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Palekyte A, Morkowska A, Billington O, Morris-Jones S, Millard J, Marakalala MJ, Owolabi O, Sambou B, Zumla A, Sutherland JS, McHugh TD, Honeyborne I. Acetic Acid Enables Molecular Enumeration of Mycobacterium tuberculosis from Sputum and Eliminates the Need for a Biosafety Level 3 Laboratory. Clin Chem 2024; 70:642-652. [PMID: 38479728 DOI: 10.1093/clinchem/hvae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/08/2023] [Indexed: 04/04/2024]
Abstract
BACKGROUND Improved monitoring of Mycobacterium tuberculosis response to treatment is urgently required. We previously developed the molecular bacterial load assay (MBLA), but it is challenging to integrate into the clinical diagnostic laboratory due to a labor-intensive protocol required at biosafety level 3 (BSL-3). A modified assay was needed. METHODS The rapid enumeration and diagnostic for tuberculosis (READ-TB) assay was developed. Acetic acid was tested and compared to 4 M guanidine thiocyanate to be simultaneously bactericidal and preserve mycobacterial RNA. The extraction was based on silica column technology and incorporated low-cost reagents: 3 M sodium acetate and ethanol for the RNA extraction to replace phenol-chloroform. READ-TB was fully validated and compared directly to the MBLA using sputa collected from individuals with tuberculosis. RESULTS Acetic acid was bactericidal to M. tuberculosis with no significant loss in 16S rRNA or an unprotected mRNA fragment when sputum was stored in acetic acid at 25°C for 2 weeks or -20°C for 1 year. This novel use of acetic acid allows processing of sputum for READ-TB at biosafety level 2 (BSL-2) on sample receipt. READ-TB is semiautomated and rapid. READ-TB correlated with the MBLA when 85 human sputum samples were directly compared (R2 = 0.74). CONCLUSIONS READ-TB is an improved version of the MBLA and is available to be adopted by clinical microbiology laboratories as a tool for tuberculosis treatment monitoring. READ-TB will have a particular impact in low- and middle-income countries (LMICs) for laboratories with no BSL-3 laboratory and for clinical trials testing new combinations of anti-tuberculosis drugs.
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Affiliation(s)
- Ana Palekyte
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Anna Morkowska
- Imperial College London, Infection and Immunity, Department of Microbiology, Charing Cross Hospital, London, United Kingdom
| | | | - Stephen Morris-Jones
- Department of Clinical Microbiology, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - James Millard
- Liverpool Centre for Global Health Research, University of Liverpool, Liverpool, United Kingdom
- Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
- Africa Health Research Institute, Durban, South Africa
| | | | - Olumuyiwa Owolabi
- Vaccines and Immunity, MRC Unit The Gambia at The London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Basil Sambou
- Vaccines and Immunity, MRC Unit The Gambia at The London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Alimuddin Zumla
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, United Kingdom
- National Institute of Health and Research Biomedical Research Centre, UCL Hospitals National Health Service Foundation Trust, London, United Kingdom
| | - Jayne S Sutherland
- Vaccines and Immunity, MRC Unit The Gambia at The London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Timothy D McHugh
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Isobella Honeyborne
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, United Kingdom
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Peters JS, McIvor A, Papadopoulos AO, Masangana T, Gordhan BG, Waja Z, Otwombe K, Letutu M, Kamariza M, Sterling TR, Bertozzi CR, Martinson NA, Kana BD. Differentially culturable tubercle bacteria as a measure of tuberculosis treatment response. Front Cell Infect Microbiol 2023; 12:1064148. [PMID: 36710965 PMCID: PMC9877613 DOI: 10.3389/fcimb.2022.1064148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/22/2022] [Indexed: 01/13/2023] Open
Abstract
Introduction Routine efficacy assessments of new tuberculosis (TB) treatments include quantitative solid culture or routine liquid culture, which likely miss quantification of drug tolerant bacteria. To improve these assessments, comparative analyses using additional measures such as quantification of differentially culturable tubercle bacteria (DCTB) are required. Essential for enabling this is a comparative measure of TB treatment responses using routine solid and liquid culture with liquid limiting dilutions (LLDs) that detect DCTB in sputum. Methods We recruited treatment-naïve TB patients, with and without HIV-infection, and serially quantified their sputum for DCTB over the course of treatment. Results Serial sputum sampling in 73 individuals during their first 14 days of treatment demonstrated that clearance of DCTB was slower compared to routine solid culture. Treatment response appeared to be characterized by four patterns: (1) Classic bi-phasic bacterial clearance; (2) early non-responders with slower clearance; (3) paradoxical