Diagnostic Pathology: Infectious Diseases

SECTION 1: OVERVIEW

4 Standard Methods for Infectious Diseases
Zoe Freeman Weiss, MD, Nicole Pecora, MD, PhD, and Shira Winters, MD

10 Emerging Techniques
Jessica Crothers, MD

12 Biosafety Considerations
Jessica Crothers, MD

16 Pitfalls and Artifacts
Jessica Crothers, MD, Alvaro C. Laga, MD, MMSc, and Isaac H. Solomon, MD, PhD

SECTION 2: VIRAL INFECTIONS
DNA VIRUSES

22 Herpes Simplex Virus 1 and 2 (HSV-1, HSV-2) Infections
Isaac H. Solomon, MD, PhD, Leigh Compton, MD, and Dan Milner, MD, MSc(Epi), MBA

28 Varicella-Zoster Virus (HHV-3) Infections
Isaac H. Solomon, MD, PhD, Eleanor Russell-Goldman, MD, PhD, and Dan Milner, MD, MSc(Epi), MBA

32 Epstein-Barr Virus (HHV-4) Infection
Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA

38 Cytomegalovirus (HHV-5) Infections
Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA

44 Human Herpesvirus 6 and 7 (HHV-6, HHV-7) Infections
Isaac H. Solomon, MD, PhD

46 Kaposi Sarcoma-Associated Herpesvirus (HHV-8) Infection
Isaac H. Solomon, MD, PhD, Leigh Compton, MD, and Dan Milner, MD, MSc(Epi), MBA

52 Herpes B Virus Infection
Isaac H. Solomon, MD, PhD

54 Adenovirus Infection
Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA

58 Hepatitis B and D Virus Infections
Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA

62 Parvovirus B19 Infection
Isaac H. Solomon, MD, PhD, Leigh Compton, MD, and Dan Milner, MD, MSc(Epi), MBA

66 JC Virus, BK Virus, and Other Polyomavirus Infections
Isaac H. Solomon, MD, PhD

72 Human Papillomavirus Infection
Isaac H. Solomon, MD, PhD, T. Rinda Soong, MD, PhD, MPH, and Dan Milner, MD, MSc(Epi), MBA

78 Molluscum Contagiosum
Isaac H. Solomon, MD, PhD

80 Smallpox, Mpox, and Other Pox Virus Infections
Alvaro C. Laga, MD, MMSc, Dan Milner, MD, MSc(Epi), MBA, and Isaac H. Solomon, MD, PhD

RNA VIRUSES

86 Arbovirus Infections
Isaac H. Solomon, MD, PhD

92 Zika Virus Infection
Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA

96 Ebola, Marburg, and Other Hemorrhagic Fever Virus Infections
Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA

102 Enterovirus Infections
Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi),MBA

104 Poliovirus Infection
Jessica Crothers, MD and Isaac H. Solomon, MD, PhD

106 Rabies Virus Infection
Isaac H. Solomon, MD, PhD

108 Lymphocytic Choriomeningitis Virus Infection
Isaac H. Solomon, MD, PhD

110 Measles Virus Infection
Isaac H. Solomon, MD, PhD

112 Mumps Virus Infection
Isaac H. Solomon, MD, PhD

114 Rubella Virus Infection
Isaac H. Solomon, MD, PhD

116 Human Immunodeficiency Virus Infection
Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA

120 Human T-Lymphotropic Virus Type I Infection
Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA

122 Influenza Virus Infections
Isaac H. Solomon, MD, PhD

126 Parainfluenza Virus Infections
Isaac H. Solomon, MD, PhD

128 Coronavirus Disease 2019 (COVID-19)
Isaac H. Solomon, MD, PhD

134 Severe Acute Respiratory Syndrome (SARS), Middle East Respiratory Syndrome (MERS), and Other Coronavirus Infections
Isaac H. Solomon, MD, PhD

136 Respiratory Syncytial Virus Infection
Isaac H. Solomon, MD, PhD and Eleanor Russell-Goldman,MD, PhD

138 Rhinoviruses, Human Metapneumovirus, and Other Respiratory Virus Infections
Isaac H. Solomon, MD, PhD

140 Rotavirus, Norovirus, and Astrovirus Infections
Isaac H. Solomon, MD, PhD

142 Hepatitis A and E Virus Infections
Isaac H. Solomon, MD, PhD

146 Hepatitis C Virus Infection
Isaac H. Solomon, MD, PhD, Eleanor Russell-Goldman, MD, PhD, and Dan Milner, MD, MSc(Epi), MBA

