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Aitken JM, Aitken JE, Agrawal G. Mycobacterium avium ssp. paratuberculosis and Crohn's Disease-Diagnostic Microbiological Investigations Can Inform New Therapeutic Approaches. Antibiotics (Basel) 2024; 13:158. [PMID: 38391544 PMCID: PMC10886072 DOI: 10.3390/antibiotics13020158] [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: 12/04/2023] [Revised: 01/24/2024] [Accepted: 02/03/2024] [Indexed: 02/24/2024] Open
Abstract
Mycobacterium avium ssp. paratuberculosis (MAP) is the cause of Johne's disease (JD), which is a chronic infectious gastrointestinal disease of ruminants and is often fatal. In humans, MAP has been associated with Crohn's disease (CD) for over a century, without conclusive evidence of pathogenicity. Numerous researchers have contributed to the subject, but there is still a need for evidence of the causation of CD by MAP. An infectious aetiology in CD that is attributable to MAP can only be proven by bacteriological investigations. There is an urgency in resolving this question due to the rising global incidence rates of CD. Recent papers have indicated the "therapeutic ceiling" may be close in the development of new biologics. Clinical trial outcomes have demonstrated mild or inconsistent improvements in therapeutic interventions over the last decades when compared with placebo. The necessity to revisit therapeutic options for CD is becoming more urgent and a renewed focus on causation is essential for progress in identifying new treatment options. This manuscript discusses newer interventions, such as vaccination, FMT, dietary remediation and gut microbiome regulation, that will become more relevant as existing therapeutic options expire. Revisiting the MAP theory as a potential infectious cause of CD, rather than the prevailing concept of an "aberrant immune response" will require expanding the current therapeutic programme to include potential new alternatives, and combinations of existing treatments. To advance research on MAP in humans, it is essential for microbiologists and medical scientists to microscopically detect CWDM and to biologically amplify the growth by directed culture.
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Affiliation(s)
- John M Aitken
- Otakaro Pathways Ltd., Innovation Park, Christchurch 7675, New Zealand
| | - Jack E Aitken
- Otakaro Pathways Ltd., Innovation Park, Christchurch 7675, New Zealand
| | - Gaurav Agrawal
- Division of Diabetes & Nutritional Sciences, Franklin-Wilkins Building, King's College London, London SE1 9NH, UK
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Omar S, Whitfield MG, Nolan MB, Ngom JT, Ismail N, Warren RM, Klopper M. Bedaquiline for treatment of non-tuberculous mycobacteria (NTM): a systematic review and meta-analysis. J Antimicrob Chemother 2024; 79:211-240. [PMID: 38134888 PMCID: PMC10832598 DOI: 10.1093/jac/dkad372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND Non-tuberculous mycobacteria (NTM) infections are increasing in incidence and associated mortality. NTM are naturally resistant to a variety of antibiotics, complicating treatment. We conducted a literature assessment on the efficacy of bedaquiline in treating NTM species in vitro and in vivo (animal models and humans); meta-analyses were performed where possible. METHOD Four databases were searched using specific terms. Publications were included according to predefined criteria. Bedaquiline's impact on NTM in vitro, MICs and epidemiological cut-off (ECOFF) values were evaluated. A meta-analysis of bedaquiline efficacy against NTM infections in animal models was performed. Culture conversion, cure and/or relapse-free cure were used to evaluate the efficacy of bedaquiline in treating NTM infection in humans. RESULTS Fifty studies met the inclusion criteria: 33 assessed bedaquiline's impact on NTM in vitro, 9 in animal models and 8 in humans. Three studies assessed bedaquiline's efficacy both in vitro and in vivo. Due to data paucity, an ECOFF value of 0.5 mg/mL was estimated for Mycobacterium abscessus only. Meta-analysis of animal studies showed a 1.86× reduction in bacterial load in bedaquiline-treated versus no treatment within 30 days. In humans, bedaquiline-including regimens were effective in treating NTM extrapulmonary infection but not pulmonary infection. CONCLUSIONS Bedaquiline demonstrated strong antibacterial activity against various NTM species and is a promising drug to treat NTM infections. However, data on the genomic mutations associated with bedaquiline resistance were scarce, preventing statistical analyses for most mutations and NTM species. Further studies are urgently needed to better inform treatment strategies.
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Affiliation(s)
- Shatha Omar
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council (SAMRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Michael G Whitfield
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, National Institute for Health Research, Imperial College London, London, UK
| | - Margaret B Nolan
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council (SAMRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Justice T Ngom
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council (SAMRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Nabila Ismail
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council (SAMRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Rob M Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council (SAMRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Marisa Klopper
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council (SAMRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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Chang YS, Li SY, Pertinez H, Betoudji F, Lee J, Rannard SP, Owen A, Nuermberger EL, Ammerman NC. Using Dynamic Oral Dosing of Rifapentine and Rifabutin to Simulate Exposure Profiles of Long-Acting Formulations in a Mouse Model of Tuberculosis Preventive Therapy. Antimicrob Agents Chemother 2023; 67:e0048123. [PMID: 37338374 PMCID: PMC10353356 DOI: 10.1128/aac.00481-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/18/2023] [Indexed: 06/21/2023] Open
Abstract
Administration of tuberculosis preventive therapy (TPT) to individuals with latent tuberculosis infection is an important facet of global tuberculosis control. The use of long-acting injectable (LAI) drug formulations may simplify and shorten regimens for this indication. Rifapentine and rifabutin have antituberculosis activity and physiochemical properties suitable for LAI formulation, but there are limited data available for determining the target exposure profiles required for efficacy in TPT regimens. The objective of this study was to determine exposure-activity profiles of rifapentine and rifabutin to inform development of LAI formulations for TPT. We used a validated paucibacillary mouse model of TPT in combination with dynamic oral dosing of both drugs to simulate and understand exposure-activity relationships to inform posology for future LAI formulations. This work identified several LAI-like exposure profiles of rifapentine and rifabutin that, if achieved by LAI formulations, could be efficacious as TPT regimens and thus can serve as experimentally determined targets for novel LAI formulations of these drugs. We present novel methodology to understand the exposure-response relationship and inform the value proposition for investment in development of LAI formulations that have utility beyond latent tuberculosis infection.
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Affiliation(s)
- Yong S. Chang
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Si-Yang Li
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Henry Pertinez
- Centre of Excellence in Long-Acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool, United Kingdom
| | - Fabrice Betoudji
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jin Lee
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Steven P. Rannard
- Centre of Excellence in Long-Acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool, United Kingdom
| | - Andrew Owen
- Centre of Excellence in Long-Acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool, United Kingdom
| | - Eric L. Nuermberger
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Nicole C. Ammerman
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Medical Microbiology and Infectious Diseases, University Medical Center Rotterdam, Erasmus MC, Rotterdam, The Netherlands
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4
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Beraldi-Magalhaes F, Parker SL, Sanches C, Garcia LS, Souza Carvalho BK, Costa AA, Fachi MM, de Liz MV, de Souza AB, Safe IP, Pontarolo R, Wallis S, Lipman J, Roberts JA, Cordeiro-Santos M. Is the Pharmacokinetics of First-Line Anti-TB Drugs a Cause of High Mortality Rates in TB Patients Admitted to the ICU? A Non-Compartmental Pharmacokinetic Analysis. Trop Med Infect Dis 2023; 8:312. [PMID: 37368730 DOI: 10.3390/tropicalmed8060312] [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: 02/24/2023] [Revised: 05/28/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Patients with tuberculosis (TB) may develop multi-organ failure and require admission to intensive care. In these cases, the mortality rates are as high as 78% and may be caused by suboptimal serum concentrations of first-line TB drugs. This study aims to compare the pharmacokinetics of oral rifampin, isoniazid, pyrazinamide and ethambutol patients in intensive care units (ICU) to outpatients and to evaluate drug serum concentrations as a potential cause of mortality. METHODS A prospective pharmacokinetic (PK) study was performed in Amazonas State, Brazil. The primary PK parameters of outpatients who achieved clinical and microbiological cure were used as a comparative target in a non-compartmental analysis. RESULTS Thirteen ICU and twenty outpatients were recruited. The clearance and volume of distribution were lower for rifampin, isoniazid, pyrazinamide and ethambutol. ICU thirty-day mortality was 77% versus a cure rate of 89% in outpatients. CONCLUSIONS ICU patients had a lower clearance and volume of distribution for rifampin, isoniazid, pyrazinamide and ethambutol compared to the outpatient group. These may reflect changes to organ function, impeded absorption and distribution to the site of infection in ICU patients and have the potential to impact clinical outcomes.
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Affiliation(s)
- Francisco Beraldi-Magalhaes
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus 69040-000, Brazil
- Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus 69040-000, Brazil
- Secretaria de Estado da Saúde do Paraná, Curitiba 80010-130, Brazil
- School of Medicine, Faculdades Pequeno Príncipe, Curitiba 80230-020, Brazil
| | - Suzanne L Parker
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4029, Australia
| | - Cristina Sanches
- Department of Pharmacy, Campus Centro-Oeste Dona Lindu, Universidade Federal de São João del-Rei, Divinopolis 35501-296, Brazil
| | - Leandro Sousa Garcia
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus 69040-000, Brazil
- Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus 69040-000, Brazil
| | - Brenda Karoline Souza Carvalho
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus 69040-000, Brazil
- Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus 69040-000, Brazil
| | - Amanda Araujo Costa
- Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus 69040-000, Brazil
| | - Mariana Millan Fachi
- Department of Pharmacy, Campus Jardim Botânico, Universidade Federal do Paraná, Curitiba 80210-170, Brazil
| | - Marcus Vinicius de Liz
- Department of Chemistry & Biology, Campus Curitiba, Universidade Tecnológica Federal do Paraná, Curitiba 81280-340, Brazil
| | - Alexandra Brito de Souza
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus 69040-000, Brazil
- Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus 69040-000, Brazil
| | - Izabella Picinin Safe
- Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus 69040-000, Brazil
| | - Roberto Pontarolo
- Department of Pharmacy, Campus Jardim Botânico, Universidade Federal do Paraná, Curitiba 80210-170, Brazil
| | - Steven Wallis
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4029, Australia
| | - Jeffrey Lipman
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4029, Australia
- Department of Intensive Care Medicine, Royal Brisbane and Women's Hospital, Brisbane, QLD 4029, Australia
- Division of Anaesthesiology Critical Care Emergency and Pain Medicine, Nîmes University Hospital, University of Montpellier, 30900 Nimes, France
| | - Jason A Roberts
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4029, Australia
- Department of Intensive Care Medicine, Royal Brisbane and Women's Hospital, Brisbane, QLD 4029, Australia
- Division of Anaesthesiology Critical Care Emergency and Pain Medicine, Nîmes University Hospital, University of Montpellier, 30900 Nimes, France
- Department of Pharmacy, Royal Brisbane and Women's Hospital, Brisbane, QLD 4029, Australia
| | - Marcelo Cordeiro-Santos
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus 69040-000, Brazil
- Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus 69040-000, Brazil
- School of Medicine, Universidade Nilton Lins, Manaus 69058-040, Brazil
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Chaiyachat P, Kaewseekhao B, Chaiprasert A, Kamolwat P, Nonghanphithak D, Phetcharaburanin J, Sirichoat A, Ong RTH, Faksri K. Metabolomic analysis of Mycobacterium tuberculosis reveals metabolic profiles for identification of drug-resistant tuberculosis. Sci Rep 2023; 13:8655. [PMID: 37244948 DOI: 10.1038/s41598-023-35882-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 05/25/2023] [Indexed: 05/29/2023] Open
Abstract
The detection of pre-extensively (pre-XDR) and extensively drug-resistant tuberculosis (XDR-TB) is challenging. Drug-susceptibility tests for some anti-TB drugs, especially ethambutol (ETH) and ethionamide (ETO), are problematic due to overlapping thresholds to differentiate between susceptible and resistant phenotypes. We aimed to identify possible metabolomic markers to detect Mycobacterium tuberculosis (Mtb) strains causing pre-XDR and XDR-TB. The metabolic patterns of ETH- and ETO-resistant Mtb isolates were also investigated. Metabolomics of 150 Mtb isolates (54 pre-XDR, 63 XDR-TB and 33 pan-susceptible; pan-S) were investigated. Metabolomics of ETH and ETO phenotypically resistant subgroups were analyzed using UHPLC-ESI-QTOF-MS/MS. Orthogonal partial least-squares discriminant analysis revealed distinct separation in all pairwise comparisons among groups. Two metabolites (meso-hydroxyheme and itaconic anhydride) were able to differentiate the pre-XDR and XDR-TB groups from the pan-S group with 100% sensitivity and 100% specificity. In comparisons of the ETH and ETO phenotypically resistant subsets, sets of increased (ETH = 15, ETO = 7) and decreased (ETH = 1, ETO = 6) metabolites specific for the resistance phenotype of each drug were found. We demonstrated the potential for metabolomics of Mtb to differentiate among types of DR-TB as well as between isolates that were phenotypically resistant to ETO and ETH. Thus, metabolomics might be further applied for DR-TB diagnosis and patient management.
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Affiliation(s)
- Pratchakan Chaiyachat
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Benjawan Kaewseekhao
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Angkana Chaiprasert
- Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Phalin Kamolwat
- Bureau of Tuberculosis, Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Ditthawat Nonghanphithak
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Jutarop Phetcharaburanin
- Department of Systems Biosciences and Computational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Auttawit Sirichoat
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand.
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Chang YS, Li SY, Pertinez H, Betoudji F, Lee J, Rannard SP, Owen A, Nuermberger EL, Ammerman NC. Using dynamic oral dosing of rifapentine and rifabutin to simulate exposure profiles of long-acting formulations in a mouse model of tuberculosis preventive therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.12.536604. [PMID: 37090528 PMCID: PMC10120629 DOI: 10.1101/2023.04.12.536604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Administration of tuberculosis preventive therapy (TPT) to individuals with latent tuberculosis infection is an important facet of global tuberculosis control. The use of long-acting injectable (LAI) drug formulations may simplify and shorten regimens for this indication. Rifapentine and rifabutin have anti-tuberculosis activity and physiochemical properties suitable for LAI formulation, but there are limited data available for determining the target exposure profiles required for efficacy in TPT regimens. The objective of this study was to determine exposure-activity profiles of rifapentine and rifabutin to inform development of LAI formulations for TPT. We utilized a validated paucibacillary mouse model of TPT in combination with dynamic oral dosing of both drugs to simulate and understand exposure-activity relationships to inform posology for future LAI formulations. This work identified several LAI-like exposure profiles of rifapentine and rifabutin that, if achieved by LAI formulations, could be efficacious as TPT regimens and thus can serve as experimentally-determined targets for novel LAI formulations of these drugs. We present novel methodology to understand the exposure-response relationship and inform the value proposition for investment in development of LAI formulations that has utility beyond latent tuberculosis infection.
