Principles and practice of clinical bacteriology 2nd ed s gillespie (wiley sons, 2006)

Principles and Practice of Clinical Bacteriology Second Edition Editors Stephen H Gillespie Royal Free and University College Medical School, London, UK and Peter M Hawkey University of Birmingham, Birmingham, UK Copyright © 2006 John Wiley & Sons Ltd, The Atrium, Southern Gate, Chichester, West Sussex PO19 8SQ, England Telephone (+44) 1243 779777 Email (for orders and customer service enquiries): cs-books@wiley.co.uk All Rights Reserved No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning or otherwise, except under the terms of the Copyright, Designs and Patents Act 1988 or under the terms of a licence issued by the Copyright Licensing Agency Ltd, 90 Tottenham Court Road, London W1T 4LP, UK, without the permission in writing of the Publisher Requests to the Publisher should be addressed to the Permissions Department, John Wiley & Sons Ltd, The Atrium, Southern Gate, Chichester, West Sussex PO19 8SQ, England, or emailed to permreq@wiley.co.uk, or faxed to (+44) 1243 770620 Designations used by companies to distinguish their products are often claimed as trademarks 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 This publication is designed to provide accurate and authoritative information in regard to the subject matter covered It is sold on the understanding that the Publisher is not engaged in rendering professional services If professional advice or other expert assistance is required, the services of a competent professional should be sought Other Wiley Editorial Offices John Wiley & Sons Inc., 111 River Street, Hoboken, NJ 07030, USA Jossey-Bass, 989 Market Street, San Francisco, CA 94103-1741, USA Wiley-VCH Verlag GmbH, Boschstr 12, D-69469 Weinheim, Germany John Wiley & Sons Australia Ltd, 33 Park Road, Milton, Queensland 4064, Australia John Wiley & Sons (Asia) Pte Ltd, Clementi Loop #02-01, Jin Xing Distripark, Singapore 129809 John Wiley & Sons Canada Ltd, 22 Worcester Road, Etobicoke, Ontario, Canada M9W 1L1 Wiley also publishes its books in a variety of electronic formats Some content that appears in print may not be available in electronic books Library of Congress Cataloging in Publication Data Principles and practice of clinical bacteriology / editors, Stephen H Gillespie and Peter M Hawkey — 2nd ed p ; cm Includes bibliographical references and index ISBN-13: 978-0-470-84976-7 (cloth : alk paper) ISBN-10: 0-470-84976-2 (cloth : alk paper) Medical bacteriology [DNLM: Bacteriological Techniques QY 100 P957 2005] I Gillespie, S H II Hawkey, P M (Peter M.) QR46.P84 2005 616.9′041—dc22 2005013983 British Library Cataloguing in Publication Data A catalogue record for this book is available from the British Library ISBN-13 978-0-470-84976-7 (cloth: alk paper) ISBN-10 0-470-84976-2 (cloth: alk paper) Typeset in 9/10pt Times by Integra Software Services Pvt Ltd, Pondicherry, India Printed and bound in Great Britain by Antony Rowe Ltd, Chippenham, Wiltshire This book is printed on acid-free paper responsibly manufactured from sustainable forestry in which at least two trees are planted for each one used for paper production Contents List of Contributors vii Preface ix 19 Brucella spp 265 Edward J Young SECTION ONE GRAM-POSITIVE COCCI 1 β-Haemolytic Streptococci Androulla Efstratiou, Shiranee Sriskandan, Theresa Lamagni and Adrian Whatmore Oral and Other Non-β-Haemolytic Streptococci 21 Roderick McNab and Theresa Lamagni Enterococcus spp 59 Esteban C Nannini and Barbara E Murray Staphylococcus aureus 73 Sharon Peacock 99 GRAM-POSITIVE BACILLI 113 Corynebacterium spp 115 Aruni De Zoysa and Androulla Efstratiou Listeria and Erysipelothrix spp Kevin G Kerr 129 Bacillus spp and Related Genera 139 Niall A Logan and Marina Rodríguez-Díaz 159 11 Non-Tuberculosis Mycobacteria Stephen H Gillespie 12 Aerobic Actinomycetes Stephen H Gillespie 281 22 Rickettsia spp 285 James G Olson, Franca R Jones and Patrick J Blair 24 Mycoplasma spp 305 Christiane Bébéar, Sabine Pereyre and Cécile M Bébéar 25 Chlamydia spp and Related Organisms 317 S J Furrows and G L Ridgway Coagulase-Negative Staphylococci Roger G Finch 10 Mycobacterium tuberculosis Stephen H Gillespie 21 Francisella tularensis Petra C F Oyston 273 23 Bartonella spp 295 J M Rolain and D Raoult Streptococcus pneumoniae 41 Indran Balakrishnan SECTION TWO 20 Actinobacillus actinomycetemcomitans Brian Henderson and Derren Ready 171 183 26 Tropheryma whipplei 329 F Fenollar and D Raoult 27 Identification of Enterobacteriaceae Peter M Hawkey 341 28 Escherichia coli and Shigella spp 347 Christopher L Baylis, Charles W Penn, Nathan M Thielman, Richard L Guerrant, Claire Jenkins and Stephen H Gillespie 29 Salmonella spp 367 Claire Jenkins and Stephen H Gillespie 30 Klebsiella, Citrobacter, Enterobacter and Serratia spp 377 C Anthony Hart 31 Donovanosis and Klebsiella spp 387 John Richens SECTION THREE GRAM-NEGATIVE ORGANISMS 189 32 Proteus, Providencia and Morganella spp 391 Peter M Hawkey 13 Moraxella catarrhalis and Kingella kingae 191 Alex van Belkum and Cees M Verduin 33 Yersinia spp 397 M B Prentice 14 Neisseria meningitidis 205 Dlawer A A Ala’Aldeen and David P J Turner 34 Vibrio spp 407 Tom Cheasty 15 Neisseria gonorrhoeae 221 Catherine A Ison 35 Aeromonas and Plesiomonas spp 419 Alpana Bose 16 Acinetobacter spp 231 Peter Hawkey and Eugenie Bergogne-Berezin 36 Pseudomonas and Burkholderia spp 427 Tyrone L Pitt and Andrew J H Simpson 17 Haemophilus spp 245 Derrick W Crook and Derek W Hood 37 Legionella spp 445 T G Harrison 18 Bordetella spp 253 Qiushui He, Jussi Mertsola and Matti K Viljanen 38 Coxiella burnetii 457 James G Olson, Franca R Jones and Patrick J Blair vi CONTENTS SECTION FOUR SPIRAL BACTERIA 461 SECTION FIVE OBLIGATE ANAEROBIC BACTERIA 527 39 Leptospira spp 463 P N Levett 44 Anaerobic Cocci D A Murdoch 40 Helicobacter spp and Related Organisms 473 Peter J Jenks 45 Non-Sporing Gram-Negative Anaerobes 541 Sheila Patrick and Brian I Duerden 41 Campylobacter and Arcobacter spp 485 Diane E Taylor and Monika Keelan 42 Treponemes 503 Andrew J L Turner 43 Borrelia spp 511 Sudha Pabbatireddy and Benjamin J Luft 529 46 Clostridium difficile 557 Mark H Wilcox 47 Other Clostridium spp Ian R Poxton 567 48 Anaerobic Actinomycetes and Related Organisms Val Hall Index 587 575 List of Contributors Dlawer A A Ala’Aldeen Molecular Bacteriology and Immunology Group, Division of Microbiology, University Hospital, Nottingham NG7 2UH, UK Richard L Guerrant Division of Infectious Diseases, University of Virginia School of Medicine, Charlottesville, VA 22908, USA Indran Balakrishnan Department of Medical Microbiology, Royal Free Hospital, Pond Street, London NW3 2QG, UK Val Hall Anaerobe Reference Laboratory, National Public Health Service for Wales, Microbiology Cardiff, University Hospital of Wales, Heath Park, Cardiff CF4 4XW, UK Christopher L Baylis Campden & Chorleywood Food Research Association (CCFRA), Chipping Campden, Gloucestershire GL55 6LD, UK T G Harrison Respiratory and Systemic Infection Laboratory, Health Protection Agency, Centre for Infection, 61 Colindale Avenue, London NW9 5HT, UK Cécile M Bébéar Laboratoire de Bactériologie, Université Victor Segalen Bordeaux 2, 146 rue Léo Saignat, 33076 Bordeaux, France C Anthony Hart Medical Microbiology Department, Royal Liverpool Hospital, Duncan Building, Daulby Street, Liverpool L69 3GA, UK Christiane Bébéar Laboratoire de Bactériologie, Université Victor Segalen Bordeaux 2, 146 rue Léo Saignat, 33076 Bordeaux, France Alex van Belkum Department of Medical Microbiology & Infectious Diseases, Erasmus University Medical Center Rotterdam EMCR, Dr Molewaterplein 40, 3015 GD Rotterdam, The Netherlands Peter M Hawkey Division of Immunity and Infection, The Medical School, Edgbaston, Birmingham B15 2TT, UK Qiushui He Pertussis Reference Laboratory, National Public Health Institute, Kiinamyllynkatu 13, 20520 Turku, Finland Eugenie Bergogne-Berezin University Paris 7, Faculty of Medicine Bichat, 100 bis rue du Cherche-Midi, Paris 75006, France Brian Henderson Division of Infection and Immunity, Eastman Dental Institute, 256 Gray’s Inn Road, London WC1X 8LD, UK Patrick J Blair 96520-8132 Derek W Hood Molecular Infectious Diseases, Department of Paediatrics, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK US Embassy Jakarta, US NAMRU 2, FPO AP Alpana Bose Centre for Medical Microbiology, Royal Free and University College Medical School, Hampstead Campus, Rowland Hill Street, London NW3 2PF, UK Tom Cheasty HPA Colindale, Laboratory of Enteric Pathogens, Centre for Infection, 61 Colindale Avenue, London NW9 5HT, UK Derrick W Crook Department of Clinical Microbiology, John Radcliffe Hospital, Level 7, Headington, Oxford OX3 9DU, UK Aruni De Zoysa Health Protection Agency, Centre for Infection, Department of Respiratory and Systemic Infections, 61 Colindale Avenue, London NW9 5HT, UK Brian I Duerden Anaerobe Reference Laboratory, Department of Medical Microbiology, University of Wales College of Medicine, Heath Park, Cardiff CF14 4XN, UK Androulla Efstratiou Respiratory and Systemic Infection Laboratory, Health Protection Agency, Centre for Infection, 61 Colindale Avenue, London NW9 5HT, UK Florence Fenollar Unité des Rickettsies, CNRS UMR 6020A, Faculté de Médecine, Université de la Méditerranée, 27 Bd Jean Moulin, 13385 Marseille Cedex 05, France Roger G Finch Department of Microbiology and Infectious Diseases, The Nottingham City Hospital NHS Trust, The Clinical Sciences Building, Hucknall Road, Nottingham NG5 1PB, UK Catherine Ison Sexually Transmitted Bacteria Reference Laboratory, Centre for Infection, Health Protection Agency, 61 Colindale Avenue, London NW9 5HT, UK Claire Jenkins Department of Medical Microbiology, Royal Free Hospital NHS Trust, Rowland Hill Street, London NW3 2PF, UK Peter J Jenks Department of Microbiology, Plymouth Hospitals NHS Trust, Derriford Hospital, Plymouth PL6 8DH, UK Franca R Jones National Naval Medical Center, Microbiology Laboratory, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA Monika Keelan Department of Laboratory Medicine & Pathology, Division of Medical Laboratory Science, B-117 Clinical Sciences Building, University of Alberta, Edmonton, Alberta, Canada T6G 2G3 Kevin G Kerr Department of Microbiology, Harrogate District Hospital, Lancaster Park Road, Harrogate HG2 7SX, UK Theresa Lamagni Healthcare Associated Infection & Antimicrobial Resistance Department, Health Protection Agency, Centre for Infection, 61 Colindale Avenue, London NW9 5EQ, UK Paul N Levett Provincial Laboratory, Saskatchewan Health, 3211 Albert Street, Regina, Saskatchewan, Canada S4S 5W6 Sarah J Furrows Department of Clinical Parasitology, The Hospital of Tropical Diseases, Mortimer Market off Tottenham Court Road, London WC1E 6AU, UK Niall A Logan Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Cowcaddens Road, Glasgow G4 0BA, UK Stephen H Gillespie Centre for Medical Microbiology, Royal Free and University College Medical School, Hampstead Campus, Rowland Hill Street, London NW3 2PF, UK Benjamin J Luft Department of Medicine, Division of Infectious Diseases, SUNY at Stony Brook, New York, NY 11794-8160, USA viii LIST OF CONTRIBUTORS Roderick McNab Consumer Healthcare, GlaxoSmithKline, St George’s Avenue, Weybridge, Surrey KT13 0DE, UK Jussi Mertsola Department of Pediatrics, University of Turku, Kiinamyllynkatu 4-8, 20520 Turku, Finland David A Murdoch Department of Medical Microbiology, Royal Free Hospital NHS Trust, Rowland Hill Street, London NW3 2PF, UK Barbara E Murray Division of Infectious Diseases, University of Texas Health Science Center, Houston Medical School, Houston, TX 77225, USA Esteban C Nannini Division of Infectious Diseases, University of Texas Health Science Center, Houston Medical School, Houston, TX 77225, USA James G Olson Virology Department, U.S Naval Medical Research Center Detachment, Unit 3800, American Embassy, APO AA 34031 Petra C F Oyston Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, UK Sudha Pabbatireddy Department of Medicine, Division of Infectious Diseases, SUNY at Stony Brook, New York, NY 11794-8160, USA Sheila Patrick Department of Microbiology and Immunobiology, School of Medicine, Queen’s University of Belfast, Grosvenor Road, Belfast BT12 6BN, UK Sharon Peacock Nuffield Department of Clinical Laboratory Sciences, Department of Microbiology, Level 7, The John Radcliffe Hospital, Oxford OX3 9DU, UK Charles W Penn Professor of Molecular Microbiology, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK Sabine Pereyre Laboratoire de Bactériologie, Université Victor Segalen Bordeaux 2, 146 rue Léo Saignat, 33076 Bordeaux, France Tyrone L Pitt Centre for Infection, Health Protection Agency, 61 Colindale Avenue, London NW9 5HT, UK Ian R Poxton Medical Microbiology, University of Edinburgh Medical School, Edinburgh EH8 9AG, UK John Richens Centre for Sexual Health and HIV Research, Royal Free and University College Medical School, The Mortimer Market Centre, Mortimer Market, London WC1E 6AU, UK Geoff L Ridgway