Escherichia coli UhpT with mutation conferring resistance to fosfomycin

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Ontology CARD's Antibiotic Resistance Ontology
Accession ARO:3003890
CARD Short NameEcol_UhpT_FOF
DefinitionMutations to the active importer UhpT, which is involved with the uptake of many phosphorylated sugars, confer resistance to fosfomycin by reducing import of the drug into the bacteria.
AMR Gene Familyantibiotic-resistant UhpT
Drug Classphosphonic acid antibiotic
Resistance Mechanismantibiotic target alteration
Resistomes with Sequence VariantsCitrobacter amalonaticusg+wgs, Citrobacter freundiig+wgs, Citrobacter koserig+wgs, Citrobacter portucalensisg+wgs, Citrobacter werkmaniig+wgs, Citrobacter youngaeg+wgs, Enterobacter asburiaeg+wgs, Enterobacter cancerogenusg+wgs, Enterobacter chengduensiswgs, Enterobacter cloacaeg+p+wgs, Enterobacter hormaecheig+p+wgs, Enterobacter kobeig+wgs, Enterobacter roggenkampiig+wgs, Escherichia albertiig+wgs, Escherichia colig+wgs, Escherichia fergusoniiwgs, Escherichia marmotaeg+wgs, Klebsiella aerogenesg+wgs, Klebsiella huaxiensisg+wgs, Klebsiella michiganensisg+wgs, Klebsiella oxytocag+wgs, Klebsiella pneumoniaeg+p+wgs, Klebsiella quasipneumoniaeg+wgs, Raoultella planticolag+wgs, Salmonella bongorig+wgs, Salmonella entericag+wgs, Shigella boydiig+wgs, Shigella dysenteriaewgs, Shigella flexnerig+wgs, Shigella sonneiwgs
Classification8 ontology terms | Show
Parent Term(s)3 ontology terms | Show
+ confers_resistance_to_antibiotic fosfomycin [Antibiotic]
+ antibiotic resistant gene variant or mutant
+ antibiotic-resistant UhpT [AMR Gene Family]
Publications

Takahata S, et al. 2010. Int J Antimicrob Agents 35(4): 333-337. Molecular mechanisms of fosfomycin resistance in clinical isolates of Escherichia coli. (PMID 20071153)
Resistomes

Prevalence of Escherichia coli UhpT with mutation conferring resistance to fosfomycin 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 (view sequences)

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GIGRDI-AMR2
Citrobacter amalonaticus90.91%0%89.09%0%0%
Citrobacter freundii100%0%98.65%0%0%
Citrobacter koseri100%0%98.2%0%0%
Citrobacter portucalensis77.78%0%99.1%0%0%
Citrobacter werkmanii100%0%100%0%0%
Citrobacter youngae66.67%0%100%0%0%
Enterobacter asburiae35.48%0%32.02%0%0%
Enterobacter cancerogenus100%0%92.86%0%0%
Enterobacter chengduensis0%0%36%0%0%
Enterobacter cloacae73.21%1.12%72.2%0%0%
Enterobacter hormaechei97.84%0.13%98.75%0%0%
Enterobacter kobei100%0%97.38%0%0%
Enterobacter roggenkampii95.35%0%94.24%0%0%
Escherichia albertii98.57%0%100%0%0%
Escherichia coli8.43%0%15.96%0%13.08%
Escherichia fergusonii0%0%2.17%0%0%
Escherichia marmotae100%0%97.92%0%0%
Klebsiella aerogenes100%0%100%0%0%
Klebsiella huaxiensis100%0%100%0%0%
Klebsiella michiganensis98.39%0%99.47%0%0%
Klebsiella oxytoca97.44%0%100%0%0%
Klebsiella pneumoniae98.76%0.01%98.93%0%0%
Klebsiella quasipneumoniae100%0%99.87%0%0%
Raoultella planticola100%0%100%0%0%
Salmonella bongori100%0%100%0%0%
Salmonella enterica93.19%0%97.89%0%0%
Shigella boydii6.67%0%4.44%0%0%
Shigella dysenteriae0%0%20%0%0%
Shigella flexneri2%0%0.16%0%0%
Shigella sonnei0%0%0.22%0%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): 850

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
E350Qsingle resistance variantPMID:20071153

