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 sub-population tolerates prolonged drug exposure. We evaluated drug-tolerant bacilli in human sputum by comparing mRNA expression of drug-tolerant bacilli that survive the early bactericidal phase with treatment-naive bacilli. METHODS: M. tuberculosis gene expression was quantified via RT-PCR in serial sputa from 17 Ugandans treated for drug-susceptible pulmonary tuberculosis. RESULTS: Within four days, bacterial mRNA abundance declined >98%, indicating rapid killing. Thereafter, the rate of decline slowed >94%, indicating drug tolerance. After 14 days, 16S rRNA transcripts/genome declined 96%, indicating slow growth. Drug-tolerant bacilli displayed marked down-regulation of genes associated with growth, metabolism and lipid synthesis and up-regulation in stress responses and key regulatory categories - including stress-associated sigma factors, transcription factors, and toxin-antitoxin genes. Drug efflux pumps were up-regulated. The isoniazid stress signature was induced by initial drug exposure then disappeared after four days. CONCLUSIONS: Transcriptional patterns suggest that drug-tolerant bacilli in sputum are in a slow-growing, metabolically and synthetically down-regulated 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 TB treatment regimens.