Pathology Department, The London Clinic, 20 Devonshire Place, London W1G 6BW, UK Marina Rodríguez-Díaz Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Cowcaddens Road, Glasgow G4 0BA, UK J M Rolain Unité des Rickettsies, CNRS UMR 6020A, Faculté de Médecine, Université de la Méditerranée, 27 Bd Jean Moulin, 13385 Marseille Cedex 05, France Andrew J H Simpson Defence Science and Technology Laboratory, Biological Sciences Building 245, Salisbury, Wiltshire SP4 OJQ, UK Shiranee Sriskandan Gram Positive Molecular Pathogenesis Group, Department of Infectious Diseases, Faculty of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK Diane E Taylor Department of Medical Microbiology and Immunology, 1-41 Medical Sciences Building, University of Alberta, Edmonton AB T6G 2H7, Canada Nathan M Thielman Division of Infectious Diseases, University of Virginia School of Medicine, Charlottesville, VA 22908, USA Andrew J L Turner Manchester Medical Microbiology Partnership, Department of Clinical Virology, 3rd Floor Clinical Sciences Building 2, Manchester Royal Infirmary, Oxford Road, Manchester M13 9WL, UK David P J Turner Molecular Bacteriology and Immunology Group, Division of Microbiology, University Hospital of Nottingham, Nottingham NG7 2UH, UK Cees M Verduin PAMM, Laboratory of Medical Microbiology, P.O Box 2, 5500 AA Veldhoven, The Netherlands Matti K Viljanen Department of Medical Microbiology, University of Turku, Kiinamyllynkatu 13, 20520 Turku, Finland Michael B Prentice Department of Microbiology University College Cork, Cork, Ireland Adrian Whatmore Department of Statutory and Exotic Bacterial Diseases, Veterinary Laboratory Agency – Weybridge, Woodham Lane, Addlestone, Surrey KT15 3NB, UK Didier Raoult Unité des Rickettsies, CNRS UMR 6020A, Faculté de Médecine, Université de la Méditerranée, 27 Bd Jean Moulin, 13385 Marseille Cedex 05, France Mark H Wilcox Department of Microbiology, Leeds General Infirmary & University of Leeds, Old Medical School, Leeds LS1 3EX, UK Derren Ready Eastman Dental Hospital, University College London Hospitals NHS Trust, 256 Gray’s Inn Road, London WC1X 8LD, UK Edward J Young Department of Internal Medicine, Baylor College of Medicine, Veterans Affairs Medical Center, One Baylor Place, Houston, TX 77030, USA Preface Change is inevitable and nowhere more than in the world of bacteriology Since the publication of the first edition of this book in 1997 the speed of change has accelerated We have seen the publication of whole genome sequences of bacteria The first example, Mycoplasma genitalium, was heralded as a breakthrough, but this was only the first in a flood of sequences Now a wide range of human, animal and environmental bacterial species sequences are available For many important organisms, multiple genome sequences are available, allowing comparative genomics to be performed This has given us a tremendous insight into the evolution of bacterial pathogens, although this is only a part of the impact of molecular biological methods on bacteriology Tools have been harnessed to improve our understanding of the pathogenesis of bacterial infection, and methods have been developed and introduced into routine practice for diagnosis Typing techniques have been developed that have begun unravelling the routes of transmission in human populations in real time New pathogens have been described, and some species thought to have been pathogenic have been demonstrated only to be commensals Improved classification, often driven by molecular methods, has increased our ability to study the behaviour of bacteria in their interaction with the human host New treatments have become available, and in other instances, resistance has developed, making infections with some species more difficult to manage In this revision the authors and editors have endeavoured to provide up-to-date and comprehensive information that incorporates this new knowledge, while remaining relevant to the practice of clinical bacteriology We hope that you find it helpful in your daily practice Stephen H Gillespie Peter M Hawkey Section One Gram-Positive Cocci β-Haemolytic Streptococci Androulla Efstratiou1, Shiranee Sriskandan2, Theresa Lamagni1 and Adrian Whatmore3 Health Protection Agency, Centre for Infections, London; 2Department of Infectious Diseases, Imperial College School of Medicine, London; and 3Veterinary Laboratory Agency, Addlestone, Surrey, UK GENERAL INTRODUCTION Streptococcal diseases such as scarlet fever, erysipelas and puerperal fever were recognised as major problems for centuries before characterisation of the causative organisms The first attempts to differentiate streptococci were probably made by Schottmüller in 1903, who used haemolysis to distinguish them The β-haemolytic streptococci, characterised by the production of clear zones of haemolysis around colonies following overnight incubation on blood agar, turned out to contain some of the most ubiquitous bacterial colonisers of humans Although there are now numerous additional approaches for differentiating streptococci, both haemolytic activity and another early approach, Lancefield typing (based on group-specific carbohydrate antigens), remain useful for differentiating them in the modern clinical microbiology laboratory Table 1.1 lists the major β-haemolytic streptococci currently recognised Interestingly, the accumulation of molecular data in recent years has revealed that the β-haemolytic streptococci largely correspond to a phylogenetic grouping All the species listed in Table 1.1 fall within the pyogenic grouping recognised by Kawamura et al (1995) on the basis of 16S rRNA sequence, although this grouping also contains non-β-haemolytic streptococci Moreover, many other streptococci, particularly anginosus species, could on occasion show β-haemolytic activity However, these are not considered primarily β-haemolytic organisms and are discussed by Roderick McNab and Theresa Lamagni in Chapter 2, under nonhaemolytic streptococci The most important β-haemolytic streptococci are Streptococcus pyogenes and Streptococcus agalactiae Streptococcus pyogenes, also known as the group A streptococcus (GAS) – considered the most Table 1.1 Features of β-haemolytic streptococci Species Common Lancefield group(s) Major host(s) S pyogenes S agalactiae S dysgalactiae subsp equisimilis S equi subsp equi S equi subsp zooepidemicus S canis S porcinus S iniae S phoacae S didelphis A B C, G Human Human, bovine Human, animals C C G E, P, U and V None C and F None Animals Animals (humana) Dog (humana) Swine (humana) Marine life (humana) Seal Opossum a Rare causes of human infection pathogenic of the genus – appears to be essentially confined to humans and is associated with a wide spectrum of diseases These range from mild, superficial and extremely common diseases such as pharyngitis (strep throat) and impetigo to severe invasive disease from which the organism has gained public notoriety as the flesh-eating bacterium and immune-mediated sequelae such as rheumatic fever (RF) and poststreptococcal glomerulonephritis Although well adapted to asymptomatic colonisation of adults, S agalactiae, or the group B streptococcus (GBS), is a major cause of neonatal sepsis and an increasingly common pathogen of the elderly and immunocompromised as well as an important cause of mastitis in cattle Streptococcus dysgalactiae subsp equisimilis is considered a less pathogenic species than GAS but is a relatively common cause of similar superficial disease and may also be associated with invasive disease of the elderly or immunocompromised A further four members of the β-haemolytic streptococci are considered to be primarily non-human pathogens, although they have occasionally been associated with zoonotic human infection and will be discussed only briefly in this chapter Streptococcus equi subsp zooepidemicus infections are generally associated with the consumption of unpasteurised dairy products and may induce a broad disease spectrum Streptococcus equi subsp zooepidemicus has been associated with outbreaks of nephritis (Francis et al 1993) There have been some reports (although rare) of the isolation of Streptococcus canis from human blood cultures (the microbiological identification of the species does remain questionable) Streptococcus iniae has been associated with invasive disease in fish-handlers, and Streptococcus porcinus has been occasionally isolated from the human genitourinary tract, although the pathogenic potential of these isolates is unclear A further three β-haemolytic streptococcal species have not been reported as having been isolated from humans (Streptococcus equi subsp equi, Streptococcus didelphis and Streptococcus phoacae) – S phoacae and S didelphis have been isolated from seals and opossums Streptococcus iniae is also primarily animal pathogen, classically associated with infections amongst freshwater dolphins The review by Facklam (2002) provides a more detailed description of these streptococci PATHOGENESIS AND VIRULENCE FACTORS GAS Pathogenesis The status of GAS as one of the most versatile of human pathogens is reflected in the astonishing array of putative virulence determinants associated with this organism Lack of space and the remit of this chapter permit only a cursory discussion of the extensive and ever-expanding Principles and Practice of Clinical Bacteriology Second Edition Editors Stephen H Gillespie and Peter M Hawkey © 2006 John Wiley & Sons, Ltd β-HAEMOLYTIC STREPTOCOCCI Table 1.2 Putative virulence factors of group A streptococcus (GAS) Cell-surface molecules Major function(s)/role M-protein family (Emm, Mrp, Enn) Resistance to phagocytosis Multiple ligand-binding capacities Adhesion, invasion? Fibronectin-binding proteins (multiple) C5a peptidase Hyaluronic acid capsule Inhibits leukocyte recruitment Resistance to phagocytosis Adherence? Excreted molecules Probable function/role Streptolysin O/streptolysin S Streptokinase Superantigens (multiple) Protein Sic SpeB (cysteine protease) Haemolytic toxins Lysis of blood clots and tissue spread Nonspecific immune stimulation Inhibitor of complement Generates biologically active molecules Inflammation, shock and tissue damage literature in this area For a more encompassing view, readers are referred to the many excellent reviews covering the role of putative virulence factors identified in GAS (Cunningham 2000; Nizet 2002; Bisno, Brito and Collins 2003; Collin and Olsén 2003) Throughout the ensuing section the reader should bear in mind that the repertoire of putative virulence factors is now known to vary between strains and that even when the same factors are present there may be extensive genotypic and phenotypic diversity It is thus increasingly apparent that GAS pathogenesis involves a complex and interacting array of molecules and that the fine details may vary between different strains The best-studied virulence factors are listed in Table 1.2, though this table is far from exhaustive as there are numerous less-well-characterised molecules that could be involved in pathogenesis Cell-Associated Molecules The M protein has long been considered the major cell-surface protein of GAS M protein was originally defined as an antiphagocytic protein that determines the serotype of a strain and evokes serotype-specific antibody that promotes phagocytosis by neutrophils in fresh human blood Despite extensive antigenic variation all M proteins have an α-helical coiled–coil conformation and possess an array of properties that may be important in their antiphagocytic role The best-characterised activities are binding of factor H, a regulatory component of complement control system, and binding of fibrinogen that diminishes alternate complement pathway-mediated binding of C3b to bacterial cells, thus impeding recognition by polymorpholeukocytes (PMLs) The M-protein-encoding gene (emm) is now known to belong to a family of so-called M-like genes linked in a cluster that appear to have evolved by gene duplication and intergenic recombination (Whatmore and Kehoe 1994) A variety of genomic arrangements of this family has been identified, the simplest of which consists of only an emm gene flanked by a regulatory gene mga (multiple gene activator) and scpA (see Virulence Gene Regulators) However, many isolates contain an upstream gene (usually designated mrp) and/or a downstream gene (usually designated enn), and several members of the M-like gene family have been found to bind a whole array of moieties including various immunoglobulin A (IgA) and IgG subclasses, albumin, plasminogen and the factor H-like protein C4bBP In recent years it has become clear that resistance to phagocytosis is not solely dependent on the M protein itself For example, inactivation of emm49 has little impact on resistance to phagocytosis, with mrp49, emm49 and enn49 all appearing to be required (Podbielski et al 1996; Ji et al 1998) The capacity of some strains (notably M18) to resist phagocytosis is virtually entirely dependent on the extracellular nonantigenic hyaluronic acid capsule (Wessels and Bronze 1994) Many clinical isolates, particularly those epidemiologically associated with severe disease or RF, produce large mucoid capsules These may act to mask streptococcal antigens or may act as a physical barrier preventing access of phagocytes to opsonic complement proteins at the bacterial cell surface, as well as being involved in adherence In addition to the antiphagocytic molecules described above many other cellular components have postulated roles in pathogenesis All GAS harbour scpA mentioned above that encodes a C5a peptidase This protein destroys C5a complement protein that is a chemotactic signal that initially attracts neutrophils to sites of infection GAS have been shown to possess an array of fibronectin-binding proteins, indicating the importance of interactions with this molecule Fibronectin is a Principal glycoprotein in plasma, body fluids and the extracellular matrix Perhaps the best-characterised GAS fibronectinbinding protein is protein F (SfbI) that has roles in adherence and invasion (see Adherence, Colonisation and Internalisation) However, an ever-expanding array of other molecules has been shown to possess this activity, including proteins such as SfbII, SOF, proteinF2, M3, SDH, FBP-51, PFBP, Fba and glyceraldehyde-3-phosphate dehydrogenase With the recent completion of genome sequencing projects many novel cell-surface proteins have been identified Most remain to be fully characterised, but their surface location facilitates potential roles in host interaction Examples include Slr, a leucine-rich repeat protein, isogenic mutants of which are less virulent in an intraperitoneal mouse model and more susceptible to phagocytosis by human PMLs (Reid et al 2003) Two novel collagen-like proteins, SclA and SclB, have also been identified Their function is unclear, but they may be important in adherence and are of potential interest in the pathogenesis of autoimmune sequelae (Lukomski et al 2000; Rasmussen, Eden and Bjorck 2000; Whatmore 2001) A further potential virulence factor identified from the genome sequence is protein GRAB, present in most GAS and possessing high-affinity binding capacity for the dominant proteinase inhibitor of human plasma α2-macroglobulin Again, mutants are attenuated in mice and it has been suggested that α2-macroglobulin bound to the bacterial surface via protein GRAB entraps and inhibits the activity of GAS and host proteinases, thereby protecting other virulence determinants from proteolytic degradation (Rasmussen, Muller and Bjorck 1999) Excreted Products Most GAS produce two distinct haemolysins, streptolysin O (SLO) and streptolysin S (SLS) SLO is an oxygen-labile member of the cholesterol-binding thiol-activated toxin family that elicits antibodies useful for documenting recent exposure and is toxic to a variety of cells SLS belongs to the bacteriocin family of microbial toxins and is not immunogenic in natural infection but shares similar toxic activities to SLO Streptokinase facilitates the spread of organisms by promoting the lysis of blood clots Streptokinase binds to mammalian plasminogen, and this complex then converts other plasminogen molecules to the serum protease plasmin that subsequently acts on a variety of proteins including fibrin GAS have cell-surface receptors capable of binding plasminogen, which following conversion to plasmin in the presence of streptokinase may generate cell-associated proteolytic enzyme capable of causing tissue destruction GAS produce an array of superantigens These protein exotoxins have the ability to trigger excessive and aberrant activation of T cells by bypassing conventional major histocompatibility complex (MHC)restricted antigen processing (Llewelyn and Cohen 2002) Subsequent excessive and uncoordinated release of inflammatory cytokines such as tumour necrosis factor-α (TNF-α), interleukin-2 (IL-2) and interferon-γ (IFN-γ) results in many of the symptoms consistent with toxic shock INDEX Cefoxitin in GPAC 536 in rapid growing mycobacteria 178 Cefpirome in Enterobacter 384 in Serratia 384 Ceftazidime in Acinetobacter 237 in B cepacia 437 in B pseudomallei 439 in Bordetella 259 in Enterobacter 384 in N meningitidis 214 in Serratia 384 Ceftriaxone in B pseudomallei 439 in β-haemolytic disease 15 in Bordetella 259 in Donovanosis 388 in N gonorrhoeae 226 in N meningitidis 216 in otitis media 52 in Salmonella 373 in Shigella 359 in sinusitis 52 Ceftriaxone in N meningitidis 214 Cefuroxime in CONS 108, 109 in Enterobacter 383 in H influenzae 249 in N meningitidis 214 in non-sporing Gram-negative anaerobes 554 in Serratia 384 in Streptococcus pneumoniae 48 Cefuroxsime axetil in Lyme disease 519 Cellulitis 8, 249 Centers for Disease Control and Prevention (CDC) 7, 83 Central nervous system (CNS) 132, 211, 236, 578–9 Central venous catheters 107 Cephalosporinases in Alcaligenes 241 in Citrobacter 382 Cephalosporins in Acinetobacter 237 in Actinomyces 585 in B cereus 154 in brucellosis 270 in Campylobacter 490 in Chlamydia 325 in Chryseobacterium in CONS 108–9 in H influenzae 249 in meningitis 52 in N gonorrhoeae 226 in N meningitidis 214–15 in non-sporing Gram-negative anaerobes 554 in P aeruginosa 433 in S maltophilia 239 in Salmonella 373 in Yersiniosis 403 Cephamycins in Nocardia infection 186 Cephradine in CONS 109 in Enterobacter 383 in Serratia 384 Cerebrospinal fluid (CSF) 43, 84, 99, 161, 195, 269, 308, 323, 335, 348, 431 Lyme disease 517 shunt infections 108 shunting systems 104 testing 508 Cerebrovascular accidents 466 Cervicitis 321 Childhood infections 322 Chlamydia 317–26 cell culture 323–4 choice of antibiotic 325 classification 317–18 description of organism 317–20 genital infections 321–2 laboratory diagnosis 323–5 life cycle 318 management of infection 325–6 microscopy 323 prevention and control of infection 326 replications 318 serology 325 specimen collection 323 structure and major antigens 319–20 treatment regimens 325–6 vaccination 326 Chlamydia muridarum 318 Chlamydia suis 318 Chlamydia trachomatis 318–19, 320, 321, 326 clinical features 320 cytokines 320 epidemiology 320 treatment regimens 326 Chlamydiae, type III secretory system 319 Chlamydial infection 222 Chlamydophila 317 antibody response 320 genomes 318–19 life cycle 318 Chlamydophila abortus 318, 323 Chlamydophila caviae 318 Chlamydophila felis 318, 323 Chlamydophila pecorum 318 Chlamydophila pneumoniae 318, 319, 320, 322–3 treatment regimens 326 Chlamydophila psittaci 318, 320, 323 treatment regimens 326 Chloramphenicol in Actinomyces 584 in Alcaligenes 240 in B cepacia 437 in B cereus 154 in B pseudomallei 439 in Bartonella 300 in E coli 356 in enterococci 68 in Enterococcus 65–6 in GPAC 536 in H influenzae 348–9 in K kingae 195 in N meningitidis 214 in Oroya fever 300 in Rickettsia 292 in Salmonella 372–3 in Streptococcus pneumoniae 49, 51 in Whipple’s disease 337 in Yersiniosis 403 Chloramphenicol acetyltransferase (CAT) in mycoplasmas 313 in Streptococcus pneumoniae 51 Chlorhexidine in Proteeae 395 Cholera 407 biotypes 414 carriers 412 chronology 411 clinical features 412 control 409–10 epidemiology 411–12 identification 413 immunity 416 laboratory diagnosis 412–14 oxidase test 413 591 pathogenesis 408–11 presentation 412 prevention 415–16 rehydration therapy 414–15 sensitivity 413 specimen collection and transport 412 toxin (CT) 409–10 transmission 408–9 treatment 414–15 vaccines 415–16 virulence factors 409 see also Vibrio Cholesterol-dependent pore-forming toxins (CDTX) 130 Choline-binding protein A 42–3 Chromosomally mediated resistant N gonorrhoeae (CMRNG) 227 Chronic ambulatory peritoneal dialysis 136 Chronic bacteremia 297–8 Chryseobacterium 239–40 antimicrobial susceptibility 240 bacteriology 240 definition 239–40 epidemiology 240 pathogenicity 240 taxonomy 240 Chryseobacterium gleum 234 Chryseobacterium indologenes 234 Chryseobacterium meningosepticum 234 Chryseobacterium odoratum 234 Chryseomonas luteola 234 Ciprofloxacin in Acinetobacter 237 in Actinomyces 584 in B anthracis 153 in B cepacia 437 in B cereus 154 in B pseudomallei 437 in C difficile 561 in Campylobacter 491, 492 in Chlamydia 325 in Chryseobacterium 240 in Citrobacter 382 in E coli 356 in Enterobacter 383 in GPAC 326 in K kingae 195 in M haemophilum 178 in Mycobacterium intracellulare complex (MAIC) 174 in N gonorrhoeae 226–7 in N meningitidis 216 in Nocardia infection 186 in P aeruginosa 433 in Proteeae 395 in Serratia 384 in Shigella 359 in Staphylococcus aureus 77 in Streptococcus pneumoniae 48 in Yersiniosis 403 Ciprofloxacin–piperacillin in B cepacia 437 Citrobacter 381–2 antimicrobial susceptibility 382 biochemical characteristics 377 description of organism 381 diagnosis 382 epidemiology 382 infections 382 normal habitat 382 pathogenesis 381–2 prevention 382 treatment 382 Citrobacter diversus 342–4 Citrobacter freundii 342–4, 381–2 592 Citrobacter koseri 382 Citrobacter rodentium 381 Clarithromycin in GPAC 536 in H pylori 479 in legionellae 452 in M haemophilum 178 in Mycobacterium intracellulare complex (MAIC) 174 in Mycobacterium kansasii 175 in pneumonia 52 in rapid growing mycobacteria 178 Clavulanate in C difficile 560 in non-sporing Gram-negative anaerobes 553, 554 in Yersiniosis 403 Clavulanic acid in B pseudomallei 439 Clavulinate in H influenzae 249 Clindamycin in Actinomyces 584 in B cereus 154 in Campylobacter 491 in Chryseobacterium 240 in CONS 108 in diphtheria 122 in GPAC 536 in infective endocarditis 28 in K kingae 195 in S aureus 86 in Streptococcus pneumoniae 48–9 in Veillonellae 538 Clofazimine in Mycobacterium intracellulare complex (MAIC) 174 Clostridium 567–73 clinical spectrum and major toxins 568 commonly encountered 567 description of organism 567–8 exotoxins 568 genomics 573 GI disease 570 isolation 569 neurotoxic 571–2 pathogenic 568 pathogenicity 568 structure 568 virulence 568 Clostridium barati 568 Clostridium bifermentans 567 Clostridium botulinum 567–8, 571 Clostridium butyricum 567 Clostridium chauvoei 567–8, 573 Clostridium difficile 557–64, 573 antibacterial prophylaxis 563 antibiotic-related risk 560 antimicrobials predisposing to infection 560–1 biotherapy 562–3 clinical features 560–1 clinical presentation 560 colitis 68 control 563–4 cross-infection 559 culture 561 cytotoxic activity 561 decontaminating hospital environments 564 description of organism 557 epidemic strains 558 epidemiology 559–60 histopathology 561–2 historical aspects 557 hospital environment 559 hospital infection control 563–4 immune response 558–9 immunotherapy 563 INDEX incidence of diarrhoea 559, 563 laboratory diagnosis 561–2 management of infection 562–3 nosocomial transmission 563 pathogenicity 558–9 prevention 563–4 recurrence of infection 562 toxin-binding polymer 563 toxin detection 561 toxins A and B 558 treatment 562 typing 562 vaccination 563 virulence determinants 558 Clostridium difficile-associated diarrhoea (CDAD) 563 Clostridium innocuum 306 Clostridium novyi 567–8, 570–1 clinical features 570 laboratory diagnosis 571 patient management 571 prevention 571 Clostridium perfringens 146, 150, 559, 567–8, 569–70, 573 clinical features 569 food poisoning 570 gas gangrene in 569 isolation 569 major lethal toxins 569 Clostridium ramosum 306 Clostridium septicum 567–8, 573 Clostridium sordellii 557, 567–8, 573 Clostridium sporogenes 567–8 Clostridium tertium 567–8 Clostridium tetani 567–8, 572–3 Coagulase-negative staphylococci, see CONS Coagulase-reacting factor (CRF) 76 Co-amoxiclav in B pseudomallei 439 in CONS 109 Coli surface antigens (CSAs) 352 Colistin in P aeruginosa 433 Collagen adhesin-specific antibodies 89 Colonisation factor antigens (CFAs) 352 Colonisation factors (CFs) 352 Comamonas acidovorans 234 Comamonas terrigena 234 Comamonas testosteroni 234 Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) 76 Complement fixation 289, 458 Complicated gonococcal infection 223 Congo Red agar test 103 Conjunctivitis 249 CONS 99–109 antibiotic choice 109 antibiotic prophylaxis 108 antibiotic regimen 107 antibiotic susceptibility 106 attachment 102 bacteremia 104 biofilm-associated 103 capsular material 102 classification 99–102 clinical features 104–5 colonizers 106 CSF shunts/valves 104 deep wound samples 105 description of organism 99–102 dialysis infections 104–5 endocarditis 104 epidemiology 103–4 extracellular slime material 102 historical aspects 99 hospital setting 103 infective endocarditis 107 intravascular line infection 104, 107 iron-scavenging systems 103 laboratory diagnosis 105–6 laboratory media 105 laboratory specimens 105 management of infection 106–9 microcolony 103 multi-drug resistance 106 normal habitat 103 pathogenicity 102–3 pathogens 106 peritonitis 104–5 soft tissue infections 105 speciation 105 urine specimens 105 Consensus Approach for Ehrlichiosis (CAFE) 289 Continuous ambulatory peritoneal dialysis (CAPD) 81, 99, 107–8, 150 Coprococcus 529, 530 Corticosteroids in meningitis 215 Corynebacteria biochemical identification 121 potentially toxigenic 123 Corynebacterium 82, 115–25, 187 characteristic features 116 derivation 115–16 description