Table 1.

Summary of the 47 infectious agents of interest

Agent type	Species	Abbreviation
Bacterium	Aeromonas hydrophila	ae_hyd
Bacterium	Aeromonas salmonicida	ae_sal
Virus	Atlantic salmon paramyxovirus	aspv
Bacterium	Candidatus Branchiomonas cysticola	c_b_cys
Parasite	Ceratomyxa shasta	ce_sha
Parasite	Cryptobia salmositica	cr_sal
Parasite	Dermocystidium salmonis	de_sal
Parasite	Facilispora margolisi	fa_mar
Bacterium	Flavobacterium psychrophilum	fl_psy
Virus	Flavivirus salmonis	fl_sal
Parasite	Gyrodactylus salaris	gy_sal
Parasite	Ichthyophonus hoferi	ic_hof
Parasite	Ichthyophthirius multifiliis	ic_mul
Virus	Infectious hematopoietic necrosis virus	ihnv
Virus	Infectious salmon anemia virus	isav8
Parasite	Kudoa thyrsites	ku_thy
Parasite	Loma Salmonae	lo_sal
Bacterium	Moritella viscosa	mo_vis
Parasite	Myxobolus articus	my_arc
Parasite	Myxobolus cerebralis	my_cer
Parasite	Myxobolus insidiosus	my_ins
Fluke	Nanophyetus salmincola	na_sal
Parasite	Neoparamoeba perurans	ne_per
Parasite	Nucleospora salmonis	nu_sal
Virus	Salmonid herpesvirus/Oncorhynchus masou herpes virus	omv
Parasite	Parvicapsula kabatai	pa_kab
Parasite	Parvicapsula minibicornis	pa_min
Parasite	Parvicapsula pseudobranchicola	pa_pse
Parasite	Paranucleospora theridion (syn. Desmozoon lepeophtherii)	pa_ther
Bacterium	Piscichlamydia salmonis	pch_sal
Bacterium	Piscirickettsia salmonis	pisck_sal
Virus	Piscine myocarditis virus	pmcv1
Virus	Piscine reovirus	prv
Bacterium	Renibacterium salmoninarum	re_sal
Bacterium	Rickettsia-like organism	rlo
Virus	Salmon alphavirus 1, 2 and 3	sav
Bacterium	Gill chlamydia	sch
Virus	Infectious salmon anemia virus	snow7
Parasite	Sphaerothecum destructuens	sp_des
Parasite	Spironucleus salmonicida	sp_sal
Parasite	Tetracapsuloides bryosalmonae	te_bry
Bacterium	Tenacibaculum maritimum	te_mar
Virus	Viral erythrocytic necrosis virus	ven
Virus	Viral encephalopathy and retinopathy virus	ver
Bacterium	Vibrio anguillarum	vi_ang
Bacterium	Vibrio salmonicida	vi_sal
Bacterium	Yersinia ruckeri	ye_ruc