Essentials of Medical Microbiology, 3rd Edition PDF

DOC in MayKing  Essentials of Medical Microbiology https://t.me/docinmayking  Essentials of Medical Microbiology THIRD EDITION Apurba S Sastry MD (JIPMER) DNB MNAMS PDCR...

DOC in MayKing  Essentials of Medical Microbiology https://t.me/docinmayking  Essentials of Medical Microbiology THIRD EDITION Apurba S Sastry MD (JIPMER) DNB MNAMS PDCR Hospital Infection Control Officer Officer In-charge, HICC Antimicrobial Stewardship Lead Associate Professor Department of Microbiology Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry, India https://t.me/docinmayking Sandhya Bhat (Gold medalist) MD DNB MNAMS PDCR Professor Department of Microbiology Pondicherry Institute of Medical Sciences (PIMS) (A Unit of Madras Medical Mission) Puducherry, India Co-Editors Anand Bhimaray Janagond MD DNB Deepashree R MD DNB MNAMS Professor Assistant Professor Department of Microbiology Department of Microbiology S Nijalingappa Medical College JSS Medical College Bagalkot, Karnataka, India Mysuru, Karnataka, India Forewords Pallab Ray MD President, Indian Association of Medical Microbiologists (IAMM) Professor, Department of Microbiology, PGIMER, Chandigarh, India Sujatha Sistla MD Professor, Department of Microbiology, JIPMER, Puducherry, India JAYPEE BROTHERS MEdicAl PuBliSHERS The Health Sciences Publisher New Delhi | London  Jaypee Brothers Medical Publishers (P) Ltd Headquarters Jaypee Brothers Medical Publishers (P) Ltd EMCA House, 23/23-B Ansari Road, Daryaganj New Delhi - 110 002, INDIA Landline: +91-11-23272143,+91-11-23272703, +91-11-23282021,+91-11-23245672 Head Office : 011-43574357 Email: [email protected] Corporate Office Overseas Office Jaypee Brothers Medical Publishers (P) Ltd J.P. Medical Ltd 4838/24, Ansari Road, Daryaganj 83 Victoria Street, London New Delhi 110 002, India SW1H 0HW (UK) Phone: +91-11-43574357 Phone: +44 20 3170 8910 Fax: +91-11-43574314 Fax: +44 (0)20 3008 6180 https://t.me/docinmayking Email: [email protected] Email: [email protected] Website: www.jaypeebrothers.com Website: www.jaypeedigital.com © 2021, Jaypee Brothers Medical Publishers The views and opinions expressed in this book are solely those of the original contributor (s)/author (s) and do not necessarily represent those of editor (s) of the book. All rights reserved. No part of this publication may be reproduced, stored or transmitted in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, without the prior permission in writing of the publishers/editors. All brand names and product names used in this book are trade names, service marks, trademarks or registered trademarks of their respective owners. The publisher is not associated with any product or vendor mentioned in this book. Medical knowledge and practice change constantly. This book is designed to provide accurate, authoritative information about the subject matter in question. However, readers are advised to check the most current information available on procedures included and check information from the manufacturer of each product to be administered, to verify the recommended dose, formula, method and duration of administration, adverse effects and contraindications. It is the responsibility of the practitioner to take all appropriate safety precautions. Neither the publisher nor the author (s)/editor (s) assume any liability for any injury and/ or damage to persons or property arising from or related to use of material in this book. This book is sold on the understanding that the publisher is not engaged in providing professional medical services. If such advice or services are required, the services of a competent medical professional should be sought. Every effort has been made where necessary to contact holders of copyright to obtain permission to reproduce copyright material. If any have been inadvertently overlooked, the publisher will be pleased to make the necessary arrangements at the first opportunity. The CD/DVD-ROM (if any) provided in the sealed envelope with this book is complimentary and free of cost. Not meant for sale. Inquiries for bulk sales may be solicited at: [email protected] Essentials of Medical Microbiology First Edition: 2016 Second Edition: 2019 Third Edition: 2021 Revised Reprint: 2021 ISBN: 978-81-947090-1-5 Printed at  Dedicated to https://t.me/docinmayking Our Beloved Parents, Family Members And, above all, the Almighty “Life is the most difficult exam. Many fail because they tend to copy others, not realizing that everyone has a different question paper.” “Gold medalists are not made up of gold. They are made up of determination and hard work and ready to kill themselves to achieve their goals.” “Success is not the key to happiness. Happiness is the key to success. If you love what you are doing, you will be successful.” “You can succeed only if the fire inside you burns brighter than the fire around.”  Golden Rules of Goal Setting Dear Students Here are some important tips which will help you in setting your goals in studies: 1. Set Goals That Motivate You: This means making sure that they are important to you, and that there is value in achieving them 2. Set SMART Goals „ Specific: Your goal must be clear and well defined, not vague or generalized „ Measurable: Goals must have measurable objectives „ Attainable : Make sure that your goals are achievable and within your limit https://t.me/docinmayking „ Relevant: Will take you to the direction you want your life and career to go „ Time Bound: You must know when you have the deadline and can celebrate success 3. Set Goals in Writing: Written commitment in presence of your close people (parents, close friends) will always push and remind you whenever you tend to deviate from your goal 4. Make an Action Plan: Do not focus only on the outcome, but make planning of all small steps that collectively take to the outcome. This is especially important if your goal is big and demanding, or long-term 5. Monitor Yourself: Compliance to the action plan should be monitored at least weekly (for one month goal) or monthly (for a yearly goal), depending upon your goal size. Remember, "Success is not final; failure is not fatal: It is the courage to continue that counts." —Winston S Churchill “There are two types of people who will tell you that you cannot make a difference in this world: those who are afraid to try and those who are afraid you will succeed." —Ray Goforth "Success ke piche mat bhago. Kabil bano kabil. Kamyabi toh sali jhak maar ke peeche ayegi." —Aamir Khan  Foreword It gives me immense pleasure to know that the third edition of Essentials of Medical Microbiology is to be released. The first two editions were very well appreciated among faculty and students across the country. The third edition is fully updated with a simple lucid presentation style like its earlier editions. This updated edition of the book has come at a much-needed time when NMC has implemented competency based medical education (CBME) and there is a strong need for a clinical microbiology textbook with stress on the Indian perspective. There is also an urgent need for clinical microbiologists with patient-centric bedside orientation rather than the age-old microbe-based laboratory limited attitude. This textbook has been written from a syndromic rather than traditional organism-based approach, in accordance with the revised competency based MBBS curriculum. The book is aptly divided into two parts. The first part comprises of General Microbiology, Immunology and Hospital https://t.me/docinmayking Infection Control and the second part, Systemic Microbiology (Infectious Diseases), includes several sections, each starting with a clinical infective syndrome followed by chapters covering detailed information about the etiological agents and their specific pathogenetic, epidemiological and clinical characteristics. Parasitology has been added and therefore it obviates the need for a separate book. General Microbiology section has been meticulously restructured with the inclusion of chapters on general virology, general parasitology and general mycology. General bacteriology is reorganized into a single chapter with several subchapters. To help understand individual organisms better when discussed under systemic microbiology, overview chapters have been included in the general microbiology section. Hospital Infection Control section has been extensively updated with addition of contemporary topics like