| Accession | ARO:3007057 |
| CARD Short Name | Hpyl_pbp3_AMX |
| Definition | Point mutations in Helicobacter pylori pbp3 observed to confer resistance to amoxicillin. |
| AMR Gene Family | Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics |
| Drug Class | penicillin beta-lactam, cephalosporin |
| Resistance Mechanism | antibiotic target alteration |
| Resistomes with Sequence Variants | Helicobacter pylorig+wgs |
| Classification | 12 ontology terms | Show + process or component of antibiotic biology or chemistry + antibiotic molecule + mechanism of antibiotic resistance + beta-lactam antibiotic + antibiotic target alteration [Resistance Mechanism] + mutation conferring antibiotic resistance + penicillin beta-lactam [Drug Class] + determinant of antibiotic resistance + penicillin with extended spectrum + beta-lactam resistant penicillin-binding proteins + cephalosporin [Drug Class] + antibiotic resistant gene variant or mutant |
| Parent Term(s) | 2 ontology terms | Show + confers_resistance_to_antibiotic amoxicillin [Antibiotic] + Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics [AMR Gene Family] |
| Publications | Rimbara E, et al. 2008. J Antimicrob Chemother 61(5):995-8 Mutations in penicillin-binding proteins 1, 2 and 3 are responsible for amoxicillin resistance in Helicobacter pylori. (PMID 18276599) Saranathan R, et al. 2020. J Clin Microbiol 58(3): Helicobacter pylori Infections in the Bronx, New York: Surveying Antibiotic Susceptibility and Strain Lineage by Whole-Genome Sequencing. (PMID 31801839) |
Prevalence of Helicobacter pylori pbp3 conferring resistance to amoxicillin 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 |
|---|---|---|---|---|---|
| Helicobacter pylori | 12.56% | 0% | 9.42% | 0% | 0% |
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): 1000
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 |
|---|---|---|
| D2N | single resistance variant | PMID:31801839 |
| A50S | single resistance variant | PMID:31801839 |
| V374L | single resistance variant | PMID:18276599 |
| F490Y | single resistance variant | PMID:31801839 |
| A499V | single resistance variant | PMID:18276599 |
| E536K | single resistance variant | PMID:18276599 |
| A541T | single resistance variant | PMID:31801839 |
| Curator | Description | Most Recent Edit |
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