title: Sputum is a surrogate for bronchoalveolar lavage for monitoring Mycobacterium tuberculosis transcriptional profiles in TB patients.
abstract: Pathogen-targeted transcriptional profiling in human sputum may elucidate the physiologic state of Mycobacterium tuberculosis (M. tuberculosis) during infection and treatment. However, whether M. tuberculosis transcription in sputum recapitulates transcription in the lung is uncertain. We therefore compared M. tuberculosis transcription in human sputum and bronchoalveolar lavage (BAL) samples from 11 HIV-negative South African patients with pulmonary tuberculosis. We additionally compared these clinical samples with in vitro log phase aerobic growth and hypoxic non-replicating persistence (NRP-2). Of 2179 M. tuberculosis transcripts assayed in sputum and BAL via multiplex RT-PCR, 194 (8.9%) had a p-value <0.05, but none were significant after correction for multiple testing. Categorical enrichment analysis indicated that expression of the hypoxia-responsive DosR regulon was higher in BAL than in sputum. M. tuberculosis transcription in BAL and sputum was distinct from both aerobic growth and NRP-2, with a range of 396-1020 transcripts significantly differentially expressed after multiple testing correction. Collectively, our results indicate that M. tuberculosis transcription in sputum approximates M. tuberculosis transcription in the lung. Minor differences between M. tuberculosis transcription in BAL and sputum suggested lower oxygen concentrations or higher nitric oxide concentrations in BAL. M. tuberculosis-targeted transcriptional profiling of sputa may be a powerful tool for understanding M. tuberculosis pathogenesis and monitoring treatment responses in vivo.
authors.affiliation: Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA; Computational Bioscience Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA. Electronic address: benjamin.garcia@ucdenver.edu.
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Garcia
authors.affiliation: DST/NRF Centre of Excellence for Biomedical Tuberculosis Research and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.
authors.forename: Andre G
authors.initials: AG
authors.lastname: Loxton
authors.affiliation: Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
authors.forename: Gregory M
authors.initials: GM
authors.lastname: Dolganov
authors.affiliation: Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
authors.forename: Tran T
authors.initials: TT
authors.lastname: Van
authors.affiliation: Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA.
authors.forename: J Lucian
authors.initials: JL
authors.lastname: Davis
authors.affiliation: Institute of Tropical Medicine, Antwerp, Belgium.
authors.forename: Bouke C
authors.initials: BC
authors.lastname: de Jong
authors.affiliation: Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA.
authors.forename: Martin I
authors.initials: MI
authors.lastname: Voskuil
authors.affiliation: Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA; Computational Bioscience Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA.
authors.forename: Sonia M
authors.initials: SM
authors.lastname: Leach
authors.affiliation: Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
authors.forename: Gary K
authors.initials: GK
authors.lastname: Schoolnik
authors.affiliation: DST/NRF Centre of Excellence for Biomedical Tuberculosis Research and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.
authors.forename: Gerhard
authors.initials: G
authors.lastname: Walzl
authors.affiliation: Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA; Computational Bioscience Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Strong
authors.affiliation: Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA; Pulmonary Section, Denver Veterans Affairs Medical Center, Denver, CO, USA; Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA.
authors.forename: Nicholas D
authors.initials: ND
authors.lastname: Walter
mesh_terms: D000328:Adult; D000995:Antitubercular Agents / Q000494:pharmacology; D001426:Bacterial Proteins / Q000378:metabolism; D001992:Bronchoalveolar Lavage Fluid / Q000382:microbiology*; D004268:DNA-Binding Proteins; D016903:Drug Monitoring / Q000379:methods; D020869:Gene Expression Profiling / Q000379:methods; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects; D005798:Genes, Bacterial; D006801:Humans; D009169:Mycobacterium tuberculosis / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D011494:Protein Kinases / Q000378:metabolism; D012329:RNA, Bacterial / Q000032:analysis; D012333:RNA, Messenger / Q000032:analysis; D013048:Specimen Handling / Q000379:methods; D013183:Sputum / Q000382:microbiology*; D014158:Transcription, Genetic / Q000187:drug effects; D014397:Tuberculosis, Pulmonary / Q000382:microbiology*
chemical_list: D000995:Antitubercular Agents; D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; C542863:DosR protein, Mycobacterium tuberculosis; D012329:RNA, Bacterial; D012333:RNA, Messenger; D011494:Protein Kinases
keywords: *Gene expression profiling; Bronchoalveolar lavage/microbiology; Computational biology/methods; Mycobacterium tuberculosis/genetics; Mycobacterium tuberculosis/physiology; Sputum/microbiology; Tuberculosis, pulmonary/epidemiology/*microbiology