major types of HAI, monitoring of antimicrobial stewardship, escalation and de-escalation strategy, donning and doffing of PPE and transmission-based precautions. The chapter on sterilization and disinfection has been completely revised based on hospital use of sterilizers and disinfectants and shifted to hospital infection control section. Microbiology in 2020 cannot be complete without COVID-19 and a chapter has been rightly added covering details about the most catastrophic and enigmatic disease, the COVID-19 and its agent SARS-CoV-2. Annexures section has been expanded to include several new and relevant topics such as opportunistic infections, transplant infections, national health programmes for communicable diseases, vector-borne diseases, transfusion-transmitted infections and AETCOM (attitude, ethics and communication) in Microbiology. AETCOM module has been added as a new annexure, which covers topics pertaining to confidentiality in disclosing laboratory reports and demonstration of respect for patient samples. Updates and recent advances have been made in epidemiology, laboratory diagnosis, treatment guidelines and vaccine prophylaxis of infectious diseases including tuberculosis and HIV. I congratulate Dr Apurba S Sastry and his wife Dr Sandhya Bhat, for this commendable work and I am sure that this book will be widely read and appreciated by both undergraduate and postgraduate students of microbiology. Pallab Ray MD President Indian Association of Medical Microbiologists (IAMM) Professor Department of Microbiology, PGIMER, Chandigarh, India  Foreword I am happy to know that the third edition of Essentials of Medical Microbiology is to be released. This is a Clinical Microbiology textbook written in a system-wise approach, rather than traditional organism- based approach, with Indian perspective. JIPMER has implemented system-based Microbiology in MBBS curriculum since four years and we observed that students are finding it difficult to read organism- based book when the syllabus is system-based. Therefore this book has come at a much desired time when system-based Microbiology curriculum has been introduced pan India, by NMC. ™ Book is divided into two parts. „ The first part comprises of General Microbiology, Immunology and Hospital Infection Control. „ The second part ‘Systemic Microbiology (Infectious Diseases)’ comprises of several sections, each comprising a first chapter on clinical infective syndrome followed by several chapters covering detailed information about the etiological https://t.me/docinmayking agents ™ Parasitology has been incorporated and therefore it obviates the reading of a separate book. ™ Hospital Infection Control section has been thoroughly updated with the inclusion of new topics such as major HAI types, monitoring of antimicrobial stewardship, escalation vs de-escalation strategy, donning/doffing of PPE and transmission- based precautions. ™ General Microbiology section has been meticulously restructured with the inclusion of general virology, general parasitology and general mycology chapters. General bacteriology is reorganized into a single chapter with several subchapters. ™ Overview chapters have been incorporated in the general microbiology section, which will help in better understanding of individual organisms when discussed under systemic microbiology. ™ Sterilization and disinfection chapter has been completely revised based on hospital use of sterilizers and disinfectants; and has been shifted to Hospital Infection Control section. ™ A chapter on COVID-19 has been added, covering the latest pandemic in detail. ™ Annexures section has been expanded to include several new topics such as opportunistic infections, transplant infections, national health programmes for communicable diseases, vector-borne diseases, transfusion-transmitted infections and AETCOM in Microbiology. ™ AETCOM module has been added as a new annexure, which covers topics pertaining to confidentiality in disclosing laboratory reports and demonstration of respect for patient samples. ™ I really appreciate the efforts made by my student and now colleague Dr Apurba S Sastry and his wife Dr Sandhya Bhat, for this praiseworthy work and I am sure that this book will be widely read by both undergraduate and postgraduate students of Microbiology. Sujatha Sistla MD Professor Department of Microbiology Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER) Puducherry, India  Preface to the Third Edition It gives us immense pleasure to announce the release of third edition of Essentials of Medical Microbiology. The excitement reaches its pinnacle as our sleepless nights of last ten months have come to an end. The first two editions were highly appreciated among students and faculty. Many have described it as ‘highly recommended’, ‘extraordinary book’, ‘boon for exam’, ‘well organized’, etc. Clinical Microbiology, in True Sense The making of this third edition is a revolutionary event in our life, as we went through a journey where we experienced how Microbiology can be changed to suit to the need of an Indian Medical Graduate. ™ This book is prepared according to new MBBS curriculum and the content of the book was modified Apurba S Sastry from the traditional organism-based teaching to system-based teaching. The content has been https://t.me/docinmayking updated, concised and reshuffled—the three major types of changes incorporated in this edition. ™ Parasitology has also been incorporated into this book under the respective infective syndromes, thus obviates the reading of a separate parasitology book. ™ The reduction of the content is made by keeping the perspective of an Indian medical graduate in mind. The book is categorized into two parts, which is further divided into eleven sections. Part I: General Microbiology, Immunology, Hospital Infection Control Part I comprises of three sections—General Microbiology, Immunology, and Hospital Infection Control Sandhya Bhat ™ Section 1: General Microbiology section is meticulously restructured with the inclusion of general virology, general parasitology and general mycology chapters. General bacteriology is reorganized into a single chapter with several subchapters. Overview chapters have been incorporated in this section, which will help in better understanding of individual organisms when discussed under systemic microbiology. ™ Section 2: Immunology section is thoroughly updated. Various topics have been updated such as MAC ELISA, National Immunization Schedule 2020, diagnosis of type I hypersensitivity (atopy), etc. Outdated topics such as precipitation, neutralization, complement fixation, etc. have been concised. ™ Section 3: Hospital infection control (HIC) section needs a special mention. We must say that this section underwent a major update. In the era of COVID-19 pandemic, the significance of HIC is being increased to thousand folds. Every healthcare personnel is supposed to be well verse with the finer details of HIC. Therefore, the updated version of this section will be a key in making of a skilled Indian medical graduate. „ The content has been thoroughly updated with the inclusion of new topics such as Major HAI types, monitoring of antimicrobial stewardship, escalation vs de-escalation strategy, donning/doffing of PPE and transmission-based precautions. „ The sterilization and disinfection chapter is completely revised based on hospital use of sterilizers and disinfectants rather than traditional `Microbiology use’ and aptly shifted from general microbiology section to HIC section. Part II: Systemic Microbiology (Infectious Diseases) It comprises of eight sections, each comprises of a chapter on clinical infective syndrome followed by several chapters covering detailed information about the etiological agents. Chapters on clinical infective syndromes—represent the first chapter of every section; covers various infective syndromes pertaining to that system in detail. ™ Section 4: Bloodstream and cardiovascular system infections section covers topics such as infective syndromes (infective endocarditis, rheumatic fever, bloodstream infections, etc.), enteric fever, rickettsial infections, brucellosis, leptospirosis, borreliosis, HIV/AIDS, viral hemorrhagic fever, malaria, visceral leishmaniasis and trypanosomiasis, lymphatic filariasis, systemic candidiasis and systemic mycoses. ™ Section 5: Gastrointestinal (GI) infections section covers topics such as infective syndromes (diarrhea, dysentery, food poisoning, etc.), GI infections due to Enterobacteriaceae (diarrheagenic E.coli, shigellosis, yersiniosis, nontyphoidal xii Essentials of Medical Microbiology salmonellosis), cholera, Helicobacter, Campylobacter and Clostridioides difficile infections, viral gastroenteritis, intestinal protozoan and helminthic infections. ™ Section 6: Hepatobiliary system infections section covers topics such as infective syndromes (liver abscess, peritonitis, etc.), viral hepatitis, yellow fever, amoebic liver abscess, hydatid disease and Trematode infections of liver. ™ Section 7: Skin, soft tissue and musculoskeletal system infections section covers topics such as infective syndromes, staphylococcal and streptococcal infections, gas gangrene and infections due to non-sporing anaerobes, leprosy, anthrax, actinomycosis, nocardiosis, non-venereal treponematoses, viral exanthems and other cutaneous viral infections, parasitic and fungal infections of skin, soft tissue and musculoskeletal systems. ™ Section 8: Respiratory tract infections section covers topics such as infective syndromes, bacterial pharyngitis (streptococcal pharyngitis, and diphtheria), bacterial lobar pneumonia (pneumococcal pneumonia, Haemophilus influenzae pneumonia and others), bacterial atypical (interstitial) pneumonia (Mycoplasma, Chlamydia and Legionella), tuberculosis and non- tuberculous mycobacteria infections, pertussis, infections due to non-fermenting gram-negative bacilli, viral infections (myxoviruses—influenza, parainfluenza, mumps and respiratory syncytial virus, coronavirus, rhinovirus, adenovirus and infectious mononucleosis), parasitic infections (e.g. paragonimiasis) and fungal infections (zygomycosis, aspergillosis and pneumocystosis). Coronavirus has been added as a completely new chapter covering in detail about the most catastrophic disease, the COVID-19. ™ Section 9: Central nervous system infections section covers topics such as infective syndromes, bacterial meningitis (meningococcal, pneumococcal, Haemophilus influenzae, Listeria, tubercular meningitis, spirochetal meningitis, and others) tetanus, viral meningitis and myelitis (poliomyelitis and others), viral encephalitis and encephalopathy (rabies, HSV and arboviral encephalitis), parasitic infections (neurocysticercosis, free-living amoebae infections, toxoplasmosis https://t.me/docinmayking and others) and fungal infections (cryptococcal meningitis and others). ™ Section 10: Urogential tract infections section covers topics such as infective syndromes (UTI, pyelonephritis, genital ulcers, urethritis, vulvovaginitis, etc.), urinary infections (Enterobacteriaceae, Enterococcus, Schistosoma haematobium and others), and genital tract infections (syphilis, chancroid, donovanosis, gonorrhea, genital Chlamydia trachomatis infection, trichomoniasis and genital candidiasis). ™ Section 11: Miscellaneous infective syndrome section covers topics such as ocular and ear infections, congenital infections, organisms with oncogenic potential and zoonotic infections. ™ Annexures: It has been expanded to include several new topics such as opportunistic infections, post-transplantation infections, national health programmes for communicable diseases, vector-borne diseases, and transfusion-transmitted infections. AETCOM module has been added as a new annexure, which covers several case scenarios pertaining to confidentiality in disclosing laboratory reports and demonstration of respect for patient samples ™ Most features of the previous editions have been maintained: Such as concept of more content-less pages, concise, bulleted format and to-the-point text, simple and lucid language, separate boxes for summary of laboratory diagnosis and treatment for quick review, clinical case-based essay questions at the end of each chapter. As you know, human errors are inevitable; and no book is immune to it. We would request all the readers to provide any errata found and also valuable suggestions and updates via e-mail. This is probably the first book in India on ‘Clinical Microbiology’, in true sense. We are confident and hoping that you all will fall in love with this edition of the book. Apurba S Sastry Sandhya Bhat [email protected] [email protected]  Preface to the First Edition The association of man and microorganisms, and their fight to survive each other is never-ending. With the increasing complexity of interaction between man and microbes, the relevance of studying medical microbiology has increased manifold. Our book titled Essentials of Medical Microbiology attempts to provide smart ways to master the world of microbes relevant to the mankind. The idea of yet another book on the subject, but with a quite different approach was born after several discouraging and unsatisfying experiences with several existing books regarding many needs of the enthusiastic students of the subject and a strong desire to make medical microbiology more interesting, up-to-date, clinically relevant and yet palatable to mainly undergraduate students of medicine and also the postgraduate aspirants and students. This book was conceptualized and brought to reality to meet the strongly felt diverse needs of the Indian students, such as gaining essential concepts, acquiring contemporary knowledge, approaching university exams with ease and confidence, scoring high in postgraduate https://t.me/docinmayking entrance examinations, etc. The book focuses on providing good foundation in clinically important concepts and principles of microbiology. Enough (over 300) tables and flowcharts have been included along with the text. Over 200 schematic diagrams have been drawn to simplify difficult concepts, and they are easy to reproduce where necessary as in examinations. Plenty of clinical photographs (over 400) included in the book will create a real life-like picture in the minds of the reader and also are meant to help solving image-based MCQs in postgraduate entrance examinations. It has more content in fewer pages, making the book handy. The concise bulleted format and to-the-point text used in this book will be helpful in rapid revision before the examinations. Best attempts have been made to keep the language simple yet lucid to help easy comprehension. Summary of laboratory diagnosis and treatment in separate boxes makes quick review possible. Highlighted boxes are incorporated to cover the important concepts. In a nutshell, this book is carefully written targeting to meet the varied needs of undergraduate students with an approach that will orient them to build concepts and to clear undergraduate examinations as well as to equip them for postgraduate entrance examinations in future. General Microbiology section deals with principles of microscopy, morphology, physiology, culture identification of bacteria, concepts of bacterial genetics, etc. Principles of sterilization, antimicrobial chemotherapy and susceptibility testing are also explained in detail. It is our humble hope that this book would change the general feeling of the students regarding immunology as being a difficult section into immunology as an interesting and enjoyable topic. In this section, topics such as immunity, antigen, antibody, complement and structure of immune system are explained in a simple and logical manner. Chapters like Immune Response and Antigen-Antibody Reaction have been fully updated according to the current need. Appropriate diagrams and flowcharts are incorporated to make critically tough content easy to grasp. Topics such as autoimmunity, immunodeficiency and immunization provide complete and latest information compiled in tabular form at one place. Systematic Bacteriology section deals with individual bacterial pathogens in detail. Flow of information follows a very logical and clinically relevant course. More stress is given to the knowledge that helps in clinical setting and a careful attempt has been made to reduce the obsolete and not-so-useful core microbiology content. Sections like laboratory diagnosis, treatment and prophylaxis are most updated and referenced from internationally accepted literature and guidelines. Virology is another section where the readers will find a different approach from the existing books. The updated and succinct information provided in this section with emphasis on pathogenesis and laboratory diagnosis will be useful to the students. This book also addresses to the long-time complaint of the undergraduate