Main 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 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