Essentials of Medical Microbiology

Transcription

1 Contents i Essentials of Medical Microbiology

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3 Essentials of Medical Microbiology Fourth Edition Rajesh Bhatia MD (Medical Microbiology) Formerly Director National Institute of Biologicals, New Delhi and Department of Microbiology Maulana Azad Medical College, New Delhi India Rattan Lal Ichhpujani MD (Medical Microbiology) Additional Director and Chief of Division of HIV/AIDS and Related Diseases National Institute of Communicable Diseases, Delhi Formerly Department of Microbiology Medical College, Rohtak Haryana India JAYPEE BROTHERS MEDICAL PUBLISHERS (P) LTD New Delhi Ahmedabad Bengaluru Chennai Hyderabad Kochi Kolkata Lucknow Mumbai Nagpur

4 Published by Jitendar P Vij Jaypee Brothers Medical Publishers (P) Ltd B-3 EMCA House, 23/23B Ansari Road, Daryaganj New Delhi , India Phones: , , , Rel: , Fax: , jaypee@jaypeebrothers.com Visit our website: Branches 2/B, Akruti Society, Jodhpur Gam Road Satellite Ahmedabad , Phones: , Rel: Fax: , ahmedabad@jaypeebrother.com 202 Batavia Chambers, 8 Kumara Krupa Road, Kumara Park East Bengaluru , Phones: , , Rel: Fax: , bangalore@jaypeebrothers.com 282 IIIrd Floor, Khaleel Shirazi Estate, Fountain Plaza, Pantheon Road Chennai , Phones: , , Rel: Fax: , chennai@jaypeebrothers.com /1-3, 1st Floor, Balaji Building, Ramkote Cross Road Hyderabad , Phones: , Rel: Fax: , hyderabad@jaypeebrother.com No. 41/3098, B & B1, Kuruvi Building, St. Vincent Road Kochi , Kerala, Phones: , kochi@jaypeebrothers.com 1-A Indian Mirror Street, Wellington Square Kolkata , Phones: , , Rel: , Fax: , kolkata@jaypeebrothers.com Lekhraj Market III, B-2, Sector-4, Faizabad Road, Indira Nagar Lucknow , Phones: , lucknow@jaypeebrothers.com 106 Amit Industrial Estate, 61 Dr SS Rao Road, Near MGM Hospital, Parel Mumbai , Phones: , , Rel: Fax: , mumbai@jaypeebrothers.com KAMALPUSHPA 38, Reshimbag, Opp. Mohota Science College, Umred Road Nagpur (MS), Phone: Rel: , Fax: nagpur@jaypeebrothers.com Essentials of Medical Microbiology 2008, Jaypee Brothers Medical Publishers Editorial Consultant: Ms Peromila MA (English) All rights reserved. No part of this publication should 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 written permission of the authors and the publisher. This book has been published in good faith that the materials provided by authors is original. Every effort is made to ensure accuracy of material, but the publisher, printer and authors will not be held responsible for any inadvertent error(s). In case of any dispute, all legal matters are to be settled under Delhi jurisdiction only. First Edition: 1994 Second Edition: 1999 Third Edition: 2004 Fourth Edition: 2008 ISBN Typeset at JPBMP typesetting unit Printed at Ajanta

5 To Indu, Peromila, Parul, Vrinda and Tushar for being so wonderful and understanding during the genesis of this work

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7 Preface to the Fourth Edition Teaching of Medical Microbiology to the MBBS students is changing rapidly. This is primarily due to emergence of newer pathogens, newer diagnostic tools, emerging and re-emerging infections and above all shrinking time available to accommodate all this. Microbiology continues to be the backbone of understanding diagnosing and controlling the communicable diseases. Our primary focus of this Fourth Edition is to update various chapters, delete the contents that have become relatively unimportant and enhanced focus on the topics of current interest. For easy assimilation and reproducibility of the subject by the students, a lot of tables, figures and flow charts have been included. The book is for the first time being printed in colour which will definitely enhance its acceptability by our valued readers. We are deeply indebted to Shri Jitendar P Vij, Chairman and Managing Director, Jaypee Brothers Medical Publishers and his dedicated team for their magnificent support in bringing this book to its current shape. We continue to be thankful to our family members, friends, well-wishers and above all our dear students for their continuous support. We are optimistic that this revised edition will be liked by our readers. We look forward to their patronage. Rajesh Bhatia RL Ichhpujani