students about unavailability of a concise and pictorialized Mycology section. Written in a clear and concise manner with appropriate and beautiful schematic pictures, images and illustrations, this section will surely make the students enjoy reading. Applied Microbiology covers important aspects of various clinical infective syndromes with special reference to the approach towards the diagnosis. Useful information regarding hospital-acquired infections and biomedical waste management have been incorporated. The annexure incorporated at the end covers the recent topics, such as emerging pathogens, bioterrorism and laboratory-acquired infections. xiv Essentials of Medical Microbiology Clinical case-based essay questions and MCQs are given at the end of each chapter to orient and prepare students for the examinations. Advanced and newer postgraduate entrance-oriented topics like H1N1, ebola, polio eradication, bacterial drug resistance mechanisms (such as ESBL, VRSA, VRE), automations and molecular methods in microbiology, etc. are incorporated. We hope that the undergraduates, postgraduate aspirants, and postgraduate students will relish reading this book and find it useful. We also hope that we have made a good start in addressing the varied needs of students and faculty teaching medical microbiology with a single comprehensive book. We will feel glad to receive your valuable feedback, which will enable us to improve further. Apurba S Sastry Sandhya Bhat [email protected] [email protected] https://t.me/docinmayking  Acknowledgments The release of Third edition of Essentials of Medical Microbiology would not have been possible without our close association with many people. We take this opportunity to extend our sincere gratitude and appreciation to all those who made this book possible. Hearty acknowledgments to our teachers, departmental staff, family members and others, for their blessings and support. 1. We would like to sincerely thank the co-editors of this book for their constant support, hard work during the manuscipt preparation. „ Dr Anand B Janagond, Professor, Department of Microbiology, S Nijalingappa Medical College, Bagalkot, Karnataka „ Dr Deepashree R, Assistant Professor, Department of Microbiology, JSS Medical College, Mysuru, Karnataka: She https://t.me/docinmayking needs a special mention, as she has put an outstanding effort, great commitment and had several months of sleepless nights. 2. We are extremely thankful to Dr Haritha M, Ex-Senior Resident and Fellow in Hospital Infection Control, JIPMER for her help in the preparation of faculty resource material. 3. We are grateful to Dr Pallab Ray, President, Indian Association of Medical Microbiologists (IAMM) and Professor, Department of Microbiology, PGIMER, Chandigarh, India for his willingness to write an encouraging foreword. 4. We express heart-felt gratitude to Dr Sujatha Sistla, Professor, Department of Microbiology, JIPMER, for giving the foreword, for her guidance during manuscript preparation. She is an extremely friendly and knowledgeable person. She has been our ‘Google Search’; clarifying all our doubts all the time. I (Dr Apurba) am greatly indebted to you mam for your timely support and guidance. 5. We are extremely thankful to Dr Rakesh Aggarwal, Director, JIPMER, Puducherry for giving the permission to revise this textbook. 6. We are grateful to Dr Renu G Boy Varghese, Director-Principal, Pondicherry Institute of Medical Sciences (PIMS), Puducherry, for giving permission to revise this textbook. 7. We are extremely thankful to Dr Jharna Mandal, Additional Professor and Head, Department of Microbiology, JIPMER, for her constant encouragement and support during the preparation of the manuscript. 8. We would like to express our special word of thanks to Dr Reba Kanungo, Dean Research, Professor and Head, Department of Microbiology, Pondicherry Institute of Medical Sciences (PIMS). I (Dr Sandhya) am truly grateful to you mam for your wholehearted support. 9. Other Faculty of Department of Microbiology, JIPMER—Dr Rakesh Singh (Additional Professor), Dr Rahul Dhodapkar (Additional Professor), Dr Noyal M Joseph (Associate Professor), Dr Rakhi Biswas (Associate Professor), Dr Nonika Rajkumari (Associate Professor) and Dr Maanasa Bhaskar (Assistant Professor). 10. Other Faculty of Department of Microbiology, PIMS—Dr Shashikala (Professor); Dr Sheela Devi (Professor); Dr Johny Asir (Professor); Dr Vivian Joseph P (Professor), Dr Sujitha E (Associate Professor); Dr Anandhalakshmi (Associate Professor), Dr Arthi E (Associate Professor), Mrs Patricia Anita (Associate Professor), Dr Meghna (Assistant Professor) and Mrs Desdemona Rasitha (Tutor). 11. Residents and postgraduates, JIPMER—Dr Mugundan, Dr Sindhu, Dr Gopichand, Dr Radha, Dr Rachna, Dr Sarumathi, Dr Anitha, Dr Kalpana, Dr Monika, Dr Lakshmi, Dr Soundarya, Dr Kowshalya, Dr Lullu, Dr Imola, Dr Symphonia, Dr Pheba, Ms Rosemary, Ms Lakshmishree, Ms Gopika and Ms Neeshma. 12. HICC, JIPMER— Infection control nurses and other office staff such as Ms Ilaveni, Ms Ramya and Mr Venkat. 13. Special thanks to our teachers—Dr SC Parija (JIPMER, retired), Dr BN Harish (JIPMER, retired), Dr ER Nagaraj (SSMC Tumkur, retired), Dr Sharadadevi Mannur (SSMC, Tumkur) and Dr Renushree (SSMC, Tumkur). 14. We are thankful to Dr Debadutta Mishra, Fellow (Parasitology, JIPMER), Andaman & Nicobar Islands Institute of Medical Sciences, Port Blair for his inputs during the 2nd edition of Essentials of Medical Parasitology. xvi Essentials of Medical Microbiology 15. For providing photographs—We are extremely thankful to all people/institutes/companies who have agreed to provide valuable photographs. „ Head, Department of Microbiology, JIPMER, Puducherry „ Head, Department of Microbiology, Pondicherry Institute of Medical Sciences (PIMS), Puducherry „ Public Health Image Library, Centers for Disease Control and Prevention (CDC), Atlanta „ Dr Karen C Carroll, Professor, Department of Pathology, Johns Hopkins University, USA and Editor of Jawetz, Melnick & Adelberg’s Medical Microbiology, 27th edition and Mr Michael Weitz, Editorial Director, McGraw-Hill Professional Publishing, USA „ Authors of Kuby’s Immunology: Dr Judith A Owen, Jenni Punt, Dr Sharon Stranford, Dr Patricia P Jones and Ms Lauren Schultz, Senior Acquisitions Editor, WH Freeman and Company: For allowing us to modify the images from Kuby’s Immunology, fifth edition „ Dr Sherly Antony, Faculty, Pushpagiri Medical College, Kerala „ Dr Isabella Princess, Consultant, Apollo Hospitals, Chennai, Tamil Nadu „ Dr Suchitra Mahapatra, Hitech Medical College, Rourkela, Odisha „ Dr Sunitha V and Dr Subhadra, Department of Radiology, JIPMER, Puducherry „ Dr Padmaja Shenoy, Department of Microbiology, Kasturba Medical College, Manipal, Karnataka 16. Microbiology Faculty from our previous working place— „ Meenakshi Medical College, Chennai, Tamil Nadu—Dr Senthamarai, Dr Sivasankari, Dr Somasundar and others „ ESIC Medical College and PGIMSR, Chennai—Dr Manisha S Mane and others „ Sri Siddhartha Medical College, Tumkur, Karnataka, India (all faculty members) https://t.me/docinmayking 17. Dr Anand Sastry, Department of Neuromedicine, Banaras Hindu University (BHU), Varanasi, Uttar Pradesh: For giving inputs during manuscript preparation of various CNS infections 18. Ex-residents from JIPMER: Dr Prasanna, Dr Ramya, Dr Suman, Dr Sneha, Dr Sunil, Dr Subhashree, Dr Akshatha and others— for giving inputs in the correction of content errors of first edition 19. Each and every reader (faculty and students) from various parts of the country—for communicating to us by email and other electronic media about the content correction and updates from time to time 20. Our friends—Dr Godfred, Dr Sadia, Dr Ramakrishna, Dr Mridula, Dr Srinivas Acharya, Dr Chaya, Dr Manisha, Dr Ira, Dr Sreeja, Dr Wajid, Dr Kumudavathi and others. 21. Family— Parents, brother, sister and other family members, maternal and paternal cousins and all other well-wishers. Sincere Acknowledgments for Helping in Syllabus Preparation Preparation of the revised Microbiology syllabus according to NMC curriculum was an extremely difficult challenge we faced. Changing the syllabus from the traditional organism-based teaching to system-based teaching was not that easy. We express heart-felt gratitude to the following senior faculty whom we have consulted during the syllabus preparation. Their inputs were instrumental in designing the outline of the table of content. 