SECTION 3: PRION DISEASES

152 Transmissible Spongiform Encephalopathies
Isaac H. Solomon, MD, PhD

SECTION 4: BACTERIAL INFECTIONS

158 Bacterial Classification and Diagnosis
Nicole Pecora, MD, PhD

160 Botryomycosis
Isaac H. Solomon, MD, PhD and Malak Abedalthagafi, MD, MBA

162 Malakoplakia
Malak Abedalthagafi, MD, MBA and Leigh Compton, MD

GRAM-POSITIVE BACTERIA

164 Actinomycosis
Isaac H. Solomon, MD, PhD, Nicole Pecora, MD, PhD, and Leigh Compton, MD

166 Bacillus Species Infections
Zoe Freeman Weiss, MD and Nicole Pecora, MD, PhD

170 Clostridioides and Other Gram-Positive Anaerobes
Nicole Pecora, MD, PhD and Zoe Freeman Weiss, MD

174 Corynebacterium Species Infections
Nicole Pecora, MD, PhD

178 Listeria Species Infection
Zoe Freeman Weiss, MD and Nicole Pecora, MD, PhD

180 Rhodococcus Species Infection
Zoe Freeman Weiss, MD and Nicole Pecora, MD, PhD

182 Staphylococcus Species Infections
Zoe Freeman Weiss, MD and Nicole Pecora, MD, PhD

188 Streptococcus and Enterococcus Species Infections
Zoe Freeman Weiss, MD and Nicole Pecora, MD, PhD

192 Whipple Disease
Jessica Crothers, MD, Dan Milner, MD, MSc(Epi), MBA, and Isaac H. Solomon, MD, PhD

GRAM-NEGATIVE BACTERIA

196 Pathologically Important Enterobacterales: Escherichia, Shigella, Salmonella, Klebsiella, and Yersinia Species Infections
Nicole Pecora, MD, PhD and Zoe Freeman Weiss, MD

204 Fastidious Organisms: Brucella, Francisella, Haemophilus, and Legionella Species Infections
Nicole Pecora, MD, PhD

210 Nonfermentative Organisms: Acinetobacter, Burkholderia, and Pseudomonas Species Infections
Zoe Freeman Weiss, MD, Nicole Pecora, MD, PhD, and Lenette Lu, MD, PhD

216 Bacteroides, Fusobacterium, and Other Gram- Negative Anaerobes
Zoe Freeman Weiss, MD and Nicole Pecora, MD, PhD

220 Bartonella Species Infections
Isaac H. Solomon, MD, PhD and Alvaro C. Laga, MD, MMSc

222 Campylobacter and Vibrio Species Infections
Zoe Freeman Weiss, MD and Nicole Pecora, MD, PhD

226 Helicobacteriosis
Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA

228 Neisseria and Moraxella Species Infections
Nicole Pecora, MD, PhD and Dan Milner, MD, MSc(Epi), MBA

232 Pertussis
Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA

234 Intestinal Spirochetosis
Isaac H. Solomon, MD, PhD, Leigh Compton, MD, and Nicole Pecora, MD, PhD

236 Borrelia Species Infections
Isaac H. Solomon, MD, PhD and Nicole Pecora, MD, PhD

240 Leptospira Species Infection
Isaac H. Solomon, MD, PhD and Nicole Pecora, MD, PhD

242 Syphilis and Other Treponematoses
Alvaro C. Laga, MD, MMSc, Isaac H. Solomon, MD, PhD, and Dan Milner, MD, MSc(Epi), MBA

248 Anaplasmosis and Ehrlichiosis
Isaac H. Solomon, MD, PhD, Nicole Pecora, MD, PhD, andLenette Lu, MD, PhD

252 Chlamydophila and Chlamydia Species Infections
Nicole Pecora, MD, PhD

256 Coxiella Species Infection
Isaac H. Solomon, MD, PhD and Nicole Pecora, MD, PhD

258 Rickettsia and Orientia Species Infections
Isaac H. Solomon, MD, PhD and Nicole Pecora, MD, PhD

262 Mycoplasma and Ureaplasma Species Infections
Zoe Freeman Weiss, MD and Isaac H. Solomon, MD, PhD

ACID-FAST BACTERIA

264 Mycobacterium tuberculosis Complex Infections
Nicole Pecora, MD, PhD, Isaac H. Solomon, MD, PhD, and Dan Milner, MD, MSc(Epi), MBA

