Enterococcus faecium cls conferring resistance to daptomycin

Accession ARO:3003092
Synonym(s)cls1 cls2
CARD Short NameEfac_cls_DAP
Definitioncls or cardiolipin synthetase is an inner membrane protein that is involved in membrane synthesis. Specific mutations in Enterococcus can confer resistance to daptomycin.
AMR Gene Familydaptomycin resistant cls
Drug Classpeptide antibiotic
Resistance Mechanismantibiotic target alteration
Resistomes with Sequence VariantsEnterococcus faeciumg+wgs
Classification10 ontology terms | Show
Parent Term(s)3 ontology terms | Show
+ confers_resistance_to_antibiotic daptomycin [Antibiotic]
+ daptomycin resistant cls [AMR Gene Family]
+ derives_from Daptomycin sensitive cardiolipin synthetase
Publications

Arias CA, et al. 2011. N Engl J Med 365(10): 892-900. Genetic basis for in vivo daptomycin resistance in enterococci. (PMID 21899450)

Kelesidis T, et al. 2013. J Antimicrob Chemother 68(8): 1926-1928. Evolution of high-level daptomycin resistance in Enterococcus faecium during daptomycin therapy is associated with limited mutations in the bacterial genome. (PMID 23580562)

Davlieva M, et al. 2012. Antimicrob Agents Chemother 57(1): 289-296. Biochemical characterization of cardiolipin synthase mutations associated with daptomycin resistance in enterococci. (PMID 23114777)

Humphries RM, et al. 2012. Antimicrob Agents Chemother 56(11): 6051-6053. Genotypic and phenotypic evaluation of the evolution of high-level daptomycin nonsusceptibility in vancomycin-resistant Enterococcus faecium. (PMID 22948885)

Lellek H, et al. 2015. Int. J. Med. Microbiol. 305(8):902-9 Emergence of daptomycin non-susceptibility in colonizing vancomycin-resistant Enterococcus faecium isolates during daptomycin therapy. (PMID 26454536)

Resistomes

Prevalence of Enterococcus faecium cls 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 (view sequences)

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GI
Enterococcus faecium2.55%0%0.54%0%
Show Perfect Only


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): 900

Legend:

  • discovered in clinical, agricultural, or environmental isolates

  • discovered via laboratory selection experiments

  • ReSeqTB https://platform.reseqtb.org

Published Variants:

PMID: 21899450N13I H215R +MPL110-112
PMID: 23580562N13T K59T G177T
PMID: 23114777H215R
PMID: 22948885H215R
PMID: 26454536A20D D27N R267H

>gb|ALL09868.1|-|Enterococcus faecium cls conferring resistance to daptomycin [Enterococcus faecium]
MVSSIITALYLLNALIALVAILIKPRDVAAIWAWLLVLFALPGVGFVLYLFFGRGLTDKK
KFYLRQSDLKELENFQSFRGDTIEHYDPDMGDKDKQQFVDFFSSLNRMPLTRMNSVTLLT
DGQEKLDSLLQDLKKAKHSIHIEYYAFVTDNIGQQVLHVLEEKAAEGVEVRILYDAFGSH
GTKAKDFNRLIKNGGHVHTFVTSQRALLRFRLNYHDHRKIVVIDGKISYTGGFNIANQYV
NTTKKFGYWRDTHIRIFGAASSLLQLRFLTDWNVSVPEEKKVGYHLNYFFKKADRDESKL
ADTSIQLVSSGPNNEREQIKLSFIKLITSAKKRVWIQTPYLVPDESVIAALKIATASGVD
VKIMIPNKPDHPFIYRATQYYARQLIKENVQILVYENGFLHAKTLIMDDEICMVGSANQD
IRSYRLNFETSAVIYDPEFLEELATQFKEDETHCSSMTTETVKEMSNWLLFKQQISRLFS
PIL



>gb|CP013009.1|-|1008841-1010292|Enterococcus faecium cls conferring resistance to daptomycin [Enterococcus faecium]
GTGGTATCTAGTATTATAACCGCCCTTTATCTATTAAATGCACTTATTGCTTTGGTGGCTATTTTGATCAAACCCCGAGATGTAGCAGCC
ATTTGGGCATGGCTCTTAGTATTATTTGCCCTTCCTGGGGTGGGCTTTGTATTATATTTATTTTTCGGACGTGGATTAACGGATAAGAAA
AAATTCTATCTCCGACAAAGTGACTTGAAAGAATTAGAAAACTTTCAGTCTTTTAGAGGAGATACCATTGAACATTACGATCCTGACATG
GGCGATAAAGACAAACAGCAATTTGTTGACTTCTTCTCTTCATTAAATCGTATGCCGCTGACAAGAATGAATTCTGTCACTCTTCTCACA
GACGGACAAGAGAAATTGGATTCACTGCTTCAAGATCTAAAAAAAGCCAAACATTCGATCCATATCGAATATTACGCATTTGTGACAGAT
AATATCGGCCAGCAAGTCTTACATGTTTTAGAAGAAAAAGCCGCAGAAGGCGTGGAAGTTCGAATATTATATGATGCATTTGGCTCTCAT
GGCACAAAAGCAAAAGATTTCAATCGTCTAATCAAAAATGGTGGACATGTCCATACATTTGTTACCTCACAAAGGGCATTACTTCGTTTC
CGATTGAATTACCATGATCACCGAAAAATCGTTGTGATCGATGGAAAGATTAGTTATACCGGTGGTTTCAATATTGCCAATCAATATGTA
AATACAACAAAAAAATTCGGCTATTGGCGCGATACGCATATACGGATTTTCGGTGCCGCTTCTTCTTTGCTCCAGCTTCGCTTCTTAACA
GACTGGAACGTCTCGGTACCTGAAGAAAAAAAGGTCGGCTATCATTTGAATTATTTCTTTAAAAAAGCAGATCGAGATGAATCTAAGCTT
GCTGATACATCCATCCAGCTTGTTTCAAGCGGACCGAATAACGAAAGGGAACAAATCAAGCTTTCATTTATCAAATTGATTACTTCTGCT
AAAAAACGTGTTTGGATACAGACACCTTACCTTGTTCCTGATGAAAGTGTCATTGCTGCTTTAAAAATCGCAACTGCCTCTGGTGTAGAT
GTGAAAATCATGATTCCCAACAAACCGGATCATCCTTTTATTTATCGAGCAACACAATATTATGCTCGGCAGCTGATCAAGGAAAATGTA
CAAATCCTTGTCTATGAGAACGGCTTCCTCCATGCAAAAACATTGATAATGGATGATGAAATCTGCATGGTAGGTTCAGCAAATCAAGAT
ATTCGTAGCTACCGATTGAATTTTGAAACAAGTGCTGTCATTTACGATCCTGAGTTTTTAGAAGAACTTGCTACTCAGTTCAAAGAAGAT
GAGACACATTGTTCATCCATGACAACTGAAACAGTCAAGGAAATGTCTAACTGGCTATTATTCAAGCAACAAATTTCTCGATTATTTTCT
CCAATCCTATAA