Clinical Microbiology and Infectious Diseases

260 Pages·026.892 MB·English

by  W. John Spicer

Prelims-F10303.indd ii 9/10/07 2:16:32 PM
To my late great Chief, Mr Glen Buckle, who inspired me
to study Microbiology; to my patients, especially in
Bangladesh, who inspired me to study Infectious Diseases;
and to my students and colleagues, who inspire me still.
Commissioning Editor: Timothy Horne
Project Development Manager: Lulu Stader
Project Manager: Frances Affl eck
Design Direction: Erik Bigland
Prelims-F10303.indd ii 9/10/07 2:16:32 PM
To my late great Chief, Mr Glen Buckle, who inspired me
to study Microbiology; to my patients, especially in
Bangladesh, who inspired me to study Infectious Diseases;
and to my students and colleagues, who inspire me still.
Commissioning Editor: Timothy Horne
Project Development Manager: Lulu Stader
Project Manager: Frances Affl eck
Design Direction: Erik Bigland
Prelims-F10303.indd ii 9/10/07 2:16:32 PM
Clinical
SECOND EDITION
Microbiology
and Infectious
Diseases
AN ILLUSTRATED COLOUR TEXT
W. John Spicer
MB.BS (Melbourne) FRACP FRCPA FACSHP FASM DTM&H (Sydney) Dip.Bact (London)
Senior Consultant in Infectious Diseases, The Alfred Hospital, and Austin Health
Senior Consultant in Microbiology, The Alfred Hospital
Associate Professor of Microbiology and Medicine, Monash University
Consultant Microbiologist, Dorevitch Pathology
Melbourne, Australia
Illustrated by Peter Lamb and Robert Britton
EDINBURGH LONDON NEW YORK OXFORD PHILADELPHIA ST LOUIS SYDNEY TORONTO 2008
Prelims-F10303.indd iii 9/10/07 2:16:32 PM
iv
An Imprint of Elsevier Limited
© Harcourt Publishers Limited 2000
© Elsevier Limited 2008
The right of Professor W. John Spicer to be identifi ed as author of this
work has been asserted by him in accordance with the Copyright, Designs
and Patents Act 1988.
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 Publishers. Permissions may be sought directly from Elsevier’s
Health Sciences Rights Department, 1600 John F. Kennedy Boulevard,
Suite 1800, Philadelphia, PA 19103-2899, USA: phone: [phone];
fax: [phone]; or, e-mail: [email protected].
You may also complete your request on-line via the Elsevier homepage
(http://www.elsevier.com), by selecting ‘Support and contact’ and then
‘Copyright and Permission’.
First edition 2000
Second edition 2008
ISBN (10) 0-443-10303-8
ISBN (13) 978-0-443-10303-2
British Library Cataloguing in Publication Data
A catalogue record for this book is available from the British Library
Library of Congress Cataloging in Publication Data
A catalog record for this book is available from the Library of Congress
Notice
Neither the Publisher nor the Author assumes any responsibility for
any loss or injury and/or damage to persons or property arising out of
or related to any use of the material contained in this book. It is the
responsibility of the treating practitioner, relying on independent
expertise and knowledge of the patient, to determine the best
treatment and method of application for the patient.
The Publisher
Printed in China
Prelims-F10303.indd iv 9/10/07 2:16:32 PM
v
Preface to the second edition
While a three-legged table or chair can be very satisfactory, old ones with new names), new dis eases, new tests and new
most prefer the conventional four legs, so I am delighted that antim icrobials.
the major change from the fi rst edition is the addition of virol- A new table of abbreviations and a list of further reading of
ogy and viral infections to the original threesome of clinical larger, or more specialised, books have been added.
bacteriology, mycology and parasitology. This has been achieved The index has been expanded, the few typographic mistakes
both by thirteen new explicit chapters within the fi ve major in the text removed, and no new errors added, I trust.
parts of the book, and also by incorporating relevant Some of these improvements come from comments by
information on viruses throughout the text. Prions and prion readers of the fi rst edition, and I look forward to further helpful
diseases are also described. feedback through the publishers or directly to me at PO Box
Revision of the entire fi rst edition text including all tables 450, Canter bury, 3126, Victoria, Australia (nice stamps for my
and fi gures has included new knowledge, new organ isms (and grandniece, please) or by email to [email protected].