of organism 115–16 Corynebacterium amycolatum 116, 121, 124 Corynebacterium auris 116 Corynebacterium diphtheriae 116 biotypes 116, 121 causative agent of diphtheria 116 endocarditis 120 identification of potentially toxigenic 120 infections caused by non-toxigenic 119–20 management, prevention and control of infection 122–3 molecular typing schemes 118 morphological appearances 122 pathogenesis 116–17 primary isolation 120–2 septicaemia 120 skin infections 119 specimen collection and transport 120 Corynebacterium diphtheriae var belfanti 121 Corynebacterium diphtheriae var gravis 120, 121 Corynebacterium diphtheriae var intermedius 121 Corynebacterium diphtheriae var mitis 120–1 Corynebacterium imitans 121, 124 Corynebacterium jeikeium 124–5 Corynebacterium kroppenstedtii 116 Corynebacterium kutscheri 116 Corynebacterium pseudodiphtheriticum 121, 124 Corynebacterium pseudotuberculosis 116, 120–1, 123–4 Corynebacterium striatum 121, 124 Corynebacterium ulcerans 116, 119–21, 123 Corynebacterium urealyticum 125 Corynebacterium xerosis 124 Cotrimoxazole in B pseudomallei 437 in Bartonella 300 in brucellosis 270 in E coli 356 in K kingae 195 in Nocardia infection 186 in Serratia 384 in Streptococcus pneumoniae 49 in Yersiniosis 403 INDEX Coxiella burnetii 457–9 antibiotic therapy 459 bacterial isolation 458–9 culture 458–9 definition 457 description of organism 457 direct detection 459 immunofluorescence 459 isolation of 458 molecular characterization 457 see also Q fever C-reactive protein (CRP) binding 45 Crohn’s disease 179 CSF, see Cerebrospinal fluid (CSF) Cutaneous tuberculosis 161 Cysteine lactose electrolyte-deficient (CLED) medium 355, 413 Cystic fibrosis (CF) 429, 432–3, 435–6 Cytokines 210, 320, 349 Cytolethal distending toxin (CDT) 274 Cytolysin 60 Cytomegalovirus (CMV) promoter virus 326 Cytoplasmic proteins 268 Cytotoxin-associated gene A 477–8 Delftia acidovorans 427, 440–1 Dental caries 29–30 Dental procedures 276 Dermatophilus congolensis 187 Dexamethasone 329 Dialysis-associated infections 104 Diene’s test 394 Diffusely adherent E coli (DAEC) 352 Diphenoxylate in Shigella 359 Diphtheria 115 anterior nasal 119 antibiotic therapy 122 antitoxin 122 cardiac toxicity 119 clinical manifestations 118–20 control strategies 117 cutaneous 119 detection of toxigenicity 122 epidemiology 117–18 faucial 119 global annual reported incidence and DTP3 coverage 118 history 115 immunisation 117 immunity 123 laboratory diagnosis 120–2 laryngeal 119 neurologic toxicity 119 sites of infection 119 systemic complications 119 toxoid 115, 123 tracheobronchial 119 vaccination 122 Diphtheria-tetanus-pertussis immunization 260 Diphtheria toxin (DT) 116 domains 116 intoxication process 117 regulation of production 117 repressor 117 Diplococcus intracellular meningitidis 205 Diplococcus pneumoniae 41 Direct fluorescence antibody (DFA) test 258 Direct immunofluorescent test (DIF) 324 Disseminated gonococcal infection (DGI) 223 Disseminated intravascular coagulation (DIC) 210 DNA amplification techniques 163 Donovan bodies 387–8 Donovanosis 387–8 control 388 diagnosis 388 differential diagnosis 388 treatment 388 see also Klebsiella Doxycycline in Actinomyces 584 in B anthracis 153–4 in B pseudomallei 439 bacillary angiomatosis 300 in brucellosis 270 in Campylobacter 491 in Chlamydia 326 in cholera 415 in Donovanosis 388 in enterococci 68 in Leptospira 467–8 in Lyme disease 519 in Rickettsia 292 Ehrlichia 285 Ehrlichia chaffeensis 286, 288–92 Ehrlichia ewingii 286 Ehrlichiosis 286 Electron-dense layer (EDL) 545 Elek test 122 Elementary body (EB) 318, 324–5 ELISA 282, 289, 337, 458, 467, 516 Embden–Meyerhof–Parnas (EMP) (glycolytic) pathway 74 Empedobacter brevis 234 Endometritis 321 Endophthalmitis 276, 423 Endotoxin 208–9 Enteroaggregative E coli (EAggEC or EAEC) 352 Enteroaggregative heat-stable toxin-1 (EAST-1) 352 Enterobacter 341, 382–3 antimicrobial susceptibility 383 biochemical characteristics 377 description of organism 382 epidemiology 382–3 normal habitat 382–3 pathogenicity 382 prevention 383 treatment 383 Enterobacter aerogenes 343–4 Enterobacter cloacae 343–4 Enterobacteriaceae biochemical reactions 343–4 characteristics 341 identification 341–5 intrinsic antimicrobial resistance 342 Enterobacterial repetitive intragenic consensus (ERIC) sequences 282 Enterococcal bacteremia 61, 67 Enterococci biochemical characteristics 59–60 common resistances 65 description of genus 59–60 differentiation from Gram-positive organisms 59 management 67–8 multiple drug-resistant isolates 67–8 Enterococcus 59–69 acquired resistance 65 β-lactamase-producing 66 cell-wall polysaccharides 61 clinical infections 61–2 commercial identification systems 63–4 conventional tests 62–3 growth characteristics 60 habitat 60 593 intrinsic resistance 64–5 isolation procedures 62 laboratory diagnosis 62–4 molecular typing systems 64 neonatal infections 62 pathogenicity 60–1 prevention and control 68–9 resistance to antimicrobials 64 routine testing (Kirby–Bauer) 64 secreted factors 60 species identification 62–4 surface-located proteins 60–1 susceptibility testing 64 virulence factors 60–1 VRE strains 68 Enterococcus asini 62–3 Enterococcus avium 61–3 Enterococcus casseliflavus 61–5, 67–8 Enterococcus cecorum 60, 62–3 Enterococcus columbae 60, 62 Enterococcus dispar 62–3 Enterococcus durans 62–3 Enterococcus faecalis 60–4, 66, 68 Enterococcus faecium 60–4, 66 Enterococcus flavescens 62–3 Enterococcus gallinarum 61–3, 67–8 Enterococcus gilvus 62–3 Enterococcus haemoperoxidus 62 Enterococcus hirae 62–3 Enterococcus malodoratus 62–3 Enterococcus moraviensis 62 Enterococcus mundtii 62–3 Enterococcus pallens 60, 62–3 Enterococcus phoeniculicola 62 Enterococcus pseudoavium 62–3 Enterococcus raffinosus 61–3 Enterococcus ratti 62–3 Enterococcus saccharolyticus 60, 62–3 Enterococcus seriolicida 62 Enterococcus solitarius 62 Enterococcus sulfureus 62–3 Enterococcus villorum 62 Enterohaemorrhagic E coli (EHEC) 347, Enteroinvasive E coli (EIEC) 347, 349–50, 355 Enteropathogenic E coli (EPEC) 347, 349–50 Enterotoxigenic E coli (ETEC) 351–2 Enzyme immunoassays (EIA) 257–8, 289, 324, 451–2, 507, 558 Enzyme-linked immunosorbent assay, see ELISA Epididymitis 321 Epiglottitis 247 EPIYA motifs 478 Erysipelas 135, 136 Erysipeloid 135, 136 Erysipelothrix 135–6 description of organism 135 management of infection 136 Erysipelothrix inopinata 135 Erysipelothrix muriseptica 135 Erysipelothrix rhusiopathiae 134–5 clinical features 136 cutaneous infection 136 ecology 135 endocarditis 136 epidemiology 135 human infection 135 identification 136 laboratory diagnosis 136 pathogenesis of infection 135 Erysipelothrix tonsillarum 135 Erythema migrans 514 Erythrocyte sedimentation rate (ESR) 108 Erythrocyte-sensitizing substance (ESS) 289 594 INDEX Erythromycin in Actinomyces 584 in B anthracis 153 in B cereus 154 in bacillary angiomatosis 300–1 in Bordetella 259 in Campylobacter 491–2 in Chlamydia 325–6 in CONS 108 in diphtheria 122 in Donovanosis 388 in Enterococcus 67 in GAS 13 in GPAC 536 in K kingae 195 in legionellae 452 in Nocardia infection 186 in non-β-haemolytic streptococci 36 in Streptococcus pneumoniae 48 Escherichia adecarboxylata 347 Escherichia albertii 347–8 Escherichia blattae 347–8 Escherichia coli 246, 319, 343–4, 347–56, 378, 401 antibiotic resistance 356 bacteraemia 349 biochemical characteristics 348 biochemical reactions 371 clinical features of infections 348–55 description of organism 347–8 laboratory methods for isolation and detection 355 management of infection 359 molecular pathogenesis 351 pathogenicity-related characteristics of intestinal pathotypes 350 pathotypes 348 urinary tract infections 348–9 Escherichia fergusonii 347–8 Escherichia hermannii 347–8 Escherichia vulneris 347–8 Etest method 584 Ethambutol in Mycobacterium intracellulare complex (MAIC) 173 in Mycobacterium kansasii 174 in rapid growing mycobacteria 178 European Antimicrobial Resistance Surveillance System (EARSS) 48 European Laboratory Working Group on Diphtheria (ELWGD) 118 Exfoliatin A (ETA) 75 Extended-spectrum β-lactamases (ESBL) 356 Extracellular serine protease (EspP) 355 Extraintestinal pathogenic E coli 348 Extrapulmonary tuberculosis 166 Eye infection 429 Fatty acid methyl ester (FAME) profiling Femur, osteomyelitis of 84 Filamentous hemagglutinin (FHA) 255 Filobacillus 140 Finegoldia magna 529 Flavimonas oryzihabitans 234 Flavobacterium sp group IIe 234 Flavobacterium sp group IIh 234 Flavobacterium sp group Iii 234 Flea-borne typhus 286, 287, 292 Fleroxacin in Chlamydia 325 in Shigella 359 Flucloxacillin in CONS 108 in impetigo 15 in S aureus 86–7 152 Fluorescent amplified fragment length polymorphism analysis (FAFLP) 13, 208 Fluorescent antibody techniques 580 Fluorescent in situ hybridisation (FISH) 581 Fluoribacter 445 Fluoroquinolones in Acinetobacter 238 in Actinomyces 584 in Alcaligenes 240, 241 in bacillary angiomatosis 300, 301 in Bartonella 300, 301 in brucellosis 270 in C difficile 560, 561 in Campylobacter 491–2 in Chlamydia 325 in Donovanosis 387 in Enterococcus 66–7 in K kingae 195 in legionellae 452 in listeriosis 135 in Mycobacterium kansasii 175 in mycoplasmas 312–13 in N gonorrhoeae 227 in P aeruginosa 433 in Proteeae 395 in rapid growing mycobacteria 178 in S maltophilia 239 in Salmonella 372–3 in Serratia 384 in Shigella 359 in Streptococcus pneumoniae 48, 50–1 Food industry, salmonellosis in 374 Food poisoning 407 C perfringens 569 Fosfomycin-trometanol in E coli 356 Fosfomycin tromethamine in enterococci 68 Francisella tularensis 281–3 clinical features 281–2 description of organism 281 epidemiology 281 growth 281 laboratory diagnosis 282 live vaccine strain (LVS) 283 management 282–3 pathogenicity 281 prevention and control 283 taxonomy 281 Francisella tularensis subsp holarctica, vaccine 283 Francisella tularensis subsp novicida 282 Furazolidone in cholera 415 Fusidic acid in C difficile 561 in CONS 108 Fusobacteriaceae 541 Fusobacterium 542–3, 550 Fusobacterium gonidiaformans 552 Fusobacterium mortiferum 552 Fusobacterium naviforme 552 Fusobacterium necrophorum 541–2, 545, 548–9, 552 Fusobacterium nucleatum 28, 542, 548, 552 Fusobacterium pseudonecrophorum 552 Fusobacterium russi 552 Fusobacterium ulcerans 552 Fusobacterium varium 552 Gardnerella vaginalis 308 Gas gangrene in C perfringens 569 Gas–liquid chromatography (GLC) 541, 557, 581–2 GAS, see Group A streptococcus (GAS) Gastroenteritis Aeromonas 421–2 Plesiomonas shigelloides 423 Gastrointestinal tuberculosis 161 Gatifloxacin in B anthracis 153 in C difficile 561 in Chlamydia 325 GBS, see Group B streptococcus (GBS) GCS, see Group C streptococcus (GCS) Gemella 59–60 Genital tract infections 321, 326 Genitourinary tuberculosis 161 Gentamicin in Acinetobacter 237 in B cereus 154 in brucellosis 270 in Campylobacter 492 in CONS 106–7 in endocarditis 28, 67 in Enterobacter 384 in Enterococcus 61, 64 in HLR strains 67 in K kingae 195 in mycoplasmas 313 in non-sporing Gram-negative anaerobes 554 in P aeruginosa 433 in Serratia 384 in Staphylococcus aureus 73–4, 88 in Yersiniosis 403 Geobacillus 139 GGS, see Group G streptococcus (GGS) Gingivitis 548 Global antimicrobial surveillance programme (GASP) 228 Glucose metabolism products 581–2 Glycopeptides in Enterococcus 66–7 in GPAC 536 resistance 64, 65 Glycylcyclines in mycoplasmas 312 Gonocheck-II 213 Gonococcal ophthalmia 322 Gonococcal urethritis (GU) 321 Gonorrhoea 221–8 Gordona 187 Gordona bronchialis 187 Gordona rubopertincus 187 Gordona sputi 187 Gordona terrae 187 Gracilibacillus 139, 140 Gram-negative anaerobic cocci 537–8 Gram-negative bacilli 234, 238–9, 241, 295 Gram-negative bacteria 103, 207, 231, 285, 407 Gram-negative organisms 273, 447 Gram-positive anaerobic cocci (GPAC) 106, 529–37 aerotolerance 530–1 antibiotic susceptibility 536 butyrate-producing 529 characteristics of more significant species 536–7 classification 529–30 clinical importance 534–5 Clostridium Cluster I 537 Clostridium Clusters IV and XIVa 527 CNS infections 535 Collins Cluster XI 536 Collins Cluster XIII 536–7 Coriobacteriaceae (high G + C Gram-positive phylum 537 differential characteristics 532 genito-urinary tract infections 534–5 intra-abdominal infections 534 laboratory identification 531–3 laboratory isolation 530–1 maintenance 530–1 major energy source 531 INDEX modifications 534 musculoskeletal infections 535 normal flora 534 nucleic acid-based techniques 531, nutritional requirement 530 oral infections 534 pathogenesis 535–6 present classification 533 primary isolation (first stage) 533 respiratory tract infections 534 septicaemia 535 specimen transport 530–1 subculture (second stage) 533–4 superficial and soft-tissue infections 535 virulence factors 535–6 Gram-positive bacteria 152 Gram-positive organisms 59, 183 Gram-positive pathogens 103 Granulicatella 60 Granulicatella adiacens 23 Granulocyte–macrophage colony-stimulating factor (GM–CSF) 320 Granuloma inguinale 387 GRO-α 320 Group A streptococcus (GAS) 3, 119 adherence β-lactam resistance of 14 cell-associated molecules clinical syndromes associated with