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9 Preface to the First Edition The development of the science of medical microbiology from Leeuwenhoeck s astonishing observations of animalcules to Pasteur s first use of rabies vaccine on a human being; to Fleming s discovery of penicillin; to today s race to develop a vaccine against AIDS has been indeed one of the most amazing stories of mankind behind which is hidden the intricate and intimate relationship between the man and the microbe. For every single cell in the human body, ten microbes are harboured by the man. At any time an adult human being harbours 100 trillion microorganisms. These organisms are most of the times beneficial to man. Pathogenicity is a trait exhibited by only a few of them. Yet, tremendous mortality and morbidity have been inflicted on the mankind by these organisms since time immemorial. Rapid advances in medical sciences may have brought down the incidence of microbial infections in some parts of the world but an overwhelming population is still afflicted by a variety of infectious diseases. Medical microbiology is the science which deals with the study of organisms that cause infectious diseases. This book has been designed chiefly for the students pursuing an undergraduate course in medical microbiology or any of the allied fields. This has deliberately been written in a simple, straightforward, functional, easily reproducible and user-friendly style. Special attention has been given to provide the updated information. Clear, attractive and easy-to-make illustrations have been used in abundance to ensure better understanding of the subject. About three dozen coloured figures have been appended in the beginning of the book to create longlasting impressions of the appearances of the microorganisms. Numerous boxes coupled with tables have been inserted to highlight salient features. So much has been the information explosion in medical microbiology that no book, however, hefty it may be, can stake a claim to be complete and up-to-date in all aspects of the subject. Apropos to this reality we decided to present in this book a prudent mix of essentials of fundamentals, recent advances and applications to the practice of medicine. The book has been accordingly titled as Essentials of Medical Microbiology. For those desirous of going into details, a few relevant references have been appended at the end of the text of each chapter. While we derived immense pleasure in conceiving the concept of this book and giving it the shape of the manuscript, getting it through various stages of publication was also an scintillating experience. We are deeply indebted to Shri Jitendar P Vij of Jaypee Brothers, and his dedicated team for the magnificent support extended by them. Finally, we thank our affectionate families for their constant encouragement without which we would have never contemplated, let alone complete, this book. Rajesh Bhatia RL Ichhpujani

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11 Contents PART I: History and Scope of Medical Microbiology 1. History of Medical Microbiology 1 Contributions of Louis Pasteur 1; Contributions of Robert Koch 2; Antimicrobial Agents 3; Discovery of Viruses 4; Nobel Laureates 5 2. Scope of Medical Microbiology 6 Microorganism 6; Microbiology and Patient 6; Microbiology and Healthy Individual 7; Microbiology and Community 7; Branches of Microbiology 7; Role of Medical Microbiology 7 PART II: Cellular and Molecular Microbiology 3. Bacterial Morphology 8 The Bacterial Cell 9; Bacterial Spores 15; Classification of Bacteria 17; Techniques to Study Morphology of Bacteria Nutrition and Growth of Bacteria 22 Nutrients 22; Oxygen and Carbon Dioxide 22; Temperature 23; Moisture and Desiccation 24; Bacterial Metabolism 24; Bacterial Growth Bacterial Genetics 27 Mutations 29; Gene Transfer 29; Newer Approaches to Bacterial Genetics 32; Genetic Engineering Bacteriophage In Vitro Cultivation of Bacteria 41 Bacteriological Media 41; Cultivation of Bacteria 43; Anaerobic Cultures Identification of Bacteria 46 PART III: Microbial Control and Mechanism of Pathogenicity 9. Disinfection and Sterilization 49 Definitions 49; Physical Agents 49; Chemical Agents 53; Ideal Disinfectant 56; Combined Treatments Antimicrobial Chemotherapy 60 Antiviral Drugs 62; Antifungal Drugs 62; Drug Resistance 63; Biochemical Mechanisms of Drug Resistance Infection and Disease 65 Dynamics of Infectious Diseases Microbial Pathogenicity 69 Pathogenic Microorganisms 69; Virulence Factors of Microorganisms 69 PART IV: Immunology 13. Nonspecific Defenses of Host 74 Host-parasite Relationship 74; Resistance of Host to Microorganisms Overview of Acquired Immunity 78

