Table 2.

Taxa for which genetic elements can be excluded or included.

Organism option	Point mutation screening	Are certain plus genes excluded?	Taxa
Campylobacter	Yes	No	Campylobacter coli and C. jejuni
Enterococcus_faecalis	Yes	No	Enterococcus faecalis
Enterococcus_faecium	Yes	No	Enterococcus faecium
Escherichia	Yes	Yes	Escherichia sp. including Shigella, E. albertii, E. fergusonii
Klebsiella	No	Yes	Klebsiella pneumoniae, K. oxytoca
Salmonella	Yes	Yes	Salmonella sp.
Staphylococcus_aureus	Yes	No	Staphylococcus aureus
Staphylococcus_pseudintermedius	No	Yes	Staphylococcus pseudintermedius
Vibrio_cholerae	No	Yes	Vibrio cholerae

Organism option describes the value used by the  --organism flag. Taxa describes the species referred to by that flag.