Etiology | Availability* | When inclusion of NAT is indicated | Preferred testing method(s)¶ |
Bacteria | |||
Common pathogens (eg, Streptococcus pneumoniae, Haemophilus influenzae) | YesΔ | Gram stain positive, culture negative; prior antibacterial therapy | Gram stain and culture |
Fastidious organisms (Mycoplasma spp, Tropheryma spp, Brucella spp) | Yes | When clinically suspected | Serology, NAT +/– culture |
Mycobacterium tuberculosis◊ | Yes | When clinically suspected | AFB stain, culture, and NAT |
Prior antibiotic therapy§ | YesΔ | Rarely | Culture prior to antibacterial therapy |
Viruses | |||
Adenoviruses | Yes | Rarely | Testing of alternative sites (eg, respiratory) +/– CSF |
Arboviruses | Limited | When clinically suspected | Serology and NAT |
Cytomegalovirus (CMV) | YesΔ | When clinically suspected | NAT, preferably quantitative |
Epstein Barr Virus (EBV) | Yes | When clinically suspected | Serology and NAT, preferably quantitative |
Enteroviruses | WidespreadΔ | When clinically suspected | NAT |
Human herpesvirus 6 (HHV-6) | YesΔ | When clinically suspected | NAT, preferably quantitative¥ |
Herpes simplex virus (HSV) | WidespreadΔ | When clinically suspected | NAT |
Influenza | Yes | Rarely | Testing of alternative sites (eg, respiratory) +/– CSF |
Lymphocytic choriomeningitis virus | Limited | Rarely | Serology |
Mumps | Limited | Rarely | Viral culture, serology, and NAT |
Parechoviruses‡ | YesΔ | Primarily in young children (<5 years old) | NAT |
Varicella-zoster virus | YesΔ | When clinically suspected | NAT (plus CSF serology in select cases)† |
West Nile virus** | Yes | Rarely (unless immunodeficient) | Serology |
Rickettsia¶¶ | Limited | Occasionally | Serology |
Spirochetes | |||
Leptospira | Limited | Rarely | Serology |
Borrelia burgdorferi (the agent of Lyme disease) | Yes | Yes | Serology |
Treponema pallidum (syphilis) | Limited | No | Serology, CSF VDRL |
Fungal | |||
Cryptococcus spp | YesΔ | No | Antigen detection, culture |
Other fungi (eg, Coccidioides spp) | Limited | Rarely | Culture, serology |
Parasites | Limited | Rarely | Serology, histologic exam, NAT for select pathogens |
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