12 xii Essentials of Medical Microbiology 15. Functional Anatomy and Development of Immune System Biology of Immune Response 85 Dynamics of Antigen Elimination 85; Immune Response 85; Uses of Primary and Secondary Immune Responses 86; Factors Influencing Antibody Production Antigen Antibody 91 Monoclonal Antibody (Hybridomas) Cells of Immune System 95 Major Cells of Immune System The Complement System Antigen-Antibody Reactions 105 Precipitation 106; Agglutination 110; Complement Fixation Test 112; Neutralisation Tests 113; Immunofluorescence 114; Enzyme Immunoassays 115; Radioimmunoassay 115; Miscellaneous Tests 116; Opsonisation Hypersensitivity 118 Type I Hypersensitivity 118; Type II Hypersensitivity 120; Type III Hypersensitivity 121; Type IV Hypersensitivity 122; Type V Stimulatory Hypersensitivity Immunodeficiency Autoimmunity 128 Major Histocompatibility Complex (MHC) 128; Autoimmunity Transplantation and Malignancy 131 Tumour Immunology Blood Group Antigens 135 PART V: Gram-positive Bacteria 27. Staphylococcus 139 Species of Staphylococcus 139; Staphylococcus aureus 139; Coagulase Negative Staphylococci 146; Staphylococcus epidermidis 146; Staphylococcus saprophyticus 146; Micrococcus 147; Planococcus Streptococcus 148 Streptococcus pyogenes 149; Other Pathogenic Streptococci 154; Group C and G Streptococci 155; Group D Streptococci 155; Viridans Streptococci Pneumococcus Corynebacterium 162 Corynebacterium Diphtheriae 162; Other Corynebacteria Mycobacterium 169 Mycobacterium tuberculosis 169; Tests for Confirmation of Identity 175 Mycobacterium leprae 178; Atypical Mycobacteria 181; Mycobacteria Producing Skin Ulcers 182; Saprophytic mycobacteria Bacillus 184 Bacillus anthracis 184; Anthracoid bacilli 187; Bacillus cereus 187; Bacillus stearothermophilus 188; Other Bacillus Species Clostridium 189 Clostridium botulinum 190; Clostridium difficile 192; Clostridium perfringens 193; Clostridium novyi 196; Clostridium septicum 196; Other Histotoxic Clostridia 197; Clostridium tetani Actinomycetes 200 Actinomycosis 200; Nocardiosis 201; Actinomycotic Mycetoma 202

