Full Description
Revised by a collaborative, international, interdisciplinary team of editors and authors, this edition includes the latest applications of genomics and proteomics and is filled with current findings regarding infectious agents, leading-edge diagnostic methods, laboratory practices, and safety guidelines. This edition also features three new chapters on accreditation, Mycobacterium tuberculosis complex, and human herpesvirus 8. This seminal reference of microbiology continues to set the standard for state-of-the-science laboratory practice as the most authoritative reference in the field of microbiology.
Contents
section IDiagnostic Strategies andGeneral Topics / 1VOLUME EDITOR: SANDRA S. RICHTERSECTION EDITOR: JAMES KARLOWSKY1 Introduction to the 12th Edition of the Manualof Clinical Microbiology / 3KAREN C. CARROLL AND MICHAEL A. PFALLER2 Laboratory Accreditation and Compliance / 5MICHAEL LOEFFELHOLZ, LINOJ SAMUEL,AND SUSAN SHARP3 Microscopy / 16STEVEN D. DALLAS4 Laboratory Detection of Bacteremia andFungemia / 28MICHAEL L. WILSON, MELVIN P. WEINSTEIN,AND L. BARTH RELLER5 Systems for Identification of Bacteria and Fungi / 45KAREN C. CARROLL AND ROBIN PATEL6 Automation and Design of the ClinicalMicrobiology Laboratory / 72CHRISTOPHER D. DOERN ANDMARTIN HOLFELDER7 Molecular Microbiology / 86FREDERICK S. NOLTE8 Immunoassays for the Diagnosis of InfectiousDiseases / 124ELITZA S. THEEL9 Prevention of Health Care-AssociatedInfections / 139DANIEL J. DIEKEMA AND MICHAEL A. PFALLER10 Investigation of Disease Outbreaks / 155IONA MUNJAL, WENDY A. SZYMCZAK, ANDBELINDA OSTROWSKY11 Molecular Epidemiology / 167EIJA TREES, TERRY FEI FAN NG,DUNCAN MacCANNELL, PAUL A. ROTA,AND PETER GERNER-SMIDT12 Procedures for the Storage ofMicroorganisms / 197ROSEMARY C. SHE AND SUSAN M. BUTLER-WU13 Prevention of Laboratory-AcquiredInfections / 206PHILIPPE LAGACE-WIENS ANDMICHAEL PENTELLA14 Disinfection and Sterilization / 224MATTHEW J. ARDUINO ANDGERALD McDONNELL15 Biothreat Agents / 243JAMES W. SNYDER, STEVEN D. MAHLEN,SUSAN E. SHARP, AND MICHAEL LOEFFELHOLZ16 The Human Microbiome / 254JAMES VERSALOVIC, SARAH K. HIGHLANDER,BHANU P. GANESH, AND JOSEPH F. PETROSINO17 Microbial Genomics and Pathogen Discovery / 269JENNIFER K. SPINLER AND JAMES VERSALOVICsection IIBacteriology / 284VOLUME EDITORS: ROBIN PATEL ANDALEXANDER J. McADAMSECTION EDITORS: CAREY-ANN BURNHAM,J. STEPHEN DUMLER, MELISSA B. MILLER,ELISABETH NAGY, AND JOHANN PITOUTGeneral18 Taxonomy of Bacteria and Archaea / 287PAUL A. LAWSON AND KERIN L. TYRRELL19 Specimen Collection, Transport, and Processing:Bacteriology / 302ERIN McELVANIA AND KAMALJIT SINGH20 Reagents, Stains, and Media:Bacteriology / 331RONALD ATLAS