1. Dr S Sujatha, Professor, Department of Microbiology, JIPMER, Puducherry. 2. Dr Suman Singh, Professor, Department of Microbiology, Pramukhswami Medical College, Karamsad, Gujarat (contributor of the new NMC MBBS curriculum for Microbiology). 3. Dr Padma Srikanth, Professor, Department of Microbiology, Sri Ramachandra Medical College and Research Institute, Chennai (contributor of the new NMC MBBS curriculum for Microbiology). 4. All faculty, Department of Microbiology, JIPMER, Puducherry. 5. All faculty, Department of Microbiology, Pondicherry Institute of Medical Sciences, Puducherry. Special Acknowledgments to My Publishers Jaypee Brothers Medical Publishers (P) Ltd, New Delhi, India ™ Shri Jitendar P Vij (Group Chairman) ™ Mr Ankit Vij (Managing Director) ™ Mr MS Mani (Group President) ™ Dr Madhu Choudhary (Publishing Head–Education): She has been a great support throughout the manuscript preparation ™ Ms Pooja Bhandari (Production Head) ™ Ms Seema Dogra (Cover Visualizer) ™ Dr Astha Sawhney (Development Editor): Extremely dynamic, have lot of patience and available 24x7 to address to our queries  Acknowledgments xvii ™ The Development Team: Mr Deepak Saxena and Mr Omprakash Mishra (Typesetters), Mr Nitin Bhardwaj (Graphic Designer), Mr Binay Kumar and Ms Neelam (Proofreaders). These guys are simply outstanding in their work. A special mention for Mr Deepak Saxena, we must say that he is the best operator of India in medical publishing. The way Nitin Bhardwaj does the designing of photographs is extraordinary. It is a treat for us to work with all of them. These guys are extremely workaholic and have a very good team spirit. We salute them, for their professionalism. ™ Marketing heads from various zones: Mr Narendra Shekhawat (Vice President–Sales), Mr Venugopal V (South Head), Mr Rishi Sharma (North Region Head), CS Gawde (Western Head) and Sandip Gupta (Eastern Head). ™ Branch managers and Sales manager from various branches: Bengaluru branch (Ravi Kumar, A Palani, E Venkatesh, Vivek Bhagawan), Chennai branch (Maran A [Adoption Head for South], Dharani Kumar P, RK Dharani, Dharanidaran), Kochi branch (Sujeesh VS, Diffin Robin, Arun Kumar), Hyderabad branch (Parimal Guha Neogy, Marthanda Sarma, Rajesh Malothu, Hamza Ali), Mumbai branch (Sameer S Mulla), Nagpur branch (Rajesh Shrivas), Ahmedabad branch (Ms Priyanka Kansara, Dinesh Waghade), Delhi branch (Sujatha Puri), Kolkata branch (Sanjoy Chakraborthy). Lastly, we would like to keep in record that without the support of our son, parents (of both Dr Sandhya and Dr Apurba) and other family members, it would have been impossible to continue the spirit on, during the journey of the current edition. A special mention to our son (Master Adarsh), who really helped us being very much cooperative. In fact, he was encouraging us to work for the book. We deeply apologize to you as well as our parents (Mr Anooj Sastry and Ms Tarini Purohit), as we could not give enough time and care during the manuscript preparation. Apurba S Sastry Sandhya Bhat https://t.me/docinmayking  Contents Competency Number Pages (NMC Curriculum) PART I: General Microbiology, Immunology and Hospital Infection Control Section 1: General Microbiology 1. Introduction and History MI 1.1 3 2. Microscopy MI 1.1 7 3. General Bacteriology https://t.me/docinmayking 3.1. Bacterial Taxonomy MI 1.1 12 3.2. Morphology and Physiology of Bacteria MI 1.1 15 3.3. Laboratory Diagnosis of Bacterial Infections MI 1.1, 1.2, 1.6, 8.9, 8.10 25 z Specimen Collection z Direct Detection (Staining Methods and Others) z Culture, Identification and Antimicrobial Susceptibility Test z Molecular Diagnosis and Typing Methods 3.4. Bacterial Genetics MI 1.1 51 3.5. Antimicrobial Agents and Antimicrobial Resistance MI 1.6 61 3.6. Pathogenesis of Bacterial Infections MI 1.1 68 3.7. Overview of Bacterial Infections MI 1.1 72 4. General Virology and Overview of Viral Infections MI 1.1, 8.9, 8.10 80 5. General Parasitology and Overview of Parasitic Infections MI 1.1, 1.2, 8.9, 8.10 102 6. General Mycology and Overview of Fungal Infections MI 1.1, 1.2, 8.9, 8.10 115 7. Normal Human Microbiota MI 1.1 121 8. Epidemiology of Infectious Diseases MI 1.3 125 Section 2: Immunology 9. Immunity (Innate and Acquired) MI 1.7 133 10. Antigen MI 1.8 140 11. Antibody MI 1.8 144 12. Antigen-antibody Reaction MI 1.8, 8.13, 8.15 152 13. Complement MI 1.8 163 14. Components of Immune System: Organs, Cells and Products MI 1.8 169 15. Immune Responses: Cell-mediated and Antibody-mediated MI 1.8 184 16. Hypersensitivity MI 1.10 193 17. Autoimmunity MI 1.10 203 18. Immunodeficiency Disorders MI 1.10 208 19. Transplant and Cancer Immunology MI 1.11 213 20. Immunoprophylaxis MI 1.9 221 xx Essentials of Medical Microbiology Section 3: Hospital Infection Control 21. Healthcare-associated Infections MI 8.5, 8.6, 8.7 229 22. Major Healthcare-associated Infection Types MI 8.5, 8.6 241 23. Sterilization and Disinfection MI 1.4, 1.5 251 24. Biomedical Waste Management MI 8.5, 8.6 263 25. Needle Stick Injury MI 8.5, 8.6 268 26. Antimicrobial Stewardship MI 1.6 272 27. Environmental Surveillance (Bacteriology of Water, Air and Surface) MI 8.8 278 PART II: SYSTEMIC MICROBIOLOGY (INFECTIOUS DISEASES) Section 4: Bloodstream and Cardiovascular System Infections 28. Cardiovascular System Infections: Infective Endocarditis and Acute Rheumatic MI 2.1, 2.2, 2.3, 8.13, 287 Fever 8.15 29. Bloodstream Infections MI 1.1, 2.4, 8.15 295 Bacterial Infections 30. Enteric Fever (Salmonella Typhi and Salmonella Paratyphi) MI 3.3, 3.4, 8.15 302 https://t.me/docinmayking 31. Rickettsial Infections MI 1.1, 8.15 310 32. Miscellaneous Bacterial Bloodstream Infections: MI 1.1, 8.1, 8.15 316 Brucellosis, Leptospirosis and Borreliosis Viral infections 33. HIV/AIDS MI 2.7, 8.15, 8.16 325 34. Viral Hemorrhagic Fever (VHF) MI 1.1, 8.15 336 Arboviral VHF (Dengue, Chikungunya and others), Filoviral VHF (Ebola and Marburg Virus), Hantaviral and Other Agents of VHF Parasitic Infections 35. Malaria and Babesiosis MI 2.5, 2.6, 8.16 346 36. Visceral Leishmaniasis and Trypanosomiasis MI 2.5, 1.1, 8.16 360 37. Lymphatic Filariasis MI 2.5, 2.6, 8.16 370 Fungal Infections 38. Systemic Candidiasis and Systemic Mycoses MI 1.1, 8.15 377 Section 5: Gastrointestinal (GI) Infections 39. Gastrointestinal Infective Syndromes MI 3.1 387 Bacterial Infections 40. Food Poisoning: S. aureus, Bacillus cereus, Clostridium botulinum and Others MI 3.5 394 41. Gastrointestinal Infections due to Enterobacteriaceae : Diarrheagenic MI 3.1, 3.2 400 Escherichia coli, Shigellosis, Nontyphoidal Salmonellosis and Yersiniosis 42. Cholera, Halophilic Vibrio and Aeromonas Infections MI 3.1, 3.2 410 43. Miscellaneous Bacterial Infections of Gastrointestinal System: Helicobacter, MI 3.1, 3.2, 3.6 419 Campylobacter and Clostridioides difficile Infections Viral Infections 44. Viral Gastroenteritis: Rotaviruses and Others MI 3.1, 3.2 424 Parasitic Infections 45. Intestinal Protozoan Infections: Intestinal Amoebiasis, Giardiasis, Coccidian MI 3.1, 3.2, 1.2, 8.15 427 Parasitic Infections, Balantidiasis, Blastocystosis, and Others  Contents xxi 46. Intestinal Helminthic Infections MI 3.1, 3.2, 1.2, 8.15 446 Intestinal Cestode Infections: Diphyllobothrium, Taenia, Hymenolepis and Others Intestinal Trematode Infections: Fasciolopsis buski, Schistosoma mansoni, S. japonicum and Others Intestinal Nematode Infections: Trichuris, Enterobius, hookworm, Strongyloides, Ascaris and Others Section 6: Hepatobiliary System Infections 47. Infective Syndromes of Hepatobiliary System and Abdomen MI 3.1 473 Viral Infections 48. Viruses Causing Hepatitis MI 3.7, 3.8, 8.13, 8.15 476 Hepatitis Viruses, Yellow Fever and Others Parasitic Infections 49. Parasitic Infections of Hepatobiliary System MI 3.1, 3.2 491 Amoebic Liver Abscess, Hydatid Disease (Echinococcosis), Trematode Infections (Fasciola hepatica, Clonorchis and Opisthorchis) and Others Section 7: Skin, Soft Tissue and Musculoskeletal System Infections https://t.me/docinmayking 50. Infective Syndromes of Skin, Soft Tissue and Musculoskeletal Systems MI 4.1, 4.2, 4.3, 1.2 503 Bacterial Infections 51. Staphylococcal Infections MI 4.2, 4.3, 1.2 511 52. Beta-hemolytic Streptococcal Infections MI 4.3, 1.2 520 53. Gas gangrene (Clostridium perfringens) and Infections due to Nonsporing MI 4.1, 1.2 527 Anaerobes 54. Leprosy (Mycobacterium leprae) MI 4.3, 8.15, 8.16 534 55. Miscellaneous Bacterial Infections of