Helicobacter pylori pbp1 mutants conferring resistance to amoxicillin

Download Sequences
Accession ARO:3007060
CARD Short NameHpyl_pbp1_AMX
DefinitionPoint mutations in Helicobacter pylori pbp1 observed to confer resistance to amoxicillin.
AMR Gene FamilyPenicillin-binding protein mutations conferring resistance to beta-lactam antibiotics
Drug Classpenicillin beta-lactam, cephalosporin
Resistance Mechanismantibiotic target alteration
Classification12 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

Matteo MJ, et al. 2008. J Antimicrob Chemother 61(3):474-7 Helicobacter pylori amoxicillin heteroresistance due to point mutations in PBP-1A in isogenic isolates. (PMID 18192681)

Rimbara E, et al. 2007. Microbiol Immunol 51(10):939-44 Correlation between substitutions in penicillin-binding protein 1 and amoxicillin resistance in Helicobacter pylori. (PMID 17951983)

Tran TT, et al. 2022. BMC Microbiol 22(1):41 Emergence of amoxicillin resistance and identification of novel mutations of the pbp1A gene in Helicobacter pylori in Vietnam. (PMID 35114945)

Tshibangu-Kabamba E, et al. 2020. Microorganisms 8(6): Next-Generation Sequencing of the Whole Bacterial Genome for Tracking Molecular Insight into the Broad-Spectrum Antimicrobial Resistance of Helicobacter pylori Clinical Isolates from the Democratic Republic of Congo. (PMID 32545318)

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)

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)

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 pbp1 mutants 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).

Prevalence: protein variant model

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GIGRDI-AMR2
No prevalence data


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): 1300

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
N107Rsingle resistance variantPMID:31801839
A201Vsingle resistance variantPMID:31801839
V250Isingle resistance variantPMID:31801839
F366Lsingle resistance variantPMID:32545318
V374Lsingle resistance variantPMID:32708761
S402Gsingle resistance variantPMID:32545318
S405Nsingle resistance variantPMID:32545318
S414Rsingle resistance variantPMID:32545318
S414Nsingle resistance variantPMID:32708761
I450Vsingle resistance variantPMID:32708761
+E464-465insertion mutationPMID:35114945
+N464-465insertion mutationPMID:35114945
A474Tsingle resistance variantPMID:32545318
S543Tsingle resistance variantPMID:31801839
T556Ssingle resistance variantPMID:32545318
T558Ssingle resistance variantPMID:32545318
N562Ysingle resistance variantPMID:32545318
N562Hsingle resistance variantPMID:32545318
T593Ksingle resistance variantPMID:32545318
T593Asingle resistance variantPMID:17951983
T593Gsingle resistance variantPMID:32545318
T593Ssingle resistance variantPMID:32545318
G595Ssingle resistance variantPMID:17951983
+A595-596insertion mutationPMID:35114945
+G595-596insertion mutationPMID:35114945
+S595-596insertion mutationPMID:35114945
L610Ternonsense mutationPMID:32708761
R649Ksingle resistance variantPMID:37485536
R656Psingle resistance variantPMID:37485536
R656Hsingle resistance variantPMID:37485536

>gb|AAK17126.1|+|Helicobacter pylori pbp1 mutants conferring resistance to amoxicillin [Helicobacter pylori]
MLKKIFYGFIVLFLIIVGLLAILIAQVWVTTDKDIAKIKDYRPGVASQILDRKGRLIANI
YDKEFRFYARFEEIPPRFIESLLAVEDTLFFEHGGINLDAIMRAMIKNAKSGRYTEGGST
LTQQLVKNMVLTREKTLTRKLKEAIISIRIEKVLSKEEILERYLNQTFFGHGYYGVKTAS
LGYFKKPLDKLTLKEIAMLVALPRAPSFYDPTKNLEFSLSRANDILRRLYSLGWISSNEL
KSALNEVPIVYNQTSTQNIAPYVVDEVLKQLDQLDGLKTQGYIIKLTIDLDYQRLALESL
RFGHQKILEKIAKEKPKTNASNEDEDNLNASMIVTDTSTGKILALVGGIDYKKSAFNRAT
QAKRQFGSAIKPFVYQIAFDNGYSTTSKIPDTARNFENGNYSKNSKQNHAWHPSNYSRKF
LGLVTLQEALSHSLNLATINLSDQLGFEKIYQSLSDMGFKNLPKDLSIVLGSFAISPIEA
AEKYSLFSNYGTMLKPMLIESITNQQNDVKTFTPMETKKITSKEQAFLTISVLMNAVENG
TGSLAHIKGLEVAGKTGTSNNNIDAWFIGFTPTLQSVIWFGRDDNTPISKGATGGVVSAP
VYSYFMRNILSIEPSLKRKFDVPKGLRKEIVDKIPYYSTPNSITPTPKRTDDSEERLLF


