Streptococcus pneumoniae PBP1a conferring resistance to amoxicillin

Accession ARO:3003041
CARD Short NameSpne_PBP1a_AMX
DefinitionPBP1a is a penicillin-binding protein found in Streptococcus pneumoniae.
AMR Gene FamilyPenicillin-binding protein mutations conferring resistance to beta-lactam antibiotics
Drug Classpenam, cephalosporin, cephamycin
Resistance Mechanismantibiotic target alteration
Resistomes with Sequence VariantsStreptococcus pneumoniaeg+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

Stanhope MJ, et al. 2008. Infect Genet Evol 8(3): 331-339. Positive selection in penicillin-binding proteins 1a, 2b, and 2x from Streptococcus pneumoniae and its correlation with amoxicillin resistance development. (PMID 18394970)

Resistomes

Prevalence of Streptococcus pneumoniae PBP1a 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
Streptococcus pneumoniae7.18%0%2.31%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): 1350

Legend:

  • discovered in clinical, agricultural, or environmental isolates

  • discovered via laboratory selection experiments

  • ReSeqTB https://platform.reseqtb.org

Published Variants:

PMID: 18394970S575T N609D

>gb|AFC91828.1|+|Streptococcus pneumoniae PBP1a conferring resistance to amoxicillin [Streptococcus pneumoniae]
MNKPTILHLIKYLSISFLSLVIAAIVLGGGVFFYYVSKAPSLSESKLVATTSSKIYDNKN
QLIADLGSERRVNAQANDIPTDLVKAIVSIEDHRFFDHRGIDTIRILGAFLRNLQSNSLQ
GGSTLTQQLIKLTYFSTSTSDQTISRKTQEAWLAIQLEQKATKQEILTYYINKVYMSNGN
YGMQTAAQNYYGKDLNNLSLPQLALLAGMPQAPNQYDPYSHPEAAQDRRNLVLSEMKNQG
YISAEQYEKAVNTPITDGLQSLKSASNYPAYMDNYLKEVINQVEKETGYNLLTTGMDVYT
NVDQEAQKHLWDIYNTDEYVAYPDDELQVASTIVDVSNGKVIAQLGARHQSSNVSFGINQ
AVETNRDWGSTMKPITDYAPALEYGVYDSTATIVHDEPYNYPGTNTPVYNWDRGYFGNIT
LQYALQQSRNVPAVETLNKVGLNRAKTFLNGLGIDYPSIHYSNAISSNTTESDKKYGASS
EKMAAAYAAFANGGTYYKPMYIHKVVFSDGSEKEFSNVGTRAMKETTAYMMTDMMKTVLS
YGTGRNAYLAWLPQAGKTGTSNYTDEEIENHIKTSQFVAPDELFAGYTRKYSMAVWTGYS
NRLTPLVGNGLTVAAKVYRSMMTYLSEGSNPEDWNIPEGLYRNGEFVFKNGARSTWTQPA
PQQPPSTESSSSSSDSSTSQSSSTTPSTNNSTTTDPNNNTQQSNTTPDQQNQNPQPAQP



