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The Manual of Clinical Microbiology


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VOLUME 1 SECTION I GENERAL ISSUES IN CLINICAL MICROBIOLOGY VOLUME EDITOR: JAMES H. JORGENSEN SECTION EDITOR: MELVIN P. WEINSTEIN 1 Introduction to the Eighth Edition of the Manual of Clinical Microbiology PATRICK R. MURRAY 2 Laboratory Management DAVID L. SEWELL AND JAMES D. MACLOWRY 3 Laboratory Design MICHAEL L. WILSON AND L. BARTH RELLER 4 Laboratory Consultation, Communication, and Information Systems JOSEPH M. CAMPOS 5 Pathogenic and Indigenous Microorganisms of Humans PAUL A. GRANATO 6 General Principles of Specimen Collection and Handling J. MICHAEL MILLER, HARVEY T. HOLMES, AND KAREN KRISHER 7 Procedures for the Storage of Microorganisms LARRY G. REIMER AND KAREN C. CARROLL SECTION II THE CLINICAL MICROBIOLOGY LABORATORY IN INFECTION DETECTION, PREVENTION, AND CONTROL VOLUME EDITOR: MICHAEL A. PFALLER SECTION EDITOR: JOHN E. MCGOWAN, JR. 8 Decontamination, Disinfection, and Sterilization ANDREAS F. WIDMER AND RENO FREI 9 Prevention and Control of Laboratory-Acquired Infections ANDREAS VOSS AND ERIC NULENS 10 Laboratory Detection of Potential Agents of Bioterrorism JAMES W. SNYDER AND ALICE S. WEISSFELD 11 Infection Control Epidemiology and Clinical Microbiology DANIEL J. DIEKEMA AND MICHAEL A. PFALLER 12 Laboratory Procedures for the Epidemiological Analysis of Microorganisms DAVID R. SOLL, SHAWN R. LOCKHART, AND CLAUDE PUJOL 13 Investigation of Foodborne and Waterborne Disease Outbreaks JOHN BESSER, JAMES BEEBE, AND BALA SWAMINATHAN SECTION III DIAGNOSTIC TECHNOLOGIES IN CLINICAL MICROBIOLOGY / 183 VOLUME EDITOR: JAMES H. JORGENSEN SECTION EDITOR: MELVIN P. WEINSTEIN 14 Manual and Automated Systems for Detection and Identification of Microorganisms / 185 CAROLINE MOHR O'HARA, MELVIN P. WEINSTEIN, AND J. MICHAEL MILLER 15 Susceptibility Testing Instrumentation and Computerized Expert Systems for Data Analysis and Interpretation / 208 MARY JANE FERRARO AND JAMES H. JORGENSEN 16 Immunoassays for the Diagnosis of Infectious Diseases / 218 NIEL T. CONSTANTINE AND DELORES P. LANA 17 Molecular Detection and Identification of Microorganisms / 234 FREDERICK S. NOLTE AND ANGELA M. CALIENDO 18 Principles of Stains and Media / 257 KIMBERLE C. CHAPIN AND PATRICK R. MURRAY SECTION IV BACTERIOLOGY / 268 VOLUME EDITOR: ELLEN JO BARON SECTION EDITORS: J. STEPHEN DUMLER, GUIDO FUNKE, J. MICHAEL JANDA, AND ALEXANDER VON GRAEVENITZ GENERAL 19 Taxonomy and Classification of Bacteria / 271 PETER A. R. VANDAMME 20 Specimen Collection, Transport, and Processing: Bacteriology / 286 RICHARD B. THOMSON, JR., AND J. MICHAEL MILLER 21 Algorithm for Identification of Aerobic Gram-Positive Cocci / 331 KATHRYN L. RUOFF 22 Algorithm for Identification of Aerobic Gram-Positive Rods / 334 GUIDO FUNKE 23 Algorithms for Identification of Aerobic Gram-Negative Bacteria / 337 PAUL C. SCHRECKENBERGER AND JANE D. WONG 24 Algorithm for Identification of Anaerobic Bacteria / 343 DIANE M. CITRON 25 Algorithms for Identification of Curved and Spiral-Shaped Gram-Negative Rods / 345 JAMES VERSALOVIC 26 Algorithms for