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Honeyborne I, McHugh TD, Kuittinen I, Cichonska A, Evangelopoulos D, Ronacher K, van Helden PD, Gillespie SH, Fernandez-Reyes D, Walzl G, Rousu J, Butcher PD, Waddell SJ. Profiling persistent tubercule bacilli from patient sputa during therapy predicts early drug efficacy. BMC Med 2016; 14:68. [PMID: 27055815 PMCID: PMC4825072 DOI: 10.1186/s12916-016-0609-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/23/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND New treatment options are needed to maintain and improve therapy for tuberculosis, which caused the death of 1.5 million people in 2013 despite potential for an 86 % treatment success rate. A greater understanding of Mycobacterium tuberculosis (M.tb) bacilli that persist through drug therapy will aid drug development programs. Predictive biomarkers for treatment efficacy are also a research priority. METHODS AND RESULTS Genome-wide transcriptional profiling was used to map the mRNA signatures of M.tb from the sputa of 15 patients before and 3, 7 and 14 days after the start of standard regimen drug treatment. The mRNA profiles of bacilli through the first 2 weeks of therapy reflected drug activity at 3 days with transcriptional signatures at days 7 and 14 consistent with reduced M.tb metabolic activity similar to the profile of pre-chemotherapy bacilli. These results suggest that a pre-existing drug-tolerant M.tb population dominates sputum before and after early drug treatment, and that the mRNA signature at day 3 marks the killing of a drug-sensitive sub-population of bacilli. Modelling patient indices of disease severity with bacterial gene expression patterns demonstrated that both microbiological and clinical parameters were reflected in the divergent M.tb responses and provided evidence that factors such as bacterial load and disease pathology influence the host-pathogen interplay and the phenotypic state of bacilli. Transcriptional signatures were also defined that predicted measures of early treatment success (rate of decline in bacterial load over 3 days, TB test positivity at 2 months, and bacterial load at 2 months). CONCLUSIONS This study defines the transcriptional signature of M.tb bacilli that have been expectorated in sputum after two weeks of drug therapy, characterizing the phenotypic state of bacilli that persist through treatment. We demonstrate that variability in clinical manifestations of disease are detectable in bacterial sputa signatures, and that the changing M.tb mRNA profiles 0-2 weeks into chemotherapy predict the efficacy of treatment 6 weeks later. These observations advocate assaying dynamic bacterial phenotypes through drug therapy as biomarkers for treatment success.
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Affiliation(s)
- Isobella Honeyborne
- Centre for Clinical Microbiology, University College London, London, NW3 2PF, UK
| | - Timothy D McHugh
- Centre for Clinical Microbiology, University College London, London, NW3 2PF, UK
| | - Iitu Kuittinen
- Department of Computer Science, Helsinki Institute for Information Technology HIIT, Aalto University, Espoo, Finland
| | - Anna Cichonska
- Department of Computer Science, Helsinki Institute for Information Technology HIIT, Aalto University, Espoo, Finland.,Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | | | - Katharina Ronacher
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research and Medical Research Council Centre for TB Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Western Cape, South Africa
| | - Paul D van Helden
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research and Medical Research Council Centre for TB Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Western Cape, South Africa
| | - Stephen H Gillespie
- Medical and Biological Sciences Building, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9TF, UK
| | - Delmiro Fernandez-Reyes
- Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, UK.,Department of Paediatrics, University College Hospital, College of Medicine of the University of Ibadan, Ibadan, Nigeria
| | - Gerhard Walzl
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research and Medical Research Council Centre for TB Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Western Cape, South Africa
| | - Juho Rousu
- Department of Computer Science, Helsinki Institute for Information Technology HIIT, Aalto University, Espoo, Finland
| | - Philip D Butcher
- Institute for Infection and Immunity, St George's University of London, London, SW17 0RE, UK
| | - Simon J Waddell
- Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX, UK.
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Rockwood N, du Bruyn E, Morris T, Wilkinson RJ. Assessment of treatment response in tuberculosis. Expert Rev Respir Med 2016; 10:643-54. [PMID: 27030924 DOI: 10.1586/17476348.2016.1166960] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Antibiotic treatment of tuberculosis has a duration of several months. There is significant variability of the host immune response and the pharmacokinetic-pharmacodynamic properties of Mycobacterium tuberculosis sub-populations at the site of disease. A limitation of sputum-based measures of treatment response may be sub-optimal detection and monitoring of Mycobacterium tuberculosis sub-populations. Potential biomarkers and surrogate endpoints should be benchmarked against hard clinical outcomes (failure/relapse/death) and may need tailoring to specific patient populations. Here, we assess the evidence supporting currently utilized and future potential host and pathogen-based models and biomarkers for monitoring treatment response in active and latent tuberculosis. Biomarkers for monitoring treatment response in extrapulmonary, pediatric and drug resistant tuberculosis are research priorities.
