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Prelims.indd i 5/15/2012 10:20:01 AM Textbook of Microbiology and Immunology Prelims.indd i 5/15/2012 10:20:01 AM “This page intentionally left blank" Prelims.indd ii 5/15/2012 10:20:02 AM Textbook of Microbiology and Immunology 2nd Edition Subhash Chandra Parija MBBS, MD, PhD, DSc, FRCPath FAM...

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Textbook of

Microbiology and Immunology

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Textbook of

Microbiology and Immunology 2nd Edition

Subhash Chandra Parija MBBS, MD, PhD, DSc, FRCPath FAMS, FICPath, FICAI, FABMS, FISCD, FIAVP, FIATP, FIMSA

Professor and Head Department of Microbiology Jawaharlal Institute of Postgraduate Medical Education and Research Puducherry, India

ELSEVIER A division of Reed Elsevier India Private Limited

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Textbook of Microbiology and Immunology, 2/e Parija ELSEVIER A division of Reed Elsevier India Private Limited Mosby, Saunders, Churchill Livingstone, Butterworth-Heinemann and Hanley & Belfus are the Health Science imprints of Elsevier. © 2012 Elsevier First Edition 2009 Second Edition 2012 All rights are reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise without the prior permission of the publisher. ISBN: 978-81-312-2810-4 Medical knowledge is constantly changing. As new information becomes available, changes in treatment, procedures, equipment and the use of drugs become necessary. The author, editors, contributors and the publisher have, as far as it is possible, taken care to ensure that the information given in this text is accurate and up-to-date. However, readers are strongly advised to confirm that the information, especially with regard to drug dose/usage, complies with current legislation and standards of practice. Please consult full prescribing information before issuing prescriptions for any product mentioned in this publication. Published by Elsevier, a division of Reed Elsevier India Private Limited. Registered Office: 305, Rohit House, 3 Tolstoy Marg, New Delhi-110 001. Corporate Office: 14th Floor, Building No. 10B, DLF Cyber City, Phase II, Gurgaon–122 002, Haryana, India. Sr. Commissioning Editor: Shukti Mukherjee Bhattacharya Managing Editor (Development): Shabina Nasim Development Editor: Shravan Kumar Copy Editor: Shrayosee Dutta Manager Publishing Operations: Sunil Kumar Manager Production: NC Pant Typeset by Mukesh Technologies Pvt. Ltd., Pudhucherry, India. Printed and bound at EIH Unit Ltd. Press, Manesar.

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To my father

Late Shri Managovinda Parija and mother

Late Smt Nishamani Parija

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Preface to the Second Edition Like the first edition, the second edition of Textbook of Microbiology and Immunology consists of six sections. Section I and II deal with general micro biology and immunology, respectively. Section III, IV, and V deal with bacteriology, virology, and mycology, respectively. Lastly, Section VI deals with applied microbiology and includes epidemiology and control of community infections, hospital infections, antimicrobial chemotherapy, water analysis, and immunization. Medical microbiology is a rapidly changing and evolving field. The threat of emerging and reemerging pathogens and the changing epidemiology of known pathogens have made it imperative that we keep abreast of the changes and developments in the field if we are to efficiently deal with them. The second edition of the Textbook of Microbiology and Immunology has been revised thoroughly and revamped to include the latest information in the field of medical microbiology. Special emphasis has been placed on molecular methods of diagnosis, which have revolutionized the diagnosis of infectious diseases and have made it possible to detect hitherto unknown and uncultivable pathogens from clinical specimens. The problem of antimicrobial resistance with respect to emerging mechanisms, changing epidemiology, and newer ways of detection has been dealt with in detail. This text aims at not only providing basic information about microbiology and immunology, but also deals with the clinical applications of microbiology in the study of infectious diseases. In each chapter, key points are highlighted. Clinical case studies have been included so that students can evaluate their understanding of the various microbes. Photographs and pertinent line diagrams have been included to aid the learning process. The book has been trimmed down so as to include the necessary information without overburdening the students. This textbook aims at providing comprehensive information about microbiology and it’s applications for medical students, paramedical students and workers in the field of infectious diseases. I sincerely hope the book serves this purpose and also helps in creating interest towards the subject among students. Readers’ views and suggestions for further improving the book in the coming years are welcome. Suggestions may kindly be e-mailed at [email protected].

