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Rossi E, Lausen M, Øbro NF, Colque A, Nielsen BU, Møller R, de Gier C, Hald A, Skov M, Pressler T, Molin S, Ostrowski SR, Marquart HV, Johansen HK. Widespread alterations in systemic immune profile are linked to lung function heterogeneity and airway microbes in cystic fibrosis. J Cyst Fibros 2024:S1569-1993(24)00059-6. [PMID: 38702223 DOI: 10.1016/j.jcf.2024.04.015] [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: 02/18/2024] [Revised: 04/23/2024] [Accepted: 04/26/2024] [Indexed: 05/06/2024]
Abstract
BACKGROUND Excessive inflammation and recurrent airway infections characterize people with cystic fibrosis (pwCF), a disease with highly heterogeneous clinical outcomes. How the overall immune response is affected in pwCF, its relationships with the lung microbiome, and the source of clinical heterogeneity have not been fully elucidated. METHODS Peripheral blood and sputum samples were collected from 28 pwCF and an age-matched control group. Systemic immune cell subsets and surface markers were quantified using multiparameter flow cytometry. Lung microbiome composition was reconstructed using metatranscriptomics on sputum samples, and microbial taxa were correlated to circulating immune cells and surface markers expression. RESULTS In pwCF, we found a specific systemic immune profile characterized by widespread hyperactivation and altered frequencies of several subsets. These included substantial changes in B-cell subsets, enrichment of CD35+/CD49d+ neutrophils, and reduction in dendritic cells. Activation markers and checkpoint molecule expression levels differed from healthy subjects. CTLA-4 expression was increased in Tregs and, together with impaired B-cell subsets, correlated with patients' lung function. Concentrations and frequencies of key immune cells and marker expression correlated with the relative abundance of commensal and pathogenic bacteria in the lungs. CONCLUSION The CF-specific immune signature, involving hyperactivation, immune dysregulation with alteration in Treg homeostasis, and impaired B-cell function, is a potential source of lung function heterogeneity. The activity of specific microbes contributes to disrupting the balance of the immune response. Our data provide a unique foundation for identifying novel markers and immunomodulatory targets to develop the future of cystic fibrosis treatment and management.
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Affiliation(s)
- Elio Rossi
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen Ø, Denmark; Department of Biosciences, University of Milan, Milan, Italy.
| | - Mads Lausen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen Ø, Denmark
| | | | - Antonella Colque
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen Ø, Denmark
| | - Bibi Uhre Nielsen
- Department of Infectious Diseases, Rigshospitalet, Cystic Fibrosis Centre, Copenhagen Ø, Denmark
| | - Rikke Møller
- Department of Infectious Diseases, Rigshospitalet, Cystic Fibrosis Centre, Copenhagen Ø, Denmark
| | - Camilla de Gier
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen Ø, Denmark
| | - Annemette Hald
- Department of Infectious Diseases, Rigshospitalet, Cystic Fibrosis Centre, Copenhagen Ø, Denmark
| | - Marianne Skov
- Department of Pediatrics, Rigshospitalet, Cystic Fibrosis Centre, Copenhagen, Denmark
| | - Tacjana Pressler
- Department of Infectious Diseases, Rigshospitalet, Cystic Fibrosis Centre, Copenhagen Ø, Denmark; Department of Pediatrics, Rigshospitalet, Cystic Fibrosis Centre, Copenhagen, Denmark
| | - Søren Molin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Rigshospitalet, Copenhagen Ø, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Hanne Vibeke Marquart
- Department of Clinical Immunology, Rigshospitalet, Copenhagen Ø, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Helle Krogh Johansen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen Ø, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
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2
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Wynn EA, Dide-Agossou C, Reichlen M, Rossmassler K, Al Mubarak R, Reid JJ, Tabor ST, Born SEM, Ransom MR, Davidson RM, Walton KN, Benoit JB, Hoppers A, Loy DE, Bauman AA, Massoudi LM, Dolganov G, Strong M, Nahid P, Voskuil MI, Robertson GT, Moore CM, Walter ND. Transcriptional adaptation of Mycobacterium tuberculosis that survives prolonged multi-drug treatment in mice. mBio 2023; 14:e0236323. [PMID: 37905920 PMCID: PMC10746229 DOI: 10.1128/mbio.02363-23] [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: 09/13/2023] [Accepted: 09/25/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE A major reason that curing tuberculosis requires prolonged treatment is that drug exposure changes bacterial phenotypes. The physiologic adaptations of Mycobacterium tuberculosis that survive drug exposure in vivo have been obscure due to low sensitivity of existing methods in drug-treated animals. Using the novel SEARCH-TB RNA-seq platform, we elucidated Mycobacterium tuberculosis phenotypes in mice treated for with the global standard 4-drug regimen and compared them with the effect of the same regimen in vitro. This first view of the transcriptome of the minority Mycobacterium tuberculosis population that withstands treatment in vivo reveals adaptation of a broad range of cellular processes, including a shift in metabolism and cell wall modification. Surprisingly, the change in gene expression induced by treatment in vivo and in vitro was largely similar. This apparent "portability" from in vitro to the mouse provides important new context for in vitro transcriptional analyses that may support early preclinical drug evaluation.