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Affiliation(s)
- Yong S. Chang
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Touro College of Osteopathic Medicine-Middletown, Middletown, New York, USA (current address)
| | - Si-Yang Li
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Henry Pertinez
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK
| | - Fabrice Betoudji
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Veterinary Medicine Division, USAMRIID, Fort Detrick, Frederick, Maryland, USA (current address)
| | - Jin Lee
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Steven P. Rannard
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK
| | - Andrew Owen
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK
| | - Eric L. Nuermberger
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Nicole C. Ammerman
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Medical Microbiology and Infectious Diseases, University Medical Center Rotterdam, Erasmus MC, Rotterdam, The Netherlands
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7
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Finci I, Albertini A, Merker M, Andres S, Bablishvili N, Barilar I, Cáceres T, Crudu V, Gotuzzo E, Hapeela N, Hoffmann H, Hoogland C, Kohl TA, Kranzer K, Mantsoki A, Maurer FP, Nicol MP, Noroc E, Plesnik S, Rodwell T, Ruhwald M, Savidge T, Salfinger M, Streicher E, Tukvadze N, Warren R, Zemanay W, Zurek A, Niemann S, Denkinger CM. Investigating resistance in clinical Mycobacterium tuberculosis complex isolates with genomic and phenotypic antimicrobial susceptibility testing: a multicentre observational study. THE LANCET. MICROBE 2022; 3:e672-e682. [PMID: 35907429 PMCID: PMC9436784 DOI: 10.1016/s2666-5247(22)00116-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/10/2022] [Accepted: 04/14/2022] [Indexed: 01/01/2023]
Abstract
BACKGROUND Whole-genome sequencing (WGS) of Mycobacterium tuberculosis complex has become an important tool in diagnosis and management of drug-resistant tuberculosis. However, data correlating resistance genotype with quantitative phenotypic antimicrobial susceptibility testing (AST) are scarce. METHODS In a prospective multicentre observational study, 900 clinical M tuberculosis complex isolates were collected from adults with drug-resistant tuberculosis in five high-endemic tuberculosis settings around the world (Georgia, Moldova, Peru, South Africa, and Viet Nam) between Dec 5, 2014, and Dec 12, 2017. Minimum inhibitory concentrations (MICs) and resulting binary phenotypic AST results for up to nine antituberculosis drugs were determined and correlated with resistance-conferring mutations identified by WGS. FINDINGS Considering WHO-endorsed critical concentrations as reference, WGS had high accuracy for prediction of resistance to isoniazid (sensitivity 98·8% [95% CI 98·5-99·0]; specificity 96·6% [95% CI 95·2-97·9]), levofloxacin (sensitivity 94·8% [93·3-97·6]; specificity 97·1% [96·7-97·6]), kanamycin (sensitivity 96·1% [95·4-96·8]; specificity 95·0% [94·4-95·7]), amikacin (sensitivity 97·2% [96·4-98·1]; specificity 98·6% [98·3-98·9]), and capreomycin (sensitivity 93·1% [90·0-96·3]; specificity 98·3% [98·0-98·7]). For rifampicin, pyrazinamide, and ethambutol, the specificity of resistance prediction was suboptimal (64·0% [61·0-67·1], 83·8% [81·0-86·5], and 40·1% [37·4-42·9], respectively). Specificity for rifampicin increased to 83·9% when borderline mutations with MICs overlapping with the critical concentration were excluded. Consequently, we highlighted mutations in M tuberculosis complex isolates that are often falsely identified as susceptible by phenotypic AST, and we identified potential novel resistance-conferring mutations. INTERPRETATION The combined analysis of mutations and quantitative phenotypes shows the potential of WGS to produce a refined interpretation of resistance, which is needed for individualised therapy, and eventually could allow differential drug dosing. However, variability of MIC data for some M tuberculosis complex isolates carrying identical mutations also reveals limitations of our understanding of the genotype and phenotype relationships (eg, including epistasis and strain genetic background). FUNDING Bill & Melinda Gates Foundation, German Centre for Infection Research, German Research Foundation, Excellence Cluster Precision Medicine of Inflammation (EXC 2167), and Leibniz ScienceCampus EvoLUNG.
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Affiliation(s)
- Iris Finci
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | | | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; Evolution of the Resistome, Research Center Borstel, Borstel, Germany; National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Hamburg-Borstel-Lübeck-Riems, Germany
| | - Sönke Andres
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Nino Bablishvili
- National Center for Tuberculosis and Lung Diseases, Tbilisi, Georgia
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Hamburg-Borstel-Lübeck-Riems, Germany
| | - Tatiana Cáceres
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Valeriu Crudu
- Phthisiopneumology Institute Chiril Draganiuc, Chisinau, Moldova
| | - Eduardo Gotuzzo
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Nchimunya Hapeela
- Division of Medical Microbiology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Harald Hoffmann
- SYNLAB Gauting, SYNLAB MVZ Dachau, Gauting, Germany; Institute of Microbiology and Laboratory Medicine (IML Red), WHO Supranational TB Reference Laboratory, Gauting, Germany
| | | | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Hamburg-Borstel-Lübeck-Riems, Germany
| | - Katharina Kranzer
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK; Biomedical Research and Training Institute, Harare, Zimbabwe
| | | | - Florian P Maurer
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mark P Nicol
- Division of Medical Microbiology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
| | - Ecaterina Noroc
- Phthisiopneumology Institute Chiril Draganiuc, Chisinau, Moldova
| | - Sara Plesnik
- Institute of Microbiology and Laboratory Medicine (IML Red), WHO Supranational TB Reference Laboratory, Gauting, Germany
| | - Timothy Rodwell
- FIND, Geneva, Switzerland; Division of Pulmonary, Critical Care and Sleep Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Theresa Savidge
- Advanced Diagnostic Laboratories, National Jewish Health, Denver, CO, USA; Alaska State Public Health Laboratories, Anchorage, AK, USA
| | - Max Salfinger
- College of Public Health, University of South Florida, Tampa, FL, USA; Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Elizabeth Streicher
- DSI-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 Sciences, Stellenbosch University, Cape Town, South Africa
| | - Nestani Tukvadze
- National Center for Tuberculosis and Lung Diseases, Tbilisi, Georgia
| | - Robin Warren
- DSI-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 Sciences, Stellenbosch University, Cape Town, South Africa
| | - Widaad Zemanay
- Division of Medical Microbiology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Anna Zurek
- Advanced Diagnostic Laboratories, National Jewish Health, Denver, CO, USA
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Hamburg-Borstel-Lübeck-Riems, Germany
| | - Claudia M Denkinger
- FIND, Geneva, Switzerland; German Center for Infection Research, Heidelberg, Germany; Division of Clinical Tropical Medicine and German Centre for Infection Research, Heidelberg University Hospital, Heidelberg, Germany.
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8
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A long-acting formulation of rifabutin is effective for prevention and treatment of Mycobacterium tuberculosis. Nat Commun 2022; 13:4455. [PMID: 35941109 PMCID: PMC9360445 DOI: 10.1038/s41467-022-32043-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/14/2022] [Indexed: 11/08/2022] Open
Abstract
Tuberculosis (TB) is a communicable disease caused by Mycobacterium tuberculosis (Mtb) and is a major cause of morbidity and mortality. Successful treatment requires strict adherence to drug regimens for prolonged periods of time. Long-acting (LA) delivery systems have the potential to improve adherence. Here, we show the development of LA injectable drug formulations of the anti-TB drug rifabutin made of biodegradable polymers and biocompatible solvents that solidifies after subcutaneous injection. Addition of amphiphilic compounds increases drug solubility, allowing to significantly increase formulation drug load. Solidified implants have organized microstructures that change with formulation composition. Higher drug load results in smaller pore size that alters implant erosion and allows sustained drug release. The translational relevance of these observations in BALB/c mice is demonstrated by (1) delivering high plasma drug concentrations for 16 weeks, (2) preventing acquisition of Mtb infection, and (3) clearing acute Mtb infection from the lung and other tissues.
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9
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Mesfin EA, Merker M, Beyene D, Tesfaye A, Shuaib YA, Addise D, Tessema B, Niemann S. Prediction of drug resistance by Sanger sequencing of Mycobacterium tuberculosis complex strains isolated from multidrug resistant tuberculosis suspect patients in Ethiopia. PLoS One 2022; 17:e0271508. [PMID: 35930613 PMCID: PMC9355188 DOI: 10.1371/journal.pone.0271508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 07/04/2022] [Indexed: 11/25/2022] Open
Abstract
Background Ethiopia is one of the high multidrug-resistant tuberculosis (MDR-TB) burden countries. However, phenotypic drug susceptibility testing can take several weeks due to the slow growth of Mycobacterium tuberculosis complex (MTBC) strains. In this study, we assessed the performance of a Sanger sequencing approach to predict resistance against five anti-tuberculosis drugs and the pattern of resistance mediating mutations. Methods We enrolled 226 MTBC culture-positive MDR-TB suspects and collected sputum specimens and socio-demographic and TB related data from each suspect between June 2015 and December 2016 in Addis Ababa, Ethiopia. Phenotypic drug susceptibility testing (pDST) for rifampicin, isoniazid, pyrazinamide, ethambutol, and streptomycin using BACTEC MGIT 960 was compared with the results of a Sanger sequencing analysis of seven resistance determining regions in the genes rpoB, katG, fabG-inhA, pncA, embB, rpsL, and rrs. Result DNA isolation for Sanger sequencing was successfully extracted from 92.5% (209/226) of the MTBC positive cultures, and the remaining 7.5% (17/226) strains were excluded from the final analysis. Based on pDST results, drug resistance proportions were as follows: isoniazid: 109/209 (52.2%), streptomycin: 93/209 (44.5%), rifampicin: 88/209 (42.1%), ethambutol: 74/209 (35.4%), and pyrazinamide: 69/209 (33.0%). Resistance against isoniazid was mainly mediated by the mutation katG S315T (97/209, 46.4%) and resistance against rifampicin by rpoB S531L (58/209, 27.8%). The dominating resistance-conferring mutations for ethambutol, streptomycin, and pyrazinamide affected codon 306 in embB (48/209, 21.1%), codon 88 in rpsL (43/209, 20.6%), and codon 65 in pncA (19/209, 9.1%), respectively. We observed a high agreement between phenotypic and genotypic DST, such as 89.9% (at 95% confidence interval [CI], 84.2%–95.8%) for isoniazid, 95.5% (95% CI, 91.2%–99.8%) for rifampicin, 98.6% (95% CI, 95.9–100%) for ethambutol, 91.3% (95% CI, 84.6–98.1%) for pyrazinamide and 57.0% (95% CI, 46.9%–67.1%) for streptomycin. Conclusion We detected canonical mutations implicated in resistance to rifampicin, isoniazid, pyrazinamide, ethambutol, and streptomycin. High agreement with phenotypic DST results for all drugs renders Sanger sequencing promising to be performed as a complementary measure to routine phenotypic DST in Ethiopia. Sanger sequencing directly from sputum may accelerate accurate clinical decision-making in the future.
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Affiliation(s)
- Eyob Abera Mesfin
- Ethiopian Public Health Institute, National Laboratory Capacity Building Directorate, Addis Ababa, Ethiopia
- * E-mail:
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Sülfeld, Germany
- Evolution of the Resistome, Research Center Borstel, Sülfeld, Germany
| | - Dereje Beyene
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abreham Tesfaye
- Addis Ababa City Administration Health Bureau Health Research and Laboratory Services, Addis Ababa, Ethiopia
| | - Yassir Adam Shuaib
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Sülfeld, Germany
- College of Veterinary Medicine, Sudan University of Science and Technology, Khartoum North, Sudan
| | - Desalegn Addise
- Ethiopian Public Health Institute, National Laboratory Capacity Building Directorate, Addis Ababa, Ethiopia
| | - Belay Tessema
- Department of Medical Microbiology, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Sülfeld, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck- Borstel-Riems, Hamburg, Germany
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10
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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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11
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Georghiou SB, Rodwell TC, Korobitsyn A, Abbadi SH, Ajbani K, Alffenaar JW, Alland D, Alvarez N, Andres S, Ardizzoni E, Aubry A, Baldan R, Ballif M, Barilar I, Böttger EC, Chakravorty S, Claxton PM, Cirillo DM, Comas I, Coulter C, Denkinger CM, Derendinger B, Desmond EP, de Steenwinkel JE, Dheda K, Diacon AH, Dolinger DL, Dooley KE, Egger M, Ehsani S, Farhat MR, Fattorini L, Finci I, Le Ray LF, Furió V, Groenheit R, Gumbo T, Heysell SK, Hillemann D, Hoffmann H, Hsueh PR, Hu Y, Huang H, Hussain A, Ismail F, Izumi K, Jagielski T, Johnson JL, Kambli P, Kaniga K, Eranga Karunaratne G, Sharma MK, Keller PM, Kelly EC, Kholina M, Kohli M, Kranzer K, Laurenson IF, Limberis J, Grace Lin SY, Liu Y, López-Gavín A, Lyander A, Machado D, Martinez E, Masood F, Mitarai S, Mvelase NR, Niemann S, Nikolayevskyy V, Maurer FP, Merker M, Miotto P, Omar SV, Otto-Knapp R, Palaci M, Palacios Gutiérrez JJ, Peacock SJ, Peloquin CA, Perera J, Pierre-Audigier C, Pholwat S, Posey JE, Prammananan T, Rigouts L, Robledo J, Rockwood N, Rodrigues C, Salfinger M, Schechter MC, Seifert M, Sengstake S, Shinnick T, Shubladze N, Sintchenko V, Sirgel F, Somasundaram S, Sterling TR, Spitaleri A, Streicher E, Supply P, Svensson E, Tagliani E, Tahseen S, Takaki A, Theron G, Torrea G, Van Deun A, van Ingen J, Van Rie A, van Soolingen D, Vargas Jr R, Venter A, Veziris N, Villellas C, Viveiros M, Warren R, Wen S, Werngren J, Wilkinson RJ, Yang C, Yılmaz FF, Zhang T, Zimenkov D, Ismail N, Köser CU, Schön T. Updating the approaches to define susceptibility and resistance to anti-tuberculosis agents: implications for diagnosis and treatment. Eur Respir J 2022; 59:2200166. [PMID: 35422426 PMCID: PMC9059840 DOI: 10.1183/13993003.00166-2022] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/05/2022] [Indexed: 11/07/2022]
Abstract
Approximately 85 000 deaths globally in 2019 were due to drug-resistant tuberculosis (TB), which corresponds to 7% of global deaths attributable to bacterial antimicrobial resistance [1]. Yet concerns have been mounting that drug-resistant TB was being underestimated because the approaches to define susceptibility and resistance to anti-TB agents had not kept up with those used for other major bacterial pathogens [2–9]. Here, we outline the recent, evidence-based initiatives spearheaded by the World Health Organization (WHO) and others to update breakpoints (traditionally referred to as critical concentrations (CCs)) that are used for phenotypic antimicrobial susceptibility testing (AST), also called drug susceptibility testing in the TB literature. Inappropriately high breakpoints have resulted in systematic false-susceptible AST results to anti-TB drugs. MIC, PK/PD and clinical outcome data should be combined when setting breakpoints to minimise the emergence and spread of antimicrobial resistance. https://bit.ly/3i43wb6
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12
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Chung ES, Johnson WC, Aldridge BB. Types and functions of heterogeneity in mycobacteria. Nat Rev Microbiol 2022; 20:529-541. [PMID: 35365812 DOI: 10.1038/s41579-022-00721-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2022] [Indexed: 12/24/2022]
Abstract
The remarkable ability of Mycobacterium tuberculosis to survive attacks from the host immune response and drug treatment is due to the resilience of a few bacilli rather than a result of survival of the entire population. Maintenance of mycobacterial subpopulations with distinct phenotypic characteristics is key for survival in the face of dynamic and variable stressors encountered during infection. Mycobacterial populations develop a wide range of phenotypes through an innate asymmetric growth pattern and adaptation to fluctuating microenvironments during infection that point to heterogeneity being a vital survival strategy. In this Review, we describe different types of mycobacterial heterogeneity and discuss how heterogeneity is generated and regulated in response to environmental cues. We discuss how this heterogeneity may have a key role in recording memory of their environment at both the single-cell level and the population level to give mycobacterial populations plasticity to withstand complex stressors.
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Affiliation(s)
- Eun Seon Chung
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - William C Johnson
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.,Tufts University School of Graduate Biomedical Sciences, Boston, MA, USA
| | - Bree B Aldridge
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA. .,Tufts University School of Graduate Biomedical Sciences, Boston, MA, USA. .,Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Tufts University, Boston, MA, USA. .,Department of Biomedical Engineering, Tufts University School of Engineering, Medford, MA, USA.
