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, the Reference HMM Catalog for the HMMs in the latest database release, and the Reference Gene Hierarchy for the naming hierarchy which includes the relationship between HMMs and gene sequences.

Note that for AMRFinderPlus to identify mutational resistance (point mutations) the specific --organism option should be used. The organism option is only used where we have organism specific curation, 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	X
Burkholderia mallei	X	X
Burkholderia pseudomallei group	X	X	X
Campylobacter	X	X		X
Citrobacter freundii	X	X
Clostridioides difficile	X	X	X
Clostridium botulinum	X		X
Clostridium perfringens	X		X
Corynebacterium diphtheriae	X	X	X
Corynebacterium striatum	X
Cronobacter	X
Edwardsiella ictaluri	X
Edwardsiella piscicida	X
Edwardsiella tarda	X
Elizabethkingia anophelis	X
Enterobacter asburiae	X	X
Enterobacter cloacae	X	X		X
Enterococcus faecalis	X	X		X
Enterococcus faecium	X	X		X
Escherichia	X	X	X	X
Flavobacterium psychrophilum	X
Francisella tularemia
Haemophilus influenzae	X	X
Klebsiella aerogenes	X	X
Klebsiella oxytoca	X	X	X
Klebsiella penumoniae	X	X	X
Kluyvera intermedia	X
Legionella pneumophila	X
Listeria monocytogenes	X			X
Morganella morganii	X
Mycobacterium tuberculosis
Mycoplasma genitalium
Neisseria meningitidis	X	X		X
Neisseria gonorrhoeae	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	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	X
Vibrio harveyi	X
Vibrio parahaemolyticus	X	X
Vibrio vulnificus	X	X
Yersinia enterocolitica	X		X	X
Yersinia pestis	X		X
Yersinia ruckeri	X		X