Diagnostic Pathology: Infectious Diseases

Isaac H. Solomon, MD, PhD, is an Associate Pathologist in the Department of Pathology at Brigham and Women's Hospital and an Assistant Professor of Pathology at Harvard Medical School in Boston, Massachusetts. Solomon retains the status of Neurooncology Member at the Dana Farber/Harvard Cancer Center in Boston, Massachusetts. Dan Milner, MD, MSc(Epi), MBA, is a consultant pathologist, executive director, and medical director at Libragem Consulting, LLC, in Palm Springs, California, and an Associate Professor at the Department of Immunology and Infectious Diseases at Harvard T.H. Chan School of Public Health in Boston, Massachusetts

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, and Lenette 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