Helicobacter pylori 23S rRNA with mutation conferring resistance to clarithromycin

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Accession ARO:3004134
CARD Short NameHpyl_23S_CLR
DefinitionPoint mutations in Helicobacter pylori shown to confer resistance to clarithromycin, a macrolide antibiotic.
AMR Gene Family23S rRNA with mutation conferring resistance to macrolide antibiotics
Drug Classmacrolide antibiotic
Resistance Mechanismantibiotic target alteration
Resistomes with Sequence VariantsHelicobacter pylorig+wgs+gi, Klebsiella pneumoniaewgs, Moraxella catarrhaliswgs
Classification10 ontology terms | Show
Parent Term(s)2 ontology terms | Show
+ confers_resistance_to_antibiotic clarithromycin [Antibiotic]
+ 23S rRNA with mutation conferring resistance to macrolide antibiotics [AMR Gene Family]
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)
Resistomes

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 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).

Prevalence: rRNA gene variant model (view sequences)

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GIGRDI-AMR2
Helicobacter pylori100%0%96.02%100%0%
Klebsiella pneumoniae0%0%0.03%0%0%
Moraxella catarrhalis0%0%0.52%0%0%
Show Perfect Only


Detection Models

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

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).

MutationMutation typePubMed
a1410gsingle resistance variantPMID:32708761
c1707tsingle resistance variantPMID:32708761
a2142gsingle resistance variantPMID:37485536
a2143gsingle resistance variantPMID:32708761
a2144gsingle resistance variantPMID:35002447
a2146gsingle resistance variantPMID:35002447
a2146csingle resistance variantPMID:35002447
a2146tsingle resistance variantPMID:35002447
a2147csingle resistance variantPMID:35002447
a2147gsingle resistance variantPMID:35002447
a2167gsingle resistance variantPMID:32708761
c2248t,g2287amultiple resistance variantsPMID:32708761
c2922tsingle resistance variantPMID:32708761