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Affiliation(s)
- Elizabeth A. Wynn
- Rocky Mountain Regional VA Medical Center, Aurora, Colorado, USA
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Consortium for Applied Microbial Metrics, Aurora, Colorado, USA
| | - Christian Dide-Agossou
- Rocky Mountain Regional VA Medical Center, Aurora, Colorado, USA
- Consortium for Applied Microbial Metrics, Aurora, Colorado, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Matthew Reichlen
- Consortium for Applied Microbial Metrics, Aurora, Colorado, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Karen Rossmassler
- Rocky Mountain Regional VA Medical Center, Aurora, Colorado, USA
- Consortium for Applied Microbial Metrics, Aurora, Colorado, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Reem Al Mubarak
- Rocky Mountain Regional VA Medical Center, Aurora, Colorado, USA
- Consortium for Applied Microbial Metrics, Aurora, Colorado, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Justin J. Reid
- Rocky Mountain Regional VA Medical Center, Aurora, Colorado, USA
- Consortium for Applied Microbial Metrics, Aurora, Colorado, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Samuel T. Tabor
- Rocky Mountain Regional VA Medical Center, Aurora, Colorado, USA
- Consortium for Applied Microbial Metrics, Aurora, Colorado, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Sarah E. M. Born
- Consortium for Applied Microbial Metrics, Aurora, Colorado, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Monica R. Ransom
- Division of Hematology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Rebecca M. Davidson
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Kendra N. Walton
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Jeanne B. Benoit
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Amanda Hoppers
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Dorothy E. Loy
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Allison A. Bauman
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Lisa M. Massoudi
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Gregory Dolganov
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Palo Alto, California, USA
| | - Michael Strong
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Payam Nahid
- Consortium for Applied Microbial Metrics, Aurora, Colorado, USA
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, California, USA
- UCSF Center for Tuberculosis, University of California San Francisco, San Francisco, California, USA
| | - Martin I. Voskuil
- Consortium for Applied Microbial Metrics, Aurora, Colorado, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Gregory T. Robertson
- Consortium for Applied Microbial Metrics, Aurora, Colorado, USA
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Camille M. Moore
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Consortium for Applied Microbial Metrics, Aurora, Colorado, USA
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Nicholas D. Walter
- Rocky Mountain Regional VA Medical Center, Aurora, Colorado, USA
- Consortium for Applied Microbial Metrics, Aurora, Colorado, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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3
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Wynn EA, Dide-Agossou C, Reichlen M, Rossmassler K, Al Mubarak R, Reid JJ, Tabor ST, Born SEM, Ransom MR, Davidson RM, Walton KN, Benoit JB, Hoppers A, Bauman AA, Massoudi LM, Dolganov G, Nahid P, Voskuil MI, Robertson GT, Moore CM, Walter ND. Transcriptional adaptation of drug-tolerant Mycobacterium tuberculosis in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.531356. [PMID: 36945388 PMCID: PMC10028792 DOI: 10.1101/2023.03.06.531356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Transcriptome evaluation of Mycobacterium tuberculosis in the lungs of laboratory animals during long-term treatment has been limited by extremely low abundance of bacterial mRNA relative to eukaryotic RNA. Here we report a targeted amplification RNA sequencing method called SEARCH-TB. After confirming that SEARCH-TB recapitulates conventional RNA-seq in vitro, we applied SEARCH-TB to Mycobacterium tuberculosis-infected BALB/c mice treated for up to 28 days with the global standard isoniazid, rifampin, pyrazinamide, and ethambutol regimen. We compared results in mice with 8-day exposure to the same regimen in vitro. After treatment of mice for 28 days, SEARCH-TB suggested broad suppression of genes associated with bacterial growth, transcription, translation, synthesis of rRNA proteins and immunogenic secretory peptides. Adaptation of drug-stressed Mycobacterium tuberculosis appeared to include a metabolic transition from ATP-maximizing respiration towards lower-efficiency pathways, modification and recycling of cell wall components, large-scale regulatory reprogramming, and reconfiguration of efflux pumps expression. Despite markedly different expression at pre-treatment baseline, murine and in vitro samples had broadly similar transcriptional change during treatment. The differences observed likely indicate the importance of immunity and pharmacokinetics in the mouse. By elucidating the long-term effect of tuberculosis treatment on bacterial cellular processes in vivo, SEARCH-TB represents a highly granular pharmacodynamic monitoring tool with potential to enhance evaluation of new regimens and thereby accelerate progress towards a new generation of more effective tuberculosis treatment.
