Mutation in luxR Family Transcriptional Regulator Rv0890c Is Not a Marker of Linezolid Resistance

LETTER

I read with great interest the recent paper by Srivastava et al. describing the experiments on linezolid dose effectivity in the hollow-fiber model of tuberculosis (1). Some of the results described in that paper were the selection and whole-genome sequencing of linezolid-resistant mutants of the laboratory strain Mycobacterium tuberculosis H37Rv, and none of these descendants had previously described mutations in the rrl or rplC gene associated with linezolid resistance. However, I could not agree with the conclusions regarding the role of mutations in efflux genes and the transcription regulator rv0890 gene in linezolid resistance.

First, there are some errors in the mutation annotations found. Eleven single-nucleotide polymorphisms (SNPs) are not true mutations because the mutated nucleotide coincides with the wild-type nucleotide in the reference H37Rv sequence. For example, Srivastava et al. state in their Table S2 that the rv2896c mutation 457T→G leads to a Ser153Ala substitution, but the wild-type sequence in this position is G, and amino acid 153 of Rv2896c is Ala in M. tuberculosis H37Rv (NC_000962.3). This mistake occurred most likely due to errors in the reference genome used; Srivastava et al. used the previous annotation NC_000962.2 (2).

Moreover, I suppose that selection of the notable mutations from some list should be based on frequency analysis using previously sequenced clinical isolates. There are several databases available, and the most comprehensive databases are PolyTB (3) and ReSeqTB (4). I have performed such an analysis and found that only 23 of 63 SNPs described in the paper have a low frequency (0 to 2%) and, thus, are potentially associated with linezolid resistance (see Data Set S1 in the supplemental material).

Reviewing the authors' statement, I could agree only with the possible role of substitutions in Rv0545c, not in Rv0930, Rv3331, and the transcriptional regulator Rv0890c, because such mutations are present in >99% of 6,419 isolates from the ReSeqTB database.