SECTION 1: OVERVIEW<br>4 Standard Methods for Infectious Diseases<br>Zoe Freeman Weiss, MD, Nicole Pecora, MD, PhD, and Shira Winters, MD<br>10 Emerging Techniques<br>Jessica Crothers, MD<br>12 Biosafety Considerations<br>Jessica Crothers, MD<br>16 Pitfalls and Artifacts<br>Jessica Crothers, MD, Alvaro C. Laga, MD, MMSc, and Isaac H. Solomon, MD, PhD<br><br>SECTION 2: VIRAL INFECTIONS<br>DNA VIRUSES<br>22 Herpes Simplex Virus 1 and 2 (HSV-1, HSV-2) Infections<br>Isaac H. Solomon, MD, PhD, Leigh Compton, MD, and Dan Milner, MD, MSc(Epi), MBA<br>28 Varicella-Zoster Virus (HHV-3) Infections<br>Isaac H. Solomon, MD, PhD, Eleanor Russell-Goldman, MD, PhD, and Dan Milner, MD, MSc(Epi), MBA<br>32 Epstein-Barr Virus (HHV-4) Infection<br>Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA<br>38 Cytomegalovirus (HHV-5) Infections<br>Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA<br>44 Human Herpesvirus 6 and 7 (HHV-6, HHV-7) Infections<br>Isaac H. Solomon, MD, PhD<br>46 Kaposi Sarcoma-Associated Herpesvirus (HHV-8) Infection<br>Isaac H. Solomon, MD, PhD, Leigh Compton, MD, and Dan Milner, MD, MSc(Epi), MBA<br>52 Herpes B Virus Infection<br>Isaac H. Solomon, MD, PhD<br>54 Adenovirus Infection<br>Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA<br>58 Hepatitis B and D Virus Infections<br>Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA<br>62 Parvovirus B19 Infection<br>Isaac H. Solomon, MD, PhD, Leigh Compton, MD, and Dan Milner, MD, MSc(Epi), MBA<br>66 JC Virus, BK Virus, and Other Polyomavirus Infections<br>Isaac H. Solomon, MD, PhD<br>72 Human Papillomavirus Infection<br>Isaac H. Solomon, MD, PhD, T. Rinda Soong, MD, PhD, MPH, and Dan Milner, MD, MSc(Epi), MBA<br>78 Molluscum Contagiosum<br>Isaac H. Solomon, MD, PhD<br>80 Smallpox, Mpox, and Other Pox Virus Infections<br>Alvaro C. Laga, MD, MMSc, Dan Milner, MD, MSc(Epi), MBA, and Isaac H. Solomon, MD, PhD<br><br>RNA VIRUSES<br>86 Arbovirus Infections<br>Isaac H. Solomon, MD, PhD<br>92 Zika Virus Infection<br>Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA<br>96 Ebola, Marburg, and Other Hemorrhagic Fever Virus Infections<br>Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA<br>102 Enterovirus Infections<br>Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi),MBA<br>104 Poliovirus Infection<br>Jessica Crothers, MD and Isaac H. Solomon, MD, PhD<br>106 Rabies Virus Infection<br>Isaac H. Solomon, MD, PhD<br>108 Lymphocytic Choriomeningitis Virus Infection<br>Isaac H. Solomon, MD, PhD<br>110 Measles Virus Infection<br>Isaac H. Solomon, MD, PhD<br>112 Mumps Virus Infection<br>Isaac H. Solomon, MD, PhD<br>114 Rubella Virus Infection<br>Isaac H. Solomon, MD, PhD<br>116 Human Immunodeficiency Virus