Lecture notes. Medical microbiology and infection PDF
Preview Lecture notes. Medical microbiology and infection
E MEDICAL MICROBIOLOGY llio AND INFECTION tt, C MEDICAL MICROBIOLOGY a s e Lecture Notes 5th Edition y, L a AND INFECTION m Review of the previous edition b e “If it isn’t in this book, it is not worth knowing! (Lecture Notes) Medical Microbiology rt & and Infection is a concise text covering all aspects of basic science through to the S Lecture Notes clinical aspects of diagnosis and management - it is invaluable.” an d Medical Student, Hull-York Medical School o e L Medical Microbiology Lecture Notes is ideal for medical students, junior doctors, e pharmacy students, junior pharmacists, nurses, and those training in the allied health c professions. It presents a thorough introduction and overview of this core subject area. t u r e Whether you need to develop your knowledge for clinical practice, or refresh that N knowledge in the run up to examinations, Medical Microbiology and Infection Lecture o Notes will help foster a systematic approach to the clinical situation for all medical t students and hospital doctors. e s Medical Microbiology Lecture Notes has been fully revised and updated to include: AM LN • Chapters written by leading experts reflecting current research and teaching practice NE Tom Elliott DD • New chapters covering Diagnosis of Infections and Epidemiology and Prevention INIC Anna Casey & Management of Infections FA Peter Lambert • Integrated full-colour illustrations and clinical images EL C M • A self-assessment section to test understanding T Jonathan Sandoe I IC For information on all the titles in the Lecture Notes series, please visit: O R www.lecturenoteseries.com N O B 5th Edition I O L Titles of related interest All content reviewed O by students for students Medical Microbiology and Infection at a Glance, 4th Edition G Gillespie & Bamford 2012 Wiley-Blackwell Medical Education books are Y 9780470655719 designed exactly for their intended audience. All of our books are developed in collaboration with 5 IMnfceKcetinozuise Detis aela s2e0:0 C9linical Cases Uncovered sptuubdliesnhtesd. Twhiitsh myoeua,n tsh eth sattu oduern bt,o ino kms inarde. always th Ed 9781405168915 If you would like to be one itio For more information on the complete range of our student reviewers, go to n of Wiley-Blackwell medical student and www.reviewmedicalbooks.com junior doctor publishing, please visit: to find out more. www.wileymedicaleducation.com To receive automatic updates on Wiley-Blackwell books and journals, join our email list. Sign up today at www.wiley.com/email ISBN 978-1-4443-3465-4 9 781444 334654 www.wiley.com/go/medicine The Lecture Notes Series The Lecture Notes series CLINICAL CASES UNCOVERED The Lecture Notes books are designed to provide the core knowledge required by medical students in each The Lecture Notes series provides concise, yet thorough, introductions to core areas subject area. Emphasis is placed on covering each topic in concise note form, using bullet notes, summary booxef st,h aen du ncldeaerr glinrea ddiuaagtream csu. rTrhiceuselu bmoo, kcso cvane rbineg u sbeod tahs cthoenc bisae sciocu rsscei etenxctbeo oaknsd o rt hreev icsiloinni caaidls . GGeett t thhee mmoosstt ffrroomm cclliinniiccaall pprraaccttiiccee,, wwiitthh CClliinniiccaall CCaasseess U Unnccoovveereredd approaches that all medical students and junior doctors need to know. Biomedical Sciences