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VOLUME 1 SECTION I GENERAL ISSUES IN CLINICAL MICROBIOLOGY VOLUMEEDITOR: JAMES H. JORGENSEN SECTION EDITOR: MELVIN P. WEINSTEIN 1Introduction to the Eighth Edition of the Manual of Clinical MicrobiologyPATRICK R. MURRAY 2 Laboratory Management DAVID L. SEWELL AND JAMES D.MACLOWRY 3 Laboratory Design MICHAEL L. WILSON AND L. BARTH RELLER 4Laboratory Consultation, Communication, and Information Systems JOSEPH M.CAMPOS 5 Pathogenic and Indigenous Microorganisms of Humans PAUL A. GRANATO6 General Principles of Specimen Collection and Handling J. MICHAEL MILLER,HARVEY T. HOLMES, AND KAREN KRISHER 7 Procedures for the Storage ofMicroorganisms LARRY G. REIMER AND KAREN C. CARROLL SECTION II THECLINICAL MICROBIOLOGY LABORATORY IN INFECTION DETECTION, PREVENTION, ANDCONTROL VOLUME EDITOR: MICHAEL A. PFALLER SECTION EDITOR: JOHN E. MCGOWAN,JR. 8 Decontamination, Disinfection, and Sterilization ANDREAS F. WIDMERAND RENO FREI 9 Prevention and Control of Laboratory-Acquired InfectionsANDREAS VOSS AND ERIC NULENS 10 Laboratory Detection of Potential Agents ofBioterrorism JAMES W. SNYDER AND ALICE S. WEISSFELD 11 Infection ControlEpidemiology and Clinical Microbiology DANIEL J. DIEKEMA AND MICHAEL A.PFALLER 12 Laboratory Procedures for the Epidemiological Analysis ofMicroorganisms DAVID R. SOLL, SHAWN R. LOCKHART, AND CLAUDE PUJOL 13Investigation of Foodborne and Waterborne Disease Outbreaks JOHN BESSER,JAMES BEEBE, AND BALA SWAMINATHAN SECTION III DIAGNOSTIC TECHNOLOGIES INCLINICAL MICROBIOLOGY / 183 VOLUME EDITOR: JAMES H. JORGENSEN SECTIONEDITOR: MELVIN P. WEINSTEIN 14 Manual and Automated Systems for Detectionand Identification of Microorganisms / 185 CAROLINE MOHR O'HARA, MELVIN P.WEINSTEIN, AND J. MICHAEL MILLER 15 Susceptibility Testing Instrumentationand Computerized Expert Systems for Data Analysis and Interpretation / 208MARY JANE FERRARO AND JAMES H. JORGENSEN 16 Immunoassays for the Diagnosisof Infectious Diseases / 218 NIEL T. CONSTANTINE AND DELORES P. LANA 17Molecular Detection and Identification of Microorganisms / 234 FREDERICK S.NOLTE AND ANGELA M. CALIENDO 18 Principles of Stains and Media / 257KIMBERLE C. CHAPIN AND PATRICK R. MURRAY SECTION IV BACTERIOLOGY / 268VOLUME EDITOR: ELLEN JO BARON SECTION EDITORS: J. STEPHEN DUMLER, GUIDOFUNKE, J. MICHAEL JANDA, AND ALEXANDER VON GRAEVENITZ GENERAL 19 Taxonomyand Classification of Bacteria / 271 PETER A. R. VANDAMME 20 SpecimenCollection, Transport, and Processing: Bacteriology / 286 RICHARD B.THOMSON, JR., AND J. MICHAEL MILLER 21 Algorithm for Identification ofAerobic Gram-Positive Cocci / 331 KATHRYN L. RUOFF 22 Algorithm forIdentification of Aerobic Gram-Positive Rods / 334 GUIDO FUNKE 23Algorithms for Identification of Aerobic Gram-Negative Bacteria / 337 PAULC. SCHRECKENBERGER AND JANE D. WONG 24 Algorithm for Identification ofAnaerobic Bacteria / 343 DIANE