Infection<br>Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA<br>120 Human T-Lymphotropic Virus Type I Infection<br>Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA<br>122 Influenza Virus Infections<br>Isaac H. Solomon, MD, PhD<br>126 Parainfluenza Virus Infections<br>Isaac H. Solomon, MD, PhD<br>128 Coronavirus Disease 2019 (COVID-19)<br>Isaac H. Solomon, MD, PhD<br>134 Severe Acute Respiratory Syndrome (SARS), Middle East Respiratory Syndrome (MERS), and Other Coronavirus Infections<br>Isaac H. Solomon, MD, PhD<br>136 Respiratory Syncytial Virus Infection<br>Isaac H. Solomon, MD, PhD and Eleanor Russell-Goldman,MD, PhD<br>138 Rhinoviruses, Human Metapneumovirus, and Other Respiratory Virus Infections<br>Isaac H. Solomon, MD, PhD<br>140 Rotavirus, Norovirus, and Astrovirus Infections<br>Isaac H. Solomon, MD, PhD<br>142 Hepatitis A and E Virus Infections<br>Isaac H. Solomon, MD, PhD<br>146 Hepatitis C Virus Infection<br>Isaac H. Solomon, MD, PhD, Eleanor Russell-Goldman, MD, PhD, and Dan Milner, MD, MSc(Epi), MBA<br><br>SECTION 3: PRION DISEASES<br>152 Transmissible Spongiform Encephalopathies<br>Isaac H. Solomon, MD, PhD<br><br>SECTION 4: BACTERIAL INFECTIONS<br>158 Bacterial Classification and Diagnosis<br>Nicole Pecora, MD, PhD<br>160 Botryomycosis<br>Isaac H. Solomon, MD, PhD and Malak Abedalthagafi, MD, MBA<br>162 Malakoplakia<br>Malak Abedalthagafi, MD, MBA and Leigh Compton, MD<br><br>GRAM-POSITIVE BACTERIA<br>164 Actinomycosis<br>Isaac H. Solomon, MD, PhD, Nicole Pecora, MD, PhD, and Leigh Compton, MD<br>166 Bacillus Species Infections<br>Zoe Freeman Weiss, MD and Nicole Pecora, MD, PhD<br>170 Clostridioides and Other Gram-Positive Anaerobes<br>Nicole Pecora, MD, PhD and Zoe Freeman Weiss, MD<br>174 Corynebacterium Species Infections<br>Nicole Pecora, MD, PhD<br>178 Listeria Species Infection<br>Zoe Freeman Weiss, MD and Nicole Pecora, MD, PhD<br>180 Rhodococcus Species Infection<br>Zoe Freeman Weiss, MD and Nicole Pecora, MD, PhD<br>182 Staphylococcus Species Infections<br>Zoe Freeman Weiss, MD and Nicole Pecora, MD, PhD<br>188 Streptococcus and Enterococcus Species Infections<br>Zoe Freeman Weiss, MD and Nicole Pecora, MD, PhD<br>192 Whipple Disease<br>Jessica Crothers, MD, Dan Milner, MD, MSc(Epi), MBA, and Isaac H. Solomon, MD, PhD<br><br>GRAM-NEGATIVE BACTERIA<br>196 Pathologically Important Enterobacterales: Escherichia, Shigella, Salmonella, Klebsiella, and Yersinia Species Infections<br>Nicole Pecora, MD, PhD and Zoe Freeman Weiss, MD<br>204 Fastidious Organisms: Brucella, Francisella, Haemophilus, and Legionella Species Infections<br>Nicole Pecora, MD, PhD<br>210 Nonfermentative Organisms: Acinetobacter, Burkholderia, and Pseudomonas Species Infections<br>Zoe