Subhash Chandra Parija

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Preface to the First Edition The intent of the book is to provide an up-to-date information on microbial diseases which are emerging as an important health problem world wide. 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 medical microbiology. Textbook of Microbiology and Immunology consists of six sections. Section I and II deals with general micro biology and immunology, respectively. Section III, IV, and V deals with bacteriology, virology, and mycology, respectively. Lastly, Section VI deals with applied microbiology and includes epidemiology and control of community infections, hospital infections, antimicrobial chemotherapy, water analysis, and immunization. Emphasis, throughout the text, is made on the clinical applications of microbiology to study infectious diseases. Cultivation and identification of each organism along with pathogenesis of 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 summarized in the tabular format. Clinical cases are provided in most of the chapters. The book is profusely illustrated with line diagrams and photomicrographs both black & white and color. I believe this book will be a useful source of comprehensive information for students mainly the undergraduate students of medicine, allied sciences, and others who are interested in medical microbiology. 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] or at [email protected].

Subhash Chandra Parija

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Acknowledgements I am grateful for the valuable professional help and support provided by the staff at Elsevier, New Delhi, namely, Mr Sumeet Rohatgi, Mr Vidhu Goel, Ms Shabina Nasim, and Mr Shravan Kumar during a period of last more than one year. It has been really a wonderful and learning experience while working in particular with Ms Shabina Nasim and Mr Shravan Kumar; their professional contributions are immense for the development of manuscript to the present book format. I gratefully acknowledge all my colleagues, friends, and students for their valuable advice, constructive criticism, and assistance in preparation of the manuscript. I owe special debt of profound gratitude to my mother late Smt Nishamani Parija and father late Shri Managovinda Parija without whose encouragement the book would not have been possible. I am indeed grateful to my wife Smt Jyothirmayee Parija for all her support throughout the period of preparation of the manuscript of the book. It is my pleasure to thank my niece Er Kukumina Parija, son-in-law Er Subhasis Ray, nephew Er Shri Rajkumar Parija, daughterin-law Ms Smriti Parija, and daughters, Ms Dr Madhuri Parija, son-in-law Dr Ajay Halder, Ms Er Mayuri Parija and son-in-law Er Shailesh Nandan for their untiring secretarial help towards the preparation of the manuscript.

Subhash Chandra Parija

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Contents Preface to the Second Edition Preface to the First Edition Acknowledgements Color Photos

vii ix x CP1

6. Laboratory Identification of Bacteria and Taxonomy  

SECTION I



GENERAL MICROBIOLOGY

1. History of Microbiology

3

7.

Bacterial Genetics 

     

Introduction Historical Background Microorganisms as a Cause of Disease Study of Viruses Phenomenon of Immunity Chemotherapeutic Agents

2. Morphology and Physiology of Bacteria     

 

Introduction Size of Bacteria Microscopy Study of Bacteria Structure and Functions of Bacterial Cell Envelope Growth and Multiplication of Bacteria Bacterial Nutrition

3. Sterilization and Disinfection    

Introduction Definition of Frequently Used Terms Sterilization Disinfection

4. Culture Media   

Introduction Ingredients of Culture Media Types of Culture Media

5. Culture Methods   

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Introduction Methods of Culture Anaerobic Culture

3 3 3 6 7 8

9 9 9 9 12 14 21 23

24 24 24 24 29

34 34 34 34

38 38 38 39

Introduction Identification of Bacteria Bacterial Taxonomy

     

Introduction Chromosomal Substances Mutations Extrachromosomal DNA Substances Transfer of DNA Within Bacterial Cells Transfer of DNA Between Bacterial Cells Recombination

8. Genetic Engineering and Molecular Methods        

Introduction DNA: An Amazing Molecule Genetic Engineering Nucleic Acid Probes Polymerase Chain Reaction Recombinant DNA Technology Genetically Modified Organisms Gene Therapy