Skin and Soft Tissues: MI 4.3, 1.2, 8.13, 8.15 539 Anthrax (Bacillus anthracis), Actinomycosis, Nocardiosis, Nonvenereal Treponematoses and Others Viral Infections 56. Viral Exanthems and Other Cutaneous Viral Infections MI 4.3, 8.15 550 Herpesviruses (Herpes Simplex, Varicella-zoster and HHV-6 and 7 Infection), Poxviruses (Smallpox, Molluscum contagiosum), Parvovirus, Measles, Rubella, Coxsackieviruses and Others Parasitic Infections 57. Parasitic Infections of Skin, Soft Tissue and Musculoskeletal System MI 4.2, 4.3, 8.13, 8.15 565 Cutaneous Leishmaniasis, Cysticercosis, Tissue Nematodes (Filarial Tissue Nematodes, Dracunculus medinensis, Trichinella spiralis) and Larva Migrans Fungal Infections 58. Fungal Infections of Skin, Soft Tissue and Musculoskeletal System MI 4.2, 4.3, 8.13, 8.15 574 Superficial Fungal Infections, Subcutaneous Fungal Infections, Candidiasis (cutaneous and mucosal) and Penicillium marneffei Infection Section 8: Respiratory Tract Infections 59. Infective Syndromes of Respiratory Tract MI 6.1, 6.2, 6.3 587 Bacterial Infections 60. Bacterial Pharyngitis: Streptococcus pyogenes Pharyngitis, Diphtheria and MI 6.1, 6.2, 8.15 598 Others 61. Bacterial Lobar Pneumonia: Pneumococcal Pneumonia, Haemophilus influenzae MI 6.1, 6.3, 1.2, 8.15 606 Pneumonia and Others xxii Essentials of Medical Microbiology 62. Bacterial Atypical (Interstitial) Pneumonia: Mycoplasma, Chlamydia, Legionella and MI 6.1, 6.3 618 Others 63. Tuberculosis and Nontuberculous Mycobacteria Infections MI 6.1, 6.3, 1.2, 8.16 623 64. Pertussis (Bordetella pertussis) MI 6.1 638 65. Infections due to Non-fermenting Gram-negative Bacilli: Pseudomonas, MI 6.1, 6.3, 4.3 642 Acinetobacter, Burkholderia and Others Viral Infections 66. Myxovirus Infections of Respiratory Tract: Influenza, Parainfluenza, Mumps, MI 6.1, 6.2, 6.3 648 Respiratory Syncytial Virus and Others 67. Coronavirus Infections Including COVID-19 MI 6.1, 6.2, 6.3 660 68. Miscellaneous Viral Infections of Respiratory Tract: Rhinovirus, Adenovirus and MI 6.1, 6.2 672 Infectious Mononucleosis (Epstein-Barr Virus) Parasitic and Fungal Agents 69. Parasitic and Fungal Infections of Respiratory Tract MI 6.1, 6.2, 6.3 676 Parasitic Infections: Paragonimiasis and Others Fungal Infections: Zygomycosis, Aspergillosis, Pneumocystosis and Others Section 9: Central Nervous System Infections https://t.me/docinmayking 70. Infective Syndromes of Central Nervous System MI 5.1, 5.2, 5.3 687 Bacterial Infections 71. Bacterial Meningitis MI 5.1, 5.3, 1.2, 8.15 692 Acute Bacterial (Pyogenic) Meningitis: Neisseria meningitidis, Streptococcus pneumoniae, Streptococcus agalactiae, Haemophilus influenzae and Listeria Chronic Bacterial Meningitis: Tubercular Meningitis, Spirochetal Meningitis, Lyme Disease and Others 72. Tetanus MI 4.1 702 Viral Infections 73. Viral Meningitis and Myelitis: Poliomyelitis, Coxsackievirus Infections, and Others MI 5.1, 5.3, 8.16 706 74. Viral Encephalitis and Encephalopathy MI 5.2, 8.15 715 Rabies, HSV Encephalitis, Arboviral Encephalitis (Japanese Encephalitis and West Nile), Nipah and Hendra, Slow Virus and Prion Disease, and Others Parasitic and Fungal Infections 75. Parasitic and Fungal Infections of Central Nervous System MI 5.1, 5.2, 5.3, 8.15 727 Parasitic Infections: Neurocysticercosis, Free-living Amoeba Infections, Toxoplasmosis and Others Fungal Infections: Cryptococcal Meningitis and Others Section 10: Urogenital Tract Infections 76. Infective Syndromes of Urinary Tract and Sexually-transmitted Infections MI 7.1, 7.3 745 Bacterial Infections: Enterobacteriaceae, Enterococcus and Others Viral (BK Virus), Parasitic (Schistosoma haematobium) and Fungal Infections 77. Infective Syndromes of Genital Tract MI 7.1, 7.2, 8.15 756 Ulcerative Genital Disease: Syphilis, Lymphogranuloma Venerum, Granuloma Inguinale, Soft Chancre and Genital Herpes Gonorrhea and Non-gonococcal Urethritis (Chlamydia trachomatis and Others) Vulvovaginitis (Trichomoniasis, Bacterial Vaginosis, Vaginal Candidiasis) Other Genital Tract Infections of Females and Males  Contents xxiii Section 11: Miscellaneous Infective Syndromes 78. Ocular and Ear Infections MI 1.1, 8.15 779 79. Congenital Infections MI 1.1, 8.15 793 Cytomegalovirus Infections, Congenital Varicella, Neonatal Herpes, Congenital Rubella, Congenital Toxoplasmosis, Congenital Syphilis, Zika Virus Infections and Others 80. Organisms with Oncogenic Potential MI 8.3 800 Human Papilloma Virus, Kaposi Sarcoma, HTLV and HIV, Epstein-Barr Virus, Hepatitis B and C, and Others 81. Zoonotic Infections: Plague, Tularaemia and Bite Wound Infections MI 8.1 807 Annexures 1. Opportunistic Infections MI 8.2 817 2. Transplant Infections MI 1.1, 8.2 818 3. Emerging and Re-emerging Infections MI 8.4 819 4. Microbial Agents of Bioterrorism MI 1.1 820 5. Laboratory Acquired Infections MI 1.1 822 https://t.me/docinmayking 6. National Health Programmes for Communicable Diseases MI 8.16 823 7. Vector-borne Infections and Ectoparasite Infestations MI 8.1 824 8. Transfusion-transmitted Infections MI 1.1 827 9. AETCOM in Microbiology MI 8.11, 8.12, 8.14 828 10. Pandemic Management NMC’s Pandemic 834 Management Module Index 835  Organism Assignment into Various Systems This book has followed system-wise approach rather traditional organism-based approach to discuss the etiological agents of infectious diseases. The assignment of organisms under each system is mainly based on the organs/systems they principally infect and produce manifestations; not based on their mode of transmission or habitat or source (e.g. animal). For examples, ™ HIV is discussed under bloodstream, not genitourinary section. This is because HIV is only transmitted sexually, but does not produce any genital manifestations ™ Anthrax is discussed under skin and soft tissue infections; not under zoonotic infection ™ Enteric fever is discussed under bloodstream, not GIT section. This is because Salmonella Typhi is only transmitted by enteric route, but manifestations are largely extraintestinal ™ Schistosoma mansoni and S. haematobium are discussed under infections of GIT and urinary tract respectively. Although https://t.me/docinmayking called as blood flukes (because of their habitat); the manifestations are confined to GIT and urinary tract. ™ For the organism infecting more than one system, it is discussed under the major system it principally infects and is briefly discussed under other system(s) by keeping only the relevant points. The table below is a guide for the reader to find out the chapters in which the organisms are discussed. The chapter numbers in ‘bold’ are the systems in which the organisms are discussed in detail. Table 1: Etiological agents of infectious diseases Bacterial agents Chapter(s) Page Bacterial agents Chapter(s) Page Gram-positive cocci Clostridioides difficile 43 422 Staphylococcus aureus, Coagulase 51, 28, 40, 61 511, 290, Non-sporing anaerobes 53 531 negative, Staphylococcus (CoNS) 395, 518 Mycobacterium tuberculosis 63, 55, 71, 623,547, 699, Staphylococcus saprophyticus 76 752 76,77 752, 770 Streptococcus species 52 520 Non-tuberculous Mycobacteria 63, 55 636,547 Classification 52 520 Mycobacterium leprae 54 534 Streptococcus pyogenes 52, 60 520, 598 Actinomyces 55 542 Streptococcus agalactiae 52, 71, 77 525, 694, 775 Nocardia 55 544 Enterococcus 76 750 Listeria monocytogenes 71 698 Viridans streptococci 28 290 Erysipelothrix rhusiopathiae 55 547 Streptococcus pneumoniae 61,71 606, 695 Tropheryma whipplei 39 393 Gram-negative cocci Gram-negative bacilli Neisseria meningitidis 71, 55 695, 546 Enterobacteriaceae 41 400 Neisseria gonorrhoeae 77, 60 764, 605 Escherichia coli 41, 76 400 Moraxella species 61, 78 617,780 Shigella 41 404 Gram-positive bacilli Salmonella 30, 41 302, 406 Corynebacterium diphtheriae 60, 55 599, 547 Klebsiella 61 614 Diphtheroids 60 604 Enterobacter 61 615 Bacillus anthracis 55, 61 539, 616 Serratia 61 615 Bacillus cereus 40 395 Citrobacter 76 749 Proteus, Providencia, 76 749 Anaerobes 53 527 Morganella Clostridium perfringens 53 528 Yersinia pestis 81 807 Clostridium tetani 72 702 Y. enterocolitica 41 407 Clostridium botulinum 40 397 Y. pseudotuberculosis xxvi Essentials of Medical Microbiology Bacterial agents Chapter(s) Page Viral agents Chapter(s) Page Vibrio and Aeromonas 42 410, 418 RNA viruses Non-fermenting gram- 65 642 Orthomyxoviruses (Influenza 66 648 negative bacilli—Pseudomonas, viruses) Acinetobacter, Burkholderia, Paramyxoviruses 66 655 Stenotrophomonas