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13
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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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14
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Beraldi-Magalhaes F, Parker SL, Sanches C, Sousa Garcia L, Souza Carvalho BK, Fachi MM, de Liz MV, Pontarolo R, Lipman J, Cordeiro-Santos M, Roberts JA. Is Dosing of Ethambutol as Part of a Fixed-Dose Combination Product Optimal for Mechanically Ventilated ICU Patients with Tuberculosis? A Population Pharmacokinetic Study. Antibiotics (Basel) 2021; 10:antibiotics10121559. [PMID: 34943771 PMCID: PMC8698281 DOI: 10.3390/antibiotics10121559] [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: 11/01/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) patients admitted to intensive care units (ICU) have high mortality rates. It is uncertain whether the pharmacokinetics of first-line TB drugs in ICU patients are different from outpatients. This study aims to compare the pharmacokinetics of oral ethambutol in TB patients in ICU versus TB outpatients and to determine whether contemporary dosing regimens achieve therapeutic exposures. METHODS A prospective population pharmacokinetic study of ethambutol was performed in Amazonas State, Brazil. Probability of target attainment was determined using AUC/MIC > 11.9 and Cmax/MIC > 0.48 values. Optimized dosing regimens were simulated at steady state. RESULTS Ten ICU patients and 20 outpatients were recruited. Ethambutol pharmacokinetics were best described using a two-compartment model with first-order oral absorption. Neither ICU patients nor outpatients consistently achieved optimal ethambutol exposures. The absorption rate for ethambutol was 2-times higher in ICU patients (p < 0.05). Mean bioavailability for ICU patients was >5-times higher than outpatients (p < 0.0001). Clearance and volume of distribution were 93% (p < 0.0001) and 53% (p = 0.002) lower in ICU patients, respectively. CONCLUSIONS ICU patients displayed significantly different pharmacokinetics for an oral fixed-dose combination administration of ethambutol compared to outpatients, and neither patient group consistently achieved pre-defined therapeutic exposures.
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Affiliation(s)
- Francisco Beraldi-Magalhaes
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus 69040-000, Brazil; (L.S.G.); (B.K.S.C.); (M.C.-S.)
- Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus 69040-000, Brazil
- Secretaria de Estado da Saúde do Paraná, Curitiba 80010-130, Brazil
- School of Medicine, Faculdades Pequeno Príncipe, Curitiba 80230-020, Brazil
- Correspondence:
| | - Suzanne L. Parker
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4029, Australia; (S.L.P.); (J.L.); (J.A.R.)
| | - Cristina Sanches
- Department of Pharmacy, Universidade Federal de São João del-Rei, Divinopolis 35501-296, Brazil;
| | - Leandro Sousa Garcia
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus 69040-000, Brazil; (L.S.G.); (B.K.S.C.); (M.C.-S.)
- Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus 69040-000, Brazil
| | - Brenda Karoline Souza Carvalho
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus 69040-000, Brazil; (L.S.G.); (B.K.S.C.); (M.C.-S.)
- Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus 69040-000, Brazil
| | - Mariana Millan Fachi
- Department of Pharmacy, Universidade Federal do Paraná, Curitiba 80210-170, Brazil; (M.M.F.); (R.P.)
| | - Marcus Vinicius de Liz
- Department of Chemistry and Biology, Universidade Federal Tecnológica do Paraná, Curitiba 81280-340, Brazil;
| | - Roberto Pontarolo
- Department of Pharmacy, Universidade Federal do Paraná, Curitiba 80210-170, Brazil; (M.M.F.); (R.P.)
| | - Jeffrey Lipman
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4029, Australia; (S.L.P.); (J.L.); (J.A.R.)
- Department of Intensive Care Medicine, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4029, Australia
- Division of Anaesthesiology Critical Care Emergency and Pain Medicine, Nîmes University Hospital, University of Montpellier, 30900 Nimes, France
| | - Marcelo Cordeiro-Santos
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus 69040-000, Brazil; (L.S.G.); (B.K.S.C.); (M.C.-S.)
- Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus 69040-000, Brazil
- School of Medicine, Universidade Nilton Lins, Manaus 69058-040, Brazil
| | - Jason A. Roberts
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4029, Australia; (S.L.P.); (J.L.); (J.A.R.)
- Department of Intensive Care Medicine, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4029, Australia
- Division of Anaesthesiology Critical Care Emergency and Pain Medicine, Nîmes University Hospital, University of Montpellier, 30900 Nimes, France
- Department of Pharmacy, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4029, Australia
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15
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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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16
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Köser CU, Georghiou SB, Schön T, Salfinger M. On the Consequences of Poorly Defined Breakpoints for Rifampin Susceptibility Testing of Mycobacterium tuberculosis Complex. J Clin Microbiol 2021; 59:e02328-20. [PMID: 33568463 PMCID: PMC8092724 DOI: 10.1128/jcm.02328-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In a recent report of a systematic review of critical concentrations (CCs), the World Health Organization (WHO) lowered the rifampin (RIF) CC for antimicrobial susceptibility testing (AST) of the Mycobacterium tuberculosis complex using Middlebrook 7H10 medium and the Bactec Mycobacterial Growth Indicator Tube (MGIT) 960 system from 1 to 0.5 μg/ml. The previous RIF CC for 7H10 had been in use for over half a century. Because it had served as the de facto reference standard, it contributed to the endorsement of inappropriately high CCs for other AST methods, including the U.S. Food and Drug Administration (FDA)-approved MGIT system. Moreover, this resulted in confusion about the interpretation of seven borderline resistance mutations in rpoB (i.e., L430P, D435Y, H445L, H445N, H445S, L452P, and I491F). In this issue of the Journal of Clinical Microbiology, Shea et al. (J Clin Microbiol 59:e01885-20, 2021, https://doi.org/10.1128/JCM.01885-20) provide evidence that the CC endorsed by the Clinical and Laboratory Standards Institute for the Sensititre MYCOTB system, which is not FDA approved but is CE-IVD marked in the European Union, is likely also too high. These findings underscore the importance of calibrating AST methods against a rigorously defined reference standard, as recently proposed by the European Committee on Antimicrobial Susceptibility Testing, as well as the value of routine next-generation sequencing for investigating discordant AST results.
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Affiliation(s)
- Claudio U Köser
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | | | - Thomas Schön
- Department of Infectious Diseases, Kalmar County Hospital, Linköping University, Kalmar, Sweden
- Unit of Infection and Inflammation, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Infectious Diseases, Linköping University Hospital, Linköping, Sweden
| | - Max Salfinger
- University of South Florida College of Public Health and Morsani College of Medicine, Tampa, Florida, USA
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17
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Shuaib YA, Khalil EA, Wieler LH, Schaible UE, Bakheit MA, Mohamed-Noor SE, Abdalla MA, Kerubo G, Andres S, Hillemann D, Richter E, Kranzer K, Niemann S, Merker M. Mycobacterium tuberculosis Complex Lineage 3 as Causative Agent of Pulmonary Tuberculosis, Eastern Sudan 1. Emerg Infect Dis 2021; 26:427-436. [PMID: 32091355 PMCID: PMC7045825 DOI: 10.3201/eid2603.191145] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pathogen-based factors associated with tuberculosis (TB) in eastern Sudan are not well defined. We investigated genetic diversity, drug resistance, and possible transmission clusters of Mycobacterium tuberculosis complex (MTBC) strains by using a genomic epidemiology approach. We collected 383 sputum specimens at 3 hospitals in 2014 and 2016 from patients with symptoms suggestive of TB; of these, 171 grew MTBC strains. Whole-genome sequencing could be performed on 166 MTBC strains; phylogenetic classification revealed that most (73.4%; n = 122) belonged to lineage 3 (L3). Genome-based cluster analysis showed that 76 strains (45.9%) were grouped into 29 molecular clusters, comprising 2–8 strains/patients. Of the strains investigated, 9.0% (15/166) were multidrug resistant (MDR); 10 MDR MTBC strains were linked to 1 large MDR transmission network. Our findings indicate that L3 strains are the main causative agent of TB in eastern Sudan; MDR TB is caused mainly by transmission of MDR L3 strains.
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18
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Most-Probable-Number-Based Minimum Duration of Killing Assay for Determining the Spectrum of Rifampicin Susceptibility in Clinical Mycobacterium tuberculosis Isolates. Antimicrob Agents Chemother 2021; 65:AAC.01439-20. [PMID: 33257450 PMCID: PMC8092508 DOI: 10.1128/aac.01439-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/24/2020] [Indexed: 12/17/2022] Open
Abstract
Accurate antibiotic susceptibility testing is essential for successful tuberculosis treatment. Recent studies have highlighted the limitations of MIC-based phenotypic susceptibility methods in detecting other aspects of antibiotic susceptibilities in bacteria. Duration and peak of antibiotic exposure, at or above the MIC required for killing the bacterial population, has emerged as another important factor for determining antibiotic susceptibility. This is broadly defined as antibiotic tolerance. Accurate antibiotic susceptibility testing is essential for successful tuberculosis treatment. Recent studies have highlighted the limitations of MIC-based phenotypic susceptibility methods in detecting other aspects of antibiotic susceptibilities in bacteria. Duration and peak of antibiotic exposure, at or above the MIC required for killing the bacterial population, has emerged as another important factor for determining antibiotic susceptibility. This is broadly defined as antibiotic tolerance. Antibiotic tolerance can further facilitate the emergence of antibiotic resistance. Currently, there are limited methods to quantify antibiotic tolerance among clinical M. tuberculosis isolates. In this study, we develop a most-probable-number (MPN)-based minimum duration of killing (MDK) assay to quantify the spectrum of M. tuberculosis rifampicin susceptibility within subpopulations based on the duration of rifampicin exposure required for killing the bacterial population. MDK90–99 and MDK99.99 were defined as the minimum duration of antibiotic exposure at or above the MIC required for killing 90 to 99% and 99.99% of the initial (pretreatment) bacterial population, respectively. Results from the rifampicin MDK assay applied to 28 laboratory and clinical M. tuberculosis isolates showed that there is variation in rifampicin susceptibility among isolates. The rifampicin MDK99/99.99 time for isolates varied from less than 2 to 10 days. MDK was correlated with larger subpopulations of M. tuberculosis from clinical isolates that were rifampicin tolerant. Our study demonstrates the utility of MDK assays to measure the variation in antibiotic tolerance among clinical M. tuberculosis isolates and further expands clinically important aspects of antibiotic susceptibility testing.
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Lange C, Aarnoutse R, Chesov D, van Crevel R, Gillespie SH, Grobbel HP, Kalsdorf B, Kontsevaya I, van Laarhoven A, Nishiguchi T, Mandalakas A, Merker M, Niemann S, Köhler N, Heyckendorf J, Reimann M, Ruhwald M, Sanchez-Carballo P, Schwudke D, Waldow F, DiNardo AR. Perspective for Precision Medicine for Tuberculosis. Front Immunol 2020; 11:566608. [PMID: 33117351 PMCID: PMC7578248 DOI: 10.3389/fimmu.2020.566608] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/02/2020] [Indexed: 12/28/2022] Open
Abstract
Tuberculosis is a bacterial infectious disease that is mainly transmitted from human to human via infectious aerosols. Currently, tuberculosis is the leading cause of death by an infectious disease world-wide. In the past decade, the number of patients affected by tuberculosis has increased by ~20 percent and the emergence of drug-resistant strains of Mycobacterium tuberculosis challenges the goal of elimination of tuberculosis in the near future. For the last 50 years, management of patients with tuberculosis has followed a standardized management approach. This standardization neglects the variation in human susceptibility to infection, immune response, the pharmacokinetics of drugs, and the individual duration of treatment needed to achieve relapse-free cure. Here we propose a package of precision medicine-guided therapies that has the prospect to drive clinical management decisions, based on both host immunity and M. tuberculosis strains genetics. Recently, important scientific discoveries and technological advances have been achieved that provide a perspective for individualized rather than standardized management of patients with tuberculosis. For the individual selection of best medicines and host-directed therapies, personalized drug dosing, and treatment durations, physicians treating patients with tuberculosis will be able to rely on these advances in systems biology and to apply them at the bedside.
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Affiliation(s)
- Christoph Lange
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
- Cluster of Excellence Precision Medicine in Chronic Inflammation, Kiel, Germany
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Rob Aarnoutse
- Department of Internal Medicine, Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands
| | - Dumitru Chesov
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
- Department of Pulmonology and Allergology, Nicolae Testemitanu University of Medicine and Pharmacy, Chisinau, Moldova
| | - Reinout van Crevel
- Department of Internal Medicine, Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Hans-Peter Grobbel
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
| | - Barbara Kalsdorf
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
- Cluster of Excellence Precision Medicine in Chronic Inflammation, Kiel, Germany
| | - Irina Kontsevaya
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
| | - Arjan van Laarhoven
- Department of Internal Medicine, Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands
| | - Tomoki Nishiguchi
- The Global Tuberculosis Program, Texas Children's Hospital, Immigrant and Global Health, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Anna Mandalakas
- The Global Tuberculosis Program, Texas Children's Hospital, Immigrant and Global Health, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Matthias Merker
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Cluster of Excellence Precision Medicine in Chronic Inflammation, Kiel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Stefan Niemann
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Cluster of Excellence Precision Medicine in Chronic Inflammation, Kiel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Niklas Köhler
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
| | - Jan Heyckendorf
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
| | - Maja Reimann
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
| | - Morten Ruhwald
- Foundation of Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Patricia Sanchez-Carballo
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
| | - Dominik Schwudke
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Bioanalytical Chemistry, Priority Area Infection, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- Airway Research Center North, German Center for Lung Research (DZL), Borstel, Germany
| | - Franziska Waldow
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Bioanalytical Chemistry, Priority Area Infection, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Andrew R. DiNardo
- The Global Tuberculosis Program, Texas Children's Hospital, Immigrant and Global Health, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
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20
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Michael A, Kelman T, Pitesky M. Overview of Quantitative Methodologies to Understand Antimicrobial Resistance via Minimum Inhibitory Concentration. Animals (Basel) 2020; 10:ani10081405. [PMID: 32806615 PMCID: PMC7459578 DOI: 10.3390/ani10081405] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 08/05/2020] [Accepted: 08/07/2020] [Indexed: 01/07/2023] Open
Abstract
Simple Summary An emerging threat to human and food animal health is the development of antimicrobial resistance in bacteria associated with food animals. One of the primary tools for assessing resistance levels and monitoring for changes in expressed resistance is the use of minimum inhibitory concentration tests, which expose bacterial isolates to a series of dilutions of an antimicrobial agent to identify the lowest concentration of the antimicrobial that effectively prevents bacterial growth. These tests produce a minimum inhibitory value that falls within a range of concentrations instead of an exact value, a process known as censoring. Analysis of censored data is complex and careful consideration of methods of analysis is necessary. The use of regression methods such as logistic regression that divide the data into two or three categories is relatively easy to implement but may not detect important changes in the distributions of data that occur within the categories. Models that do not simplify the data may be more complex but may detect potentially relevant changes missed when the data is categorized. As a result, the analysis of minimum inhibitory concentration data requires careful consideration to identify the appropriate model for the purpose of the study. Abstract The development of antimicrobial resistance (AMR) represents a significant threat to humans and food animals. The use of antimicrobials in human and veterinary medicine may select for resistant bacteria, resulting in increased levels of AMR in these populations. As the threat presented by AMR increases, it becomes critically important to find methods for effectively interpreting minimum inhibitory concentration (MIC) tests. Currently, a wide array of techniques for analyzing these data can be found in the literature, but few guidelines for choosing among them exist. Here, we examine several quantitative techniques for analyzing the results of MIC tests and discuss and summarize various ways to model MIC data. The goal of this review is to propose important considerations for appropriate model selection given the purpose and context of the study. Approaches reviewed include mixture models, logistic regression, cumulative logistic regression, and accelerated failure time–frailty models. Important considerations in model selection include the objective of the study (e.g., modeling MIC creep vs. clinical resistance), degree of censoring in the data (e.g., heavily left/right censored vs. primarily interval censored), and consistency of testing parameters (e.g., same range of concentrations tested for a given antibiotic).