AND JAMES SNYDERGram-Positive Cocci21 General Approaches to Identification ofAerobic Gram-Positive Cocci / 362JENS JORGEN CHRISTENSEN, XIAOHUI CHENNIELSEN, AND KATHRYN L. RUOFF22 Staphylococcus, Micrococcus, and OtherCatalase-Positive Cocci / 367KARSTEN BECKER, ROBERT L. SKOV, ANDCHRISTOF von EIFF23 Streptococcus / 399BARBARA SPELLERBERG, CLAUDIA BRANDT,AND PARHAM SENDI24 Enterococcus / 418SIQUEIRA CARVALHO, RICHARD R. FACKLAM,AND PATRICIA LYNN SHEWMAKER25 Aerococcus, Abiotrophia, and OtherAerobic Catalase-Negative, Gram-PositiveCocci / 436JENS JORGEN CHRISTENSEN, XIAOHUI CHENNIELSEN, AND KATHRYN L. RUOFFGram-Positive Rods26 General Approaches to the Identification ofAerobic Gram-Positive Rods / 451KATHRYN A. BERNARD27 Bacillus and Other Aerobic Endospore-FormingBacteria / 455CHRISTINE Y. TURENNE ANDDAVID C. ALEXANDER28 Listeria and Erysipelothrix / 477NELE WELLINGHAUSEN29 Coryneform Gram-Positive Rods / 488KATHRYN A. BERNARD30 Nocardia, Rhodococcus, Gordonia,Actinomadura, Streptomyces, and OtherAerobic Actinomycetes / 525PATRICIA S. CONVILLE, BARBARA A.BROWN-ELLIOTT, AND FRANK G. WITEBSKY31 Mycobacterium: General Characteristics,Laboratory Detection, and StainingProcedures / 558ISABELLA MARTIN, GABY E. PFYFFER, ANDNICOLE PARRISH32 Mycobacterium tuberculosis Complex / 576DAVID M. WARSHAUER, MAX SALFINGER,EDWARD DESMOND, AND SHOU-YEANGRACE LIN33 Mycobacterium: Laboratory Characteristicsof Slowly Growing Mycobacteria Other thanMycobacterium tuberculosis / 595ADAM J. CAULFIELD, ELVIRA RICHTER,BARBARA A. BROWN-ELLIOTT, RICHARD J.WALLACE, JR., AND NANCY L. WENGENACK34 Mycobacterium: Clinical and LaboratoryCharacteristics of Rapidly GrowingMycobacteria / 612BARBARA A. BROWN-ELLIOTT ANDRICHARD J. WALLACE, JR.Gram-Negative Bacteria35 Approaches to the Identification of AerobicGram-Negative Bacteria / 630NIELS NORSKOV-LAURITSEN ANDWINNIE RIDDERBERG36 Neisseria / 640JOHANNES ELIAS, MATTHIAS FROSCH, ANDULRICH VOGEL37 Aggregatibacter, Capnocytophaga, Eikenella,Kingella, Pasteurella, and Other Fastidious orRarely Encountered Gram-Negative Rods / 656REINHARD ZBINDEN38 Haemophilus / 670MARK D. GONZALEZ ANDNATHAN A. LEDEBOER39 Escherichia, Shigella, and Salmonella / 688BLAKE W. BUCHAN, MATTHEW L. FARON,ROMNEY M. HUMPHRIES, JOHN DEKKER, ANDNATHAN A. LEDEBOER40 Klebsiella and Selected Enterobacterales / 724STEPHEN J. FORSYTHE, JOHANN PITOUT,ANGELLA CHARNOT-KATSIKAS, KEVIN ALBY,AND KAREN M. FRANK41 Yersinia / 751LUKE C. KINGRY, CHERYL L. TARR, ANDJEANNINE M. PETERSEN42 Aeromonas / 765BRIGITTE LAMY AND AMY J. HORNEMAN43 Vibrio and Related Organisms / 775CHERYL L. TARR, WILLIAM A. GLOVER II,YAN BOUCHER, AND JOHN J. FARMER III44 Pseudomonas / 787NIELS HOIBY, OANA CIOFU, ANDTHOMAS