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Affiliation(s)
- Elizabeth A Wynn
- Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
- Department of Biostatistics and Informatics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
| | - Christian Dide-Agossou
- Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Matthew Reichlen
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Karen Rossmassler
- Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Reem Al Mubarak
- Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Justin J Reid
- Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Samuel T Tabor
- Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Sarah E M Born
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Monica R Ransom
- Division of Hematology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Rebecca M Davidson
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Kendra N Walton
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Jeanne B Benoit
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Amanda Hoppers
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Allison A Bauman
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Lisa M Massoudi
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Gregory Dolganov
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Palo Alto, CA, USA
| | - Payam Nahid
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, CA, USA
- UCSF Center for Tuberculosis, University of California, San Francisco, CA, USA
| | - Martin I Voskuil
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Gregory T Robertson
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Camille M Moore
- Department of Biostatistics and Informatics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Nicholas D Walter
- Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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4
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Coppola M, Lai RPJ, Wilkinson RJ, Ottenhoff THM. The In Vivo Transcriptomic Blueprint of Mycobacterium tuberculosis in the Lung. Front Immunol 2022; 12:763364. [PMID: 35003075 PMCID: PMC8727759 DOI: 10.3389/fimmu.2021.763364] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/17/2021] [Indexed: 11/30/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) genes encoding proteins targeted by vaccines and drugs should be expressed in the lung, the main organ affected by Mtb, for these to be effective. However, the pulmonary expression of most Mtb genes and their proteins remains poorly characterized. The aim of this study is to fill this knowledge gap. We analyzed large scale transcriptomic datasets from specimens of Mtb-infected humans, TB-hypersusceptible (C3H/FeJ) and TB-resistant (C57BL/6J) mice and compared data to in vitro cultured Mtb gene-expression profiles. Results revealed high concordance in the most abundantly in vivo expressed genes between pulmonary Mtb transcriptomes from different datasets and different species. As expected, this contrasted with a lower correlation found with the highest expressed Mtb genes from in vitro datasets. Among the most consistently and highly in vivo expressed genes, 35 have not yet been explored as targets for vaccination or treatment. More than half of these genes are involved in protein synthesis or metabolic pathways. This first lung-oriented multi-study analysis of the in vivo expressed Mtb-transcriptome provides essential data that considerably increase our understanding of pulmonary TB infection biology, and identifies novel molecules for target-based TB-vaccine and drug development.
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Affiliation(s)
- Mariateresa Coppola
- Department Infectious Diseases, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Rachel P-J Lai
- The Francis Crick Institute, London, United Kingdom.,Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Robert J Wilkinson
- The Francis Crick Institute, London, United Kingdom.,Department of Infectious Diseases, Imperial College London, London, United Kingdom.,Department of Medicine, Institute of Infectious Disease and Molecular Medicine, Wellcome Centre for Infectious Diseases Research in Africa, Cape Town, South Africa
| | - Tom H M Ottenhoff
- Department Infectious Diseases, Leiden University Medical Center (LUMC), Leiden, Netherlands
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5
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Kateete DP, Mbabazi MM, Nakazzi F, Katabazi FA, Kigozi E, Ssengooba W, Nakiyingi L, Namiiro S, Okwera A, Joloba ML, Muwonge A. Sputum microbiota profiles of treatment-naïve TB patients in Uganda before and during first-line therapy. Sci Rep 2021; 11:24486. [PMID: 34966183 PMCID: PMC8716532 DOI: 10.1038/s41598-021-04271-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 12/14/2021] [Indexed: 11/23/2022] Open
Abstract
Information on microbiota dynamics in pulmonary tuberculosis (TB) in Africa is scarce. Here, we sequenced sputa from 120 treatment-naïve TB patients in Uganda, and investigated changes in microbiota of 30 patients with treatment-response follow-up samples. Overall, HIV-status and anti-TB treatment were associated with microbial structural and abundance changes. The predominant phyla were Bacteroidetes, Firmicutes, Proteobacteria, Fusobacteria and Actinobacteria, accounting for nearly 95% of the sputum microbiota composition; the predominant genera across time were Prevotella, Streptococcus, Veillonella, Haemophilus, Neisseria, Alloprevotella, Porphyromonas, Fusobacterium, Gemella, and Rothia. Treatment-response follow-up at month 2 was characterized by a reduction in abundance of Mycobacterium and Fretibacterium, and an increase in Ruminococcus and Peptococcus; month 5 was characterized by a reduction in Tannerella and Fusobacterium, and an increase in members of the family Neisseriaceae. The microbiota core comprised of 44 genera that were stable during treatment. Hierarchical clustering of this core's abundance distinctly separated baseline (month 0) samples from treatment follow-up samples (months 2/5). We also observed a reduction in microbial diversity with 9.1% (CI 6-14%) of the structural variation attributed to HIV-status and anti-TB treatment. Our findings show discernible microbiota signals associated with treatment with potential to inform anti-TB treatment response monitoring.
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Affiliation(s)
- David Patrick Kateete
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda.
| | - Monica M Mbabazi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Faith Nakazzi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Fred A Katabazi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Edgar Kigozi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Willy Ssengooba
- BSL-3 Mycobacteriology Laboratory, Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Lydia Nakiyingi
- Department of Medicine, School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
- Infectious Diseases Institute, Makerere University College of Health Sciences, Mulago Hospital Complex, Kampala, Uganda
| | - Sharon Namiiro
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Alphonse Okwera
- TB Clinics, Mulago National Referral Hospital, Kampala, Uganda
| | - Moses L Joloba
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Adrian Muwonge
- Division of Genetics and Genomics, The Roslin Institute, University of Edinburgh, Edinburg, UK.
