Helicobacter pylori pbp3 conferring resistance to amoxicillin [Drug Class]

Accession ARO:3007057
CARD Short NameHpyl_pbp3_AMX
DefinitionPoint mutations in Helicobacter pylori pbp3 observed to confer resistance to amoxicillin.
AMR Gene FamilyPenicillin-binding protein mutations conferring resistance to beta-lactam antibiotics
Drug Classcephalosporin, cephamycin, penam
Resistance Mechanismantibiotic target alteration
Resistomes with Sequence VariantsHelicobacter pylorig+wgs
Classification13 ontology terms | Show
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)

Resistomes

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 377 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: protein variant model (view sequences)

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GI
Helicobacter pylori12.76%0%8.26%0%
Show Perfect Only


Detection Models

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

Legend:

  • discovered in clinical, agricultural, or environmental isolates

  • discovered via laboratory selection experiments

  • ReSeqTB https://platform.reseqtb.org

Published Variants:

PMID in progress (single): V374I E536K

PMID: 18276599A499V
PMID: 31801839D2N A50S F490Y A541T

>gb|EJC52487.1|-|Helicobacter pylori pbp3 conferring resistance to amoxicillin [Helicobacter pylori Hp P-30]
MDNKNIDPNFNPERFLETQKYKGSITALIFLLLFFIFLMVAFKKAFFAQANMPNLVMSKQ
DTAARGTIYSQDNYSLAASQTLFKLGFDTRFLNPDKEDFFIDFLSIYSNIPKKSLKDAIN
TKGYIILAYDLTPNMAANIRDLNKKFLAFGVFQNFKDAHDKVWQKQGLNIEVSGVSRHYP
YQNSLEPIIGYVQKQEEDKLTLTTGKKGVEKSQDHLLKAQQNGIRTGKRDVSFNFIQNHS
YTEVERLDGYEVYLSIPLKLQREIETLLDKTKDKLKAKEILVGIINPKSGEILSLASSKR
FNPNAIKTSDYESLNLSVAEKVFEPGSTIKPIVYSLLLDKNLINPKERIDLNHGYYQLGK
YTIKDDFIPSKKAVVEDILIQSSNVGMIKISKNLNPEDFYNGLLGYGFSQKTGIDLSLEA
TGKIPPLSAFKREVLKGSVSYGYGLNATFLQLLRAYAVFSNEGKLTTPYLVQRETAPNGD
IYIPSPKPTFQVISPKSARKMKETLIKVVRYGTGKNAQFEGLYIGGKTGTARVAKNGSYS
AESYNSSFFGFAEDERQVFTIGVVILGSHGKEEYYASKIAAPIFKEITEILVRYNYLSPS
IAIQNVLEKNRFKIK



>gb|AKPU01000002.1|-|217825-219672|Helicobacter pylori pbp3 conferring resistance to amoxicillin [Helicobacter pylori Hp P-30]
ATGGATAATAAAAACATTGATCCCAACTTCAACCCAGAACGATTTTTAGAAACCCAAAAATACAAGGGCTCTATTACGGCTTTAATCTTT
TTATTGCTTTTTTTTATTTTTTTAATGGTGGCTTTTAAAAAAGCTTTTTTTGCCCAAGCCAACATGCCTAATCTAGTGATGAGCAAACAA
GACACTGCGGCTAGGGGGACTATCTATAGTCAAGACAACTACAGCCTAGCCGCTTCGCAAACCCTTTTCAAACTGGGCTTTGATACAAGG
TTTTTAAACCCGGATAAAGAAGATTTTTTCATTGATTTCCTTTCTATTTATAGCAATATCCCTAAAAAGTCCTTAAAAGACGCCATCAAT
ACGAAAGGCTATATTATTCTAGCCTATGATCTCACGCCCAATATGGCCGCTAACATTAGAGACTTGAATAAGAAATTTTTAGCCTTTGGG
GTTTTTCAAAATTTCAAAGACGCGCACGATAAGGTGTGGCAAAAGCAAGGGCTAAACATTGAAGTGAGCGGCGTTTCCAGGCATTACCCT
TATCAAAATAGCCTAGAGCCAATCATTGGCTATGTGCAAAAACAAGAAGAAGACAAGCTCACTTTAACTACCGGTAAAAAAGGCGTTGAA
AAATCTCAAGATCACTTGCTTAAAGCCCAACAAAATGGCATAAGAACAGGCAAAAGAGATGTGAGTTTTAATTTTATTCAAAACCACTCT
TACACAGAGGTTGAGCGCCTTGATGGCTATGAGGTGTATTTGAGCATTCCTTTAAAACTCCAAAGAGAAATTGAAACCCTATTGGATAAA
ACCAAAGACAAACTCAAGGCTAAAGAAATCCTAGTGGGTATCATTAACCCTAAAAGCGGGGAAATCTTATCGCTAGCTTCAAGCAAGCGC
TTCAATCCTAACGCCATTAAAACCAGCGATTATGAAAGCTTGAATTTGAGCGTTGCCGAAAAGGTTTTTGAGCCAGGCAGCACGATCAAA
CCCATTGTTTATTCCTTGCTGTTAGACAAGAATTTGATCAACCCTAAAGAACGCATTGATTTAAACCATGGCTATTACCAATTAGGAAAA
TACACCATTAAAGACGACTTTATCCCTAGTAAAAAAGCCGTTGTGGAAGATATTTTGATCCAATCTAGCAATGTGGGCATGATAAAAATC
AGCAAAAATCTCAACCCGGAGGATTTCTATAATGGGCTTTTAGGCTATGGATTTTCTCAAAAAACCGGCATTGATTTATCCTTAGAAGCC
ACAGGAAAGATCCCTCCTTTGTCCGCTTTCAAGCGTGAAGTGTTAAAGGGGAGCGTCTCTTATGGCTATGGGCTGAACGCGACTTTTTTG
CAGCTTTTAAGGGCTTATGCGGTGTTTTCTAATGAAGGCAAATTGACTACCCCCTATTTAGTGCAACGAGAGACCGCCCCTAATGGCGAT
ATTTACATCCCTAGCCCCAAACCCACTTTTCAAGTCATTAGCCCCAAAAGCGCCAGGAAAATGAAAGAAACCTTAATCAAAGTGGTGCGT
TATGGCACAGGCAAAAACGCTCAATTTGAAGGGTTATACATAGGGGGCAAAACAGGCACGGCTAGGGTTGCTAAAAACGGGAGTTACAGC
GCGGAATCCTACAACAGCTCTTTTTTTGGGTTCGCTGAAGATGAAAGGCAGGTTTTTACTATCGGCGTGGTTATCTTAGGCTCGCACGGC
AAGGAAGAATATTATGCTAGCAAGATTGCAGCCCCTATTTTTAAAGAAATCACCGAAATTTTAGTGCGTTACAATTACCTATCGCCCTCT
ATTGCGATTCAAAACGTGCTCGAGAAAAACCGCTTTAAGATAAAATAA