9. Antimicrobial Agents: Therapy and Resistance  

   

Introduction Mechanisms of Action of Antimicrobial Drugs Resistance to Antimicrobial Drugs Basis of Resistance Antibiotic Sensitivity Testing Antibacterial Assays in Body Fluids

41 41 41 45

47 47 47 48 49 50 51 54

55 55 55 55 57 57 59 60 60

61 61 61 64 65 68 71

10. Microbial Pathogenesis

72

Introduction Types of Microorganisms Infection

72 72 72

  

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CONTENTS  

Stages of Pathogenesis of Infections Stages of an Infectious Disease

73 82

17. Immune Response  

SECTION II

IMMUNOLOGY

 

11. Immunity  

Introduction Types of Immunity

85 85 85



90

 

         

Introduction Determinants of Antigenicity Antigenic Specificity Species Specificity Isospecificity Autospecificity Organ Specificity Heterophile Specificity Haptens Superantigens

13. Antibodies   

Introduction Immunoglobulins Abnormal Immunoglobulins

14. Antigen–Antibody Reactions  

 

Introduction General Features of Antigen–Antibody Reactions Stages of Antigen–Antibody Reactions Types of Antigen–Antibody Reactions

90 90 91 92 92 92 92 92 93 93

94 94 94 100

101 101 101 102 102

       

Introduction The Complement System Activation of Complement Regulation of Complement System Biological Effects of Complement Deficiency of Complement Biosynthesis of Complement Quantitation of Complement

16. Structure and Function of Immune System     

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Introduction Lymphoid Tissues and Organs Lymphatic Circulatory System Cells of the Lymphoreticular System Major Histocompatibility Complex

116 116 116 116 119 120 121 121 121

134 134 138 142 142

143

Introduction Primary Immunodeficiencies Secondary Immunodeficiencies

143 143 147

19. Hypersensitivity     



    

149

Introduction Type I (Anaphylactic) Hypersensitivity Type II (Cytotoxic) Hypersensitivity Type III (Immune-Complex) Hypersensitivity Type IV Delayed (Cell-Mediated) Hypersensitivity Type V (Stimulatory Type) Hypersensitivity

20. Autoimmunity Introduction Tolerance Pathogenesis of Autoimmunity Animal Models of Autoimmunity Autoimmune Diseases

149 149 152 153 154 155

156 156 156 156 158 158

21. Immunology of Transplantation and Malignancy

161

Introduction Transplant Immunology Tumor Immunology

161 161 164

  

15. Complement System

Introduction Humoral Immunity Cell-Mediated Immunity Transfer Factor Immunological Tolerance

18. Immunodeficiency 

12. Antigen

134

22. Immunohematology     



Introduction ABO Blood Group System Rh Blood Group System Blood Transfusion Hemolytic Disease of Newborn (Erythroblastosis Fetalis) ABO Hemolytic Diseases

SECTION III

167 167 167 168 168 169 170

BACTERIOLOGY

122 122 122 124 124 131

23. Staphylococcus    

Introduction Staphylococcus Staphylococcus aureus Coagulase-Negative Staphylococci

173 173 173 173 181

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CONTENTS   

Micrococcus Planococcus Stomatococcus

182 182 182

   

24. Streptococcus and Enterococcus       

Introduction Streptococcus Streptococcus pyogenes Streptococcus agalactiae Other Hemolytic Streptococci Viridans Streptococci Enterococcus

183 183 183 184 191 191 192 192

     

32. Salmonella 

25. Pneumococcus  

Introduction Streptococcus pneumoniae

26. Neisseria    

Introduction Neisseria gonorrhoeae Neisseria meningitidis Other Neisseria Species

194 194 194

201 201 201 207 211

  

   

Introduction Corynebacterium diphtheriae Other Pathogenic Corynebacterium Species Other Coryneform Genera

213 213 213 220 221

 

  

Introduction Bacillus anthracis Anthracoid Bacilli

29. Clostridium      

Introduction Clostridium Clostridium perfringens Clostridium tetani Clostridium botulinum Clostridium difficile

