| Accession | ARO:3005059 |
| CARD Short Name | LptD |
| Definition | LptD is involved in LPS transport in a ABC Transporter efflux system. It confers resistance to rifamycin, aminocoumarin, and peptide antibiotics. |
| AMR Gene Family | ATP-binding cassette (ABC) antibiotic efflux pump |
| Drug Class | peptide antibiotic, aminocoumarin antibiotic, carbapenem, rifamycin antibiotic |
| Resistance Mechanism | antibiotic efflux |
| Efflux Component | efflux pump complex or subunit conferring antibiotic resistance |
| Resistomes with Perfect Matches | Klebsiella pneumoniaeg+wgs |
| Resistomes with Sequence Variants | Klebsiella aerogenesg+wgs, Klebsiella huaxiensisg+wgs, Klebsiella michiganensisg+wgs, Klebsiella oxytocag+wgs, Klebsiella pneumoniaeg+wgs, Klebsiella quasipneumoniaeg+wgs, Raoultella planticolag+wgs |
| Classification | 14 ontology terms | Show + process or component of antibiotic biology or chemistry + antibiotic molecule + peptide antibiotic [Drug Class] + mechanism of antibiotic resistance + lipopeptide antibiotic + antibiotic efflux [Resistance Mechanism] + beta-lactam antibiotic + determinant of antibiotic resistance + polymyxin antibiotic + aminocoumarin antibiotic [Drug Class] + carbapenem [Drug Class] + efflux pump complex or subunit conferring antibiotic resistance [Efflux Component] + antibiotic mixture + rifamycin antibiotic [Drug Class] |
| Parent Term(s) | 8 ontology terms | Show + ATP-binding cassette (ABC) antibiotic efflux pump [AMR Gene Family] + confers_resistance_to_drug_class rifamycin antibiotic [Drug Class] + confers_resistance_to_drug_class peptide antibiotic [Drug Class] + confers_resistance_to_drug_class aminocoumarin antibiotic [Drug Class] + confers_resistance_to_antibiotic novobiocin [Antibiotic] + confers_resistance_to_antibiotic imipenem [Antibiotic] + confers_resistance_to_antibiotic rifampin [Antibiotic] + confers_resistance_to_antibiotic polymyxin B [Antibiotic] |
| Publications | Snitkin ES, et al. 2012. Sci Transl Med 4(148):148ra116 Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. (PMID 22914622) Huang L, et al. 2019. Front Microbiol 10:1443 Role of LptD in Resistance to Glutaraldehyde and Pathogenicity in Riemerella anatipestifer. (PMID 31281307) |
Prevalence of LptD 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 |
|---|---|---|---|---|
| Klebsiella aerogenes | 90% | 0% | 70.06% | 0% |
| Klebsiella huaxiensis | 100% | 0% | 66.67% | 0% |
| Klebsiella michiganensis | 100% | 0% | 69.15% | 0% |
| Klebsiella oxytoca | 94.87% | 0% | 73.11% | 0% |
| Klebsiella pneumoniae | 99.53% | 0% | 57.33% | 0% |
| Klebsiella quasipneumoniae | 100% | 0% | 73.82% | 0% |
| Raoultella planticola | 100% | 0% | 94.87% | 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): 1500