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Walsh KF, Lee MH, Zainabadi K, Vilbrun SC, Jean Juste MA, Joseph Y, Royal G, Saito K, McAulay K, Pape JW, Fitzgerald D. High variance in quantification of Mycobacterium tuberculosis at low bacterial loads and with differentially detectable mycobacteria. Antimicrob Agents Chemother 2024; 68:e0160123. [PMID: 38829050 PMCID: PMC11232379 DOI: 10.1128/aac.01601-23] [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: 12/04/2023] [Accepted: 05/04/2024] [Indexed: 06/05/2024] Open
Abstract
We examined the correlation between three different methods of Mycobacterium tuberculosis quantification: time to positivity (TTP), log10 CFU, and an assay to detect differentially detectable M. tuberculosis (DD Mtb) from three different prospective studies. Participants with DD Mtb have significantly more variation in the CFU/TTP correlation than participants with no DD Mtb (P < 0.001). This may impact the design of early bactericidal activity studies that use TTP as the primary outcome.
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Affiliation(s)
- Kathleen F. Walsh
- Center for Global Health, Weill Cornell Medicine, New York, New York, USA
- Division of General Internal Medicine, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Myung Hee Lee
- Center for Global Health, Weill Cornell Medicine, New York, New York, USA
| | - Kayvan Zainabadi
- Center for Global Health, Weill Cornell Medicine, New York, New York, USA
| | - Stalz Charles Vilbrun
- Department of Medicine, Groupe Haïtien d'Étude du Sarcome de Kaposi et des Infectieuses Opportunistes (GHESKIO), Port-au-Prince, Haiti
| | - Marc Antoine Jean Juste
- Department of Medicine, Groupe Haïtien d'Étude du Sarcome de Kaposi et des Infectieuses Opportunistes (GHESKIO), Port-au-Prince, Haiti
| | - Yvetot Joseph
- Department of Medicine, Groupe Haïtien d'Étude du Sarcome de Kaposi et des Infectieuses Opportunistes (GHESKIO), Port-au-Prince, Haiti
| | - Gertrude Royal
- Department of Medicine, Groupe Haïtien d'Étude du Sarcome de Kaposi et des Infectieuses Opportunistes (GHESKIO), Port-au-Prince, Haiti
| | - Kohta Saito
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Kathrine McAulay
- Center for Global Health, Weill Cornell Medicine, New York, New York, USA
| | - Jean W. Pape
- Center for Global Health, Weill Cornell Medicine, New York, New York, USA
- Department of Medicine, Groupe Haïtien d'Étude du Sarcome de Kaposi et des Infectieuses Opportunistes (GHESKIO), Port-au-Prince, Haiti
| | - Daniel Fitzgerald
- Center for Global Health, Weill Cornell Medicine, New York, New York, USA
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Gordhan BG, Padarath K, Sewcharran A, McIvor A, VanNieuwenhze MS, Waja Z, Martinson N, Kana BD. Clinical Strains of Mycobacterium tuberculosis Representing Different Genotype Families Exhibit Distinct Propensities to Adopt the Differentially Culturable State. Pathogens 2024; 13:318. [PMID: 38668273 PMCID: PMC11054447 DOI: 10.3390/pathogens13040318] [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: 01/31/2024] [Revised: 03/20/2024] [Accepted: 03/27/2024] [Indexed: 04/29/2024] Open
Abstract
Growing evidence points to the presence of differentially culturable tubercle bacteria (DCTB) in clinical specimens from individuals with active tuberculosis (TB) disease. These bacteria are unable to grow on solid media but can resuscitate in liquid media. Given the epidemiological success of certain clinical genotype families of Mycobacterium tuberculosis, we hypothesize that different strains may have distinct mechanisms of adaptation and tolerance. We used an in vitro carbon starvation model to determine the propensity of strains from lineages 2 and 4 that included the Beijing and LAM families respectively, to generate DCTB. Beijing strains were associated with a greater propensity to produce DCTB compared to LAM strains. Furthermore, LAM strains required culture filtrate (CF) for resuscitation whilst starved Beijing strains were not dependent on CF. Moreover, Beijing strains showed improved resuscitation with cognate CF, suggesting the presence of unique growth stimulatory molecules in this family. Analysis of starved Beijing and LAM strains showed longer cells, which with resuscitation were restored to a shorter length. Cell wall staining with fluorescent D-amino acids identified strain-specific incorporation patterns, indicating that cell surface remodeling during resuscitation was distinct between clinical strains. Collectively, our data demonstrate that M. tuberculosis clinical strains from different genotype lineages have differential propensities to generate DCTB, which may have implications for TB treatment success.
