 26538509 DOI: 10.1093/jac/dkv353] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 09/29/2015] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Fluoroquinolones (FQs) are important in the treatment of MDR-TB and in the definition of XDR-TB. Our objective was to investigate how discrepancies in the phenotypic and genotypic methods for antimicrobial susceptibility testing could affect the interpretation of antimicrobial susceptibility test results. METHODS We analysed MICs of ofloxacin and levofloxacin in Middlebrook 7H10 broth (7H10) as well as sequencing of the quinolone resistance-determining region of the gyrA gene and the MTBDRsl assay in 75 resistant isolates, including MDR and XDR strains of Mycobacterium tuberculosis. RESULTS Among 75 resistant isolates, 27 had mutations associated with FQ resistance. Among isolates with resistance mutations in gyrA, 26% (seven of 27) were susceptible to levofloxacin and ofloxacin by phenotypic testing at 1 mg/L and 2 mg/L. The most common mutation was in codon 94 and these isolates had significantly increased MICs of levofloxacin (2-8 mg/L) compared with isolates with mutations in codon 90 (0.25-2 mg/L, P < 0.05). The sensitivity and specificity for the MTBDRsl assay compared with gyrA sequencing were 96% and 98%, respectively. CONCLUSION Current critical concentrations may classify up to 26% of isolates with gyrA mutations as susceptible to FQs due to a close relationship between susceptible and resistant populations. These results should be considered while improving clinical breakpoints for M. tuberculosis and may have an impact on the definition of XDR-TB.
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Affiliation(s)
- Katarina Niward
- Department of Infectious Diseases, Linköping University Hospital, Linköping, Sweden Department of Clinical and Experimental medicine, Linköping University, Linköping, Sweden
| | - Kristian Ängeby
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden Department of Microbiology, The University of the West Indies, Kingston, Jamaica
| | - Erja Chryssanthou
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Jakob Paues
- Department of Infectious Diseases, Linköping University Hospital, Linköping, Sweden Department of Clinical and Experimental medicine, Linköping University, Linköping, Sweden
| | - Judith Bruchfeld
- Unit of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden Department of Medicine, Karolinska Institute, Solna, Sweden
| | - Pontus Jureen
- The Public Health Agency of Sweden, Stockholm, Sweden
| | - Christian G Giske
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Gunnar Kahlmeter
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden Department of Clinical Microbiology, Växjö Hospital, Växjö, Sweden
| | - Thomas Schön
- Department of Clinical Microbiology and Infectious Diseases, Kalmar County Hospital, Kalmar, Sweden Department of Medical microbiology, Linköping University, Linköping, Sweden
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Nguyen VAT, Nguyen HQ, Vu TT, Nguyen NAT, Duong CM, Tran THT, Nguyen HV, Dang DA, Bañuls AL. Reduced turn-around time for Mycobacterium tuberculosis drug susceptibility testing with a proportional agar microplate assay. Clin Microbiol Infect 2015; 21:1084-92. [PMID: 26348263 DOI: 10.1016/j.cmi.2015.08.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 08/04/2015] [Accepted: 08/27/2015] [Indexed: 10/23/2022]
Abstract
Multidrug-resistant tuberculosis is a major issue worldwide; however, accessibility to drug susceptibility testing (DST) is still limited in developing countries, owing to high costs and complexity. We developed a proportion method on 12-well microplates for DST. The assay reduced the time to results to <12 days and <10 days when bacterial growth was checked with the naked eye or a microscope, respectively. Comparison with the Canetti-Grosset method showed that the results of the two assays almost overlapped (kappa index 0.98 (95% CI 0.91-1.00) for isoniazid, rifampicin, streptomycin; and kappa index 0.92 (95% CI 0.85-0.99) for ethambutol). The sequencing of genes involved in drug resistance showed similar level of phenotype-genotype agreement between techniques. Finally, measurement of the MICs of rifampicin and ethambutol suggests that the currently used critical ethambutol concentration should be revised, and that the current molecular drug susceptibility tests for rifampicin need to be re-evaluated, as in vitro rifampicin-sensitive isolates could harbour drug resistance-associated mutation(s).
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Affiliation(s)
- V A T Nguyen
- Department of Bacteriology, National Institute of Hygiene Epidemiology, Hanoi, Vietnam.