Freeman Weiss, MD, Nicole Pecora, MD, PhD, and Lenette Lu, MD, PhD<br>216 Bacteroides, Fusobacterium, and Other Gram- Negative Anaerobes<br>Zoe Freeman Weiss, MD and Nicole Pecora, MD, PhD<br>220 Bartonella Species Infections<br>Isaac H. Solomon, MD, PhD and Alvaro C. Laga, MD, MMSc<br>222 Campylobacter and Vibrio Species Infections<br>Zoe Freeman Weiss, MD and Nicole Pecora, MD, PhD<br>226 Helicobacteriosis<br>Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA<br>228 Neisseria and Moraxella Species Infections<br>Nicole Pecora, MD, PhD and Dan Milner, MD, MSc(Epi), MBA<br>232 Pertussis<br>Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA<br>234 Intestinal Spirochetosis<br>Isaac H. Solomon, MD, PhD, Leigh Compton, MD, and Nicole Pecora, MD, PhD<br>236 Borrelia Species Infections<br>Isaac H. Solomon, MD, PhD and Nicole Pecora, MD, PhD<br>240 Leptospira Species Infection<br>Isaac H. Solomon, MD, PhD and Nicole Pecora, MD, PhD<br>242 Syphilis and Other Treponematoses<br>Alvaro C. Laga, MD, MMSc, Isaac H. Solomon, MD, PhD, and Dan Milner, MD, MSc(Epi), MBA<br>248 Anaplasmosis and Ehrlichiosis<br>Isaac H. Solomon, MD, PhD, Nicole Pecora, MD, PhD, andLenette Lu, MD, PhD<br>252 Chlamydophila and Chlamydia Species Infections<br>Nicole Pecora, MD, PhD<br>256 Coxiella Species Infection<br>Isaac H. Solomon, MD, PhD and Nicole Pecora, MD, PhD<br>258 Rickettsia and Orientia Species Infections<br>Isaac H. Solomon, MD, PhD and Nicole Pecora, MD, PhD<br>262 Mycoplasma and Ureaplasma Species Infections<br>Zoe Freeman Weiss, MD and Isaac H. Solomon, MD, PhD<br><br>ACID-FAST BACTERIA<br>264 Mycobacterium tuberculosis Complex Infections<br>Nicole Pecora, MD, PhD, Isaac H. Solomon, MD, PhD, and Dan Milner, MD, MSc(Epi), MBA<br>270 Leprosy<br>Malak Abedalthagafi, MD, MBA, Dan Milner, MD, MSc(Epi), MBA, and Isaac H. Solomon, MD, PhD<br>274 Buruli Ulcer<br>Alvaro C. Laga, MD, MMSc<br>276 Mycobacterium avium Complex and Other Nontuberculous Mycobacterial Infections<br>Nicole Pecora, MD, PhD and Zoe Freeman Weiss, MD<br>280 Nocardiosis<br>Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA<br><br>SECTION 5: FUNGAL INFECTIONS<br>286 Fungal Classification and Diagnosis<br>Alvaro C. Laga, MD, MMSc and Dan Milner, MD, MSc(Epi), MBA<br><br>MOLDS<br>290 Aspergillosis<br>Zoe Freeman Weiss, MD, Alvaro C. Laga, MD, MMSc, and Isaac H. Solomon, MD, PhD<br>296 Entomophthoramycosis<br>Alvaro C. Laga, MD, MMSc<br>300 Fusariosis<br>Alvaro C. Laga, MD, MMSc, Zoe Freeman Weiss, MD, and Nicole Pecora, MD, PhD<br>302 Mucormycosis<br>Zoe Freeman Weiss, MD, Alvaro C. Laga, MD, MMSc, and Isaac H. Solomon, MD, PhD<br>306 Mycetoma<br>Alvaro C. Laga, MD, MMSc, T. Rinda Soong, MD, PhD, MPH, and Brian J. Hall, MD<br>310 