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Affiliation(s)
- Alec Michael
- Department of Population Health and Reproduction, School of Veterinary Medicine, UC Davis, 1089 Veterinary Medicine Dr., VM3B, Davis, CA 95616, USA;
- Correspondence:
| | - Todd Kelman
- Department of Population Health and Reproduction, School of Veterinary Medicine, UC Davis, 1089 Veterinary Medicine Dr., VM3B, Davis, CA 95616, USA;
| | - Maurice Pitesky
- Department of Population Health and Reproduction, School of Veterinary Medicine-Cooperative Extension, UC Davis, 1089 Veterinary Medicine Dr., VM3B, Davis, CA 95616, USA;
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21
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Kouanda S, Ouedraogo HG, Cisse K, Compaoré TR, Sulis G, Diagbouga S, Roggi A, Tarnagda G, Villani P, Sangare L, Simporé J, Regazzi M, Matteelli A. Pharmacokinetic study of two different rifabutin doses co-administered with lopinavir/ritonavir in African HIV and tuberculosis co-infected adult patients. BMC Infect Dis 2020; 20:449. [PMID: 32590942 PMCID: PMC7318514 DOI: 10.1186/s12879-020-05169-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 06/17/2020] [Indexed: 12/04/2022] Open
Abstract
Background This study aimed to assess the pharmacokinetic profile of 150 mg rifabutin (RBT) taken every other day (every 48 h) versus 300 mg RBT taken every other day (E.O.D), both in combination with lopinavir/ritonavir (LPV/r), in adult patients with human immunodeficiency virus (HIV) and tuberculosis (TB) co-infection. Methods This is a two-arm, open-label, pharmacokinetic, randomised study conducted in Burkina Faso between May 2013 and December 2015. Enrolled patients were randomised to receive either 150 mg RBT EOD (arm A, 9 subjects) or 300 mg RBT EOD (arm B, 7 subjects), both associated with LPV/r taken twice daily. RBT plasma concentrations were evaluated after 2 weeks of combined HIV and TB treatment. Samples were collected just before drug ingestion and at 1, 2, 3, 4, 6, 8, and 12 h after drug ingestion to measure plasma drug concentration using an HPLC-MS/MS assay. Results The Cmax and AUC0–12h medians in arm A (Cmax = 296 ng/mL, IQR: 205–45; AUC0–12h = 2528 ng.h/mL, IQR: 1684–2735) were lower than those in arm B (Cmax = 600 ng/mL, IQR: 403–717; AUC0–12h = 4042.5 ng.h/mL, IQR: 3469–5761), with a statistically significant difference in AUC0–12h (p = 0.044) but not in Cmax (p = 0.313). No significant differences were observed in Tmax (3 h versus 4 h). Five patients had a Cmax below the plasma therapeutic limit (< 300 ng/mL) in the 150 mg RBT arm, while the Cmax was above this threshold for all patients in the 300 mg RBT arm. Additionally, at 48 h after drug ingestion, all patients had a mycobacterial minimum inhibitory concentration (MIC) above the limit (> 64 ng/mL) in the 300 mg RBT arm, while 4/9 patients had such values in the 150 mg RBT arm. Conclusion This study confirmed that the 150 mg dose of rifabutin ingested EOD in combination with LPV/r is inadequate and could lead to selection of rifamycin-resistant mycobacteria. Trial registration PACTR201310000629390, 28th October 2013.
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Affiliation(s)
- Seni Kouanda
- Biomedical and Public Health Department, Institut de Recherche en Sciences de la Santé (IRSS), Ouagadougou, 03BP7192, Burkina Faso.
| | - Henri Gautier Ouedraogo
- Biomedical and Public Health Department, Institut de Recherche en Sciences de la Santé (IRSS), Ouagadougou, 03BP7192, Burkina Faso
| | - Kadari Cisse
- Biomedical and Public Health Department, Institut de Recherche en Sciences de la Santé (IRSS), Ouagadougou, 03BP7192, Burkina Faso
| | - Tegwinde Rebeca Compaoré
- Biomedical and Public Health Department, Institut de Recherche en Sciences de la Santé (IRSS), Ouagadougou, 03BP7192, Burkina Faso
| | - Giorgia Sulis
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada.,McGill International TB Centre, McGill University, Montreal, QC, Canada
| | - Serge Diagbouga
- Biomedical and Public Health Department, Institut de Recherche en Sciences de la Santé (IRSS), Ouagadougou, 03BP7192, Burkina Faso
| | - Alberto Roggi
- Institute of Infectious and Tropical Diseases, Brescia University Hospital, Brescia, Italy
| | - Grissoum Tarnagda
- Biomedical and Public Health Department, Institut de Recherche en Sciences de la Santé (IRSS), Ouagadougou, 03BP7192, Burkina Faso
| | - Paola Villani
- Institute of Pharmacology, IRCCS, San Matteo University Hospital, Pavia, Italy
| | - Lassana Sangare
- Yalgado Ouedraogo University Teaching Hospital, Ouagadougou, Burkina Faso
| | - Jacques Simporé
- Centre de Recherche Biomoléculaire Pietro Annigoni (CERBA), Ouagadougou, Burkina Faso
| | - Mario Regazzi
- Institute of Pharmacology, IRCCS, San Matteo University Hospital, Pavia, Italy
| | - Alberto Matteelli
- Institute of Infectious and Tropical Diseases, Brescia University Hospital, Brescia, Italy
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22
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Model-based integration of genomics and metabolomics reveals SNP functionality in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2020; 117:8494-8502. [PMID: 32229570 DOI: 10.1073/pnas.1915551117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Human tuberculosis is caused by members of the Mycobacterium tuberculosis complex (MTBC) that vary in virulence and transmissibility. While genome-wide association studies have uncovered several mutations conferring drug resistance, much less is known about the factors underlying other bacterial phenotypes. Variation in the outcome of tuberculosis infection and diseases has been attributed primarily to patient and environmental factors, but recent evidence indicates an additional role for the genetic diversity among MTBC clinical strains. Here, we used metabolomics to unravel the effect of genetic variation on the strain-specific metabolic adaptive capacity and vulnerability. To define the functionality of single-nucleotide polymorphisms (SNPs) systematically, we developed a constraint-based approach that integrates metabolomic and genomic data. Our model-based predictions correctly classify SNP effects in pyruvate kinase and suggest a genetic basis for strain-specific inherent baseline susceptibility to the antibiotic para-aminosalicylic acid. Our method is broadly applicable across microbial life, opening possibilities for the development of more selective treatment strategies.
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23
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Kaniga K, Aono A, Borroni E, Cirillo DM, Desmaretz C, Hasan R, Joseph L, Mitarai S, Shakoor S, Torrea G, Ismail NA, Omar SV. Validation of Bedaquiline Phenotypic Drug Susceptibility Testing Methods and Breakpoints: a Multilaboratory, Multicountry Study. J Clin Microbiol 2020; 58:e01677-19. [PMID: 31969421 PMCID: PMC7098739 DOI: 10.1128/jcm.01677-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/13/2020] [Indexed: 02/08/2023] Open
Abstract
Drug-resistant tuberculosis persists as a major public health concern. Alongside efficacious treatments, validated and standardized drug susceptibility testing (DST) is required to improve patient care. This multicountry, multilaboratory external quality assessment (EQA) study aimed to validate the sensitivity, specificity, and reproducibility of provisional bedaquiline MIC breakpoints and World Health Organization interim critical concentrations (CCs) for categorizing clinical Mycobacterium tuberculosis isolates as susceptible/resistant to the drug. Three methods were used: Middlebrook 7H11 agar proportion (AP) assay, broth microdilution (BMD) assay, and mycobacterial growth indicator tube (MGIT) assay. Each of the five laboratories tested the 40-isolate (20 unique isolates, duplicated) EQA panel at three time points. The study validated the sensitivity and specificity of a bedaquiline MIC susceptibility breakpoint of 0.12 μg/ml for the BMD method and WHO interim CCs of 1 μg/ml for MGIT and 0.25 μg/ml for the 7H11 AP methods. Categorical agreements between observed and expected results and sensitivities/specificities for correctly identifying an isolate as susceptible/resistant were highest at the 0.25, 0.12, and 1 μg/ml bedaquiline concentrations for the AP method, BMD (frozen or dry plates), and MGIT960, respectively. At these concentrations, the very major error rates for erroneously categorizing an isolate as susceptible when it was resistant were the lowest and within CLSI guidelines. The most highly reproducible bedaquiline DST methods were MGIT960 and BMD using dry plates. These findings validate the use of standardized DST methodologies and interpretative criteria to facilitate routine phenotypic bedaquiline DST and to monitor the emergence of bedaquiline resistance.
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Affiliation(s)
- Koné Kaniga
- Johnson & Johnson Global Public Health, Titusville, New Jersey, USA
| | - Akio Aono
- Department of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-tuberculosis Association, Kiyose, Japan
| | - Emanuele Borroni
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Christel Desmaretz
- Department of Biomedical Sciences, Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
- Faculty of Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Lavania Joseph
- Center for Tuberculosis, National and WHO Supranational TB Reference Laboratory, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa
| | - Satoshi Mitarai
- Department of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-tuberculosis Association, Kiyose, Japan
| | - Sadia Shakoor
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - Gabriela Torrea
- Department of Biomedical Sciences, Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Nazir Ahmed Ismail
- Center for Tuberculosis, National and WHO Supranational TB Reference Laboratory, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
- Department of Internal Medicine, University of Witwatersrand, Johannesburg, South Africa
| | - Shaheed V Omar
- Center for Tuberculosis, National and WHO Supranational TB Reference Laboratory, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa
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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] [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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Kontsevaya I, Werngren J, Holicka Y, Klaos K, Tran A, Nikolayevskyy V. Non-commercial phenotypic assays for the detection of Mycobacterium tuberculosis drug resistance: a systematic review. Eur J Clin Microbiol Infect Dis 2019; 39:415-426. [PMID: 31667670 DOI: 10.1007/s10096-019-03723-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 09/24/2019] [Indexed: 10/25/2022]
Abstract
Several rapid non-commercial culture-based methods and assays for drug susceptibility testing (DST) of Mycobacterium tuberculosis have emerged over the last decades. The aim of the current review was to summarise evidence on the performance of microscopic observation of drug susceptibility (MODS), thin-layer agar (TLA) and colorimetric redox-indicator (CRI) assays for detection of resistance to first- and second-line anti-tuberculosis (TB) drugs. Forty-three publications satisfying selection criteria were selected for data extraction. MODS and CRI assays demonstrated pooled sensitivity and specificity of > 93% for the detection of resistance to rifampicin and isoniazid and confirmed their utility for an accurate detection of multidrug-resistant TB (MDR-TB) in various settings. Sensitivity and specificity values for indirect DST for ethambutol (EMB) using CRI assays were 94.0% and 82.0%, respectively, suggesting that CRIs could be used to rule out resistance to EMB. Performance for other drugs varied more substantially across the reports. There was no sufficient evidence on the performance of the TLA assay for making any conclusion on its utility for DST. Our data suggests that non-commercial assays could be used for a rapid and accurate DST in settings where the use of commercial World Health Organization-endorsed assays could be limited due to a variety of reasons including limited resources, laboratory facilities or trained personnel. While inexpensive and easy-to-perform MODS and TLA assays can be used in low-income settings, using CRI assays for determination of minimal inhibitory concentrations may be implemented in middle- and high-income countries with high MDR-TB burden to guide clinical management of TB patients.
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Affiliation(s)
- Irina Kontsevaya
- Imperial College London, Du Cane Road, London, W12 0NN, UK.,Research Center Borstel, Parkallee 1-40, D-23845, Borstel, Germany
| | - Jim Werngren
- Public Health Agency of Sweden, Nobels väg 18, 17165, Solna, Sweden
| | - Yen Holicka
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Kadri Klaos
- Department of Pulmonary Medicine, University of Tartu, Puusepa 8, 50406, Tartu, Estonia.,Department of Mycobacteriology, United Laboratories, Tartu University Hospital, Puusepa 1A, 50406, Tartu, Estonia
| | - Anh Tran
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Vladyslav Nikolayevskyy
- Imperial College London, Du Cane Road, London, W12 0NN, UK. .,Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK.
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26
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Grobbelaar M, Louw GE, Sampson SL, van Helden PD, Donald PR, Warren RM. Evolution of rifampicin treatment for tuberculosis. INFECTION GENETICS AND EVOLUTION 2019; 74:103937. [PMID: 31247337 DOI: 10.1016/j.meegid.2019.103937] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/20/2019] [Accepted: 06/21/2019] [Indexed: 02/07/2023]
Abstract
Rifampicin was discovered in 1965 and remains one of the most important drugs in tuberculosis treatment that is valued for its sterilizing activity and ability to shorten treatment. Antimicrobial activity of rifampicin was initially proved in vitro; subsequently numerous in vivo studies showed the bactericidal properties and dose-dependent effect of rifampicin. Rifampicin was first during the late 1960s to treat patients suffering from chronic drug-resistant pulmonary TB. Decades later, rifampicin continues to be studied with particular emphasis on whether higher doses could shorten the duration of treatment without increasing relapse or having adverse effects. Lesion-specific drug penetration and pharmacokinetics of rifampicin are improving our understanding of effective concentration while potentially refining drug regimen designs. Another prospective aspect of high-dose rifampicin is its potential use in treating discrepant mutation thereby eliminating the need for MDR treatment. To date, several clinical trials have shown the safety, efficacy, and tolerability of high-dose rifampicin. Currently, high-dose rifampicin has been used successfully in a routine clinical setting for the treatment of high-risk patients. However, the WHO and other relevant policy makers have not committed to implementing a controlled rollout thereof. This review describes the course that rifampicin has travelled to the present-day exploration of high-dose rifampicin treatment.
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Affiliation(s)
- Melanie Grobbelaar
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
| | - Gail E Louw
- Institute of Infectious Diseases and Molecular Medicine, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Samantha L Sampson
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Paul D van Helden
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Peter R Donald
- Department of Paediatrics and Child Health, Desmond Tutu TB Centre, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Robin M Warren
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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27
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Mu R, Kong C, Yu W, Wang H, Ma Y, Li X, Wu J, Somersan-Karakaya S, Li H, Sun Z, Liu G. Nitrooxidoreductase Rv2466c-Dependent Fluorescent Probe for Mycobacterium tuberculosis Diagnosis and Drug Susceptibility Testing. ACS Infect Dis 2019; 5:949-961. [PMID: 30916931 DOI: 10.1021/acsinfecdis.9b00006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Firstly, this study demonstrated that natural product-inspired coumarin-based nitrofuranyl calanolides (NFCs) can form the Rv2466c-mycothiol (MSH)-NFC (RvMN) ternary complex via NFC binding to W21, N51, and Y61 of Rv2466c and be specifically reduced by Rv2466c, which is accompanied by the generation of a high level of fluorescence. Additionally, the results unveiled that the acetylated cysteine-glucosamine (AcCys-GlcN) motif of MSH is sufficient to interact with Rv2466c and adopt the active conformation that is essential for fully reducing NFCs. Further clinical translational investigation in this Article indicated that the novel fluorescent NFC probe can serve as a much needed high-throughput and low-cost detection method for detection of living Mycobacterium tuberculosis ( Mtb) and can precisely determine MIC values for a full range of available drugs. This method can greatly facilitate the development of phenotypic drug-susceptibility testing (pDST) that will allow the point-of-care treatment of tuberculosis (TB) within a week after diagnosis.
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Affiliation(s)
- Ran Mu
- School of Pharmaceutical Sciences, Tsinghua University, Haidian District, Beijing 100084, P. R. China
| | - Chengcheng Kong
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, P. R. China
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, P. R. China
| | - Wenjun Yu
- School of Pharmaceutical Sciences, Tsinghua University, Haidian District, Beijing 100084, P. R. China
| | - Hongyao Wang
- School of Pharmaceutical Sciences, Tsinghua University, Haidian District, Beijing 100084, P. R. China
| | - Yao Ma
- School of Pharmaceutical Sciences, Tsinghua University, Haidian District, Beijing 100084, P. R. China
| | - Xueyuan Li
- School of Pharmaceutical Sciences, Tsinghua University, Haidian District, Beijing 100084, P. R. China
| | - Jie Wu
- School of Pharmaceutical Sciences, Tsinghua University, Haidian District, Beijing 100084, P. R. China
| | - Selin Somersan-Karakaya
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Haitao Li
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Haidian District, Beijing 100084, P. R. China
| | - Zhaogang Sun
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, P. R. China
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, P. R. China
| | - Gang Liu
- School of Pharmaceutical Sciences, Tsinghua University, Haidian District, Beijing 100084, P. R. China
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28
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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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29
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GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions. Nat Commun 2019; 10:2128. [PMID: 31086182 PMCID: PMC6513847 DOI: 10.1038/s41467-019-10110-6] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/18/2019] [Indexed: 01/28/2023] Open
Abstract
Drug resistance diagnostics that rely on the detection of resistance-related mutations could expedite patient care and TB eradication. We perform minimum inhibitory concentration testing for 12 anti-TB drugs together with Illumina whole-genome sequencing on 1452 clinical Mycobacterium tuberculosis (MTB) isolates. We evaluate genome-wide associations between mutations in MTB genes or non-coding regions and resistance, followed by validation in an independent data set of 792 patient isolates. We confirm associations at 13 non-canonical loci, with two involving non-coding regions. Promoter mutations are measured to have smaller average effects on resistance than gene body mutations. We estimate the heritability of the resistance phenotype to 11 anti-TB drugs and identify a lower than expected contribution from known resistance genes. This study highlights the complexity of the genomic mechanisms associated with the MTB resistance phenotype, including the relatively large number of potentially causal loci, and emphasizes the contribution of the non-coding portion of the genome.
