| Accession | ARO:3004654 |
| CARD Short Name | Cdif_23S_MULT |
| Definition | SNP causing high-level ERY resistance and low-level CLI resistance. |
| AMR Gene Family | 23S rRNA with mutation conferring resistance to macrolide antibiotics |
| Drug Class | lincosamide antibiotic, macrolide antibiotic |
| Resistance Mechanism | antibiotic target alteration |
| Resistomes with Sequence Variants | Chlamydia psittaciwgs, Clostridioides difficilegi, Clostridium perfringenswgs, Escherichia coliwgs, Streptococcus pneumoniaewgs |
| Classification | 11 ontology terms | Show + process or component of antibiotic biology or chemistry + mechanism of antibiotic resistance + antibiotic target alteration [Resistance Mechanism] + mutation conferring antibiotic resistance + determinant of antibiotic resistance + antibiotic resistant gene variant or mutant + rRNA with mutation conferring antibiotic resistance + antibiotic molecule + 23S rRNA with mutation conferring antibiotic resistance + lincosamide antibiotic [Drug Class] + macrolide antibiotic [Drug Class] |
| Parent Term(s) | 3 ontology terms | Show + confers_resistance_to_antibiotic erythromycin [Antibiotic] + confers_resistance_to_antibiotic clindamycin [Antibiotic] + 23S rRNA with mutation conferring resistance to macrolide antibiotics [AMR Gene Family] |
| Publications | Schmidt C, et al. 2007. Diagn. Microbiol. Infect. Dis. 59(1):1-5 Antimicrobial phenotypes and molecular basis in clinical strains of Clostridium difficile. (PMID 17509804) |
Prevalence of Clostridioides difficile 23S rRNA with mutation conferring resistance to erythromycin and clindamycin among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI or IslandViewer for 414 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 | GRDI-AMR2 |
|---|---|---|---|---|---|
| Chlamydia psittaci | 0% | 0% | 4.17% | 0% | 0% |
| Clostridioides difficile | 0% | 0% | 0% | 8.33% | 0% |
| Clostridium perfringens | 0% | 0% | 0.24% | 0% | 0% |
| Escherichia coli | 0% | 0% | 0.02% | 0% | 0% |
| Streptococcus pneumoniae | 0% | 0% | 0.01% | 0% | 0% |
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
PubMed: mutation data hand curated from the scientific literature, evaluated as conferring resistance (R). CRyPTIC: mutation data acquired from the CRyPTIC catalog, evaluated as resistant (R), susceptible (S), or undetermined (U). ReSeqTB: mutation data acquired from the ReSeqTB catalog, evaluated as conferring resistance (Minimal, Moderate, High), not conferring resistance (None), or Indeterminate. WHO: mutation data acquired from the WHO 2023 catalog, evaluated as resistant (R), susceptible (S), or undetermined (U).| Mutation | Mutation type | PubMed |
|---|---|---|
| c656t | single resistance variant | PMID:17509804 |
| Curator | Description | Most Recent Edit |
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