Staphylococcus aureus 23S rRNA with mutation conferring resistance to linezolid

Accession ARO:3004058
CARD Short NameSaur_23S_LZD
DefinitionPoint mutations in the 23S rRNA subunit of the large ribosomal bacterial subunit in Staphylococcus aureus, which confer resistance to linezolid by disrupting antibiotic target binding.
AMR Gene Family23S rRNA with mutation conferring resistance to linezolid antibiotics
Drug Classoxazolidinone antibiotic, pleuromutilin antibiotic, phenicol antibiotic, glycopeptide antibiotic, streptogramin antibiotic, lincosamide antibiotic, macrolide antibiotic
Resistance Mechanismantibiotic target alteration
Resistomes with Sequence VariantsStaphylococcus aureusg+wgs, Staphylococcus capitisg+wgs, Staphylococcus epidermidisg+wgs+gi, Staphylococcus haemolyticusg
Classification17 ontology terms | Show
Parent Term(s)2 ontology terms | Show
+ confers_resistance_to_antibiotic linezolid [Antibiotic]
+ 23S rRNA with mutation conferring resistance to linezolid antibiotics [AMR Gene Family]
Publications

Musumeci R, et al. 2016. New Microbiol. 39(4):269-273 Resistance to linezolid in Staphylococcus spp. clinical isolates associated with ribosomal binding site modifications: novel mutation in domain V of 23S rRNA. (PMID 27727405)

Resistomes

Prevalence of Staphylococcus aureus 23S rRNA with mutation conferring resistance to linezolid among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI or IslandViewer for 413 important pathogens (see methodological details and complete list of analyzed pathogens). Values reflect percentage of genomes, plasmids, genome islands, or whole-genome shotgun assemblies that have at least one hit to the AMR detection model. Default view includes percentages calculated based on Perfect plus Strict RGI hits. Select the checkbox to view percentages based on only Perfect matches to AMR reference sequences curated in CARD (note: this excludes resistance via mutation as references in protein variant models are often wild-type, sensitive sequences).

Prevalence: rRNA gene variant model (view sequences)

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GI
Staphylococcus aureus0.26%0%0.02%0%
Staphylococcus capitis20%0%1.27%0%
Staphylococcus epidermidis21.29%0%0.25%2.86%
Staphylococcus haemolyticus6.9%0%0%0%
Show Perfect Only


Detection Models

Model Type: rRNA gene variant model

Model Definition: Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.

Bit-score Cut-off (blastN): 5000

Legend:

  • discovered in clinical, agricultural, or environmental isolates

  • discovered via laboratory selection experiments

  • ReSeqTB https://platform.reseqtb.org

Published Variants:

PMID: 27727405C2579T G2604T


>gb|NZ_CP009828.1|+|497114-500039|Staphylococcus aureus 23S rRNA with mutation conferring resistance to linezolid [Staphylococcus aureus]
AGATTAAGTTATTAAGGGCGCACGGTGGATGCCTTGGCACTAGAAGCCGATGAAGGACGTTACTAACGACGATATGCTTTGGGGAGCTGT
AAGTAAGCTTTGATCCAGAGATTTCCGAATGGGGAAACCCAGCATGAGTTATGTCATGTTATCGATATGTGAATACATAGCATATCAGAA
GGCACACCCGGAGAACTGAAACATCTTAGTACCCGGAGGAAGAGAAAGAAAATTCGATTCCCTTAGTAGCGGCGAGCGAAACGGGAAGAG
CCCAAACCAACAAGCTTGCTTGTTGGGGTTGTAGGACACTCTATACGGAGTTACAAAGGACGACATTAGACGAATCATCTGGAAAGATGA
ATCAAAGAAGGTAATAATCCTGTAGTCGAAAATGTTGTCTCTCTTGAGTGGATCCTGAGTACGACGGAGCACGTGAAATTCCGTCGGAAT
CTGGGAGGACCATCTCCTAAGGCTAAATACTCTCTAGTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGTGAAAAGCACCCCGGAAGG
GGAGTGAAATAGAACCTGAAACCGTGTGCTTACAAGTAGTCAGAGCCCGTTAATGGGTGATGGCGTGCCTTTTGTAGAATGAACCGGCGA
GTTACGATTTGATGCAAGGTTAAGCAGTAAATGTGGAGCCGTAGCGAAAGCGAGTCTGAATAGGGCGTTTAGTATTTGGTCGTAGACCCG
AAACCAGGTGATCTACCCTTGGTCAGGTTGAAGTTCAGGTAACACTGAATGGAGGACCGAACCGACTTACGTTGAAAAGTGAGCGGATGA
ACTGAGGGTAGCGGAGAAATTCCAATCGAACCTGGAGATAGCTGGTTCTCTCCGAAATAGCTTTAGGGCTAGCCTCAAGTGATGATTATT
GGAGGTAGAGCACTGTTTGGACGAGGGGCCCCTCTCGGGTTACCGAATTCAGACAAACTCCGAATGCCAATTAATTTAACTTGGGAGTCA
GAACATGGGTGATAAGGTCCGTGTTCGAAAGGGAAACAGCCCAGACCACCAGCTAAGGTCCCAAAATATATGTTAAGTGGAAAAGGATGT
GGCGTTGCCCAGACAACTAGGATGTTGGCTTAGAAGCAGCCATCATTTAAAGAGTGCGTAATAGCTCACTAGTCGAGTGACACTGCGCCG
AAAATGTACCGGGGCTAAACATATTACCGAAGCTGTGGATTGTCCTTTGGACAATGGTAGGAGAGCGTTCTAAGGGCGTTGAAGCATGAT
CGTAAGGACATGTGGAGCGCTTAGAAGTGAGAATGCCGGTGTGAGTAGCGAAAGACGGGTGAGAATCCCGTCCACCGATTGACTAAGGTT
TCCAGAGGAAGGCTCGTCCGCTCTGGGTTAGTCGGGTCCTAAGCTGAGGCCGACAGGCGTAGGCGATGGATAACAGGTTGATATTCCTGT
ACCACCTATAATCGTTTTAATCGATGGGGGGACGCAGTAGGATAGGCGAAGCGTGCGATTGGATTGCACGTCTAAGCAGTAAGGCTGAGT
ATTAGGCAAATCCGGTACTCGTTAAGGCTGAGCTGTGATGGGGAGAAGACATTGTGTCTTCGAGTCGTTGATTTCACACTGCCGAGAAAA
GCCTCTAGATAGAAAATAGGTGCCCGTACCGCAAACCGACACAGGTAGTCAAGATGAGAATTCTAAGGTGAGCGAGCGAACTCTCGTTAA
GGAACTCGGCAAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTTTAGGGTTAACGCCCAGAAGAGCCGCAGTGAATAGGCCCAAGCG
ACTGTTTATCAAAAACACAGGTCTCTGCTAAACCGTAAGGTGATGTATAGGGGCTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGAGTG
GTTAGCTTCTGCGAAGCTACGAATCGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTA
AGTTCCGACCCGCACGAAAGGCGTAACGATTTGGGCACTGTCTCAACGAGAGACTCGGTGAAATCATAGTACCTGTGAAGATGCAGGTTA
CCCGCGACAGGACGGAAAGACCCCGTGGAGCTTTACTGTAGCCTGATATTGAAATTCGGCACAGCTTGTACAGGATAGGTAGGAGCCTTT
GAAACGTGAGCGCTAGCTTACGTGGAGGCGCTGGTGGGATACTACCCTAGCTGTGTTGGCTTTCTAACCCGCACCACTTATCGTGGTGGG
AGACAGTGTCAGGCGGGCAGTTTGACTGGGGCGGTCGCCTCCTAAAAGGTAACGGAGGCGCTCAAAGGTTCCCTCAGAATGGTTGGAAAT
CATTCATAGAGTGTAAAGGCATAAGGGAGCTTGACTGCGAGACCTACAAGTCGAGCAGGGTCGAAAGACGGACTTAGTGATCCGGTGGTT
CCGCATGGAAGGGCCATCGCTCAACGGATAAAAGCTACCCCGGGGATAACAGGCTTATCTCCCCCAAGAGTTCACATCGACGGGGAGGTT
TGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGTAGTCGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGTACGCGAGCTGG
GTTCAGAACGTCGTGAGACAGTTCGGTCCCTATCCGTCGTGGGCGTAGGAAATTTGAGAGGAGCTGTCCTTAGTACGAGAGGACCGGGAT
GGACATACCTCTGGTGTACCAGTTGTCGTGCCAACGGCATAGCTGGGTAGCTATGTGTGGACGGGATAAGTGCTGAAAGCATCTAAGCAT
GAAGCCCCCCTCAAGATGAGATTTCCCAACTTCGGTTATAAGATCCCTCAAAGATGATGAGGTTAATAGGTTCGAGGTGGAAGCATGGTG
ACATGTGGAGCTGACGAATACTAATCGATCGAAGACTTAATCAAAA