clcD

Accession ARO:3004599
CARD Short NameclcD
DefinitionclcD gene can provide resistance to representatives of five of the six antibiotic groups previously shown to be affected by Cfr. clcD was originally found in Clostridioides difficile and is cfr-like.
AMR Gene FamilyCfr 23S ribosomal RNA methyltransferase
Drug Classstreptogramin antibiotic, phenicol antibiotic, oxazolidinone antibiotic, streptogramin B antibiotic, streptogramin A antibiotic, lincosamide antibiotic, pleuromutilin antibiotic
Resistance Mechanismantibiotic target alteration
Resistomes with Sequence VariantsEnterococcus faecalisg, Enterococcus faeciumg+p+wgs, Staphylococcus aureusg+wgs
Classification21 ontology terms | Show
Parent Term(s)6 ontology terms | Show
+ confers_resistance_to_antibiotic clindamycin [Antibiotic]
+ confers_resistance_to_antibiotic linezolid [Antibiotic]
+ confers_resistance_to_antibiotic florfenicol [Antibiotic]
+ confers_resistance_to_antibiotic tiamulin [Antibiotic]
+ confers_resistance_to_antibiotic quinupristin-dalfopristin [Antibiotic]
+ Cfr Group
Publications

Hansen LH, et al. 2015. Antimicrob. Agents Chemother. 59(9):5841-3 A cfr-like gene from Clostridium difficile confers multiple antibiotic resistance by the same mechanism as the cfr gene. (PMID 26149991)

Resistomes

Prevalence of clcD 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 homolog model (view sequences)

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GI
Enterococcus faecalis0.91%0%0%0%
Enterococcus faecium0.64%0.06%0.1%0%
Staphylococcus aureus0.09%0%0.01%0%
Show Perfect Only


Detection Models

Model Type: protein homolog model

Model Definition: Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.

Bit-score Cut-off (blastP): 650

Type of Antibiotic Resistance: Acquired


>gb|AIX48090.1|+|clcD [Clostridioides difficile]
MQQKNKYIRIQEFLKQNKFPNYRMKQITNAIFPGRINNFNEITVLPKSLRDMLIEEFGESILNIVPLKAQQSTQVSKVLFGISGDEKIET
VNMKYKAGWESFCISSQCGCNFGCKFCATGDIGLKRNLTSDEITDQILYFHLQGHSIDSISFMGMGEALANVQVFDALNVLTDPALFALS
PRRLSISTIGIIPNIKKLTQNYPQVNLTFSLHSPFNEQRSELMPINERYPLSDVMDTLDEHIRVTSKKVYIAYIMLHGVNDSIEHAKEVV
NLLRGRYRSGNLYHVNIIRYNPTISSRMRFEEANEKCLVNFYKELKSAGIKVTIRSQFGIDIDAACGQLYGNYQKTNSQ


>gb|KM359438.1|+|1-1050|clcD [Clostridioides difficile]
ATGCAACAAAAAAATAAGTATATAAGAATTCAAGAGTTCTTGAAGCAGAATAAATTTCCTAATTATAGAATGAAACAAATTACAAATGCT
ATATTCCCAGGGAGAATAAATAATTTCAACGAAATAACGGTTCTTCCTAAATCACTAAGAGATATGTTAATTGAGGAGTTTGGAGAATCG
ATTTTAAATATTGTTCCTTTAAAAGCACAACAATCTACACAAGTTTCAAAAGTCTTATTTGGAATTTCAGGAGACGAAAAAATAGAAACG
GTAAATATGAAATATAAAGCTGGTTGGGAGTCATTTTGTATATCATCGCAGTGCGGTTGTAATTTTGGTTGTAAATTTTGTGCAACTGGA
GATATAGGTTTAAAACGTAACTTAACTTCAGATGAAATTACTGACCAGATTTTGTACTTTCACTTACAAGGGCATTCAATTGACAGTATT
TCTTTTATGGGAATGGGAGAAGCATTAGCGAATGTACAAGTTTTTGATGCTTTAAATGTACTTACAGATCCTGCGTTGTTTGCTTTAAGT
CCGCGTAGGTTATCTATATCCACTATAGGAATTATTCCAAACATTAAAAAATTGACTCAAAACTATCCGCAGGTCAACCTGACATTTTCA
TTACATTCTCCTTTTAATGAACAGCGAAGTGAGTTAATGCCAATTAATGAACGCTACCCATTATCAGATGTGATGGATACATTAGATGAG
CATATACGAGTAACCTCAAAAAAAGTTTATATTGCTTATATTATGTTGCACGGAGTTAATGATTCTATTGAACATGCGAAAGAAGTCGTA
AACCTTTTAAGAGGTAGATATAGGAGTGGGAACTTGTATCATGTGAACATCATTAGATATAACCCGACTATTAGTTCACGGATGCGGTTT
GAAGAAGCAAATGAGAAATGTCTTGTCAACTTTTATAAAGAATTAAAGTCAGCAGGAATTAAAGTTACCATTAGAAGTCAATTTGGCATT
GATATAGACGCTGCTTGCGGTCAATTGTATGGAAACTATCAAAAAACCAATAGCCAGTAA