Curated organisms

In the following table an 'X' indicates that the AMRFinderPlus curators believe the database has relatively good coverage of phenotypically informative genes or point mutations for that taxon and element type. We strive to make sure AMRFinderPlus with the latest database version can identify most known phenotypically informative genes/point mutations for that organism. If there are important genes or point mutations we're missing please let us know by emailing us at [email protected]. See the Reference Gene Catalog for the complete list of proteins and point mutations, and the Reference HMM Catalog for the HMMs in the latest database release.

Note that for AMRFinderPlus to identify mutational resistance (point mutations) the specific --organism option should be used. See the --organism option documentation for more information on how to use that.

Organism	Acquired resistance	Mutational resistance	Virulence genes	Stress response genes	Notes
Acinetobacter baumannii	X	X		X
Aeromonas hydrophila	X
Aeromonas salmonicida	X
Aeromonas sobria	X
Aeromonas veronii	X
Bacillus cereus	X		X
Bordetella pertussis
Burkholderia cepacia complex	X	X
Burkholderia pseudomallei group	X	X
Campylobacter	X	X		X
Citrobacter freundii	X
Clostridioides difficile	X	X	X
Clostridium botulinum	X
Clostridium perfringens	X		X
Corynebacterium striatum	X
Cronobacter	X
Edwardsiella ictaluri	X
Edwardsiella piscicida	X
Edwardsiella tarda	X
Elizabethkingia anophelis	X
Enterobacter	X			X
Enterococcus faecalis	X	X		X
Enterococcus faecium	X	X		X
Escherichia	X	X	X	X
Flavobacterium psychrophilum	X
Francisella tularemia
Klebsiella	X	X	X
Kluyvera_intermedia	X
Legionella pneumophila	X
Listeria monocytogenes	X			X
Morganella morganii	X
Mycobacterium tuberculosis
Mycoplasma genitalium
Neisseria	X	X		X
Photobacterium damselae	X
Providencia alcalifaciens	X
Pseudomonas aeruginosa	X	X		X
Pseudomonas putida	X
Salmonella	X	X	X	X
Serratia marcescens	X
Shewanella algae	X
Shigella	X	X	X	X
Staphylococcus aureus	X	X	X	X
Staphylococcus pseudintermedius	X	X	X
Streptococcus agalactiae	X	X
Streptococcus iniae	X
Streptococcus pneumoniae	X	X
Streptococcus pyogenes	X	X
Vibrio cholerae	X
Vibrio harveyi	X
Vibrio parahaemolyticus	X
Vibrio vulnificus	X
Yersinia enterocolitica	X		X	X
Yersinia pestis	X		X
Yersinia ruckeri	X		X