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30
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Chen ML, Doddi A, Royer J, Freschi L, Schito M, Ezewudo M, Kohane IS, Beam A, Farhat M. Beyond multidrug resistance: Leveraging rare variants with machine and statistical learning models in Mycobacterium tuberculosis resistance prediction. EBioMedicine 2019; 43:356-369. [PMID: 31047860 PMCID: PMC6557804 DOI: 10.1016/j.ebiom.2019.04.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/21/2019] [Accepted: 04/05/2019] [Indexed: 01/04/2023] Open
Abstract
Background Methods Findings Interpretation
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31
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Abstract
PURPOSE OF REVIEW To summarize data regarding categories, detection methods, prevalence and patterns of drug resistance among patients with tuberculous pleural effusion (TPE) and to comment on the management of suspected drug-resistant TPE. RECENT FINDINGS Pleural and pulmonary tuberculosis (TB) present similar patterns of drug resistance. Approximately 10% and 6-10% of pleural Mycobacterium tuberculosis isolates are resistant to at least one first-line anti-TB drug or at least isoniazid, respectively. The prevalence of multidrug-resistant-pleural and extensively drug-resistant-pleural TB is 1-3% and 0-1%, respectively. SUMMARY Although guidelines suggest the empirical standard anti-TB regimen (i.e. 2 months of isoniazid, rifampicin, pyrazinamide and ethambutol followed by 4 months of isoniazid and rifampicin) for TPE treatment, the data regarding drug resistance among TPE patients are limited. The few studies examining the issue report a notable drug resistance. In suspected drug-resistant TPE, every effort is warranted to isolate M. tuberculosis to perform drug susceptibility testing and provide guided therapy. For this purpose, the use of cultures or molecular methods with pleural biopsies is superior to their use in pleural fluid. If still M. tuberculosis cannot be detected, prolonged administration of ethambutol with isoniazid and rifampicin during the continuation phase of treatment might be considered.
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Affiliation(s)
- Vasileios S Skouras
- Department of Pulmonary Medicine, 401 General Army Hospital.,1st Department of Pulmonary Medicine, Hygeia Hospital
| | - Ioannis Kalomenidis
- 1st Department of Critical Care & Pulmonary Medicine, Medical School of Athens University, 'Evangelismos' General Hospital, Athens, Greece
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32
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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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33
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'Those who cannot remember the past are condemned to repeat it': Drug-susceptibility testing for bedaquiline and delamanid. Int J Infect Dis 2019; 80S:S32-S35. [PMID: 30818049 DOI: 10.1016/j.ijid.2019.02.027] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/18/2019] [Accepted: 02/20/2019] [Indexed: 11/22/2022] Open
Abstract
Despite being fundamental to all treatment decisions, the breakpoints that define susceptibility and resistance to conventional anti-tuberculosis (TB) drugs were traditionally defined based on expert opinion as opposed to modern microbiological principles. As a result, the breakpoints for several key drugs (i.e. amikacin, levofloxacin, and moxifloxacin) were too high, resulting in the systematic misclassification of a proportion of resistant strains as susceptible. Moreover, a recent systematic review of clinical outcome data prompted the World Health Organization (WHO) to make significant changes to its treatment guidelines. For example, capreomycin and kanamycin are no longer recommended for TB treatment because their use correlates with worse clinical outcomes. This history notwithstanding, robust breakpoints still do not exist for bedaquiline and delamanid six years after their approval. This was compounded by the fact that access to both agents for drug-susceptibility testing had initially been restricted. It is incumbent upon the European Medicines Agency, the United States Food and Drug Administration, and WHO to ensure that drug developers generate the necessary data to set breakpoints as a prerequisite for the approval of new agents.
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34
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Mvelase NR, Pillay M, Sibanda W, Ngozo JN, Brust JCM, Mlisana KP. rpoB Mutations Causing Discordant Rifampicin Susceptibility in Mycobacterium tuberculosis: Retrospective Analysis of Prevalence, Phenotypic, Genotypic, and Treatment Outcomes. Open Forum Infect Dis 2019; 6:ofz065. [PMID: 31024968 PMCID: PMC6475586 DOI: 10.1093/ofid/ofz065] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 02/08/2019] [Indexed: 02/07/2023] Open
Abstract
Background Discordant genotypic/phenotypic rifampicin susceptibility testing in Mycobacterium tuberculosis is a significant challenge, yet there are limited data on its prevalence and how best to manage such patients. Whether to treat isolates with rpoB mutations not conferring phenotypic resistance as susceptible or multidrug-resistant tuberculosis (MDR-TB) is unknown. We describe phenotypic and genotypic characteristics of discordant isolates and clinical characteristics and treatment outcomes of affected patients in KwaZulu-Natal, South Africa. Methods We analyzed clinical isolates showing rifampicin resistance on GenoType MTBDRplus while susceptible on 1% agar proportion method. We measured rifampicin minimum inhibitory concentrations (MICs) using Middlebrook 7H10 agar dilution and BACTEC MGIT 960. Sensititre MYCOTB plates were used for drug-susceptibility testing, and rpoB gene sequencing was performed on all isolates. Local MDR-TB program data were reviewed for clinical information and patient outcomes. Results Discordant isolates constituted 4.6% (60) of 1302 rifampicin-resistant cases over the study period. Of these, 62% remained susceptible to isoniazid and 98% remained susceptible to rifabutin. Rifampicin MICs were close to the critical concentration of 1 µg/mL (0.5–2 µg/mL) for 83% of isolates. The most frequent rpoB mutations were Q513P (25.3%), D516V (19.2%), and D516Y (13.3%). Whereas 70% were human immunodeficiency virus infected, the mean CD4 count was 289 cells/mm3 and 87% were receiving antiretroviral therapy. Standard therapy for MDR-TB was used and 53% achieved successful treatment outcomes. Conclusions Rifampicin-discordant TB is not uncommon and sequencing is required to confirm results. The high susceptibility to rifabutin and isoniazid and poor treatment outcomes with the current regimen suggest a potential utility for rifabutin-based therapy.
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Affiliation(s)
- Nomonde R Mvelase
- Department of Medical Microbiology, KwaZulu-Natal Academic Complex, National Health Laboratory Service, Durban, South Africa.,Department of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Melendhran Pillay
- Department of Medical Microbiology, KwaZulu-Natal Academic Complex, National Health Laboratory Service, Durban, South Africa
| | - Wilbert Sibanda
- Department of Biostatistics, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Jacqueline N Ngozo
- Department of Health, KwaZulu-Natal Province, Pietermaritzburg, South Africa
| | - James C M Brust
- Department of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York
| | - Koleka P Mlisana
- Department of Medical Microbiology, KwaZulu-Natal Academic Complex, National Health Laboratory Service, Durban, South Africa.,Department of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
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35
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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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36
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Gröschel MI, Walker TM, van der Werf TS, Lange C, Niemann S, Merker M. Pathogen-based precision medicine for drug-resistant tuberculosis. PLoS Pathog 2018; 14:e1007297. [PMID: 30335850 PMCID: PMC6193714 DOI: 10.1371/journal.ppat.1007297] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Matthias I. Gröschel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- Department of Pulmonary Diseases & Tuberculosis, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- * E-mail:
| | - Timothy M. Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Tjip S. van der Werf
- Department of Pulmonary Diseases & Tuberculosis, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Christoph Lange
- Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- International Health / Infectious Diseases, University of Lübeck, Lübeck, Germany
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
- German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany
| | - Stefan Niemann
- 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
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37
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Liu Y, Matsumoto M, Ishida H, Ohguro K, Yoshitake M, Gupta R, Geiter L, Hafkin J. Delamanid: From discovery to its use for pulmonary multidrug-resistant tuberculosis (MDR-TB). Tuberculosis (Edinb) 2018; 111:20-30. [DOI: 10.1016/j.tube.2018.04.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/09/2018] [Accepted: 04/30/2018] [Indexed: 10/17/2022]
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38
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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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Rominski A, Schulthess B, Müller DM, Keller PM, Sander P. Effect of β-lactamase production and β-lactam instability on MIC testing results for Mycobacterium abscessus. J Antimicrob Chemother 2018; 72:3070-3078. [PMID: 28961987 DOI: 10.1093/jac/dkx284] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 07/09/2017] [Indexed: 12/27/2022] Open
Abstract
Objectives Limited treatment options available for Mycobacterium abscessus infections include the parenteral β-lactam antibiotics cefoxitin and imipenem, which show moderate in vitro activity. Other β-lactam antibiotics (except meropenem) have no considerable in vitro activity, due to their rapid hydrolysis by a broad-spectrum β-lactamase (Bla_Mab). We here addressed the impact of β-lactamase production and β-lactam in vitro stability on M. abscessus MIC results and determined the epidemiological cut-off (ECOFF) values of cefoxitin, imipenem and meropenem. Methods By LC high-resolution MS (LC-HRMS), we assessed the in vitro stability of cefoxitin, imipenem and meropenem. M. abscessus ATCC 19977 strain and its isogenic blaMab deletion mutant were used for MIC testing. Based on MIC distributions for M. abscessus clinical strains, we determined ECOFFs of cefoxitin, imipenem and meropenem. Results A functional Bla_Mab increased MICs of penicillins, ceftriaxone and meropenem. LC-HRMS data showed significant degradation of cefoxitin, imipenem and meropenem during standard antibiotic susceptibility testing procedures. MIC, MIC50 and ECOFF values of cefoxitin, imipenem and meropenem are influenced by incubation time. Conclusions The results of our study support administration of imipenem, meropenem and cefoxitin, for treatment of patients infected with M. abscessus. Our findings on in vitro instability of imipenem, meropenem and cefoxitin explain the problematic correlation between in vitro susceptibility and in vivo activity of these antibiotics and question the clinical utility of susceptibility testing of these chemotherapeutic agents.
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Affiliation(s)
- Anna Rominski
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Bettina Schulthess
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland.,Nationales Zentrum für Mykobakterien, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Daniel M Müller
- Institut für Klinische Chemie, UniversitätsSpital Zürich, Rämistrasse 100, 8091 Zürich, Switzerland
| | - Peter M Keller
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland.,Nationales Zentrum für Mykobakterien, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Peter Sander
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland.,Nationales Zentrum für Mykobakterien, Gloriastrasse 30/32, 8006 Zürich, Switzerland
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40
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Zignol M, Cabibbe AM, Dean AS, Glaziou P, Alikhanova N, Ama C, Andres S, Barbova A, Borbe-Reyes A, Chin DP, Cirillo DM, Colvin C, Dadu A, Dreyer A, Driesen M, Gilpin C, Hasan R, Hasan Z, Hoffner S, Hussain A, Ismail N, Kamal SMM, Khanzada FM, Kimerling M, Kohl TA, Mansjö M, Miotto P, Mukadi YD, Mvusi L, Niemann S, Omar SV, Rigouts L, Schito M, Sela I, Seyfaddinova M, Skenders G, Skrahina A, Tahseen S, Wells WA, Zhurilo A, Weyer K, Floyd K, Raviglione MC. Genetic sequencing for surveillance of drug resistance in tuberculosis in highly endemic countries: a multi-country population-based surveillance study. THE LANCET. INFECTIOUS DISEASES 2018; 18:675-683. [PMID: 29574065 PMCID: PMC5968368 DOI: 10.1016/s1473-3099(18)30073-2] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/05/2018] [Accepted: 01/30/2018] [Indexed: 12/02/2022]
Abstract
Background In many countries, regular monitoring of the emergence of resistance to anti-tuberculosis drugs is hampered by the limitations of phenotypic testing for drug susceptibility. We therefore evaluated the use of genetic sequencing for surveillance of drug resistance in tuberculosis. Methods Population-level surveys were done in hospitals and clinics in seven countries (Azerbaijan, Bangladesh, Belarus, Pakistan, Philippines, South Africa, and Ukraine) to evaluate the use of genetic sequencing to estimate the resistance of Mycobacterium tuberculosis isolates to rifampicin, isoniazid, ofloxacin, moxifloxacin, pyrazinamide, kanamycin, amikacin, and capreomycin. For each drug, we assessed the accuracy of genetic sequencing by a comparison of the adjusted prevalence of resistance, measured by genetic sequencing, with the true prevalence of resistance, determined by phenotypic testing. Findings Isolates were taken from 7094 patients with tuberculosis who were enrolled in the study between November, 2009, and May, 2014. In all tuberculosis cases, the overall pooled sensitivity values for predicting resistance by genetic sequencing were 91% (95% CI 87–94) for rpoB (rifampicin resistance), 86% (74–93) for katG, inhA, and fabG promoter combined (isoniazid resistance), 54% (39–68) for pncA (pyrazinamide resistance), 85% (77–91) for gyrA and gyrB combined (ofloxacin resistance), and 88% (81–92) for gyrA and gyrB combined (moxifloxacin resistance). For nearly all drugs and in most settings, there was a large overlap in the estimated prevalence of drug resistance by genetic sequencing and the estimated prevalence by phenotypic testing. Interpretation Genetic sequencing can be a valuable tool for surveillance of drug resistance, providing new opportunities to monitor drug resistance in tuberculosis in resource-poor countries. Before its widespread adoption for surveillance purposes, there is a need to standardise DNA extraction methods, recording and reporting nomenclature, and data interpretation. Funding Bill & Melinda Gates Foundation, United States Agency for International Development, Global Alliance for Tuberculosis Drug Development.
