Systematic review of mutations associated with resistance to the new and repurposed Mycobacterium tuberculosis drugs bedaquiline, clofazimine, linezolid, delamanid and pretomanid

Abstract

Background: Improved genetic understanding of Mycobacterium tuberculosis (MTB) resistance to novel and repurposed anti-tubercular agents can aid the development of rapid molecular diagnostics.

Methods: Adhering to PRISMA guidelines, in March 2018, we performed a systematic review of studies implicating mutations in resistance through sequencing and phenotyping before and/or after spontaneous resistance evolution, as well as allelic exchange experiments. We focused on the novel drugs bedaquiline, delamanid, pretomanid and the repurposed drugs clofazimine and linezolid. A database of 1373 diverse control MTB whole genomes, isolated from patients not exposed to these drugs, was used to further assess genotype-phenotype associations.

Results: Of 2112 papers, 54 met the inclusion criteria. These studies characterized 277 mutations in the genes atpE, mmpR, pepQ, Rv1979c, fgd1, fbiABC and ddn and their association with resistance to one or more of the five drugs. The most frequent mutations for bedaquiline, clofazimine, linezolid, delamanid and pretomanid resistance were atpE A63P, mmpR frameshifts at nucleotides 192-198, rplC C154R, ddn W88* and ddn S11*, respectively. Frameshifts in the mmpR homopolymer region nucleotides 192-198 were identified in 52/1373 (4%) of the control isolates without prior exposure to bedaquiline or clofazimine. Of isolates resistant to one or more of the five drugs, 59/519 (11%) lacked a mutation explaining phenotypic resistance.

Conclusions: This systematic review supports the use of molecular methods for linezolid resistance detection. Resistance mechanisms involving non-essential genes show a diversity of mutations that will challenge molecular diagnosis of bedaquiline and nitroimidazole resistance. Combined phenotypic and genotypic surveillance is needed for these drugs in the short term.

Figure 1.

Study selection process performed for bedaquiline and reasons for exclusion of studies. The same selection process was performed for all five drugs (see Figures S1 to S4).

Figure 2.

Mutations in mmpR with relative MIC fold changes for bedaquiline (BDQ) or clofazimine (CFZ). Round and square brackets are used as exclusive and inclusive of the listed concentration, respectively. This figure appears in colour in the online version of JAC and in black and white in the print version of JAC.

Figure 3.

Secondary structure of the peptidyltransferase loop of domain V of 23S rRNA. Likely MTB linezolid resistance mutations are circled in red (nucleotide positions for these mutations are also highlighted in red).^,,,,,,, The most common mutations occurred at four sites based on our systematic review (rrl G2299T, G2814T, G2270T/C and G2746A). Asterisks indicate mutations found in clinical isolates. Nucleotides forming the linezolid-binding pocket are indicated by blue arrowheads. Nucleotide changes correlating with linezolid MIC increases for various organisms are indicated in grey using the E. coli numbering system. Two-letter abbreviations are used for corresponding organisms (Ec, E. coli; Em, Enterococcus faecium; Es, Enterococcus faecalis; Hh, Halobacterium halobium; Sa, Staphylococcus aureus; Se, Staphylococcus epidermidis; Sh, Staphylococcus haemolyticus; Sp, Streptococcus pneumoniae; Ms, Mycobacterium smegmatis; and Mt, MTB). This figure appears in colour in the online version of JAC and in black and white in the print version of JAC.