2007 W. J. S.
Preface to the fi rst edition
All medical students, and all nurses, gen eral practitioners and organisms in more detail (micro biology), and then the fourth
medical specialists seeing patients, need to understand the section on clinical infections in each body organ system and
basics of microbiology and infections. Infection cannot be some special categories, with extensive cross-references between
understood without knowing some microbiology; and infec- the third and fourth sections. The fi fth and fi nal section is on
tion is one of the major mechanisms causing disease and can the extrinsic defences we have invented, such as vaccines, asep-
affect every body tissue and organ. sis and antisepsis, and antimicrobials.
This book aims to present – clearly, concisely and mem- The format of the book is exciting, being specifi cally
orably – the clinically relevant basic facts and processes in the designed to help both initial learning and revision. Each subject
twin disciplines of microbiology and infectious diseases. The is presented in an ‘easy learning’ module complete on a single
range of the book is wide, including fungi and para sites as well or double page spread, with numerous coloured photo graphs,
as bacteria and their cons equent infections. coloured graphics, integrated tables, and a ‘key point’ sum-
The organisation of any book on microbiology and infectious mary in the bottom right hand corner, useful both for initial
diseases depends particularly on one question – to present the orientation and for revision.
twins integrated in each chapter, or separately? If all infections In a book of this size it is obviously impossible to give
were like tetanus or anthrax, where one organism causes only extended detail, or cover all organisms and diseases, yet I
one disease which is in turn caused only by that organism, have intentionally included rarer and ‘tropical’ infections. Every
the integrated approach would be obvious and easy. But life, GP and Emer gency Department clinician must be able to
apparently, was not meant to be easy. Consider the amaz- recognise the rare meningococcal bacteraemia or meningitis,
ing Group A streptococcus (S. pyogenes, p. 36–37), causing which they may never have seen before, yet the patient’s life
numerous diseases by numerous mechanisms in numerous depends on early recogni tion and emergency treatment by
organs; or the versatile ‘golden staph’ (S. aureus, p. 34–35), the fi rst doctor to see them. Similarly, any GP or other ‘front
causing infections ranging from a trivial pimple through line’ doctor in a tem perate industrialised country may be
cellulitis to serious deep abscesses and bone infections, to confronted by a sick patient with malaria or typhoid fever in
endocarditis and over whelming septicaemia with septic shock. a returned traveller or immigrant, needing early recognition
Conversely, many common disease presentations such as and urgent relevant investigation and treatment. I aimed to
pneumonia, uri nary infections and gut infections have more make this book useful in both industrialised and devel oping
than one possible causative organ ism. So I have chosen, after countries.
an introd uctory section on general characteristics of the I have enjoyed writing this book, and I hope you enjoy and
organisms and a second section on their attack on us and our profi t from read ing it. I will be interested to hear your opinions
intrinsic defences, to present the third section on specifi c and suggestions.
2000 W. J. S.
Prelims-F10303.indd v 9/10/07 2:16:32 PM
v
Preface to the second edition
While a three-legged table or chair can be very satisfactory, old ones with new names), new dis eases, new tests and new
most prefer the conventional four legs, so I am delighted that antim icrobials.
the major change from the fi rst edition is the addition of virol- A new table of abbreviations and a list of further reading of
ogy and viral infections to the original threesome of clinical larger, or more specialised, books have been added.
bacteriology, mycology and parasitology. This has been achieved The index has been expanded, the few typographic mistakes
both by thirteen new explicit chapters within the fi ve major in the text removed, and no new errors added, I trust.
parts of the book, and also by incorporating relevant Some of these improvements come from comments by
information on viruses throughout the text. Prions and prion readers of the fi rst edition, and I look forward to further helpful
diseases are also described. feedback through the publishers or directly to me at PO Box
Revision of the entire fi rst edition text including all tables 450, Canter bury, 3126, Victoria, Australia (nice stamps for my
and fi gures has included new knowledge, new organ isms (and grandniece, please) or by email to [email protected].
2007 W. J. S.
Preface to the fi rst edition
All medical students, and all nurses, gen eral practitioners and organisms in more detail (micro biology), and then the fourth
medical specialists seeing patients, need to understand the section on clinical infections in each body organ system and
basics of microbiology and infections. Infection cannot be some special categories, with extensive cross-references between
understood without knowing some microbiology; and infec- the third and fourth sections. The fi fth and fi nal section is on
tion is one of the major mechanisms causing disease and can the extrinsic defences we have invented, such as vaccines, asep-
affect every body tissue and organ. sis and antisepsis, and antimicrobials.