Endocrinology and Diabetes Neurology 9e No other series is quite like Clinical Cases Background to the subject and how to 9781405157117 9781405153454 9781405177221 No other series is quite like Clinical Cases Background to the subject and how to approach Uncovered, where you can rehearse for life approach the patient are covered in an Biomedical Sciences Endocrinology and Diabetes Neurology 9e Uncovered, where you can rehearse for life in the patient are covered in an introductory section Ca9r7d8i1o4lo0g5y1 557e117 Epi9d7e8m14io0l5o1g5y3 a4n5d4 Public Obs9te7t8r1ic4s0 a5n1d7 7G2y2n1aecology 3e cilnin ciclianl ipcraalc ptircaec wtiicthe weaistyh- teoa-suys-et aon-ud swe ealnl-idn s tructed ainndtr oondcuec ytooruy h saevcet iwoonr kaendd t ohnrocueg yho tuh eh aravneg e of 9781405157087 Health Medicine 5e 9781405178013 well-instructed walk-through scenarios. worked through the range of cases you can walk-through scenarios. Each case is presented as cases you can test yourself with a selection of MCQs, 9781405106740 ClCinaicrdailo Alongaye s5tehesia 3e Epidemiology and OncOolbosgtye t2reics and Gynaecology 3e yEoauc who cualsde s iese pitr easnedn tthede uasse y oofu re walo-luifled e sxepee ritie nces EtMesQt ys oaunrds SeAlfQ ws.i tThh ais s deilsetcinticotn b loefn Md oCf Qlesa,r nEiMngQs 97987184104510750135873087 GaPsturobelicn tHereoallothg yM aenddicine 5e 97819470851149051531378013 maneadn tsh teh eu dsee coisfi orenasl -alnifde oeuxtpceormieens caerse mfacetaunasll ythe maneadn Ss AyoQus .w Thill iism dpirsotivnec tti mblee anndd o afg laeianr,n girnegat ly He9p7a8to1l4o0g5y106740 bdaesecdis. iAolnosn agn tdh eo wutacyo tmo dese taerrem fiancitnuga all dy ibaganseodsi.s emnheaanncsi nyog uy owuirl ld iemcipsiroonv-em taimkine ga snkdil lasg. aWinit,h such ClCinliincaicl aBli oAcnhaeemstishtersyi a8 e3e 9781405183215 OphOthnaclomloogloyg 2ye 10e aAndlo indgen tthifey winagy t rteoa dtmeteenrtms, iynoinu gle aa rdni aagbnouots ivsa riable ag wreidatel yra ennghe aonf csiunbgje ycotsu cro dveecreisdi oynou-m wailkl isnogo n see 97987184104510953107504383 Gastroenterology and 97819470851145070591495133 saynmdp tiodmenst, idfyainngge rt rseigantms aenndt sg,e yt oouv elrevairenw as boof ualtl tshkei lblse.n Wefiitt hof s tuhceh C aC wUi adpep rraonacghe .of subjects GeHneerpaal tSoulorggeyry 11e thvaer cioamblme soynm, cpltaossmicsa,l daanndg aetry psiigcanls p arnesde ngteatt ions. covered you will soon see the benefit of ClCinliincaicl aMl eBdioiccinhee m6eistry 8e 97891748015413095111833215 OrthOopphatehdailcms oalnodg yF r1a1cetures 4e 9780632065059 9781405133296 overviews of all the common, classical the CCU approach. 9781405193054 9781444335583 Haematology 8e and atypical presentations. General Surgery 11e Clinical Pharmacology and 9781405180504 Paediatrics 8e ThCelrinaipceaul tMices d8iecine 7e 9781405139113 9781O4r0t5h1o4p50a9e1dics and Fractures 4e The series so far... Paediatrics: Clinical Cases Uncovered 978-1-4051-5984-5 97987184104510957175876148 Human Physiology 5e 9781405133296 978H1a40e5m13a6to51lo8gy 8e Psychiatry 10e ATcuhtee M seedriciienes: Csloin ifcaal rC…ases Uncovered POsybcshtieattrriyc:s C alinndic aGl yCnaaseesc oUlnocgoyv:e red ClCinliincaicl aSlk Pilhlsa 4remacology 9781405180504 9781P4a0e51d9ia1t3r7ic1s 8e 978-1-4051-6883-0 9C78li-n1i-c4a05l 1C-a59s8e3s- 8U ncovered 97a8n0d63 T2h0e65ra11p0eutics 8e Immunology 6e 9781405145091 9781405191364 Radiology 3e CAacrduitoel oMgye:d