title: Transcriptional Adaptation of Drug-tolerant Mycobacterium tuberculosis During Treatment of Human Tuberculosis.
abstract: BACKGROUND
  Treatment initiation rapidly kills most drug-susceptible Mycobacterium tuberculosis, but a bacterial subpopulation tolerates prolonged drug exposure. We evaluated drug-tolerant bacilli in human sputum by comparing messenger RNA (mRNA) expression of drug-tolerant bacilli that survive the early bactericidal phase with treatment-naive bacilli.
  
  
  METHODS
  M. tuberculosis gene expression was quantified via reverse-transcription polymerase chain reaction in serial sputa from 17 Ugandans treated for drug-susceptible pulmonary tuberculosis.
  
  
  RESULTS
  Within 4 days, bacterial mRNA abundance declined >98%, indicating rapid killing. Thereafter, the rate of decline slowed >94%, indicating drug tolerance. After 14 days, 16S ribosomal RNA transcripts/genome declined 96%, indicating slow growth. Drug-tolerant bacilli displayed marked downregulation of genes associated with growth, metabolism, and lipid synthesis and upregulation in stress responses and key regulatory categories-including stress-associated sigma factors, transcription factors, and toxin-antitoxin genes. Drug efflux pumps were upregulated. The isoniazid stress signature was induced by initial drug exposure, then disappeared after 4 days.
  
  
  CONCLUSIONS
  Transcriptional patterns suggest that drug-tolerant bacilli in sputum are in a slow-growing, metabolically and synthetically downregulated state. Absence of the isoniazid stress signature in drug-tolerant bacilli indicates that physiological state influences drug responsiveness in vivo. These results identify novel drug targets that should aid in development of novel shorter tuberculosis treatment regimens.
authors.affiliation: Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Aurora Pulmonary Division, Denver Veterans Administration Medical Center, Colorado.
authors.forename: Nicholas D
authors.initials: ND
authors.lastname: Walter
authors.affiliation: Department of Microbiology and Immunology, Stanford University, California.
authors.forename: Gregory M
authors.initials: GM
authors.lastname: Dolganov
authors.affiliation: Integrated Center for Genes, Environment, and Health, National Jewish Health, Denver Computational Bioscience Program, University of Colorado Denver, Aurora.
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Garcia
authors.affiliation: Makerere University-University of California, San Francisco Research Collaboration, Kampala, Uganda.
authors.forename: William
authors.initials: W
authors.lastname: Worodria
authors.affiliation: Makerere University-University of California, San Francisco Research Collaboration, Kampala, Uganda.
authors.forename: Alfred
authors.initials: A
authors.lastname: Andama
authors.affiliation: Makerere University-University of California, San Francisco Research Collaboration, Kampala, Uganda.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Musisi
authors.affiliation: Makerere University-University of California, San Francisco Research Collaboration, Kampala, Uganda.
authors.forename: Irene
authors.initials: I
authors.lastname: Ayakaka
authors.affiliation: Department of Microbiology and Immunology, Stanford University, California.
authors.forename: Tran T
authors.initials: TT
authors.lastname: Van
authors.affiliation: Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora.
authors.forename: Martin I
authors.initials: MI
authors.lastname: Voskuil
authors.affiliation: Institute of Tropical Medicine, Antwerp, Belgium.
authors.forename: Bouke C
authors.initials: BC
authors.lastname: de Jong
authors.affiliation: Integrated Center for Genes, Environment, and Health, National Jewish Health, Denver.
authors.forename: Rebecca M
authors.initials: RM
authors.lastname: Davidson
authors.affiliation: Department of Epidemiology and Biostatistics Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora.
authors.forename: Tasha E
authors.initials: TE
authors.lastname: Fingerlin
authors.affiliation: Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora.
authors.forename: Katerina
authors.initials: K
authors.lastname: Kechris
authors.affiliation: Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora.
authors.forename: Claire
authors.initials: C
authors.lastname: Palmer
authors.affiliation: Division of Pulmonary and Critical Care Medicine, University of California San Francisco.
authors.forename: Payam
authors.initials: P
authors.lastname: Nahid
authors.affiliation: Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Aurora Division of Mycobacterial and Respiratory Infections, National Jewish Health, Denver, Colorado.
authors.forename: Charles L
authors.initials: CL
authors.lastname: Daley
authors.affiliation: Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Aurora.
authors.forename: Mark
authors.initials: M
authors.lastname: Geraci
authors.affiliation: Division of Pulmonary and Critical Care Medicine, University of California San Francisco HIV/AIDS Division, University of California San Francisco.
authors.forename: Laurence
authors.initials: L
authors.lastname: Huang
authors.affiliation: Division of Pulmonary and Critical Care Medicine, University of California San Francisco.
authors.forename: Adithya
authors.initials: A
authors.lastname: Cattamanchi
authors.affiliation: Integrated Center for Genes, Environment, and Health, National Jewish Health, Denver.
authors.forename: Michael
authors.initials: M
authors.lastname: Strong
authors.affiliation: Department of Microbiology and Immunology, Stanford University, California.
authors.forename: Gary K
authors.initials: GK
authors.lastname: Schoolnik
authors.affiliation: Division of Pulmonary and Critical Care Medicine, University of California San Francisco.
authors.forename: John Lucian
authors.initials: JL
authors.lastname: Davis
mesh_terms: D000222:Adaptation, Physiological; D000995:Antitubercular Agents / Q000494:pharmacology / Q000627:therapeutic use*; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects*; D006801:Humans; D009169:Mycobacterium tuberculosis / Q000187:drug effects* / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D013183:Sputum / Q000382:microbiology; D014158:Transcription, Genetic; D059467:Transcriptome; D014397:Tuberculosis, Pulmonary / Q000188:drug therapy / Q000453:epidemiology / Q000382:microbiology*; D014454:Uganda / Q000453:epidemiology
chemical_list: D000995:Antitubercular Agents; D012333:RNA, Messenger
keywords: Mycobacterium tuberculosis/genetics; Mycobacterium tuberculosis/physiology; gene expression profiling; pulmonary/epidemiology; sputum/microbiology; tuberculosis