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Affiliation(s)
- Bhavna Gowan Gordhan
- Department of Science and Innovation and the National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2017, South Africa; (B.G.G.); (K.P.); (A.S.); (A.M.)
- National Health Laboratory Service, Johannesburg 2000, South Africa
| | - Kiyasha Padarath
- Department of Science and Innovation and the National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2017, South Africa; (B.G.G.); (K.P.); (A.S.); (A.M.)
- National Health Laboratory Service, Johannesburg 2000, South Africa
| | - Astika Sewcharran
- Department of Science and Innovation and the National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2017, South Africa; (B.G.G.); (K.P.); (A.S.); (A.M.)
- National Health Laboratory Service, Johannesburg 2000, South Africa
| | - Amanda McIvor
- Department of Science and Innovation and the National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2017, South Africa; (B.G.G.); (K.P.); (A.S.); (A.M.)
- National Health Laboratory Service, Johannesburg 2000, South Africa
| | | | - Ziyaad Waja
- Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg 2017, South Africa; (Z.W.); (N.M.)
| | - Neil Martinson
- Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg 2017, South Africa; (Z.W.); (N.M.)
- Center for TB Research, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Bavesh Davandra Kana
- Department of Science and Innovation and the National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2017, South Africa; (B.G.G.); (K.P.); (A.S.); (A.M.)
- National Health Laboratory Service, Johannesburg 2000, South Africa
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Zainabadi K, Vilbrun SC, Mathurin LD, Walsh KF, Pape JW, Fitzgerald DW, Lee MH. A bedaquiline, pyrazinamide, levofloxacin, linezolid, clofazimine second line regimen for tuberculosis displays similar early bactericidal activity as the standard rifampin based first line regimen. J Infect Dis 2023:jiad564. [PMID: 38060827 DOI: 10.1093/infdis/jiad564] [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: 08/07/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND In 2018 the World Health Organization (WHO) recommended a switch to an all oral bedaquiline based second line regimen for treatment of drug resistant (DR) tuberculosis (TB). How these new second line regimens fare in comparison to first line regimens for treatment of drug sensitive (DS) tuberculosis is not well known. METHODS In this study, we contemporaneously enrolled subjects with DS (n = 31) and DR (n = 23) TB and assessed their response to therapy with first-line (rifampin, isoniazid, ethambutol, pyrazinamide) or second-line (bedaquiline, pyrazinamide, levofloxacin, linezolid, clofazimine) regimens, respectively. RESULTS We found that the early bactericidal activity of first and second line regimens was similar during the first two weeks of therapy as determined by BACTEC MGIT, colony forming units (CFU), and a liquid limiting dilution (LD) assays capable of detecting differentially detectable/culturable Mtb (DD Mtb). Further, an identical percentage (77.8%) of subjects from the DS and DR cohorts converted to culture negative after two months of therapy. CONCLUSIONS Despite presenting with more advanced disease at time of treatment, subjects with DR TB receiving an all oral bedaquiline based second line treatment regimen displayed a similar microbiological response to therapy as subjects with DS TB receiving a first-line treatment regimen.