Identification of Mycoplasma, Ureaplasma, and Obligate Intracellular Bacteria / 349 J. STEPHEN DUMLER 27 Reagents, Stains, and Media: Bacteriology / 354 KIMBERLE C. CHAPIN AND TSAI-LING LAUDERDALE GRAM-POSITIVE COCCI 28 Staphylococcus, Micrococcus, and Other Catalase-Positive Cocci That Grow Aerobically / 384 TAMMY L. BANNERMAN 29 Streptococcus / 405 KATHRYN L. RUOFF, R. A. WHILEY, AND D. BEIGHTON 30 Enterococcus / 422 LU CIA MARTINS TEIXEIRA AND RICHARD R. FACKLAM 31 Aerococcus, Abiotrophia, and Other Infrequently Isolated Aerobic Catalase-Negative, Gram-Positive Cocci / 434 KATHRYN L. RUOFF GRAM-POSITIVE RODS 32 Bacillus and Other Aerobic Endospore-Forming Bacteria / 445 NIALL A. LOGAN AND PETER C. B. TURNBULL 33 Listeria and Erysipelothrix / 461 JACQUES BILLE, JOCELYNE ROCOURT, AND BALA SWAMINATHAN 34 Coryneform Gram-Positive Rods / 472 GUIDO FUNKE AND KATHRYN A. BERNARD 35 Nocardia, Rhodococcus, Gordonia, Actinomadura, Streptomyces, and Other Aerobic Actinomycetes / 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. 37 Mycobacterium: Phenotypic and Genotypic Identification / 560 VE RONIQUE VINCENT, 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 Encountered Gram-Negative Rods / 609 ALEXANDER VON GRAEVENITZ, REINHARD ZBINDEN, AND REINIER 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, PATRICIA I. FIELDS, JOY G. WELLS, AND NANCY A. STROCKBINE 43 Yersinia / 672 JOCHEN BOCKEMU HL AND JANE D. WONG 44 Klebsiella, Enterobacter, Citrobacter, Serratia, Plesiomonas, and Other Enterobacteriaceae / 684 SHARON L. ABBOTT 45 Aeromonas / 701 SHARON L. ABBOTT 46 Vibrio / 706 J. J. FARMER III, J. MICHAEL JANDA, AND KAREN BIRKHEAD 47 Pseudomonas / 719 DEANNA L. KISKA AND PETER 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 49 Acinetobacter, Achromobacter, Chryseobacterium, Moraxella, and Other Nonfermentative Gram-Negative Rods / 749 PAUL C. SCHRECKENBERGER, MARYAM I. DANESHVAR, ROBBIN S. WEYANT, AND DANNIE G. HOLLIS 50 Bordetella / 780 MIKE J. 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. YU 53 Bartonella and Afipia / 824 DAVID F. WELCH AND LEONARD N. SLATER ANAEROBIC BACTERIA 54 Clostridium / 835 STEPHEN D. ALLEN, CHRISTOPHER L. EMERY, AND DAVID M. LYERLY 55 Peptostreptococcus, Propionibacterium, Lactobacillus, Actinomyces, and Other Non- Spore-Forming Anaerobic Gram-Positive Bacteria / 857 BERNARD J. MONCLA AND SHARON L. HILLIER 56 Bacteroides, Porphyromonas, Prevotella, Fusobacterium, and Other Anaerobic Gram- 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 and Arcobacter / 902 IRVING NACHAMKIN 58 Helicobacter / 915 JAMES VERSALOVIC AND JAMES G. FOX 59 Leptospira and Leptonema / 929 PAUL N. LEVETT 60 Borrelia / 937 BETTINA WILSKE AND MARTIN E. SCHRIEFER 61 Treponema and Other Human Host-Associated Spirochetes / 955 STEVEN J. NORRIS, VICTORIA POPE, ROBERT E. JOHNSON, AND SANDRA A. LARSEN MYCOPLASMAS AND OBLIGATE INTRACELLULAR 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, AND DIDIER RAOULT SECTION V ANTIBACTERIAL AGENTS AND SUSCEPTIBILITY TEST METHODS / 1037 VOLUME EDITOR: JAMES H. JORGENSEN SECTION EDITORS: MARY JANE FERRARO AND JOHN D. TURNIDGE 67 Antibacterial Agents / 1039 JOSEPH D. C. YAO