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburg, UK.
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Transcriptomic Characterization of Tuberculous Sputum Reveals a Host Warburg Effect and Microbial Cholesterol Catabolism. mBio 2021; 12:e0176621. [PMID: 34872348 PMCID: PMC8649757 DOI: 10.1128/mbio.01766-21] [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] [Indexed: 11/23/2022] Open
Abstract
The crucial transmission phase of tuberculosis (TB) relies on infectious sputum and yet cannot easily be modeled. We applied one-step RNA sequencing (RNA-Seq) to sputum from infectious TB patients to investigate the host and microbial environments underlying transmission of Mycobacterium tuberculosis. In such TB sputa, compared to non-TB controls, transcriptional upregulation of inflammatory responses, including an interferon-driven proinflammatory response and a metabolic shift toward glycolysis, was observed in the host. Among all bacterial sequences in the sputum, approximately 1.5% originated from M. tuberculosis, and its transcript abundance was lower in HIV-1-coinfected patients. Commensal bacterial abundance was reduced in the presence of M. tuberculosis infection. Direct alignment to the genomes of the predominant microbiota species also reveals differential adaptation, whereby firmicutes (e.g., streptococci) displayed a nonreplicating phenotype with reduced transcription of ribosomal proteins and reduced activities of ATP synthases, while Neisseria and Prevotella spp. were less affected. The transcriptome of sputum M. tuberculosis more closely resembled aerobic replication and shared similarity in carbon metabolism to in vitro and in vivo models with significant upregulation of genes associated with cholesterol metabolism and downstream propionate detoxification pathways. In addition, and counter to previous reports on intracellular M. tuberculosis infection in vitro, M. tuberculosis in sputum was zinc, but not iron, deprived, and the phoP loci were also significantly downregulated, suggesting that the pathogen is likely extracellular in location.
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7
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Mekonnen D, Derbie A, Mihret A, Yimer SA, Tønjum T, Gelaw B, Nibret E, Munshae A, Waddell SJ, Aseffa A. Lipid droplets and the transcriptome of Mycobacterium tuberculosis from direct sputa: a literature review. Lipids Health Dis 2021; 20:129. [PMID: 34602073 PMCID: PMC8487580 DOI: 10.1186/s12944-021-01550-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/09/2021] [Indexed: 11/21/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the main etiology of tuberculosis (TB), is predominantly an intracellular pathogen that has caused infection, disease and death in humans for centuries. Lipid droplets (LDs) are dynamic intracellular organelles that are found across the evolutionary tree of life. This review is an evaluation of the current state of knowledge regarding Mtb-LD formation and associated Mtb transcriptome directly from sputa.Based on the LD content, Mtb in sputum may be classified into three groups: LD positive, LD negative and LD borderline. However, the clinical and evolutionary importance of each state is not well elaborated. Mounting evidence supports the view that the presence of LD positive Mtb bacilli in sputum is a biomarker of slow growth, low energy state, towards lipid degradation, and drug tolerance. In Mtb, LD may serve as a source of chemical energy, scavenger of toxic compounds, prevent destruction of Mtb through autophagy, delay trafficking of lysosomes towards the phagosome, and contribute to Mtb persistence. It is suggest that LD is a key player in the induction of a spectrum of phenotypic and metabolic states of Mtb in the macrophage, granuloma and extracellular sputum microenvironment. Tuberculosis patients with high proportion of LD positive Mtb in pretreatment sputum was associated with higher rate of poor treatment outcome, indicating that LD may have a clinical application in predicting treatment outcome.The propensity for LD formation among Mtb lineages is largely unknown. The role of LD on Mtb transmission and disease phenotype (pulmonary TB vs extra-pulmonary TB) is not well understood. Thus, further studies are needed to understand the relationships between LD positivity and Mtb lineage, Mtb transmission and clinical types.
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Affiliation(s)
- Daniel Mekonnen
- Department of Medical Microbiology, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia.
- Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia.
