section I Diagnostic Strategies and General Topics / 1 VOLUME EDITOR: SANDRA S. RICHTER SECTION EDITOR: JAMES KARLOWSKY 1 Introduction to the 12th Edition of the Manual of Clinical Microbiology / 3 KAREN C. CARROLL AND MICHAEL A. PFALLER 2 Laboratory Accreditation and Compliance / 5 MICHAEL LOEFFELHOLZ, LINOJ SAMUEL, AND SUSAN SHARP 3 Microscopy / 16 STEVEN D. DALLAS 4 Laboratory Detection of Bacteremia and Fungemia / 28 MICHAEL L. WILSON, MELVIN P. WEINSTEIN, AND L. BARTH RELLER 5 Systems for Identification of Bacteria and Fungi / 45 KAREN C. CARROLL AND ROBIN PATEL 6 Automation and Design of the Clinical Microbiology Laboratory / 72 CHRISTOPHER D. DOERN AND MARTIN HOLFELDER 7 Molecular Microbiology / 86 FREDERICK S. NOLTE 8 Immunoassays for the Diagnosis of Infectious Diseases / 124 ELITZA S. THEEL 9 Prevention of Health Care-Associated Infections / 139 DANIEL J. DIEKEMA AND MICHAEL A. PFALLER 10 Investigation of Disease Outbreaks / 155 IONA MUNJAL, WENDY A. SZYMCZAK, AND BELINDA OSTROWSKY 11 Molecular Epidemiology / 167 EIJA TREES, TERRY FEI FAN NG, DUNCAN MacCANNELL, PAUL A. ROTA, AND PETER GERNER-SMIDT 12 Procedures for the Storage of Microorganisms / 197 ROSEMARY C. SHE AND SUSAN M. BUTLER-WU 13 Prevention of Laboratory-Acquired Infections / 206 PHILIPPE LAGACE-WIENS AND MICHAEL PENTELLA 14 Disinfection and Sterilization / 224 MATTHEW J. ARDUINO AND GERALD McDONNELL 15 Biothreat Agents / 243 JAMES W. SNYDER, STEVEN D. MAHLEN, SUSAN E. SHARP, AND MICHAEL LOEFFELHOLZ 16 The Human Microbiome / 254 JAMES VERSALOVIC, SARAH K. HIGHLANDER, BHANU P. GANESH, AND JOSEPH F. PETROSINO 17 Microbial Genomics and Pathogen Discovery / 269 JENNIFER K. SPINLER AND JAMES VERSALOVIC section II Bacteriology / 284 VOLUME EDITORS: ROBIN PATEL AND ALEXANDER J. McADAM SECTION EDITORS: CAREY-ANN BURNHAM, J. STEPHEN DUMLER, MELISSA B. MILLER, ELISABETH NAGY, AND JOHANN PITOUT General 18 Taxonomy of Bacteria and Archaea / 287 PAUL A. LAWSON AND KERIN L. TYRRELL 19 Specimen Collection, Transport, and Processing: Bacteriology / 302 ERIN McELVANIA AND KAMALJIT SINGH 20 Reagents, Stains, and Media: Bacteriology / 331 RONALD ATLAS AND JAMES SNYDER Gram-Positive Cocci 21 General Approaches to Identification of Aerobic Gram-Positive Cocci / 362 JENS JORGEN CHRISTENSEN, XIAOHUI CHEN NIELSEN, AND KATHRYN L. RUOFF 22 Staphylococcus, Micrococcus, and Other Catalase-Positive Cocci / 367 KARSTEN BECKER, ROBERT L. SKOV, AND CHRISTOF von EIFF 23 Streptococcus / 399 BARBARA SPELLERBERG, CLAUDIA BRANDT, AND PARHAM SENDI 24 Enterococcus / 418 LUCIA MARTINS TEIXEIRA, MARIA DA GLORIA SIQUEIRA CARVALHO, RICHARD R. FACKLAM, AND PATRICIA LYNN SHEWMAKER 25 Aerococcus, Abiotrophia, and Other Aerobic Catalase-Negative, Gram-Positive Cocci / 436 JENS JORGEN CHRISTENSEN, XIAOHUI