Parainfluenza viruses 66 655 Haemophilus influenzae 61, 71 610, 697 Mumps virus 66, 73 656, 709 Haemophilus ducreyi 77 762 Measles virus 56, 74 559, 724 Haemophilus aegyptius 78 780 Respiratory syncytial virus 66 657 HACEK group 28 291 Nipah and Hendra viruses 74 718 Bordetella 64 638 Rubella virus 56, 79 562, 794 Brucella 32 316 Picornaviruses 73 707 Other gram-negative bacilli Polioviruses 73 709 Campylobacter 43 419 Coxsackie viruses 73 707 Helicobacter 43 420 Other enteroviruses 73 707 Legionella 62 621 Rhinoviruses 68 675 Klebsiella granulomatis 77 763 Arboviruses 34 336 Agents of rat bite fever 81 813 (Streptobacillus, Spirillum) Classification 34 337 https://t.me/docinmayking Miscellaneous bacterial agents Dengue, Chikungunya 34 338, 341 Spirochetes 32 319 Kyasanur forest disease virus 34 342 Treponema pallidum 77, 71, 79 756, 700, 799 Japanese encephalitis virus 74 716, 718 West Nile virus Non-venereal treponematoses 55 545 Yellow fever 48 489 Borrelia 32 322 Zika virus 79 798 Leptospira 32 319 Rabies virus 74 718 Rickettsiae and related genera 31 310 — Rickettsia, Orientia, Bartonella, HIV and other retroviruses 33, 80 325, 801 Ehrlichia Hantaviruses and Arenaviruses 34 345 Chlamydia trachomatis 77, 78, 62 766, 781, 621 Ebola and Marburg viruses 34 343 Chlamydophila psittaci 62 620 Coronaviruses 67 660 Chlamydophila pneumoniae 62 620 Viral gastroenteritis (Rotaviruses, 44 424 Mycoplasma pneumoniae 62 618 Noroviruses and others) Urogenital Mycoplasma 77 770 Slow viruses and prion disease 74 724 Other group of viruses Viral agents Chapter(s) Page Hepatitis viruses 48, 80 476 DNA viruses Oncogenic viruses 80 800 Herpesviruses 56 550 Parasitic agents Chapter(s) Page Herpes simplex virus 56, 73,74, 77, 551,708, 78, 79 716,762, 785, Protozoan parasites 797 Amoeba Varicella-zoster virus 56, 78, 79 554, 785, 797 Entamoeba histolytica 45, 49 427, 491 Epstein-Barr virus 68, 80, 56 672, 802, 550 Nonpathogenic Amoebae 45 432 Cytomegalovirus 79, 56 795, 550 Free-living Amoebae: Naegleria, 75 727, 729, 730 Human herpes virus 6 and 7 56 556 Acanthamoeba, Balamuthia, Sappinia Human herpes virus 8 80, 56 803, 556 Flagellates Other DNA viruses Giardia lamblia 45 433 Parvoviruses 56, 79 556, 798 Trichomonas vaginalis 77 771 Papillomaviruses 80, 56, 77 803, 557, 771 Leishmania 36, 57 360, 565 Poxviruses 56 557 Trypanosoma cruzi 36, 57, 78,79 366, 572, Adenoviruses 68, 78, 44 674 787, 799 Bacteriophages 4 97 Trypanosoma brucei complex 36, 75 368, 735  Organism Assignment into Various Systems xxvii Parasitic agents Chapter(s) Page Parasitic agents Chapter(s) Page Apicomplexa Nematodes of lower animals Malaria parasites and Babesia 35, 75, 79 346, 734, 799 Visceral larva migrans 49 499 Toxoplasma 75, 78, 79 731, 787, 793 Cutaneous larva migrans 57 572 Cryptosporidium, Cyclospora, 45 437 Toxocara canis 49 498 Cystoisospora Angiostrongylus cantonensis 75 739 Sarcocystis 45, 57 442, 572 Dioctophyme renale 76 755 Miscellaneous Protozoa Capillaria species 46, 49 469, 499 Balantidium coli 45 441 Ectoparasites Blastocystis 45 442 Sarcoptes scabiei Annexure-7 824 Helminths Cestodes Fungal agents Chapter(s) Page Diphyllobothrium latum 46 450 Superficial mycoses Taenia saginata 46 447 Tinea versicolor: Malassezia furfur 58 574 Taenia solium (intestinal) 46 447 Tinea nigra: Hortaea werneckii 58 575 Taenia solium (cysticercosis) 75, 57, 78 735, 573, 788 Piedra: Trichosporon beigelii, Piedraia 58 575 Echinococcus granulosus 49 493 hortae Hymenolepis nana 46 450 Dermatophytosis: Trichophyton, 58 575 https://t.me/docinmayking Microsporum, Epidermophyton Dipylidium caninum 46 450 Subcutaneous mycoses Trematodes Mycetoma: Madurella mycetomatis 58 578 Schistosoma haematobium 76 753 and others Schistosoma mansoni 46, 75, 49 454, 738, 498 Sporothrix schenckii 58 580 Schistosoma japonicum 46, 75, 49 455, 738, 498 Chromoblastomycosis 58 581 Fasciolopsis buski 46 456 Phaeohyphomycosis 58 581 Fasciola hepatica 49 497 Rhinosporidium seeberi 58 582 Clonorchis sinensis 49, 80 498, 806 Systemic mycoses Opisthorchis viverrini 49, 80 498, 806 Histoplasma, Blastomyces, 38 379, 381, 382 Paragonimus westermani 69 676 Coccidioides, Paracoccidioides Intestinal Nematodes Opportunistic mycoses Trichuris trichiura 46 458 Candida species 38, 58, 77 377, 583, 774 Enterobius vermicularis 46 459 Cryptococcus neoformans 75, 69 739,684 Ascaris lumbricoides 46, 69 461, 678 Zygomycosis: Rhizopus, Mucor, 69, 78 680, 789 Hookworm: Ancylostoma and 46, 57, 69 463, 572, 678 Lichtheimia Necator Aspergillosis: Aspergillus flavus, 69 681 Strongyloides stercoralis 46, 75 466, 739 A. fumigatus, A. niger Somatic Nematodes Penicillium marneffei 58 582 Lymphatic filarial 37 370 Other Penicillium species 69 684 nematodes Wuchereria bancrofti Brugia malayi, B. timori Pneumocystis jirovecii 69 679 Cutaneous filarial nematodes: Loa 57 567 Fusarium species 78 789 loa, Onchocerca, Mansonella Others Dracunculus medinensis 57 569 Microsporidia species 45, 58, 78 443, 582, 790 Trichinella spiralis 57 570 Mycotoxicoses 40 398  Further Reading 1. Abbas’ Cellular and Molecular Immunology, 8th Edition. 2. Bailey & Scott’s Diagnostic Microbiology, 14th Edition. 3. Gillespie’s Medical Microbiology and Infection at a Glance, 4th Edition. 4. Harrison’s Principles of Internal Medicine, 20th Edition. 5. Indian Council of Medical Research, New Delhi, India 6. Jawetz Melnick and Adelbergs’ Medical Microbiology, 28th Edition. 7. Koneman’s Color Atlas and Textbook of Diagnostic Microbiology, 7th Edition. 8. Kuby’s Immunology, 8th Edition. 9. Mackie and McCartney’s Practical Medical Microbiology, 14th Edition. 10. Mandell, Douglas, and Bennett’s Principles and Practice of Infectious Diseases, 9th Edition. https://t.me/docinmayking 11. Manson’s Tropical Diseases, 23rd Edition. 12. National AIDS Control Organisation (NACO), India. 13. National Center for Disease Control (NCDC) Guidelines, India. 14. National Vector Borne Disease Control Program (NVBDCP), India. 15. Patrick R Murray’s Medical Microbiology, 9th Edition. 16. Plotkin’s Vaccines, 7th Edition. 17. Prescott’s Microbiology, 10th Edition. 18. Revised National Tuberculosis Control Program (RNTCP), India. 19. Robbins & Cotran Pathologic Basis of Disease, 9th Edition. 20. Stites’ Medical Immunology, 10th Edition. 21. Topley and Wilson’s Microbiology and Microbial Infections, 10th Edition. 22. Garcia’s Diagnostic Medical Parasitology, 6th edition. 23. Gillespie’s Medical Parasitology at a Glance, 4th Edition. 24. Various national and international journals and other internet sources. 25. World Health Organization (WHO). 26. Centers for Disease Control and Prevention, Atlanta, USA.  PART I General Microbiology, Immunology and Hospital Infection Control Section 1: General Microbiology Section 2: Immunology Section 3: Hospital Infection Control https://t.me/docinmayking SECTION SECTION OUTLINE General Microbiology 1 1. Introduction and History 2. Microscopy 3. General Bacteriology 3.1 Bacterial Taxonomy 3.2 Morphology and Physiology of Bacteria 3.3 Laboratory Diagnosis of Bacterial Infections 3.4 Bacterial Genetics 3.5 Antimicrobial Agents and Antimicrobial Resistance 3.6 Pathogenesis of Bacterial Infections 3.7 Overview of Bacterial Infections 4. General Virology and Overview of Viral Infections 5. General Parasitology and Overview of Parasitic Infections 6. General Mycology and Overview of Fungal Infections 7. Normal Human Microbiota 8. Epidemiology of Infectious Diseases https://t.me/docinmayking  CHAPTER Introduction and History 1 CHAPTER PREVIEW „ Clinical Microbiology „ Classification of Microorganisms „ History CLINICAL MICROBIOLOGY Table 1.1: Characteristics of prokaryotes and eukaryotes. Medical microbiology is a branch of medicine that deals Characteristics Prokaryotes Eukaryotes with the study of microorganisms such as such as bacteria, Major groups Bacteria, blue Fungi, parasites, other viruses, parasites or fungi; which produce disease in green algae algae, plants and animals https://t.me/docinmayking humans, called as infectious diseases. Nucleus Diffuse Well defined Clinical microbiology is a branch of medical science Nuclear membrane Absent Present concerned with the prevention, diagnosis and treatment Nucleolus Absent Present of infectious diseases. The various branches of clinical Ribonucleoprotein Absent Present microbiology include: Cell division Binary fission Mitosis, meiosis ™ General microbiology: It deals with the study of general Chromosome One, circular