Cicliinnieca: lC Cliansiecsa lU Cnacsoevse rUendcovered 978-1-4051-8671-1 9781405197786 Human Physiology 5e Radiology: Clinical Cases Uncovered Dermatology 10e 9781405195140 997788-1-1-4-045015-17-860808-36-0 9781405195713 Inf9e7ct8i1o4u0s5 D1i3s6e5a1se8s 6e Psychiatry 10e 9P7a8-e1d-4ia05tr1i-c8s4:7 C4-l8inical Cases Uncovered Clinical Skills 4e 9781405108201 Resp9i7r8a1to4r0y5 1M9e1d3i7c1ine 7e ECnadrodciroinloogloyg: yC alinndic Dali aCbaesteess :U Cnlicnoicvael rCeadses R9e7s8p-i1r-a4t0o5r1y- 5M9e84d-i5cine: Clinical Cases Uncovered Di9s7e8a0s6e3s 2o0f6 t5h1e1 E0ar, Nose and Immunology 6e 9781405153447 Uncovered 978-1-4051-7800-6 978-1-4051-5895-4 Throat 10e Me9d7i8ca1l4 G05e1n9e1ti3c6s 43e Radiology 3e 978-1-4051-5726-1 Psychiatry: Clinical Cases Uncovered 97D8e14rm05a1t4o5l0o8g4y 10e 9781405130035 The 9S7o8c1ia4l0 B5a1s9i5s 1o4f0 Medicine 9781405195713 Infectious Diseases 6e 9781405139120 GEenndeoracrl iPnroalcotigcey: aCnlidn iDcaila Cbaesteess :U ncovered S997u78r8-g1-e1-4r-0y45:0 1C5-1l5i-n859i9c88a-35l -C8a ses Uncovered Elderly Care Medicine 7e Medical Law and Ethics 9C78li-n1i-c4a05l 1C-a61s4e0s- 4U ncovered 9781405108201 Respiratory Medicine 8e Radiology: Clinical Cases Uncovered 9781405157124 9781405118682 Tropical Medicine 6e 978-1-4051-5726-1 Diseases of the Ear, 9780470654422 9781405180481 Haematology: Clinical Cases Uncovered 978-1-4051-8474-8 EmNeorsgee anncyd MTherdoiacitn 1e0 3ee MeMdiecdailc Mali cGroebnieotliocgs y3 aend 9G78e-n1-e4r0a5l1 P-8r3a2c2t-i2ce: Clinical Cases Uncovered 97987184104510252174353084 Inf9e7ct8i1o4n0 45e130035 UrolTohgey S6oecial Basis of Medicine CRoesmpiirnatgo rsyo Moend.i.c.ine: Clinical Cases 978-1-4051-6140-4 9781405129329 97819470851142027501239120 Infectious Disease: Clinical Cases Uncovered Uncovered Elderly Care Medicine 7e Medical Law and Ethics 978-1-4051-6891-5 Hepatology: Clinical Cases Uncovered Haematology: Clinical Cases Uncovered 978-1-4051-5895-4 9781405157124 9781405118682 Tropical Medicine 6e 9781444332469 N9e7p8h-1r-o4l0o5g1y-:8 C32li2n-i2cal Cases Uncovered 9781405180481 978-1-4051-8990-3 NSeuurrgoeloryg:y C: Clilninicicaal lC Caasseess UUnnccoovveerreedd Emergency Medicine 3e Medical Microbiology Hepatology: Clinical Cases Uncovered 997788-1-1-4-045015-16-252809-83-5 9781405122733 and Infection 5e Urology 6e Obstetrics and Gynaecology: Clinical Cases 978-1-4443-3246-9 9781444334654 9781405122702 Uncovered Gastroenterology: Clinical Cases Uncovered 978-1-4051-8671-1 Infectious Disease: Clinical Cases Uncovered 978-1-4051-6975-2 978-1-4051-6891-5 Nephrology: Clinical Cases Uncovered 978-1-4051-8990-3 Neurology: Clinical Cases Uncovered 978-1-4051-6220-3 Medical Microbiology and Infection Lecture Notes Edited by Tom Elliott BMBSBMedSciPhDDScMRCPFRCPath ConsultantMedicalMicrobiologist TheQueenElizabethHospital UniversityHospitalsBirminghamNHSFoundationTrust Birmingham,UK Anna Casey BScPhD ClinicalResearchScientist DepartmentofClinicalMicrobiology TheQueenElizabethHospital UniversityHospitalsBirminghamNHSFoundationTrust Birmingham,UK Peter Lambert BScPhDDSc ProfessorofMicrobiology SchoolofLifeandHealthSciences AstonUniversity Birmingham,UK Jonathan Sandoe MbChBPhDFRCPath ConsultantMicrobiologistandHonorarySeniorLecturer DepartmentofMicrobiology LeedsTeachingHospitalsNHSTrustandUniversityofLeeds Leeds,UK Fifth Edition Thiseditionfirstpublished2011(cid:1)2011byBlackwellPublishingLtd BlackwellPublishingwasacquiredbyJohnWiley&SonsinFebruary2007.Blackwell’spublishingprogramhasbeen