| | - H Q Nguyen
- Department of Bacteriology, National Institute of Hygiene Epidemiology, Hanoi, Vietnam; MIVEGEC (IRD 224-CNRS 5290-Université de Montpellier), Centre IRD, Montpellier, France; Department of Biotechnology Pharmacology, University of Science and Technology of Hanoi, Vietnam
| | - T T Vu
- Department of Bacteriology, National Institute of Hygiene Epidemiology, Hanoi, Vietnam
| | - N A T Nguyen
- Department of Bacteriology, National Institute of Hygiene Epidemiology, Hanoi, Vietnam
| | - C M Duong
- Department of Bacteriology, National Institute of Hygiene Epidemiology, Hanoi, Vietnam
| | - T H T Tran
- Department of Bacteriology, National Institute of Hygiene Epidemiology, Hanoi, Vietnam
| | - H V Nguyen
- Department of Microbiology, National Lung Hospital, Hanoi, Vietnam
| | - D A Dang
- Department of Bacteriology, National Institute of Hygiene Epidemiology, Hanoi, Vietnam
| | - A-L Bañuls
- Department of Bacteriology, National Institute of Hygiene Epidemiology, Hanoi, Vietnam; MIVEGEC (IRD 224-CNRS 5290-Université de Montpellier), Centre IRD, Montpellier, France
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Mutations Found in embCAB, embR, and ubiA Genes of Ethambutol-Sensitive and -Resistant Mycobacterium tuberculosis Clinical Isolates from China. BIOMED RESEARCH INTERNATIONAL 2015; 2015:951706. [PMID: 26417605 PMCID: PMC4568347 DOI: 10.1155/2015/951706] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 08/07/2015] [Accepted: 08/19/2015] [Indexed: 11/18/2022]
Abstract
To better understand the molecular mechanisms of Ethambutol (EMB) resistance, the mutant hot spot region of five genes (embB, embA, embC, embR, and ubiA) was amplified and sequenced in 109 EMB-resistant and 153 EMB-susceptible clinical isolates from China. Twenty-seven EMB-susceptible isolates were found to have nonsynonym mutations, 23 of which were in embB. The mutations occurred most frequently in embB (85.3%, 93) and were seldom in embC (2.8%, 3), embA (3.7%, 4), embR (3.7%, 4), and ubiA (8.3%, 9) in EMB-resistant isolates. For the embB gene, 63 isolates showed mutations at embB306, 20 at embB406, nine at embB497, and five at embB354 in EMB-resistant isolates. In addition, the particular mutants at embB406 and embB497 indicated both high levels of EMB resistance (MICs > 5 μg/mL) and broad anti-TB drug resistance spectrums. Our data supported the facts that embB306 could be used as a marker for EMB resistance with a sensitivity of 57.8% and a specificity of 78.8%.
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Walker TM, Kohl TA, Omar SV, Hedge J, Del Ojo Elias C, Bradley P, Iqbal Z, Feuerriegel S, Niehaus KE, Wilson DJ, Clifton DA, Kapatai G, Ip CLC, Bowden R, Drobniewski FA, Allix-Béguec C, Gaudin C, Parkhill J, Diel R, Supply P, Crook DW, Smith EG, Walker AS, Ismail N, Niemann S, Peto TEA. Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study. THE LANCET. INFECTIOUS DISEASES 2015; 15:1193-1202. [PMID: 26116186 PMCID: PMC4579482 DOI: 10.1016/s1473-3099(15)00062-6] [Citation(s) in RCA: 417] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/03/2015] [Accepted: 05/15/2015] [Indexed: 12/14/2022]
Abstract
BACKGROUND Diagnosing drug-resistance remains an obstacle to the elimination of tuberculosis. Phenotypic drug-susceptibility testing is slow and expensive, and commercial genotypic assays screen only common resistance-determining mutations. We used whole-genome sequencing to characterise common and rare mutations predicting drug resistance, or consistency with susceptibility, for all first-line and second-line drugs for tuberculosis. METHODS Between Sept 1, 2010, and Dec 1, 2013, we sequenced a training set of 2099 Mycobacterium tuberculosis genomes. For 23 candidate genes identified from the drug-resistance scientific literature, we algorithmically characterised genetic mutations as not conferring resistance (benign), resistance determinants, or uncharacterised. We then assessed the ability of these characterisations to predict phenotypic drug-susceptibility testing for an independent validation set of 1552 genomes. We sought mutations under similar selection pressure to those characterised as resistance determinants outside candidate genes to account for residual phenotypic resistance. FINDINGS We characterised 120 training-set mutations as resistance determining, and 772 as benign. With these mutations, we could predict 89·2% of the validation-set phenotypes with a mean 92·3% sensitivity (95% CI 90·7-93·7) and 98·4% specificity (98·1-98·7). 10·8% of validation-set phenotypes could not be predicted because uncharacterised mutations were present. With an in-silico comparison, characterised resistance determinants had higher sensitivity than the mutations from three line-probe assays (85·1% vs 81·6%). No additional resistance determinants were identified among mutations under selection pressure in non-candidate genes. INTERPRETATION A broad catalogue of genetic mutations enable data from whole-genome sequencing to be used clinically to predict drug resistance, drug susceptibility, or to identify drug phenotypes that cannot yet be genetically predicted. This approach could be integrated into routine diagnostic workflows, phasing out phenotypic drug-susceptibility testing while reporting drug resistance early. FUNDING Wellcome Trust, National Institute of Health Research, Medical Research Council, and the European Union.