>gb|AB162858.1|+|1-2975|Helicobacter pylori 23S rRNA with mutation conferring resistance to clarithromycin [Helicobacter pylori]
AAGGCAGTGGTAGCGCTGAAGAATATTCGTGCAATTGTCGTTATTCATTATAAAAGGGCAGGTTTTAAAGGATATTTTAAAATTTAAAAC
AAGCTTTTAAGAGCAGATGGCGGATGCCTTGCCAAAGAGAGGCGATGAAGGACGTACTAGACTGCGATAAGCTATGCGGAGCTGTCAAGG
AGCTTTGATGCGTAGATGTCCGAATGGGGCAACCCAACTAATAGAGATATTAGTTACTCTAATTTAGAGAGCGAACCTAGTGAAGTGAAA
CATCTCAGTAACTAGAGGAAAAGAAATCAACGAGATTCCCTAAGTAGTGGCGAGCGAACGGGGAAAAGGGCAAACCGAGTGCTTGCATTC
GGGGTTGAGGACTGCAACATCCAAGAGAACGCTTTAGCAGAGTTACCTGGAAAGGTAAGCCATAGAAAGTGATAGCCTTGTATGCGACAA
GGCGTTCTTAGGTAGCAGGATCCAGAGTAGGCCAGGACACGAGAAATCCAGGTTGAAGCTGGGGAGACCACTCTCCAACCCTAAATACTA
CTCTTTGAGCGATAGCGAACAAGTACCGTGAGGGAAAGGTGAAAAGAACCGCAGTGAGCGGAGTGAAATAGAACCTGAAACCATCTGCTT
ACAATCATTCAGAGCCCTATGATTTATCAGGGTGATGGACTGCCTTTTGCATAATGATCCTGCGAGTTGTGGTATCTGGCAAGGTTAAGC
GGATGCGAAGCCGTAGCGAAAGCGAGTCTTAATAGGGCGGTTTAAGTCAGATGCTGCAGACCCGAAGCTAAGTGATCTATCCATGGCCAA
GTTGAAACGCGTGTAATAGCGCGTGGAGGACTGAACTCGTACCCATTGAAACGGGTTGGGATGAGCTGTGGATAGGGGTGAAAGGTCAAA
CAAACTTAGTGATAGCTGGTTCTCTTCGAAATATATTTAGGTATAGCCTCAAGTGATAATAAAAGGGGGTAGAGCTCTGATTGGGCTAGG
GCTGCTCGCCGCGGTACCAAACCCTATCAAACTTCGAATACCTTTTATCGTATCTTGGGAGTCAGGCGGTGGGTGATAAAATCAATCGTC
AAAAGGGGAACAACCCAGACTACCAAATAAGGTCCCTAAGTTCTATTCTGAGTGGAAAAAGATGTGTGGCTACTCAAACAACCAGGAGGT
TGGCTTAGAAGCAGCCATCCTTTAAAGAAAGCGTAACAGCTCACTGGTCTAGTGGTCATGCGCTGAAAATATAACGGGGCTAAGATAGAC
ACCGAATTTGTAGATTGTGTTAAACACAGTGGTAGAAGAGCGTTCATACCAGCGTTGAAGGTATACCGGTAAGGAGTGCTGGAGCGGTAT
GAAGTGAGCATGCAGGAATGAGTAACGATAAGATATATGAGAATTGTATCCGCCGTAAATCTAAGGTTTCCTACGCGATGGTCGTCATCG
TAGGGTTAGTCGGGTCCTAAGCCGAGTCCGAAAGGGGTAGGTGATGGCAAATTGGTTAATATTCCAATACCGACTCATGGAGCGTGATGG
GGGGACGCATAGGGTTAAGCGAGCTAGCTGATGGAAGTGCTAGTCTAAGGGCGTAGATTGGAGGGAAGGCAAATCCACCTCTGTATTTGA
AACCCAAACAGGCTCTTTGAGTCCTTTCAGGACAAAGGGAGAATCGCTGATACCGTCGTGCCAAGAAAAGCCTCTAAGCATATCCATAGT
CGTCCGTACCGCAAACCGACACAGGTAGATGAGATGAGTATTCTAAGGCGCGTGAAAGAACTCTGGTTAAGGAACTCTGCAAACTAGCAC
CGTAAGTTCGCGATAAGGTGTGCCGCAGCAATGCGGTCTCAGCAAAGAGTCCCTCCCGACTGTTTACCAAAAACACAGCACTTTGCCAAC
TCGTAAGAGGAAGTATAAGGTGTGACGCCTGCCCGGTGCTCGAAGGTTAAGAGGATGCGTCAGTCGCAAGATGAAGCGTTGAATTGAAGC
CCGAGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGTTAAATACCGACCTGCATGAATGGCGTAACGAG
ATGGGAGCTGTCTCAACCAGAGATTCAGTGAAATTGTAGTGGAGGTGAAAATTCCTCCTACCCGCGGCAAGACGGAAAGACCCCGTGGAC
CTTTACTACAACTTAGCACTGCTAACGGGAATATCATGTGCAGGATAGGTGGGAGGCTTTGAAGTAAGGGCTTTGGCTCTTATGGAGCCA
TCCTTGAGATACCACCCTTGATGTTTCTGTTAGCTAACTGGCCTGTGTTATCCACAGGCAGGACAATGCTTGGTGGGTAGTTTGACTGGG
GCGGTCGCCTCCTAAAAAGTAACGGAGGCTTGCAAAGGTTGGCTCATTGCGGTTGGAAATCGCAAGTTGAGTGTAATGGCACAAGCCAGC
CTGACTGTAAGACATACAAGTCAAGCAGAGACGAAAGTCGGTCATAGTGATCCGGTGGTTCTGTGTGGAAGGGCCATCGCTCAAAGGATA
AAAGGTACCCCGGGGATAACAGGCTGATCTCCCCCAAGAGCTCACATCGACGGGGAGGTTTGGCACCTCGATGTCGGCTCATCGCATCCT
GGGGCTGGAGCAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGCGGTACGCGAGCTGGGTTCAGAACGTCGTGAGACAGTTCGGTCCC
TATCTGCCGTGGGCGTAGGAAAGTTGAGGAGAGCTGTCCCTAGTACGAGAGGACCGGGATGGACGTGTCACTGGTGCACCAGTTGTTCTG
CCAAGAGCATCGCTGGGTAGCTACACACGGATGTGATAACTGCTGAAAGCATCTAAGCAGGAAGCCAACTCCAAGATAAACTTTCCCTGA
AGCTCGCACAAAGACTATGTGCTTGATAGGGTAGATGTGTAAGCGCAGTAATGCGTTTAGCTGACTACTACTAATAGAGCGTTTGGCTTG
TTTTT

Curator Acknowledgements
Curator Description Most Recent Edit