M. CITRON 25 Algorithms for Identificationof Curved and Spiral-Shaped Gram-Negative Rods / 345 JAMES VERSALOVIC 26Algorithms for Identification of Mycoplasma, Ureaplasma, and ObligateIntracellular Bacteria / 349 J. STEPHEN DUMLER 27 Reagents, Stains, andMedia: Bacteriology / 354 KIMBERLE C. CHAPIN AND TSAI-LING LAUDERDALEGRAM-POSITIVE COCCI 28 Staphylococcus, Micrococcus, and OtherCatalase-Positive Cocci That Grow Aerobically / 384 TAMMY L. BANNERMAN 29Streptococcus / 405 KATHRYN L. RUOFF, R. A. WHILEY, AND D. BEIGHTON 30Enterococcus / 422 LU CIA MARTINS TEIXEIRA AND RICHARD R. FACKLAM 31Aerococcus, Abiotrophia, and Other Infrequently Isolated AerobicCatalase-Negative, Gram-Positive Cocci / 434 KATHRYN L. RUOFF GRAM-POSITIVERODS 32 Bacillus and Other Aerobic Endospore-Forming Bacteria / 445 NIALLA. LOGAN AND PETER C. B. TURNBULL 33 Listeria and Erysipelothrix / 461JACQUES BILLE, JOCELYNE ROCOURT, AND BALA SWAMINATHAN 34 CoryneformGram-Positive Rods / 472 GUIDO FUNKE AND KATHRYN A. BERNARD 35 Nocardia,Rhodococcus, Gordonia, Actinomadura, Streptomyces, and Other AerobicActinomycetes / 502 JUNE M. BROWN AND MICHAEL M. MCNEIL 36 Mycobacterium:General Characteristics, Isolation, and Staining Procedures / 532 GABY E.PFYFFER, BARBARA A. BROWN-ELLIOTT, AND RICHARD J. WALLACE, JR. 37Mycobacterium: Phenotypic and Genotypic Identification / 560 VE RONIQUEVINCENT, BARBARA A. BROWN-ELLIOTT, KENNETH C. JOST, JR., AND RICHARD J.WALLACE, JR. GRAM-NEGATIVE BACTERIA 38 Neisseria and Moraxella catarrhalis/ 585 WILLIAM M. JANDA AND JOAN S. KNAPP 39 Actinobacillus, Capnocytophaga,Eikenella, Kingella, Pasteurella, and Other Fastidious or Rarely EncounteredGram-Negative Rods / 609 ALEXANDER VON GRAEVENITZ, REINHARD ZBINDEN, ANDREINIER MUTTERS 40 Haemophilus / 623 MOGENS KILIAN 41 Enterobacteriaceae:Introduction and Identification / 636 J. J. FARMER III 42 Escherichia,Shigella, and Salmonella / 654 CHERYL A. BOPP, FRANCES W. BRENNER, PATRICIAI. FIELDS, JOY G. WELLS, AND NANCY A. STROCKBINE 43 Yersinia / 672 JOCHENBOCKEMU HL AND JANE D. WONG 44 Klebsiella, Enterobacter, Citrobacter,Serratia, Plesiomonas, and Other Enterobacteriaceae / 684 SHARON L. ABBOTT45 Aeromonas / 701 SHARON L. ABBOTT 46 Vibrio / 706 J. J. FARMER III, J.MICHAEL JANDA, AND KAREN BIRKHEAD 47 Pseudomonas / 719 DEANNA L. KISKA ANDPETER H. GILLIGAN 48 Burkholderia, Stenotrophomonas, Ralstonia,Brevundimonas, Comamonas, Delftia, Pandoraea, and Acidovorax / 729 PETER H.GILLIGAN, GARY LUM,PETER A. R. VANDAMME, AND SUSAN WHITTIER 49Acinetobacter, Achromobacter, Chryseobacterium, Moraxella, and OtherNonfermentative Gram-Negative Rods / 749 PAUL C. SCHRECKENBERGER, MARYAM I.DANESHVAR, ROBBIN S. WEYANT, AND DANNIE G. HOLLIS 50 Bordetella / 780 MIKEJ. LOEFFELHOLZ 51 Francisella and Brucella / 789 MAY C. CHU AND ROBBIN S.WEYANT 52 Legionella / 809 JANET E. STOUT, JOHN D. RIHS, AND VICTOR L. YU53 Bartonella and Afipia / 824 DAVID F. WELCH AND