Title | Subhash Chandra Parija Textbook of Microbiology and Immunology Elsevier India (2012) |
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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...