Staphylococcus aureus rpoB mutants conferring resistance to daptomycin

Accession ARO:3003287
CARD Short NameSaur_rpoB_DAP
DefinitionPoint mutations that occurs in Staphylococcus aureus rpoB resulting in resistance to daptomycin.
AMR Gene Familydaptomycin resistant beta-subunit of RNA polymerase (rpoB)
Drug Classpeptide antibiotic, rifamycin antibiotic
Resistance Mechanismantibiotic target alteration
Classification12 ontology terms | Show
Parent Term(s)2 ontology terms | Show
+ confers_resistance_to_antibiotic daptomycin [Antibiotic]
+ daptomycin resistant beta-subunit of RNA polymerase (rpoB) [AMR Gene Family]
Publications

Friedman L, et al. 2006. Antimicrob Agents Chemother 50(6): 2137-2145. Genetic changes that correlate with reduced susceptibility to daptomycin in Staphylococcus aureus. (PMID 16723576)

Cui L, et al. 2010. Antimicrob Agents Chemother 54(12): 5222-5233. An RpoB mutation confers dual heteroresistance to daptomycin and vancomycin in Staphylococcus aureus. (PMID 20837752)

Resistomes

Prevalence of Staphylococcus aureus rpoB mutants conferring resistance to daptomycin 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: protein variant model

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GI
No prevalence data


Detection Models

Model Type: protein variant model

Model Definition: Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein 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 BLASTP bit-score above the curated BLASTP 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 BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.

Bit-score Cut-off (blastP): 2300

Legend:

  • discovered in clinical, agricultural, or environmental isolates

  • discovered via laboratory selection experiments

  • ReSeqTB https://platform.reseqtb.org

Published Variants:

PMID: 16723576I953S A1085V
PMID: 20837752A621E

>gb|CAG39568.1|+|Staphylococcus aureus rpoB mutants conferring resistance to daptomycin [Staphylococcus aureus subsp. aureus MRSA252]
MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYEWFLREGLIEMFRDISPIEDFTG
NLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLIIKETGEVKEQEVFMGDFPLMT
DTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGRENYDATIIPNRGAWLEYETDAKDVV
YVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYLRNTLEKDGTENTEQALLEIYERL
RPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKTNKKLHLKHRLFNQKLAEPIVNTETG
EIVVEEGTVLDRRKIDEIMDVLESNANSEVFELHGSVIDEPVEIQSIKVYVPNDDEGRTT
TVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYTDDIDHLGNRRLRSVGELLQNQFR
IGLSRMERVVRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELT
HKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFG
FIETPYRKVDLDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFMDDEVVCRFRGNNT
VMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTG
MEHVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKFKRSNSG
TCYNQRPIVAVGDVVEFNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAVIMSERL
VKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYIGAEVKDGDI
LVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGDDT
LSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPL
GVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWSTIEEAGMARDGKTVLYDG
RTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEV
WALEAYGAAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQSLGL
DVKVMDEQDNEIEMTDVDDDDVVERKVDLQQNDAPETQKEVTD