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Affiliation(s)
- Timothy M Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
| | - Thomas A Kohl
- Molecular Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany
| | - Shaheed V Omar
- Centre for Tuberculosis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Jessica Hedge
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Carlos Del Ojo Elias
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Phelim Bradley
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Zamin Iqbal
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Silke Feuerriegel
- Molecular Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany; German Center for Infection Research, Borstel Site, Borstel, Germany
| | - Katherine E Niehaus
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK
| | - Daniel J Wilson
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - David A Clifton
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK
| | | | - Camilla L C Ip
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Rory Bowden
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Francis A Drobniewski
- Public Health England National Mycobacterial Reference Laboratory, Queen Mary's School of Medicine and Dentistry, London, UK; Department of Infectious Diseases, Imperial College, London, UK
| | | | | | | | - Roland Diel
- Institute for Epidemiology, University Medical Hospital Schleswig-Holstein, Airway Research Center North, Kiel, Germany
| | - Philip Supply
- Genoscreen, Lille, France; Centre National de la Recherche Scientifique, Lille, France; INSERM, Université de Lille, and Campus de l'Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK; National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - E Grace Smith
- Public Health England West Midlands Public Health Laboratory, Heartlands Hospital, Birmingham, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK; National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Nazir Ismail
- Centre for Tuberculosis, National Institute for Communicable Diseases, Johannesburg, South Africa; Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - Stefan Niemann
- Molecular Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany; German Center for Infection Research, Borstel Site, Borstel, Germany
| | - Tim E A Peto
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK; National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
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Coll F, McNerney R, Preston MD, Guerra-Assunção JA, Warry A, Hill-Cawthorne G, Mallard K, Nair M, Miranda A, Alves A, Perdigão J, Viveiros M, Portugal I, Hasan Z, Hasan R, Glynn JR, Martin N, Pain A, Clark TG. Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Med 2015; 7:51. [PMID: 26019726 PMCID: PMC4446134 DOI: 10.1186/s13073-015-0164-0] [Citation(s) in RCA: 277] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 04/16/2015] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium tuberculosis drug resistance (DR) challenges effective tuberculosis disease control. Current molecular tests examine limited numbers of mutations, and although whole genome sequencing approaches could fully characterise DR, data complexity has restricted their clinical application. A library (1,325 mutations) predictive of DR for 15 anti-tuberculosis drugs was compiled and validated for 11 of them using genomic-phenotypic data from 792 strains. A rapid online ‘TB-Profiler’ tool was developed to report DR and strain-type profiles directly from raw sequences. Using our DR mutation library, in silico diagnostic accuracy was superior to some commercial diagnostics and alternative databases. The library will facilitate sequence-based drug-susceptibility testing.
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Affiliation(s)
- Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Mark D Preston
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - José Afonso Guerra-Assunção
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Andrew Warry
- Advanced Data Analysis Centre, University of Nottingham, Wollaton Road, Nottingham, NG8 1BB UK
| | - Grant Hill-Cawthorne
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia ; Sydney Emerging Infections and Biosecurity Institute and School of Public Health, University of Sydney, Sydney, Australia
| | - Kim Mallard
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Mridul Nair
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Anabela Miranda
- Tuberculosis Laboratory, Instituto Nacional de Saude Dr. Ricardo Jorge, Porto, Portugal
| | - Adriana Alves
- Tuberculosis Laboratory, Instituto Nacional de Saude Dr. Ricardo Jorge, Porto, Portugal
| | - João Perdigão
- Centro de Patogénese Molecular, Faculdade de Farmácia da Universidade de Lisboa, Lisbon, Portugal
| | - Miguel Viveiros
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Isabel Portugal
- Centro de Patogénese Molecular, Faculdade de Farmácia da Universidade de Lisboa, Lisbon, Portugal
| | - Zahra Hasan
- Department of Pathology & Microbiology, Aga Khan University Hospital, Karachi, Pakistan
| | - Rumina Hasan
- Department of Pathology & Microbiology, Aga Khan University Hospital, Karachi, Pakistan
| | - Judith R Glynn
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK ; Karonga Prevention Study, Chilumba, Malawi
| | - Nigel Martin
- Department of Computer Science, Birkbeck College, University of London, Malet Street, London, WC1E 7HX UK
| | - Arnab Pain
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
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Determination of MIC distribution and epidemiological cutoff values for bedaquiline and delamanid in Mycobacterium tuberculosis using the MGIT 960 system equipped with TB eXiST. Antimicrob Agents Chemother 2015; 59:4352-5. [PMID: 25941226 DOI: 10.1128/aac.00614-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 04/29/2015] [Indexed: 11/20/2022] Open
Abstract
Bedaquiline (Sirturo) and delamanid (Deltyba) have recently been approved by the regulatory authorities for treatment of multidrug-resistant tuberculosis (MDR-TB). Antimicrobial susceptibility testing is not established for either substance. On the basis of the use of the MGIT 960 system equipped with EpiCenter/TB eXiST, we determined a mean bedaquiline MIC for wild-type strains of 0.65 mg/liter (median, 0.4 mg/liter) and an epidemiological cutoff (ECOFF) of 1.6 mg/liter; for delamanid, a mean wild-type drug MIC of 0.013 mg/liter (median, 0.01 mg/liter) and an ECOFF of 0.04 mg/liter were determined.
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Stehr M, Elamin AA, Singh M. Pyrazinamide: the importance of uncovering the mechanisms of action in mycobacteria. Expert Rev Anti Infect Ther 2015; 13:593-603. [PMID: 25746054 DOI: 10.1586/14787210.2015.1021784] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Pyrazinamide (PZA) is still one of the key drugs used in current therapeutic regimens for tuberculosis (TB). Despite its importance for TB therapy, the mode of action of PZA remains unknown. PZA has to be converted to its active form pyrazinoic acid (POA) by the nicotinamidase PncA and is then excreted by an unknown efflux pump. At acidic conditions, POA is protonated to HPOA and is reabsorbed into the cell where it causes cellular damage. For a long time, it has been thought that PZA/POA has no defined target of action, but recent studies have shown that both PZA and POA have several different targets interfering with diverse biochemical pathways, especially in the NAD(+) and energy metabolism. PZA resistance seems to depend not only on a defective pyrazinamidase but is also rather a result of the interplay of many different enzyme targets and transport mechanisms.