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Affiliation(s)
- Kayvan Zainabadi
- Center for Global Health, Weill Cornell Medicine, New York, New York, USA
| | | | | | - Kathleen Frances Walsh
- Center for Global Health, Weill Cornell Medicine, New York, New York, USA
- Division of General Internal Medicine, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Jean William Pape
- Center for Global Health, Weill Cornell Medicine, New York, New York, USA
- Les Centres GHESKIO, Port-au-Prince, Haiti
| | | | - Myung Hee Lee
- Center for Global Health, Weill Cornell Medicine, New York, New York, USA
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Ealand CS, Sewcharran A, Peters JS, Gordhan BG, Kamariza M, Bertozzi CR, Waja Z, Martinson NA, Kana BD. The performance of tongue swabs for detection of pulmonary tuberculosis. Front Cell Infect Microbiol 2023; 13:1186191. [PMID: 37743867 PMCID: PMC10512057 DOI: 10.3389/fcimb.2023.1186191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023] Open
Abstract
Introduction Oral and/or tongue swabs have demonstrated ability to detect Mycobacterium tuberculosis (Mtb) in adults with pulmonary tuberculosis (TB). Swabs provide useful alternative specimens for diagnosis of TB using molecular assays however, the diagnostic pickup by culture requires further improvement and development. Several studies identified the presence of differentially culturable tubercle bacilli (DCTB) populations in a variety of clinical specimens. These organisms do not grow in routine laboratory media and require growth factors in the form of culture filtrate (CF) from logarithmic phase cultures of Mtb H37Rv. Methods Herein, we compared the diagnostic performance of sputum and tongue swabs using Mycobacterial Growth Indicator Tube (MGIT) assays, Auramine smear, GeneXpert and DCTB assays supplemented with or without CF. Results From 89 eligible participants, 83 (93%), 66 (74%) and 79 (89%) were sputum positive by MGIT, smear and GeneXpert, respectively. The corresponding tongue swabs displayed a lower sensitivity with 39 (44%), 2 (2.0%) and 18 (20%) participants respectively for the same tests. We aimed to improve the diagnostic yield by utilizing DCTB assays. Sputum samples were associated with a higher positivity rate for CF-augmented DCTB at 82/89 (92%) relative to tongue swabs at 36/89 (40%). Similarly, sputum samples had a higher positivity rate for DCTB populations that were CF-independent at 64/89 (72%) relative to tongue swabs at 26/89 (29%). DCTB positivity increased significantly, relative to MGIT culture, for tongue swabs taken from HIV-positive participants. We next tested whether the use of an alternative smear stain, DMN-Trehalose, would improve diagnostic yield but noted no substantial increase. Discussion Collectively, our data show that while tongue swabs yield lower bacterial numbers for diagnostic testing, the use of growth supplementation may improve detection of TB particularly in HIV-positive people but this requires further interrogation in larger studies.
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Affiliation(s)
- Christopher S. Ealand
- Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Astika Sewcharran
- Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Julian S. Peters
- Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Bhavna G. Gordhan
- Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Mireille Kamariza
- Department of Biology, Stanford University, Stanford, CA, United States
| | - Carolyn R. Bertozzi
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, United States
- Department of Chemistry, Stanford University, Stanford, CA, United States
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, United States
| | - Ziyaad Waja
- Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa
| | - Neil A. Martinson
- Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
- Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa
- Johns Hopkins University, Centre for Tuberculosis Research, Baltimore, MD, United States
| | - Bavesh D. Kana
- Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
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Lanni A, Iacobino A, Fattorini L, Giannoni F. Eradication of Drug-Tolerant Mycobacterium tuberculosis 2022: Where We Stand. Microorganisms 2023; 11:1511. [PMID: 37375013 DOI: 10.3390/microorganisms11061511] [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: 04/28/2023] [Revised: 05/26/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
The lungs of tuberculosis (TB) patients contain a spectrum of granulomatous lesions, ranging from solid and well-vascularized cellular granulomas to avascular caseous granulomas. In solid granulomas, current therapy kills actively replicating (AR) intracellular bacilli, while in low-vascularized caseous granulomas the low-oxygen tension stimulates aerobic and microaerophilic AR bacilli to transit into non-replicating (NR), drug-tolerant and extracellular stages. These stages, which do not have genetic mutations and are often referred to as persisters, are difficult to eradicate due to low drug penetration inside the caseum and mycobacterial cell walls. The sputum of TB patients also contains viable bacilli called differentially detectable (DD) cells that, unlike persisters, grow in liquid, but not in solid media. This review provides a comprehensive update on drug combinations killing in vitro AR and drug-tolerant bacilli (persisters and DD cells), and sterilizing Mycobacterium tuberculosis-infected BALB/c and caseum-forming C3HeB/FeJ mice. These observations have been important for testing new drug combinations in noninferiority clinical trials, in order to shorten the duration of current regimens against TB. In 2022, the World Health Organization, following the results of one of these trials, supported the use of a 4-month regimen for the treatment of drug-susceptible TB as a possible alternative to the current 6-month regimen.