LEONARD N. SLATERANAEROBIC BACTERIA 54 Clostridium / 835 STEPHEN D. ALLEN, CHRISTOPHER L.EMERY, AND DAVID M. LYERLY 55 Peptostreptococcus, Propionibacterium,Lactobacillus, Actinomyces, and Other Non- Spore-Forming AnaerobicGram-Positive Bacteria / 857 BERNARD J. MONCLA AND SHARON L. HILLIER 56Bacteroides, Porphyromonas, Prevotella, Fusobacterium, and Other AnaerobicGram- Negative Bacteria / 880 HANNELE R. JOUSIMIES-SOMER, PAULA H.SUMMANEN, HANNAH WEXLER, SYDNEY M. FINEGOLD, SAHEER E. GHARBIA, AND HAROUN N.SHAH CURVED AND SPIRAL-SHAPED GRAM-NEGATIVE RODS 57 Campylobacter andArcobacter / 902 IRVING NACHAMKIN 58 Helicobacter / 915 JAMES VERSALOVICAND JAMES G. FOX 59 Leptospira and Leptonema / 929 PAUL N. LEVETT 60Borrelia / 937 BETTINA WILSKE AND MARTIN E. SCHRIEFER 61 Treponema andOther Human Host-Associated Spirochetes / 955 STEVEN J. NORRIS, VICTORIAPOPE, ROBERT E. JOHNSON, AND SANDRA A. LARSEN MYCOPLASMAS AND OBLIGATEINTRACELLULAR BACTERIA 62 Mycoplasma and Ureaplasma / 972 KEN B. WAITES,YASUKO RIKIHISA, AND DAVID TAYLOR-ROBINSON 63 Chlamydia and Chlamydophila /991 JAMES B. MAHONY, BRIAN K. COOMBES, AND MAX A. CHERNESKY 64 Rickettsia /1005 DAVID H. WALKER AND DONALD H. BOUYER 65 Ehrlichia, Anaplasma,Neorickettsia, and Aegyptianella / 1015 MARIA E. AGUERO-ROSENFELD AND J.STEPHEN DUMLER 66 Coxiella / 1030 PHILIPPE BROUQUI, THOMAS J. MARRIE, ANDDIDIER RAOULT SECTION V ANTIBACTERIAL AGENTS AND SUSCEPTIBILITY TESTMETHODS / 1037 VOLUME EDITOR: JAMES H. JORGENSEN SECTION EDITORS: MARY JANEFERRARO AND JOHN D. TURNIDGE 67 Antibacterial Agents / 1039 JOSEPH D. C.YAO AND ROBERT C. MOELLERING, JR. 68 Mechanisms of Resistance toAntibacterial Agents / 1074 LOUIS B. RICE, DANIEL SAHM, AND ROBERT A. BONOMO69 Susceptibility Test Methods: General Considerations / 1102 JOHN D.TURNIDGE, MARY JANE FERRARO, AND JAMES H. JORGENSEN 70 Susceptibility TestMethods: Dilution and Disk Diffusion Methods / 1108 JAMES H. JORGENSEN ANDJOHN D. TURNIDGE 71 Susceptibility Test Methods: Fastidious Bacteria / 1128JANET FICK HINDLER AND JANA M. SWENSON 72 Susceptibility Test Methods:Anaerobic Bacteria / 1141 DIANE M. CITRON AND DAVID W. HECHT 73Susceptibility Test Methods: Mycobacteria / 1149 CLARK B. INDERLIED AND GABYE. PFYFFER 74 Special Phenotypic Methods for Detecting AntibacterialResistance / 1178 JANA M. SWENSON, JANET FICK HINDLER, AND JAMES H.JORGENSEN 75 Detection and Characterization of Antimicrobial ResistanceGenes in Bacteria / 1196 J. KAMILE RASHEED AND FRED C. TENOVER VOLUME 2SECTION VI VIROLOGY / 1214 VOLUME EDITOR: ROBERT H. YOLKEN SECTIONEDITORS: MARIE LOUISE LANDRY, THOMAS F. SMITH, AND JOSEPH L. WANER GENERAL76 Taxonomy and Classification of Viruses / 1217 CORNELIA BU CHEN-OSMOND77 Specimen Collection, Transport, and Processing: Virology / 1227 MICHAELS. FORMAN AND ALEXANDRA VALSAMAKIS 78 Algorithms for Detection andIdentification of Viruses / 1242 ROBERT H. YOLKEN, THOMAS