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Affiliation(s)
- Matthias Stehr
- LIONEX Diagnostics and Therapeutics GmbH, Salzdahlumer Straße 196, D-38126, Braunschweig, Germany
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69
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Srivastava S. Minimum inhibitory concentration, pharmacokinetics/pharmacodynamics and therapeutic drug monitoring: An integrated approach for multidrug-resistant tuberculosis. Lung India 2015; 32:402-3. [PMID: 26180397 PMCID: PMC4502212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Shashikant Srivastava
- Center for Infectious Diseases Research and Experimental therapeutics, Baylor Institute for Immunology Research, Dallas, Texas, and Department of Immunology, UT Southwestern Medical Center, Dallas, Texas, USA. E-mail:
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Ajbani K, Lin SYG, Rodrigues C, Nguyen D, Arroyo F, Kaping J, Jackson L, Garfein RS, Catanzaro D, Eisenach K, Victor TC, Crudu V, Gler MT, Ismail N, Desmond E, Catanzaro A, Rodwell TC. Evaluation of pyrosequencing for detecting extensively drug-resistant Mycobacterium tuberculosis among clinical isolates from four high-burden countries. Antimicrob Agents Chemother 2015; 59:414-20. [PMID: 25367911 PMCID: PMC4291380 DOI: 10.1128/aac.03614-14] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Accepted: 10/28/2014] [Indexed: 12/15/2022] Open
Abstract
Reliable molecular diagnostics, which detect specific mutations associated with drug resistance, are promising technologies for the rapid identification and monitoring of drug resistance in Mycobacterium tuberculosis isolates. Pyrosequencing (PSQ) has the ability to detect mutations associated with first- and second-line anti-tuberculosis (TB) drugs, with the additional advantage of being rapidly adaptable for the identification of new mutations. The aim of this project was to evaluate the performance of PSQ in predicting phenotypic drug resistance in multidrug- and extensively drug-resistant tuberculosis (M/XDR-TB) clinical isolates from India, South Africa, Moldova, and the Philippines. A total of 187 archived isolates were run through a PSQ assay in order to identify M. tuberculosis (via the IS6110 marker), and to detect mutations associated with M/XDR-TB within small stretches of nucleotides in selected loci. The molecular targets included katG, the inhA promoter and the ahpC-oxyR intergenic region for isoniazid (INH) resistance; the rpoB core region for rifampin (RIF) resistance; gyrA for fluoroquinolone (FQ) resistance; and rrs for amikacin (AMK), capreomycin (CAP), and kanamycin (KAN) resistance. PSQ data were compared to phenotypic mycobacterial growth indicator tube (MGIT) 960 drug susceptibility testing results for performance analysis. The PSQ assay illustrated good sensitivity for the detection of resistance to INH (94%), RIF (96%), FQ (93%), AMK (84%), CAP (88%), and KAN (68%). The specificities of the assay were 96% for INH, 100% for RIF, FQ, AMK, and KAN, and 97% for CAP. PSQ is a highly efficient diagnostic tool that reveals specific nucleotide changes associated with resistance to the first- and second-line anti-TB drug medications. This methodology has the potential to be linked to mutation-specific clinical interpretation algorithms for rapid treatment decisions.
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Affiliation(s)
- Kanchan Ajbani
- P. D. Hinduja National Hospital & Medical Research Centre, Department of Microbiology, Veer Sarvarkar Marg, Mahim, Mumbai, India
| | - Shou-Yean Grace Lin
- California Department of Public Health, Microbial Diseases Laboratory, Richmond, California, USA
| | - Camilla Rodrigues
- P. D. Hinduja National Hospital & Medical Research Centre, Department of Microbiology, Veer Sarvarkar Marg, Mahim, Mumbai, India
| | - Duylinh Nguyen
- California Department of Public Health, Microbial Diseases Laboratory, Richmond, California, USA
| | - Francine Arroyo
- California Department of Public Health, Microbial Diseases Laboratory, Richmond, California, USA
| | - Janice Kaping
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Lynn Jackson
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Richard S Garfein
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Donald Catanzaro
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Kathleen Eisenach
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Thomas C Victor
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Valeru Crudu
- Microbiology and Morphology Laboratory, Institute of Phthisiopneumology, Chisinau, Moldova
| | - Maria Tarcela Gler
- Tropical Disease Foundation/Makati Medical Center, Makati City, Philippines
| | - Nazir Ismail
- National Tuberculosis Reference Laboratory, Johannesburg, South Africa
| | - Edward Desmond
- California Department of Public Health, Microbial Diseases Laboratory, Richmond, California, USA
| | - Antonino Catanzaro
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Timothy C Rodwell
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
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Srivastava S. Minimum inhibitory concentration, pharmacokinetics/pharmacodynamics and therapeutic drug monitoring: An integrated approach for multidrug-resistant tuberculosis. Lung India 2015. [DOI: 10.4103/0970-2113.159600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Genetic determinants involved in p-aminosalicylic acid resistance in clinical isolates from tuberculosis patients in northern China from 2006 to 2012. Antimicrob Agents Chemother 2014; 59:1320-4. [PMID: 25421465 DOI: 10.1128/aac.03695-14] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
p-Aminosalicylic acid (PAS) is an important compound for treating multidrug-resistant tuberculosis (TB). Previous studies showed that thyA mutations are often related to PAS resistance in clinical isolates. We performed a systematic analysis of isolate genotypes and detected mutations in three folate pathway genes (folC, thyA, and ribD) in 61.1% (127/208) of PAS-resistant isolates, including 11 double mutants. This result expands our knowledge about the distribution and frequency of mutations related to PAS resistance in mycobacterial clinical isolates.