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Affiliation(s)
- Alessio Lanni
- Department of Infectious Diseases, Istituto Superiore di Sanità, Via Regina Elena 299, 00161 Rome, Italy
| | - Angelo Iacobino
- Department of Infectious Diseases, Istituto Superiore di Sanità, Via Regina Elena 299, 00161 Rome, Italy
| | - Lanfranco Fattorini
- Department of Infectious Diseases, Istituto Superiore di Sanità, Via Regina Elena 299, 00161 Rome, Italy
| | - Federico Giannoni
- Department of Infectious Diseases, Istituto Superiore di Sanità, Via Regina Elena 299, 00161 Rome, Italy
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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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Zainabadi K, Saito K, Mishra S, Walsh KF, Mathurin LD, Vilbrun SC, Ocheretina O, Pape JW, Fitzgerald DW, Nathan CF, Lee MH. Transcriptional Biomarkers of Differentially Detectable Mycobacterium tuberculosis in Patient Sputum. mBio 2022; 13:e0270122. [PMID: 36326252 PMCID: PMC9765512 DOI: 10.1128/mbio.02701-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/06/2022] [Indexed: 11/05/2022] Open
Abstract
Certain populations of Mycobacterium tuberculosis go undetected by standard diagnostics but can be enumerated using limiting dilution assays. These differentially detectable M. tuberculosis (DD M. tuberculosis) populations may have relevance for persistence due to their drug tolerance. It is unclear how well DD M. tuberculosis from patients is modeled by a recently developed in vitro model in which M. tuberculosis starved in phosphate-buffered saline is incubated with rifampin to produce DD M. tuberculosis (the PBS-RIF model). This study attempted to answer this question. We selected 14 genes that displayed differential expression in the PBS-RIF model and evaluated their expression in patient sputa containing various proportions of DD M. tuberculosis. The expression of 12/14 genes correlated with the relative abundance of DD M. tuberculosis in patient sputa. Culture filtrate (CF), which promotes recovery of DD M. tuberculosis from certain patient sputa, improved these correlations in most cases. The gene whose reduced expression relative to M. tuberculosis 16S rRNA showed the greatest association with the presence and relative abundance of DD M. tuberculosis in patient sputa, icl1, was recently shown to play a functional role in restraining DD M. tuberculosis formation in the PBS-RIF model. Expression of icl1, combined with two additional DD M. tuberculosis-related genes, showed strong performance for predicting the presence or absence of DD M. tuberculosis in patient sputa (receiver operating characteristic [ROC] area under the curve [AUC] = 0.88). Thus, the in vitro DD M. tuberculosis model developed by Saito et al. (K. Saito, T. Warrier, S. Somersan-Karakaya, L. Kaminski, et al., Proc Natl Acad Sci U S A 114:E4832-E4840, 2017, https://doi.org/10.1073/pnas.1705385114) bears a resemblance to DD M. tuberculosis found in tuberculosis (TB) patients, and DD M. tuberculosis transcriptional profiles may be useful for monitoring DD M. tuberculosis populations in patient sputum. IMPORTANCE Differentially detectable M. tuberculosis (DD M. tuberculosis), which is detectable by limiting dilution assays but not by CFU, is present and enriched for in TB patient sputum after initiation of first-line therapy. These cryptic cells may play a role in disease persistence due to their phenotypic tolerance to anti-TB drugs. A recently developed in vitro model of DD M. tuberculosis (the PBS-RIF model) has expanded our understanding of these cells, though how well it translates to DD M. tuberculosis in patients is currently unknown. To answer this question, we selected 14 genes that displayed differential expression in the PBS-RIF model and evaluated their expression in TB patient sputa. We found that 12/14 of these genes showed a similar expression profile in patient sputa that correlated with the relative abundance of DD M. tuberculosis. Further, the expression of three of these genes showed strong performance for predicting the presence or absence of DD M. tuberculosis in patient sputa. The use of DD M. tuberculosis transcriptional profiles may allow for easier monitoring of DD M. tuberculosis populations in patient sputum in comparison to limiting dilution assays.