>gb|AF315503.1|+|78-2057|Helicobacter pylori pbp1 mutants conferring resistance to amoxicillin [Helicobacter pylori]
ATGCTAAAAAAGATTTTTTATGGTTTTATCGTTTTATTTTTGATTATCGTAGGGTTGTTAGCCATTCTTATCGCTCAAGTTTGGGTAACT
ACGGATAAGGATATTGCTAAAATTAAAGATTATCGCCCGGGCGTCGCTTCACAGATTTTAGACCGAAAAGGGCGTTTGATCGCTAATATC
TATGATAAGGAATTTCGTTTTTATGCGCGTTTTGAAGAAATCCCCCCACGATTTATTGAAAGCCTTTTAGCGGTAGAAGACACCCTCTTT
TTTGAACATGGGGGGATCAATTTAGACGCTATCATGCGCGCTATGATTAAAAACGCTAAAAGCGGTCGTTACACCGAGGGGGGTAGCACC
CTAACCCAACAACTCGTTAAAAACATGGTGCTCACACGAGAAAAAACCCTAACCAGAAAACTCAAAGAAGCTATCATTTCCATACGCATT
GAAAAAGTCTTAAGCAAAGAAGAAATTTTAGAGCGCTATTTGAACCAAACTTTTTTTGGGCATGGGTATTATGGCGTGAAAACCGCAAGT
TTAGGGTATTTTAAAAAACCCCTTGACAAACTCACGCTTAAAGAAATCGCCATGTTAGTCGCCTTGCCTAGGGCTCCGAGTTTTTATGAT
CCTACCAAAAATTTAGAATTTTCACTTTCTAGGGCTAATGATATTTTAAGGCGGTTGTATTCTTTAGGCTGGATTTCTTCTAACGAGCTC
AAATCCGCTCTCAATGAAGTGCCAATCGTCTATAACCAAACTTCCACGCAAAATATCGCTCCCTATGTCGTGGATGAAGTATTGAAGCAA
TTGGATCAATTAGACGGGTTAAAAACTCAAGGCTATATTATAAAGCTCACGATAGATTTGGATTACCAACGCTTAGCGTTAGAGTCCTTG
CGTTTTGGGCATCAAAAAATCTTAGAAAAAATCGCTAAAGAAAAGCCAAAAACTAACGCGTCTAATGAAGATGAAGACAACTTGAACGCT
AGCATGATAGTTACAGACACGAGCACCGGTAAGATTTTAGCTTTAGTGGGAGGGATTGATTATAAAAAAAGCGCTTTCAATCGCGCCACG
CAAGCCAAACGGCAATTTGGGAGCGCGATCAAGCCTTTTGTGTATCAAATCGCTTTTGATAATGGCTATTCCACGACTTCTAAAATCCCT
GATACCGCGCGAAACTTTGAAAATGGCAATTATAGTAAAAACAGCAAACAAAACCATGCATGGCACCCCAGCAATTATTCTCGCAAGTTT
TTAGGGCTTGTAACCTTGCAAGAAGCTTTGAGCCATTCATTAAATCTAGCCACGATCAATTTAAGCGATCAGCTTGGCTTTGAAAAAATT
TATCAATCTTTAAGCGATATGGGGTTTAAAAACCTCCCTAAAGACTTGTCTATTGTGTTAGGGAGCTTTGCTATCTCACCCATTGAAGCG
GCTGAAAAGTATTCTTTATTTTCTAATTACGGCACTATGCTCAAACCCATGCTCATTGAAAGCATCACTAACCAACAAAACGATGTCAAA
ACTTTCACGCCTATGGAAACCAAAAAGATCACCTCCAAAGAACAGGCTTTTTTAACCATTTCAGTGCTGATGAATGCGGTAGAAAACGGC
ACAGGGAGTTTGGCTCACATTAAAGGTTTAGAAGTCGCCGGTAAAACCGGAACTTCTAACAACAATATTGACGCTTGGTTCATTGGCTTT
ACCCCCACCTTGCAAAGCGTGATCTGGTTTGGGAGGGACGATAACACGCCTATTAGCAAAGGAGCGACAGGAGGCGTTGTGAGCGCGCCT
GTGTATTCGTATTTCATGCGTAATATTCTAAGCATTGAACCTTCTTTAAAAAGAAAGTTTGATGTCCCCAAAGGCTTGCGTAAAGAAATT
GTGGATAAAATCCCCTACTATTCAACCCCCAATTCCATCACCCCCACCCCCAAAAGAACAGACGATAGCGAAGAACGCTTGTTGTTCTAA

Curator Acknowledgements
Curator Description Most Recent Edit