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Disparities in capreomycin resistance levels associated with the rrs A1401G mutation in clinical isolates of Mycobacterium tuberculosis. Antimicrob Agents Chemother 2014; 59:444-9. [PMID: 25385119 DOI: 10.1128/aac.04438-14] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
As the prevalence of multidrug-resistant and extensively drug-resistant tuberculosis strains continues to rise, so does the need to develop accurate and rapid molecular tests to complement time-consuming growth-based drug susceptibility testing. Performance of molecular methods relies on the association of specific mutations with phenotypic drug resistance and while considerable progress has been made for resistance detection of first-line antituberculosis drugs, rapid detection of resistance for second-line drugs lags behind. The rrs A1401G allele is considered a strong predictor of cross-resistance between the three second-line injectable drugs, capreomycin (CAP), kanamycin, and amikacin. However, discordance is often observed between the rrs A1401G mutation and CAP resistance, with up to 40% of rrs A1401G mutants being classified as CAP susceptible. We measured the MICs to CAP in 53 clinical isolates harboring the rrs A1401G mutation and found that the CAP MICs ranged from 8 μg/ml to 40 μg/ml. These results were drastically different from engineered A1401G mutants generated in isogenic Mycobacterium tuberculosis, which exclusively exhibited high-level CAP MICs of 40 μg/ml. These data support the results of prior studies, which suggest that the critical concentration of CAP (10 μg/ml) used to determine resistance by indirect agar proportion may be too high to detect all CAP-resistant strains and suggest that a larger percentage of resistant isolates could be identified by lowering the critical concentration. These data also suggest that differences in resistance levels among clinical isolates are possibly due to second site or compensatory mutations located elsewhere in the genome.
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74
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Little difference between minimum inhibitory concentrations of Mycobacterium tuberculosis wild-type organisms determined with BACTEC MGIT 960 and Middlebrook 7H10. Clin Microbiol Infect 2014; 21:148.e5-7. [PMID: 25640156 DOI: 10.1016/j.cmi.2014.08.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 08/18/2014] [Accepted: 08/20/2014] [Indexed: 11/20/2022]
Abstract
The MIC wild-type (WT) distribution for Mycobacterium tuberculosis in BACTEC 960 MGIT is not defined, which may result in poor reproducibility for drug susceptibility testing (DST), as several DST methods with different breakpoints are in use. In a comparison between MGIT and Middlebrook 7H10 medium of seven first- and second-line drugs, including 133 MIC determinations of 15 WT isolates, we found an agreement of 91.7% within ± one MIC dilution step. The results confirm the agreement in MIC testing between 7H10 and MGIT and indicate that breakpoints could be harmonized in order to avoid misclassification.
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75
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Resistance to rifampicin: a review. J Antibiot (Tokyo) 2014; 67:625-30. [PMID: 25118103 DOI: 10.1038/ja.2014.107] [Citation(s) in RCA: 217] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Revised: 06/28/2014] [Accepted: 07/04/2014] [Indexed: 11/08/2022]
Abstract
Resistance to rifampicin (RIF) is a broad subject covering not just the mechanism of clinical resistance, nearly always due to a genetic change in the β subunit of bacterial RNA polymerase (RNAP), but also how studies of resistant polymerases have helped us understand the structure of the enzyme, the intricacies of the transcription process and its role in complex physiological pathways. This review can only scratch the surface of these phenomena. The identification, in strains of Escherichia coli, of the positions within β of the mutations determining resistance is discussed in some detail, as are mutations in organisms that are therapeutic targets of RIF, in particular Mycobacterium tuberculosis. Interestingly, changes in the same three codons of the consensus sequence occur repeatedly in unrelated RIF-resistant (RIF(r)) clinical isolates of several different bacterial species, and a single mutation predominates in mycobacteria. The utilization of our knowledge of these mutations to develop rapid screening tests for detecting resistance is briefly discussed. Cross-resistance among rifamycins has been a topic of controversy; current thinking is that there is no difference in the susceptibility of RNAP mutants to RIF, rifapentine and rifabutin. Also summarized are intrinsic RIF resistance and other resistance mechanisms.
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76
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Köser CU, Ellington MJ, Peacock SJ. Whole-genome sequencing to control antimicrobial resistance. Trends Genet 2014; 30:401-7. [PMID: 25096945 PMCID: PMC4156311 DOI: 10.1016/j.tig.2014.07.003] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 07/10/2014] [Accepted: 07/14/2014] [Indexed: 11/18/2022]
Abstract
Following recent improvements in sequencing technologies, whole-genome sequencing (WGS) is positioned to become an essential tool in the control of antibiotic resistance, a major threat in modern healthcare. WGS has already found numerous applications in this area, ranging from the development of novel antibiotics and diagnostic tests through to antibiotic stewardship of currently available drugs via surveillance and the elucidation of the factors that allow the emergence and persistence of resistance. Numerous proof-of-principle studies have also highlighted the value of WGS as a tool for day-to-day infection control and, for some pathogens, as a primary diagnostic tool to detect antibiotic resistance. However, appropriate data analysis platforms will need to be developed before routine WGS can be introduced on a large scale.