| | - Awoke Derbie
- Department of Medical Microbiology, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia
- Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
- The Centre for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), Addis Ababa University, Addis Ababa, Ethiopia
| | - Adane Mihret
- Armauer Hansen Research Institute, Jimma Road, ALERT Compound, PO Box 1005, Addis Ababa, Ethiopia
- Department of Medical Microbiology, Immunology and Parasitology, College of Medicine and Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Solomon Abebe Yimer
- Department of Microbiology, University of Oslo, PO Box 1071, Blindern, NO-0316, Oslo, Norway
- Coalition for Epidemic Preparedness Innovations, CEPI, P.O. Box 123, Torshov, 0412, Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, University of Oslo, PO Box 1071, Blindern, NO-0316, Oslo, Norway
- Department of Microbiology, Oslo University Hospital, PO Box 4950, Nydalen, NO-0424, Oslo, Norway
| | - Baye Gelaw
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Endalkachew Nibret
- Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
- Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Abaineh Munshae
- Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
- Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Simon J Waddell
- Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX, UK
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Jimma Road, ALERT Compound, PO Box 1005, Addis Ababa, Ethiopia
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8
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Mishra R, Yadav V, Guha M, Singh A. Heterogeneous Host-Pathogen Encounters Coordinate Antibiotic Resilience in Mycobacterium tuberculosis. Trends Microbiol 2021; 29:606-620. [PMID: 33309526 PMCID: PMC7611257 DOI: 10.1016/j.tim.2020.10.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/25/2020] [Accepted: 10/26/2020] [Indexed: 12/11/2022]
Abstract
Successful treatment of tuberculosis (TB) depends on the eradication of its causative agent Mycobacterium tuberculosis (Mtb) in the host. However, the emergence of phenotypically drug-resistant Mtb in the host environment tempers the ability of antibiotics to cure disease. Host immunity produces diverse microenvironmental niches that are exploited by Mtb to mobilize adaptation programs. Such differential interactions amplify pre-existing heterogeneity in the host-pathogen milieu to influence disease pathology and therapy outcome. Therefore, comprehending the intricacies of phenotypic heterogeneity can be an empirical step forward in potentiating drug action. With this goal, we review the interconnectedness of the lesional, cellular, and bacterial heterogeneity underlying phenotypic drug resistance. Based on this information, we anticipate the development of new therapeutic strategies targeting host-pathogen heterogeneity to cure TB.
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Affiliation(s)
- Richa Mishra
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru-560012, India; Centre for Infectious Disease and Research (CIDR), Indian Institute of Science, Bengaluru-560012, India
| | - Vikas Yadav
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru-560012, India; Centre for Infectious Disease and Research (CIDR), Indian Institute of Science, Bengaluru-560012, India
| | - Madhura Guha
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru-560012, India; Centre for Infectious Disease and Research (CIDR), Indian Institute of Science, Bengaluru-560012, India
| | - Amit Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru-560012, India; Centre for Infectious Disease and Research (CIDR), Indian Institute of Science, Bengaluru-560012, India.
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Which sample type is better for Xpert MTB/RIF to diagnose adult and pediatric pulmonary tuberculosis? Biosci Rep 2020; 40:225865. [PMID: 32701147 PMCID: PMC7403955 DOI: 10.1042/bsr20200308] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 02/05/2023] Open
Abstract
Objective: This review aimed to identify proper respiratory-related sample types for adult and pediatric pulmonary tuberculosis (PTB), respectively, by comparing performance of Xpert MTB/RIF when using bronchoalveolar lavage (BAL), induced sputum (IS), expectorated sputum (ES), nasopharyngeal aspirates (NPAs), and gastric aspiration (GA) as sample. Methods: Articles were searched in Web of Science, PubMed, and Ovid from inception up to 29 June 2020. Pooled sensitivity and specificity were calculated, each with a 95% confidence interval (CI). Quality assessment and heterogeneity evaluation across included studies were performed. Results: A total of 50 articles were included. The respective sensitivity and specificity were 87% (95% CI: 0.84–0.89), 91% (95% CI: 0.90–0.92) and 95% (95% CI: 0.93–0.97) in the adult BAL group; 90% (95% CI: 0.88–0.91), 98% (95% CI: 0.97–0.98) and 97% (95% CI: 0.95–0.99) in the adult ES group; 86% (95% CI: 0.84–0.89) and 97% (95% CI: 0.96–0.98) in the adult IS group. Xpert MTB/RIF showed the sensitivity and specificity of 14% (95% CI: 0.10–0.19) and 99% (95% CI: 0.97–1.00) in the pediatric ES group; 80% (95% CI: 0.72–0.87) and 94% (95% CI: 0.92–0.95) in the pediatric GA group; 67% (95% CI: 0.62–0.72) and 99% (95% CI: 0.98–0.99) in the pediatric IS group; and 54% (95% CI: 0.43–0.64) and 99% (95% CI: 0.97–0.99) in the pediatric NPA group. The heterogeneity across included studies was deemed acceptable. Conclusion: Considering diagnostic accuracy, cost and sampling process, ES was a better choice than other sample types for diagnosing adult PTB, especially HIV-associated PTB. GA might be more suitable than other sample types for diagnosing pediatric PTB. The actual choice of sample types should also consider the needs of specific situations.