30. Nonsporing Anaerobes   

Introduction Anaerobic Cocci Anaerobic Bacilli

31. Coliforms   

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Introduction Escherichia Escherichia coli

222 222 222 229

231 231 231 232 237 242 245

247 247 247 247

251 251 252 252

Introduction Shigella

34. Yersinia   

Introduction Yersinia pestis Yersinia enterocolitica Yersinia pseudotuberculosis

35. Vibrio, Aeromonas, and Plesiomonas 

28. Bacillus

Introduction Salmonella Salmonella Gastroenteritis Salmonella Bacteremia

33. Shigella



27. Corynebacterium

Edwardsiella Citrobacter Klebsiella Enterobacter Hafnia Serratia Proteus Morganella Providencia Erwinia

      

Introduction Vibrio cholerae Noncholera Vibrios Vibrio mimicus Halophilic Vibrios Other Vibrio Species Aeromonas Plesiomonas

36. Campylobacter and Helicobacter     

Introduction Campylobacter Helicobacter Helicobacter pylori Other Helicobacter Species

37. Pseudomonas, Burkholderia, and Moraxella      

Introduction Pseudomonas Pseudomonas aeruginosa Other Pseudomonas Species Burkholderia Moraxella

xiii 261 261 261 263 264 264 265 267 268 268

269 269 269 280 280

281 281 281

286 286 286 291 292

294 294 294 302 302 302 303 304 304

305 305 305 308 308 311

313 313 313 313 318 318 319

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CONTENTS

38. Haemophilus, Pasteurella, and Actinobacillus       

Introduction Haemophilus Haemophilus influenzae Other Haemophilus Species Pasteurella Actinobacillus HACEK Group of Bacteria

45. Mycoplasma and Ureaplasma 321 321 321 321 326 327 327 328

    

46. Actinomycetes 

39. Bordetella and Francisella

330

 

     

Introduction Bordetella Bordetella pertussis Bordetella parapertussis Bordetella bronchiseptica Francisella tularensis

40. Brucella  

Introduction Brucella

41. Mycobacterium tuberculosis  

Introduction Mycobacterium tuberculosis

330 330 330 334 335 335

338 338 338

345 345 346

     

358

Introduction Photochromogens Scotochromogens Nonphotochromogens Rapid Growers

358 358 359 359 360

    

43. Mycobacterium leprae and Mycobacterium lepraemurium

     

  

Introduction Mycobacterium leprae Mycobacterium lepraemurium

       

362 362 362 370

          

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Introduction Treponema Treponema pallidum Nonvenereal Treponematosis Nonpathogenic Treponemes Borrelia Borrelia recurrentis Borrelia vincenti Borrelia burgdorferi Leptospira Leptospira interrogans Complex

Introduction Listeria monocytogenes Erysipelothrix rhusiopathiae Alcaligenes faecalis Chromobacterium violaceum Flavobacterium meningosepticum Calymmatobacterium Streptobacillus and Spirillum Streptobacillus moniliformis Spirillum minus Legionella Legionella pneumophila Bartonella Capnocytophaga Gardnerella vaginalis

48. Rickettsia, Orientia, Ehrlichia, and Coxiella  

44. Treponema, Borrelia, and Leptospira

Introduction Actinomyces Nocardia Rhodococcus Gordonia and Tsukamurella Thermophilic Actinomyces Tropheryma whippelii Dermatophilus Oerskovia

47. Miscellaneous Bacteria



42. Nontuberculous Mycobacteria

Introduction Mycoplasma pneumoniae Genital Mycoplasma Species Ureaplasma urealyticum Atypical Pneumonia

371



371 371 371 377 378 378 378 381 381 381 382





  

     

Introduction Genus Rickettsia Typhus Fever Group Rickettsia prowazekii Rickettsia typhi Spotted Fever Group Rickettsia rickettsiae Other Rickettsial Species in the Spotted Fever Group Rickettsia akari Genus Orientia Orientia tsutsugamushi Genus Ehrlichia Genus Coxiella Coxiella burnetii

386 386 38...