vga(E) Staphylococcus cohnii

Accession ARO:3004715
CARD Short NameScoh_vga(E)
Definitionvga(E) gene variant that confers resistance to pleuromutilins, lincosamides and streptogramin A antibiotics in staphylococci.
AMR Gene Familyvga-type ABC-F protein
Drug Classstreptogramin antibiotic, pleuromutilin antibiotic, streptogramin A antibiotic, lincosamide antibiotic
Resistance Mechanismantibiotic target protection
Resistomes with Perfect MatchesStaphylococcus aureuswgs
Resistomes with Sequence VariantsStaphylococcus aureuswgs
Classification11 ontology terms | Show
Parent Term(s)7 ontology terms | Show
+ vga-type ABC-F protein [AMR Gene Family]
+ confers_resistance_to_antibiotic valnemulin [Antibiotic]
+ confers_resistance_to_antibiotic tiamulin [Antibiotic]
+ confers_resistance_to_antibiotic retapamulin [Antibiotic]
+ confers_resistance_to_antibiotic virginiamycin M1 [Antibiotic]
+ confers_resistance_to_antibiotic clindamycin [Antibiotic]
+ confers_resistance_to_antibiotic lincomycin [Antibiotic]
Publications

Li J, et al. 2014. J. Antimicrob. Chemother. 69(4):919-23 Identification of a novel vga(E) gene variant that confers resistance to pleuromutilins, lincosamides and streptogramin A antibiotics in staphylococci of porcine origin. (PMID 24324222)

Resistomes

Prevalence of vga(E) Staphylococcus cohnii among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI or IslandViewer for 413 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 homolog model (view sequences)

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GI
Staphylococcus aureus0%0%0.02%0%
Show Perfect Only


Detection Models

Model Type: protein homolog model

Model Definition: Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.

Bit-score Cut-off (blastP): 1000


>gb|AHB37625.1|-|vga(E) Staphylococcus cohnii [Staphylococcus cohnii]
MLLFEGTSIKKQLHDRVLFDIDLIQVHDNQRIGLVGRNGTGKTSLLKIITGEELPDEGNISPFTSVKLVPQFKESRLEKSGGEITQQYLQ
NAFNGNPGLLLLDEPTTHLDTERIAWLEKKIRNYQGAAVVVSHDRTFLNNVCTDIWEIEKNTLKIFKGNYDEYAKQKEILKKQKQTEFEK
YEREKQKLERAIRQKEERAQRATKKPKNLSSSEARIVGAKTHYANIQKKLRSSAKALETRLEQLDKVDKVKELPEIKMDMLNEENLTNQS
VLRAENIKGEIEERKLWEPFSLYLYGGDKVAIIGKNGSGKTTLLKKIVKQDEGVTIPEKVKIGYFSQHLTILNDEKSIIENVQSTSSQNE
TLIRTVLARMHFWDEDVYKKVGILSGGEKVKLALAKLFLSEVNMLVLDEPTNFLDIAALEALETLMKSYHGTILFVTHDRMLVKNIATKI
IDIKDGKITVFDGSYEAYEEWLENKTKSNNDDQLLLIETKISDVLGRLSLEPSQELEDEFQRLLKEKKELTRGE


>gb|KF540226.1|-|3570-5144|vga(E) Staphylococcus cohnii [Staphylococcus cohnii]
ATGCTATTATTTGAAGGAACATCAATCAAAAAACAATTACATGACAGAGTGCTATTTGATATTGATTTAATACAAGTGCATGATAATCAA
CGTATAGGCTTAGTAGGTAGGAATGGAACAGGAAAAACAAGCCTATTAAAAATTATTACAGGTGAAGAATTACCTGATGAAGGTAATATC
TCTCCTTTTACCTCTGTGAAATTAGTGCCACAATTTAAAGAATCAAGATTGGAGAAAAGTGGTGGCGAAATAACACAGCAATATTTACAG
AACGCATTCAATGGGAATCCAGGCTTACTGCTTTTAGATGAACCGACAACACACTTAGATACGGAAAGAATTGCTTGGCTAGAAAAAAAG
ATAAGAAACTATCAAGGAGCAGCTGTCGTAGTATCTCATGATCGGACATTTTTAAATAATGTATGTACTGACATATGGGAAATTGAAAAA
AATACGTTAAAAATATTTAAAGGAAATTATGATGAATATGCAAAGCAAAAAGAAATACTTAAAAAACAAAAACAAACTGAATTTGAAAAG
TATGAACGTGAGAAACAAAAATTAGAAAGAGCAATACGTCAAAAAGAAGAAAGAGCTCAACGAGCAACAAAAAAACCTAAGAATCTAAGT
TCATCTGAAGCGAGAATAGTGGGTGCTAAAACCCACTACGCCAACATACAGAAAAAGCTGAGAAGTTCGGCAAAAGCTTTAGAAACAAGA
CTGGAACAATTGGATAAGGTTGACAAGGTGAAAGAGCTGCCTGAAATTAAGATGGATATGTTAAATGAAGAAAACTTAACAAACCAATCT
GTATTACGTGCTGAAAATATTAAGGGAGAGATTGAAGAACGTAAGCTCTGGGAACCCTTTAGCTTATATTTATATGGAGGAGATAAAGTT
GCTATCATTGGAAAAAATGGCTCAGGTAAAACAACGTTGCTTAAAAAAATAGTGAAGCAAGATGAAGGAGTGACAATTCCAGAAAAAGTA
AAGATAGGTTACTTCTCTCAACACTTAACCATCCTAAATGATGAGAAATCAATCATAGAAAATGTACAATCGACCTCTAGTCAAAATGAG
ACATTAATAAGAACAGTTTTAGCAAGAATGCATTTTTGGGATGAAGATGTCTATAAAAAGGTAGGCATATTAAGTGGTGGTGAAAAAGTA
AAGCTAGCTTTAGCTAAACTATTTTTAAGTGAGGTGAATATGCTCGTTTTAGATGAGCCGACTAACTTTTTAGACATTGCAGCTTTAGAA
GCGCTAGAAACATTAATGAAAAGTTATCATGGAACGATTCTATTTGTTACTCACGACCGAATGTTAGTAAAAAATATAGCTACAAAAATA
ATTGATATAAAAGATGGTAAGATAACAGTATTCGATGGATCGTACGAAGCATATGAAGAGTGGCTGGAGAATAAAACAAAGTCTAACAAT
GATGACCAACTTTTATTAATTGAAACTAAAATATCTGATGTTCTGGGTAGGTTGAGCTTGGAACCTTCGCAAGAGTTAGAAGATGAATTT
CAAAGATTATTGAAAGAAAAGAAAGAACTGACTAGAGGGGAATAA