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Gabrielian A, Engle E, Harris M, Wollenberg K, Glogowski A, Long A, Hurt DE, Rosenthal A. Comparative analysis of genomic variability for drug-resistant strains of Mycobacterium tuberculosis: The special case of Belarus. INFECTION GENETICS AND EVOLUTION 2020; 78:104137. [DOI: 10.1016/j.meegid.2019.104137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 01/27/2023]
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Gordhan BG, Peters J, Kana BD. Application of model systems to study adaptive responses of Mycobacterium tuberculosis during infection and disease. ADVANCES IN APPLIED MICROBIOLOGY 2019; 108:115-161. [PMID: 31495404 DOI: 10.1016/bs.aambs.2019.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Tuberculosis (TB) claims more human lives than any other infectious organism. The lethal synergy between TB-HIV infection and the rapid emergence of drug resistant strains has created a global public health threat that requires urgent attention. Mycobacterium tuberculosis, the causative agent of TB is an exquisitely well-adapted human pathogen, displaying the ability to promptly remodel metabolism when encountering stressful environments during pathogenesis. A careful study of the mechanisms that enable this adaptation will enhance the understanding of key aspects related to the microbiology of TB disease. However, these efforts require microbiological model systems that mimic host conditions in the laboratory. Herein, we describe several in vitro model systems that generate non-replicating and differentially culturable mycobacteria. The changes that occur in the metabolism of M. tuberculosis in some of these models and how these relate to those reported for human TB disease are discussed. We describe mechanisms that tubercle bacteria use to resuscitate from these non-replicating conditions, together with phenotypic heterogeneity in terms of culturabiliy of M. tuberculosis in sputum. Transcriptional changes in M. tuberculosis that allow for adaptation of the organism to the lung environment are also summarized. Finally, given the emerging importance of the microbiome in various infectious diseases, we provide a description of how the lung and gut microbiome affect susceptibility to TB infection and response to treatment. Consideration of these collective aspects will enhance the understanding of basic metabolism, physiology, drug tolerance and persistence in M. tuberculosis to enable development of new therapeutic interventions.
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Affiliation(s)
- Bhavna Gowan Gordhan
- Department of Science and Technology/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 Peters
- Department of Science and Technology/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
| | - Bavesh Davandra Kana
- Department of Science and Technology/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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12
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Multiplex Real-Time PCR-short TUB Assay for Detection of the Mycobacterium tuberculosis Complex in Smear-Negative Clinical Samples with Low Mycobacterial Loads. J Clin Microbiol 2019; 57:JCM.00733-19. [PMID: 31189585 DOI: 10.1128/jcm.00733-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/09/2019] [Indexed: 01/20/2023] Open
Abstract
Tuberculosis (TB) remains a major health problem worldwide. Control of TB requires rapid, accurate diagnosis of active disease. However, extrapulmonary TB is very difficult to diagnose because the clinical specimens have very low bacterial loads. Several molecular methods involving direct detection of the Mycobacterium tuberculosis complex (MTBC) have emerged in recent years. Real-time PCR amplification simultaneously combines the amplification and detection of candidate sequences by using fluorescent probes (mainly TaqMan or Molecular Beacons) in automated systems. The multiplex real-time PCR-short assay is performed using locked nucleic acid (LNA) probes (length, 8 to 9 nucleotides) in combination with CodUNG to detect multiple pathogens in clinical samples. In this study, we evaluated the performance of this novel multiplex assay for detecting the MTBC in comparison with that of the conventional culture-based method. The multiplex real-time PCR-shortTUB assay targets two genes, whiB3 (redox-responsive transcriptional regulator) and pstS1 (phosphate-specific transporter), yielding limits of detection (LOD) of 10 copies and 100 copies, respectively, and amplification efficiencies of 92% and 99.7%, respectively. A total of 94 extrapulmonary samples and pulmonary samples with low mycobacterial loads (all smear negative; 75 MTBC culture positive) were analyzed using the test, yielding an overall sensitivity of 88% and a specificity of 95%. For pleural fluid and tissues/biopsy specimens, the sensitivity was 83% and 85%, respectively. In summary, this technique could be implemented in routine clinical microbiology testing to reduce the overall turnaround time for MTBC detection and may therefore be a useful tool for the diagnosis of extrapulmonary tuberculosis and diagnosis using pulmonary samples with low mycobacterial loads.
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13
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Rockwood N, Lai RP, Seldon R, Young DB, Wilkinson RJ. Variation in pre-therapy levels of selected Mycobacterium tuberculosis transcripts in sputum and their relationship with 2-month culture conversion. Wellcome Open Res 2019. [DOI: 10.12688/wellcomeopenres.15332.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background:The abundance of transcripts arising fromMycobacterium tuberculosis(MTB) in sputum pre-chemotherapy may enhance our understanding of factors influencing treatment response. We hypothesized that differences in the prevalence of pre-existing slowly metabolizing MTB in sputum may be partially responsible for differences in the rate of sputum clearance during treatment.Methods:Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was used to characterize a selected limited transcription profile of MTB in sputum pre-chemotherapy and assess inter-individual variation. The difference in cycle threshold (Ct) per gene, normalized to 16S, between exponential/stationary phase culture and sputum was calculated and stratified by 2-month culture converter status.Results:HIV-1 uninfected patients with rifampicin-susceptible tuberculosis provided sputum pre-chemotherapy; 11 patients were negative for MTB culture after two months of therapy and 8 remained culture-positive.Increasedicl1andprpDandrpsN2:rpsN1in sputum relative to culture suggested cholesterol utilization and a low-zinc environment respectively. IncreasedhspXand decreasedatpAandnuoGrelative to exponential culture suggested a slowly metabolizing subpopulation of MTB. While the thehspXhiatpAlonuoGlosignal varied, we did not observe statistically significant enrichment of this phenotype in the non-converter population nor an association with MTB-lineage.Conclusion:Differential abundance of selected informative transcripts suggested a metabolically less-active subpopulation with a prevalence that varied between individual untreated patients.
