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Predicting nitroimidazole antibiotic resistance mutations in Mycobacterium tuberculosis with protein engineering
Author(s) -
Lee Brendon,
Almeida Deepak,
Afriat-Jurnou Livnat,
Aung Htin,
Forde Brian,
Harold Liam,
Hards Kiel,
Pidot Sacha,
Ahmed Hafna,
Mohamed Elaaf,
Taylor Mathew,
West Nicholas,
Stinear Timothy,
Greening Chris,
Beatson Scott,
Cook Gregory,
Nuermberger Eric,
Jackson Colin
Publication year - 2020
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.2020.34.s1.04923
Subject(s) - mycobacterium tuberculosis , biology , nitroreductase , tuberculosis , drug resistance , antibiotic resistance , genetics , mutation , antibiotics , microbiology and biotechnology , medicine , gene , pathology
Our inability to predict which mutations could result in antibiotic resistance has made it difficult to rapidly identify the emergence of resistance, identify pre‐existing resistant populations, and manage our use of antibiotics to effectively treat patients and prevent or slow the spread of resistance. Here we investigated the potential for resistance against the new antitubercular nitroimidazole prodrugs pretomanid and delamanid to emerge in Mycobacterium tuberculosis , the causative agent of tuberculosis (TB). Deazaflavin‐dependent nitroreductase (Ddn) is the only identified enzyme within M. tuberculosis that activates these prodrugs, via an F 420 H 2 ‐dependent reaction. We show that the native menaquinone‐reductase activity of Ddn is essential for emergence from dormancy, which suggests that for resistance to spread and pose a threat to human health, the native activity of Ddn must be at least partially retained. We tested 75 unique mutations, including all known sequence polymorphisms identified among ~15,000 sequenced M. tuberculosis genomes. Several mutations abolished pretomanid and delamanid activation in vitro , without causing complete loss of the native activity. We confirmed that a transmissible M. tuberculosis isolate from the hypervirulent Beijing family already possesses one such mutation and is resistant to pretomanid, before being exposed to the drug. Notably, delamanid was still effective against this strain, which is consistent with structural analysis that indicates delamanid and pretomanid bind to Ddn differently. We suggest that the mutations identified in this work be monitored for informed use of delamanid and pretomanid treatment and to slow the emergence of resistance. Support or Funding Information This work was supported by by NHMRC Project Grant APP1128929 (to C. J. J., C. G., and G. M. C.). In addition, this work was supported by an ARC DECRA Fellowship DE170100310, and NHMRC New Investigator Grant APP1139832 (to C. G.). SAB is supported by an NHMRC Career Development Fellowship GNT1090456 (to SAB). DVA and ELN acknowledge the support of the U.S. National Institutes of Health (R01‐AI111992).