mergedwithWiley’sglobalScientific,TechnicalandMedicalbusinesstoformWiley-Blackwell. Registeredoffice:JohnWiley&Sons,Ltd,TheAtrium,SouthernGate,Chichester,WestSussex,PO198SQ,UK Editorialoffices: 9600GarsingtonRoad,Oxford,OX42DQ,UK TheAtrium,SouthernGate,Chichester,WestSussex,PO198SQ,UK 111RiverStreet,Hoboken,NJ07030-5774,USA Fordetailsofourglobaleditorialoffices,forcustomerservicesandforinformationabouthowtoapplyforpermissionto reuse the copyrigh t material in this book please see our website at www.wil ey.com/wiley -blackwell. TherightoftheauthortobeidentifiedastheauthorofthisworkhasbeenassertedinaccordancewiththeUKCopyright, DesignsandPatentsAct1988. Allrightsreserved.Nopartofthispublicationmaybereproduced,storedinaretrievalsystem,ortransmitted,inanyform orbyanymeans,electronic,mechanical,photocopying,recordingorotherwise,exceptaspermittedbytheUKCopyright, DesignsandPatentsAct1988,withoutthepriorpermissionofthepublisher. Firstpublished(AsLectureNotesonBacteriology)1967 FirstEdition1975 SecondEdition1978 Reprinted1979,1983,1986 ThirdEdition1997 Internationaledition1997 Reprinted2003,2004 FourthEdition2007 FifthEdition2011 Designationsusedbycompaniestodistinguishtheirproductsareoftenclaimedastrademarks.Allbrandnamesand productnamesusedinthisbookaretradenames,servicemarks,trademarksorregisteredtrademarksoftheirrespective owners.Thepublisherisnotassociatedwithanyproductorvendormentionedinthisbook.Thispublicationisdesignedto provideaccurateandauthoritativeinformationinregardtothesubjectmattercovered.Itissoldontheunderstandingthat thepublisherisnotengagedinrenderingprofessionalservices.Ifprofessionaladviceorotherexpertassistanceisrequired, theservicesofacompetentprofessionalshouldbesought. LibraryofCongressCataloging-in-PublicationData Lecturenotes.Medicalmicrobiologyandinfection/TomElliott...[etal.].–5thed. p.;cm. Medicalmicrobiologyandinfection Includesbibliographicalreferencesandindex. ISBN-13:978-1-4443-3465-4(pbk.:alk.paper) ISBN-10:1-4443-3465-4(pbk.:alk.paper)1. Medicalmicrobiology–Outlines,syllabi,etc.I. Elliott,Tom (ThomasStuartJackson)II. Title:Medicalmicrobiologyandinfection. [DNLM:1. Microbiology.2. CommunicableDiseases–microbiology. QW4] QR46.G492011 616.9’041–dc22 2011012045 AcataloguerecordforthisbookisavailablefromtheBritishLibrary. Setin8.5pt/11ptUtopiafontbyThomsonDigital,Noida,India. 1 2011 Contents Preface v 17 Basicmycologyandclassificationoffungi, 93 Contributors vii ElizabethJohnson 18 Parasitology:protozoa, 101 PeterChiodini Basic microbiology 19 Parasitology:helminths, 112 PeterChiodini 1 Basicbacteriology, 3 PeterLambert 2 Classificationofbacteria, 12 PeterLambert Antimicrobialagents 3 Staphylococci, 16 20 Antibacterialagents, 127 TomElliottandPeterLambert PeterLambert 4 Streptococciandenterococcci, 20 21 Antifungalagents, 144 AnnaCasey ElizabethJohnson 5 Clostridia, 26 22 Antiviralagents, 147 TonyWorthington EleniNastouli 6 OtherGram-positivebacteria, 30 AnnaCasey 7 Gram-negativecocci, 36 Infection JonathanSandoe 23 Diagnosticlaboratorymethods, 157 8 Enterobacteriaceae, 40 TonyWorthington PeterLambert 24 Epidemiologyandpreventionofinfection, 167 9 HaemophilusandotherfastidiousGram-negative BarryCookson bacteria, 45 JonathanSandoe 25 Upperrespiratorytractinfections, 177 JonathanSandoe 10 Pseudomonas,Legionellaandotherenvironmental Gram-negativebacilli, 51 26 Lowerrespiratorytractinfections, 183 PeterLambert ShrutiKhurana 11 Campylobacter,HelicobacterandVibrio, 