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Shockey AC, Dabney J, Pepperell CS. Effects of Host, Sample, and in vitro Culture on Genomic Diversity of Pathogenic Mycobacteria. Front Genet 2019; 10:477. [PMID: 31214242 PMCID: PMC6558051 DOI: 10.3389/fgene.2019.00477] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 05/03/2019] [Indexed: 12/16/2022] Open
Abstract
Mycobacterium tuberculosis (M. tb), an obligate human pathogen and the etiological agent of tuberculosis (TB), remains a major threat to global public health. Comparative genomics has been invaluable for monitoring the emergence and spread of TB and for gaining insight into adaptation of M. tb. Most genomic studies of M. tb are based on single bacterial isolates that have been cultured for several weeks in vitro. However, in its natural human host, M. tb comprises complex, in some cases massive bacterial populations that diversify over the course of infection and cannot be wholly represented by a single genome. Recently, enrichment via hybridization capture has been used as a rapid diagnostic tool for TB, circumventing culturing protocols and enabling the recovery of M. tb genomes directly from sputum. This method has further applicability to the study of M. tb adaptation, as it enables a higher resolution and more direct analysis of M. tb genetic diversity within hosts with TB. Here we analyzed genomic material from M. tb and Mycobacterium bovis populations captured directly from sputum and from cultured samples using metagenomic and Pool-Seq approaches. We identified effects of sampling, patient, and sample type on bacterial genetic diversity. Bacterial genetic diversity was more variable and on average higher in sputum than in culture samples, suggesting that manipulation in the laboratory reshapes the bacterial population. Using outlier analyses, we identified candidate bacterial genetic loci mediating adaptation to these distinct environments. The study of M. tb in its natural human host is a powerful tool for illuminating host pathogen interactions and understanding the bacterial genetic underpinnings of virulence.
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Affiliation(s)
- Abigail C. Shockey
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Jesse Dabney
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Caitlin S. Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
- Department of Medicine, Division of Infectious Diseases, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
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15
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Burel JG, Babor M, Pomaznoy M, Lindestam Arlehamn CS, Khan N, Sette A, Peters B. Host Transcriptomics as a Tool to Identify Diagnostic and Mechanistic Immune Signatures of Tuberculosis. Front Immunol 2019; 10:221. [PMID: 30837989 PMCID: PMC6389658 DOI: 10.3389/fimmu.2019.00221] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 01/25/2019] [Indexed: 12/15/2022] Open
Abstract
Tuberculosis (TB) is a major infectious disease worldwide, and is associated with several challenges for control and eradication. First, more accurate diagnostic tools that better represent the spectrum of infection states are required; in particular, identify the latent TB infected individuals with high risk of developing active TB. Second, we need to better understand, from a mechanistic point of view, why the immune system is unsuccessful in some cases for control and elimination of the pathogen. Host transcriptomics is a powerful approach to identify both diagnostic and mechanistic immune signatures of diseases. We have recently reported that optimal study design for these two purposes should be guided by different sets of criteria. Here, based on already published transcriptomics signatures of tuberculosis, we further develop these guidelines and identify additional factors to consider for obtaining diagnostic vs. mechanistic signatures in terms of cohorts, samples, data generation and analysis. Diagnostic studies should aim to identify small disease signatures with high discriminatory power across all affected populations, and against similar pathologies to TB. Specific focus should be made on improving the diagnosis of infected individuals at risk of developing active disease. Conversely, mechanistic studies should focus on tissues biopsies, immune relevant cell subsets, state of the art transcriptomic techniques and bioinformatics tools to understand the biological meaning of identified gene signatures that could facilitate therapeutic interventions. Finally, investigators should ensure their data are made publicly available along with complete annotations to facilitate metadata and cross-study analyses.
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Affiliation(s)
- Julie G Burel
- Department of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Mariana Babor
- Department of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Mikhail Pomaznoy
- Department of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | | | - Nabeela Khan
- Department of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Alessandro Sette
- Department of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States.,Department of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Bjoern Peters
- Department of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States.,Department of Medicine, University of California, San Diego, La Jolla, CA, United States
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16
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High-resolution in situ transcriptomics of Pseudomonas aeruginosa unveils genotype independent patho-phenotypes in cystic fibrosis lungs. Nat Commun 2018; 9:3459. [PMID: 30150613 PMCID: PMC6110831 DOI: 10.1038/s41467-018-05944-5] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/30/2018] [Indexed: 12/30/2022] Open
Abstract
Life-long bacterial infections in cystic fibrosis (CF) airways constitute an excellent model both for persistent infections and for microbial adaptive evolution in complex dynamic environments. Using high-resolution transcriptomics applied on CF sputum, we profile transcriptional phenotypes of Pseudomonas aeruginosa populations in patho-physiological conditions. Here we show that the soft-core genome of genetically distinct populations, while maintaining transcriptional flexibility, shares a common expression program tied to the lungs environment. We identify genetically independent traits defining P. aeruginosa physiology in vivo, documenting the connection between several previously identified mutations in CF isolates and some of the convergent phenotypes known to develop in later stages of the infection. In addition, our data highlight to what extent this organism can exploit its extensive repertoire of physiological pathways to acclimate to a new niche and suggest how alternative nutrients produced in the lungs may be utilized in unexpected metabolic contexts.