This book aims to present – clearly, concisely and mem- The format of the book is exciting, being specifi cally
orably – the clinically relevant basic facts and processes in the designed to help both initial learning and revision. Each subject
twin disciplines of microbiology and infectious diseases. The is presented in an ‘easy learning’ module complete on a single
range of the book is wide, including fungi and para sites as well or double page spread, with numerous coloured photo graphs,
as bacteria and their cons equent infections. coloured graphics, integrated tables, and a ‘key point’ sum-
The organisation of any book on microbiology and infectious mary in the bottom right hand corner, useful both for initial
diseases depends particularly on one question – to present the orientation and for revision.
twins integrated in each chapter, or separately? If all infections In a book of this size it is obviously impossible to give
were like tetanus or anthrax, where one organism causes only extended detail, or cover all organisms and diseases, yet I
one disease which is in turn caused only by that organism, have intentionally included rarer and ‘tropical’ infections. Every
the integrated approach would be obvious and easy. But life, GP and Emer gency Department clinician must be able to
apparently, was not meant to be easy. Consider the amaz- recognise the rare meningococcal bacteraemia or meningitis,
ing Group A streptococcus (S. pyogenes, p. 36–37), causing which they may never have seen before, yet the patient’s life
numerous diseases by numerous mechanisms in numerous depends on early recogni tion and emergency treatment by
organs; or the versatile ‘golden staph’ (S. aureus, p. 34–35), the fi rst doctor to see them. Similarly, any GP or other ‘front
causing infections ranging from a trivial pimple through line’ doctor in a tem perate industrialised country may be
cellulitis to serious deep abscesses and bone infections, to confronted by a sick patient with malaria or typhoid fever in
endocarditis and over whelming septicaemia with septic shock. a returned traveller or immigrant, needing early recognition
Conversely, many common disease presentations such as and urgent relevant investigation and treatment. I aimed to
pneumonia, uri nary infections and gut infections have more make this book useful in both industrialised and devel oping
than one possible causative organ ism. So I have chosen, after countries.
an introd uctory section on general characteristics of the I have enjoyed writing this book, and I hope you enjoy and
organisms and a second section on their attack on us and our profi t from read ing it. I will be interested to hear your opinions
intrinsic defences, to present the third section on specifi c and suggestions.
2000 W. J. S.
Prelims-F10303.indd v 9/10/07 2:16:32 PM
vi
Acknowledgements
While many of the slides and images illustrating this book Richard Stawell, Peter Thompson, Jonathan Tversky, John
came from my own collection of the last 40 years, I am Waterston, Robert West and Bob Zacharin, and also Ms Karen
indebted to many colleagues for fi lling gaps with particular Flett and Mr Guy Brown. If I have unk nowingly been pro vided
slides I needed. My own staff in the Departments of Infec- with previously published slides, I apologize in advance. Sev-
tious Diseases and Microbiology, Alfred Hospital, were always eral slides from the former Fairfi eld Hospital and the Royal
wonderfully help ful, especially Associate Professor Denis Victorian Eye and Ear Hospital Slide Libraries were used with
Spelman and Dr Andrew Fuller, also Drs Ashley Watson, Sally permission, and my thanks to Ms Caroline Hedt, Mr Gavin
Roberts, Adam Jenney and numerous other registrars and Hawkins and Mr Cam Harvey in the Alfred Visual Commu-
residents in the ID Unit; Mr Grant Perry, Ms Clare Franklin, nications Department who were always helpful in duplicat-
Mrs Jenni Williams and the late Mr Glen Buckle in Micro- ing slides, with which the Monash University Department
biology; and Ms Glenys Harrington in Infection Control. I am at Alfred also assisted at times. For the second edition I am
very grateful to all the patients who gave permission to be particularly indebted to Drs Andrew Fuller, Mike Catton and
photographed, and to Alfred Hospital and Monash University John Marshall and Professor Catriona McLean for most of
Departments and individual colleagues who willingly provided the new digital images, and for additional images from
particular slides from their patients in Melbourne or overseas: Dr Philip du Cros, Dr Reuben Glass, Prof Stephen Kent and
in the Departments of Radiology and Nuclear Medicine, Asso- his son Tom.