invasive disease colonisation complications of invasive disease erythromycin resistance 14 excreted products 4–5 host immune response to infection internalisation international quality assurance programmes for characterisation 14 invasive diseases caused by invasive infections caused by 8–10 macrolide resistance 14–15 pathogenesis 3–6 predisposition to invasive disease putative virulence factors risk factors for acquiring invasive disease signs and symptoms of pharyngitis 12 typing 12–13 virulence gene regulators Group B streptococcus (GBS) adult disease 10–11 invasive disease caused by 7, 10 neonatal disease 10 neonatal infection pathogenesis pregnancy-related disease 10 typing 13–14 vaccines 16 Group C streptococcus (GCS) invasive disease caused by 8, 10 typing 13 Group D antisera 59 Group G streptococcus (GGS) invasive disease caused by 8, 10 typing 13 Group Q antisera 59 Guillain–Barré syndrome 119, 466 HAART (highly active antiretroviral therapy) 173 HACEK group 191, 276 Haemodialysis 81 Haemolysins 75 Haemolytic uraemic syndrome (HUS) 423 Haemophilus 245–50 antibiotic susceptibility testing 249 characteristics 245–6 description of organism 245–6 differentiation of species 249 neighbourhood joining tree 246 taxonomy 245 Haemophilus aegyptius 245–6, 249 Haemophilus aphrophilus 245–6, 250 Haemophilus ducreyi 245–6, 250 Haemophilus haemolyticus 245–6 Haemophilus influenzae 52, 84, 209, 236, 245–6 antibiotic resistance 248 capsular typing 249 capsule 246–7 characteristics 245 epidemiology 247–8 incidence 248 laboratory diagnosis 249 lipopolysaccharide (LPS) 247 noncapsulate 248 pathogenicity 246–7 phase and antigenic variation 247 pili and other adhesion proteins 247 population genetics 245–6 treatment of infection 249 Haemophilus influenzae type b (Hib) 247–8 antibiotic prophylaxis 249 clinical features 248–9 disease manifestations 247 prevention and control 249 Haemophilus Neisseria identification panel 191 Haemophilus parahaemolyticus 246 Haemophilus parainfluenzae 245–6, 250 Haemophilus paraphrohaemolyticus 246 Haemophilus paraphrophilus 245–6, 250 Haemophilus segnis 245–6, 250 Hafnia alvei 343–4 Halobacillus 140 Hazard analysis critical control point (HACCP) systems 369 Heat-labile enterotoxin 351 Heat-labile phospholipase C(PLC) 429 Heat shock proteins 313–14 Heat-stable rhamnolipid 429 Helcococcus 60 Helicobacter 473–80 description of organism 473 species and their hosts 473 Helicobacter cinaedi 474 Helicobacter fennelliae 474 Helicobacter mainz 474 Helicobacter pylori 465, 473 acid tolerance 476 adhesion 476 animal models 480 cag type IV secretion system 478 chromosome 475 cytotoxin-associated gene A (CagA) 477–8 diagnosis 478–9 epidemiology 473–4 gene regulation 475 genome, genomics and genetic diversity 475 human disease 474 induction of pathological changes 477–8 lipopolysaccharide (LPS) 478 microbiology 474 morphology 474 oxidative stress resistance 476–7 pathogenesis 476–8 pathogenicity island (PAI) 477–8 prevention and eradication 480 scavenging mechanisms 475 595 susceptibility testing 479 treatment 479 vaccines 480 vacuolating cytotoxin 477 Helicobacter westmeadii 474 Herpes simplex 321 Hexose monophosphate pathway (HMP) 74 Hib, see Haemophilus influenzae type b (Hib) Highly active antiretroviral therapy (HAART) 173 HIV/AIDS 132, 159, 228, 250, 268, 295, 309, 505–6 in Nocardia infection 186 and tuberculosis 160 Hospital-acquired infections 84 Hospital infection control measures 87–8 Hospital Infection Control Practices Advisory Committee (HICPAC) 68 Human granulocytic ehrlichiosis (HGE) 286, 288, 290 Human monocytic ehrlichiosis (HME) 286, 288, 291 Hyaluronidase 43 Imipenem in Acinetobacter 237 in Actinomyces 584 in B cereus 154 in B pseudomallei 439 in Citrobacter 382 in Enterobacter 383 in Nocardia infection 186 in P aeruginosa 433 in Serratia 384 Immunocompromised patients, streptococcal infections in patients with cancer 29 Immunofluorescence 518 Immunofluorescence assay (IFA) 288 Immunoglobulin A (IgA) 320, 333 Immunoglobulin G (IgG) 320, 333, 559 Immunoglobulin M (IgM) 268, 320, 333 Impetigo 15 Indirect Fluorescent Antibody (IFA) assay 289, 458 Indirect haemagglutination (IHA) 289 Indirect immunofluorescent antibody test (IFAT) 452 Infective endocarditis 24–8, 276 antimicrobial treatment 27 children 28 clinical and laboratory considerations 29 clinical features 27 in CONS 107 epidemiology 26 laboratory diagnosis 27 management 27 pathogenesis 25, 28–9 prevention and control 28 prophylactic regimens 28 recommended antibiotic prophylaxis 28 streptococcal virulence properties 25 streptococci isolated from 26 treatment regimens 27 Intercellular adhesion molecule-1 (ICAM-1) 45 Interferon-γ (IFN-γ) 4, 333–4, 337 Interleukin-1 (IL-1) 42, 44, 429, 431 Interleukin-1α (IL-1α) 320, 349 Interleukin-1β (IL-1β) 44, 211, 349 Interleukin-2 (IL-2) Interleukin-4 (IL-4) 329 Interleukin-6 (IL-6) 45, 210, 320, 349 Interleukin-8 (IL-8) 210, 320, 349, 352, 478 Interleukin-10 (IL-10) 329 Interleukin-12 (IL-12) 333–4, 337 Interleukin-18 (IL-18) 431 Interstitial myocarditis 286 596 Intestinal infectious disease (IID) 559 Intestinal pathogenic E coli 347 Intra-abdominal infections 61 Intracranial pressure (ICP) 211 Intrauterine contraceptive devices (IUCDs) and Actinomyces 577 Intravenous immunoglobulin (IVIG) in GAS 15 Isoniazid in M kansasii 175 in M tuberculosis 165 in tuberculosis 164 Ixodes dammini 511 Ixodes pacificus 513 Ixodes ricinus 513 Ixodes scapularis 513 Jeotgalibacillus 140 Johne’s disease 179 Joint infection 431 Joint sepsis 87 Joint tuberculosis 161 Jonesia denitrificans 129 Kanamycin in B pseudomallei 439 in Campylobacter 491–2 in HLR strains 67 Keratitis 423 Ketolides in Streptococcus pneumoniae 50 Kingella denitrificans 191–2 pericellular structures 196 Kingella indologenes 192 Kingella kingae 191–9 antimicrobial susceptibility 195 bacteremia 193 bacteremia in children 193–4 β-lactamase production 191–2 bone and joint infections 193 carriage rate 192 description of organism 191 endocarditis 194 epidemiology 192 infections in adults 194 laboratory diagnosis 194 mediated diseases in childhood 193–4 typing systems 192 virulence 197 Kingella oralis 191 Klebsiella 377–84 adhesins 379 antimicrobial susceptibility 381 biochemical characteristics 377–8 capsule 377 clinical features 381, 387–8 description of organism 377, 387 diagnosis 381 epidemiology 380–1, 387 natural habitat 380 pathogenesis 387 typing methods 381 see also Donovanosis Klebsiella granulomatis 345, 387 Klebsiella oxytoca 342–4, 377 Klebsiella pneumoniae 235, 342–4, 387 electron micrograph 379 iron scavenging 380 LPS 379 nosocomial and opportunistic infection 380 pathogenicity 378–80 prevention 381 toxins 380 treatment 381 Klebsiella pneumoniae subsp aerogenes 378 Klebsiella pneumoniae subsp pneumoniae 378 INDEX Klebsiella pneumoniae subsp rhinoscleromatis 378, 381 Klebsiella rhinoscleromatis 387 Lacrimal canaliculitis 579 Lactobacilli, differentiation from Gram-positive organisms 59 Lactococci, differentiation from Gram-positive organisms 59 Lactococcus lactis 82 Large clostridial toxins (LCT) 355 Laryngeal tuberculosis 160 Laryngitis, M catarrhalis infection 194 Legionella 445–53 biochemical reactions 451 colonial appearance 450 description of organism 445–6 human infection 449 microscopic appearance 450 molecular methods of detection 452 phenotypic characteristics 451 taxonomy 445 Legionella anisa 449 Legionella erythra 450 Legionella feeleii 449 Legionella gresilensis 446 Legionella micdadei 449 Legionella pneumophila 445–6, 449–50, 452 antigen detection 451 cellular constituents 447 Dot/Icm system 447 LPS 447 virulence factors 447 Legionella rubrilucens 450 Legionella sainthelensi 450 Legionella santicrucis 450 Legionellaceae 445 differentiation of species 450 members of family 446 Legionellae antigenic properties 450–1 control of infection 453 definition 445–6 epidemiology 447–8 growth requirements 450 management 452 normal habitat 447–8 pathogenicity 446 prevention 453 Legionnaires’ disease (LD) 445 alternatives to culture 451 causative agent 445 clinical features 449 diagnosis by estimation of antibody levels 452 diagnostic methods 450–2 incidence 448–9 laboratory tests 450 microscopy 451 nosocomially acquired 449 risk factors 448–9 specimens for culture 450 travel-associated 449 Leishman-Donovan bodies 387 Lentibacillus 140 Leptospira 463–9 clinical features 464–6 culture 466 epidemiology 464 geographical distribution 464 histopathology 466 laboratory diagnosis 466–7 life cycle 464 microscopic agglutination 467 microscopy 466 molecular methods of diagnosis 467 molecular typing 467 named species and distribution of serogroups 464 occupational and recreational exposure 464 paradoxical reactions 467 serological assays 466–7 transmission routes 464 Leptospira biflexa 463 Leptospira interrogans 463 Leptospires classification 463–4 definition 463 serovars 463–4 Leptospirosis 463 antibiotics 467 biphasic nature 465 cell-mediated immunity 469 clinical presentation 465 complications 466 control 469 fatality 466 icteric 466–8 immunization of animals 469 jaundice in 466 management 467–8 prevention 469 symptoms 465 treatment 467–8 vaccination 469 Leptospiruria, prevention 468 Leptotrichia 543 Leptotrichia buccalis 541 Leuconostoc 59–60 differentiation from Gram-positive organisms 59 Leukotoxin (LtxA) 275–6 Levofloxacin in B anthracis 153 in C difficile 561 in Streptococcus pneumoniae 48 Lincosamides in Enterococcus 65–6 in Streptococcus pneumoniae 50–1 Linezolid in CONS 107 in enterococci 67, 68 in listeriosis 135 Lipooligosaccharides (LOS) 196, 207–8, 218 Lipopeptide–daptomycin in enterococci 68 Lipopolysaccharide (LPS)-binding protein (LBP) 74 Lipopolysaccharides (LPS) 208, 247, 265–6, 319, 378, 478, 547 Lipoteichoic acid (LTA) 5, 74 Listerella hepatolytica 129 Listeria 129–36 antigenic determinants 129 differentiation of species 134 endocarditis 133 general description of genus 129–30 history 129 pathogenesis 130 Listeria denitrificans 129 Listeria grayi 129 Listeria grayi subsp grayi 134 Listeria grayi subsp murrayi 134 Listeria innocua 129, 134 Listeria ivanovii 129, 134 Listeria monocytogenes 129, 134 animals and human carriers 130 clinical manifestations of infection 132 differences in virulence 130 INDEX direct detection in clinical material 133–4 environmental sources 130 epidemiology 130–2 food products 130–1 human infection 131 identification 131–2, 133 isolation from clinical material 133 minimum infectious dose 130 molecular epidemiology 131–2 nosocomial spread 131 routes of transmission 131 typing 131–2 Listeria murrayi 129 Listeria seeligeri 129, 134 Listeria welshimeri 129, 134 Listeriolysin, detection of antibodies 133 Listeriosis adults 132 antimicrobial therapy 135 association with consumption of poultry 130 CNS 132 food-borne infection 130 food-borne vector 131 invasive 132 laboratory diagnosis 133 management of infection 134–5 maternal genital 132 maternofetal 131 miscellaneous syndromes 133 neonatal 132 neurological infection 132–3 ocular infections 133 pregnancy 132 zoonotic cases 131 Localized aggressive periodontitis (LAP) 273–4, 276 Lomefloxacin in Chlamydia 325 Loperamide in Shigella 359 Louse-borne typhus 286, 287 Lyme arthritis 515–16 Lyme borreliosis diagnosis 517–18 nervous system 516 Lyme disease 511–20 carditis 515 clinical manifestations 513–17 coincident infections 514 control 520 CSF 516 immune response 518 immunological tests 518–19 lymphocytoma 514–15 molecular diagnosis 519 organ systems affected 517 post-treatment 516–17 prevention 520 serologic assays 518–19 skin infection 514 treatment 519–20 vaccine 520 see also Borrelia burgdorferi Lymph node tuberculosis 161 Lymphadenitis in M haemophilum 178 Mycobacterium intracellulare complex (MAIC) 173–4 non-tuberculosis mycobacteria (NTM) 171–2 rapid growing mycobacteria 177 Lymphocytoma, Lyme disease 514–15 Lymphogranuloma venereum (LGV) 317, 320, 322 Macrolide-lincosamide-streptogramin-ketolide (MLSK) group 312–13 Macrolides in Bartonella 301 in Campylobacter 492 in Chlamydia 325 in CONS 106 in Enterococcus 63 in GAS 14 in GPAC 536 in legionellae 452 in pertussis 259 in Streptococcus pneumoniae 49–50 Madura foot 183, 185 Major histocompatibility complex (MHC) 4, 446 Major outer membrane protein (MOMP) 317–18, 319, 446 Mann–Rogosa–Sharpe (MRS) Lactobacillus 60 Marinibacillus 139 Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) 86 MDR efflux pumps 51 Megasphaera elsdenii 538 Melioidosis, presentation and diagnosis 438 Meningitis 45, 46, 52, 62, 87, 132, 148, 161, 208, 235, 245–7, 422 cerebrospinal fluid (CSF) in 213 epidemic outbreaks 205 epidemiology 46–7 Meningitis-associated E coli 348 Meningococcaemia 211 Meningococcal disease 212–13 morbidity and mortality 212–13 Meningococcal genome sequence project 218 Meningococcal septicaemia 211–12, 215 Meningococcal vaccines 215–17 Meropenem in B cepacia 437 in B pseudomallei 439 in Campylobacter 491 in K kingae 195 in P aeruginosa 433 Methicillin in CONS 106 in N meningitidis 215–16 Methicillin-resistant S aureus (MRSA) 68, 80, 81–2, 87–8 Methicillin-susceptible