Transcriptional Adaptation of Drug-tolerant Mycobacterium tuberculosis During Treatment of Human Tuberculosis

Nicholas D. Walter, Gregory M. Dolganov, Benjamin J. Garcia, William Worodria, Alfred Andama, Emmanuel Musisi, Irene Ayakaka, Tran T. Van, Martin I. Voskuil, Bouke C. De Jong, Rebecca M. Davidson, Tasha E. Fingerlin, Katerina Kechris, Claire Palmer, Payam Nahid, Charles L. Daley, Mark Geraci, Laurence Huang, Adithya Cattamanchi, Michael StrongGary K. Schoolnik, John Lucian Davis

Research output: Contribution to journalArticle

31 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)990-998
Number of pages9
JournalJournal of Infectious Diseases
Volume212
Issue number6
DOIs
StatePublished - Sep 15 2015
Externally publishedYes

Fingerprint

Mycobacterium tuberculosis
Tuberculosis
Pharmaceutical Preparations
Bacillus
Sputum
Isoniazid
Down-Regulation
Bacterial RNA
16S Ribosomal RNA
Drug Tolerance
Antitoxins
Sigma Factor
Messenger RNA
Growth
Lipid Metabolism
Pulmonary Tuberculosis
Genes
Reverse Transcription
Transcription Factors
Up-Regulation

Keywords

  • gene expression profiling
  • Mycobacterium tuberculosis/genetics
  • Mycobacterium tuberculosis/physiology
  • pulmonary/epidemiology
  • sputum/microbiology
  • tuberculosis

ASJC Scopus subject areas

  • Infectious Diseases
  • Immunology and Allergy

Cite this

Walter, N. D., Dolganov, G. M., Garcia, B. J., Worodria, W., Andama, A., Musisi, E., ... Davis, J. L. (2015). Transcriptional Adaptation of Drug-tolerant Mycobacterium tuberculosis During Treatment of Human Tuberculosis. Journal of Infectious Diseases, 212(6), 990-998. https://doi.org/10.1093/infdis/jiv149

Transcriptional Adaptation of Drug-tolerant Mycobacterium tuberculosis During Treatment of Human Tuberculosis. / Walter, Nicholas D.; Dolganov, Gregory M.; Garcia, Benjamin J.; Worodria, William; Andama, Alfred; Musisi, Emmanuel; Ayakaka, Irene; Van, Tran T.; Voskuil, Martin I.; De Jong, Bouke C.; Davidson, Rebecca M.; Fingerlin, Tasha E.; Kechris, Katerina; Palmer, Claire; Nahid, Payam; Daley, Charles L.; Geraci, Mark; Huang, Laurence; Cattamanchi, Adithya; Strong, Michael; Schoolnik, Gary K.; Davis, John Lucian.

In: Journal of Infectious Diseases, Vol. 212, No. 6, 15.09.2015, p. 990-998.

Research output: Contribution to journalArticle

Walter, ND, Dolganov, GM, Garcia, BJ, Worodria, W, Andama, A, Musisi, E, Ayakaka, I, Van, TT, Voskuil, MI, De Jong, BC, Davidson, RM, Fingerlin, TE, Kechris, K, Palmer, C, Nahid, P, Daley, CL, Geraci, M, Huang, L, Cattamanchi, A, Strong, M, Schoolnik, GK & Davis, JL 2015, 'Transcriptional Adaptation of Drug-tolerant Mycobacterium tuberculosis During Treatment of Human Tuberculosis', Journal of Infectious Diseases, vol. 212, no. 6, pp. 990-998. https://doi.org/10.1093/infdis/jiv149
Walter, Nicholas D. ; Dolganov, Gregory M. ; Garcia, Benjamin J. ; Worodria, William ; Andama, Alfred ; Musisi, Emmanuel ; Ayakaka, Irene ; Van, Tran T. ; Voskuil, Martin I. ; De Jong, Bouke C. ; Davidson, Rebecca M. ; Fingerlin, Tasha E. ; Kechris, Katerina ; Palmer, Claire ; Nahid, Payam ; Daley, Charles L. ; Geraci, Mark ; Huang, Laurence ; Cattamanchi, Adithya ; Strong, Michael ; Schoolnik, Gary K. ; Davis, John Lucian. / Transcriptional Adaptation of Drug-tolerant Mycobacterium tuberculosis During Treatment of Human Tuberculosis. In: Journal of Infectious Diseases. 2015 ; Vol. 212, No. 6. pp. 990-998.
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AU - Andama, Alfred

AU - Musisi, Emmanuel

AU - Ayakaka, Irene

AU - Van, Tran T.

AU - Voskuil, Martin I.

AU - De Jong, Bouke C.

AU - Davidson, Rebecca M.

AU - Fingerlin, Tasha E.

AU - Kechris, Katerina

AU - Palmer, Claire

AU - Nahid, Payam

AU - Daley, Charles L.

AU - Geraci, Mark

AU - Huang, Laurence

AU - Cattamanchi, Adithya

AU - Strong, Michael

AU - Schoolnik, Gary K.

AU - Davis, John Lucian

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N2 - 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.

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