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Microorganism	Microscopy	Culture	Nucleic Acid Amplification Test (NAAT)	Antigen Detection	Antibody Detection
Bacteria
Bacillus anthracis	✓	✓	✓
Bartonella species	✓		✓
Bordetella pertussis		✓	✓		✓
Borrelia species		✓	✓		✓
Brucella species	✓	✓	✓
Clostridium botulinum	✓	✓		✓	✓
Clostridioides difficile		✓	✓	✓
Clostridium tetani	✓	✓
Corynebacterium diphtheriae		✓
Erysipelothrix species	✓	✓
Francisella tularensis		✓			✓
Haemophilus ducreyi	✓	✓		✓
Helicobacter pylori	✓	✓		✓	✓
Kingella species	✓	✓	✓
Klebsiella species	✓		✓
Legionella species		✓	✓	✓	✓
Listeria species	✓	✓	✓
Mycoplasma species			✓		✓
Neisseria species	✓	✓	✓
Nocardia	✓	✓	✓
Rhodococcus equus	✓	✓
Streptococcus species	✓	✓	✓	✓	✓
Treponema pallidum	✓		✓		X
Tropheryma whipplei	✓		✓
Vibrio species		✓	✓
Yersinia pestis	✓	✓	✓		✓
Mycobacteria
Nontuberculous	✓	✓
Tuberculosis and ulcerans	✓	✓	✓
Intracellular Organisms
Anaplasma species	✓		✓		✓
Chlamydia species			✓		✓
Coxiella species			✓		✓
Leishmania species	✓	✓	✓		✓
Leptospira species		✓	✓		✓
Borrelia species	✓	✓	✓		✓
Fungi
Aspergillus species	✓	✓	✓	✓
Blastomyces species	✓	✓	✓	✓	✓
Candida species	✓	✓	✓
Coccidiodes species	✓	✓	✓	✓	✓
Cryptococcus neoformans	✓	✓	✓	✓
Dermatophytes	✓	✓
Histoplasma capsulatum	✓	✓	✓	✓	✓
Malassezia species	✓	✓
Mucorales species	✓	✓	✓
Pneumocystis jirovecii	✓			✓	✓
Sporothrix species	✓			✓	✓
Viruses
Adenovirus		✓	✓
BK virus	✓		✓
COVID-19 (SARS-CoV2)			✓		✓
Cytomegalovirus (CMV)	✓	✓	✓		✓
Enteroviruses		✓	✓		✓
Epstein-Barr Virus (EBV)			✓		✓
Hepatitis A, B, C, D and E			✓		✓
Herpes simplex virus	✓	✓	✓		✓
Herpes virus 6			✓		✓
HIV			✓	✓	✓
Human papillomavirus (HPV)	✓		✓
Influenza	✓		✓	✓
JC virus			✓		✓
LaCrosse virus					✓
Lymphocytic choriomeningitis virus (LCMV)			✓		✓
Measles			✓		✓
Mumps			✓		✓
Norovirus			✓	✓
Parainfluenza		✓	✓
Parvovirus B19		✓	✓		✓
Powassan virus			✓		✓
Rabies	✓		✓	✓	✓
Respiratory syncytial virus (RSV)		✓	✓	✓
Rubella					✓
St Louis encephalitis virus			✓
Tickborne encephalitis virus					✓
Varicella zoster	✓	✓	✓		✓
West Nile virus			✓		✓
Zika virus			✓		✓
Protozoa and Parasites
Babesia	✓		✓		✓
Cryptosporidium	✓		✓	✓
Cyclospora	✓		✓
Entamoeba	✓		✓	✓	✓
Enterobius vermicularis	✓
Giardia	✓		✓
Intestinal nematodes	✓			✓	✓
Plasmodium species	✓		✓	✓
Scabies	✓
Taenia solium	✓				✓
Toxocara species	✓				✓
Trichinella spiralis	✓				✓
Trypanosoma species	✓	✓	✓	✓	✓
Adapted from Bennett JE, Dolin R, Blaser MJ: Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases, 9th Edition. Elsevier, 2020.