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Affiliation(s)
- Matteo Zignol
- Global Tuberculosis Programme, World Health Organization, Geneva, Switzerland.
| | - Andrea Maurizio Cabibbe
- Global Tuberculosis Programme, World Health Organization, Geneva, Switzerland; San Raffaele Scientific Institute, Milan, Italy
| | - Anna S Dean
- Global Tuberculosis Programme, World Health Organization, Geneva, Switzerland
| | - Philippe Glaziou
- Global Tuberculosis Programme, World Health Organization, Geneva, Switzerland
| | - Natavan Alikhanova
- Scientific Research Institute of Lung Diseases, Ministry of Health, Baku, Azerbaijan
| | - Cecilia Ama
- National Tuberculosis Reference Laboratory, Manila, Philippines
| | - Sönke Andres
- National Reference Laboratory for Mycobacteria, Borstel Research Centre, Borstel, Germany
| | - Anna Barbova
- Central Reference Laboratory on Tuberculosis Microbiological Diagnostics, Ministry of Health, Kiev, Ukraine
| | | | | | | | - Charlotte Colvin
- Bureau for Global Health, US Agency for International Development, Washington, DC, USA
| | - Andrei Dadu
- Regional Office for Europe, World Health Organization, Copenhagen, Denmark
| | - Andries Dreyer
- National Institute for Communicable Diseases, Sandringham, South Africa
| | - Michèle Driesen
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Christopher Gilpin
- Global Tuberculosis Programme, World Health Organization, Geneva, Switzerland
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Sven Hoffner
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Alamdar Hussain
- National Reference Laboratory, National Tuberculosis Control Programme, Islamabad, Pakistan
| | - Nazir Ismail
- National Institute for Communicable Diseases, Sandringham, South Africa; Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - S M Mostofa Kamal
- Department of Pathology and Microbiology, National Institute of Diseases of the Chest and Hospital, Dhaka, Bangladesh
| | - Faisal Masood Khanzada
- National Reference Laboratory, National Tuberculosis Control Programme, Islamabad, Pakistan
| | | | - Thomas Andreas Kohl
- Molecular and Experimental Mycobacteriology, Borstel Research Centre, Borstel, Germany
| | - Mikael Mansjö
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | | | - Ya Diul Mukadi
- Bureau for Global Health, US Agency for International Development, Washington, DC, USA
| | - Lindiwe Mvusi
- Tuberculosis Control and Management Unit, National Department of Health, Pretoria, South Africa
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Borstel Research Centre, Borstel, Germany
| | - Shaheed V Omar
- National Institute for Communicable Diseases, Sandringham, South Africa
| | - Leen Rigouts
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Ivita Sela
- Department of Mycobacteriology, Tuberculosis and Lung Disease Centre, Riga East University Hospital, Riga, Latvia
| | - Mehriban Seyfaddinova
- Scientific Research Institute of Lung Diseases, Ministry of Health, Baku, Azerbaijan
| | - Girts Skenders
- Department of Mycobacteriology, Tuberculosis and Lung Disease Centre, Riga East University Hospital, Riga, Latvia
| | - Alena Skrahina
- Republican Scientific and Practical Centre for Pulmonology and Tuberculosis, Minsk, Belarus
| | - Sabira Tahseen
- National Reference Laboratory, National Tuberculosis Control Programme, Islamabad, Pakistan
| | - William A Wells
- Bureau for Global Health, US Agency for International Development, Washington, DC, USA
| | - Alexander Zhurilo
- National Institute of Phthisiology And Pulmonology, National Academy of Medical Science of Ukraine, Kiev, Ukraine
| | - Karin Weyer
- Global Tuberculosis Programme, World Health Organization, Geneva, Switzerland
| | - Katherine Floyd
- Global Tuberculosis Programme, World Health Organization, Geneva, Switzerland
| | - Mario C Raviglione
- Global Tuberculosis Programme, World Health Organization, Geneva, Switzerland
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Martin IW, Dionne K, Deml SM, Wengenack NL, Parrish NM. Automated broth-based systems versus the MYCOTB plate for antimicrobial susceptibility testing of the Mycobacterium tuberculosis complex: challenges in interpretation. Diagn Microbiol Infect Dis 2018; 91:38-41. [PMID: 29422273 DOI: 10.1016/j.diagmicrobio.2018.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/20/2017] [Accepted: 01/01/2018] [Indexed: 11/25/2022]
Abstract
We examined categorical agreement between automated mycobacterial susceptibility testing methods (Mycobacterial Growth Indicator Tube [MGIT] 960 System and the VersaTREK Mycobacteria Detection and Susceptibility System) which are based on single critical concentration (CC) "breakpoints" and a commercial microbroth dilution method (Sensititre Mycobacterium tuberculosis MIC Plate [MYCOTB]) which provides an MIC value. Mycobacterium tuberculosis isolates (n=355) were tested against three first-line antimycobacterial agents (ethambutol [EMB], isoniazid [INH], rifampin [RIF]) using the MYCOTB plate and either the MGIT 960 (site 1, n=142) or VersaTREK (site 2, n=213) systems. Overall categorical agreement was 96.8%. When stratified by drug and CC-defined susceptible and resistant isolates, concordance ranged from 75% to 100%. Interpretation of MIC-based results versus established CC-based results was challenging for drugs whose CC was not represented by an exactly equivalent concentration in the manufacturer-defined dilutions on the MYCOTB plate (EMB, INH). We propose interpretations of MYCOTB plate MICs using the currently available plate configuration.
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Affiliation(s)
- Isabella W Martin
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Kim Dionne
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Sharon M Deml
- Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, USA
| | | | - Nicole M Parrish
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, USA.
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42
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Heyckendorf J, Andres S, Köser CU, Olaru ID, Schön T, Sturegård E, Beckert P, Schleusener V, Kohl TA, Hillemann D, Moradigaravand D, Parkhill J, Peacock SJ, Niemann S, Lange C, Merker M. What Is Resistance? Impact of Phenotypic versus Molecular Drug Resistance Testing on Therapy for Multi- and Extensively Drug-Resistant Tuberculosis. Antimicrob Agents Chemother 2018; 62:e01550-17. [PMID: 29133554 PMCID: PMC5786814 DOI: 10.1128/aac.01550-17] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 10/26/2017] [Indexed: 12/29/2022] Open
Abstract
Rapid and accurate drug susceptibility testing (DST) is essential for the treatment of multi- and extensively drug-resistant tuberculosis (M/XDR-TB). We compared the utility of genotypic DST assays with phenotypic DST (pDST) using Bactec 960 MGIT or Löwenstein-Jensen to construct M/XDR-TB treatment regimens for a cohort of 25 consecutive M/XDR-TB patients and 15 possible anti-TB drugs. Genotypic DST results from Cepheid GeneXpert MTB/RIF (Xpert) and line probe assays (LPAs; Hain GenoType MTBDRplus 2.0 and MTBDRsl 2.0) and whole-genome sequencing (WGS) were translated into individual algorithm-derived treatment regimens for each patient. We further analyzed if discrepancies between the various methods were due to flaws in the genotypic or phenotypic test using MIC results. Compared with pDST, the average agreement in the number of drugs prescribed in genotypic regimens ranged from just 49% (95% confidence interval [CI], 39 to 59%) for Xpert and 63% (95% CI, 56 to 70%) for LPAs to 93% (95% CI, 88 to 98%) for WGS. Only the WGS regimens did not contain any drugs to which pDST showed resistance. Importantly, MIC testing revealed that pDST likely underestimated the true rate of resistance for key drugs (rifampin, levofloxacin, moxifloxacin, and kanamycin) because critical concentrations (CCs) were too high. WGS can be used to rule in resistance even in M/XDR strains with complex resistance patterns, but pDST for some drugs is still needed to confirm susceptibility and construct the final regimens. Some CCs for pDST need to be reexamined to avoid systematic false-susceptible results in low-level resistant isolates.
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Affiliation(s)
- Jan Heyckendorf
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel, Borstel, Germany
- International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - Sönke Andres
- Division of Mycobacteriology (National Tuberculosis Reference Laboratory), Research Center Borstel, Borstel, Germany
| | - Claudio U Köser
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Ioana D Olaru
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel, Borstel, Germany
| | - Thomas Schön
- Department of Infectious Diseases and Clinical Microbiology, Kalmar County Hospital, Kalmar, Sweden
- Department of Clinical and Experimental Medicine, Division of Medical Microbiology, Linköping University, Linköping, Sweden
| | - Erik Sturegård
- Clinical Microbiology, Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Patrick Beckert
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel, Borstel, Germany
- Division of Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Viola Schleusener
- Division of Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Thomas A Kohl
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel, Borstel, Germany
- Division of Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Doris Hillemann
- Division of Mycobacteriology (National Tuberculosis Reference Laboratory), Research Center Borstel, Borstel, Germany
| | | | | | - Sharon J Peacock
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Stefan Niemann
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel, Borstel, Germany
- Division of Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Christoph Lange
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel, Borstel, Germany
- International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Medicine, University of Namibia School of Medicine, Windhoek, Namibia
| | - Matthias Merker
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel, Borstel, Germany
- Division of Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
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Ismail NA, Omar SV, Joseph L, Govender N, Blows L, Ismail F, Koornhof H, Dreyer AW, Kaniga K, Ndjeka N. Defining Bedaquiline Susceptibility, Resistance, Cross-Resistance and Associated Genetic Determinants: A Retrospective Cohort Study. EBioMedicine 2018; 28:136-142. [PMID: 29337135 PMCID: PMC5835552 DOI: 10.1016/j.ebiom.2018.01.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 12/22/2017] [Accepted: 01/04/2018] [Indexed: 10/26/2022] Open
Abstract
BACKGROUND Bedaquiline (BDQ) is a novel agent approved for use in combination treatment of multi-drug resistant tuberculosis (MDR-TB). We sought to determine BDQ epidemiological cut-off values (ECVs), define and assess interpretive criteria against putative resistance associated variants (RAVs), microbiological outcomes and cross resistance with clofazimine (CFZ). METHODS A retrospective cohort study was conducted. Minimal inhibitory concentrations (MIC) to BDQ were determined using 7H9 broth microdilution (BMD) and MGIT960. RAVs were genetically characterised using whole genome sequencing. BDQ ECVs were determined using ECOFFinder and compared with 6-month culture conversion status and CFZ MICs. FINDINGS A total of 391 isolates were analysed. Susceptible and intermediate categories were determined to have MICs of ≤0.125μg/ml and 0.25μg/ml using BMD and ≤1μg/ml and 2μg/ml using MGIT960 respectively. Microbiological failures occurred among BDQ exposed patients with a non-susceptible BDQ MIC, an Rv0678 mutation and ≤2 active drug classes. The Rv0678 RAVs were not the dominant mechanism of CFZ resistance and cross resistance was limited to isolates with an Rv0678 mutation. INTERPRETATION Criteria for BDQ susceptibility are defined and will facilitate improved early detection of resistance. Cross- resistance between BDQ and CFZ is an emerging concern but in this study was primarily among those with an Rv0678 mutation.
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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.
| | - Shaheed V Omar
- National Institute for Communicable Diseases, Centre for Tuberculosis, Johannesburg, 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
| | - Farzana Ismail
- National Institute for Communicable Diseases, Centre for Tuberculosis, Johannesburg, South Africa; Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - Hendrik Koornhof
- National Institute for Communicable Diseases, Centre for Tuberculosis, Johannesburg, South Africa
| | - Andries W Dreyer
- National Institute for Communicable Diseases, Centre for Tuberculosis, Johannesburg, South Africa
| | - Koné Kaniga
- Janssen Research & Development, Titusville, NJ, United States
| | - Norbert Ndjeka
- National Department of Health, Tuberculosis Control and Management Cluster, Pretoria, South Africa
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44
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Nakatani Y, Opel-Reading HK, Merker M, Machado D, Andres S, Kumar SS, Moradigaravand D, Coll F, Perdigão J, Portugal I, Schön T, Nair D, Devi KRU, Kohl TA, Beckert P, Clark TG, Maphalala G, Khumalo D, Diel R, Klaos K, Aung HL, Cook GM, Parkhill J, Peacock SJ, Swaminathan S, Viveiros M, Niemann S, Krause KL, Köser CU. Role of Alanine Racemase Mutations in Mycobacterium tuberculosis d-Cycloserine Resistance. Antimicrob Agents Chemother 2017; 61:e01575-17. [PMID: 28971867 PMCID: PMC5700341 DOI: 10.1128/aac.01575-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 09/25/2017] [Indexed: 11/23/2022] Open
Abstract
A screening of more than 1,500 drug-resistant strains of Mycobacterium tuberculosis revealed evolutionary patterns characteristic of positive selection for three alanine racemase (Alr) mutations. We investigated these mutations using molecular modeling, in vitro MIC testing, as well as direct measurements of enzymatic activity, which demonstrated that these mutations likely confer resistance to d-cycloserine.
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Affiliation(s)
- Yoshio Nakatani
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
| | - Helen K Opel-Reading
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Borstel-Lübeck, Germany
| | - Diana Machado
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Sönke Andres
- Division of Mycobacteriology (National Tuberculosis Reference Laboratory), Research Center Borstel, Borstel, Germany
| | - S Siva Kumar
- National Institute for Research in Tuberculosis, Chennai, India
| | | | - Francesc Coll
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - João Perdigão
- Med.ULisboa-Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Portugal
- Med.ULisboa-Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Thomas Schön
- Department of Clinical and Experimental Medicine, Division of Medical Microbiology, Linköping University, Linköping, Sweden
- Department of Clinical Microbiology and Infectious Diseases, Kalmar County Hospital, Kalmar, Sweden
| | - Dina Nair
- National Institute for Research in Tuberculosis, Chennai, India
| | - K R Uma Devi
- National Institute for Research in Tuberculosis, Chennai, India
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Patrick Beckert
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Borstel-Lübeck, Germany
| | - Taane G Clark
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Gugu Maphalala
- National Reference Laboratory, Ministry of Health, Mbabane, Swaziland
| | - Derrick Khumalo
- National Tuberculosis Control Program, Ministry of Health, Manzini, Swaziland
| | - Roland Diel
- Institute of Epidemiology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Kadri Klaos
- Tartu University Hospital, United Laboratories, Mycobacteriology, Tartu, Estonia
| | - Htin Lin Aung
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
| | | | - Sharon J Peacock
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Soumya Swaminathan
- Department of Health Research and Director General, Indian Council of Medical Research, New Delhi, India
| | - Miguel Viveiros
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Borstel-Lübeck, Germany
| | - Kurt L Krause
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
| | - Claudio U Köser
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
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Xie YL, Chakravorty S, Armstrong DT, Hall SL, Via LE, Song T, Yuan X, Mo X, Zhu H, Xu P, Gao Q, Lee M, Lee J, Smith LE, Chen RY, Joh JS, Cho Y, Liu X, Ruan X, Liang L, Dharan N, Cho SN, Barry CE, Ellner JJ, Dorman SE, Alland D. Evaluation of a Rapid Molecular Drug-Susceptibility Test for Tuberculosis. N Engl J Med 2017; 377:1043-1054. [PMID: 28902596 PMCID: PMC5727572 DOI: 10.1056/nejmoa1614915] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Fluoroquinolones and second-line injectable drugs are the backbone of treatment regimens for multidrug-resistant tuberculosis, and resistance to these drugs defines extensively drug-resistant tuberculosis. We assessed the accuracy of an automated, cartridge-based molecular assay for the detection, directly from sputum specimens, of Mycobacterium tuberculosis with resistance to fluoroquinolones, aminoglycosides, and isoniazid. METHODS We conducted a prospective diagnostic accuracy study to compare the investigational assay against phenotypic drug-susceptibility testing and DNA sequencing among adults in China and South Korea who had symptoms of tuberculosis. The Xpert MTB/RIF assay and sputum culture were performed. M. tuberculosis isolates underwent phenotypic drug-susceptibility testing and DNA sequencing of the genes katG, gyrA, gyrB, and rrs and of the eis and inhA promoter regions. RESULTS Among the 308 participants who were culture-positive for M. tuberculosis, when phenotypic drug-susceptibility testing was used as the reference standard, the sensitivities of the investigational assay for detecting resistance were 83.3% for isoniazid (95% confidence interval [CI], 77.1 to 88.5), 88.4% for ofloxacin (95% CI, 80.2 to 94.1), 87.6% for moxifloxacin at a critical concentration of 0.5 μg per milliliter (95% CI, 79.0 to 93.7), 96.2% for moxifloxacin at a critical concentration of 2.0 μg per milliliter (95% CI, 87.0 to 99.5), 71.4% for kanamycin (95% CI, 56.7 to 83.4), and 70.7% for amikacin (95% CI, 54.5 to 83.9). The specificity of the assay for the detection of phenotypic resistance was 94.3% or greater for all drugs except moxifloxacin at a critical concentration of 2.0 μg per milliliter (specificity, 84.0% [95% CI, 78.9 to 88.3]). When DNA sequencing was used as the reference standard, the sensitivities of the investigational assay for detecting mutations associated with resistance were 98.1% for isoniazid (95% CI, 94.4 to 99.6), 95.8% for fluoroquinolones (95% CI, 89.6 to 98.8), 92.7% for kanamycin (95% CI, 80.1 to 98.5), and 96.8% for amikacin (95% CI, 83.3 to 99.9), and the specificity for all drugs was 99.6% (95% CI, 97.9 to 100) or greater. CONCLUSIONS This investigational assay accurately detected M. tuberculosis mutations associated with resistance to isoniazid, fluoroquinolones, and aminoglycosides and holds promise as a rapid point-of-care test to guide therapeutic decisions for patients with tuberculosis. (Funded by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, and the Ministry of Science and Technology of China; ClinicalTrials.gov number, NCT02251327 .).
