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.
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
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