Manual of Clinical Microbiology, 2 Volume Set

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 LAGACÉ-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 JØRGEN 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
LÚCIA MARTINS TEIXEIRA, MARIA DA GLÓRIA
SIQUEIRA CARVALHO, RICHARD R. FACKLAM,
AND PATRICIA LYNN SHEWMAKER
25 Aerococcus, Abiotrophia, and Other
Aerobic Catalase-Negative, Gram-Positive
Cocci / 436
JENS JØRGEN 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 NØRSKOV-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 HØIBY, 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 KÄMPFER,
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 KÖNÖNEN
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. SEÑA, ALLAN PILLAY, AND
JUSTIN D. RADOLF
Mycoplasmas and Obligate
Intracellular Bacteria
63 General Approaches to Identification of
Mycoplasma, Ureaplasma, and Obligate
Intracellular Bacteria / 1109
CÉCILE BÉBÉAR AND J. STEPHEN DUMLER
64 Mycoplasma and Ureaplasma / 1117
KEN B. WAITES AND CÉCILE BÉBÉAR
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 GEIßDÖRFER, 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 JOSÉ 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-STÖCKL AND
STEPHAN W. ABERLE
102 Human Cytomegalovirus / 1770
RICHARD L. HODINKA
103 Epstein-Barr Virus / 1797
BARBARA C. GÄRTNER 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
FRANÇOISE DROMER
125 Histoplasma, Blastomyces, Coccidioides,
Paracoccidioides, and Other Dimorphic Fungi
Causing Systemic Mycoses / 2187
GEORGE R. THOMPSON III AND
BEATRIZ L. GÓMEZ
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
JÉRÔME CLAIN
154 Susceptibility Test Methods: Parasites / 2682
JÉRÔME CLAIN, JACQUES LE BRAS, AND
W. EVAN SECOR