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Affiliation(s)
- Claudio U Köser
- Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Matthew J Ellington
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, UK; Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK; Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
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77
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Prevalence of Extensively Drug Resistant Tuberculosis among Archived Multidrug Resistant Tuberculosis Isolates in Zimbabwe. Tuberc Res Treat 2014; 2014:349141. [PMID: 24967101 PMCID: PMC4054961 DOI: 10.1155/2014/349141] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Revised: 04/27/2014] [Accepted: 04/28/2014] [Indexed: 11/17/2022] Open
Abstract
We conducted a cross-sectional study of second line drug resistance patterns and genetic diversity of MDR-TB isolates archived at the BRTI-TB Laboratory, Harare, between January 2007 and December 2011. DSTs were performed for second line antituberculosis drugs. XDR-TB strains were defined as MDR-TB strains with resistance to either kanamycin and ofloxacin or capreomycin and ofloxacin. Strain types were identified by spoligotyping. No resistance to any second line drugs was shown in 73% of the isolates, with 23% resistant to one or two drugs but not meeting the definition of XDR-TB. A total of 26 shared types were identified, and 18 (69%) matched preexisting shared types in the current published spoligotype databases. Of the 11 out of 18 clustered SITs, 4 predominant (>6 isolates per shared type) were identified. The most and least abundant types were SIT 1468 (LAM 11-ZWE) with 12 (18%) isolates and SIT 53 (T1) with 6 (9%) isolates, respectively. XDR-TB strains are rare in Zimbabwe, but the high proportion of “pre-XDR-TB” strains and treatment failure cases is of concern. The genetic diversity of the MDR-TB strains showed no significant association between SITs and drug resistance.
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Rodwell TC, Valafar F, Douglas J, Qian L, Garfein RS, Chawla A, Torres J, Zadorozhny V, Kim MS, Hoshide M, Catanzaro D, Jackson L, Lin G, Desmond E, Rodrigues C, Eisenach K, Victor TC, Ismail N, Crudu V, Gler MT, Catanzaro A. Predicting extensively drug-resistant Mycobacterium tuberculosis phenotypes with genetic mutations. J Clin Microbiol 2014; 52:781-9. [PMID: 24353002 PMCID: PMC3957771 DOI: 10.1128/jcm.02701-13] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 12/12/2013] [Indexed: 01/20/2023] Open
Abstract
Molecular diagnostic methods based on the detection of mutations conferring drug resistance are promising technologies for rapidly detecting multidrug-/extensively drug-resistant tuberculosis (M/XDR TB), but large studies of mutations as markers of resistance are rare. The Global Consortium for Drug-Resistant TB Diagnostics analyzed 417 Mycobacterium tuberculosis isolates from multinational sites with a high prevalence of drug resistance to determine the sensitivities and specificities of mutations associated with M/XDR TB to inform the development of rapid diagnostic methods. We collected M/XDR TB isolates from regions of high TB burden in India, Moldova, the Philippines, and South Africa. The isolates underwent standardized phenotypic drug susceptibility testing (DST) to isoniazid (INH), rifampin (RIF), moxifloxacin (MOX), ofloxacin (OFX), amikacin (AMK), kanamycin (KAN), and capreomycin (CAP) using MGIT 960 and WHO-recommended critical concentrations. Eight genes (katG, inhA, rpoB, gyrA, gyrB, rrs, eis, and tlyA) were sequenced using Sanger sequencing. Three hundred seventy isolates were INHr, 356 were RIFr, 292 were MOXr/OFXr, 230 were AMKr, 219 were CAPr, and 286 were KANr. Four single nucleotide polymorphisms (SNPs) in katG/inhA had a combined sensitivity of 96% and specificities of 97 to 100% for the detection of INHr. Eleven SNPs in rpoB had a combined sensitivity of 98% for RIFr. Eight SNPs in gyrA codons 88 to 94 had sensitivities of 90% for MOXr/OFXr. The rrs 1401/1484 SNPs had 89 to 90% sensitivity for detecting AMKr/CAPr but 71% sensitivity for KANr. Adding eis promoter SNPs increased the sensitivity to 93% for detecting AMKr and to 91% for detecting KANr. Approximately 30 SNPs in six genes predicted clinically relevant XDR-TB phenotypes with 90 to 98% sensitivity and almost 100% specificity.