>gb|JN645776.1|+|1-2160|Streptococcus pneumoniae PBP1a conferring resistance to amoxicillin [Streptococcus pneumoniae]
ATGAACAAACCAACGATTCTGCACCTAATCAAGTATCTGAGCATTAGCTTCTTAAGCTTGGTTATCGCAGCCATTGTCTTAGGCGGAGGA
GTTTTTTTCTACTACGTTAGCAAGGCTCCTAGCCTATCCGAGAGTAAACTAGTTGCAACAACTTCTAGTAAAATCTACGACAATAAAAAT
CAACTCATTGCTGACTTGGGTTCTGAACGCCGCGTCAATGCCCAAGCTAATGATATTCCCACAGATTTGGTTAAGGCAATCGTTTCTATC
GAAGACCATCGCTTCTTCGACCACAGGGGGATTGATACCATCCGTATCCTGGGAGCTTTCTTGCGCAATCTGCAAAGCAATTCCCTCCAA
GGTGGATCAACTCTCACCCAACAGTTGATTAAGTTGACTTACTTTTCAACTTCGACTTCCGACCAGACTATTTCTCGTAAGACTCAGGAA
GCTTGGTTAGCGATTCAGTTAGAACAAAAAGCAACCAAGCAAGAAATCTTGACCTACTATATAAATAAGGTCTACATGTCTAATGGCAAC
TATGGAATGCAGACAGCAGCTCAAAACTACTATGGTAAAGACCTCAATAATTTAAGTTTACCTCAGTTAGCCTTGCTGGCTGGAATGCCT
CAGGCACCAAACCAATATGACCCCTATTCACATCCAGAAGCAGCCCAAGACCGCCGAAACTTGGTCTTATCTGAAATGAAAAATCAAGGC
TACATCTCTGCTGAACAGTATGAGAAAGCAGTCAATACACCAATTACTGATGGACTACAAAGTCTCAAATCAGCAAGTAATTACCCTGCT
TACATGGATAATTACCTCAAGGAAGTCATCAATCAAGTTGAAAAAGAAACAGGCTATAACCTGCTCACAACTGGGATGGATGTCTACACA
AATGTAGACCAAGAAGCTCAAAAACATCTGTGGGATATTTACAATACAGACGAATACGTTGCCTATCCAGACGATGAATTGCAAGTCGCT
TCTACCATTGTTGATGTTTCTAACGGTAAAGTCATTGCCCAGCTAGGAGCACGCCATCAGTCAAGTAATGTTTCCTTCGGAATTAACCAA
GCAGTAGAAACAAACCGCGACTGGGGATCAACTATGAAACCGATCACAGACTATGCTCCTGCCTTGGAGTACGGTGTCTACGATTCAACT
GCTACTATCGTTCACGATGAGCCCTATAACTACCCTGGGACAAATACTCCTGTTTATAACTGGGATAGGGGCTACTTTGGCAACATCACC
TTGCAATACGCCCTGCAACAATCGCGAAACGTCCCAGCCGTGGAAACTCTAAACAAGGTCGGACTCAACCGCGCCAAGACTTTCCTAAAT
GGTCTCGGAATCGACTACCCAAGTATTCACTACTCAAATGCCATTTCAAGTAACACAACCGAATCAGACAAAAAATATGGAGCAAGTAGT
GAAAAGATGGCTGCTGCTTACGCTGCCTTTGCAAATGGTGGAACTTACTATAAACCAATGTATATCCATAAAGTCGTCTTTAGTGATGGG
AGTGAAAAAGAGTTCTCTAATGTCGGAACTCGTGCCATGAAGGAAACAACAGCCTATATGATGACCGACATGATGAAAACAGTCTTGAGT
TATGGAACTGGACGAAATGCCTATCTTGCTTGGCTCCCTCAGGCTGGTAAAACAGGAACCTCTAACTATACAGACGAGGAAATTGAAAAC
CACATCAAGACCTCTCAATTTGTAGCACCTGACGAACTATTTGCTGGCTATACGCGTAAATATTCAATGGCTGTATGGACAGGCTATTCT
AACCGTCTGACACCACTTGTAGGCAATGGCCTTACGGTCGCTGCCAAAGTTTACCGCTCTATGATGACCTACCTGTCTGAAGGAAGCAAT
CCAGAGGATTGGAATATACCAGAGGGGCTCTACAGAAATGGAGAATTCGTATTTAAAAATGGTGCTCGTTCTACGTGGACTCAACCTGCT
CCACAACAACCCCCATCAACTGAAAGTTCAAGCTCATCATCAGATAGTTCAACTTCACAGTCTAGCTCAACCACTCCAAGCACAAATAAT
AGTACGACTACCGATCCTAACAATAATACGCAACAATCAAATACAACCCCTGATCAACAAAATCAGAATCCTCAACCAGCACAACCATAA