Staphylococcus aureus (MSSA) 77, 87, 89 Methionine sulphoxide reductase (MSR) 26 Methyl-α-D-glucopyranoside (MGP) 63 Metronidazole in Actinomyces 584 in Clostridium difficile 573 in GPAC 536 in H pylori 479 in non-sporing Gram-negative anaerobes 552–3 in Veillonellae 538 Mezlocillin, in Bordetella 259 MIC (minimum inhibitory concentration) determination 48, 65, 583–4 Microbe septicèmique du salive 41 Micrococcus 73 Micrococcus pasteuri 41 Micromonas micros 529 MLSK group in mycoplasmas 312 Mobiluncus 554 Mobiluncus curtisii 548, 554 Mobiluncus mulieris 554 Modified Thayer–Martin (MTM) medium 195 Monobactams in Acinetobacter 237 in P aeruginosa 433 597 Monomeric heat-stable enterotoxin 351 Moraxella catarrhalis 52, 191–98, 248 adherence 197 animal models 197 antibody responses to whole bacteria 198 antimicrobial susceptibility 195 β-lactamase production 195–6 carriage rate 192 cell-wall structures 196 complement resistance 197 description of organism 191–2 epidemiology 192 history 191 immunogenicity of outer membrane proteins 198 infections in adults 198 infections in children 197 laboratory diagnosis 197–8 local antibody response 198 LOS immunogenicity 198 lower respiratory tract infections 197 mediated diseases in childhood 192–3 pericellular structures 196 respiratory tract infections 197–8 typing systems 192 vaccines 198 virulence 197 Morganella 391–94 clinical manifestations 394 description of organism 391 epidemiology 393 habitat 393 human infections 393 isolation 394 laboratory diagnosis 394 pathogenicity 391–2 resistance to antimicrobials 394–5 resistance to chemotherapy 394–5 taxonomy 391 typing methods 393 Morganella morganii 342–4, 391 Mouse pneumonitis 317 Moxifloxacin in C difficile 561 in Chlamydia 325 in GPAC 536 in Streptococcus pneumoniae 48 MRSA, see Methicillin resistant S aureus (MRSA) MSSA, see Methicillin-susceptible Staphylococcus aureus (MSSA) Mucosa-associated lymphoid tissue (MALT) lymphoma 473–4 Multidrug-resistant Streptococcus pneumoniae (MDRSP) 51–2 Multidrug-resistant tuberculosis (MDRTB) 159, 162, 165–6 Multilocus enzyme electrophoresis (MLEE) 13, 207–8, 347, 414, 439 Multilocus sequence typing (MLST) 13, 47, 77, 86, 207–8, 226, 246, 258, 414, 439, 489 Mupirocin in S aureus 88 Mutant prevention concentration (MPC) 51 Mycobacteria decontamination 162 identification 162 see also Non-tuberculosis mycobacteria (NTM); Rapid growing mycobacteria Mycobacterial lymphadenitis 171–2 Mycobacterium abscessus 173, 177–8 Mycobacterium africanum 159 Mycobacterium avium 163, 172, 334 Mycobacterium avium-intracellulare 172–3, 179 Mycobacterium bohemicum 172 Mycobacterium bovis 159 598 Mycobacterium branderi 172 Mycobacterium canetti 159 Mycobacterium celatum 172–3 Mycobacterium chelonae 173 Mycobacterium chelonae-abscessus 172 Mycobacterium chelonei 177 Mycobacterium conspicuum 172 Mycobacterium dorcium 172 Mycobacterium elephantis 172 Mycobacterium fortuitum 172–3, 177–8 Mycobacterium genavense 172–3, 179 Mycobacterium goodi 172, 177 Mycobacterium gordoni 163 Mycobacterium haemophilum 172–3, 178 clinical features 178 cutaneous lesions 178 epidemiology 178 laboratory diagnosis 178 management of infection 178 Mycobacterium heckeshornense 172 Mycobacterium heidelburgense 172 Mycobacterium immunogenum 172, 177 Mycobacterium interjectum 172 Mycobacterium intermedium 172 Mycobacterium avuim-intracelluare complex (MAIC) 173 antibiotics 174 clinical features 173 disseminated disease 173 epidemiology 173–4 management 173–4 organisms 173 prophylaxis 174 pulmonary disease 173–4 respiratory infection 173 Mycobacterium kansasii 163, 171, 174–5 cavitation 174 clinical features 174 cutaneous infection 174 epidemiology 174 extrapulmonary infection 175 management 174–5 pulmonary infections 174–5 Mycobacterium kubicae 172 Mycobacterium lentiflavum 172 Mycobacterium malmoense 171, 172, 173 clinical features 175 epidemiology 175 extrapulmonary disease 175 management 175 pulmonary disease 175 Mycobacterium marinum 176–8 clinical features 176 epidemiology 176 management 176 Mycobacterium microti 159 Mycobacterium palustre 172 Mycobacterium paratuberculosis 179 Mycobacterium perigrinum 177 Mycobacterium scrofulaceae 173 Mycobacterium scrofulaceum 173, 179 Mycobacterium simiae 179 Mycobacterium smegmatis 172, 177 Mycobacterium szulgai 179 Mycobacterium triplex 172 Mycobacterium tuberculosis 159–67 clinical features 160–2 cross-contamination 163 culture 163 description of organism 159 history 159 immunocompetent individuals 160 laboratory diagnosis 162 microscopy 162 INDEX molecular mechanism of resistance 165 molecular susceptibility 164 molecular techniques 161 pathogenesis 159–60 response to infection 159–60 specimen collection 162 stages of infection 159 staining methods 162–3 Mycobacterium ulcerans 172–3 clinical features 176–7 control 177 epidemiology 176 management 177 pathology 177 Mycobacterium wolinskyi 172 Mycobacterium xenopi 171, 173, 175–6 clinical features 176 epidemiology 175–6 management 176 pulmonary disease 176 Mycoplasma 305, 318 Mycoplasma arginini 306, 309 Mycoplasma buccale 306 Mycoplasma faucium 306 Mycoplasma felis 309 Mycoplasma fermentans 305–8, 309–10, 311 Mycoplasma genitalium 305–14, 321 Mycoplasma hominis 305–14 fried-egg colonies 307 Mycoplasma hyorhinis 306 Mycoplasma lipophilum 306 Mycoplasma mycoides spp mycoides 305 Mycoplasma orale 306 Mycoplasma penetrans 305–7, 309–11 Mycoplasma pirum 306, 310 Mycoplasma pneumoniae 305–14, 323 Mycoplasma primatum 306 Mycoplasma salivarium 306 Mycoplasma spermatophilum 306 Mycoplasmas 305–14 activities of antibiotics used for treatment 312–13 animal 309 antibiotic susceptibility testing 312 antigenic structure 307 biochemical characteristics 307 clinical characteristics 308–9 culture 310–11 description of organism 305–6 detection of growth 310 diagnostic methods 309–10 epidemiology 308–9 general characteristics 305 genital 308, 311–12, 314 growth media 310 habitat 306 identification 310 interpretation of culture results 310–11 intrinsic antibiotic resistance 312 morphology 306–7 neonatal infections 309 non-culture methods for detection 311 nutritional requirements 307 pathogenesis 307–8 phylogeny 305–6 pregnancy 309 principal properties 306–7 reproduction disorders 309 respiratory infections 308–9 serology 311–12 specimens 310 structure 311–12 systemic infections 309 taxonomy 305–6 treatment, prevention and control 313–14 urinary tract disorders 309 urogenital tract infections 308–9 Myroides odoratus 234 Nalidixic acid in B cepacia 437 in Campylobacter 488 in E coli 356 National Committee for Clinical Laboratory Standards (NCCLS) 48–51, 85 Native valve endocarditis 87, 107 Nearchus programme 48 Neisseria cinerea 221 Neisseria gonorrhoeae 65, 191, 205, 221–8, 321, 325 antimicrobial resistance 226–7 attachment 221–2 auxotyping 225 cell envelope antigens 221 clinical features 223 description of organism 221 epidemiology 222–3 genetic diversity 226 genetic variation 222 genotyping 226 identification 224–5 immune response 222 invasion 221–2 iron acquisition 222 isolation 223–4 laboratory diagnosis 223 management of infection 226–8 molecular detection 225 pathogenesis 222 presumptive diagnosis 223 prevention and control 228 serotyping 225 surveillance 228 susceptibility testing 227 typing methods 225–6 Neisseria lactamica 221, 224 Neisseria meningitidis 205–18, 221, 224 activated complement cascades 210 age-specific rates for infection 206 antibiotic treatment 214 biochemical reactions 205 blood cultures 213 capsular polysaccharides 208 carriage 206 cell envelope 207 cell envelope antigens 221 classification systems of clinical isolates 207 clinical manifestations 211–12 coagulopathy 210 consequences of bacterial insults 211 cultural characteristics 199 description of organism 205–6 detection of meningococcal antigens, antibodies and DNA 214 DNA sequences 205–6 epidemiology 206 genome sequence and analysis 205 glycoconjugate serogroup A and C vaccines 217 history 205 host factors 211 identification 213 IgA1 protease and other autotransporter proteins 209–10 incidence 248 isolation 213 laboratory diagnosis 213–14 management of infection 214–15 INDEX natural immunity 216 Opa and OpcA 209 outer membrane vesicles 218 pathogenesis 209 pathophysiology 210–11 peripheral white cell count 214 polysaccharide capsule 209 PorA 208 PorB 208 prevention and control 216–18 raised intracranial pressure 215 serogroup A capsular polysaccharide 217 serogroup antigens 208 serogroup B capsular polysaccharide 217 serogroup B vaccines 217–18 serogroup C capsular polysaccharide 217 serosubtype antigens 208 sex-specific rates for infection 206 skin lesions 213 specimen collection 213 throat and nasopharynx 213 Type IV Pili 209 Neonatal infections 309, 322 Neorickettsia 285 Neorickettsia sennetsu 286, 288 Nervous system, Lyme borreliosis 514 Neuraminidases 43, 546 Neurobrucellosis 270 Nitrofurantoin in C difficile 561 in E coli 356 in enterococci 67 in Proteeae 395 Nocardia 183–6 animal infection 183 antigens 183–4 clinical features 184–5 colonization of respiratory tract 184 culture 185–6 description of organism 183–4 differentiation of species 186 direct examination 185 disseminated infection 184 epidemiology 184 habitat 184 human infection 184 identification 186 interaction with phagocytes 184 isolation 185–6 laboratory diagnosis 185–6 management of infection 186–7 morphological characteristics 183 pathogenesis 183–4 physiological characteristics 183 prevention and control 186–7 pulmonary disease serodiagnostic tests 186 species-specific drug resistance 186 specimen collection 185 systemic infection 185 taxonomy 183 tissue sections 185 Nocardia amarae 183 Nocardia asteroides 183–6 Nocardia brasiliensis 183–6 Nocardia brevicatena 183 Nocardia carea 183 Nocardia farcinica 183, 185–6 Nocardia nova 183 Nocardia otidiscaviarum 183 Nocardia pseudobrasiliensis 183 Nocardia seriolae 183 Nocardia transvalensis 183, 185–6 Nocardia vacinii 183 Nocardia veterana 183 Nocardosis, cutaneous 185 Non-cholera Vibrios 408 Non-cystic fibrosis 431 Non-gonococcal urethritis (NGU) 321 Non-Salmonella typhi serotypes 367–8 Non-sporing Gram-negative anaerobes 541–54 antibiotic susceptibility 552–3 bone and joint infection 549 chemotaxonomic characters 543 clinical features 547–9 control 554 description of organisms 541–3 establishing infection 546 evasion of host defence 546 gastrointestinal tract 544 general properties 542–3 genito-urinary infections 548 genito-urinary tract 544 genome sequencing projects 545 growth conditions 543 identification 550 infections with oral anaerobes 548–9 invasion 545 laboratory diagnosis 549–53 laboratory examination 550 management of infections 553–4 mouth 544 non-culture detection methods 552 normal human microbiota 544–7 pathogenicity 544–5 prevention 554 specimen collection 549 superficial soft-tissue infections 549 surface variation 545 taxonomy 541–3 tissue damage 546 transport of samples 549–50 Non-treponemal tests 507 Non-tuberculosis mycobacteria (NTM) 171–9 cutaneous infection 174 description of organism 171–2 pulmonary infection 171 rapid-growing organisms 171 slow-growing organisms 171 taxonomy 171 Non-typhoid Salmonella, azithromycin in 373 Non-typhoid salmonellosis 368–9 Norfloxacin in Campylobacter 492 in cholera 415 in Shigella 359 Nosocomial infections 62, 84, 88, 194, 236 Nosocomial meningitis 236 Novobiocin 154 Nucleic acid amplification technology (NAAT) 223, 225, 322, 324–5 Octal conversion of binary code 342 Ocular infections 423 Oerskovia turbata 187 Oerskovia xanthineolytica 187 Ofloxacin in B pseudomallei 439 in Campylobacter 492 in Salmonella 372 in Shigella 359 omc proteins 319 Oral infections 548 Orientia 285 Orientia tsutsugamushi 286–8, 290 Oroya fever 300 Osteomyelitis 47, 84, 193, 276 Otitis media 47, 52, 193 599 Outer membrane proteins (OMPs) 192, 196, 198, 207, 208, 266 Oxazolidinones in enterococci 68 Oxidase test 418 Oxidation/fermentation (O/F) tests 424 Paenibacillus 139 Paenibacillus alvei 141, 143, 145, 150 Paenibacillus glucanolyticus 144 Paenibacillus lautus 144 Paenibacillus macerans 145, 150 Paenibacillus polymyxa 139, 141, 143, 145, 150, 154 Paenibacillus popilliae 150 PAF receptor 45 PALCAM agar 133 Pandoraea apista 441 Pandoraea pnomenusa 441 Pandoraea pulmonicola 441 Pandoraea sputorum 441 Panton–Valentine leukocidin (PVL) 75 Para-amino salicylic (PAS) acid 164 Pasteurella multocida 246 Pediococcus 59 differentiation from Gram-positive organisms 60 Peliosis hepatis 300, 301 Pelvic infections 61 Pelvic inflammatory disease (PID) 223, 309, 320–1 Penems in rapid growing mycobacteria 178 Penicillin in Acinetobacter 237 in Actinomyces 584 in B anthracis 152–3 in B cereus 154 in β-haemolytic streptococci 15 in C difficile infection 560 in Campylobacter 491 in Chlamydia 325 in Chryseobacterium 238 in CONS 107 in diphtheria 122 in endocarditis 66 in Enterococcus 64, 66–7 in GPAC 536 in H influenzae 248 in infective endocarditis 26 in Leptospira 468 in Lyme disease 519 in M catarrhalis 195 in N gonorrhoeae 226–7 in N meningitidis 213 in non-β-haemolytic streptococci 35 in P aeruginosa 433 