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Safi H, Gopal P, Lingaraju S, Ma S, Levine C, Dartois V, Yee M, Li L, Blanc L, Ho Liang HP, Husain S, Hoque M, Soteropoulos P, Rustad T, Sherman DR, Dick T, Alland D. Phase variation in Mycobacterium tuberculosis glpK produces transiently heritable drug tolerance. Proc Natl Acad Sci U S A 2019; 116:19665-19674. [PMID: 31488707 PMCID: PMC6765255 DOI: 10.1073/pnas.1907631116] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The length and complexity of tuberculosis (TB) therapy, as well as the propensity of Mycobacterium tuberculosis to develop drug resistance, are major barriers to global TB control efforts. M. tuberculosis is known to have the ability to enter into a drug-tolerant state, which may explain many of these impediments to TB treatment. We have identified a mechanism of genetically encoded but rapidly reversible drug tolerance in M. tuberculosis caused by transient frameshift mutations in a homopolymeric tract (HT) of 7 cytosines (7C) in the glpK gene. Inactivating frameshift mutations associated with the 7C HT in glpK produce small colonies that exhibit heritable multidrug increases in minimal inhibitory concentrations and decreases in drug-dependent killing; however, reversion back to a fully drug-susceptible large-colony phenotype occurs rapidly through the introduction of additional insertions or deletions in the same glpK HT region. These reversible frameshift mutations in the 7C HT of M. tuberculosis glpK occur in clinical isolates, accumulate in M. tuberculosis-infected mice with further accumulation during drug treatment, and exhibit a reversible transcriptional profile including induction of dosR and sigH and repression of kstR regulons, similar to that observed in other in vitro models of M. tuberculosis tolerance. These results suggest that GlpK phase variation may contribute to drug tolerance, treatment failure, and relapse in human TB. Drugs effective against phase-variant M. tuberculosis may hasten TB treatment and improve cure rates.
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Affiliation(s)
- Hassan Safi
- Center for Emerging Pathogens, New Jersey Medical School, Rutgers University, Newark, NJ 07103;
- Department of Medicine, New Jersey Medical School, Rutgers University, Newark, NJ 07103
| | - Pooja Gopal
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 117597 Singapore, Republic of Singapore
| | - Subramanya Lingaraju
- Center for Emerging Pathogens, New Jersey Medical School, Rutgers University, Newark, NJ 07103
- Department of Medicine, New Jersey Medical School, Rutgers University, Newark, NJ 07103
| | - Shuyi Ma
- Center for Infectious Disease, Seattle Children's Hospital, Seattle, WA 98105
| | - Carly Levine
- Center for Emerging Pathogens, New Jersey Medical School, Rutgers University, Newark, NJ 07103
- Department of Medicine, New Jersey Medical School, Rutgers University, Newark, NJ 07103
| | - Veronique Dartois
- The Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110
| | - Michelle Yee
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117597 Singapore, Republic of Singapore
| | - Liping Li
- The Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110
| | - Landry Blanc
- The Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103
| | - Hsin-Pin Ho Liang
- The Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110
| | - Seema Husain
- Genomics Center, New Jersey Medical School, Rutgers University, Newark, NJ 07103
| | - Mainul Hoque
- Genomics Center, New Jersey Medical School, Rutgers University, Newark, NJ 07103
| | | | - Tige Rustad
- Center for Infectious Disease, Seattle Children's Hospital, Seattle, WA 98105
| | - David R Sherman
- Center for Infectious Disease, Seattle Children's Hospital, Seattle, WA 98105
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110
| | - David Alland
- Center for Emerging Pathogens, New Jersey Medical School, Rutgers University, Newark, NJ 07103;
- Department of Medicine, New Jersey Medical School, Rutgers University, Newark, NJ 07103
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