BJARNSHOLT45 Burkholderia, Stenotrophomonas, Ralstonia,Cupriavidus, Pandoraea, Brevundimonas,Comamonas, Delftia, and Acidovorax / 807JOHN J. LiPUMA, BART J. CURRIE, SHARON J.PEACOCK, AND PETER A. R. VANDAMME46 Acinetobacter, Chryseobacterium,Moraxella, and Other NonfermentativeGram-Negative Rods / 829PIET COOLS, ALEXANDR NEMEC, PETER KAEMPFER,AND MARIO VANEECHOUTTE47 Bordetella and Related Genera / 858PAUL E. KILGORE AND TOM COENYE48 Francisella / 871ELIZABETH A. DIETRICH ANDJEANNINE M. PETERSEN49 Brucella / 883GEORGE F. ARAJ50 Bartonella / 893J. STEPHEN DUMLER, KAREN C. CARROLL,AND ROBIN PATEL51 Legionella / 905PAUL H. EDELSTEINAnaerobic Bacteria52 Approaches to the Identification of AnaerobicBacteria / 921ANDREJ WEINTRAUB53 Peptostreptococcus, Finegoldia,Anaerococcus, Peptoniphilus, Parvimonas,Murdochiella, Veillonella, and OtherAnaerobic Cocci / 925ALIDA C. M. VELOO AND CRYSTAL N. JOHNSON54 Actinomyces, Lactobacillus, Cutibacterium,and Other Non-Spore-Forming AnaerobicGram-Positive Rods / 938SUSAN M. BUTLER-WU AND ROSEMARY C. SHE55 Clostridium and Clostridioides / 968ED KUIJPER AND FREDERIC BARBUT56 Bacteroides, Porphyromonas, Prevotella,Fusobacterium, and Other AnaerobicGram-Negative Rods / 995GEORG CONRADS, ELISABETH NAGY,AND EIJA KOENOENENCurved and Spiral-ShapedGram-Negative Rods57 Algorithms for Identification ofCurved and Spiral-Shaped Gram-NegativeRods / 1024IRVING NACHAMKIN58 Campylobacter and Arcobacter / 1028IRVING NACHAMKIN59 Helicobacter / 1044MARC ROGER COUTURIER60 Leptospira / 1058PAUL N. LEVETT AND RENEE L. GALLOWAY61 Borrelia / 1066MARIA E. AGUERO-ROSENFELD ANDGEROLD STANEK62 Treponema and Brachyspira: HumanHost-Associated Spirochetes / 1083ARLENE C. SENA, ALLAN PILLAY, ANDJUSTIN D. RADOLFMycoplasmas and ObligateIntracellular Bacteria63 General Approaches to Identification ofMycoplasma, Ureaplasma, and ObligateIntracellular Bacteria / 1109CECILE BEBEAR AND J. STEPHEN DUMLER64 Mycoplasma and Ureaplasma / 1117KEN B. WAITES AND CECILE BEBEAR65 Chlamydia / 1137JULIUS SCHACHTER AND MAX CHERNESKY66 Rickettsia and Orientia / 1149LUCAS S. BLANTON, DAVID H. WALKER, ANDDONALD H. BOUYER67 Ehrlichia, Anaplasma, and Related IntracellularBacteria / 1163BOBBI S. PRITT AND J. STEPHEN DUMLER68 Coxiella / 1180GILBERT J. KERSH ANDCHANTAL P. BLEEKER-ROVERS69 Tropheryma whipplei / 1189WALTER GEIssDOERFER, ANNETTE MOTER,AND CHRISTIAN BOGDANsection IIIAntibacterial Agentsand Susceptibility TestMethods / 1199VOLUME EDITOR: SANDRA S. RICHTERSECTION EDITOR: JEAN B. PATEL70 Antibacterial Agents / 120171 Mechanisms of Resistance to AntibacterialAgents / 1242PATRICIA A. BRADFORD ANDMARIANA CASTANHEIRA72 Susceptibility Test Methods: GeneralConsiderations / 1277JOHN