| Accession | ARO:3002956 |
| Synonym(s) | vanYB vanY-B |
| CARD Short Name | vanY_in_vanB_cl |
| Definition | Also known as vanYB, is a vanY variant found in the vanB gene cluster. |
| AMR Gene Family | glycopeptide resistance gene cluster, vanY |
| Drug Class | glycopeptide antibiotic |
| Resistance Mechanism | antibiotic target alteration |
| Resistomes with Perfect Matches | Enterococcus faecalisg+wgs+gi, Enterococcus faeciumwgs |
| Resistomes with Sequence Variants | Achromobacter xylosoxidansg+wgs, Alloiococcus otitiswgs, Anaerostipes hadrusg+wgs, Bacillus amyloliquefaciensg+wgs, Bacillus anthracisg+wgs, Bacillus cereusg+wgs, Bacillus halotoleransg, Bacillus subtilisg+wgs, Bacillus tequilensisg+wgs, Bacillus thuringiensisg+p+wgs, Bacillus velezensisg+p+wgs, Bifidobacterium bifidumg+wgs, Borrelia crociduraewgs, Borrelia hermsiig, Borrelia miyamotoig, Brevibacillus brevisg+wgs, Burkholderia multivoranswgs, Clostridium botulinumg+wgs, Clostridium butyricumwgs, Clostridium perfringensg+wgs, Clostridium sporogenesg+wgs, Dysosmobacter welbionisg+wgs, Enterobacter roggenkampiiwgs, Enterocloster clostridioformiswgs, Enterococcus aviumg+wgs, Enterococcus faecalisg+wgs+gi, Enterococcus faeciumg+p+wgs+gi, Enterococcus gilvusg+wgs, Enterococcus hiraeg+wgs, Enterococcus pallenswgs, Erysipelatoclostridium ramosumg+wgs, Erysipelothrix rhusiopathiaeg+wgs, Eubacterium limosumg+wgs, Eubacterium maltosivoransg+wgs, Faecalibacterium prausnitziig+wgs, Francisella philomiragiag+wgs, Francisella tularensisg+wgs, Gemella haemolysansg+wgs, Gemella sanguinisg+wgs, Jeotgalibaca porcig, Kocuria palustrisg, Lactococcus garvieaeg+wgs, Listeria innocuag+wgs, Listeria monocytogeneswgs, Macrococcus canisg, Moraxella catarrhaliswgs, Mycolicibacterium fortuitumg+wgs, Mycolicibacterium septicumg+wgs, Nocardia asiaticawgs, Nocardia farcinicag+wgs, Nocardia terpenicag, Paeniclostridium sordelliig+wgs, Parabacteroides distasoniswgs, Pseudomonas aeruginosawgs, Pseudomonas putidawgs, Rhodococcus rhodochrouswgs, Roseburia hominiswgs, Rothia mucilaginosag+wgs, Ruthenibacterium lactatiformansg+wgs, Staphylococcus arlettaewgs, Staphylococcus aureuswgs, Staphylococcus capitiswgs, Staphylococcus epidermidisg+wgs, Staphylococcus haemolyticusg+wgs, Staphylococcus hominisg+wgs, Staphylococcus saprophyticusg+wgs, Staphylococcus warneriwgs, Streptococcus agalactiaeg+wgs, Streptococcus anginosusg+wgs, Streptococcus canisg+wgs, Streptococcus constellatusg+wgs, Streptococcus cristatuswgs, Streptococcus dysgalactiaeg+wgs, Streptococcus equig+wgs, Streptococcus gallolyticusg+wgs, Streptococcus gordoniig+wgs, Streptococcus iniaeg+wgs, Streptococcus intermediuswgs, Streptococcus lutetiensisg+wgs, Streptococcus pasteurianusg+wgs, Streptococcus pneumoniaeg+wgs, Streptococcus porcinusg+wgs, Streptococcus pseudoporcinusg+wgs, Streptococcus pyogenesg+wgs, Streptococcus sanguinisg+wgs, Streptococcus suisg+wgs, Streptococcus uberisg+wgs, Vibrio choleraewgs |
| Classification | 12 ontology terms | Show + process or component of antibiotic biology or chemistry + mechanism of antibiotic resistance + antibiotic target alteration [Resistance Mechanism] + restructuring of bacterial cell wall conferring antibiotic resistance + determinant of antibiotic resistance + antibiotic molecule + antibiotic resistance gene cluster, cassette, or operon + glycopeptide antibiotic [Drug Class] + protein(s) conferring antibiotic resistance via molecular bypass + gene(s) or protein(s) associated with a glycopeptide resistance cluster + glycopeptide resistance gene cluster [AMR Gene Family] + vancomycin [Antibiotic] |
| Parent Term(s) | 2 ontology terms | Show |
| Publications | Courvalin P. 2005. Clin Infect Dis 42(SUPPL 1): S25-S34. Vancomycin resistance in gram-positive cocci. (PMID 16323116) Evers S and Courvalin P. 1996. J Bacteriol 178(5): 1302-1309. Regulation of VanB-type vancomycin resistance gene expression by the VanS(B)-VanR (B) two-component regulatory system in Enterococcus faecalis V583. (PMID 8631706) |
Prevalence of vanY gene in vanB cluster 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).
