Streptococcus pneumoniae PBP2x conferring resistance to amoxicillin

Accession ARO:3003043
CARD Short NameSpne_PBP2x_AMX
DefinitionPBP2x is a penicillin-binding protein found in Streptococcus pneumoniae.
AMR Gene FamilyPenicillin-binding protein mutations conferring resistance to beta-lactam antibiotics
Drug Classcephamycin, penam, cephalosporin
Resistance Mechanismantibiotic target alteration
Resistomes with Sequence VariantsStreptococcus pneumoniaeg+wgs, Streptococcus pseudopneumoniaewgs
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 PBP2x 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 pneumoniae4.62%0%5.83%0%
Streptococcus pseudopneumoniae0%0%3.42%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): 1450

Legend:

  • discovered in clinical, agricultural, or environmental isolates

  • discovered via laboratory selection experiments

  • ReSeqTB https://platform.reseqtb.org

Published Variants:

PMID in progress (single): M339F I371T R384G M400T N514H L546V N605T


>gb|AFC91898.1|+|Streptococcus pneumoniae PBP2x conferring resistance to amoxicillin [Streptococcus pneumoniae]
MKWTKRVIRYATKNRKSPAENRRRVGKSLSLLSVFVFAIFLVNFAVIIGTGTRFGTDLAK
EAKKVHQTTRTVPAKRGTIYDRNGVPIAEDATSYNVYAVIDENYKSATGKILYVEKTQFN
KVAEVFHKYLDMEESYVREQLSQPNLKQVSFGAKGNGITYANMMSIKKELETAEVKGIDF
TTSPNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGKDGIITYEKDR
LGNVVPGTEQVSQQTVDGKDVYTTISSTLQSFMETQMNAFQEKVKGKYMTATLVSAKTGE
ILATTQRPTFDADTKEGLTKDFVWRDILYQSNYEPGSPMKVMTLAASIDNNTFPGGEYFN
SSELKIADVTIRDWDVNESLTGGGMMTFSQGFAHSSNVGMTLLEQKMGDATWLDYLNRFK
FGVPTRFGLTDEYAGQLPADNIVNIAQSSFGQGISVTQTQMIRAFTAIANDGVMLEPKFI
SAIYDPNDQTARKSQKEVVGNPVSKDAASLTRTNMILVGTDPVYGTMYNHSTGKPTVTVP
GQNVALKSGTAQIADEKNGGYLVGLTNYIFSAVSMNPAENPDFILYVTVQQPEHYSGIQL
GEFANPILERASAMKDSLNLQTTAKALEQVSQQSPYPMPSVKDISPGDLAEELRRNLVQP
IVVGTGTKIKESSVEEGTNLAPNQQVILLSDKVEEIPDMYGWKKETAEAFAKWLDIELEF
EGSGSVVQKQDVRTNTAIKNIKKITLTLGD