D. TURNIDGE AND JAMES H. JORGENSEN73 Antimicrobial Susceptibility Test Methods:Dilution and Disk Diffusion Methods / 1284LAURA M. KOETH AND LINDA A. MILLER74 Antimicrobial Susceptibility TestingSystems / 1300JAMES A. KARLOWSKY AND SANDRA S. RICHTER75 Special Phenotypic Methods for DetectingAntibacterial Resistance / 1316PATRICIA J. SIMNER AND ROMNEY HUMPHRIES76 Susceptibility Test Methods: FastidiousBacteria / 1348ROMNEY M. HUMPHRIES ANDJENNIFER DIEN BARD77 Susceptibility Test Methods: AnaerobicBacteria / 1377AUDREY N. SCHUETZ ANDDARCIE E. CARPENTER78 Susceptibility Test Methods: Mycobacteria,Nocardia, and Other Actinomycetes / 1398GAIL L. WOODS, SHOU-YEAN GRACE LIN,BARBARA A. BROWN-ELLIOTT, ANDEDWARD P. DESMOND79 Molecular Detection of Antibacterial DrugResistance / 1420APRIL N. ABBOTT AND FERRIC C. FANGVolume 2section IVVirology / 1432VOLUME EDITOR: MARIE LOUISE LANDRYSECTION EDITORS: ANGELA M. CALIENDO,CHRISTINE C. GINOCCHIO, RANDALL T. HAYDEN,AND YI-WEI TANGGeneral80 Taxonomy and Classification ofViruses / 1435ELLIOT J. LEFKOWITZ81 Specimen Collection, Transport, andProcessing: Virology / 1446JAMES J. DUNN AND BENJAMIN A. PINSKY82 Reagents, Stains, Media, and Cell Cultures:Virology / 1462GERALD A. CAPRARO ANDCHRISTINE C. GINOCCHIO83 Algorithms for Detection and Identificationof Viruses / 1472MARIE LOUISE LANDRY, ANGELA M.CALIENDO, CHRISTINE C. GINOCCHIO,RANDALL HAYDEN, AND YI-WEI TANGRNA Viruses84 Human Immunodeficiency Viruses / 1477S. MICHELE OWEN85 Human T-Cell Lymphotropic Viruses / 1498WILLIAM M. SWITZER, WALID HENEINE,AND S. MICHELE OWEN86 Influenza Viruses / 1510ROBERT L. ATMAR87 Parainfluenza and Mumps Viruses / 1528RYAN F. RELICH AND DIANE S. LELAND88 Respiratory Syncytial Virus and HumanMetapneumovirus / 1541N. ESTHER BABADY AND YI-WEI TANG89 Measles and Rubella Viruses / 1560CAROLE J. HICKMAN ANDJOSEPH P. ICENOGLE90 Enteroviruses and Parechoviruses / 1576KATHLEEN A. STELLRECHT, DARYL M.LAMSON, AND JOSE R. ROMERO91 Rhinoviruses / 1592MARIE LOUISE LANDRY AND XIAOYAN LU92 Coronaviruses / 1606NAOMI J. GADSBY AND KATE E. TEMPLETON93 Hepatitis A and E Viruses / 1625JACQUES IZOPET AND NASSIM KAMAR94 Hepatitis C Virus / 1640MICHAEL S. FORMAN, BRYAN R. COBB,AND ALEXANDRA VALSAMAKIS95 Gastroenteritis Viruses / 1656XIAOLI PANG AND MAREK SMIEJA96 Rabies Lyssavirus / 1674LILLIAN A. ORCIARI, PAMELA A. YAGER,AND P. S. SATHESHKUMAR97 Arboviruses / 1685ELIZABETH A. HUNSPERGER98 Hantaviruses / 1706JOHN D. KLENA, CHENG-FENG CHIANG,AND WUN-JU SHIEH99 Arenaviruses and Filoviruses / 1719JONATHAN S. TOWNER, PIERRE E. ROLLIN,YI-WEI TANG, AND THOMAS G. KSIAZEKDNA Viruses100 Herpes Simplex Viruses and Herpes BVirus / 1740ALEXANDER L. GRENINGER, RHODA ASHLEYMORROW, AND