54 27 Tuberculosisandmycobacteria, 189 MartinSkirrow,CliodnaMcNultyandTomElliott SumeetSinghania 12 Treponema,BorreliaandLeptospira, 58 28 Gastrointestinalinfections, 193 SusanO’Connell TariqIqbal 13 Gram-negativeanaerobicbacteria, 62 29 Liverandbiliarytractinfections, 202 PeterLambert DavidMutimer 14 Chlamydiaceae,Rickettsia,Coxiella,Mycoplasma- 30 Urinarytractinfections, 207 taceaeandAnaplasmataceae, 64 ChrisCatchpole JonathanSandoe 31 Genitalinfections, 210 15 Basicvirology, 69 KavehManavi PeterMackie 32 Infectionsofthecentralnervoussystem, 220 16 Majorvirusgroups, 75 ErwinBrown PeterMackie iv Contents 33 Bacteraemiaandbloodstreaminfections, 229 40 Perinatalandcongenitalinfections, 264 TomElliott JamesGray 34 Device-relatedinfections, 233 41 Humanimmunodeficiencyvirus, 271 TomElliott KavehManavi 35 Cardiovascularinfections, 238 42 Miscellaneousviralinfections, 277 RichardWatkin JohnCheesbrough 36 Boneandjointinfections, 241 JonathanSandoe 37 Skinandsoft-tissueinfections, 246 Self-assessment SupriyaNarasimhanandRabihDarouiche Self-assessmentquestions, 285 38 Infectionsinthecompromisedhost, 257 Answerstoself-assessmentquestions, 300 TomElliott 39 Infectionscausedbyantimicrobial-resistant Generalsubjectindex, 309 bacteria, 260 DavidLivermore Organismindex, 317 Preface The magnitude of recent changes in the field of andinfection.Itcoversallaspectsofmicrobiology, medical microbiology has warranted this fifth including bacteriology, virology, mycology and edition of Lecture Notes: Medical Microbiology parasitology. As in previous editions, the text and Infection. While these changes have been is supported throughout with colour figures to encompassed in new chapters, this edition illustratethekeypoints. continues to maintain the well-received and Thisbookiswrittenspecificallyforstudentsin user-friendlyformatofearliereditions,highlight- medicine,biomedicine,biology,dentistry,science ingthepertinentkeyfactsinmedicalmicrobiology and also pharmacology, who have an interest in and providing a sound foundation of knowledge medicalmicrobiologyatbothundergraduateand whichstudentscanbuildon.Thebookforthefirst postgraduate levels. In addition, this book will time is multi-authored, with chapters being serveasausefulaidememoirefordoctorssitting writtenbyrecognisedexpertsintheirfield. MRCS and MRCP examinations, as well as other This fifth edition is arranged into three main healthcareprofessionals,forexamplebiomedical sections:basicmicrobiology,antimicrobialagents scientists,workingtowardsstateregistration. Contributors ErwinBrown ConsultantMicrobiologist,Depart- ShrutiKhurana SpecialistRegistrar,Department mentofMedicalMicrobiology,FrenchayHospital, ofRespiratoryMedicine,ManchesterRoyalInfir- NorthBristolNHSTrust,Bristol,UK mary, Central Manchester University Hospitals NHSFoundationTrust,Manchester,UK AnnaCasey ClinicalResearchScientist,Depart- ment of Clinical Microbiology, The Queen PeterLambert ProfessorofMicrobiology,School ElizabethHospital,UniversityHospitalsBirming- of Life and Health Sciences, Aston University, hamNHSFoundationTrust,Birmingham,UK Birmingham,UK ChrisCatchpole ConsultantMicrobiologist,De- DavidLivermore Director,AntibioticResistance partmentofClinicalMicrobiology,Worcestershire Monitoring and Reference Laboratory, Health Royal Hospital, Worcestershire Acute Hospitals Protection Agency, Microbiology Services, Colin- NHSTrust,Worcester,UK dale,London,UK John Cheesbrough Consultant Microbiologist, Peter