Manual of Clinical Microbiology, 2 Volume Set

Dr. Karen Carroll is a professor of pathology at the Johns Hopkins University School of Medicine.

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