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Affiliation(s)
- Timothy C. Rodwell
- Department of Medicine, University of California San Diego, San Diego, California, USA
| | - Faramarz Valafar
- Department of Bioinformatics and Medical Informatics, San Diego State University, San Diego, California, USA
| | - James Douglas
- Department of Microbiology, University of Hawaii Manoa, Honolulu, Hawaii, USA
| | - Lishi Qian
- Department of Microbiology, University of Hawaii Manoa, Honolulu, Hawaii, USA
| | - Richard S. Garfein
- Department of Medicine, University of California San Diego, San Diego, California, USA
| | - Ashu Chawla
- Department of Bioinformatics and Medical Informatics, San Diego State University, San Diego, California, USA
| | - Jessica Torres
- Department of Bioinformatics and Medical Informatics, San Diego State University, San Diego, California, USA
| | - Victoria Zadorozhny
- Department of Bioinformatics and Medical Informatics, San Diego State University, San Diego, California, USA
| | - Min Soo Kim
- Department of Bioinformatics and Medical Informatics, San Diego State University, San Diego, California, USA
| | - Matt Hoshide
- Department of Microbiology, University of Hawaii Manoa, Honolulu, Hawaii, USA
| | - Donald Catanzaro
- Department of Bioinformatics and Medical Informatics, San Diego State University, San Diego, California, USA
| | - Lynn Jackson
- Department of Medicine, University of California San Diego, San Diego, California, USA
| | - Grace Lin
- California Department of Public Health, Microbial Diseases Laboratory, Richmond, California, USA
| | - Edward Desmond
- California Department of Public Health, Microbial Diseases Laboratory, Richmond, California, USA
| | | | - Kathy Eisenach
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Thomas C. Victor
- Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa
| | - Nazir Ismail
- National Tuberculosis Reference Laboratory, Johannesburg, South Africa
| | - Valeru Crudu
- Microbiology and Morphology Laboratory, Institute of Phthisiopneumology, Chisinau, Moldova
| | | | - Antonino Catanzaro
- Department of Medicine, University of California San Diego, San Diego, California, USA
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Garcia-Prats AJ, Rose PC, Hesseling AC, Schaaf HS. Linezolid for the treatment of drug-resistant tuberculosis in children: A review and recommendations. Tuberculosis (Edinb) 2014; 94:93-104. [DOI: 10.1016/j.tube.2013.10.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 10/11/2013] [Accepted: 10/20/2013] [Indexed: 11/30/2022]
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Sensititre MYCOTB MIC plate for testing Mycobacterium tuberculosis susceptibility to first- and second-line drugs. Antimicrob Agents Chemother 2013; 58:11-8. [PMID: 24100497 DOI: 10.1128/aac.01209-13] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
For Mycobacterium tuberculosis, phenotypic methods for drug susceptibility testing of second-line drugs are poorly standardized and technically challenging. The Sensititre MYCOTB MIC plate (MYCOTB) is a microtiter plate containing lyophilized antibiotics and configured for determination of MICs to first- and second-line antituberculosis drugs. To evaluate the performance of MYCOTB for M. tuberculosis drug susceptibility testing using the Middlebrook 7H10 agar proportion method (APM) as the comparator, we conducted a two-site study using archived M. tuberculosis isolates from Uganda and the Republic of Korea. Thawed isolates were subcultured, and dilutions were inoculated into MYCOTB wells and onto 7H10 agar. MYCOTB results were read at days 7, 10, 14, and 21; APM results were read at 21 days. A total of 222 isolates provided results on both platforms. By APM, 106/222 (47.7%) of isolates were resistant to at least isoniazid and rifampin. Agreement between MYCOTB and APM with respect to susceptibility or resistance was ≥92% for 7 of 12 drugs when a strict definition was used and ≥96% for 10 of 12 drugs when agreement was defined by allowing a ± one-well range of dilutions around the APM critical concentration. For ethambutol, agreement was 80% to 81%. For moxifloxacin, agreement was 83% to 85%; incorporating existing DNA sequencing information for discrepant analysis raised agreement to 91% to 96%. For MYCOTB, the median time to plate interpretation was 10 days and interreader agreement was ≥95% for all drugs. MYCOTB provided reliable results for M. tuberculosis susceptibility testing of first- and second-line drugs except ethambutol, and results were available sooner than those determined by APM.
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Wells WA, Boehme CC, Cobelens FG, Daniels C, Dowdy D, Gardiner E, Gheuens J, Kim P, Kimerling ME, Kreiswirth B, Lienhardt C, Mdluli K, Pai M, Perkins MD, Peter T, Zignol M, Zumla A, Schito M. Alignment of new tuberculosis drug regimens and drug susceptibility testing: a framework for action. THE LANCET. INFECTIOUS DISEASES 2013; 13:449-58. [PMID: 23531393 PMCID: PMC4012744 DOI: 10.1016/s1473-3099(13)70025-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
New tuberculosis drug regimens are creating new priorities for drug susceptibility testing (DST) and surveillance. To minimise turnaround time, rapid DST will need to be prioritised, but developers of these assays will need better data about the molecular mechanisms of resistance. Efforts are underway to link mutations with drug resistance and to develop strain collections to enable assessment of new diagnostic assays. In resource-limited settings, DST might not be appropriate for all patients with tuberculosis. Surveillance data and modelling will help country stakeholders to design appropriate DST algorithms and to decide whether to change drug regimens. Finally, development of practical DST assays is needed so that, in countries where surveillance and modelling show that DST is advisable, these assays can be used to guide clinical decisions for individual patients. If combined judiciously during both development and implementation, new tuberculosis regimens and new DST assays have enormous potential to improve patient outcomes and reduce the burden of disease.