worsening with an increase in bacterial count upon treatment initiation; and (4) non-responders with no change in bacterial load. During treatment, LLDs displayed greater bacterial yield when compared with quantitative solid culture. Upon treatment completion, 74% [46/62] of specimens displayed residual DCTB and within this group, two recurrences were diagnosed. Residual DCTB upon treatment completion was associated with a higher proportion of MGIT culture, GeneXpert, and smear positivity at two months post treatment. No recurrences occurred in the group without residual DCTB. Discussion These data indicate that DCTB assays detect distinct subpopulations of organisms in sputum that are missed by routine solid and liquid culture, and offer important alternatives for efficacy assessments of new TB treatments. The residual DCTB observed upon treatment completion suggests that TB treatment does not always eliminate all bacterial populations, a finding that should be investigated in larger cohorts.
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Affiliation(s)
- Julian S. Peters
- Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, The National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Amanda McIvor
- Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, The National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Andrea O. Papadopoulos
- Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, The National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tshepiso Masangana
- Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, The National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Bhavna G. Gordhan
- Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, The National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ziyaad Waja
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Kennedy Otwombe
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Matebogo Letutu
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Mireille Kamariza
- Department of Biology, Stanford University, Stanford, CA, United States
| | | | - Carolyn R. Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA, United States,Howard Hughes Medical Institute, Stanford University, Stanford, CA, United States
| | - Neil A. Martinson
- Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, The National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa,Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa,Johns Hopkins University Center for TB Research, Baltimore, MD, United States
| | - Bavesh D. Kana
- Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, The National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa,*Correspondence: Bavesh D. Kana,
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Mishra S, Saito K. Clinically encountered growth phenotypes of tuberculosis-causing bacilli and their in vitro study: A review. Front Cell Infect Microbiol 2022; 12:1029111. [PMID: 36439231 PMCID: PMC9684195 DOI: 10.3389/fcimb.2022.1029111] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/20/2022] [Indexed: 07/11/2024] Open
Abstract
The clinical manifestations of tuberculosis (TB) vary widely in severity, site of infection, and outcomes of treatment-leading to simultaneous efforts to individualize therapy safely and to search for shorter regimens that can be successfully used across the clinical spectrum. In these endeavors, clinicians and researchers alike employ mycobacterial culture in rich media. However, even within the same patient, individual bacilli among the population can exhibit substantial variability in their culturability. Bacilli in vitro also demonstrate substantial heterogeneity in replication rate and cultivation requirements, as well as susceptibility to killing by antimicrobials. Understanding parallels in clinical, ex vivo and in vitro growth phenotype diversity may be key to identifying those phenotypes responsible for treatment failure, relapse, and the reactivation of bacilli that progresses TB infection to disease. This review briefly summarizes the current role of mycobacterial culture in the care of patients with TB and the ex vivo evidence of variability in TB culturability. We then discuss current advances in in vitro models that study heterogenous subpopulations within a genetically identical bulk culture, with an emphasis on the effect of oxidative stress on bacillary cultivation requirements. The review highlights the complexity that heterogeneity in mycobacterial growth brings to the interpretation of culture in clinical settings and research. It also underscores the intricacies present in the interplay between growth phenotypes and antimicrobial susceptibility. Better understanding of population dynamics and growth requirements over time and space promises to aid both the attempts to individualize TB treatment and to find uniformly effective therapies.
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Affiliation(s)
- Saurabh Mishra
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, United States
| | - Kohta Saito
- Department of Medicine, Weill Cornell Medicine, New York, NY, United States
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