ciate Professors Nina Sacharias and Victor Kalff, and Drs Chris In Churchill Livingstone, now part of Elsevier, I received
O’Donnell and Stephen Booth; in the Department of Ana tomi- particular help, expert advice, and unfailing courtesy from
cal Pathology, Professor John Dowling, the late Asso ciate Mr Jim Killgore, Ms Frances Affl eck and Mr Timothy Horne,
Professor Brian Essex and Drs Shant Khan, S K Tang, the late with much help behind the scenes from Dr Jane Ward, Leslie
Ross Anderson and Mr John Hall; in Monash Micro biology, Smillie, Dr Laurence Errington and Dr Susan Boobis, and from
Drs Geoff Cross, Ian Denham, Mrs Lyn Howden and Mrs Jan Peter Lamb and Robert Britton who transformed my line
Savage. Individually, Professors Hugh Taylor, Suzanne Garland, drawings, examples and directions to the excellent fi gures you
John Murtagh and Dan Sexton (Duke University, USA), see. Dr Lulu Stader has been an excellent editorial colleague in
Associate Professors Geoff Hogg, John Kelly, Hector McLean Scotland and I have much enjoyed our 12 months working
and Alison Street, and Drs David Abell, Barry Elliott, Reuben together though so far apart.
Glass, Tony Hall, Robin Hooper, the late Don Jacobs, David Finally I thank my wife Heather and my family, who are
Looke (Bris bane), Fiona McCurragh, Hugh Newton-John, almost as pleased as I am to see such a beautiful book emerge
Jo Sabto, Jack Swann, Hugo Standish, the late Brian Smith, again!
Prelims-F10303.indd vi 9/10/07 2:16:32 PM
ix
Microbial names changed from the fi rst edition:
OLD NAME NEW NAME
Actinobacillus actinomycetemcomitans Haemophilus actinomycetemcomitans
Branhamella catarrhalis Moraxella catarrhalis
Borrelia burgdorferi Borrelia burgdorferi group now includes two other species.
Calymmatobacterium granulomatis Klebsiella granulomatis
Chlamydia pneumoniae Chlamydophila pneumoniae
Flavobacterium spp. Chryseobacterium spp.
Opisthorchis sinensis Clonorchis sinensis
Pneumocystis carinii Pneumocystis jirovecii
Pseudomonas pseudomallei Burkholderia pseudomallei
Pseudomonas mallei Burkholderia mallei
Pseudomonas cepacia Burkholderia cepacia
Rochalimaea henselae Bartonella henselae
Rochalimaea quintana Bartonella quintana
Xanthomonas maltophilia Stenotrophomonas maltophilia
Abbreviations
Abbreviation Meaning Abbreviation Meaning
AFB Acid-Fast Bacilli (usually mycobacteria) HSV, HZV Herpes Simplex Virus, H. Zoster Virus
AGN Acute Glomerulo-Nephritis IFA Indirect Fluorescent Antibody (test)
AIDS Acquired Immune Defi ciency Syndrome IgA, E, G, M Immunoglobulin A, E, G, M
ASOT Anti-Streptolysin O Titre (Test) IL-1 Interleukin-1 (cytokine from macrophages)
BCG Bacillus Calmette-Guérin LFTs Liver Function Tests
CD4 Cluster of Differentiation (T-cell receptors) LPS LipoPolySaccharide (endotoxin)
CMI Cell-Mediated Immunity MAC Mycobacterium avium Complex
CMV CytoMegaloVirus MRI Magnetic Resonance Imaging
CT Computed Tomography (Scan) NAD No Abnormality Detected
DFA Direct Fluorescent Antibody (Test) NGU/NSU Non-Gonococcal/Non-Specifi c Urethritis
DGM Dark Ground Microscopy NK Natural Killer (Cells)
DIC Disseminated Intravascular Coagulation PCR Polymerase Chain Reaction (Test)
DNA De-oxyribo Nucleic Acid PMEC Pseudo-Membranous Entero-Colitis
EBV Epstein-Barr Virus PPD Purifi ed Protein Derivative (of Myco. TB)
EIA Enzyme Immuno-Assay RNA Ribo Nucleic Acid
ELISA Enzyme-Linked Immuno-Sorbent Assay RPR Rapid Plasma Reagin (test for syphilis)
FTA Fluorescent Treponemal Antibody (test) SOL Space Occupying Lesion (in body organ)
GLC Gas-Liquid Chromatography (S)SSS (Staphylococcal) Scalded Skin Syndrome
GNR/B/C Gram Negative Rod/Bacillus/Coccus STD/I Sexually Transmitted Disease/Infection
GPR/C Gram Positive Rod/Coccus TNF Tumour Necrosis Factor
HACEK Rare causes of endocarditis TPHA/TPPA T. pallidum Haem/Particle Agglutination
HAV, HBV, Hepatitis A Virus, Hepatitis B Virus, TSS/TSST Toxic Shock Syndrome (Toxin)
HCV, HDV, Hepatitis C Virus, Hepatitis D Virus, UTI Urinary Tract Infection
HEV, HGV Hepatitis E Virus, Hepatitis G Virus VDRL Venereal Disease Research Lab. (test)
HIV Human Immunodefi ciency Virus VZV Varicella-Zoster Virus
HPF High Powered Field (in microscopy) XR XRay
Prelims-F10303.indd ix 9/10/07 2:16:33 PM
ix
Microbial names changed from the fi rst edition:
OLD NAME NEW NAME
Actinobacillus actinomycetemcomitans Haemophilus actinomycetemcomitans
Branhamella catarrhalis Moraxella catarrhalis
Borrelia burgdorferi Borrelia burgdorferi group now includes two other species.