270 Leprosy
Malak Abedalthagafi, MD, MBA, Dan Milner, MD, MSc(Epi), MBA, and Isaac H. Solomon, MD, PhD

274 Buruli Ulcer
Alvaro C. Laga, MD, MMSc

276 Mycobacterium avium Complex and Other Nontuberculous Mycobacterial Infections
Nicole Pecora, MD, PhD and Zoe Freeman Weiss, MD

280 Nocardiosis
Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA

SECTION 5: FUNGAL INFECTIONS

286 Fungal Classification and Diagnosis
Alvaro C. Laga, MD, MMSc and Dan Milner, MD, MSc(Epi), MBA

MOLDS

290 Aspergillosis
Zoe Freeman Weiss, MD, Alvaro C. Laga, MD, MMSc, and Isaac H. Solomon, MD, PhD

296 Entomophthoramycosis
Alvaro C. Laga, MD, MMSc

300 Fusariosis
Alvaro C. Laga, MD, MMSc, Zoe Freeman Weiss, MD, and Nicole Pecora, MD, PhD

302 Mucormycosis
Zoe Freeman Weiss, MD, Alvaro C. Laga, MD, MMSc, and Isaac H. Solomon, MD, PhD

306 Mycetoma
Alvaro C. Laga, MD, MMSc, T. Rinda Soong, MD, PhD, MPH, and Brian J. Hall, MD

310 Phaeohyphomycosis
Alvaro C. Laga, MD, MMSc, Dan Milner, MD, MSc(Epi), MBA, and Isaac H. Solomon, MD, PhD

312 Scedosporiosis and Lomentosporiosis
Alvaro C. Laga, MD, MMSc, Zoe Freeman Weiss, MD, and Eleanor Russell-Goldman, MD, PhD

314 Scopulariopsis Infections
Zoe Freeman Weiss, MD, Alvaro C. Laga, MD, MMSc, and Eleanor Russell-Goldman, MD, PhD

316 Tineasis
Malak Abedalthagafi, MD, MBA, Leigh Compton, MD, and Isaac H. Solomon, MD, PhD

318 Trichosporonosis
Isaac H. Solomon, MD, PhD, Alvaro C. Laga, MD, MMSc, and Dan Milner, MD, MSc(Epi), MBA

320 Superficial Mycoses
Alvaro C. Laga, MD, MMSc

YEASTS AND YEAST-LIKE ORGANISMS

324 Blastomycosis
Jessica Crothers, MD

330 Candidiasis
Jessica Crothers, MD, T. Rinda Soong, MD, PhD, MPH, and Isaac H. Solomon, MD, PhD

336 Chromoblastomycosis
Alvaro C. Laga, MD, MMSc, T. Rinda Soong, MD, PhD, MPH, and Nicole Pecora, MD, PhD

340 Coccidioidomycosis
Malak Abedalthagafi, MD, MBA and Isaac H. Solomon, MD, PhD

344 Cryptococcosis
Alvaro C. Laga, MD, MMSc, T. Rinda Soong, MD, PhD, MPH, and Isaac H. Solomon, MD, PhD

350 Histoplasmosis
Alvaro C. Laga, MD, MMSc, T. Rinda Soong, MD, PhD, MPH, and Nicole Pecora, MD, PhD

356 Lobomycosis
Alvaro C. Laga, MD, MMSc

358 Paracoccidioidomycosis
Isaac H. Solomon, MD, PhD and Eleanor Russell-Goldman, MD, PhD

360 Pneumocystosis
Jessica Crothers, MD, Eleanor Russell-Goldman, MD, PhD, and Isaac H. Solomon, MD, PhD

364 Sporotrichosis
Alvaro C. Laga, MD, MMSc, Isaac H. Solomon, MD, PhD, and Dan Milner, MD, MSc(Epi), MBA

368 Talaromycosis
Alvaro C. Laga, MD, MMSc, Dan Milner, MD, MSc(Epi), MBA, and Isaac H. Solomon, MD, PhD

370 Rhinosporidiosis
Alvaro C. Laga, MD, MMSc

372 Protothecosis
Jessica Crothers, MD

SECTION 6: PROTOZOAN PARASITIC INFECTIONS

376 Parasite Classification and Diagnosis
Alvaro C. Laga, MD, MMSc, Isaac H. Solomon, MD, PhD, and Dan Milner, MD, MSc(Epi), MBA