F. SMITH, JOSEPHL. WANER, AND MARIE LOUISE LANDRY 79 Reagents, Stains, Media, and CellLines: Virology / 1246 KIMBERLE C. CHAPIN AND FRED W. WESTENFELD VIRUSES80 Human Immunodeficiency Viruses / 1253 JO RG SCHU PBACH 81 Human T-CellLymphotropic Virus Types 1 and 2 / 1282 CHARLENE S. DEZZUTTI, ELLIOT P.COWAN, AND RENU B. LAL 82 Herpes Simplex Viruses and Herpes B Virus / 1291KEITH R. JEROME AND RHODA L. ASHLEY 83 Human Cytomegalovirus / 1304 RICHARDL. HODINKA 84 Varicella-Zoster Virus / 1319 ANNE A. GERSHON, PHILIPLARUSSA, AND SHARON P. STEINBERG 85 Epstein-Barr Virus / 1331 ANNIKA LINDE86 Human Herpesviruses 6, 7, and 8 / 1341 PHILIP E. PELLETT AND GRAHAMTIPPLES 87 Influenza Viruses / 1360 NANCY J. COX AND THEDI ZIEGLER 88Mumps and Parainfluenza Viruses / 1368 JOSEPH L. WANER AND ELLA M. SWIERKOSZ89 Respiratory Syncytial Virus / 1378 DEBRA A. TRISTRAM 90 Measles andRubella Viruses / 1389 WILLIAM J. BELLINI AND JOSEPH P. ICENOGLE 91Adenoviruses / 1404 PAUL D. SWENSON, GO RAN WADELL, ANNIKA ALLARD, AND JOHNC. HIERHOLZER 92 Rhinoviruses / 1418 MARIE LOUISE LANDRY 93 Enteroviruses/ 1427 JOSE R. ROMERO AND HARLEY A. ROTBART 94 Rotaviruses, Caliciviruses,Astroviruses, and Other Diarrheic Viruses / 1439 MARTIN PETRIC AND RAYMONDTELLIER 95 Hepatitis A Virus / 1452 EDWIN A. BROWN AND JACK T. STAPLETON96 Hepatitis B and D Viruses / 1464 REBECCA T. HORVAT AND GARY E. TEGTMEIER97 Hepatitis C and G Viruses / 1480 MARGARET C. SHUHART AND DAVID R. GRETCH98 Hepatitis E Virus / 1495 GEORGE G. SCHLAUDER AND GEORGE J. DAWSON 99Human Papillomavirus / 1512 QINGHUA FENG AND NANCY B. KIVIAT 100 HumanPolyomaviruses / 1524 EUGENE O. MAJOR, MANETH GRAVELL, AND JEAN HOU 101Human Parvoviruses / 1534 MARIALUISA ZERBINI AND MONICA MUSIANI 102 RabiesVirus / 1544 JEAN S. SMITH 103 Arboviruses / 1553 THEODORE F. TSAI ANDLAURA J. CHANDLER 104 Filoviruses and Arenaviruses / 1570 PETER B.JAHRLING, STUART T. NICHOL, PIERRE E. ROLLIN, AND THOMAS G. KSIAZEK 105Poxviruses That Infect Humans / 1583 INGER K. DAMON AND JOSEPH J. ESPOSITO106 Transmissible Spongiform Encephalopathies / 1592 DAVID M. ASHER SECTIONVII ANTIVIRAL AGENTS AND SUSCEPTIBILITY TEST METHODS / 1605 VOLUME EDITOR:JAMES H. JORGENSEN SECTION EDITOR: JOHN D. TURNIDGE 107 Antiviral Agents /1607 ELLA M. SWIERKOSZ 108 Mechanisms of Resistance to Antiviral Agents /1625 ROBERT W. SHAFER AND SUNWEN CHOU 109 Susceptibility Test Methods:Viruses / 1638 ELLA M. SWIERKOSZ AND MAX Q. ARENS SECTION VIII MYCOLOGY /1651 VOLUME EDITOR: MICHAEL A. PFALLER SECTION EDITOR: ROBERT A. FROMTLINGGENERAL 110 Taxonomy, Classification, and Morphology of the Fungi / 1653ROBERT A. FROMTLING, JUDITH C. RHODES, AND DENNIS M. DIXON 111 SpecimenCollection, Transport, and Processing: Mycology / 1659 DEANNA A. SUTTON 112Algorithms for Detection and Identification of Fungi / 1668 WILLIAM G. MERZAND GLENN D. ROBERTS 113 Reagents, Stains, and Media: Mycology / 1686 MARKT. LAROCCO FUNGI 114 