Calymmatobacterium granulomatis Klebsiella granulomatis
Chlamydia pneumoniae Chlamydophila pneumoniae
Flavobacterium spp. Chryseobacterium spp.
Opisthorchis sinensis Clonorchis sinensis
Pneumocystis carinii Pneumocystis jirovecii
Pseudomonas pseudomallei Burkholderia pseudomallei
Pseudomonas mallei Burkholderia mallei
Pseudomonas cepacia Burkholderia cepacia
Rochalimaea henselae Bartonella henselae
Rochalimaea quintana Bartonella quintana
Xanthomonas maltophilia Stenotrophomonas maltophilia
Abbreviations
Abbreviation Meaning Abbreviation Meaning
AFB Acid-Fast Bacilli (usually mycobacteria) HSV, HZV Herpes Simplex Virus, H. Zoster Virus
AGN Acute Glomerulo-Nephritis IFA Indirect Fluorescent Antibody (test)
AIDS Acquired Immune Defi ciency Syndrome IgA, E, G, M Immunoglobulin A, E, G, M
ASOT Anti-Streptolysin O Titre (Test) IL-1 Interleukin-1 (cytokine from macrophages)
BCG Bacillus Calmette-Guérin LFTs Liver Function Tests
CD4 Cluster of Differentiation (T-cell receptors) LPS LipoPolySaccharide (endotoxin)
CMI Cell-Mediated Immunity MAC Mycobacterium avium Complex
CMV CytoMegaloVirus MRI Magnetic Resonance Imaging
CT Computed Tomography (Scan) NAD No Abnormality Detected
DFA Direct Fluorescent Antibody (Test) NGU/NSU Non-Gonococcal/Non-Specifi c Urethritis
DGM Dark Ground Microscopy NK Natural Killer (Cells)
DIC Disseminated Intravascular Coagulation PCR Polymerase Chain Reaction (Test)
DNA De-oxyribo Nucleic Acid PMEC Pseudo-Membranous Entero-Colitis
EBV Epstein-Barr Virus PPD Purifi ed Protein Derivative (of Myco. TB)
EIA Enzyme Immuno-Assay RNA Ribo Nucleic Acid
ELISA Enzyme-Linked Immuno-Sorbent Assay RPR Rapid Plasma Reagin (test for syphilis)
FTA Fluorescent Treponemal Antibody (test) SOL Space Occupying Lesion (in body organ)
GLC Gas-Liquid Chromatography (S)SSS (Staphylococcal) Scalded Skin Syndrome
GNR/B/C Gram Negative Rod/Bacillus/Coccus STD/I Sexually Transmitted Disease/Infection
GPR/C Gram Positive Rod/Coccus TNF Tumour Necrosis Factor
HACEK Rare causes of endocarditis TPHA/TPPA T. pallidum Haem/Particle Agglutination
HAV, HBV, Hepatitis A Virus, Hepatitis B Virus, TSS/TSST Toxic Shock Syndrome (Toxin)
HCV, HDV, Hepatitis C Virus, Hepatitis D Virus, UTI Urinary Tract Infection
HEV, HGV Hepatitis E Virus, Hepatitis G Virus VDRL Venereal Disease Research Lab. (test)
HIV Human Immunodefi ciency Virus VZV Varicella-Zoster Virus
HPF High Powered Field (in microscopy) XR XRay
Prelims-F10303.indd ix 9/10/07 2:16:33 PM