CHEN NIELSEN, AND KATHRYN L. RUOFF Gram-Positive Rods 26 General Approaches to the Identification of Aerobic Gram-Positive Rods / 451 KATHRYN A. BERNARD 27 Bacillus and Other Aerobic Endospore-Forming Bacteria / 455 CHRISTINE Y. TURENNE AND DAVID C. ALEXANDER 28 Listeria and Erysipelothrix / 477 NELE WELLINGHAUSEN 29 Coryneform Gram-Positive Rods / 488 KATHRYN A. BERNARD 30 Nocardia, Rhodococcus, Gordonia, Actinomadura, Streptomyces, and Other Aerobic Actinomycetes / 525 PATRICIA S. CONVILLE, BARBARA A. BROWN-ELLIOTT, AND FRANK G. WITEBSKY 31 Mycobacterium: General Characteristics, Laboratory Detection, and Staining Procedures / 558 ISABELLA MARTIN, GABY E. PFYFFER, AND NICOLE PARRISH 32 Mycobacterium tuberculosis Complex / 576 DAVID M. WARSHAUER, MAX SALFINGER, EDWARD DESMOND, AND SHOU-YEAN GRACE LIN 33 Mycobacterium: Laboratory Characteristics of Slowly Growing Mycobacteria Other than Mycobacterium tuberculosis / 595 ADAM J. CAULFIELD, ELVIRA RICHTER, BARBARA A. BROWN-ELLIOTT, RICHARD J. WALLACE, JR., AND NANCY L. WENGENACK 34 Mycobacterium: Clinical and Laboratory Characteristics of Rapidly Growing Mycobacteria / 612 BARBARA A. BROWN-ELLIOTT AND RICHARD J. WALLACE, JR. Gram-Negative Bacteria 35 Approaches to the Identification of Aerobic Gram-Negative Bacteria / 630 NIELS NORSKOV-LAURITSEN AND WINNIE RIDDERBERG 36 Neisseria / 640 JOHANNES ELIAS, MATTHIAS FROSCH, AND ULRICH VOGEL 37 Aggregatibacter, Capnocytophaga, Eikenella, Kingella, Pasteurella, and Other Fastidious or Rarely Encountered Gram-Negative Rods / 656 REINHARD ZBINDEN 38 Haemophilus / 670 MARK D. GONZALEZ AND NATHAN A. LEDEBOER 39 Escherichia, Shigella, and Salmonella / 688 BLAKE W. BUCHAN, MATTHEW L. FARON, ROMNEY M. HUMPHRIES, JOHN DEKKER, AND NATHAN A. LEDEBOER 40 Klebsiella and Selected Enterobacterales / 724 STEPHEN J. FORSYTHE, JOHANN PITOUT, ANGELLA CHARNOT-KATSIKAS, KEVIN ALBY, AND KAREN M. FRANK 41 Yersinia / 751 LUKE C. KINGRY, CHERYL L. TARR, AND JEANNINE M. PETERSEN 42 Aeromonas / 765 BRIGITTE LAMY AND AMY J. HORNEMAN 43 Vibrio and Related Organisms / 775 CHERYL L. TARR, WILLIAM A. GLOVER II, YAN BOUCHER, AND JOHN J. FARMER III 44 Pseudomonas / 787 NIELS HOIBY, OANA CIOFU, AND THOMAS BJARNSHOLT 45 Burkholderia, Stenotrophomonas, Ralstonia, Cupriavidus, Pandoraea, Brevundimonas, Comamonas, Delftia, and Acidovorax / 807 JOHN J. LiPUMA, BART J. CURRIE, SHARON J. PEACOCK, AND PETER A. R. VANDAMME 46 Acinetobacter, Chryseobacterium, Moraxella, and Other Nonfermentative Gram-Negative Rods / 829 PIET COOLS, ALEXANDR NEMEC, PETER KAEMPFER, AND MARIO VANEECHOUTTE 47 Bordetella and Related Genera / 858 PAUL E. KILGORE AND TOM COENYE 48 Francisella / 871 ELIZABETH A. DIETRICH AND JEANNINE M. PETERSEN 49 Brucella / 883 GEORGE F. ARAJ 50 Bartonella / 893 J. STEPHEN DUMLER, KAREN C. CARROLL, AND ROBIN PATEL 51 Legionella / 905 PAUL H. EDELSTEIN Anaerobic Bacteria 52 Approaches to the Identification of Anaerobic Bacteria / 921 ANDREJ WEINTRAUB 53 Peptostreptococcus, Finegoldia, Anaerococcus, Peptoniphilus, Parvimonas, Murdochiella, Veillonella, and Other Anaerobic Cocci / 925 ALIDA C. M. VELOO AND CRYSTAL N. JOHNSON 54 Actinomyces, Lactobacillus, Cutibacterium, and Other Non-Spore-Forming Anaerobic Gram-Positive Rods / 938 SUSAN M. BUTLER-WU AND ROSEMARY C. SHE 55 Clostridium and Clostridioides / 968 ED KUIJPER AND FREDERIC BARBUT 56 Bacteroides, Porphyromonas, Prevotella, Fusobacterium, and Other Anaerobic Gram-Negative Rods / 995 GEORG CONRADS, ELISABETH NAGY, AND EIJA KOENOENEN Curved and Spiral-Shaped Gram-Negative Rods 57 Algorithms for Identification of Curved and Spiral-Shaped Gram-Negative Rods / 1024 IRVING NACHAMKIN 58 Campylobacter and Arcobacter / 1028 IRVING NACHAMKIN 59 Helicobacter / 1044 MARC ROGER COUTURIER 60 Leptospira / 1058 PAUL N. LEVETT AND RENEE L. GALLOWAY 61 Borrelia / 1066 MARIA E. AGUERO-ROSENFELD AND GEROLD STANEK 62 Treponema and Brachyspira: Human Host-Associated Spirochetes / 1083 ARLENE C. SENA, ALLAN PILLAY, AND JUSTIN D. RADOLF Mycoplasmas and Obligate Intracellular Bacteria 63 General Approaches to Identification of Mycoplasma, Ureaplasma, and Obligate Intracellular Bacteria / 1109 CECILE BEBEAR AND J. STEPHEN DUMLER 64 Mycoplasma and Ureaplasma / 1117 KEN B. WAITES AND CECILE BEBEAR 65 Chlamydia / 1137 JULIUS SCHACHTER AND MAX CHERNESKY 66 Rickettsia and Orientia / 1149 LUCAS S. BLANTON, DAVID H. WALKER, AND DONALD H. BOUYER 67 Ehrlichia, Anaplasma, and Related Intracellular Bacteria / 1163 BOBBI S. PRITT AND J. STEPHEN DUMLER 68 Coxiella / 1180 GILBERT J. KERSH AND CHANTAL P. BLEEKER-ROVERS 69 Tropheryma whipplei / 1189 WALTER GEIssDOERFER, ANNETTE MOTER, AND CHRISTIAN BOGDAN section III Antibacterial Agents and Susceptibility Test Methods / 1199 VOLUME EDITOR: SANDRA S. RICHTER SECTION EDITOR: JEAN B. PATEL 70 Antibacterial Agents / 1201 JAMES S. LEWIS II AND KAREN BUSH 71 Mechanisms of Resistance to Antibacterial Agents / 1242 PATRICIA A. BRADFORD AND MARIANA CASTANHEIRA 72 Susceptibility Test Methods: General Considerations / 1277 JOHN D. TURNIDGE AND JAMES H. JORGENSEN 73 Antimicrobial Susceptibility Test Methods: Dilution and Disk Diffusion Methods / 1284 LAURA M. KOETH AND LINDA A. MILLER 74 Antimicrobial Susceptibility Testing Systems / 1300 JAMES A. KARLOWSKY AND SANDRA S. RICHTER 75 Special Phenotypic Methods for Detecting Antibacterial Resistance / 1316 PATRICIA J. SIMNER AND ROMNEY HUMPHRIES 76 Susceptibility Test Methods: Fastidious Bacteria / 1348 ROMNEY M. HUMPHRIES AND JENNIFER DIEN BARD 77 Susceptibility Test