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Affiliation(s)
- Kayvan Zainabadi
- Center for Global Health, Weill Cornell Medicine, New York, New York, USA
| | - Kohta Saito
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA
| | - Saurabh Mishra
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, New York, USA
| | - Kathleen Frances Walsh
- Center for Global Health, Weill Cornell Medicine, New York, New York, USA
- Department of Medicine, Division of General Internal Medicine, Weill Cornell Medicine, New York, New York, USA
| | | | | | - Oksana Ocheretina
- Center for Global Health, Weill Cornell Medicine, New York, New York, USA
| | - Jean William Pape
- Center for Global Health, Weill Cornell Medicine, New York, New York, USA
- Les Centres GHESKIO, Port-au-Prince, Haiti
| | | | - Carl F. Nathan
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, New York, USA
| | - Myung Hee Lee
- Center for Global Health, Weill Cornell Medicine, New York, New York, USA
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8
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Demina GR, Shleeva MO, Bagaeva DI, Vostroknutova GV, Kaprelyants AS. Detection of “Non-culturable” Mycobacterium tuberculosis Cells by Culture Methods. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822100064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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9
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Chengalroyen MD, Beukes GM, Otwombe K, Gordhan BG, Martinson N, Kana B. The detection of mixed tuberculosis infections using culture filtrate and resuscitation promoting factor deficient filtrate. Front Cell Infect Microbiol 2022; 12:1072073. [PMID: 36506007 PMCID: PMC9729742 DOI: 10.3389/fcimb.2022.1072073] [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: 10/17/2022] [Accepted: 11/08/2022] [Indexed: 11/25/2022] Open
Abstract
Tuberculosis (TB) infected individuals harbor a heterogenous population of differentially culturable tubercle bacilli (DCTB). Herein, we describe how DCTB assays using culture filtrate either containing or deficient in resuscitation promoting factors can uncover mixed infections. We demonstrate that Mycobacterium tuberculosis (Mtb) strain genotypes can be separated in DCTB assays based on their selective requirement for growth stimulatory factors. Beijing mixed infections appear to be associated with a higher bacterial load and reduced reliance on growth stimulatory factors. These data have important implications for identifying mixed infections and hetero-resistance, which in turn can affect selection of treatment regimen and establishment of transmission links.
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Affiliation(s)
- Melissa D. Chengalroyen
- National Health Laboratory Service, DST/NRF Centre of Excellence for Biomedical TB Research, University of the Witwatersrand, Johannesburg, South Africa
| | - Germar M. Beukes
- National Health Laboratory Service, DST/NRF Centre of Excellence for Biomedical TB Research, University of the Witwatersrand, Johannesburg, South Africa
| | - Kennedy Otwombe
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Bhavna G. Gordhan
- National Health Laboratory Service, DST/NRF Centre of Excellence for Biomedical TB Research, University of the Witwatersrand, Johannesburg, South Africa
| | - Neil Martinson
- National Health Laboratory Service, DST/NRF Centre of Excellence for Biomedical TB Research, University of the Witwatersrand, Johannesburg, South Africa,Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa,Center for TB Research, Johns Hopkins University, Baltimore, MD, United States
| | - Bavesh Kana
- National Health Laboratory Service, DST/NRF Centre of Excellence for Biomedical TB Research, University of the Witwatersrand, Johannesburg, South Africa,*Correspondence: Bavesh Kana,
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10
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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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Zainabadi K, Lee MH, Walsh KF, Vilbrun SC, Mathurin LD, Ocheretina O, Pape JW, Fitzgerald DW. An optimized method for purifying, detecting and quantifying Mycobacterium tuberculosis RNA from sputum for monitoring treatment response in TB patients. Sci Rep 2022; 12:17382. [PMID: 36253384 PMCID: PMC9574834 DOI: 10.1038/s41598-022-19985-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/07/2022] [Indexed: 02/05/2023] Open
Abstract
