Recommendations To Address the Difficulties Encountered When Determining Linezolid Resistance from Whole-Genome Sequencing Data

Abstract

Mutations associated with linezolid resistance within the V domain of 23S rRNA are annotated using an Escherichia coli numbering system. The 23S rRNA gene varies in length, nucleotide sequence, and copy number among bacterial species. Consequently, this numbering system is not intuitive and can lead to confusion when mutation sites are being located using whole-genome sequencing data. Using the mutation G2576T as an example, we demonstrate the difficulties associated with using the E. coli numbering system.

Keywords: G2576T; linezolid resistance; whole-genome sequencing.

FIG 1

(a) Alignment of the 23S rRNA genes from Escherichia coli, Enterococcus faecalis, Enterococcus faecium, Mycobacterium tuberculosis, Staphylococcus aureus, Streptococcus pneumoniae, and Staphylococcus epidermidis (GenBank accession numbers NC_010468, NC_004668, NC_017022, NC_000962, NC_017341, NC_011900, and CP022247, respectively) with 23S rRNA from the E. coli rRNA operon (rrnB) (GenBank accession number J01695). (b) Expanded purple section with the location of the G2576T (E. coli numbering) mutation highlighted and annotated with the nucleotide position for the respective bacterial species.