Methods: Anaerobic Bacteria / 1377 AUDREY N. SCHUETZ AND DARCIE E. CARPENTER 78 Susceptibility Test Methods: Mycobacteria, Nocardia, and Other Actinomycetes / 1398 GAIL L. WOODS, SHOU-YEAN GRACE LIN, BARBARA A. BROWN-ELLIOTT, AND EDWARD P. DESMOND 79 Molecular Detection of Antibacterial Drug Resistance / 1420 APRIL N. ABBOTT AND FERRIC C. FANG Volume 2 section IV Virology / 1432 VOLUME EDITOR: MARIE LOUISE LANDRY SECTION EDITORS: ANGELA M. CALIENDO, CHRISTINE C. GINOCCHIO, RANDALL T. HAYDEN, AND YI-WEI TANG General 80 Taxonomy and Classification of Viruses / 1435 ELLIOT J. LEFKOWITZ 81 Specimen Collection, Transport, and Processing: Virology / 1446 JAMES J. DUNN AND BENJAMIN A. PINSKY 82 Reagents, Stains, Media, and Cell Cultures: Virology / 1462 GERALD A. CAPRARO AND CHRISTINE C. GINOCCHIO 83 Algorithms for Detection and Identification of Viruses / 1472 MARIE LOUISE LANDRY, ANGELA M. CALIENDO, CHRISTINE C. GINOCCHIO, RANDALL HAYDEN, AND YI-WEI TANG RNA Viruses 84 Human Immunodeficiency Viruses / 1477 S. MICHELE OWEN 85 Human T-Cell Lymphotropic Viruses / 1498 WILLIAM M. SWITZER, WALID HENEINE, AND S. MICHELE OWEN 86 Influenza Viruses / 1510 ROBERT L. ATMAR 87 Parainfluenza and Mumps Viruses / 1528 RYAN F. RELICH AND DIANE S. LELAND 88 Respiratory Syncytial Virus and Human Metapneumovirus / 1541 N. ESTHER BABADY AND YI-WEI TANG 89 Measles and Rubella Viruses / 1560 CAROLE J. HICKMAN AND JOSEPH P. ICENOGLE 90 Enteroviruses and Parechoviruses / 1576 KATHLEEN A. STELLRECHT, DARYL M. LAMSON, AND JOSE R. ROMERO 91 Rhinoviruses / 1592 MARIE LOUISE LANDRY AND XIAOYAN LU 92 Coronaviruses / 1606 NAOMI J. GADSBY AND KATE E. TEMPLETON 93 Hepatitis A and E Viruses / 1625 JACQUES IZOPET AND NASSIM KAMAR 94 Hepatitis C Virus / 1640 MICHAEL S. FORMAN, BRYAN R. COBB, AND ALEXANDRA VALSAMAKIS 95 Gastroenteritis Viruses / 1656 XIAOLI PANG AND MAREK SMIEJA 96 Rabies Lyssavirus / 1674 LILLIAN A. ORCIARI, PAMELA A. YAGER, AND P. S. SATHESHKUMAR 97 Arboviruses / 1685 ELIZABETH A. HUNSPERGER 98 Hantaviruses / 1706 JOHN D. KLENA, CHENG-FENG CHIANG, AND WUN-JU SHIEH 99 Arenaviruses and Filoviruses / 1719 JONATHAN S. TOWNER, PIERRE E. ROLLIN, YI-WEI TANG, AND THOMAS G. KSIAZEK DNA Viruses 100 Herpes Simplex Viruses and Herpes B Virus / 1740 ALEXANDER L. GRENINGER, RHODA ASHLEY MORROW, AND KEITH R. JEROME 101 Varicella-Zoster Virus / 1757 ELISABETH PUCHHAMMER-STOECKL AND STEPHAN W. ABERLE 102 Human Cytomegalovirus / 1770 RICHARD L. HODINKA 103 Epstein-Barr Virus / 1797 BARBARA C. GAERTNER AND FAUSTO BALDANTI 104 Human Herpesviruses 6A, 6B, and 7 / 1814 ALEXANDER L. GRENINGER, RUTH HALL SEDLAK, AND KEITH R. JEROME 105 Human Herpesvirus 8 / 1826 SHEILA C. DOLLARD AND CLIFFORD J. GUNTHEL 106 Adenoviruses / 1831 ALBERT HEIM AND RANDALL T. HAYDEN 107 Human