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Affiliation(s)
- Yingda L Xie
- From the Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (Y.L.X., L.E.V., R.Y.C., C.E.B.), and Johns Hopkins University School of Medicine, Baltimore (D.T.A., S.E.D.) - both in Maryland; the Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark (S.C., L.E.S., N.D., D.A.); Boston Medical Center and Boston University School of Medicine, Boston (S.L.H., J.J.E.); the International Tuberculosis Research Center, Changwon (T.S., M.L., J.L., S.-N.C.), and the National Medical Center (J.S.J.), Seoul Metropolitan Seobuk Hospital (Y.C.), and the Department of Microbiology, College of Medicine, Yonsei University (S.-N.C.), Seoul - all in South Korea; Henan Provincial Chest Hospital (X.Y., X.M., X.L., X.R., L.L.) and Sino-U.S. Tuberculosis Research Collaboration (H.Z.), Zhengzhou, and Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science, Fudan University, Shanghai (P.X., Q.G.) - all in China; and the Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa (C.E.B.)
| | - Soumitesh Chakravorty
- From the Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (Y.L.X., L.E.V., R.Y.C., C.E.B.), and Johns Hopkins University School of Medicine, Baltimore (D.T.A., S.E.D.) - both in Maryland; the Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark (S.C., L.E.S., N.D., D.A.); Boston Medical Center and Boston University School of Medicine, Boston (S.L.H., J.J.E.); the International Tuberculosis Research Center, Changwon (T.S., M.L., J.L., S.-N.C.), and the National Medical Center (J.S.J.), Seoul Metropolitan Seobuk Hospital (Y.C.), and the Department of Microbiology, College of Medicine, Yonsei University (S.-N.C.), Seoul - all in South Korea; Henan Provincial Chest Hospital (X.Y., X.M., X.L., X.R., L.L.) and Sino-U.S. Tuberculosis Research Collaboration (H.Z.), Zhengzhou, and Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science, Fudan University, Shanghai (P.X., Q.G.) - all in China; and the Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa (C.E.B.)
| | - Derek T Armstrong
- From the Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (Y.L.X., L.E.V., R.Y.C., C.E.B.), and Johns Hopkins University School of Medicine, Baltimore (D.T.A., S.E.D.) - both in Maryland; the Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark (S.C., L.E.S., N.D., D.A.); Boston Medical Center and Boston University School of Medicine, Boston (S.L.H., J.J.E.); the International Tuberculosis Research Center, Changwon (T.S., M.L., J.L., S.-N.C.), and the National Medical Center (J.S.J.), Seoul Metropolitan Seobuk Hospital (Y.C.), and the Department of Microbiology, College of Medicine, Yonsei University (S.-N.C.), Seoul - all in South Korea; Henan Provincial Chest Hospital (X.Y., X.M., X.L., X.R., L.L.) and Sino-U.S. Tuberculosis Research Collaboration (H.Z.), Zhengzhou, and Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science, Fudan University, Shanghai (P.X., Q.G.) - all in China; and the Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa (C.E.B.)
| | - Sandra L Hall
- From the Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (Y.L.X., L.E.V., R.Y.C., C.E.B.), and Johns Hopkins University School of Medicine, Baltimore (D.T.A., S.E.D.) - both in Maryland; the Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark (S.C., L.E.S., N.D., D.A.); Boston Medical Center and Boston University School of Medicine, Boston (S.L.H., J.J.E.); the International Tuberculosis Research Center, Changwon (T.S., M.L., J.L., S.-N.C.), and the National Medical Center (J.S.J.), Seoul Metropolitan Seobuk Hospital (Y.C.), and the Department of Microbiology, College of Medicine, Yonsei University (S.-N.C.), Seoul - all in South Korea; Henan Provincial Chest Hospital (X.Y., X.M., X.L., X.R., L.L.) and Sino-U.S. Tuberculosis Research Collaboration (H.Z.), Zhengzhou, and Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science, Fudan University, Shanghai (P.X., Q.G.) - all in China; and the Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa (C.E.B.)
| | - Laura E Via
- From the Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (Y.L.X., L.E.V., R.Y.C., C.E.B.), and Johns Hopkins University School of Medicine, Baltimore (D.T.A., S.E.D.) - both in Maryland; the Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark (S.C., L.E.S., N.D., D.A.); Boston Medical Center and Boston University School of Medicine, Boston (S.L.H., J.J.E.); the International Tuberculosis Research Center, Changwon (T.S., M.L., J.L., S.-N.C.), and the National Medical Center (J.S.J.), Seoul Metropolitan Seobuk Hospital (Y.C.), and the Department of Microbiology, College of Medicine, Yonsei University (S.-N.C.), Seoul - all in South Korea; Henan Provincial Chest Hospital (X.Y., X.M., X.L., X.R., L.L.) and Sino-U.S. Tuberculosis Research Collaboration (H.Z.), Zhengzhou, and Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science, Fudan University, Shanghai (P.X., Q.G.) - all in China; and the Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa (C.E.B.)
| | - Taeksun Song
- From the Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (Y.L.X., L.E.V., R.Y.C., C.E.B.), and Johns Hopkins University School of Medicine, Baltimore (D.T.A., S.E.D.) - both in Maryland; the Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark (S.C., L.E.S., N.D., D.A.); Boston Medical Center and Boston University School of Medicine, Boston (S.L.H., J.J.E.); the International Tuberculosis Research Center, Changwon (T.S., M.L., J.L., S.-N.C.), and the National Medical Center (J.S.J.), Seoul Metropolitan Seobuk Hospital (Y.C.), and the Department of Microbiology, College of Medicine, Yonsei University (S.-N.C.), Seoul - all in South Korea; Henan Provincial Chest Hospital (X.Y., X.M., X.L., X.R., L.L.) and Sino-U.S. Tuberculosis Research Collaboration (H.Z.), Zhengzhou, and Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science, Fudan University, Shanghai (P.X., Q.G.) - all in China; and the Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa (C.E.B.)
| | - Xing Yuan
- From the Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (Y.L.X., L.E.V., R.Y.C., C.E.B.), and Johns Hopkins University School of Medicine, Baltimore (D.T.A., S.E.D.) - both in Maryland; the Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark (S.C., L.E.S., N.D., D.A.); Boston Medical Center and Boston University School of Medicine, Boston (S.L.H., J.J.E.); the International Tuberculosis Research Center, Changwon (T.S., M.L., J.L., S.-N.C.), and the National Medical Center (J.S.J.), Seoul Metropolitan Seobuk Hospital (Y.C.), and the Department of Microbiology, College of Medicine, Yonsei University (S.-N.C.), Seoul - all in South Korea; Henan Provincial Chest Hospital (X.Y., X.M., X.L., X.R., L.L.) and Sino-U.S. Tuberculosis Research Collaboration (H.Z.), Zhengzhou, and Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science, Fudan University, Shanghai (P.X., Q.G.) - all in China; and the Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa (C.E.B.)
| | - Xiaoying Mo
- From the Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (Y.L.X., L.E.V., R.Y.C., C.E.B.), and Johns Hopkins University School of Medicine, Baltimore (D.T.A., S.E.D.) - both in Maryland; the Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark (S.C., L.E.S., N.D., D.A.); Boston Medical Center and Boston University School of Medicine, Boston (S.L.H., J.J.E.); the International Tuberculosis Research Center, Changwon (T.S., M.L., J.L., S.-N.C.), and the National Medical Center (J.S.J.), Seoul Metropolitan Seobuk Hospital (Y.C.), and the Department of Microbiology, College of Medicine, Yonsei University (S.-N.C.), Seoul - all in South Korea; Henan Provincial Chest Hospital (X.Y., X.M., X.L., X.R., L.L.) and Sino-U.S. Tuberculosis Research Collaboration (H.Z.), Zhengzhou, and Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science, Fudan University, Shanghai (P.X., Q.G.) - all in China; and the Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa (C.E.B.)
| | - Hong Zhu
- From the Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (Y.L.X., L.E.V., R.Y.C., C.E.B.), and Johns Hopkins University School of Medicine, Baltimore (D.T.A., S.E.D.) - both in Maryland; the Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark (S.C., L.E.S., N.D., D.A.); Boston Medical Center and Boston University School of Medicine, Boston (S.L.H., J.J.E.); the International Tuberculosis Research Center, Changwon (T.S., M.L., J.L., S.-N.C.), and the National Medical Center (J.S.J.), Seoul Metropolitan Seobuk Hospital (Y.C.), and the Department of Microbiology, College of Medicine, Yonsei University (S.-N.C.), Seoul - all in South Korea; Henan Provincial Chest Hospital (X.Y., X.M., X.L., X.R., L.L.) and Sino-U.S. Tuberculosis Research Collaboration (H.Z.), Zhengzhou, and Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science, Fudan University, Shanghai (P.X., Q.G.) - all in China; and the Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa (C.E.B.)
| | - Peng Xu
- From the Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (Y.L.X., L.E.V., R.Y.C., C.E.B.), and Johns Hopkins University School of Medicine, Baltimore (D.T.A., S.E.D.) - both in Maryland; the Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark (S.C., L.E.S., N.D., D.A.); Boston Medical Center and Boston University School of Medicine, Boston (S.L.H., J.J.E.); the International Tuberculosis Research Center, Changwon (T.S., M.L., J.L., S.-N.C.), and the National Medical Center (J.S.J.), Seoul Metropolitan Seobuk Hospital (Y.C.), and the Department of Microbiology, College of Medicine, Yonsei University (S.-N.C.), Seoul - all in South Korea; Henan Provincial Chest Hospital (X.Y., X.M., X.L., X.R., L.L.) and Sino-U.S. Tuberculosis Research Collaboration (H.Z.), Zhengzhou, and Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science, Fudan University, Shanghai (P.X., Q.G.) - all in China; and the Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa (C.E.B.)
| | - Qian Gao
- From the Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (Y.L.X., L.E.V., R.Y.C., C.E.B.), and Johns Hopkins University School of Medicine, Baltimore (D.T.A., S.E.D.) - both in Maryland; the Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark (S.C., L.E.S., N.D., D.A.); Boston Medical Center and Boston University School of Medicine, Boston (S.L.H., J.J.E.); the International Tuberculosis Research Center, Changwon (T.S., M.L., J.L., S.-N.C.), and the National Medical Center (J.S.J.), Seoul Metropolitan Seobuk Hospital (Y.C.), and the Department of Microbiology, College of Medicine, Yonsei University (S.-N.C.), Seoul - all in South Korea; Henan Provincial Chest Hospital (X.Y., X.M., X.L., X.R., L.L.) and Sino-U.S. Tuberculosis Research Collaboration (H.Z.), Zhengzhou, and Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science, Fudan University, Shanghai (P.X., Q.G.) - all in China; and the Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa (C.E.B.)
| | - Myungsun Lee
- From the Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (Y.L.X., L.E.V., R.Y.C., C.E.B.), and Johns Hopkins University School of Medicine, Baltimore (D.T.A., S.E.D.) - both in Maryland; the Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark (S.C., L.E.S., N.D., D.A.); Boston Medical Center and Boston University School of Medicine, Boston (S.L.H., J.J.E.); the International Tuberculosis Research Center, Changwon (T.S., M.L., J.L., S.-N.C.), and the National Medical Center (J.S.J.), Seoul Metropolitan Seobuk Hospital (Y.C.), and the Department of Microbiology, College of Medicine, Yonsei University (S.-N.C.), Seoul - all in South Korea; Henan Provincial Chest Hospital (X.Y., X.M., X.L., X.R., L.L.) and Sino-U.S. Tuberculosis Research Collaboration (H.Z.), Zhengzhou, and Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science, Fudan University, Shanghai (P.X., Q.G.) - all in China; and the Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa (C.E.B.)
| | - Jongseok Lee
- From the Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (Y.L.X., L.E.V., R.Y.C., C.E.B.), and Johns Hopkins University School of Medicine, Baltimore (D.T.A., S.E.D.) - both in Maryland; the Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark (S.C., L.E.S., N.D., D.A.); Boston Medical Center and Boston University School of Medicine, Boston (S.L.H., J.J.E.); the International Tuberculosis Research Center, Changwon (T.S., M.L., J.L., S.-N.C.), and the National Medical Center (J.S.J.), Seoul Metropolitan Seobuk Hospital (Y.C.), and the Department of Microbiology, College of Medicine, Yonsei University (S.-N.C.), Seoul - all in South Korea; Henan Provincial Chest Hospital (X.Y., X.M., X.L., X.R., L.L.) and Sino-U.S. Tuberculosis Research Collaboration (H.Z.), Zhengzhou, and Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science, Fudan University, Shanghai (P.X., Q.G.) - all in China; and the Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa (C.E.B.)
| | - Laura E Smith
- From the Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (Y.L.X., L.E.V., R.Y.C., C.E.B.), and Johns Hopkins University School of Medicine, Baltimore (D.T.A., S.E.D.) - both in Maryland; the Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark (S.C., L.E.S., N.D., D.A.); Boston Medical Center and Boston University School of Medicine, Boston (S.L.H., J.J.E.); the International Tuberculosis Research Center, Changwon (T.S., M.L., J.L., S.-N.C.), and the National Medical Center (J.S.J.), Seoul Metropolitan Seobuk Hospital (Y.C.), and the Department of Microbiology, College of Medicine, Yonsei University (S.-N.C.), Seoul - all in South Korea; Henan Provincial Chest Hospital (X.Y., X.M., X.L., X.R., L.L.) and Sino-U.S. Tuberculosis Research Collaboration (H.Z.), Zhengzhou, and Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science, Fudan University, Shanghai (P.X., Q.G.) - all in China; and the Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa (C.E.B.)
| | - Ray Y Chen
- From the Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (Y.L.X., L.E.V., R.Y.C., C.E.B.), and Johns Hopkins University School of Medicine, Baltimore (D.T.A., S.E.D.) - both in Maryland; the Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark (S.C., L.E.S., N.D., D.A.); Boston Medical Center and Boston University School of Medicine, Boston (S.L.H., J.J.E.); the International Tuberculosis Research Center, Changwon (T.S., M.L., J.L., S.-N.C.), and the National Medical Center (J.S.J.), Seoul Metropolitan Seobuk Hospital (Y.C.), and the Department of Microbiology, College of Medicine, Yonsei University (S.-N.C.), Seoul - all in South Korea; Henan Provincial Chest Hospital (X.Y., X.M., X.L., X.R., L.L.) and Sino-U.S. Tuberculosis Research Collaboration (H.Z.), Zhengzhou, and Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science, Fudan University, Shanghai (P.X., Q.G.) - all in China; and the Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa (C.E.B.)
| | - Joon Sung Joh
- From the Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (Y.L.X., L.E.V., R.Y.C., C.E.B.), and Johns Hopkins University School of Medicine, Baltimore (D.T.A., S.E.D.) - both in Maryland; the Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark (S.C., L.E.S., N.D., D.A.); Boston Medical Center and Boston University School of Medicine, Boston (S.L.H., J.J.E.); the International Tuberculosis Research Center, Changwon (T.S., M.L., J.L., S.-N.C.), and the National Medical Center (J.S.J.), Seoul Metropolitan Seobuk Hospital (Y.C.), and the Department of Microbiology, College of Medicine, Yonsei University (S.-N.C.), Seoul - all in South Korea; Henan Provincial Chest Hospital (X.Y., X.M., X.L., X.R., L.L.) and Sino-U.S. Tuberculosis Research Collaboration (H.Z.), Zhengzhou, and Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science, Fudan University, Shanghai (P.X., Q.G.) - all in China; and the Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa (C.E.B.)
| | - YoungSoo Cho
- From the Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (Y.L.X., L.E.V., R.Y.C., C.E.B.), and Johns Hopkins University School of Medicine, Baltimore (D.T.A., S.E.D.) - both in Maryland; the Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark (S.C., L.E.S., N.D., D.A.); Boston Medical Center and Boston University School of Medicine, Boston (S.L.H., J.J.E.); the International Tuberculosis Research Center, Changwon (T.S., M.L., J.L., S.-N.C.), and the National Medical Center (J.S.J.), Seoul Metropolitan Seobuk Hospital (Y.C.), and the Department of Microbiology, College of Medicine, Yonsei University (S.-N.C.), Seoul - all in South Korea; Henan Provincial Chest Hospital (X.Y., X.M., X.L., X.R., L.L.) and Sino-U.S. Tuberculosis Research Collaboration (H.Z.), Zhengzhou, and Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science, Fudan University, Shanghai (P.X., Q.G.) - all in China; and the Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa (C.E.B.)