13 Contents xiii PART VI: Gram-negative Bacteria 35. Neisseria 203 Neisseria meningitidis 203; Neisseria gonorrhoeae 206; Other Neisseriae Haemophilus 209 Haemophilus influenzae 209; Other Haemophilus Species 212; Gardnerella vaginalis Bordetella 214 Bordetella parapertussis 217; Bordetella bronchiseptica 217; Bordetella avium Brucella Enterobacteriaceae 222 Escherichia coli 224; Klebsiella 228; Proteeae 228; Other Members of Enterobacteriaceae Salmonella 232 Enteric Fever 235; Salmonella Gastroenteritis 240; Salmonella bacteraemia with Focal Lesions Shigella Yersinia 245 Yersinia pestis 245; Yersinia pseudotuberculosis 248; Yersinia enterocolitica Vibrio 251 Vibrio cholerae 251; V. parahaemolyticus 256; Aeromonas 256; Plesiomonas Pseudomonas 258 Pseudomonas aeruginosa 258; Other Species of Pseudomonas 260; Burkholderia mallei 260; Burkholderia pseudomallei 260; Burkholderia cepacia 260 PART VII: Spirochaetes and Other Bacteria 45. Treponemes 261 Treponema 262; Treponema Pallidum 262; Pinta 269; Endemic Syphilis Leptospira Borrelia 274 Borrelia vincenti 275; Lyme Disease Mycoplasma Chlamydia 278 Psittacosis 280; Trachoma 280; Lymphogranuloma venereum Rickettsia 282 Epidemic Typhus 284; Brill-Zinsser Disease 284; Endemic or Murine Typhus 284; Scrub Typhus 284; Trench Fever (Quintana Fever) 285; Rocky Mountain Spotted Fever 285 Q-fever 285; Laboratory Diagnosis of Rickettsial Diseases 286; Ehrlichia 287; Rochalimaea Non-sporing Anaerobes 288 Anaerobic Gram-negative Bacilli 288; Bacteroides, Prevotella and Porphyromonas 288; Fusobacteria and Leptotrichia 290; Anaerobic Gram-positive Bacilli 290; Anaerobic Cocci 290; Peptostreptococcus and Peptococcus 290; Veillonella and Acidaminococcus 291; Spiral Shaped Motile Anaerobes Legionella 292 Legionella pneumophila Campylobacter and Helicobacter 294 Helicobacter pylori 295; Gastrospirillum hominis 296

14 xiv Essentials of Medical Microbiology 54. Miscellaneous Bacteria 297 Pasteurella multocida 297; Actinobacillus 297; Francisella tularensis 297; Streptobacillus moniliformis 298; Spirillum minus 298; Listeria monocytogenes 298; Erysipelothrix rhusiopathiae 299; Calymmatobacterium granulomatis 299; Eikenella 299; Cardiobacterium 300; Chromobacterium 300; Achromobacter 300; Capnocytophaga 300; DF-2 Bacteria 300; Flavobacterium meningosepticum 300; Kingella 300; acinetobacter 301; Alcaligenes 301; Bartonella Normal Microbial Flora of the Human Body 302 Sites with Normal Flora 303 PART VIII: General Virology 56. Nature and Classification of Viruses 306 Viroids 308; Prions Morphology of Viruses Replication of Viruses 313 Release 314; Defective Viruses Cultivation and Assay of Viruses Genetics of Viruses 320 Mutations 320; Genetic Recombination Between Viruses 320; Interaction Between Viral Gene Products 320; Genetic Variation in Nature 321; Viral Vectors Viral Pathogenesis and Host Response 322 Pathogenicity of Viruses 322; Host Response to Viral Infections Oncogenic and Teratogenic Viruses 328 Oncogenic Viruses 328; Teratogenic Viruses 329 PART IX: DNA Viruses 63. Adenoviruses 330 Adenoviruses Associated Defective Viruses Herpesviruses 333 Herpes Simplex Virus 334; Varicella-zoster Virus 336; Cytomegalovirus 337; Human Herpesvirus 6 339; Human Herpesvirus Poxviruses 341 Smallpox 341; Human Monkeypox 342; Cowpox 342; Buffalopox 342; Tanapox 343; Milker s Nodules 343; ORF 343; Molluscum contagiosum Papovaviruses 344 Human Papillomaviruses 344; Human Polyomaviruses Parvoviruses 346 PART X: RNA Viruses 68. Picornaviruses 348 Poliovirus 348; Coxsackieviruses 351; Echoviruses 352; Enteroviruses Types ; Enterovirus ; Rhinoviruses Paramyxoviruses 355 Measles 355; Mumps 357; Infections Caused by Parainfluenza Viruses 359; Infections Caused by Respiratory Syncytial Virus 359