>gb|CDJ73208.1|+|Escherichia coli UhpT with mutation conferring resistance to fosfomycin [Escherichia coli str. K-12 substr. MC4100]
MLAFLNQVRKPTLDLPLEVRRKMWFKPFMQSYLVVFIGYLTMYLIRKNFNIAQNDMISTY
GLSMTQLGMIGLGFSITYGVGKTLVSYYADGKNTKQFLPFMLILSAICMLGFSASMGSGS
VSLFLMIAFYALSGFFQSTGGSCSYSTITKWTPRRKRGTFLGFWNISHNLGGAGAAGVAL
FGANYLFDGHVIGMFIFPSIIALIVGFIGLRYGSDSPESYGLGKAEELFGEEISEEDKET
ESTDMTKWQIFVEYVLKNKVIWLLCFANIFLYVVRIGIDQWSTVYAFQELKLSKAVAIQG
FTLFEAGALVGTLLWGWLSDLANGRRGLVACIALALIIATLGVYQHASNEYIYLASLFAL
GFLVFGPQLLIGVAAVGFVPKKAIGAADGIKGTFAYLIGDSFAKLGLGMIADGTPVFGLT
GWAGTFAALDIAAIGCICLMAIVAVMEERKIRREKKIQQLTVA


>gb|HG738867.1|+|2934267-2935658|Escherichia coli UhpT with mutation conferring resistance to fosfomycin [Escherichia coli str. K-12 substr. MC4100]
ATGCTGGCTTTCTTAAACCAGGTTCGCAAGCCGACCCTGGACCTTCCGCTCGAAGTGCGGCGCAAAATGTGGTTCAAACCGTTCATGCAA
TCCTACCTGGTGGTCTTTATCGGCTACCTGACGATGTACCTGATTCGCAAGAACTTTAACATCGCGCAGAACGATATGATTTCGACCTAC
GGGTTGAGCATGACGCAGCTGGGGATGATCGGCCTGGGTTTCTCCATCACTTATGGCGTGGGTAAAACGCTGGTTTCCTACTACGCCGAC
GGCAAAAACACCAAACAATTCCTGCCGTTCATGCTGATCCTCTCTGCTATTTGTATGCTGGGCTTCAGTGCCAGTATGGGCAGCGGCTCG
GTTAGCCTGTTCCTGATGATTGCCTTCTACGCCTTAAGCGGCTTTTTCCAGAGTACCGGCGGTTCGTGCAGTTACTCCACCATCACCAAA
TGGACGCCGCGTCGTAAACGCGGGACATTCCTCGGTTTCTGGAATATTTCTCACAACCTTGGCGGTGCAGGCGCAGCAGGTGTGGCGCTG
TTCGGGGCAAATTACCTGTTCGATGGCCATGTCATCGGCATGTTTATCTTCCCGTCGATTATCGCGCTGATTGTCGGTTTTATCGGCCTG
CGTTACGGCAGCGACTCCCCGGAATCTTATGGCCTCGGCAAAGCTGAAGAACTGTTCGGCGAGGAGATCAGCGAAGAGGACAAAGAGACA
GAATCTACCGATATGACCAAGTGGCAGATCTTTGTTGAGTATGTGCTGAAAAACAAAGTGATCTGGCTGCTGTGCTTCGCCAACATTTTC
CTCTATGTGGTACGTATTGGTATCGACCAGTGGTCAACCGTATACGCGTTCCAGGAACTGAAACTCTCTAAAGCGGTGGCGATTCAGGGC
TTTACGCTGTTTGAAGCTGGTGCGCTGGTCGGTACGCTGCTGTGGGGCTGGCTCTCTGACCTGGCGAACGGTCGCCGTGGCCTGGTGGCC
TGCATCGCGCTGGCGCTGATTATCGCCACGCTCGGTGTGTATCAACATGCCAGTAACGAATATATCTATCTGGCTTCTCTCTTTGCGTTG
GGTTTCCTGGTCTTTGGCCCGCAATTGTTGATTGGTGTGGCTGCTGTTGGCTTTGTACCTAAAAAAGCGATTGGCGCTGCCGATGGTATT
AAAGGCACCTTTGCTTACCTGATTGGTGACAGCTTTGCCAAGTTAGGTCTGGGAATGATTGCCGATGGGACGCCGGTATTCGGCCTTACC
GGCTGGGCAGGCACCTTCGCCGCGCTGGATATCGCCGCGATTGGTTGTATCTGCCTGATGGCGATAGTGGCGGTAATGGAAGAACGCAAA
ATCCGCCGCGAGAAAAAAATTCAGCAGTTGACAGTGGCATAA

Curator Acknowledgements
Curator Description Most Recent Edit