Many, linear properties of microorganisms—taxonomy, morphology, Extrachromosomal Found in Found in mitochondria pathogenesis, laboratory diagnosis, and treatment for DNA plasmid their effective killing Cell membrane Does not contain Contain sterols ™ Immunology: It deals with the study of the immune sterols except in system, immunological mechanisms of infectious Mycoplasma diseases and various immunological methods for Cellular organelles like Absent (except Present diagnosis of infectious diseases mitochondria, etc. ribosome) ™ Hospital infection control: It deals with the study of Ribosome 70S 80S various control measures to prevent the transmission of Site of respiration Mesosome Mitochondria healthcare associated infections Pinocytosis Absent Present ™ Systemic microbiology (infectious diseases): Microorganisms infect various organ systems of our Abbreviation: S, Svedberg unit. body. Accordingly, the infectious diseases are classified into various clinical syndromes ™ Bacteria and blue green algae are placed under „ Bloodstream and cardiovascular system infections prokaryotes. They have a primitive nucleus, and other „ Gastrointestinal and hepatobiliary system infections properties of a prokaryotic cell (Table 1.1) „ Skin, soft tissue and musculoskeletal system infec- ™ Whereas other algae, fungi and parasites (protozoa and tions helminths) belong to eukaryotes; having a well-defined „ Central nervous system infections nucleus and various eukaryotic cellular organelles „ Respiratory tract infections ™ Viruses are neither considered as prokaryotes nor „ Urinary tract infections eukaryotes because they lack the characteristics of living „ Genital tract infections things, except the ability to replicate. „ Infections of eye, ear and others. HISTORY CLASSIFICATION OF MICROORGANISMS The existence of microorganisms was hypothesized for Microorganisms are grouped under both prokaryotes and many centuries before their actual discovery. The teaching eukaryotes. of Mahavira (Jainism, 6th century BC) and the postulation 4 SECTION 1  General Microbiology ™ He had proposed the principles of fermentation for preservation of food ™ He introduced the sterilization techniques and developed steam sterilizer, hot air oven and autoclave ™ He described the method of pasteurization of milk ™ He had also contributed for the vaccine development against several diseases, such as anthrax, fowl cholera and rabies ™ He disproved the theory of spontaneous generation of disease and postulated the ‘germ theory of disease’. He stated that disease cannot be caused by bad air or vapor, A B but it is produced by the microorganisms present in air ™ Liquid media concept: He used nutrient broth to grow microorganisms ™ He was the founder of the Pasteur Institute, Paris. Joseph Lister Joseph Lister (1867) is considered to be the ‘father of antiseptic surgery’. He had observed that postoperative infections were greatly reduced by using disinfectants https://t.me/docinmayking such as diluted carbolic acid during surgery to sterilize the instruments and to clean the wounds. C D Robert Koch Figs 1.1A to D: Eminent microbiologists: A. Antonie van Robert Koch provided remarkable contributions to Leeuwenhoek; B. Louis Pasteur; C. Robert Koch; D. Paul Ehrlich. the field of microbiology. He was a German general Source: Wikipedia (with permission). practitioner (1843–1910) (Fig. 1.1C). His contributions are as follows: of Varo and Columella (who named the invisible organisms ™ He introduced solid media for the culture of bacteria. as ‘Animalia minuta’) were some of those attempts. The Eilshemius Hesse, the wife of, one of the Koch’s assistants eminent personalities in the field of Microbiology and their had suggested the use of agar as solidifying agents important contributions have been described below. ™ He also introduced methods for isolation of bacteria in pure culture Antonie Philips van Leeuwenhoek (1676) ™ He described hanging drop method for testing motility He was the first scientist who observed bacteria and ™ He discovered bacteria such as the anthrax bacilli, other microorganisms, using a single-lens microscope tubercle bacilli and cholera bacilli constructed by him and he named those small organisms ™ He introduced staining techniques by using aniline dye as ‘Little animalcules’ (Fig. 1.1A). ™ Koch’s phenomenon: Robert Koch observed that guinea pigs already infected with tubercle bacillus developed a Edward Jenner hypersensitivity reaction when injected with tubercle Edward Jenner 1796, developed the first vaccine of the bacilli or its protein. Since then, this observation is called world, the smallpox vaccine. He used the cowpox virus as Koch’s phenomenon (Variolae vaccinae) to immunize children against smallpox ™ Koch’s postulates: Robert Koch had postulated that a from which the term ‘vaccine’ has been derived. The same microorganism can be accepted as the causative agent principles are even used today for developing vaccines. of an infectious disease only if four criteria are fulfilled. These criteria are as follows: Louis Pasteur 1. The microorganism should be constantly associated Microbiology developed as a scientific discipline from with the lesions of the disease the era of Louis Pasteur (1822–1895). He is also known as 2. It should be possible to isolate the organism in pure ‘father of microbiology’. He was a professor of chemistry in culture from the lesions of the disease France. His studies on fermentation led him to take interest 3. The same disease must result when the isolated mi- to work in microbiology (Fig. 1.1B). His contributions to croorganism is inoculated into a suitable laboratory microbiology are as follows: animal  CHAPTER 1  Introduction and History 5 4. It should be possible to re-isolate the organism the first effective medicinal treatment for syphilis, in pure culture from the lesions produced in the thereby initiating and also naming the concept of experimental animals. chemotherapy An additional fifth criterion was introduced ™ The bacteria ‘Ehrlichia’ was named after him subsequently which states that antibody to the causative ™ In 1908, he received the Nobel prize in Physiology or organism should be demonstrable in the patient’s serum. Medicine for his contributions to immunology Exceptions to Koch’s postulates: It is observed that it is ™ He was the founder and first director of what is known not always possible to apply these postulates to study all now as the Paul Ehrlich Institute, Germany. the human infectious diseases. There are some bacteria that do not satisfy one or more of the four criteria of Koch’s Other Important Contributors postulates. Those organisms are: ™ Hans Christian Gram (in 1884): He developed a method ™ Mycobacterium leprae and Treponema pallidum: of staining bacteria which was named as ‘Gram stain’ They cannot be grown in vitro; however, they can be to make them more visible and differentiable under a maintained in experimental animals microscope ™ Neisseria gonorrhoeae: There is no animal model; ™ Ernst Ruska: He was the founder of electron microscope however, it can be grown in vitro. (1931) ™ Alexander Fleming (in 1929): He discovered the most Paul Ehrlich commonly used antibiotic substance of the last century, Paul Ehrlich (1854–1915) was a German scientist and is i.e. penicillin also known as ‘father of chemotherapy’ (Fig. 1.1D). His ™ Goodpasture: He described the viral culture technique https://t.me/docinmayking contributions are as follows: in chick embryo ™ He was the first to report the acid-fast nature of tubercle ™ Barbara McClintock: She described the mobile genetic bacillus elements in bacteria called transposons ™ He developed techniques to stain tissues and blood ™ Walter Gilbert and Frederick Sanger were the first to cells develop (1977) the method of DNA sequencing ™ He proposed a toxin-antitoxin interaction called ™ Karry B Mullis: Discovered polymerase chain reaction Ehrlich phenomenon and also introduced methods of (PCR) and was awarded Noble prize in 1993. standardising toxin and antitoxin ™ He proposed the ‘side chain theory for antibody Discovery of Microorganisms production’ Several microorganisms were discovered by the scientists ™ Chemotherapy: He discovered salvarsan, an arseni- (Table 1.2). The names of some of the bacteria have been cal compound (also called as the ‘magic bullet’) as coined in the honor of the scientists who discovered them (Table 1.3). Table 1.2: Discovery of impo