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Affiliation(s)
- Neesha Rockwood
- a Department of Medicine , Imperial College London , London , UK.,b Clinical Infectious Diseases Research Initiative, Institute of Infectious Diseases and Molecular Medicine and Department of Medicine , University of Cape Town , Observatory , South Africa
| | - Elsa du Bruyn
- b Clinical Infectious Diseases Research Initiative, Institute of Infectious Diseases and Molecular Medicine and Department of Medicine , University of Cape Town , Observatory , South Africa
| | - Thomas Morris
- a Department of Medicine , Imperial College London , London , UK
| | - Robert J Wilkinson
- a Department of Medicine , Imperial College London , London , UK.,b Clinical Infectious Diseases Research Initiative, Institute of Infectious Diseases and Molecular Medicine and Department of Medicine , University of Cape Town , Observatory , South Africa.,c The Francis Crick Institute Mill Hill Laboratory , London , UK
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Phenotypically Adapted Mycobacterium tuberculosis Populations from Sputum Are Tolerant to First-Line Drugs. Antimicrob Agents Chemother 2016; 60:2476-83. [PMID: 26883695 PMCID: PMC4808147 DOI: 10.1128/aac.01380-15] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 02/06/2016] [Indexed: 12/12/2022] Open
Abstract
Tuberculous sputum contains multiple Mycobacterium tuberculosis populations with different requirements for isolation in vitro. These include cells that form colonies on solid media (plateable M. tuberculosis), cells requiring standard liquid medium for growth (nonplateable M. tuberculosis), and cells requiring supplementation of liquid medium with culture supernatant (SN) for growth (SN-dependent M. tuberculosis). Here, we describe protocols for the cryopreservation and direct assessment of antimicrobial tolerance of these M. tuberculosis populations within sputum. Our results show that first-line drugs achieved only modest bactericidal effects on all three populations over 7 days (1 to 2.5 log10 reductions), and SN-dependent M. tuberculosis was more tolerant to streptomycin and isoniazid than the plateable and nonplateable M. tuberculosis strains. Susceptibility of plateable M. tuberculosis to bactericidal drugs was significantly increased after passage in vitro; thus, tolerance observed in the sputum samples from the population groups was likely associated with mycobacterial adaptation to the host environment at some time prior to expectoration. Our findings support the use of a simple ex vivo system for testing drug efficacies against mycobacteria that have phenotypically adapted during tuberculosis infection.
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54
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Barr DA, Kamdolozi M, Nishihara Y, Ndhlovu V, Khonga M, Davies GR, Sloan DJ. Serial image analysis of Mycobacterium tuberculosis colony growth reveals a persistent subpopulation in sputum during treatment of pulmonary TB. Tuberculosis (Edinb) 2016; 98:110-5. [PMID: 27156626 PMCID: PMC4869592 DOI: 10.1016/j.tube.2016.03.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 03/02/2016] [Accepted: 03/10/2016] [Indexed: 12/01/2022]
Abstract
Faster elimination of drug tolerant ‘persister’ bacteria may shorten treatment of tuberculosis (TB) but no method exists to quantify persisters in clinical samples. We used automated image analysis to assess whether studying growth characteristics of individual Mycobacterium tuberculosis colonies from sputum on solid media during early TB treatment facilitates ‘persister’ phenotyping. As Time to Detection (TTD) in liquid culture inversely correlates with total bacterial load we also evaluated the relationship between individual colony growth parameters and TTD. Sputum from TB patients in Malawi was prepared for solid and liquid culture after 0, 2 and 4 weeks of treatment. Serial photography of agar plates was used to measure time to appearance (lag time) and radial growth rate for each colony. Mixed-effects modelling was used to analyse changing growth characteristics from serial samples. 20 patients had colony measurements recorded at ≥1 time-point. Overall lag time increased by 6.5 days between baseline and two weeks (p = 0.0001). Total colony count/ml showed typical biphasic elimination, but long lag time colonies (>20days) had slower, monophasic decline. TTD was associated with minimum lag time (time to appearance of first colony1). Slower elimination of long lag time colonies suggests that these may represent a persister subpopulation of bacilli.