KEITH R. JEROME101 Varicella-Zoster Virus / 1757ELISABETH PUCHHAMMER-STOECKL ANDSTEPHAN W. ABERLE102 Human Cytomegalovirus / 1770RICHARD L. HODINKA103 Epstein-Barr Virus / 1797BARBARA C. GAERTNER ANDFAUSTO BALDANTI104 Human Herpesviruses 6A, 6B, and 7 / 1814ALEXANDER L. GRENINGER, RUTH HALLSEDLAK, AND KEITH R. JEROME105 Human Herpesvirus 8 / 1826SHEILA C. DOLLARD ANDCLIFFORD J. GUNTHEL106 Adenoviruses / 1831ALBERT HEIM AND RANDALL T. HAYDEN107 Human Papillomaviruses / 1847KATE CUSCHIERI AND ELIZABETH R. UNGER108 Human Polyomaviruses / 1863GREGORY A. STORCH ANDRICHARD S. BULLER109 Parvovirus B19 and Bocaviruses / 1880KEVIN E. BROWN110 Poxviruses / 1891VICTORIA A. OLSON, P. S. SATHESHKUMAR,AND INGER K. DAMON111 Hepatitis B and D Viruses / 1905YI-WEI TANG, REBECCA T. HORVAT, ANDMARIE-LOUISE LANDRYSubviral Agents112 Prion Diseases / 1923DANIEL D. RHOADS AND JIRI G. SAFARsection VAntiviral Agents andSusceptibility TestMethods / 1935VOLUME EDITOR: MARIE LOUISE LANDRYSECTION EDITORS: ANGELA M. CALIENDO,CHRISTINE C. GINOCCHIO, RANDALL T. HAYDEN,AND YI-WEI TANG113 Antiviral Agents / 1937CARLOS A. Q. SANTOS AND NELL S. LURAIN114 Mechanisms of Resistance to AntiviralAgents / 1962ROBERT W. SHAFER, GUY BOIVIN, ANDSUNWEN CHOU115 Susceptibility Test Methods: Viruses / 1985DIANA D. HUANG, BENJAMIN A. PINSKY,AND MATTHEW J. BANKOWSKIsection VIMycology / 2005VOLUME EDITOR: DAVID W. WARNOCKSECTION EDITORS: MARY E. BRANDT ANDELIZABETH M. JOHNSONGeneral116 Taxonomy, Classification, and Nomenclatureof Fungi / 2007MARY E. BRANDT AND DAVID W. WARNOCKCONTENTS n ix117 Specimen Collection, Transport, and Processing:Mycology / 2016ELIZABETH L. BERKOW ANDKARIN L. McGOWAN118 Reagents, Stains, and Media: Mycology / 2025MARK D. LINDSLEY119 General Approaches for Direct Detection andIdentification of Fungi / 2035H. RUTH ASHBEEFungi120 Candida, Cryptococcus, and Other Yeasts ofMedical Importance / 2056ANDREW M. BORMAN ANDELIZABETH M. JOHNSON121 Pneumocystis / 2087MELANIE T. CUSHION AND M. ALI RAI122 Aspergillus, Talaromyces, and Penicillium / 2103SHARON C.-A. CHEN, WIELAND MEYER, TANIAC. SORRELL, AND CATRIONA L. HALLIDAY123 Fusarium and Other Opportunistic HyalineFungi / 2132SEAN X. ZHANG, KERRY O'DONNELL, ANDDEANNA A. SUTTON124 Agents of Systemic andSubcutaneous Mucormycosis andEntomophthoromycosis / 2163DEA GARCIA-HERMOSO, ALEXANDREALANIO, OLIVIER LORTHOLARY, ANDFRANCOISE DROMER125 Histoplasma, Blastomyces, Coccidioides,Paracoccidioides, and Other Dimorphic FungiCausing Systemic Mycoses / 2187GEORGE R. THOMPSON III ANDBEATRIZ L. GOMEZ126 Trichophyton, Microsporum, Epidermophyton,and Agents of Superficial Mycoses / 2208ANDREW M. BORMAN ANDRICHARD C. SUMMERBELL127 Curvularia, Exophiala, Scedosporium,Sporothrix, and