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Subhash Chandra Parija Textbook of Microbiology and Immunology Fourth Edition Textbook of Microbiology and Immunology Subhash Chandra Parija Textbook of Microbiology and Immunology Fourth Edition SubhashChandraParija SriBalajiVidyapeeth(Deemed-to-be-university) Pondicherry,India ISBN978-981-19-3314-1 ISBN978-981-19-3315-8 (eBook) https://doi.org/10.1007/978-981-19-3315-8 3rdedition:#Elsevier2016 #TheEditor(s)(ifapplicable)andTheAuthor(s),underexclusivelicensetoSpringerNature SingaporePteLtd.2009,2012,2016,2023 Thisworkissubjecttocopyright.AllrightsaresolelyandexclusivelylicensedbythePublisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting,reuseofillustrations,recitation,broadcasting,reproductiononmicrofilmsorinany otherphysicalway,andtransmissionorinformationstorageandretrieval,electronicadaptation, computersoftware,orbysimilarordissimilarmethodologynowknownorhereafterdeveloped. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthis publication does not imply, even in the absence of a specific statement, that such names are exemptfromtherelevantprotectivelawsandregulationsandthereforefreeforgeneraluse. Thepublisher,theauthors,andtheeditorsaresafetoassumethattheadviceandinformationin thisbookarebelievedtobetrueandaccurateatthedateofpublication.Neitherthepublishernor the authors or the editors give a warranty, expressed or implied, with respect to the material containedhereinorforanyerrorsoromissionsthatmayhavebeenmade.Thepublisherremains neutralwithregardtojurisdictionalclaimsinpublishedmapsandinstitutionalaffiliations. ThisSpringerimprintispublishedbytheregisteredcompanySpringerNatureSingaporePteLtd. The registered company address is: 152 Beach Road, #21-01/04 Gateway East, Singapore 189721,Singapore Lotus Feet of Divine Mother, Maa Sarala, Almighty Goddess of Learning and Wisdom My Father Late Shri Managovinda Parija Mother Late Smt Nishamani Parija Wife Ms Jyotirmayee Parija and My Professional Colleagues and Mentors Preface to the Fourth Edition ItismygreatpleasuretoauthorthefourtheditionofTextbookofMicrobiol- ogy and Immunology, a book which has received huge support from the readersacrossIndiaandabroadforthepreviouseditions.Alargenumberof suggestions and feedback were received from the faculty members and students using the previous edition of the book and a sincere attempt has been made to incorporate the appropriate suggestions while preparing this edition. In the backdrop of the transitions of modern healthcare from generic to personalized, One health replacing the health, medical education is going through transformations to accommodate the new and revise or update the basics.Inthislandscape,theresurgenceofexistingpathogens,emergingand re-emerging infections, and the worldwide phenomenon of antimicrobial resistance have made microbiology more relevant where contextual clinical interventions demand more corroboration with accurate diagnosis and syndrome-based investigation rather than classical organismal views. It has beenfuturetriggeredbyourpresentcentury’sexperiencewiththeCOVID-19 pandemic where parallel scientific advances in terms of molecular tools and technology and their affordability as a whole have brought whole new revolutions in our understandings and dealings with pathogens. As such, a reflectionofthesedevelopmentsintheexistingacademicbookwasnecessary forthefraternityincludingthestudentandteachers. The recent introduction of “Competency-Based Medical Education” (CBME) by the National Medical Commission, India, has resulted in a sea change in the microbiology syllabus for the undergraduate (MBBS) and postgraduate (MD) students of this country. The approach has shifted from organism-relatedteachingtosystemandsyndrome-basedexpositionofinfec- tiousdiseaseswhichismorerelevantforthetrainingofamedicalstudentin FacultyofMedicine. This fourth edition of Textbook of Microbiology and Immunology has, therefore,madethefirstattempttobemoreinclusiveandcontextualtomeet the current demand gap in simplistic approaches keeping stock of the latest development in the field of medical microbiology and immunology. While doingso,thisbookhasblendedthetraditionalorganism-basedlearninganda syndromic approach to infectious disease, together with the introduction of newandmodifiedchaptersincorporatingthelatestinformationinthisfield. Thisbookcontains72chaptersdistributedinsixspecificsections. vii viii PrefacetotheFourthEdition PartIdealswiththeaspectsofGeneralMicrobiology.Whereastheearlier books in the subject dealt almost exclusively with bacteria in focus, in this editiondueimportancehasbeengiventootherclassesofmicrobeslikefungi, viruses,etc.Separatechaptershavebeenassignedtotheseorganismssothat the student can have a baseline knowledge about them. In addition, the chapters on antimicrobial agents and diagnostic methods have been completely rewritten to encompass all pathogenic microbes and parasites. A notablefeatureistheadditionofanewchapterongenomicsandproteomics which are gaining increasing importance not only in Microbiology but in almostallspecialtiesofmedicalsciences. Part II deals with immunology in the context of medical education and requirements. It has been revised to make it more concise and updated to accommodatethenewerdevelopmentsinthisfield.Eachchapterhasdetailed componentsofimmunesystems,diseases,etc.andhasdescribedtheunderly- ingprocesses. Parts III, IV and V deal with bacteriology, virology and basic mycology, respectively. Wherein the first few chapters of these sections describe the historyandcurrentstatusandapproachesinvolvingantimicrobialtherapyand