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Affiliation(s)
| | | | - Frank G.J. Cobelens
- Department of Global Health, Academic Medical Center; and Amsterdam Institute of Global Health and Development, Amsterdam, The Netherlands
| | | | - David Dowdy
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Jan Gheuens
- Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Peter Kim
- National Institutes of Allergy and Infectious Disease, Bethesda, MD, USA
| | | | - Barry Kreiswirth
- University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
| | | | - Khisi Mdluli
- Global Alliance for TB Drug Development, New York, NY, USA
| | - Madhukar Pai
- Department of Epidemiology and Biostatistics, McGill University, Montreal, Canada
| | - Mark D. Perkins
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - Trevor Peter
- Clinton Health Access Initiative, Boston, MA, USA
| | - Matteo Zignol
- Stop TB Department, World Health Organization, Geneva, Switzerland
| | | | - Marco Schito
- HJF-DAIDS, a Division of The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Contractor to NIAID, NIH, DHHS, Bethesda, MD, USA
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Sirgel FA, Warren RM, Böttger EC, Klopper M, Victor TC, van Helden PD. The rationale for using rifabutin in the treatment of MDR and XDR tuberculosis outbreaks. PLoS One 2013; 8:e59414. [PMID: 23527189 PMCID: PMC3602005 DOI: 10.1371/journal.pone.0059414] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 02/14/2013] [Indexed: 11/18/2022] Open
Abstract
Genetically related Mycobacterium tuberculosis strains with alterations at codon 516 in the rpoB gene were observed amongst a substantial number of patients with drug resistant tuberculosis in the Eastern Cape Province (ECP) of South Africa. Mutations at codon 516 are usually associated with lower level rifampicin (RIF) resistance, while susceptibility to rifabutin (RFB) remains intact. This study was conducted to assess the rationale for using RFB as a substitution for RIF in the treatment of MDR and XDR tuberculosis outbreaks. Minimum inhibitory concentrations (MICs) of 34 drug resistant clinical isolates of M tuberculosis were determined by MGIT 960 and correlated with rpoB mutations. RFB MICs ranged from 0.125 to 0.25 µg/ml in the 34 test isolates thereby confirming phenotypic susceptibility as per critical concentration (CC) of 0.5 µg/ml. The corresponding RIF MICs ranged between 5 and 15 µg/ml, which is well above the CC of 1.0 µg/ml. Molecular-based drug susceptibility testing provides important pharmacogenetic insight by demonstrating a direct correlation between defined rpoB mutation and the level of RFB susceptibility. We suggest that isolates with marginally reduced susceptibility as compared to the epidemiological cut-off for wild-type strains (0.064 µg/ml), but lower than the current CC (≤0.5 µg/ml), are categorised as intermediate. Two breakpoints (0.064 µg/ml and 0.5 µg/ml) are recommended to distinguish between susceptible, intermediate and RFB resistant strains. This concept may assist clinicians and policy makers to make objective therapeutic decisions, especially in situations where therapeutic options are limited. The use of RFB in the ECP may improve therapeutic success and consequently minimise the risk of ongoing transmission of drug resistant M. tuberculosis strains.
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Affiliation(s)
- Frederick A Sirgel
- DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Faculty of Health Science, Stellenbosch University, Stellenbosch, South Africa.
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83
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Minion J, Gallant V, Wolfe J, Jamieson F, Long R. Multidrug and extensively drug-resistant tuberculosis in Canada 1997-2008: demographic and disease characteristics. PLoS One 2013; 8:e53466. [PMID: 23326436 PMCID: PMC3541271 DOI: 10.1371/journal.pone.0053466] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 11/30/2012] [Indexed: 11/18/2022] Open
Abstract
Setting Nationwide Canadian public health surveillance. Objective Description of demographic features and disease characteristics of drug-resistant tuberculosis (TB) in Canada over a 12 year period. Design Continuous surveillance of all cases of culture-confirmed TB in Canada. Demographic and microbiologic features were analyzed and comparisons between drug-susceptible, multidrug-resistant (MDR), and drug-resistant not-MDR were made. Cases of extensively drug resistant TB are described. Results 15,993 cases of culture-confirmed TB were reported during the study period. There were 5 cases of XDR-TB, 177 cases of MDR-TB, and 1,234 cases of first-line drug resistance not-MDR. The majority of drug-resistant cases were reported in foreign-born individuals, with drug-resistant cases diagnosed earlier post-arrival in Canada compared to drug-susceptible cases. In MDR-TB isolates, there was a high rate of drug-resistance to other first- and second-line drugs, making reliable empiric therapeutic recommendations for MDR-TB difficult. There was a statistically significant association between both MDR and drug-resistance not-MDR, and the risk of a negative treatment outcome (defined as treatment failure, absconded, or treatment ongoing >3 yrs). Conclusion Drug-resistance complicates TB management even in developed nations with well-established TB control programs. The predominantly international origin of drug-resistant cases highlights the need for global strategies to combat TB.
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Affiliation(s)
- Jessica Minion
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Canada
| | - Victor Gallant
- HIV/AIDS and TB Core Surveillance, Public Health Agency of Canada, Ottawa, Canada
| | - Joyce Wolfe
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Winnipeg, Canada
| | - Frances Jamieson
- Public Health Laboratories, Public Health Ontario, (representing the Canadian Public Health Laboratory Networks), Toronto, Canada
| | - Richard Long
- Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, Canada
- * E-mail:
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Importance of the genetic diversity within the Mycobacterium tuberculosis complex for the development of novel antibiotics and diagnostic tests of drug resistance. Antimicrob Agents Chemother 2012; 56:6080-7. [PMID: 23006760 DOI: 10.1128/aac.01641-12] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite being genetically monomorphic, the limited genetic diversity within the Mycobacterium tuberculosis complex (MTBC) has practical consequences for molecular methods for drug susceptibility testing and for the use of current antibiotics and those in clinical trials. It renders some representatives of MTBC intrinsically resistant against one or multiple antibiotics and affects the spectrum and consequences of resistance mutations selected for during treatment. Moreover, neutral or silent changes within genes responsible for drug resistance can cause false-positive results with hybridization-based assays, which have been recently introduced to replace slower phenotypic methods. We discuss the consequences of these findings and propose concrete steps to rigorously assess the genetic diversity of MTBC to support ongoing clinical trials.
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