GASTROINTESTINAL AND OTHER LUMINAL PROTOZOA

380 Balantidiasis
Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA

382 Cryptosporidiosis and Other Coccidia Infections
Isaac H. Solomon, MD, PhD, Malak Abedalthagafi, MD, MBA, and Dan Milner, MD, MSc(Epi), MBA

386 Entamebiasis
Malak Abedalthagafi, MD, MBA and Isaac H. Solomon, MD, PhD

390 Giardiasis
Malak Abedalthagafi, MD, MBA, Eleanor Russell-Goldman, MD, PhD, and Isaac H. Solomon, MD, PhD

392 Microsporidiosis
Isaac H. Solomon, MD, PhD, Malak Abedalthagafi, MD, MBA, and Dan Milner, MD, MSc(Epi), MBA

394 Trichomoniasis
Isaac H. Solomon, MD, PhD and T. Rinda Soong, MD, PhD, MPH

INTRAVASCULAR PROTOZOA

396 African Trypanosomiasis
Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA

398 Babesiosis
Malak Abedalthagafi, MD, MBA, Dan Milner, MD, MSc(Epi), MBA, and Lenette Lu, MD, PhD

402 Malaria
Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA

DEEP TISSUE PROTOZOA

408 Free-Living Amebiasis
Alvaro C. Laga, MD, MMSc, Isaac H. Solomon, MD, PhD, and Dan Milner, MD, MSc(Epi), MBA

414 American Trypanosomiasis
Isaac H. Solomon, MD, PhD, Malak Abedalthagafi, MD, MBA, and Eleanor Russell-Goldman, MD, PhD

416 Leishmaniasis
Malak Abedalthagafi, MD, MBA, Dan Milner, MD, MSc(Epi), MBA, and Isaac H. Solomon, MD, PhD

420 Toxoplasmosis
Isaac H. Solomon, MD, PhD, Malak Abedalthagafi, MD, MBA, and Dan Milner, MD, MSc(Epi), MBA

SECTION 7: HELMINTHIC PARASITIC INFECTIONS
NEMATODES

426 Ancylostomiasis and Necatoriasis
Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA

428 Angiostrongyliasis
Isaac H. Solomon, MD, PhD

430 Ascariasis
Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA

434 Enterobiasis
Jessica Crothers, MD and Isaac H. Solomon, MD, PhD

438 Gnathostomiasis
Alvaro C. Laga, MD, MMSc

440 Human Filariasis
Malak Abedalthagafi, MD, MBA, Isaac H. Solomon, MD, PhD, and Eleanor Russell-Goldman, MD, PhD

444 Onchocerciasis
Malak Abedalthagafi, MD, MBA

446 Strongyloidiasis
Malak Abedalthagafi, MD, MBA and Isaac H. Solomon, MD, PhD

450 Trichuriasis
Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA

454 Trichinellosis
Jessica Crothers, MD

TREMATODES

456 Clonorchiasis and Opisthorchiasis
Jessica Crothers, MD

460 Fascioliasis and Fasciolopsiasis
Jessica Crothers, MD

462 Paragonimiasis
Jessica Crothers, MD

464 Schistosomiasis
Dan Milner, MD, MSc(Epi), MBA and Isaac H. Solomon, MD, PhD

CESTODES

470 Coenurosis
Isaac H. Solomon, MD, PhD

472 Cysticercosis
Isaac H. Solomon, MD, PhD

478 Diphyllobothriasis and Hymenolepiasis
Jessica Crothers, MD

482 Echinococcosis
Dan Milner, MD, MSc(Epi), MBA and Isaac H. Solomon, MD, PhD

486 Sparganosis
Isaac H. Solomon, MD, PhD

SECTION 8: INFESTATIONS AND OTHER INVERTEBRATE-RELATED MALADIES

490 Tissue Damage From Arachnids and Insects
Alvaro C. Laga, MD, MMSc, Isaac H. Solomon, MD, PhD, and Dan Milner, MD, MSc(Epi), MBA

498 Myiasis
Malak Abedalthagafi, MD, MBA and Dan Milner, MD, MSc(Epi), MBA

500 Scabies
Malak Abedalthagafi, MD, MBA, Leigh Compton, MD, and Dan Milner, MD, MSc(Epi), MBA

502 Demodex Infestations
Malak Abedalthagafi, MD, MBA and Dan Milner, MD, MSc(Epi), MBA

504 Tungiasis
Malak Abedalthagafi, MD, MBA and Dan Milner, MD, MSc(Epi), MBA