Diagnostics that more accurately detect and quantify viable Mycobacterium tuberculosis (Mtb) in the sputum of patients undergoing therapy are needed. Current culture- and molecular-based tests have shown limited efficacy for monitoring treatment response in TB patients, either due to the presence of viable sub-populations of Mtb which fail to grow under standard culture conditions (termed differentially detectable/culturable Mtb, DD Mtb) or the prolonged half-life of Mtb DNA in sputum. Here, we report an optimized RNA-based method for detecting and quantifying viable Mtb from patient sputum during the course of therapy. We first empirically derived a novel RNA extraction protocol from sputum that improves recovery of Mtb RNA while almost completely eliminating contamination from Mtb DNA and host nucleic acids. Next, we identified five Mtb 16S rRNA primer sets with varying limits of detection that were capable of distinguishing between live versus dead H37Rv Mtb. This combined protocol was then tested on sputa from a longitudinal cohort of patients receiving therapy for drug sensitive (DS) or drug resistant (DR) TB with first-line or second-line regimens, respectively. Results were compared with that of culture, including CFU, BACTEC MGIT, and a limiting dilution assay capable of detecting DD Mtb. The five 16S rRNA primer sets positively identified nearly all (range 94-100%) culture positive sputa, and a portion (19-37%) of culture negative sputa. In comparison, ten highly expressed Mtb mRNAs showed positivity in 72-86% of culture positive sputa, and in 0-13% of culture negative sputa. Two of the five 16S rRNA primer sets were able to positively identify 100% of culture positive sputa, and when tested on culture negative sputa from the DS cohort at 2 months post-initiation of therapy, identified 40% of samples as positive; a percentage that is in line with expected treatment failure rates when first-line therapy is discontinued early. These two primer sets also detected 16S rRNA in 13-20% of sputa at 6 months post-initiation of therapy in the DR cohort. Cycle threshold values for 16S rRNA showed a strong correlation with Mtb numbers as determined by culture (R > 0.87), including as Mtb numbers declined during the course of treatment with first-line and second-line regimens. The optimized molecular assay outlined here may have utility for monitoring treatment response in TB patients.
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Affiliation(s)
- Kayvan Zainabadi
- Center for Global Health, Weill Cornell Medicine, New York, NY, USA.
| | - Myung Hee Lee
- Center for Global Health, Weill Cornell Medicine, New York, NY, USA
| | - Kathleen Frances Walsh
- Center for Global Health, Weill Cornell Medicine, New York, NY, USA
- Division of General Internal Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | | | | | - Jean William Pape
- Center for Global Health, Weill Cornell Medicine, New York, NY, USA
- Les Centres GHESKIO, Port-au-Prince, Haiti
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Liebenberg D, Gordhan BG, Kana BD. Drug resistant tuberculosis: Implications for transmission, diagnosis, and disease management. Front Cell Infect Microbiol 2022; 12:943545. [PMID: 36211964 PMCID: PMC9538507 DOI: 10.3389/fcimb.2022.943545] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 09/06/2022] [Indexed: 01/17/2023] Open
Abstract
Drug resistant tuberculosis contributes significantly to the global burden of antimicrobial resistance, often consuming a large proportion of the healthcare budget and associated resources in many endemic countries. The rapid emergence of resistance to newer tuberculosis therapies signals the need to ensure appropriate antibiotic stewardship, together with a concerted drive to develop new regimens that are active against currently circulating drug resistant strains. Herein, we highlight that the current burden of drug resistant tuberculosis is driven by a combination of ongoing transmission and the intra-patient evolution of resistance through several mechanisms. Global control of tuberculosis will require interventions that effectively address these and related aspects. Interrupting tuberculosis transmission is dependent on the availability of novel rapid diagnostics which provide accurate results, as near-patient as is possible, together with appropriate linkage to care. Contact tracing, longitudinal follow-up for symptoms and active mapping of social contacts are essential elements to curb further community-wide spread of drug resistant strains. Appropriate prophylaxis for contacts of drug resistant index cases is imperative to limit disease progression and subsequent transmission. Preventing the evolution of drug resistant strains will require the development of shorter regimens that rapidly eliminate all populations of mycobacteria, whilst concurrently limiting bacterial metabolic processes that drive drug tolerance, mutagenesis and the ultimate emergence of resistance. Drug discovery programs that specifically target bacterial genetic determinants associated with these processes will be paramount to tuberculosis eradication. In addition, the development of appropriate clinical endpoints that quantify drug tolerant organisms in sputum, such as differentially culturable/detectable tubercle bacteria is necessary to accurately assess the potential of new therapies to effectively shorten treatment duration. When combined, this holistic approach to addressing the critical problems associated with drug resistance will support delivery of quality care to patients suffering from tuberculosis and bolster efforts to eradicate this disease.