15 Contents xv 70. Orthomyxoviruses 361 Avian Influenza (Bird Flu) Retroviruses 367 Human T Cell Leukaemia Viruses 367; Human Immunodeficiency Virus Rhabdoviruses 382 PART XI: Multiple Viral Complexes 73. Viral Hepatitis 389 Hepatitis A Virus 389; Hepatitis B Virus 391; Hepatitis C 396; Hepatitis E 397; Hepatitis D 398; Hepatitis G 399; Hepatitis F 400; Overview of Viral Hepatitis Arboviruses 401 Definition 401; Virology of Common Arboviruses 401; Togaviridae 402; Bunyaviridae 402; General Clinical Features 403; Laboratory Diagnosis of Arboviruses 404; Arboviral Diseases in India 404; Dengue Fever and Dengue Haemorrhagic Fever 405; Kyasanur Forest Disease 406; Chikungunya Virus Miscellaneous Viruses 408 Rubella 408; Rotavirus 410; Coronaviridae 411; Arenaviridae 412; Lymphocytic Choriomeningitis 413; Argentinian Haemorrhagic Fever 413; Bolivian Haemorrhagic Fever 413; Lassa Fever 413; Filoviruses (Ebola and Marburg Virus) 413 PART XII: Mycotic Infections 76. Medical Mycology 415 Spore Formation in Fungi 416; Economic Importance of Fungi 419; Mycoses 419; Tinea Versicolor 419; White Piedra (Piedra Alba) 420; Black Piedra (Piedra Nigra) 420; Dermatophytes 421; Dermatophytids (ID Reaction) 424; Paracoccidioidomycosis 424; Blastomycosis 425; Histoplasmosis (Darling s Disease) 426; Candidiasis 427; Mycetoma 429; Cryptococcosis 430; Rhinosporidiosis 431; Sporotrichosis 432; Coccidioidomycosis 433; Opportunistic Fungi 434; Otomycosis 435; Fungal Contaminants 435; Absidia Species 436; Mucor Species 436; Rhizopus Species 436; Septate Contaminants 437; Dematiaceous Contaminants 437; Alternaria Species 437; Cladosporium (Hormodendrum Species) 437; Curvularia Species 438; Penicillium Species 438; Mycotoxicosis 438; Immunodiagnosis of Fungal Infections 438 PART XIII: Applied Microbiology 77. Microbiology of Water, Milk and Air 440 Examination of Milk 444; Bacteriological Examination of Milk 445; Examination of Milk for Specific Pathogens 446; Examination of Air Nosocomial Infections 448 Role of Microbiology Laboratory in Prevention and Control of Nosocomial Infections Blood Transfusion Associated Infections 452 Blood Culture Quality Assurance in Microbiology Immunoprophylaxis Against Infectious Diseases 458 Vaccine 458; Immunoglobulins and Antisera 460

16 xvi Essentials of Medical Microbiology PART XIV: Clinical Microbiology 82. Laboratory Diagnosis of Important Clinical Syndromes 462 Laboratory Diagnosis of Meningitis 462; Laboratory Diagnosis of Tetanus 465; Laboratory Diagnosis of Gas Gangrene 466; Laboratory Diagnosis of Urinary Tract Infections 467; Laboratory Diagnosis of Pertussis 468; Laboratory Diagnosis of Pyrexia of Unknown Origin 470; Laboratory Diagnosis of AIDS 472; Molecular Level Detection 474; Laboratory Diagnosis of Syphilis 474; Laboratory Diagnosis of Sore Throat 476; Laboratory Diagnosis of Cholera 478; Laboratory Diagnosis of Diarrhoeal Diseases (Gastroenteritis) 480; Laboratory Diagnosis of Acute Respiratory Infections (ARI) 484 Index 489