AND ROBERT C. MOELLERING, JR. 68 Mechanisms of Resistance to Antibacterial Agents / 1074 LOUIS B. RICE, DANIEL SAHM, AND ROBERT A. BONOMO 69 Susceptibility Test Methods: General Considerations / 1102 JOHN D. TURNIDGE, MARY JANE FERRARO, AND JAMES H. JORGENSEN 70 Susceptibility Test Methods: Dilution and Disk Diffusion Methods / 1108 JAMES H. JORGENSEN AND JOHN D. TURNIDGE 71 Susceptibility Test Methods: Fastidious Bacteria / 1128 JANET FICK HINDLER AND JANA M. SWENSON 72 Susceptibility Test Methods: Anaerobic Bacteria / 1141 DIANE M. CITRON AND DAVID W. HECHT 73 Susceptibility Test Methods: Mycobacteria / 1149 CLARK B. INDERLIED AND GABY E. PFYFFER 74 Special Phenotypic Methods for Detecting Antibacterial Resistance / 1178 JANA M. SWENSON, JANET FICK HINDLER, AND JAMES H. JORGENSEN 75 Detection and Characterization of Antimicrobial Resistance Genes in Bacteria / 1196 J. KAMILE RASHEED AND FRED C. TENOVER VOLUME 2 SECTION VI VIROLOGY / 1214 VOLUME EDITOR: ROBERT H. YOLKEN SECTION EDITORS: MARIE LOUISE LANDRY, THOMAS F. SMITH, AND JOSEPH L. WANER GENERAL 76 Taxonomy and Classification of Viruses / 1217 CORNELIA BU CHEN-OSMOND 77 Specimen Collection, Transport, and Processing: Virology / 1227 MICHAEL S. FORMAN AND ALEXANDRA VALSAMAKIS 78 Algorithms for Detection and Identification of Viruses / 1242 ROBERT H. YOLKEN, THOMAS F. SMITH, JOSEPH L. WANER, AND MARIE LOUISE LANDRY 79 Reagents, Stains, Media, and Cell Lines: Virology / 1246 KIMBERLE C. CHAPIN AND FRED W. WESTENFELD VIRUSES 80 Human Immunodeficiency Viruses / 1253 JO RG SCHU PBACH 81 Human T-Cell Lymphotropic Virus Types 1 and 2 / 1282 CHARLENE S. DEZZUTTI, ELLIOT P. COWAN, AND RENU B. LAL 82 Herpes Simplex Viruses and Herpes B Virus / 1291 KEITH R. JEROME AND RHODA L. ASHLEY 83 Human Cytomegalovirus / 1304 RICHARD L. HODINKA 84 Varicella-Zoster Virus / 1319 ANNE A. GERSHON, PHILIP LARUSSA, AND SHARON P. STEINBERG 85 Epstein-Barr Virus / 1331 ANNIKA LINDE 86 Human Herpesviruses 6, 7, and 8 / 1341 PHILIP E. PELLETT AND GRAHAM TIPPLES 87 Influenza Viruses / 1360 NANCY J. COX AND THEDI ZIEGLER 88 Mumps and Parainfluenza Viruses / 1368 JOSEPH L. WANER AND ELLA M. SWIERKOSZ 89 Respiratory Syncytial Virus / 1378 DEBRA A. TRISTRAM 90 Measles and Rubella Viruses / 1389 WILLIAM J. BELLINI AND JOSEPH P. ICENOGLE 91 Adenoviruses / 1404 PAUL D. SWENSON, GO RAN WADELL, ANNIKA ALLARD, AND JOHN C. 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 RAYMOND TELLIER 95 Hepatitis A Virus / 1452 EDWIN A. BROWN AND JACK T. STAPLETON 96 Hepatitis B and D Viruses / 1464 REBECCA T. HORVAT AND GARY E. TEGTMEIER 97 Hepatitis C and G Viruses / 1480 MARGARET C. SHUHART AND DAVID R. GRETCH 98 Hepatitis E Virus / 1495 GEORGE G. SCHLAUDER AND GEORGE J. DAWSON 99 Human Papillomavirus / 1512 QINGHUA FENG AND NANCY B. KIVIAT 100 Human Polyomaviruses / 1524 EUGENE O. MAJOR, MANETH GRAVELL, AND JEAN HOU 101 Human Parvoviruses / 1534 MARIALUISA ZERBINI AND MONICA MUSIANI 102 Rabies Virus / 1544 JEAN S. SMITH 103 Arboviruses / 1553 THEODORE F. TSAI AND LAURA J. CHANDLER 104 Filoviruses and Arenaviruses / 1570 PETER B. JAHRLING, STUART T. NICHOL, PIERRE E. ROLLIN, AND THOMAS G. KSIAZEK 105 Poxviruses That