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Gordhan BG, Sewcharran A, Letsoalo M, Chinappa T, Yende-Zuma N, Padayatchi N, Naidoo K, Kana BD. Detection of differentially culturable tubercle bacteria in sputum from drug-resistant tuberculosis patients. Front Cell Infect Microbiol 2022; 12:949370. [PMID: 36159642 PMCID: PMC9500503 DOI: 10.3389/fcimb.2022.949370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Several studies described the presence of non-replicating, drug-tolerant differentially culturable tubercle bacteria (DCTB) in sputum from patients with active tuberculosis (TB). These organisms are unable to form colonies on agar but can be recovered in liquid media supplemented with culture filtrate as a source of growth factors. Herein, we undertook to investigate the response of DCTB during the treatment of individuals with drug-resistant TB. A cohort of 100 participants diagnosed with rifampicin-resistant TB were enrolled and prospectively followed to monitor response to therapy using routine culture and limiting dilution assays, supplemented with culture filtrate (CF) to quantify DCTB. Fifteen participants were excluded due to contamination, and of the remaining 85 participants, 29, 49, and 7 were infected with rifampicin mono-resistant (RMR), multidrug-resistant (MDR), or extremely drug-resistant (XDR) TB, respectively. Analysis of baseline sputum demonstrated that CF supplementation of limiting dilution assays detected notable amounts of DCTB. Prevalence of DCTB was not influenced by smear status or mycobacterial growth indicator tube time to positivity. CF devoid of resuscitation promoting factors (Rpfs) yielded a greater amount of DCTB in sputum from participants with MDR-TB compared with those with RMR-TB. A similar effect was noted in DCTB assays without CF supplementation, suggesting that CF is dispensable for the detection of DCTB from drug-resistant strains. The HIV status of participants, and CD4 count, did not affect the amount of DCTB recovered. During treatment with second-line drug regimens, the probability of detecting DCTB from sputum specimens in liquid media with or without CF was higher compared with colony forming units, with DCTB detected up to 16 weeks post treatment. Collectively, these data point to differences in the ability of drug-resistant strains to respond to CF and Rpfs. Our findings demonstrate the possible utility of DCTB assays to diagnose and monitor treatment response for drug-resistant TB, particularly in immune compromised individuals with low CD4 counts.
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Affiliation(s)
- Bhavna G. Gordhan
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis (TB) Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Astika Sewcharran
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis (TB) Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Marothi Letsoalo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Thilgavathy Chinappa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nonhlanhla Yende-Zuma
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC)-Centre for the AIDS Programme of Research in South Africa (CAPRISA) Human Immunodeficiency Virus- Tuberculosis (HIV-TB) Pathogenesis and Treatment Research Unit, University of KwaZulu-Natal, Durban, South Africa
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC)-Centre for the AIDS Programme of Research in South Africa (CAPRISA) Human Immunodeficiency Virus- Tuberculosis (HIV-TB) Pathogenesis and Treatment Research Unit, University of KwaZulu-Natal, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC)-Centre for the AIDS Programme of Research in South Africa (CAPRISA) Human Immunodeficiency Virus- Tuberculosis (HIV-TB) Pathogenesis and Treatment Research Unit, University of KwaZulu-Natal, Durban, South Africa
| | - Bavesh D. Kana
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis (TB) Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
- *Correspondence: Bavesh D. Kana,
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