laboratory diagnosis including molecular; the rest of the chapters give a specific look into different types of pathogenic bacteria and viruses. This book contains the latest updates on their description, taxonomic status and diseasesincludingthesymptoms.Italsoconsidersthedetectionandmanage- ment roadmaps that have been prescribed by the competent national and internationalregulatorybodies. PartVIdescribestheappliedaspectsofclinicalmicrobiology.Itdealswith pathogens in water, milk, air and food, and also collects information on the plethora of healthcare-associated infections. It also updates knowledge on waste handling, management, diagnostic modalities and quality assurance strategiesandprogram ina diagnostic laboratory. As such, this section shall actasahandbookforthepractitionerandthelaboratorypersonneltoprovide good services by maintaining appropriate measures and regulatory compliances. GlossaryandFurtherreadingsarealsoincluded,attheend,forthebenefit ofall. I hope that the book in its new format will be well appreciated by the readers and can serve not only as a textbook for undergraduate medical students but will also form a foundation base for the postgraduate students onwhichtheycanbuilduptheirmoreadvancedknowledge.Anysuggestion orfeedbackfromthereaderswillbehighlyappreciatedandcanbeaddressed to me [email protected] for further improvement in subsequent editions. Pondicherry,India SubhashChandraParija Preface to the First Edition The intent of the book is to provide an up-to-date information on microbial diseaseswhichareemergingasanimportanthealthproblemworldwide.This book has been written to provide a comprehensive coverage of basic and clinical microbiology, including immunology, bacteriology, virology and mycology, in a clear and succinct manner. The book also intends to provide an accurate presentation of clinically relevant information to the learners of medicalmicrobiology. TextbookofMicrobiologyandImmunologyconsistsofsixsections.PartsI and II deals with general microbiology and immunology, respectively. Parts III, IV and V deals with bacteriology, virology and mycology, respectively. Lastly, Part VI deals with applied microbiology and includes epidemiology and control of community infections, hospital infections, antimicrobial che- motherapy,wateranalysisandimmunisation. Emphasis, throughout the text, is made on the clinical applications of microbiologytostudyinfectiousdiseases. Cultivationandidentificationofeachorganismalongwithpathogenesisof diseases, clinical manifestations, diagnostic laboratory tests, treatment and prevention and control of resulting infections are thoroughly updated to include most recent advances in the field. Details are summarised in the tabular format. Clinical cases are provided in most of the chapters. The book is profusely illustrated with line diagrams and photomicrographs both blackandwhiteandcolour. I believe this book will be a useful source of comprehensive information for students mainly the undergraduate students of medicine, allied sciences andotherswhoareinterestedinmedicalmicrobiology. I welcome reader’s views and suggestions for further improvement of the book in the future edition. Suggestions may kindly be e-mailed at [email protected]. Pondicherry,India SubhashChandraParija ix Editorial Board ProfAbhijitChaudhuryMD,DNB Professor, Department of Microbiology, Sri Venkateswara Institute of MedicalSciences,Tirupati,AndhraPradesh,India Prof Shivaprakash M Rudramurthy, MD, PhD (RU, Netherlands), FECMM,MNAMS,MNASc Professor, and In-Charge, Mycology Division Head, WHO Collaborating Center&CenterofAdvancedResearchinMedicalMycology,Departmentof Medical Microbiology, Postgraduate Institute of Medical Education and Research,Chandigarh,India ProfTuhinaBanerjeeMD,DNB,PhD,PGDHHM Professor, Department of Microbiology, Institute of Medical Sciences, BanarasHinduUniversity,Varanasi,UttarPradesh,India xi Acknowledgements I wish to place on record my sincere thanks to all those who helped us in bringingoutthisfourtheditionTextbookofMicrobiologyandImmunology. First, I like to thank members of the Editorial Board of the book, my professional colleagues, Prof Abhijit Chaudhury (SVIMS, Tirupati), Prof Shivaprakash M Rudramurthy (PGIMER, Chandigarh) and Prof Tuhina Banerjee(IMS,BHU,Varanasi),fortheirimmensecontributioninenriching the contents and also for sharing many images that have found place in thebook. My thanks to my elder brother Shri Kailash Chandra Parija, niece Er Kukumina Ray, son-in-law Er Subhasis Ray, nephew Er Rajkumar Parija, daughter-in-lawMs.SmrithiParija,daughtersDrMadhuriParija,son-in-law Dr Ajay Halder, Er Ms. Mayuri Parija and son-in-law Er Shailesh Nandan, and grandchildren Sri Harihar, Ms Shyama and Sri Ram and brother-in-law DrBirajaPrasannaDasfortheirsupportduringpreparationofthemanuscript. Thanks are due to Prof Ujjala Ghosal (SGPGI, Lucknow), Prof Pramodhini, Dr Namratha Bhosle, Dr Vanathy and Dr Abhijit Poddar of DepartmentofMicrobiology,ProfS.Padmavathy,DepartmentofPharmacol- ogy, and Prof Richa Gupta, Department of Physiology, Shri Balaji Vidyapeeth, Pondicherry, for their assistance during preparation of the manuscript. I like to thank Sri Ram Kumar, IT,Shri Balaji Vidyapeeth and Mr Tamilselvanforpreparingimagesandillustrationsofthebook. IamespeciallythankfultoDrNarenAggarwalandDrBhavikSawhneyof SpringerNature,thePublisherofthebook,fortheirwholeheartedsupportto meincarryingoutthisprojectandlookingafterthecountlessthingswhichgo beforethepublicationofabook. Pondicherry,India SubhashChandraParija xiii