>gb|BX571856.1|+|590831-594382|Staphylococcus aureus rpoB mutants conferring resistance to daptomycin [Staphylococcus aureus subsp. aureus MRSA252]
TTGGCAGGTCAAGTTGTCCAATATGGAAGACATCGTAAACGTAGAAACTACGCGAGAATTTCAGAAGTATTAGAATTACCAAACTTAATA
GAAATTCAAACTAAATCTTACGAGTGGTTCCTAAGAGAAGGTTTAATCGAAATGTTTAGAGACATTTCTCCAATTGAAGATTTTACTGGT
AATTTGTCATTAGAGTTTGTGGATTACCGTTTAGGAGAACCAAAATATGATTTAGAAGAATCTAAAAACCGTGACGCTACTTATGCTGCA
CCTCTTCGTGTAAAAGTGCGTCTAATCATTAAAGAAACAGGAGAAGTTAAAGAACAAGAAGTCTTTATGGGTGATTTCCCATTAATGACT
GATACAGGTACGTTCGTTATCAATGGTGCAGAACGTGTAATCGTATCTCAATTAGTTCGTTCACCATCCGTTTATTTCAATGAAAAAATC
GACAAAAATGGTCGTGAAAACTATGATGCAACAATTATTCCAAACCGAGGTGCATGGTTAGAATATGAAACAGATGCTAAAGATGTTGTA
TACGTGCGTATTGATAGAACACGTAAACTACCATTAACAGTATTGTTACGTGCATTAGGTTTCTCAAGTGACCAAGAAATTGTTGACCTT
TTAGGTGACAATGAATATTTACGTAATACTTTAGAGAAAGACGGCACTGAAAACACTGAACAAGCGTTATTAGAAATCTATGAACGTTTA
CGTCCAGGTGAACCACCAACTGTTGAAAATGCTAAAAGTCTATTGTATTCACGTTTCTTTGATCCAAAACGCTATGACTTAGCAAGCGTG
GGTCGTTATAAAACAAACAAAAAATTACATTTAAAACATCGTTTATTCAATCAAAAATTAGCTGAGCCAATTGTGAATACTGAAACTGGT
GAAATTGTAGTTGAAGAAGGTACAGTGCTTGATCGTCGTAAAATCGACGAAATCATGGATGTACTTGAATCAAACGCAAACAGCGAAGTG
TTTGAATTGCATGGTAGCGTTATAGACGAGCCAGTAGAAATTCAATCAATTAAAGTATATGTTCCTAACGATGATGAAGGTCGTACGACA
ACTGTAATTGGTAATGCTTTCCCTGACTCAGAAGTTAAATGTATTACACCGGCAGATATCATCGCTTCAATGAGTTACTTCTTTAACTTA
TTAAGTGGTATTGGATATACAGATGATATTGACCATTTAGGTAACCGTCGTTTACGTTCTGTAGGTGAATTACTACAAAACCAATTCCGT
ATCGGTTTATCAAGAATGGAAAGAGTTGTACGTGAAAGAATGTCAATTCAAGATACTGAGTCTATCACACCTCAACAATTAATTAATATT
CGACCTGTTATTGCATCTATTAAAGAATTCTTTGGTAGCTCTCAATTATCACAATTCATGGACCAAGCAAATCCATTAGCTGAGTTAACG
CATAAACGTCGTCTATCAGCATTAGGACCTGGTGGTTTAACACGTGAACGTGCTCAAATGGAAGTGCGTGACGTTCACTACTCTCACTAT
GGCCGTATGTGTCCAATTGAAACGCCTGAGGGACCAAACATTGGATTGATTAACTCATTATCAAGTTATGCACGTGTAAATGAATTCGGC
TTTATTGAAACACCATATCGTAAAGTTGATTTAGATACACATGCTATCACTGATCAAATTGACTATTTAACAGCTGACGAAGAAGATAGC
TATGTTGTAGCACAAGCAAACTCTAAATTAGATGAAAATGGTCGTTTCATGGATGATGAAGTTGTATGTCGTTTCCGTGGTAACAATACA
GTTATGGCTAAAGAAAAAATGGATTATATGGATGTATCGCCGAAGCAAGTTGTTTCAGCAGCGACAGCATGTATTCCATTCTTAGAAAAT
GATGACTCAAACCGTGCATTGATGGGTGCGAACATGCAACGTCAAGCAGTGCCTTTGATGAATCCAGAAGCACCATTTGTTGGTACAGGT
ATGGAACACGTTGCAGCACGTGATTCTGGTGCAGCTATTACAGCTAAGCACAGAGGTCGTGTTGAACATGTTGAATCTAATGAAATTCTT
GTACGTCGTCTAGTTGAAGAGAACGGCGTTGAGCATGAAGGTGAATTAGATCGCTATCCATTAGCTAAATTTAAACGTTCAAACTCAGGT
ACATGTTACAACCAACGTCCAATCGTTGCAGTTGGAGATGTTGTTGAGTTTAACGAGATTTTAGCAGATGGACCATCTATGGAATTAGGA
GAAATGGCATTAGGTAGAAACGTAGTAGTTGGTTTCATGACTTGGGACGGTTACAACTATGAGGATGCCGTTATCATGAGTGAAAGACTT
GTGAAAGATGACGTGTATACTTCTATTCATATTGAAGAGTATGAATCAGAAGCACGTGATACTAAGTTAGGACCTGAAGAAATCACAAGA
GATATTCCTAATGTTTCTGAAAGTGCACTTAAGAACTTAGACGATCGTGGTATCGTTTATATTGGTGCAGAAGTAAAAGATGGAGATATT
TTAGTTGGTAAAGTAACGCCTAAAGGTGTAACTGAGTTAACTGCCGAAGAAAGATTGTTACATGCAATCTTTGGTGAAAAAGCACGTGAA
GTTAGAGATACTTCATTACGTGTACCTCACGGCGCTGGCGGTATCGTTCTTGATGTAAAAGTATTCAATCGTGAAGAAGGCGACGACACA
TTATCACCTGGTGTAAACCAATTAGTACGTGTATATATCGTTCAAAAACGTAAAATTCATGTTGGTGATAAGATGTGTGGTCGACATGGT
AACAAAGGTGTCATTTCTAAGATTGTTCCTGAAGAAGATATGCCTTACTTACCAGATGGACGTCCGATTGATATCATGTTAAATCCTCTT
GGTGTACCATCTCGTATGAACATCGGACAAGTATTAGAGCTACACTTAGGTATGGCTGCTAAAAATCTTGGTATTCACGTTGCATCACCA
GTATTTGACGGTGCAAACGATGACGATGTATGGTCAACAATTGAAGAAGCTGGTATGGCTCGTGATGGTAAAACTGTACTTTATGATGGA
CGTACAGGTGAACCATTCGATAACCGTATTTCAGTAGGTGTAATGTACATGTTGAAACTTGCGCACATGGTTGATGATAAATTACATGCG
CGTTCAACAGGACCATATTCACTTGTTACACAACAACCACTTGGCGGTAAAGCGCAATTCGGTGGACAACGTTTCGGTGAGATGGAGGTA
TGGGCACTTGAAGCATATGGTGCTGCATACACATTACAAGAAATCTTAACTTACAAATCCGATGATACAGTAGGACGTGTGAAAACATAC
GAGGCTATTGTTAAAGGTGAAAACATCTCTAGACCAAGTGTTCCAGAATCATTCCGAGTATTGATGAAAGAATTACAAAGTTTAGGTTTA
GATGTAAAAGTTATGGATGAGCAAGATAATGAAATCGAAATGACAGACGTTGATGACGATGATGTTGTAGAACGCAAAGTAGATTTACAA
CAAAATGATGCTCCTGAAACACAAAAAGAAGTTACTGATTAA