Other MelanizedFungi / 2234JOSEP GUARRO, HUGO MADRID, ANDSYBREN de HOOG128 Fungi Causing Eumycotic Mycetoma / 2261SARAH ABDALLAH AHMED, G. SYBREN deHOOG, AND WENDY W. J. van de SANDE129 Mycotoxins / 2278JOANNA TANNOUS AND NANCY P. KELLER130 Lacazia, Lagenidium, Pythium, andRhinosporidium / 2291RAQUEL VILELA AND LEONEL MENDOZA131 Microsporidia / 2305RAINER WEBER, PETER DEPLAZES, ANDALEXANDER MATHISsection VIIAntifungal Agentsand Susceptibility TestMethods / 2317VOLUME EDITOR: DAVID W. WARNOCKSECTION EDITORS: MARY E. BRANDT ANDELIZABETH M. JOHNSON132 Antifungal Agents / 2319SHAWN R. LOCKHART ANDELIZABETH L. BERKOW133 Mechanisms of Resistance to AntifungalAgents / 2334DAVID S. PERLIN134 Susceptibility Test Methods: Yeasts andFilamentous Fungi / 2351ELIZABETH M. JOHNSON ANDMAIKEN CAVLING ARENDRUPsection VIIIParasitology / 2377VOLUME EDITOR: DAVID W. WARNOCKSECTION EDITORS: BOBBI S. PRITT ANDGARY W. PROCOPGeneral135 Taxonomy and Classification of HumanEukaryotic Parasites / 2379SINA M. ADL AND BLAINE A. MATHISON136 Specimen Collection, Transport, andProcessing: Parasitology / 2389ROBYN Y. SHIMIZU AND LYNNE S. GARCIA137 Reagents, Stains, and Media:Parasitology / 2406ANDREA J. LINSCOTT AND SUSAN E. SHARP138 General Approaches for Detection andIdentification of Parasites / 2414LYNNE S. GARCIA, GRAEME P. PALTRIDGE, ANDROBYN Y. SHIMIZUParasites139 Plasmodium and Babesia / 2438BOBBI S. PRITT140 Leishmania and Trypanosoma / 2458DAVID A. BRUCKNER AND JAIME A. LABARCA141 Toxoplasma / 2473JAMES B. McAULEY AND KAMALJIT SINGH142 Pathogenic and Opportunistic Free-LivingAmebae / 2486JENNIFER R. COPE, IBNE KARIM M. ALI,AND GOVINDA S. VISVESVARA143 Intestinal and Urogenital Amebae, Flagellates,and Ciliates / 2497SUSAN NOVAK-WEEKLEY AND AMY L. LEBER144 Cystoisospora, Cyclospora, andSarcocystis / 2526DAVID S. LINDSAY AND LOUIS M. WEISS145 Cryptosporidium / 2536LIHUA XIAO AND VITALIANO CAMA146 Nematodes / 2551HARSHA SHEOREY, BEVERLEY-ANN BIGGS,AND NORBERT RYAN147 Filarial Nematodes / 2570CARMELLE T. NORICE-TRA ANDTHOMAS B. NUTMAN148 Cestodes / 2582HECTOR H. GARCIA, JUAN A. JIMENEZ, ANDHERMES ESCALANTE149 Trematodes / 2590MALCOLM K. JONES, JENNIFER KEISER, ANDDONALD P. McMANUS150 Less Common Helminths / 2606GARY W. PROCOP AND RONALD C. NEAFIE151 Arthropods of Medical Importance / 2620SAM R. TELFORD III AND BLAINE A. MATHISONsection IXAntiparasitic Agentsand Susceptibility TestMethods / 2643VOLUME EDITOR: DAVID W. WARNOCKSECTION EDITORS: GARY W. PROCOP152 Antiparasitic Agents / 2645KARIN LEDER, SARAH L. McGUINNESS, ANDPETER F. WELLER153 Mechanisms of Resistance to AntiparasiticAgents / 2669JEROME CLAIN154 Susceptibility Test Methods: Parasites / 2682W. EVAN SECOR