Candida, Cryptococcus, and Other Yeasts of MedicalImportance / 1693 KEVIN C. HAZEN AND SUSAN A. HOWELL 115 Pneumocystis /1712 MELANIE T. CUSHION 116 Aspergillus, Fusarium, and Other OpportunisticMoniliaceous Fungi / 1726 LYNNE SIGLER AND PAUL E. VERWEIJ 117 Rhizopus,Rhizomucor, Absidia, and Other Agents of Systemic and SubcutaneousZygomycoses / 1761 MALCOLM D. RICHARDSON, PIRKKO KOUKILA-KA HKO LA , ANDGILLIAN S. SHANKLAND 118 Histoplasma, Blastomyces, Coccidioides, and OtherDimorphic Fungi Causing Systemic Mycoses / 1781 THOMAS J. WALSH, DAVISE H.LARONE, WILEY A. SCHELL, AND THOMAS G. MITCHELL 119 Trichophyton,Microsporum, Epidermophyton, and Agents of Superficial Mycoses / 1798RICHARD C. SUMMERBELL 120 Bipolaris, Exophiala, Scedosporium, Sporothrix,and Other Dematiaceous Fungi / 1820 WILEY A. SCHELL, IRA F. SALKIN, ANDMICHAEL R. MCGINNIS 121 Fungi Causing Eumycotic Mycetoma / 1848 MICHAEL R.MCGINNIS AND ARVIND A. PADHYE SECTION IX ANTIFUNGAL AGENTS ANDSUSCEPTIBILITY TEST METHODS / 1857 VOLUME EDITOR: JAMES H. JORGENSENSECTION EDITOR: JOHN D. TURNIDGE 122 Antifungal Agents / 1859 SEVTAP ARIKANAND JOHN H. REX 123 Mechanisms of Resistance to Antifungal Agents / 1869THEODORE C. WHITE 124 Susceptibility Test Methods: Yeasts and FilamentousFungi / 1880 ANA V. ESPINEL-INGROFF AND MICHAEL A. PFALLER SECTION XPARASITOLOGY / 1895 VOLUME EDITOR: MICHAEL A. PFALLER SECTION EDITOR: LYNNES. GARCIA GENERAL 125 Taxonomy and Classification of Human Parasites / 1897FRANCES E. G. COX 126 Specimen Collection, Transport, and Processing:Parasitology / 1903 LYNNE S. GARCIA, ROBYN Y. SHIMIZU, AND PETER DEPLAZES127 Algorithms for Detection and Identification of Parasites / 1920 LYNNE S.GARCIA, ROBYN Y. SHIMIZU, AND GRAEME P. PALTRIDGE 128 Reagents, Stains, andMedia: Parasitology / 1939 SUSAN E. SHARP PARASITES 129 Plasmodium andBabesia / 1944 WILLIAM O. ROGERS 130 Leishmania and Trypanosoma / 1960DAVID A. BRUCKNER AND JAIME A. LABARCA 131 Toxoplasma / 1970 MARIANNAWILSON, JEFFERY L. JONES, AND JAMES B. MCAULEY 132 Pathogenic andOpportunistic Free-Living Amebae / 1981 GOVINDA S. VISVESVARA 133Intestinal and Urogenital Amebae, Flagellates, and Ciliates / 1990 AMY L.LEBER AND SUSAN M. NOVAK 134 Cryptosporidium, Cyclospora, and Isospora /2008 YNES R. ORTEGA AND MICHAEL ARROWOOD 135 Microsporidia / 2020 RAINERWEBER AND ELIZABETH U. CANNING 136 Intestinal Helminths / 2031 LAWRENCE R.ASH AND THOMAS C. ORIHEL 137 Tissue Helminths / 2047 THOMAS C. ORIHEL ANDLAWRENCE R. ASH 138 Arthropods of Medical Importance / 2061 THOMAS R.FRITSCHE SECTION XI ANTIPARASITIC AGENTS AND SUSCEPTIBILITY TEST METHODS /2079 VOLUME EDITOR: JAMES H. JORGENSEN SECTION EDITOR: MARY JANE FERRARO139 Antiparasitic Agents / 2081 KAREN LEDER AND PETER F. WELLER 140Mechanisms of Resistance to Antiparasitic Agents / 2098 W. EVAN SECOR ANDPHUC NGUYEN-DINH 141 Susceptibility Test Methods: Parasites / 2108 PHUCNGUYEN-DINH AND W. EVAN SECOR