Phaeohyphomycosis<br>Alvaro C. Laga, MD, MMSc, Dan Milner, MD, MSc(Epi), MBA, and Isaac H. Solomon, MD, PhD<br>312 Scedosporiosis and Lomentosporiosis<br>Alvaro C. Laga, MD, MMSc, Zoe Freeman Weiss, MD, and Eleanor Russell-Goldman, MD, PhD<br>314 Scopulariopsis Infections<br>Zoe Freeman Weiss, MD, Alvaro C. Laga, MD, MMSc, and Eleanor Russell-Goldman, MD, PhD<br>316 Tineasis<br>Malak Abedalthagafi, MD, MBA, Leigh Compton, MD, and Isaac H. Solomon, MD, PhD<br>318 Trichosporonosis<br>Isaac H. Solomon, MD, PhD, Alvaro C. Laga, MD, MMSc, and Dan Milner, MD, MSc(Epi), MBA<br>320 Superficial Mycoses<br>Alvaro C. Laga, MD, MMSc<br><br>YEASTS AND YEAST-LIKE ORGANISMS<br>324 Blastomycosis<br>Jessica Crothers, MD<br>330 Candidiasis<br>Jessica Crothers, MD, T. Rinda Soong, MD, PhD, MPH, and Isaac H. Solomon, MD, PhD<br>336 Chromoblastomycosis<br>Alvaro C. Laga, MD, MMSc, T. Rinda Soong, MD, PhD, MPH, and Nicole Pecora, MD, PhD<br>340 Coccidioidomycosis<br>Malak Abedalthagafi, MD, MBA and Isaac H. Solomon, MD, PhD<br>344 Cryptococcosis<br>Alvaro C. Laga, MD, MMSc, T. Rinda Soong, MD, PhD, MPH, and Isaac H. Solomon, MD, PhD<br>350 Histoplasmosis<br>Alvaro C. Laga, MD, MMSc, T. Rinda Soong, MD, PhD, MPH, and Nicole Pecora, MD, PhD<br>356 Lobomycosis<br>Alvaro C. Laga, MD, MMSc<br>358 Paracoccidioidomycosis<br>Isaac H. Solomon, MD, PhD and Eleanor Russell-Goldman, MD, PhD<br>360 Pneumocystosis<br>Jessica Crothers, MD, Eleanor Russell-Goldman, MD, PhD, and Isaac H. Solomon, MD, PhD<br>364 Sporotrichosis<br>Alvaro C. Laga, MD, MMSc, Isaac H. Solomon, MD, PhD, and Dan Milner, MD, MSc(Epi), MBA<br>368 Talaromycosis<br>Alvaro C. Laga, MD, MMSc, Dan Milner, MD, MSc(Epi), MBA, and Isaac H. Solomon, MD, PhD<br>370 Rhinosporidiosis<br>Alvaro C. Laga, MD, MMSc<br>372 Protothecosis<br>Jessica Crothers, MD<br><br>SECTION 6: PROTOZOAN PARASITIC INFECTIONS<br>376 Parasite Classification and Diagnosis<br>Alvaro C. Laga, MD, MMSc, Isaac H. Solomon, MD, PhD, and Dan Milner, MD, MSc(Epi), MBA<br><br>GASTROINTESTINAL AND OTHER LUMINAL PROTOZOA<br>380 Balantidiasis<br>Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA<br>382 Cryptosporidiosis and Other Coccidia Infections<br>Isaac H. Solomon, MD, PhD, Malak Abedalthagafi, MD, MBA, and Dan Milner, MD, MSc(Epi), MBA<br>386 Entamebiasis<br>Malak Abedalthagafi, MD, MBA and Isaac H. Solomon, MD, PhD<br>390 Giardiasis<br>Malak Abedalthagafi, MD, MBA, Eleanor Russell-Goldman, MD, PhD, and Isaac H. Solomon, MD, PhD<br>392 Microsporidiosis<br>Isaac H. Solomon, MD, PhD, Malak Abedalthagafi, MD, MBA, and Dan Milner, MD, MSc(Epi), MBA<br>394 Trichomoniasis<br>Isaac H. Solomon, MD, PhD and T. Rinda Soong, MD, PhD, MPH<br><br>INTRAVASCULAR PROTOZOA<br>396 African