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17
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Ofori-Anyinam B, Dolganov G, Van T, Davis JL, Walter ND, Garcia BJ, Voskuil M, Fissette K, Diels M, Driesen M, Meehan CJ, Yeboah-Manu D, Coscolla M, Gagneux S, Antonio M, Schoolnik G, Gehre F, de Jong BC. Significant under expression of the DosR regulon in M. tuberculosis complex lineage 6 in sputum. Tuberculosis (Edinb) 2017; 104:58-64. [PMID: 28454650 PMCID: PMC5421582 DOI: 10.1016/j.tube.2017.03.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/21/2017] [Accepted: 03/02/2017] [Indexed: 11/19/2022]
Abstract
Mycobacterium africanum lineage (L) 6 is an important pathogen in West Africa, causing up to 40% of pulmonary tuberculosis (TB). The biology underlying the clinical differences between M. africanum and M. tuberculosis sensu stricto remains poorly understood. We performed ex vivo expression of 2179 genes of the most geographically dispersed cause of human TB, M. tuberculosis L4 and the geographically restricted, M. africanum L6 directly from sputa of 11 HIV-negative TB patients from The Gambia who had not started treatment. The DosR regulon was the most significantly decreased category in L6 relative to L4. Further, we identified nonsynonymous mutations in major DosR regulon genes of 44 L6 genomes of TB patients from The Gambia and Ghana. Using Lebek's test, we assessed differences in oxygen requirements for growth. L4 grew only at the aerobic surface while L6 grew throughout the medium. In the host, the DosR regulon is critical for M. tuberculosis in adaptation to oxygen limitation. However, M. africanum L6 appears to have adapted to growth under hypoxic conditions or to different biological niches. The observed under expression of DosR in L6 fits with the genomic changes in DosR genes, microaerobic growth and the association with extrapulmonary disease.
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Affiliation(s)
- Boatema Ofori-Anyinam
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2000, Antwerp, Belgium; Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, The Gambia, Atlantic Boulevard, Fajara, P.O. Box 273, Banjul, Gambia
| | - Gregory Dolganov
- Department of Microbiology and Immunology, Stanford University, 299 Campus Drive, Stanford, CA, 94305, USA
| | - Tran Van
- Department of Microbiology and Immunology, Stanford University, 299 Campus Drive, Stanford, CA, 94305, USA
| | - J Lucian Davis
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College Street, P.O. Box 208034, New Haven, CT, 06520-8034, USA; Department of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, P.O. Box 208057, 300 Cedar Street TAC - 441 South, New Haven, CT, 06520-8057, USA
| | - Nicholas D Walter
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Building 500 - 13001 E, 17th Place, Campus Box C290, Aurora, CO, 80045, USA; Pulmonary Section, Denver Veterans Affairs Medical Center, 1055 Clermont Street, Denver, CO, 80220, USA; Integrated Center for Genes, Environment, & Health, National Jewish Health, Smith Building; A647, 1400 Jackson Street, Denver, CO, 80206, USA
| | - Benjamin J Garcia
- Integrated Center for Genes, Environment, & Health, National Jewish Health, Smith Building; A647, 1400 Jackson Street, Denver, CO, 80206, USA; Computational Bioscience Program, University of Colorado Denver, Building 500 - 13001 E, 17th Place, Campus Box C290, Aurora, CO, 80045, USA
| | - Marty Voskuil
- Department of Immunology and Microbiology, University of Colorado School of Medicine, 12800 E. 19th Ave., Mail Stop 8333, Aurora, CO, 80045, USA
| | - Kristina Fissette
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2000, Antwerp, Belgium
| | - Maren Diels
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2000, Antwerp, Belgium
| | - Michèle Driesen
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2000, Antwerp, Belgium
| | - Conor J Meehan
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2000, Antwerp, Belgium
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, P.O. Box LG 581, Legon, Accra, Ghana
| | - Mireia Coscolla
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, P.O. Box 4002, Basel, Switzerland; University of Basel, Petersplatz 1, P.O. Box 4001, Basel, Switzerland
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, P.O. Box 4002, Basel, Switzerland; University of Basel, Petersplatz 1, P.O. Box 4001, Basel, Switzerland
| | - Martin Antonio
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, The Gambia, Atlantic Boulevard, Fajara, P.O. Box 273, Banjul, Gambia
| | - Gary Schoolnik
- Department of Microbiology and Immunology, Stanford University, 299 Campus Drive, Stanford, CA, 94305, USA
| | - Florian Gehre
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2000, Antwerp, Belgium; Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, The Gambia, Atlantic Boulevard, Fajara, P.O. Box 273, Banjul, Gambia
| | - Bouke C de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2000, Antwerp, Belgium.
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