1
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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,
| |
Collapse
|
2
|
Nkosi T, Chasara C, Papadopoulos AO, Nguni TL, Karim F, Moosa MYS, Gazy I, Jambo K, Hanekom W, Sigal A, Ndhlovu ZM. Unsuppressed HIV infection impairs T cell responses to SARS-CoV-2 infection and abrogates T cell cross-recognition. eLife 2022; 11:e78374. [PMID: 35880744 PMCID: PMC9355563 DOI: 10.7554/elife.78374] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 07/20/2022] [Indexed: 11/15/2022] Open
Abstract
In some instances, unsuppressed HIV has been associated with severe COVID-19 disease, but the mechanisms underpinning this susceptibility are still unclear. Here, we assessed the impact of HIV infection on the quality and epitope specificity of SARS-CoV-2 T cell responses in the first wave and second wave of the COVID-19 epidemic in South Africa. Flow cytometry was used to measure T cell responses following peripheral blood mononuclear cell stimulation with SARS-CoV-2 peptide pools. Culture expansion was used to determine T cell immunodominance hierarchies and to assess potential SARS-CoV-2 escape from T cell recognition. HIV-seronegative individuals had significantly greater CD4+ T cell responses against the Spike protein compared to the viremic people living with HIV (PLWH). Absolute CD4 count correlated positively with SARS-CoV-2-specific CD4+ and CD8+ T cell responses (CD4 r=0.5, p=0.03; CD8 r=0.5, p=0.001), whereas T cell activation was negatively correlated with CD4+ T cell responses (CD4 r=-0.7, p=0.04). There was diminished T cell cross-recognition between the two waves, which was more pronounced in individuals with unsuppressed HIV infection. Importantly, we identify four mutations in the Beta variant that resulted in abrogation of T cell recognition. Taken together, we show that unsuppressed HIV infection markedly impairs T cell responses to SARS-Cov-2 infection and diminishes T cell cross-recognition. These findings may partly explain the increased susceptibility of PLWH to severe COVID-19 and also highlights their vulnerability to emerging SARS-CoV-2 variants of concern.
Collapse
Affiliation(s)
- Thandeka Nkosi
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of Kwa-Zulu NatalDurbanSouth Africa
| | - Caroline Chasara
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of Kwa-Zulu NatalDurbanSouth Africa
| | - Andrea O Papadopoulos
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of Kwa-Zulu NatalDurbanSouth Africa
| | - Tiza L Nguni
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of Kwa-Zulu NatalDurbanSouth Africa
| | - Farina Karim
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of Kwa-Zulu NatalDurbanSouth Africa
| | - Mahomed-Yunus S Moosa
- HIV Pathogenesis Program, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
| | - Inbal Gazy
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-NatalDurbanSouth Africa
| | - Kondwani Jambo
- Malawi-Liverpool-Wellcome Trust Clinical Research ProgrammeBlantyreMalawi
- Liverpool School of Tropical MedicineLiverpoolUnited Kingdom
| | - COMMIT-KZN-Team
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of Kwa-Zulu NatalDurbanSouth Africa
| | - Willem Hanekom
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of Kwa-Zulu NatalDurbanSouth Africa
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Alex Sigal
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of Kwa-Zulu NatalDurbanSouth Africa
| | - Zaza M Ndhlovu
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of Kwa-Zulu NatalDurbanSouth Africa
- HIV Pathogenesis Program, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
| |
Collapse
|
3
|
Hassim F, Papadopoulos AO, Kana BD, Gordhan BG. A combinatorial role for MutY and Fpg DNA glycosylases in mutation avoidance in Mycobacterium smegmatis. Mutat Res 2015; 779:24-32. [PMID: 26125998 DOI: 10.1016/j.mrfmmm.2015.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 05/26/2015] [Accepted: 06/01/2015] [Indexed: 10/23/2022]
Abstract
Hydroxyl radical (OH) among reactive oxygen species cause damage to nucleobases with thymine being the most susceptible, whilst in contrast, the singlet oxygen ((1)02) targets only guanine bases. The high GC content of mycobacterial genomes predisposes these organisms to oxidative damage of guanine. The exposure of cellular DNA to OH and one-electron oxidants results in the formation of two main degradation products, the pro-mutagenic 8-oxo-7,8-dihydroguanine (8-oxoGua) and the cytotoxic 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyGua). These lesions are repaired through the base excision repair (BER) pathway and we previously, demonstrated a combinatorial role for the mycobacterial Endonuclease III (Nth) and the Nei family of DNA glycosylases in mutagenesis. In addition, the formamidopyrimidine (Fpg/MutM) and MutY DNA glycosylases have also been implicated in mutation avoidance and BER in mycobacteria. In this study, we further investigate the combined role of MutY and the Fpg/Nei DNA glycosylases in Mycobacterium smegmatis and demonstrate that deletion of mutY resulted in enhanced sensitivity to oxidative stress, an effect which was not exacerbated in Δfpg1 Δfpg2 or Δnei1 Δnei2 double mutant backgrounds. However, combinatorial loss of the mutY, fpg1 and fpg2 genes resulted in a significant increase in mutation rates suggesting interplay between these enzymes. Consistent with this, there was a significant increase in C → A mutations with a corresponding change in cell morphology of rifampicin resistant mutants in the Δfpg1 Δfpg2 ΔmutY deletion mutant. In contrast, deletion of mutY together with the nei homologues did not result in any growth/survival defects or changes in mutation rates. Taken together these data indicate that the mycobacterial mutY, in combination with the Fpg DNA N-glycosylases, plays an important role in controlling mutagenesis under oxidative stress.
Collapse
Affiliation(s)
- Farzanah Hassim
- DST/NRF Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, P.O. Box 1038, Johannesburg 2000, South Africa
| | - Andrea O Papadopoulos
- DST/NRF Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, P.O. Box 1038, Johannesburg 2000, South Africa
| | - Bavesh D Kana
- DST/NRF Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, P.O. Box 1038, Johannesburg 2000, South Africa
| | - Bhavna G Gordhan
- DST/NRF Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, P.O. Box 1038, Johannesburg 2000, South Africa.
| |
Collapse
|