>gb|JN645706.1|+|1-2253|Streptococcus pneumoniae PBP2x conferring resistance to amoxicillin [Streptococcus pneumoniae]
ATGAAGTGGACAAAAAGAGTAATCCGTTATGCGACCAAAAATCGGAAATCGCCGGCTGAAAACAGACGCAGAGTTGGAAAAAGTCTGAGT
TTATTATCTGTCTTTGTTTTTGCCATTTTTTTAGTCAATTTTGCGGTCATTATTGGGACAGGCACTCGCTTTGGAACAGATTTAGCGAAG
GAAGCTAAGAAGGTTCATCAAACCACCCGTACAGTTCCTGCCAAACGTGGGACTATTTATGACCGAAATGGAGTCCCGATTGCTGAGGAT
GCAACCTCCTATAATGTCTATGCGGTCATTGATGAGAACTATAAGTCAGCAACGGGTAAGATTCTTTACGTAGAAAAAACACAATTTAAC
AAGGTTGCAGAGGTCTTTCATAAGTATCTGGACATGGAAGAATCCTATGTAAGAGAGCAACTCTCGCAACCTAATCTCAAGCAAGTTTCC
TTTGGAGCAAAGGGCAATGGGATTACCTATGCCAATATGATGTCTATCAAAAAAGAGTTGGAAACTGCAGAGGTCAAGGGGATTGATTTT
ACAACCAGTCCTAATCGTAGTTACCCAAACGGACAATTTGCTTCTAGTTTTATCGGACTAGCTCAGCTCCATGAAAATGAAGATGGGAGC
AAGAGTTTGCTGGGAACTTCTGGGATGGAGAGTTCCTTGAACAGTATTCTCGCAGGGAAAGATGGCATTATTACTTATGAAAAGGATCGT
CTAGGTAATGTTGTACCCGGAACAGAACAAGTTTCCCAACAAACGGTAGATGGCAAGGATGTTTATACAACGATTTCCAGCACCCTTCAG
TCCTTCATGGAGACCCAGATGAATGCCTTTCAAGAAAAAGTAAAAGGTAAGTATATGACGGCGACCTTGGTCAGTGCTAAAACAGGGGAA
ATTCTTGCAACAACGCAGAGACCAACCTTTGATGCCGATACTAAGGAAGGACTTACCAAGGACTTTGTTTGGCGTGATATCCTCTATCAA
AGTAACTATGAGCCGGGGTCACCCATGAAGGTCATGACGCTAGCAGCTTCTATTGATAACAATACCTTCCCAGGTGGAGAATACTTCAAT
AGCAGTGAATTAAAAATAGCGGATGTGACAATTCGAGATTGGGACGTTAATGAAAGTTTGACCGGTGGTGGTATGATGACATTTTCTCAA
GGATTTGCTCACTCAAGTAACGTTGGGATGACCCTCCTTGAGCAAAAGATGGGAGATGCTACCTGGCTTGATTATCTTAATCGTTTTAAA
TTTGGTGTTCCGACCCGTTTCGGTTTGACGGATGAGTATGCTGGTCAGCTTCCTGCGGATAATATCGTTAACATTGCGCAAAGCTCATTT
GGGCAAGGGATTTCAGTGACCCAGACGCAAATGATTCGTGCCTTTACAGCTATTGCTAATGACGGTGTCATGCTGGAACCTAAATTTATT
AGTGCCATTTATGATCCAAATGATCAAACTGCTCGGAAATCTCAAAAAGAAGTTGTGGGAAATCCTGTTTCCAAAGATGCAGCTAGTCTA
ACTCGGACTAACATGATTTTGGTAGGGACGGATCCGGTTTATGGAACCATGTATAACCACAGCACAGGCAAGCCAACTGTAACTGTTCCT
GGGCAAAATGTAGCCCTCAAGTCTGGTACGGCTCAGATTGCTGACGAGAAAAATGGTGGTTATCTAGTCGGGTTAACCAACTATATTTTC
TCGGCTGTATCAATGAACCCTGCTGAAAATCCTGATTTTATCTTGTATGTGACGGTCCAACAACCTGAACATTATTCAGGTATTCAGTTG
GGAGAATTTGCCAATCCTATCTTGGAGCGGGCTTCAGCTATGAAAGACTCTCTCAATCTTCAAACAACAGCTAAAGCTTTGGAGCAAGTA
AGTCAACAAAGTCCTTATCCTATGCCTAGTGTCAAGGATATTTCACCTGGTGATTTAGCAGAAGAATTGCGTCGCAATCTTGTACAACCC
ATCGTTGTGGGAACAGGAACAAAGATTAAAGAATCATCTGTAGAAGAAGGGACCAATCTTGCACCAAACCAACAAGTTATCCTTTTATCG
GATAAGGTAGAAGAAATTCCAGACATGTATGGCTGGAAAAAAGAGACTGCTGAGGCCTTTGCTAAATGGTTGGATATCGAGCTGGAATTT
GAAGGTTCAGGTTCCGTCGTTCAGAAGCAGGATGTTCGGACTAATACAGCTATCAAAAACATTAAAAAAATTACATTAACTTTAGGAGAC
TAA