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Affiliation(s)
- David A Barr
- Wellcome Trust Liverpool Glasgow Centre for Global Health Research, University of Liverpool, 70 Pembroke Place, Liverpool, L69 3GF, UK; Brownlee Centre for Infectious Disease, Gartnavel General Hospital, 1053 Great Western Road, Glasgow, G12 0YN, UK.
| | - Mercy Kamdolozi
- Department of Microbiology, College of Medicine, University of Malawi, Mahatma Gandhi Road, Blantyre 3, Malawi.
| | - Yo Nishihara
- Queen Elizabeth Central Hospital, P.O. Box 95, Blantyre 3, Malawi; Malawi Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Mahatma Gandhi Road, Blantyre 3, Malawi.
| | - Victor Ndhlovu
- Department of Microbiology, College of Medicine, University of Malawi, Mahatma Gandhi Road, Blantyre 3, Malawi.
| | - Margaret Khonga
- Department of Microbiology, College of Medicine, University of Malawi, Mahatma Gandhi Road, Blantyre 3, Malawi.
| | - Geraint R Davies
- Department of Microbiology, College of Medicine, University of Malawi, Mahatma Gandhi Road, Blantyre 3, Malawi; Institute of Infection and Global Health, The Ronald Ross Building, University of Liverpool, 8 West Derby Street, Liverpool, L69 7BE, UK; Malawi Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Mahatma Gandhi Road, Blantyre 3, Malawi.
| | - Derek J Sloan
- Liverpool Heart and Chest Hospital, Thomas Drive, Liverpool, L14 3PE, UK; Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
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Phillips PPJ, Mendel CM, Burger DA, Crook AM, Nunn AJ, Dawson R, Diacon AH, Gillespie SH, Gillespie SH. Limited role of culture conversion for decision-making in individual patient care and for advancing novel regimens to confirmatory clinical trials. BMC Med 2016; 14:19. [PMID: 26847437 PMCID: PMC4743210 DOI: 10.1186/s12916-016-0565-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 01/23/2016] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Despite recent increased clinical trials activity, no regimen has proved able to replace the standard 6-month regimen for drug-sensitive tuberculosis. Understanding the relationship between microbiological markers measured during treatment and long-term clinical outcomes is critical to evaluate their usefulness for decision-making for both individual patient care and for advancing novel regimens into time-consuming and expensive pivotal phase III trials. METHODS Using data from the randomized controlled phase III trial REMoxTB, we evaluated sputum-based markers of speed of clearance of bacilli: time to smear negative status; time to culture negative status on LJ or in MGIT; daily rate of change of log10(TTP) to day 56; and smear or culture results at weeks 6, 8 or 12; as individual- and trial-level surrogate endpoints for long-term clinical outcome. RESULTS Time to culture negative status on LJ or in MGIT, time to smear negative status and daily rate of change in log10(TTP) were each independent predictors of clinical outcome, adjusted for treatment (p <0.001). However, discrimination between low and high risk patients, as measured by the c-statistic, was modest and not much higher than the reference model adjusted for BMI, history of smoking, HIV status, cavitation, gender and MGIT TTP. CONCLUSIONS Culture conversion during treatment for tuberculosis, however measured, has only a limited role in decision-making for advancing regimens into phase III trials or in predicting the outcome of treatment for individual patients. REMoxTB ClinicalTrials.gov number: NCT00864383.
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Affiliation(s)
- Patrick P J Phillips
- MRC Clinical Trials Unit at UCL, Aviation House, 125 Kingsway, London, WC2B 6NH, UK.
| | - Carl M Mendel
- Global Alliance for TB Drug Development, New York, NY, USA
| | - Divan A Burger
- Department of Mathematical Statistics and Actuarial Science, University of the Free State, Bloemfontein, South Africa
| | | | - Andrew J Nunn
- MRC Clinical Trials Unit at UCL, Aviation House, 125 Kingsway, London, WC2B 6NH, UK
| | - Rodney Dawson
- Division of Pulmonology and Department of Medicine, University of Cape Town Lung Institute, Mowbray, Cape Town, South Africa
| | - Andreas H Diacon
- Division of Physiology, Department of Medical Biochemistry, Stellenbosch University, Tygerberg, Cape Town, South Africa.,TASK Applied Science, Bellville, Cape Town, South Africa
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Kayigire XA, Friedrich SO, van der Merwe L, Donald PR, Diacon AH. Simultaneous staining of sputum smears for acid-fast and lipid-containing Myobacterium tuberculosis can enhance the clinical evaluation of antituberculosis treatments. Tuberculosis (Edinb) 2015; 95:770-779. [DOI: 10.1016/j.tube.2015.08.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 07/24/2015] [Accepted: 08/02/2015] [Indexed: 10/23/2022]
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