Prevalence of oqxA among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI for 82 important pathogens (see methodological details and complete list of analyzed pathogens). Values reflect percentage of genomes, plasmids, 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 |
|---|---|---|---|
| Acinetobacter baumannii | 0% | 0% | 0.11% |
| Citrobacter amalonaticus | 66.67% | 0% | 77.78% |
| Citrobacter freundii | 0% | 0% | 0.78% |
| Enterobacter asburiae | 80% | 0% | 96.88% |
| Enterobacter cloacae | 96.67% | 0% | 90.74% |
| Enterobacter hormaechei | 91.89% | 0.9% | 91.44% |
| Enterobacter kobei | 100% | 0% | 95.31% |
| Enterococcus faecium | 0% | 0% | 0% |
| Escherichia coli | 0% | 0.48% | 1.16% |
| Klebsiella oxytoca | 100% | 0% | 91.59% |
| Klebsiella pneumoniae | 0% | 0% | 0% |
| Pseudomonas aeruginosa | 0% | 0% | 0% |
| Salmonella enterica | 0% | 0.7% | 0.18% |
| Shigella flexneri | 0% | 0% | 0.26% |
| Shigella sonnei | 0% | 0% | 0.08% |
| Vibrio parahaemolyticus | 0% | 0% | 0.17% |
Model Type: protein homolog model
Model Definition: The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.
Bit-score Cut-off (blastP): 670