Infect Humans / 1583 INGER K. DAMON AND JOSEPH J. ESPOSITO 106 Transmissible Spongiform Encephalopathies / 1592 DAVID M. ASHER SECTION VII 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. FROMTLING GENERAL 110 Taxonomy, Classification, and Morphology of the Fungi / 1653 ROBERT A. FROMTLING, JUDITH C. RHODES, AND DENNIS M. DIXON 111 Specimen Collection, Transport, and Processing: Mycology / 1659 DEANNA A. SUTTON 112 Algorithms for Detection and Identification of Fungi / 1668 WILLIAM G. MERZ AND GLENN D. ROBERTS 113 Reagents, Stains, and Media: Mycology / 1686 MARK T. LAROCCO FUNGI 114 Candida, Cryptococcus, and Other Yeasts of Medical Importance / 1693 KEVIN C. HAZEN AND SUSAN A. HOWELL 115 Pneumocystis / 1712 MELANIE T. CUSHION 116 Aspergillus, Fusarium, and Other Opportunistic Moniliaceous Fungi / 1726 LYNNE SIGLER AND PAUL E. VERWEIJ 117 Rhizopus, Rhizomucor, Absidia, and Other Agents of Systemic and Subcutaneous Zygomycoses / 1761 MALCOLM D. RICHARDSON, PIRKKO KOUKILA-KA HKO LA , AND GILLIAN S. SHANKLAND 118 Histoplasma, Blastomyces, Coccidioides, and Other Dimorphic 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 / 1798 RICHARD C. SUMMERBELL 120 Bipolaris, Exophiala, Scedosporium, Sporothrix, and Other Dematiaceous Fungi / 1820 WILEY A. SCHELL, IRA F. SALKIN, AND MICHAEL R. MCGINNIS 121 Fungi Causing Eumycotic Mycetoma / 1848 MICHAEL R. MCGINNIS AND ARVIND A. PADHYE SECTION IX ANTIFUNGAL AGENTS AND SUSCEPTIBILITY TEST METHODS / 1857 VOLUME EDITOR: JAMES H. JORGENSEN SECTION EDITOR: JOHN D. TURNIDGE 122 Antifungal Agents / 1859 SEVTAP ARIKAN AND JOHN H. REX 123 Mechanisms of Resistance to Antifungal Agents / 1869 THEODORE C. WHITE 124 Susceptibility Test Methods: Yeasts and Filamentous Fungi / 1880 ANA V. ESPINEL-INGROFF AND MICHAEL A. PFALLER SECTION X PARASITOLOGY / 1895 VOLUME EDITOR: MICHAEL A. PFALLER SECTION EDITOR: LYNNE S. GARCIA GENERAL 125 Taxonomy and Classification of Human Parasites / 1897 FRANCES E. G. COX 126 Specimen Collection, Transport, and Processing: Parasitology / 1903 LYNNE S. GARCIA, ROBYN Y. SHIMIZU, AND PETER DEPLAZES 127 Algorithms for Detection and Identification of Parasites / 1920 LYNNE S. GARCIA, ROBYN Y. SHIMIZU, AND GRAEME P. PALTRIDGE 128 Reagents, Stains, and Media: Parasitology / 1939 SUSAN E. SHARP PARASITES 129 Plasmodium and Babesia / 1944 WILLIAM O. ROGERS 130 Leishmania and Trypanosoma / 1960 DAVID A. BRUCKNER AND JAIME A. LABARCA 131 Toxoplasma / 1970 MARIANNA WILSON, JEFFERY L. JONES, AND JAMES B. MCAULEY 132 Pathogenic and Opportunistic Free-Living Amebae / 1981 GOVINDA S. VISVESVARA 133 Intestinal 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 RAINER WEBER AND ELIZABETH U. CANNING 136 Intestinal Helminths / 2031 LAWRENCE R. ASH AND THOMAS C. ORIHEL 137 Tissue Helminths / 2047 THOMAS C. ORIHEL AND LAWRENCE 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 FERRARO 139 Antiparasitic Agents / 2081 KAREN LEDER AND PETER F. WELLER 140 Mechanisms of Resistance to Antiparasitic Agents / 2098 W. EVAN SECOR AND PHUC NGUYEN-DINH 141 Susceptibility Test Methods: Parasites / 2108 PHUC NGUYEN-DINH AND W. EVAN SECOR

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