| Accession | ARO:3004441 |
| Synonym(s) | tet59 |
| CARD Short Name | tet(59) |
| Definition | Tet(59) is a chromosome-encoded tetracycline efflux pump described from a Chinese pig manure sample. |
| AMR Gene Family | major facilitator superfamily (MFS) antibiotic efflux pump |
| Drug Class | tetracycline antibiotic |
| Resistance Mechanism | antibiotic efflux |
| Efflux Component | efflux pump complex or subunit conferring antibiotic resistance |
| Resistomes with Perfect Matches | Citrobacter portucalensiswgs, Klebsiella aerogeneswgs, Providencia rettgerig+wgs |
| Resistomes with Sequence Variants | Actinobacillus pleuropneumoniaeg, Citrobacter portucalensiswgs, Escherichia coliwgs, Klebsiella aerogeneswgs, Proteus mirabiliswgs, Providencia alcalifacienswgs, Providencia heimbachaeg+wgs, Providencia rettgerig+wgs, Providencia stuartiiwgs, Vibrio alginolyticusg, Vibrio choleraewgs, Vibrio fluvialiswgs, Vibrio harveyiwgs, Vibrio neocaledonicusg, Vibrio owensiig+wgs, Vibrio parahaemolyticusg+wgs, Vibrio vulnificusg+wgs |
| Classification | 7 ontology terms | Show + process or component of antibiotic biology or chemistry + mechanism of antibiotic resistance + determinant of antibiotic resistance + antibiotic molecule + antibiotic efflux [Resistance Mechanism] + efflux pump complex or subunit conferring antibiotic resistance [Efflux Component] + tetracycline antibiotic [Drug Class] |
| Parent Term(s) | 4 ontology terms | Show + confers_resistance_to_antibiotic tetracycline [Antibiotic] + major facilitator superfamily (MFS) antibiotic efflux pump [AMR Gene Family] + confers_resistance_to_antibiotic chlortetracycline [Antibiotic] + confers_resistance_to_antibiotic oxytetracycline [Antibiotic] |
| Publications | Leclercq SO, et al. 2016. Appl. Environ. Microbiol. 82(21):6454-6462 Diversity of the Tetracycline Mobilome within a Chinese Pig Manure Sample. (PMID 27565618) |
Prevalence of tet(59) 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).
| Species | NCBI Chromosome | NCBI Plasmid | NCBI WGS | NCBI GI | GRDI-AMR2 |
|---|---|---|---|---|---|
| Actinobacillus pleuropneumoniae | 2.78% | 0% | 0% | 0% | 0% |
| Citrobacter portucalensis | 0% | 0% | 0.9% | 0% | 0% |
| Escherichia coli | 0% | 0% | 0.01% | 0% | 0% |
| Klebsiella aerogenes | 0% | 0% | 0.28% | 0% | 0% |
| Proteus mirabilis | 0% | 0% | 0.5% | 0% | 0% |
| Providencia alcalifaciens | 0% | 0% | 20.69% | 0% | 0% |
| Providencia heimbachae | 100% | 0% | 100% | 0% | 0% |
| Providencia rettgeri | 91.18% | 0% | 77.07% | 0% | 0% |
| Providencia stuartii | 0% | 0% | 9.09% | 0% | 0% |
| Vibrio alginolyticus | 2.47% | 0% | 0% | 0% | 0% |
| Vibrio cholerae | 0% | 0% | 8.69% | 0% | 0% |
| Vibrio fluvialis | 0% | 0% | 21.33% | 0% | 0% |
| Vibrio harveyi | 0% | 0% | 2% | 0% | 0% |
| Vibrio neocaledonicus | 50% | 0% | 0% | 0% | 0% |
| Vibrio owensii | 16.67% | 0% | 5.26% | 0% | 0% |
| Vibrio parahaemolyticus | 0.65% | 0% | 2.16% | 0% | 0% |
| Vibrio vulnificus | 1.82% | 0% | 1.22% | 0% | 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): 500
Type of Antibiotic Resistance: Intrinsic or chromosomally-encoded
| Curator | Description | Most Recent Edit |
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