in Streptococcus pneumoniae 47 in syphilis 508 in Whipple’s disease 333 Penicillin-binding in CONS 106 Penicillin-binding proteins (PBPs) 74 Peptidoglycan 74, 196 Peptococcus 529 Peptostreptococcus 529 Periodontal disease 273, 494, 544 Periodontitis 273, 276 Periodontium 273 Peripheral neutrophil leucocytosis 46 Periplasmic proteins 268 Peritonitis 47, 107–8, 136, 423 Pertussis chemoprophylaxis 259 clinical manifestations 251 detection of serum antibodies 258 epidemiologic characteristics 256 600 Pertussis (Continued) immunization 253–4 incidence 256–7, 260 laboratory diagnosis 257 mortality 256–7 prevention and control 259 re-emergence in immunised population 257 toxin (PT) 255–6 treatment 259 vaccination 256–7, 259–60 Peyer’s patches, inflammation of 276 Phage therapy in β-haemolytic streptococcal disease 15 Pharyngitis Phenoxymethylpenicillin in N meningitidis 215 PHOENIX 342 PHLS Anaerobe Reference Unit 584 Phospholipase D (PLD) 123 Phospholipids 207 Pinta 503 Piperacillin in Acinetobacter 237 in B cepacia 435 in B pseudomallei 437 in C difficile 561 in Chryseobacterium 240 in M catarrhalis 195 in Serratia 384 Pivmecillinam in Shigella 359 Plague 401 control 403 laboratory diagnosis 402 prevention 403 streptomycin in 403 Plasmid-encoded toxin (Pet) 350 Platelet-activating factor (PAF) 42 Platelet aggregation-associated protein (PAAP) 26 Plesiomonas 419–25 antibiotic susceptibility 424 characteristics 420 control 425 description of organism 419 epidemiology 421, 422 laboratory diagnosis 423–4 management of extragastrointestinal infections 424 pathogenesis 420 prevention 425 taxonomy 419 Plesiomonas shigelloides 420, 423 Pneumococcal conjugate vaccine 53 Pneumococcal endocarditis 47 Pneumococcal infection, see Streptococcus pneumoniae Pneumococcal pneumonia, risk factors 43 Pneumococcal polysaccharide vaccine 53 Pneumococcal surface adhesin A (PsaA) 42 Pneumococcal surface protein A (PspA) 43 Pneumococcal vaccines 53 administration 53 adverse reactions 53 contraindications 54 dosage 53 effectiveness 53 recommendations 53 Pneumocystis jiroveci 184 Pneumolysin 43–4 Pneumonia 45, 46, 52, 81, 248 epidemiology 46 intravenous therapy 52 M catarrhalis 196 Pneumonic plague 401 Pneumonitis 322 INDEX Polyacrylamide gel electrophoresis (PAGE) analysis 152 Polymerase chain reaction (PCR) 47, 77, 85, 122, 225, 257–8, 269, 282, 291–2, 295, 318, 355, 383, 384, 388, 402, 458, 459, 478, 552, 558, 563 Polymeric immunoglobulin receptor (pIgR) 43 Polymorphic outer membrane proteins 319 Polymorpholeukocytes (PMLs) Polymorphonuclear leucocytes (PMNL) 320, 352 Polymyxins in B cepacia 437 in P aeruginosa 434 in Proteeae 392 Polysaccharide intercellular adhesin (PIA) 76 C-polysaccharide (PnC) 44–5 Poly-N-succinyl-β-1–6-glucosamine (PNSG) 88 Pontiac fever 449 Porphyromonas 541–3, 550, 553 Preisz–Nocard bacillus 123 Prevotella 541–3, 550, 553 Prevotella bivia 551 Prevotella buccae 551 Prevotella buccalis 551 Prevotella corporis 551 Prevotella denticola 551 Prevotella disiens 551 Prevotella heparinolytica 551 Prevotella intermedia 28–9, 551 Prevotella loescheii 551 Prevotella melaninogenica 551 Prevotella nigrescens 551 Prevotella oralis 551 Prevotella oris 551 Prevotella oulora 551 Prevotella veroralis 551 Prevotella zoogleoformans 551 Probenecid in Lyme disease 519 Propionibacterium 108 Propionibacterium propionicum 575 direct detection by specific probes 581 epidemiology 577 morphology 576 Prospective Resistant Organism Tracking and Epidemiology for the Ketolide Telithromycin (PROTEKT) study 14 Prosthetic joint infections 108–9 Prosthetic valve endocarditis (PVE) 87, 107 Proteus 391–4 clinical manifestations 394 description of organism 391 epidemiology 393 habitat 393 human infections 393 isolation 394 laboratory diagnosis 394 pathogenicity 391–3 resistance to antimicrobials 394–5 resistance to chemotherapy 394–5 taxonomy 391 typing methods 393 Proteus mirabilis 341–3, 392–3 biochemical characteristics 392 swarming culture 392 Proteus myxofaciens, biochemical characteristics 391 Proteus penneri 342, 391 Proteus vulgaris 343–4, 391 Providencia 391–5 clinical manifestations 394 description of organism 391 epidemiology 393 habitat 393 human infections 393 isolation 394 laboratory diagnosis 394 pathogenicity resistance to antimicrobials 394–5 resistance to chemotherapy 394–5 taxonomy 391 typing methods 393 Providencia alcalifaciens 343–4, 392 Providencia heimbachae 392 Providencia rettgeri 342, 392, 395 Providencia rustiganii 392 Providencia stuartii 342, 392, 395 Pseudomembranous colitis (PMC) 557 Pseudomonads, key tests 427 Pseudomonas 427–41 description of organisms 427–8 early descriptions 427 taxonomy 427 Pseudomonas acidovorans 241 Pseudomonas aeruginosa 88, 231, 427 adherence 428 antibiotic resistance and therapy 433–4 bacteraemia 431 biochemistry 428 colonial forms 428 control 434–9 cultural characteristics 428 cytotoxin 429–30 epidemiology 430 ETA 429 exoenzymes 429 extracellular polysaccharides 429 flagella 428–9 haemolysins 429 infections due to 430–3 isolates from CF 432 laboratory diagnosis and strain typing 433 LasA and LasB 429 LPS 429 LPS-deficient strains 433 pathogenicity 428–30 pigments 428 prevention 434–5 pyocyanin 430 quorum sensing 430 siderophores 430 typing methods 433 vaccines 434–9 virulence-associated factors 428–9 Pseudomonas aeruginosa exotoxin A (rEPA) 373 Pseudomonas alcaligenes 234, 427 Pseudomonas chlororaphis 234, 428 Pseudomonas delafieldii 234 Pseudomonas fluorescens 234, 427, 435 Pseudomonas maltophilia 238 Pseudomonas mendocina 234 Pseudomonas pertucinogena 234 Pseudomonas pseudoalcaligenes 234, 427, 435 Pseudomonas putida 234, 427 Pseudomonas pyocyanea 427 Pseudomonas sp group 234 Pseudomonas sp group 234 Pseudomonas stutzeri 234, 241, 427, 435 Pseudomonas testosteroni 241 Pulmonary infections 84 Pulsed-field gel electrophoresis (PFGE) 13, 86, 131, 226, 236, 259–60, 414, 427, 467, 488, 562 Putative colonisation factors (PCFs) 352 Pyogenic meningitis 205, 214 Pyrazinamide in M kansasii 173 in M tuberculosis 163 in tuberculosis 164 L-pyrrolidonyl-β-naphthylamide (PYR) 60, 63 INDEX histological diagnosis 335 immunohistochemical diagnosis 329 immunology 333–4 molecular biology 336 nonspecific diagnosis 335 pathogenesis 333 pathology 333–4 physiopathology 333 serology 337 specific diagnosis 335–7 specific staining 335 treatment 337 see also Tropheryma whipplei Widal test for typhoid 372 Widespread Colonization Island 274–5 Wolbachia 285 Wounds, infected 431 Yaws 503 Yersinia 397–403 characteristics of 403 description of organisms epidemiology 401 397–8 factors in mouse-lethal 400 laboratory diagnosis 402–3 morphology and growth 397 normal habitat 397–8 pathogenicity 398–401 plasmid-specified type III secretion system 399 simplified model of evolution 400 staining, culture and antigen detection 402 taxonomy 397 Yersinia enterocolitica 343–4, 397–403 antimicrobial sensitivities 403 characteristics of 403 clinical features 401 epidemiology 401 identification 402–3 serology 402 type III secretion system 398 Yersinia frederiksenii, characteristics of 403 Yersinia intermedia, characteristics of 403 Yersinia kristensenii, characteristics of 403 Yersinia pestis 343–5, 397–403 antimicrobial sensitivities 403 characteristics of 403 605 epidemiology 401 factors unique to 398 laboratory diagnosis 402 lipopolysaccharide (LPS) 399 pathogenicity 398 pathogenicity factors 398 serology 402 Yersinia pseudotuberculosis 343–4, 397–403 antimicrobial sensitivities 403 characteristics of 403 clinical features 401–2 epidemiology 393 identification 402–3 pathogenicity factors 398–9 Yersiniabactin 398 Yersiniae enteropathogenic 397 mouse-lethal 398 Yersiniosis 397 clinical features 401–2 laboratory diagnosis 402 Zoonotic infection 318 INDEX Q fever 457 clinical features 457–8 complement fixation (CF) assay 458 epidemiology 457–8 indirect fluorescent antibody (IFA) assay 458 laboratory diagnosis 458 microimmunofluorescence cut-off values 458 pathogenesis 457–8 prevention 459 serology 458 treatment 459 QRDR mutations 51 Quinolones in Bordetella 259 in brucellosis 295 in Chlamydia 325 in CONS 106 in GPAC 536 in H influenzae 249 in K kingae 195 in legionellae 452 in Mycobacterium intracellulare complex (MAIC) 174 in Nocardia infection 186 in Salmonella 373 in Shigella 359 in Yersiniosis 403 Quinupristin/dalfopristin in CONS 106 in Enterococcus 61, 64, 68 in listeriosis 135 in S mitis 34 Rabbit infectivity testing (RIT) 507 Ralstonia gilardii 440 Ralstonia mannitolilytica 440 Ralstonia paucula 440 Ralstonia pickettii 427, 440 Ralstonia solanacearum 437 Ramoplanin in enterococci 69 Random amplified polymorphic DNA (RAPD) analysis 131, 439, 558 Rapid growing mycobacteria 177–8 clinical features 177 disseminated cutaneous infection 178 disseminated disease 173 epidemiology 177 extrapulmonary disease 178 management of infection 178 pathology 177 pulmonary disease 178 pulmonary infection 174 wound infections 178 Reiter’s syndrome 321 Relapsing fever clinical manifestations 520 diagnosis 520 pathogenesis 520 Renal tuberculosis 161 Repetitive extragenic palindromic (REP) sequences 282 Respiratory tract infections 423 Restriction endonuclease analysis (REA) 562 Restriction fragment length polymorphism (RFLP) 153, 208, 258, 288, 291, 299, 435, 485, 488–9, 491, 508, 512, 538, 583 Reticulate body (RB) 318 Rhabdomyolysis 466 Rheumatic fever (RF) 11 Rhinoscleroma 378 Rhodococcus 186 Ribotyping 131 Rickettsia 285–92 culture/isolation 290–1 description of organisms 285 diagnostic criteria 290 direct detection of organisms 291–2 groups 285 immune mechanisms 292 immunofluorescence 291 laboratory diagnosis 288–90 molecular characterization 285 pathogenesis 285–6 prevention and control 292 primary isolation 290–1 propagation of isolates 291 serology 288–9 treatment 292 vaccine 292 Rickettsia akari 286, 290 Rickettsia australis 286 Rickettsia conorii 286, 290 Rickettsia japonica 286 Rickettsia prowazekii 286–8, 291 Rickettsia rickettsii 286–8, 290–2 spotted fever group (SFG) 286 Rickettsia siberica 286 Rickettsia typhi 286, 287, 288, 290–2 Rickettsiae, definition 285 Rickettsiales 285 classification 285 clinical and epidemiological features 286–8 diseases associated with 286 Rickettsialpox 287–8 Rifabutin in M haemophilum 178 in Mycobacterium intracellulare complex (MAIC) 173 Rifampicin in B cepacia 437 in C difficile 560 in Campylobacter 491 in Chlamydia 325 in Chryseobacterium 238 in CONS 106–7 in diphtheria 122 in H influenzae 249 in M kansasii 174 in M tuberculosis 164 in meningitis 51 in N meningitidis 216 in rapid growing mycobacteria 175 in S maltophilia 238 in S pneumoniae 51 in S pyogenes 15 in Serratia 384 in tuberculosis 164 Rifampin 154 in Bartonella 300 in brucellosis 300 in M haemophilum 178 Rifamycin in Mycobacterium intracellulare complex (MAIC) 174 Rochalimaea quintana 295 Rochalimaea vinsonii 295 Rocky Mountain spotted fever (RMSF) 286–7, 290–2 Rothia dentocariosa 187 RTX toxins 275 Ruminococcus 529 Saccharomyces boulardii 562–3 Saccharomyces cerevisiae 563 Salibacillus 139, 145 Salmonella 367–74 antigen detection 372 attenuation strategies 374 601 classification 367 clinical features 370–1 definitive identification 371–2 description of organism 367 infective dose 369 intracellular survival 368 isolation 371 laboratory diagnosis 371–2 molecular methods for detecting and typing 372 outbreaks in hospitals and institutions 369 pathogenicity 367 population structure 367 prevention and control 373 screening identification 371 serotypes 343–4 specimens 371 subspecies 367 treatment 372–3 treatment of chronic carriers 373 virulence plasmids 368 Salmonella bongori 367 Salmonella bovis-morbificans 369 Salmonella cholerasuis 368 Salmonella dublin 368 Salmonella enterica 367 Salmonella enteritidis 368–9 Salmonella enteritidis PT4 368–9 Salmonella enteritidis PT 6a 369 Salmonella gallinarum-pullorum 368 Salmonella paratyphi 371 Salmonella paratyphi A 371, 372 Salmonella pullorum 371 Salmonella sofia 369 Salmonella typhi 343–4, 367, 268–9 azithromycin in 373 epidemiology 368–70 natural history of infection 368 vaccination 373 virulence 368 Salmonella typhimurium 368 Salmonella virchow 368 Salmonellosis community outbreaks 370 food industry 374 hospital environment 374 non-typhoid 367–8 symptoms of 370 Salpingitis 223, 321 SARA 322, 326 Sarcina 529 Scalded skin syndrome 86 Scarlet fever 9–10 Scrub typhus 285 Sennetsu fever 288 SENTRY Antimicrobial Surveillance Programme 36 Septic arthritis 82, 84, 133 Septicaemia 534 Septicaemic plague 401 Serratia 383–4 antimicrobial susceptibility 384 biochemical characteristics 377 clinical features 384 description of organism 383 diagnosis 384 epidemiology 383–4 infections 383–4 normal habitat 383–4 pathogenicity 383 prevention 384 treatment 384 Serratia liquefaciens 343–4 Serratia marcescens 341–4, 383 Sexually acquired reactive arthritis 321–2 602 Sexually transmitted infections (STIs) 222, 223, 228, 351 Shigella 356–9 antimicrobial sensitivities 359 antimicrobial therapy 359 biochemical identification 356–7 classification 357 clinical features 358 description of