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taxa curation
Arjun Prasad edited this page Jun 7, 2022
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| Organism | Acquired resistance | Mutational resistance | Virulence genes | Stress response genes |
|---|---|---|---|---|
| Acinetobacter baumannii | Yes | Yes | Yes | |
| Aeromonas hydrophila | Yes | |||
| Aeromonas salmonicida | Yes | |||
| Aeromonas sobria | Yes | |||
| Aeromonas veronii | Yes | |||
| Bacillus cereus | Yes | Yes | ||
| Bordetella pertussis | ||||
| Burkholderia sp. | Yes | |||
| Campylobacter | Yes | Yes | Yes | |
| Citrobacter freundii | Yes | Yes | ||
| Clostridioides difficile | Yes | Yes | Yes | |
| Clostridium botulinum | Yes | |||
| Clostridium perfringens | Yes | Yes | ||
| Corynebacterium striatum | Yes | |||
| Cronobacter | Yes | |||
| Edwardsiella ictaluri | Yes | |||
| Edwardsiella piscicida | Yes | |||
| Edwardsiella tarda | Yes | |||
| Elizabethkingia anophelis | Yes | |||
| Enterobacter | Yes | Yes | Yes | |
| Enterococcus faecalis | Yes | Yes | Yes | |
| Enterococcus faecium | Yes | Yes | Yes | |
| Escherichia | Yes | Yes | Yes | Yes |
| Flavobacterium psychrophilum | Yes | |||
| Francisella tularemia | ||||
| Klebsiella | Yes | Yes | Yes | |
| Kluyvera_intermedia | Yes | |||
| Legionella pneumophila | Yes | |||
| Listeria monocytogenes | Yes | Yes | ||
| Morganella morganii | Yes | |||
| Mycobacterium tuberculosis | ||||
| Mycoplasma genitalium | ||||
| Neisseria | Yes | Yes | Yes | |
| Photobacterium damselae | Yes | |||
| Providencia alcalifaciens | Yes | |||
| Pseudomonas aeruginosa | Yes | Yes | Yes | Yes |
| Pseudomonas putida | Yes | |||
| Salmonella | Yes | Yes | Yes | Yes |
| Serratia marcescens | Yes | |||
| Shewanella algae | Yes | |||
| Shigella | Yes | Yes | Yes | Yes |
| Staphylococcus aureus | Yes | Yes | Yes | Yes |
| Staphylococcus pseudintermedius | Yes | Yes | Yes | |
| Streptococcus agalactiae | Yes | Yes | ||
| Streptococcus iniae | Yes | |||
| Streptococcus pneumoniae | Yes | Yes | ||
| Streptococcus pyogenes | Yes | Yes | ||
| Vibrio cholerae | Yes | |||
| Vibrio harveyi | Yes | |||
| Vibrio parahaemolyticus | Yes | |||
| Vibrio vulnificus | Yes | |||
| Yersinia enterocolitica | Yes | Yes | Yes | |
| Yersinia pestis | Yes | Yes | ||
| Yersinia ruckeri | Yes | Yes |
- New in AMRFinderPlus
- Documentation for AMRFinder v1 (Depricated)
- Overview
- Install with bioconda (recommended)
- Docker Image
- Install with binary
- Compile from source
- Test your installation
- Usage (syntax/options)
- --organism option
- Examples
- Input file formats
- Output format
- Common errors
- Known issues
- Tips and tricks
- Database updates
- Software upgrades
- Genotypes vs. Phenotypes
- Scope: plus vs. core
- AMRFinderPlus "Method" column
- Element type and Subtype
- Class and Subclass
- Point mutation nomenclature
- StxTyper output