Prevalence of Escherichia coli soxS with mutation conferring antibiotic resistance among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI or IslandViewer for 263 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 |
|---|---|---|---|---|
| Citrobacter amalonaticus | 100% | 0% | 87.5% | 0% |
| Citrobacter freundii | 99.23% | 0% | 57.72% | 0% |
| Citrobacter koseri | 100% | 0% | 46.67% | 0% |
| Citrobacter portucalensis | 100% | 0% | 86% | 0% |
| Citrobacter werkmanii | 100% | 0% | 100% | 0% |
| Citrobacter youngae | 100% | 0% | 100% | 0% |
| Enterobacter cloacae | 0% | 0% | 0.91% | 0% |
| Enterobacter hormaechei | 0% | 0% | 0.24% | 0% |
| Escherichia albertii | 100% | 0% | 97.7% | 0% |
| Escherichia coli | 61.46% | 0.03% | 74.67% | 0% |
| Escherichia fergusonii | 100% | 0% | 44.62% | 0% |
| Escherichia marmotae | 100% | 0% | 69.05% | 0% |
| Klebsiella aerogenes | 97.5% | 0% | 76.73% | 0% |
| Klebsiella oxytoca | 0% | 0.95% | 0% | 0% |
| Klebsiella pneumoniae | 0% | 0% | 0.09% | 0% |
| Salmonella enterica | 94.6% | 0% | 89.22% | 0% |
| Shigella boydii | 92.86% | 0% | 94.62% | 0% |
| Shigella dysenteriae | 90.91% | 0% | 100% | 0% |
| Shigella flexneri | 94.74% | 0% | 83.33% | 0% |
| Shigella sonnei | 100% | 0% | 95.34% | 0% |
Model Type: protein overexpression model
Model Definition: This model detects protein overexpression based on the presence of mutations. The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s).
Bit-score Cut-off (blastP): 200
Legend:
Published Variants:
| PMID: 25921515 | A12S |