Table 2.

Outline of standard follow-up and confirmatory tests at the Infectious Diseases Pathology Laboratory (IDPL), CDC-Atlanta.

Category	Primary testing	Findings that trigger follow-up assay	Follow-up assay
Fungal	H&Ea	Frothy intra-alveolar eosinophilic material	Pneumocystis spp IHCb
	GMSc	Crescentic fungal forms	Pneumocystis spp IHC
	H&E and H&E	Fungal hyphae and yeast	Fungal IHC assaysd; Broad-range fungal PCRe,f
Viral	H&E and PCR	Phase I viral panel negative and interstitial pneumonitis	Additional PCRg; Mycoplasma spp; Rhinovirus; Human metapneumovirus
	GMS and IHC	Pneumocystis organisms	CMVh IHC
	H&E	Compatible viral inclusions	CMV IHC
	H&E, GMS, IHC and clinical history	Concomitant diseases associated with immunosuppression	CMV IHC
Bacterial	H&E, LTi, and GMS	Gram-negative bacteria	Klebsiella /Enterobacteriaceae IHCj (and confirmatory PCR)
	H&E and LT/GMS	Acute inflammation without bacteria on special stains	Mycobacterium spp IHC; Streptococcus spp IHC; Staphylococcus spp IHC; Group B Streptococcus spp IHC; Group A Streptococcus spp IHC; Warthin starry special stain
	H&E, LT/GMS, and IHC	Acute inflammation without bacteria on special stains or IHC	Pan eubacterial PCR
	LT	Gram-positive cocci	Streptococcus spp IHC; Group A Streptococcus spp IHC
	LT	Small Gram-negative coccobacilli	Haemophilus influenzae IHC

^aH&E: Hematoxylin & Eosin.

^bIHC: immunohistochemistry.

^cGMS: Grocott's methenamine silver.

^dFungal IHC panel consists of one or more of the following based on H&E and GMS morphology and Gram stain characteristics when applicable: Polyfungal IHC, mucormycete fungus IHC, Aspergillus spp IHC, and Candida spp IHC.

^eBroad-range fungal PCR performed by colleagues at the Mycotics Diseases Branch.

^fPCR: polymerase chain reaction.

^gAdditional pneumonia-associated PCR assays based on H&E, clinical history, and TAC results.

^hCMV: cytomegalovirus.

ⁱLT: Lillie-Twort Gram.

^jPolyclonal IHC known to cross-react with other Enterobacteriaceae bacteria.