Papillomaviruses / 1847 KATE CUSCHIERI AND ELIZABETH R. UNGER 108 Human Polyomaviruses / 1863 GREGORY A. STORCH AND RICHARD S. BULLER 109 Parvovirus B19 and Bocaviruses / 1880 KEVIN E. BROWN 110 Poxviruses / 1891 VICTORIA A. OLSON, P. S. SATHESHKUMAR, AND INGER K. DAMON 111 Hepatitis B and D Viruses / 1905 YI-WEI TANG, REBECCA T. HORVAT, AND MARIE-LOUISE LANDRY Subviral Agents 112 Prion Diseases / 1923 DANIEL D. RHOADS AND JIRI G. SAFAR section V Antiviral Agents and Susceptibility Test Methods / 1935 VOLUME EDITOR: MARIE LOUISE LANDRY SECTION EDITORS: ANGELA M. CALIENDO, CHRISTINE C. GINOCCHIO, RANDALL T. HAYDEN, AND YI-WEI TANG 113 Antiviral Agents / 1937 CARLOS A. Q. SANTOS AND NELL S. LURAIN 114 Mechanisms of Resistance to Antiviral Agents / 1962 ROBERT W. SHAFER, GUY BOIVIN, AND SUNWEN CHOU 115 Susceptibility Test Methods: Viruses / 1985 DIANA D. HUANG, BENJAMIN A. PINSKY, AND MATTHEW J. BANKOWSKI section VI Mycology / 2005 VOLUME EDITOR: DAVID W. WARNOCK SECTION EDITORS: MARY E. BRANDT AND ELIZABETH M. JOHNSON General 116 Taxonomy, Classification, and Nomenclature of Fungi / 2007 MARY E. BRANDT AND DAVID W. WARNOCK CONTENTS n ix 117 Specimen Collection, Transport, and Processing: Mycology / 2016 ELIZABETH L. BERKOW AND KARIN L. McGOWAN 118 Reagents, Stains, and Media: Mycology / 2025 MARK D. LINDSLEY 119 General Approaches for Direct Detection and Identification of Fungi / 2035 H. RUTH ASHBEE Fungi 120 Candida, Cryptococcus, and Other Yeasts of Medical Importance / 2056 ANDREW M. BORMAN AND ELIZABETH M. JOHNSON 121 Pneumocystis / 2087 MELANIE T. CUSHION AND M. ALI RAI 122 Aspergillus, Talaromyces, and Penicillium / 2103 SHARON C.-A. CHEN, WIELAND MEYER, TANIA C. SORRELL, AND CATRIONA L. HALLIDAY 123 Fusarium and Other Opportunistic Hyaline Fungi / 2132 SEAN X. ZHANG, KERRY O'DONNELL, AND DEANNA A. SUTTON 124 Agents of Systemic and Subcutaneous Mucormycosis and Entomophthoromycosis / 2163 DEA GARCIA-HERMOSO, ALEXANDRE ALANIO, OLIVIER LORTHOLARY, AND FRANCOISE DROMER 125 Histoplasma, Blastomyces, Coccidioides, Paracoccidioides, and Other Dimorphic Fungi Causing Systemic Mycoses / 2187 GEORGE R. THOMPSON III AND BEATRIZ L. GOMEZ 126 Trichophyton, Microsporum, Epidermophyton, and Agents of Superficial Mycoses / 2208 ANDREW M. BORMAN AND RICHARD C. SUMMERBELL 127 Curvularia, Exophiala, Scedosporium, Sporothrix, and Other Melanized Fungi / 2234 JOSEP GUARRO, HUGO MADRID, AND SYBREN de HOOG 128 Fungi Causing Eumycotic Mycetoma / 2261 SARAH ABDALLAH AHMED, G. SYBREN de HOOG, AND WENDY W. J. van de SANDE 129 Mycotoxins / 2278 JOANNA TANNOUS AND NANCY P. KELLER 130 Lacazia, Lagenidium, Pythium, and Rhinosporidium / 2291 RAQUEL VILELA AND LEONEL MENDOZA 131 Microsporidia / 2305 RAINER WEBER, PETER DEPLAZES, AND ALEXANDER