| Accession | ARO:3004134 |
| CARD Short Name | Hpyl_23S_CLR |
| Definition | Point mutations in Helicobacter pylori shown to confer resistance to clarithromycin, a macrolide antibiotic. |
| AMR Gene Family | 23S rRNA with mutation conferring resistance to macrolide antibiotics |
| Drug Class | macrolide antibiotic |
| Resistance Mechanism | antibiotic target alteration |
| Resistomes with Sequence Variants | Helicobacter pylorig+wgs+gi, Klebsiella pneumoniaewgs, Moraxella catarrhaliswgs |
| Classification | 10 ontology terms | Show + process or component of antibiotic biology or chemistry + mechanism of antibiotic resistance + antibiotic target alteration [Resistance Mechanism] + determinant of antibiotic resistance + mutation conferring antibiotic resistance + antibiotic resistant gene variant or mutant + rRNA with mutation conferring antibiotic resistance + antibiotic molecule + macrolide antibiotic [Drug Class] + 23S rRNA with mutation conferring antibiotic resistance |
| Parent Term(s) | 2 ontology terms | Show + 23S rRNA with mutation conferring resistance to macrolide antibiotics [AMR Gene Family] + confers_resistance_to_antibiotic clarithromycin [Antibiotic] |
| Publications | Vester B, et al. 2001. Antimicrob. Agents Chemother. 45(1):1-12 Macrolide resistance conferred by base substitutions in 23S rRNA. (PMID 11120937) Azzaya D, et al. 2020. Microorganisms 8(7): High Antibiotic Resistance of Helicobacter pylori and Its Associated Novel Gene Mutations among the Mongolian Population. (PMID 32708761) Hussein RA, et al. 2022. Saudi J Biol Sci 29(1):513-520 Detection of clarithromycin resistance and 23SrRNA point mutations in clinical isolates of Helicobacter pylori isolates: Phenotypic and molecular methods. (PMID 35002447) Guzman K, et al. 2023. Front Microbiol 14:1198325 The Helicobacter pylori single nucleotide polymorphisms SNPs associated with multiple therapy resistance in Colombia. (PMID 37485536) |
Prevalence of Helicobacter pylori 23S rRNA with mutation conferring resistance to clarithromycin 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 |
|---|---|---|---|---|
| Helicobacter pylori | 100% | 0% | 75.4% | 100% |
| Klebsiella pneumoniae | 0% | 0% | 0.03% | 0% |
| Moraxella catarrhalis | 0% | 0% | 0.52% | 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): 2000
Legend:
Published Variants:
| PMID: 32708761 | A1410G C1707T A2143G A2167G C2248T,G2287A C2922T |
| PMID: 35002447 | A2144G A2146U A2146G A2146C A2147G A2147C |
| PMID: 37485536 | A2142G |