Table 2.
Nonsynonymous nucleotide mutations identified between strain 8019 (daptomycin susceptible) and strains 5938 and 5994 (daptomycin NS) by WGS
| Nucleotide mutation (predicted amino acid mutation) |
Mutation class |
E. faecium DO |
Predicted gene product | ||
|---|---|---|---|---|---|
| 5938 | 5994 | Locus | Locus tag | ||
| Deletion of 227 bp (fs)a | WTb | Indelc | HMPREF0351_11791 HMPREF0351_11792 | Hypothetical protein PTS system, mannose-specific IIA component | |
| Insertion of T at 2508 (fs) | Insertion of T at 2508 (fs) | Indel | No match | NtrC family transcriptional regulator | |
| WT | Deletion of T at 1839 (fs) | Indel | HMPREF0351_10870 | Hypothetical protein | |
| WT | Insertion of A at 229 (fs) | Indel | pspC | HMPREF0351_12014 | Conserved hypothetical protein |
| WT | Insertion of T at 704 (fs) | Indel | No match | ABC transporter | |
| G187A (R63-) | WT | Nonsense | lepB | HMPREF0351_11130 | Signal peptidase I |
| C236T (G79E) | C236T (G79E) | SNV | HMPREF0351_11658 | Hypothetical protein | |
| G1253A (C418Y) | G1253A (C418Y) | SNV | aad | HMPREF0351_10204 | Alcohol dehydrogenase |
| G303T (L101F) | WT | SNV | HMPREF0351_10668 | NrdR-regulated deoxyribonucleotide transporter | |
| G712A (L238F) | G712A (L238F) | SNV | HMPREF0351_12883 | PTS system, mannose-specific IID component | |
| G979A (A327T) | G979A (A327T) | SNV | ezrA | HMPREF0351_12190 | EzrA |
| T38C (N12S) | T644C (H215R) | SNV | cls | HMPREF0351_11068 | Cardiolipin synthetase |
| T874A (S292T) | T874A (S292T) | SNV | HMPREF0351_12498 | Alpha-mannosidase | |
| WT | A749T (V250E) | SNV | HMPREF0351_11298 | Outer surface protein of unknown function | |
| WT | G35A (G12E) | SNV | HMPREF0351_10875 | Hypothetical protein | |
| WT | T98C (V33A) | SNV | sdhC | HMPREF0351_10830 | Hypothetical protein |
a
fs, frameshift.
b
WT, wild type (i.e., same as strain 8019).
c
Indel, insertion or deletion of a nucleotide(s).