| | - Xin Liu
- From the Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (Y.L.X., L.E.V., R.Y.C., C.E.B.), and Johns Hopkins University School of Medicine, Baltimore (D.T.A., S.E.D.) - both in Maryland; the Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark (S.C., L.E.S., N.D., D.A.); Boston Medical Center and Boston University School of Medicine, Boston (S.L.H., J.J.E.); the International Tuberculosis Research Center, Changwon (T.S., M.L., J.L., S.-N.C.), and the National Medical Center (J.S.J.), Seoul Metropolitan Seobuk Hospital (Y.C.), and the Department of Microbiology, College of Medicine, Yonsei University (S.-N.C.), Seoul - all in South Korea; Henan Provincial Chest Hospital (X.Y., X.M., X.L., X.R., L.L.) and Sino-U.S. Tuberculosis Research Collaboration (H.Z.), Zhengzhou, and Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science, Fudan University, Shanghai (P.X., Q.G.) - all in China; and the Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa (C.E.B.)
| | - Xianglin Ruan
- From the Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (Y.L.X., L.E.V., R.Y.C., C.E.B.), and Johns Hopkins University School of Medicine, Baltimore (D.T.A., S.E.D.) - both in Maryland; the Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark (S.C., L.E.S., N.D., D.A.); Boston Medical Center and Boston University School of Medicine, Boston (S.L.H., J.J.E.); the International Tuberculosis Research Center, Changwon (T.S., M.L., J.L., S.-N.C.), and the National Medical Center (J.S.J.), Seoul Metropolitan Seobuk Hospital (Y.C.), and the Department of Microbiology, College of Medicine, Yonsei University (S.-N.C.), Seoul - all in South Korea; Henan Provincial Chest Hospital (X.Y., X.M., X.L., X.R., L.L.) and Sino-U.S. Tuberculosis Research Collaboration (H.Z.), Zhengzhou, and Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science, Fudan University, Shanghai (P.X., Q.G.) - all in China; and the Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa (C.E.B.)
| | - Lili Liang
- From the Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (Y.L.X., L.E.V., R.Y.C., C.E.B.), and Johns Hopkins University School of Medicine, Baltimore (D.T.A., S.E.D.) - both in Maryland; the Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark (S.C., L.E.S., N.D., D.A.); Boston Medical Center and Boston University School of Medicine, Boston (S.L.H., J.J.E.); the International Tuberculosis Research Center, Changwon (T.S., M.L., J.L., S.-N.C.), and the National Medical Center (J.S.J.), Seoul Metropolitan Seobuk Hospital (Y.C.), and the Department of Microbiology, College of Medicine, Yonsei University (S.-N.C.), Seoul - all in South Korea; Henan Provincial Chest Hospital (X.Y., X.M., X.L., X.R., L.L.) and Sino-U.S. Tuberculosis Research Collaboration (H.Z.), Zhengzhou, and Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science, Fudan University, Shanghai (P.X., Q.G.) - all in China; and the Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa (C.E.B.)
| | - Nila Dharan
- From the Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (Y.L.X., L.E.V., R.Y.C., C.E.B.), and Johns Hopkins University School of Medicine, Baltimore (D.T.A., S.E.D.) - both in Maryland; the Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark (S.C., L.E.S., N.D., D.A.); Boston Medical Center and Boston University School of Medicine, Boston (S.L.H., J.J.E.); the International Tuberculosis Research Center, Changwon (T.S., M.L., J.L., S.-N.C.), and the National Medical Center (J.S.J.), Seoul Metropolitan Seobuk Hospital (Y.C.), and the Department of Microbiology, College of Medicine, Yonsei University (S.-N.C.), Seoul - all in South Korea; Henan Provincial Chest Hospital (X.Y., X.M., X.L., X.R., L.L.) and Sino-U.S. Tuberculosis Research Collaboration (H.Z.), Zhengzhou, and Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science, Fudan University, Shanghai (P.X., Q.G.) - all in China; and the Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa (C.E.B.)
| | - Sang-Nae Cho
- From the Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (Y.L.X., L.E.V., R.Y.C., C.E.B.), and Johns Hopkins University School of Medicine, Baltimore (D.T.A., S.E.D.) - both in Maryland; the Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark (S.C., L.E.S., N.D., D.A.); Boston Medical Center and Boston University School of Medicine, Boston (S.L.H., J.J.E.); the International Tuberculosis Research Center, Changwon (T.S., M.L., J.L., S.-N.C.), and the National Medical Center (J.S.J.), Seoul Metropolitan Seobuk Hospital (Y.C.), and the Department of Microbiology, College of Medicine, Yonsei University (S.-N.C.), Seoul - all in South Korea; Henan Provincial Chest Hospital (X.Y., X.M., X.L., X.R., L.L.) and Sino-U.S. Tuberculosis Research Collaboration (H.Z.), Zhengzhou, and Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science, Fudan University, Shanghai (P.X., Q.G.) - all in China; and the Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa (C.E.B.)
| | - Clifton E Barry
- From the Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (Y.L.X., L.E.V., R.Y.C., C.E.B.), and Johns Hopkins University School of Medicine, Baltimore (D.T.A., S.E.D.) - both in Maryland; the Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark (S.C., L.E.S., N.D., D.A.); Boston Medical Center and Boston University School of Medicine, Boston (S.L.H., J.J.E.); the International Tuberculosis Research Center, Changwon (T.S., M.L., J.L., S.-N.C.), and the National Medical Center (J.S.J.), Seoul Metropolitan Seobuk Hospital (Y.C.), and the Department of Microbiology, College of Medicine, Yonsei University (S.-N.C.), Seoul - all in South Korea; Henan Provincial Chest Hospital (X.Y., X.M., X.L., X.R., L.L.) and Sino-U.S. Tuberculosis Research Collaboration (H.Z.), Zhengzhou, and Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science, Fudan University, Shanghai (P.X., Q.G.) - all in China; and the Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa (C.E.B.)
| | - Jerrold J Ellner
- From the Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (Y.L.X., L.E.V., R.Y.C., C.E.B.), and Johns Hopkins University School of Medicine, Baltimore (D.T.A., S.E.D.) - both in Maryland; the Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark (S.C., L.E.S., N.D., D.A.); Boston Medical Center and Boston University School of Medicine, Boston (S.L.H., J.J.E.); the International Tuberculosis Research Center, Changwon (T.S., M.L., J.L., S.-N.C.), and the National Medical Center (J.S.J.), Seoul Metropolitan Seobuk Hospital (Y.C.), and the Department of Microbiology, College of Medicine, Yonsei University (S.-N.C.), Seoul - all in South Korea; Henan Provincial Chest Hospital (X.Y., X.M., X.L., X.R., L.L.) and Sino-U.S. Tuberculosis Research Collaboration (H.Z.), Zhengzhou, and Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science, Fudan University, Shanghai (P.X., Q.G.) - all in China; and the Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa (C.E.B.)
| | - Susan E Dorman
- From the Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (Y.L.X., L.E.V., R.Y.C., C.E.B.), and Johns Hopkins University School of Medicine, Baltimore (D.T.A., S.E.D.) - both in Maryland; the Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark (S.C., L.E.S., N.D., D.A.); Boston Medical Center and Boston University School of Medicine, Boston (S.L.H., J.J.E.); the International Tuberculosis Research Center, Changwon (T.S., M.L., J.L., S.-N.C.), and the National Medical Center (J.S.J.), Seoul Metropolitan Seobuk Hospital (Y.C.), and the Department of Microbiology, College of Medicine, Yonsei University (S.-N.C.), Seoul - all in South Korea; Henan Provincial Chest Hospital (X.Y., X.M., X.L., X.R., L.L.) and Sino-U.S. Tuberculosis Research Collaboration (H.Z.), Zhengzhou, and Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science, Fudan University, Shanghai (P.X., Q.G.) - all in China; and the Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa (C.E.B.)
| | - David Alland
- From the Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (Y.L.X., L.E.V., R.Y.C., C.E.B.), and Johns Hopkins University School of Medicine, Baltimore (D.T.A., S.E.D.) - both in Maryland; the Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark (S.C., L.E.S., N.D., D.A.); Boston Medical Center and Boston University School of Medicine, Boston (S.L.H., J.J.E.); the International Tuberculosis Research Center, Changwon (T.S., M.L., J.L., S.-N.C.), and the National Medical Center (J.S.J.), Seoul Metropolitan Seobuk Hospital (Y.C.), and the Department of Microbiology, College of Medicine, Yonsei University (S.-N.C.), Seoul - all in South Korea; Henan Provincial Chest Hospital (X.Y., X.M., X.L., X.R., L.L.) and Sino-U.S. Tuberculosis Research Collaboration (H.Z.), Zhengzhou, and Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science, Fudan University, Shanghai (P.X., Q.G.) - all in China; and the Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa (C.E.B.)
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46
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Burke RM, Coronel J, Moore D. Minimum inhibitory concentration distributions for first- and second-line antimicrobials against Mycobacterium tuberculosis. J Med Microbiol 2017; 66:1023-1026. [PMID: 28759352 DOI: 10.1099/jmm.0.000534] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report the range of minimum inhibitory concentrations for six antimicrobial drugs in 228 clinical Mycobacterium tuberculosis (MTB) isolates from three distinct groups of patients (unselected patients, patients at high risk of drug-resistant TB and HIV-positive patients) in Lima, Peru. These data highlight the challenges of and discriminatory characteristics required for MTB drug susceptibility testing.
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Affiliation(s)
- Rachael M Burke
- Hospital for Tropical Diseases, University College London Hospitals NHS Trust, London, UK
| | - Jorge Coronel
- Laboratorio de Investigación de Enfermedades Infecciosas, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - David Moore
- TB Centre, London School of Hygiene and Tropical Medicine, London, UK.,Laboratorio de Investigación de Enfermedades Infecciosas, Universidad Peruana Cayetano Heredia, Lima, Peru.,Hospital for Tropical Diseases, University College London Hospitals NHS Trust, London, UK
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47
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Critical Review: What Dose of Rifabutin Is Recommended With Antiretroviral Therapy? J Acquir Immune Defic Syndr 2017; 72:138-52. [PMID: 26855245 DOI: 10.1097/qai.0000000000000944] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Since the advent of combination antiretroviral therapy to successfully treat HIV infection, drug-drug interactions (DDIs) have become a significant problem as many antiretrovirals (ARVs) are metabolized in the liver. Antituberculous therapy traditionally includes rifamycins, particularly rifampicin. Rifabutin (RBT) has shown similar efficacy as rifampicin but induces CYP3A4 to a lesser degree and is less likely to have DDIs with ARVs. We identified 14 DDI pharmacokinetic studies on HIV monoinfected and HIV-tuberculosis coinfected individuals, and the remaining studies were healthy volunteer studies. Although RBT may be coadministered with most nonnucleoside reverse transcriptase inhibitors, identifying the optimal dose with ritonavir-boosted or cobicistat-boosted protease inhibitors is challenging because of concern about adverse effects with increased RBT exposure. Limited healthy volunteer studies on other ARV drug classes and RBT suggest that dose modification may be unnecessary. The paucity of data assessing clinical tuberculosis endpoints concurrently with RBT and ARV pharmacokinetics limits evidence-based recommendations on the optimal dose of RBT within available ARV drug classes.
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48
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Schleusener V, Köser CU, Beckert P, Niemann S, Feuerriegel S. Mycobacterium tuberculosis resistance prediction and lineage classification from genome sequencing: comparison of automated analysis tools. Sci Rep 2017; 7:46327. [PMID: 28425484 PMCID: PMC7365310 DOI: 10.1038/srep46327] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 03/15/2017] [Indexed: 11/25/2022] Open
Abstract
Whole-genome sequencing (WGS) has the potential to accelerate drug-susceptibility testing (DST) to design appropriate regimens for drug-resistant tuberculosis (TB). Several recently developed automated software tools promise to standardize the analysis and interpretation of WGS data. We assessed five tools (CASTB, KvarQ, Mykrobe Predictor TB, PhyResSE, and TBProfiler) with regards to DST and phylogenetic lineage classification, which we compared with phenotypic DST, Sanger sequencing, and traditional typing results for a collection of 91 strains. The lineage classifications by the tools generally only differed in the resolution of the results. However, some strains could not be classified at all and one strain was misclassified. The sensitivities and specificities for isoniazid and rifampicin resistance of the tools were high, whereas the results for ethambutol, pyrazinamide, and streptomycin resistance were more variable. False-susceptible DST results were mainly due to missing mutations in the resistance catalogues that the respective tools employed for data interpretation. Notably, we also found cases of false-resistance because of the misclassification of polymorphisms as resistance mutations. In conclusion, the performance of current WGS analysis tools for DST is highly variable. Sustainable business models and a shared, high-quality catalogue of resistance mutations are needed to ensure the clinical utility of these tools.
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Affiliation(s)
- Viola Schleusener
- Division of Molecular and Experimental Mycobacteriology Group, Research Center Borstel, Borstel, Germany
| | - Claudio U. Köser
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Patrick Beckert
- Division of Molecular and Experimental Mycobacteriology Group, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Borstel Site, Borstel Germany
| | - Stefan Niemann
- Division of Molecular and Experimental Mycobacteriology Group, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Borstel Site, Borstel Germany
| | - Silke Feuerriegel
- Division of Molecular and Experimental Mycobacteriology Group, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Borstel Site, Borstel Germany
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49
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Hu Y, Wu X, Luo J, Fu Y, Zhao L, Ma Y, Li Y, Liang Q, Shang Y, Huang H. Detection of pyrazinamide resistance of Mycobacterium tuberculosis using nicotinamide as a surrogate. Clin Microbiol Infect 2017; 23:835-838. [PMID: 28411185 DOI: 10.1016/j.cmi.2017.03.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 03/28/2017] [Accepted: 03/28/2017] [Indexed: 11/18/2022]
Abstract
OBJECTIVES Despite the importance of pyrazinamide (PZA) in tuberculosis treatment, PZA susceptibility testing is not routinely performed because of its acid pH requirement. We evaluated the Microplate Alamar Blue assay (MABA) to detect resistance to PZA using nicotinamide (NIC) as a surrogate in neutral pH and identify the appropriate cutoff point for the assay. METHODS The NIC minimal inhibition concentrations (MICs) for 125 Mycobacterium tuberculosis clinical isolates were tested by MABA at nine different concentrations (8-2000 μg/mL). The PZA susceptibility testing by the BACTEC MGIT 960 system was used as a reference method. The pncA gene and its promoter region were sequenced for all the recruited strains. RESULTS A total of 64 of 125 clinical isolates were identified as resistant by MGIT 960. Using a minimum inhibitory concentration (MIC) of >500 μg/mL as the cutoff concentration to define resistance presented the best fit of the MABA assay with the MGIT 960 outcomes. MABA demonstrated sensitivity of 100% (95% confidence interval, 92.6-100), specificity of 95.2% (95% confidence interval, 86.0-98.8) and an accuracy of 97.6% compared to the MGIT 960 method. Nine PZA susceptible strains defined by MGIT 960 also had pncA mutations; however, three of them were defined as PZA resistant by NIC MABA with MIC ≥2000 μg/mL. CONCLUSIONS The NIC substitution method for PZA susceptibility test is reliable, cheap, rapid and easy, which makes it promising for use in clinical laboratories.
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Affiliation(s)
- Y Hu
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - X Wu
- Department of Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - J Luo
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Y Fu
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - L Zhao
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Y Ma
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Y Li
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Q Liang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Y Shang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - H Huang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China.
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50
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Some Synonymous and Nonsynonymous gyrA Mutations in Mycobacterium tuberculosis Lead to Systematic False-Positive Fluoroquinolone Resistance Results with the Hain GenoType MTBDR sl Assays. Antimicrob Agents Chemother 2017; 61:AAC.02169-16. [PMID: 28137812 PMCID: PMC5365657 DOI: 10.1128/aac.02169-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/16/2017] [Indexed: 11/20/2022] Open
Abstract
In this study, using the Hain GenoType MTBDRsl assays (versions 1 and 2), we found that some nonsynonymous and synonymous mutations in gyrA in Mycobacterium tuberculosis result in systematic false-resistance results to fluoroquinolones by preventing the binding of wild-type probes. Moreover, such mutations can prevent the binding of mutant probes designed for the identification of specific resistance mutations. Although these mutations are likely rare globally, they occur in approximately 7% of multidrug-resistant tuberculosis strains in some settings.
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