| Species | NCBI Chromosome | NCBI Plasmid | NCBI WGS | NCBI GI |
|---|---|---|---|---|
| Achromobacter xylosoxidans | 8.7% | 0% | 2.29% | 0% |
| Alloiococcus otitis | 0% | 0% | 100% | 0% |
| Anaerostipes hadrus | 33.33% | 0% | 20.69% | 0% |
| Bacillus amyloliquefaciens | 100% | 0% | 82.02% | 0% |
| Bacillus anthracis | 100% | 0% | 78.07% | 0% |
| Bacillus cereus | 100% | 0% | 85.54% | 0% |
| Bacillus halotolerans | 9.09% | 0% | 0% | 0% |
| Bacillus subtilis | 3.23% | 0% | 0.58% | 0% |
| Bacillus tequilensis | 100% | 0% | 66.67% | 0% |
| Bacillus thuringiensis | 100% | 0.72% | 90.75% | 0% |
| Bacillus velezensis | 100% | 0.9% | 83.15% | 0% |
| Bifidobacterium bifidum | 100% | 0% | 63.18% | 0% |
| Borrelia crocidurae | 0% | 0% | 100% | 0% |
| Borrelia hermsii | 100% | 0% | 0% | 0% |
| Borrelia miyamotoi | 100% | 0% | 0% | 0% |
| Brevibacillus brevis | 100% | 0% | 100% | 0% |
| Burkholderia multivorans | 0% | 0% | 0.24% | 0% |
| Clostridium botulinum | 83.58% | 0% | 39.95% | 0% |
| Clostridium butyricum | 0% | 0% | 3.92% | 0% |
| Clostridium perfringens | 97.5% | 0% | 46.7% | 0% |
| Clostridium sporogenes | 100% | 0% | 91.45% | 0% |
| Dysosmobacter welbionis | 100% | 0% | 100% | 0% |
| Enterobacter roggenkampii | 0% | 0% | 0.36% | 0% |
| Enterocloster clostridioformis | 0% | 0% | 2.33% | 0% |
| Enterococcus avium | 100% | 0% | 78.95% | 0% |
| Enterococcus faecalis | 29.55% | 0% | 20.97% | 16.67% |
| Enterococcus faecium | 98.73% | 0.52% | 57.01% | 15.69% |
| Enterococcus gilvus | 100% | 0% | 100% | 0% |
| Enterococcus hirae | 100% | 0% | 77.31% | 0% |
| Enterococcus pallens | 0% | 0% | 100% | 0% |
| Erysipelatoclostridium ramosum | 100% | 0% | 51.16% | 0% |
| Erysipelothrix rhusiopathiae | 100% | 0% | 80% | 0% |
| Escherichia coli | 0% | 0% | 0% | 0% |
| Eubacterium limosum | 100% | 0% | 100% | 0% |
| Eubacterium maltosivorans | 100% | 0% | 100% | 0% |
| Faecalibacterium prausnitzii | 100% | 0% | 79.61% | 0% |
| Francisella philomiragia | 100% | 0% | 20.45% | 0% |
| Francisella tularensis | 100% | 0% | 67.73% | 0% |
| Gemella haemolysans | 100% | 0% | 75% | 0% |
| Gemella sanguinis | 100% | 0% | 83.33% | 0% |
| Jeotgalibaca porci | 100% | 0% | 0% | 0% |
| Kocuria palustris | 100% | 0% | 0% | 0% |
| Lactococcus garvieae | 100% | 0% | 77.78% | 0% |
| Listeria innocua | 88.24% | 0% | 37.59% | 0% |
| Listeria monocytogenes | 0% | 0% | 0.24% | 0% |