Trypanosomiasis<br>Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA<br>398 Babesiosis<br>Malak Abedalthagafi, MD, MBA, Dan Milner, MD, MSc(Epi), MBA, and Lenette Lu, MD, PhD<br>402 Malaria<br>Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA<br><br>DEEP TISSUE PROTOZOA<br>408 Free-Living Amebiasis<br>Alvaro C. Laga, MD, MMSc, Isaac H. Solomon, MD, PhD, and Dan Milner, MD, MSc(Epi), MBA<br>414 American Trypanosomiasis<br>Isaac H. Solomon, MD, PhD, Malak Abedalthagafi, MD, MBA, and Eleanor Russell-Goldman, MD, PhD<br>416 Leishmaniasis<br>Malak Abedalthagafi, MD, MBA, Dan Milner, MD, MSc(Epi), MBA, and Isaac H. Solomon, MD, PhD<br>420 Toxoplasmosis<br>Isaac H. Solomon, MD, PhD, Malak Abedalthagafi, MD, MBA, and Dan Milner, MD, MSc(Epi), MBA<br><br>SECTION 7: HELMINTHIC PARASITIC INFECTIONS<br>NEMATODES<br>426 Ancylostomiasis and Necatoriasis<br>Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA<br>428 Angiostrongyliasis<br>Isaac H. Solomon, MD, PhD<br>430 Ascariasis<br>Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA<br>434 Enterobiasis<br>Jessica Crothers, MD and Isaac H. Solomon, MD, PhD<br>438 Gnathostomiasis<br>Alvaro C. Laga, MD, MMSc<br>440 Human Filariasis<br>Malak Abedalthagafi, MD, MBA, Isaac H. Solomon, MD, PhD, and Eleanor Russell-Goldman, MD, PhD<br>444 Onchocerciasis<br>Malak Abedalthagafi, MD, MBA<br>446 Strongyloidiasis<br>Malak Abedalthagafi, MD, MBA and Isaac H. Solomon, MD, PhD<br>450 Trichuriasis<br>Isaac H. Solomon, MD, PhD and Dan Milner, MD, MSc(Epi), MBA<br>454 Trichinellosis<br>Jessica Crothers, MD<br><br>TREMATODES<br>456 Clonorchiasis and Opisthorchiasis<br>Jessica Crothers, MD<br>460 Fascioliasis and Fasciolopsiasis<br>Jessica Crothers, MD<br>462 Paragonimiasis<br>Jessica Crothers, MD<br>464 Schistosomiasis<br>Dan Milner, MD, MSc(Epi), MBA and Isaac H. Solomon, MD, PhD<br><br>CESTODES<br>470 Coenurosis<br>Isaac H. Solomon, MD, PhD<br>472 Cysticercosis<br>Isaac H. Solomon, MD, PhD<br>478 Diphyllobothriasis and Hymenolepiasis<br>Jessica Crothers, MD<br>482 Echinococcosis<br>Dan Milner, MD, MSc(Epi), MBA and Isaac H. Solomon, MD, PhD<br>486 Sparganosis<br>Isaac H. Solomon, MD, PhD<br><br>SECTION 8: INFESTATIONS AND OTHER INVERTEBRATE-RELATED MALADIES<br>490 Tissue Damage From Arachnids and Insects<br>Alvaro C. Laga, MD, MMSc, Isaac H. Solomon, MD, PhD, and Dan Milner, MD, MSc(Epi), MBA<br>498 Myiasis<br>Malak Abedalthagafi, MD, MBA and Dan Milner, MD, MSc(Epi), MBA<br>500 Scabies<br>Malak Abedalthagafi, MD, MBA, Leigh Compton, MD, and Dan Milner, MD, MSc(Epi), MBA<br>502 Demodex Infestations<br>Malak Abedalthagafi, MD, MBA and Dan Milner, MD, MSc(Epi), MBA<br>504 Tungiasis<br>Malak Abedalthagafi, MD, MBA and Dan Milner, MD, MSc(Epi), MBA