Mackie Consultant Clinical Scientist, Department of Microbiology, Royal Preston DepartmentofMicrobiology,TheGeneralInfirma- Hospital, Lancashire Teaching Hospitals NHS ryatLeeds,LeedsTeachingHospitalsNHSTrust, FoundationTrust,Preston,Lancashire,UK Leeds,UK Peter Chiodini Consultant Parasitologist and Kaveh Manavi Consultant Physician HIV/ Honorary Professor, The Hospital for Tropical Genitourinary Medicine, Department of DiseasesandTheLondonSchoolofHygieneand Genitourinary Medicine, The Queen Elizabeth TropicalMedicine,London,UK Hospital, University Hospitals Birmingham NHS Barry Cookson Director of the Laboratory of FoundationTrust,Birmingham,UK Healthcare-associated Infection, Health Protec- Cliodna McNulty Consultant Microbiologist, tion Agency, Microbiology Services, Colindale, Health Protection Agency, Microbiology Depart- London,UK ment,GloucestershireRoyalHospital,Gloucester- Rabih Darouiche VA Distinguished Service shireHospitalsNHSTrust,Gloucester,UK Professor,DepartmentsofMedicine,Surgeryand PhysicalMedicine&RehabilitationandDirector, David Mutimer Consultant Hepatologist, De- CenterforProsthesesInfection,BaylorCollegeof partmentofLiverMedicine,TheQueenElizabeth Medicine,Houston,Texas,USA Hospital, University Hospitals Birmingham NHS FoundationTrust,Birmingham,UK Tom Elliott Consultant Microbiologist, The Queen Elizabeth Hospital, University Hospitals Supriya Narasimhan Assistant Professor, NHSFoundationTrust,Birmingham,UK Division of Infectious Diseases, Department of Medicine,DrexelUniversity,Pittsburgh,USA James Gray Consultant Microbiologist, Depart- ment of Medical Microbiology, Birmingham EleniNastouli ConsultantVirologistandHonor- Children’s Hospital NHS Foundation Trust, ary Consultant in Paediatric Infectious Diseases, Birmingham,UK Department of Virology, University College TariqIqbal ConsultantPhysicianandGastroen- London Hospitals NHS Trust and Great Ormond Street Hospital for Children NHS Trust, London, terologist, Department of Gastrointestinal Medi- UK cine, The Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Susan O’Connell Consultant Microbiologist, Birmingham,UK Lyme Borreliosis Unit, Health Protection Agency ElizabethJohnson DirectoroftheHealthProtec- Microbiology Laboratory, Southampton General tion Agency Mycology Reference Laboratory, Hospital,SouthamptonUniversityHospitalsNHS Bristol,UK Trust,Southampton,UK viii Contributors JonathanSandoe ConsultantMicrobiologistand Richard Watkin Consultant Cardiologist, Good HonorarySeniorLecturer,DepartmentofMicro- HopeHospital,HeartofEnglandNHSFoundation biology,LeedsTeachingHospitalsNHSTrustand Trust,SuttonColdfield,Birmingham,UK UniversityofLeeds,Leeds,UK Mark Woodhead Consultant in General and Sumeet Singhania Specialist Registrar, Depart- Respiratory Medicine and Honorary Senior mentofRespiratoryMedicine,ManchesterRoyal Lecturer, Department of Respiratory Medicine, Infirmary, Central Manchester University Hospi- ManchesterRoyalInfirmary,Central Manchester talsNHSFoundationTrust,Manchester,UK University Hospitals NHS Foundation Trust and UniversityofManchester,Manchester,UK Martin Skirrow Honorary Emeritus Consultant Microbiologist,HealthProtectionAgency,Micro- TonyWorthington SeniorLecturerinMicrobiol- biology Department, Gloucestershire Royal ogy, School of Life and Health Sciences, Aston Hospital, Gloucestershire Hospitals NHS Trust, University,Birmingham,UK Gloucester,UK
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