| Macrococcus canis | 42.86% | 0% | 0% | 0% |
| Moraxella catarrhalis | 0% | 0% | 17.62% | 0% |
| Mycolicibacterium fortuitum | 100% | 0% | 93.1% | 0% |
| Mycolicibacterium septicum | 100% | 0% | 100% | 0% |
| Nocardia asiatica | 0% | 0% | 75% | 0% |
| Nocardia farcinica | 100% | 0% | 29.31% | 0% |
| Nocardia terpenica | 50% | 0% | 0% | 0% |
| Paeniclostridium sordellii | 50% | 0% | 94.92% | 0% |
| Parabacteroides distasonis | 0% | 0% | 0.47% | 0% |
| Pseudomonas aeruginosa | 0% | 0% | 0.01% | 0% |
| Pseudomonas putida | 0% | 0% | 0.53% | 0% |
| Rhodococcus rhodochrous | 0% | 0% | 11.11% | 0% |
| Roseburia hominis | 0% | 0% | 33.33% | 0% |
| Rothia mucilaginosa | 20% | 0% | 21.05% | 0% |
| Ruthenibacterium lactatiformans | 100% | 0% | 76.67% | 0% |
| Staphylococcus arlettae | 0% | 0% | 7.5% | 0% |
| Staphylococcus aureus | 0% | 0% | 0.05% | 0% |
| Staphylococcus capitis | 0% | 0% | 8.23% | 0% |
| Staphylococcus epidermidis | 0.65% | 0% | 4.85% | 0% |
| Staphylococcus haemolyticus | 31.03% | 0% | 12.75% | 0% |
| Staphylococcus hominis | 6.25% | 0% | 4.39% | 0% |
| Staphylococcus saprophyticus | 23.53% | 0% | 11.19% | 0% |
| Staphylococcus warneri | 0% | 0% | 3.28% | 0% |
| Streptococcus agalactiae | 97.2% | 0% | 77.84% | 0% |
| Streptococcus anginosus | 76.47% | 0% | 36.26% | 0% |
| Streptococcus canis | 100% | 0% | 100% | 0% |
| Streptococcus constellatus | 100% | 0% | 81.82% | 0% |
| Streptococcus cristatus | 0% | 0% | 2.86% | 0% |
| Streptococcus dysgalactiae | 98% | 0% | 57.94% | 0% |
| Streptococcus equi | 100% | 0% | 75.23% | 0% |
| Streptococcus gallolyticus | 100% | 0% | 61.36% | 0% |
| Streptococcus gordonii | 7.14% | 0% | 8.97% | 0% |
| Streptococcus iniae | 100% | 0% | 98.84% | 0% |
| Streptococcus intermedius | 0% | 0% | 34.09% | 0% |
| Streptococcus lutetiensis | 100% | 0% | 44.9% | 0% |
| Streptococcus pasteurianus | 100% | 0% | 80% | 0% |
| Streptococcus pneumoniae | 24.27% | 0% | 27.35% | 0% |
| Streptococcus porcinus | 100% | 0% | 100% | 0% |
| Streptococcus pseudoporcinus | 100% | 0% | 100% | 0% |
| Streptococcus pyogenes | 100% | 0% | 21.2% | 0% |
| Streptococcus sanguinis | 57.14% | 0% | 34.02% | 0% |
| Streptococcus suis | 88% | 0% | 72.09% | 0% |
| Streptococcus uberis | 75% | 0% | 41.96% | 0% |
| Vibrio cholerae | 0% | 0% | 0.06% | 0% |
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): 50