MATHIS section VII Antifungal Agents and Susceptibility Test Methods / 2317 VOLUME EDITOR: DAVID W. WARNOCK SECTION EDITORS: MARY E. BRANDT AND ELIZABETH M. JOHNSON 132 Antifungal Agents / 2319 SHAWN R. LOCKHART AND ELIZABETH L. BERKOW 133 Mechanisms of Resistance to Antifungal Agents / 2334 DAVID S. PERLIN 134 Susceptibility Test Methods: Yeasts and Filamentous Fungi / 2351 ELIZABETH M. JOHNSON AND MAIKEN CAVLING ARENDRUP section VIII Parasitology / 2377 VOLUME EDITOR: DAVID W. WARNOCK SECTION EDITORS: BOBBI S. PRITT AND GARY W. PROCOP General 135 Taxonomy and Classification of Human Eukaryotic Parasites / 2379 SINA M. ADL AND BLAINE A. MATHISON 136 Specimen Collection, Transport, and Processing: Parasitology / 2389 ROBYN Y. SHIMIZU AND LYNNE S. GARCIA 137 Reagents, Stains, and Media: Parasitology / 2406 ANDREA J. LINSCOTT AND SUSAN E. SHARP 138 General Approaches for Detection and Identification of Parasites / 2414 LYNNE S. GARCIA, GRAEME P. PALTRIDGE, AND ROBYN Y. SHIMIZU Parasites 139 Plasmodium and Babesia / 2438 BOBBI S. PRITT 140 Leishmania and Trypanosoma / 2458 DAVID A. BRUCKNER AND JAIME A. LABARCA 141 Toxoplasma / 2473 JAMES B. McAULEY AND KAMALJIT SINGH 142 Pathogenic and Opportunistic Free-Living Amebae / 2486 JENNIFER R. COPE, IBNE KARIM M. ALI, AND GOVINDA S. VISVESVARA 143 Intestinal and Urogenital Amebae, Flagellates, and Ciliates / 2497 SUSAN NOVAK-WEEKLEY AND AMY L. LEBER 144 Cystoisospora, Cyclospora, and Sarcocystis / 2526 DAVID S. LINDSAY AND LOUIS M. WEISS 145 Cryptosporidium / 2536 LIHUA XIAO AND VITALIANO CAMA 146 Nematodes / 2551 HARSHA SHEOREY, BEVERLEY-ANN BIGGS, AND NORBERT RYAN 147 Filarial Nematodes / 2570 CARMELLE T. NORICE-TRA AND THOMAS B. NUTMAN 148 Cestodes / 2582 HECTOR H. GARCIA, JUAN A. JIMENEZ, AND HERMES ESCALANTE 149 Trematodes / 2590 MALCOLM K. JONES, JENNIFER KEISER, AND DONALD P. McMANUS 150 Less Common Helminths / 2606 GARY W. PROCOP AND RONALD C. NEAFIE 151 Arthropods of Medical Importance / 2620 SAM R. TELFORD III AND BLAINE A. MATHISON section IX Antiparasitic Agents and Susceptibility Test Methods / 2643 VOLUME EDITOR: DAVID W. WARNOCK SECTION EDITORS: GARY W. PROCOP 152 Antiparasitic Agents / 2645 KARIN LEDER, SARAH L. McGUINNESS, AND PETER F. WELLER 153 Mechanisms of Resistance to Antiparasitic Agents / 2669 W. EVAN SECOR, JACQUES LE BRAS, AND JEROME CLAIN 154 Susceptibility Test Methods: Parasites / 2682 JEROME CLAIN, JACQUES LE BRAS, AND W. EVAN SECOR

"The Manual of Clinical Microbiology is the key resource for understanding what, why, and how in clinical microbiology. It is truly a must-have document for guiding current practice," says Carol A. Rauch, MD, PhD, FCAP, Associate Professor of Pathology, Microbiology, and Immunology at Vanderbilt University Medical Center.