| Accession | ARO:3004599 |
| CARD Short Name | clcD |
| Definition | clcD 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 Family | Cfr 23S ribosomal RNA methyltransferase |
| Drug Class | streptogramin antibiotic, phenicol antibiotic, oxazolidinone antibiotic, streptogramin B antibiotic, streptogramin A antibiotic, lincosamide antibiotic, pleuromutilin antibiotic |
| Resistance Mechanism | antibiotic target alteration |
| Resistomes with Sequence Variants | Enterococcus faecalisg, Enterococcus faeciumg+p+wgs, Staphylococcus aureusg+wgs |
| Classification | 21 ontology terms | Show + process or component of antibiotic biology or chemistry + mechanism of antibiotic resistance + determinant of antibiotic resistance + antibiotic target alteration [Resistance Mechanism] + antibiotic target modifying enzyme + ribosomal alteration conferring antibiotic resistance + rRNA methyltransferase conferring antibiotic resistance + antibiotic molecule + 23S ribosomal RNA methyltransferase + streptogramin antibiotic [Drug Class] + S-adenosylmethionine (SAM) superfamily + phenicol antibiotic [Drug Class] + oxazolidinone antibiotic [Drug Class] + streptogramin B antibiotic [Drug Class] + streptogramin A antibiotic [Drug Class] + lincosamide antibiotic [Drug Class] + antibiotic mixture + dalfopristin [Antibiotic] + pleuromutilin antibiotic [Drug Class] + quinupristin [Antibiotic] + Cfr 23S ribosomal RNA methyltransferase [AMR Gene Family] |
| 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) |
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).
| Species | NCBI Chromosome | NCBI Plasmid | NCBI WGS | NCBI GI |
|---|---|---|---|---|
| Enterococcus faecalis | 0.91% | 0% | 0% | 0% |
| Enterococcus faecium | 0.64% | 0.06% | 0.1% | 0% |
| Staphylococcus aureus | 0.09% | 0% | 0.01% | 0% |
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