organism 356–7 epidemiology 358 infection control 359–60 laboratory diagnosis 358 management of infection 359 oral rehydration therapy (ORT) 359 pathogenesis 357–8 safety 359 serogroups A, B and C 343–4 spread by personal contact 360 Shigella boydii 357 Shigella dysenteriae 352, 354, 356–9 biochemical reactions 357 identification 358–9 Shigella flexneri 350, 352, 356–8 Shigella sonnei 341, 343–4, 349, 356, 357, 358, 359, 360, 420 Shigellosis 358–9 vaccines 360 Shunt infections 62 Sinusitis 47, 52, 192, 248 Skin infections 430–1 Soft-tissue infections 87 Spectinomycin in Campylobacter 492 in N gonorrhoeae 226 Sphingobacterium mizutaii 234 Sphingobacterium multivorum 234 Sphingobacterium spiritivorum 234 Sphingobacterium thalpophilum 234 Sphingobacterium yabuuchiae 234 Sphingomonas paucimobilis 234 Sporadic zoonotic abortion 323 Sporosarcina ureae 139 Spotted fever group rickettsiae 289 Spotted fevers 287 Staphylococcal enterotoxin A (SEA) 75, 89 Staphylococcal enterotoxin B (SEB) 75, 89 Staphylococcal enterotoxin C (SEC) 75 Staphylococcal enterotoxins (SEs) 75 Staphylococcal food poisoning 83 Staphylococcal scalded skin syndrome (SSSS) 75, 76 Staphylococcal toxic shock syndrome (TSS) 75 Staphylococcus albus 73, 99, 101 Staphylococcus arlettae 101 Staphylococcus aureus 24, 60–1, 66, 73–89, 100, 102, 119, 557, 560 antibiotic prophylaxis 87–8 antibiotic resistance 80–4 antibiotic susceptibility testing 85 antimicrobial resistance 77 bacteremia 80–1 bacterial adhesins 74 bacterial determinants of infection 82 bacteriophages 80 biofilm formation 102 capsular serotypes 76 carriage patterns 81–2 cell membrane 74 cell morphology 73 cell–surface-associated adhesins 73–4 cell wall 73, 74 cellular components 76–7 clinical identifiers 83 clinical interpretation of cultures positive for 85 INDEX clinical manifestations 84, 86 clinical syndromes 82–3 colonization resistance 81 colony morphology 73, 84 cultural characteristics 73 description of organism 73–4 endocarditis 82 epidemiology 85 epidermolytic toxins (ETs) 75 eradication of carriage 88 extracellular components 76 extracellular proteases 76 extracellular toxins 75 gene expression 76–7 genetic elements 77 genetic exchange 77 genome sequence 75 growth characteristics 73 host factors 82 infection determinants 82 invasive disease 86–7 laboratory diagnosis 84–5 light microscopy 73 metabolism 73 mild skin and soft-tissue sepsis 87 newborn infants 82 pathogenicity 75–6 plasmids 78 prevention and control 87–8 reversible phenotypic switching 73 secreted adhesins 74–5 secreted components 74–5 small-colony variants (SCVs) 73 staining reactions 73 taxonomic history 73 toxin-mediated disease 86 toxins 76 treatment 83–6 typing techniques 85 vaccination 88 Staphylococcus auricularis 99–100 Staphylococcus capitis 99, 100, 102 Staphylococcus capitis subsp capitis 103 Staphylococcus capitis subsp ureolyticus 102 Staphylococcus caprae 99, 101 Staphylococcus carnosus 99, 101 Staphylococcus caseolyticus 101 Staphylococcus chromogenes 100 Staphylococcus coagulase-negative (CONS), see CONS Staphylococcus cohnii 99 Staphylococcus cohnii subsp cohnii 99 Staphylococcus epidermidis 76–7, 99–104, 147 Staphylococcus equorum 101 Staphylococcus gallinarum 101 Staphylococcus haemolyticus 99–100, 105–6 Staphylococcus hominis 99, 100 Staphylococcus hominis subsp hominis 100 Staphylococcus hominis subsp novobiosepticus 77 Staphylococcus hyicus 99–102 Staphylococcus intermedius 85, 99–100 Staphylococcus kloosii 101 Staphylococcus, laboratory characteristics 100–1 Staphylococcus lentus 101 Staphylococcus lugdunensis 85, 99, 101, 103 Staphylococcus pasteuri 99 Staphylococcus pyogenes 24, 99, 136 Staphylococcus saccharolyticus 100 Staphylococcus saprophyticus 99, 100, 102–3 Staphylococcus saprophyticus subsp saprophyticus 100 Staphylococcus schleiferi 99 Staphylococcus schleiferi subsp schleiferi 99 Staphylococcus sciuri 77, 101 Staphylococcus simulans 99–100 Staphylococcus warneri 99–100, 102–3 Staphylococcus xylosus 99, 101 Staphylokinase 76 Stenotrophomonas maltophilia 231, 234, 427, 440 bacteriological characteristics 239 habitat and pathogenicity 238 nosocomial infections 239 susceptibility/resistance to antibiotics 239 taxonomy 238–9 Sterne attenuated live spore vaccine 154–5 Streptococcal cysteine protease (SPEB) 16 Streptococcal diseases Streptococcal necrotising fasciitis Streptococcal pharyngitis 11, 15, 120 Streptococcal pyrogenic exotoxin A (SPEA) Streptococcal toxic shock syndrome (STSS) 8–10 clinical syndrome 10 consensus definition for diagnosis 10 Streptococci anginosus group 22–4, 26, 28–9 β-haemolytic 6–16 antimicrobial resistance 14–15 antimicrobial therapy 15 bacteremia caused by biochemical characteristics 12 burden of disease caused by clinical aspects of infection 8–11 clinical presentation of disease complications of superficial disease epidemiology 6–8 features of genomes genomics global trends in severe diseases caused by 7–8 immunologically mediated disease 11 infection 6–8 laboratory diagnosis and identification 11–14 nonsuppurative sequelae 11 overview pathogenesis 3–6 prevention and control 15–16 proteomics rapid identification assays 12 serological classification 12 severe disease caused by superficial infections 7–8 surgery 15 treatment strategies 15 typing 12–14 vaccines 15–16 virulence factors 3–6 see also Group A streptococcus (GAS); Group B streptococcus (GBS) bovis group 23 infections in immunocompromised patients 29 mitis group 23–5 mutans group 23–4 non-β-haemolytic 21–36 abscesses caused by 28–9 anginosus group 33 antibiotic susceptibility 34–6 bacteremia caused by 24 colonial morphology 30 current taxonomic status 21–3 description of organisms 21–3 differential biochemical characteristics 33 epidemiology 24 identification to species level 32–3 infections caused by 23–30 initial screening tests 30 laboratory diagnosis 30–4 mitis group 34 INDEX mutans group 35 salivarius group 34 serology 33–4 specimens and growth media 30 nutritionally variant (NVS) 23, 27 oral 23 phylogenetic relationships 22 salivarius group 23, 24, 26 sanguis group 23 see also Group A streptococcus (GAS); Group B streptococcus (GBS) Streptococcus differential characteristics of other genera 33 taxonomic revision 33 Streptococcus adjacens 23 Streptococcus agalactiae 3, 6, 11–12 Streptococcus alactolyticus 22 Streptococcus anginosus 21–2, 24, 25, 26, 28, 29 Streptococcus aureus 8, 15 Streptococcus bovis 22, 23, 26, 27, 31, 35, 36, 59 Streptococcus bovis/Streptococcus equinus complex 22–3, 35 Streptococcus canis 3, 6, 12 Streptococcus constellatus 22, 28–9 Streptococcus cricetus 21, 23, 35 Streptococcus crista 21, 23, 34 Streptococcus cristatus 21 Streptococcus defectivus 23 Streptococcus didelphis Streptococcus downei 21, 23, 35 Streptococcus dysgalactiae subsp equisimilis 3, 6, 11–12 Streptococcus equi subsp equi 3, 6, 11–12 Streptococcus equi subsp zooepidemicus 3, 11–12 Streptococcus equines 59 Streptococcus faecalis 59 Streptococcus faecalis var liquefaciens 60 Streptococcus faecalis var zymogenes 60 Streptococcus faecium 59 Streptococcus ferus 23 Streptococcus gallolyticus 23, 27, 35 Streptococcus gallolyticus subsp gallolyticus 22, 35 Streptococcus gallolyticus subsp macedonicus 22 Streptococcus gallolyticus subsp pasteurianus 22, 35 Streptococcus gordonii 21–3, 25–6, 34 Streptococcus hyovaginalis 23 Streptococcus infantarius 23, 35 Streptococcus infantarius subsp coli 22, 35 Streptococcus infantarius subsp infantarius 22, 35 Streptococcus infantarius subsp macedonicus 35 Streptococcus infantis 23 Streptococcus iniae Streptococcus intermedius 21–2, 25, 28, 31 Streptococcus macacae 21, 23, 35 Streptococcus macedonicus 22 Streptococcus milleri 22, 24, 34 Streptococcus mitis 21–4, 25–6, 29–31, 33, 34, 36 Streptococcus mutans 21, 23–4, 25, 26, 30, 31, 35 Streptococcus oralis 21, 23–4, 25, 26, 34, 36, 49 Streptococcus orisratti 21 Streptococcus parasanguinis 21 Streptococcus parasanguis 21, 23–6, 33, 42 Streptococcus peroris 21, 23 Streptococcus phoacae Streptococcus pneumoniae 14, 21, 26, 29, 41–54, 84, 248 adhesion 42 antigen detection 47 antimicrobial resistance rates 49 attachment 42 clinical syndromes 46–7 colonial appearance 41 culture 47 description of organism 41 differences between opaque and transparent phenotypes 42 disc susceptibility testing 47–8 epidemiology 46 Gram stain appearance 41 high-risk groups 46 history 41 immunopathology 45–6 incidence 247 inflammation and shock 44 invasion 43 laboratory diagnosis 47–52 laboratory identification 41 management 52 MIC determination 48 microscopy 47 multidrug-resistant 51–2 nonmeningeal infection 49 nucleic acid amplification 47–8 opacity 42 pathogenicity 41–6 phase variation 42 physiology 41 prevention and control 53–4 serotype distribution 46 susceptibility profiles 48–52 susceptibility testing 47–8 Streptococcus porcinus 3, 11–12 Streptococcus pyogenes 3, 8–9, 11–12, 14–16 Streptococcus rattus 23, 35 Streptococcus salivarius 21, 23, 30, 34 Streptococcus sanguinis 21 Streptococcus sanguis 21–4, 25–6, 29, 31, 34, 36, 42 Streptococcus sobrinus 21, 23, 35 Streptococcus suis 59 Streptococcus thermophilus 21, 23, 34 Streptococcus vestibularis 21, 23, 34 Streptococcus viridans 26 Streptogramins in Enterococcus 65 in Streptococcus pneumoniae 50 Streptolysin O (SLO) Streptolysin S (SLS) Streptomyces somaliensis 185 Streptomycin 282 in brucellosis 270 in Campylobacter 492 in endocarditis 66 in HLR strains 67 HLR to 64 in M tuberculosis 162 in plague 401 in tuberculosis 161 in Whipple’s disease 333 Streptothrix madurae 186 String test 424 Sulbactam in B pseudomallei 439 Sulfamethoxazole in Campylobacter 491 Sulfurospirillum 485 Sulphamethoxazole in B cepacia 437 in B pseudomallei 439 in Shigella 359 see also Trimethoprim-sulphamethoxazole Sulphonamides in Actinomyces 584 in B cereus 154 in Chlamydia 325–6 in Neisseria meningitidis 214 in Nocardia infection 186 in rapid growing mycobacteria 178 Sulphur granules, detection of 578 603 Superantigens (SAgs) 75 Suphamethoxazole in Alcaligenes 238–9 Surgical wounds 431 Syphilis 222, 503 clinical features 506 congenital 506 control 508–9 epidemiology 505–6 FTA-abs 507–8 and HIV infection 503 prevention 508–9 primary 506 secondary 506 treatment 508 see also Treponemes Systemic infections, mycoplasmas 309 Systemic inflammatory response syndrome (SIRS) 546–7 Tatlockia 445 Tazobactam in C difficile 561 in non-sporing Gram-negative anaerobes 553 Teichoic acid 74 Teicoplanin in CONS 106 in infective endocarditis 26 Tetanus laboratory diagnosis 561 pathogenesis 568 patient management 573 prevention 572 Tetracycline in A actinomycetemcomitans 273 in Acinetobacter 231 in Actinomyces 575 in Alcaligenes 231 in B cepacia 435 in B cereus 150 in B pseudomallei 427 in Bartonella 295 in brucellosis 265 in Campylobacter 485 in Chlamydia 317–18 in cholera 408 in CONS 106 in diphtheria 135 in E coli 356 in Enterococcus 65, 67–8 in H influenzae 245–50 in H pylori 473 in K kingae 191 in mycoplasmas 312–14 in N gonorrhoeae 221 in non-β-haemolytic streptococci 34 in non-sporing Gram-negative anaerobes 553 in Rickettsia 285 in Streptococcus pneumoniae 41, 48–9, 51 in Whipple’s disease 333 in Yersiniosis 401 Thayer–Martin medium 191 Thermobacillus 140 Ticarcillin in B cepacia 427 in C difficile 557 in P aeruginosa 427 in S maltophilia 231, 234 Tick infestations 292, 520 Tigecycline in S maltophilia 239 Tobramycin in S maltophilia 239 Toll-like receptors (TLRs) 82, 547 Toxic shock syndrome toxin-1 (TSST-1) 75, 83, 86 604 Toxin-coregulated pilus (TCP) 409–10 Toxin-mediated staphylococcal diseases 83 Toxoplasma gondii 184 Tracheal colonisation factor 254 Tracheal cytotoxin 254 Trachoma 314, 317 Trench fever 295, 297–8 Treponema carateum 503–4 Treponema denticola 504 Treponema pallidum 518 antigenicity 505–7 cultivation 504 description of organism 503–5 direct detection 507 epidemiology 505–6 immunoblots 508 laboratory diagnosis 507–8 microscopy 507 molecular biology 504–5 morphology 503 particle agglutination test (TPPA) 507 pathogenicity 505 phylogeny 504 physiology 504 rapid tests 508 response to treatment 508 serology 507 ultrastructure 504 Treponema pallidum subsp endemicum 503 Treponema pallidum subsp pallidum 504, 505 Treponema pallidum subsp pertenue 504 Treponematoses 503, 506 Treponemes 503–9 characteristics 503 oral 507 see also Syphilis Trichomonas vaginalis 309, 321 Trimethoprim in Alcaligenes 238–40 in B cepacia 437 in B cereus 154 in B pseudomallei 435 in C difficile 557 in Campylobacter 485 in E coli 356 in H influenzae 248–9 in K kingae 191 in M catarrhalis 191 in Proteeae 391 in Salmonella 367 in Shigella 356 in Streptococcus pneumoniae 48 Trimethoprim–sulphamethoxazole in B pseudomallei 437–8 in brucellosis 265 in cholera 407 in Nocardia infection 184 in S maltophilia 238 in Whipple’s disease 333 see also Sulphamethoxazole Tropheryma whipplei 329–37 description of organism 329–32 immunohistochemical study 329–32 molecular characterisation 330–3 morphology 329 phylogenic taxonomy 331 subspecies 332 see also Whipple’s disease TSS 83 Tsukamurella 183 Tsukamurella paurometabola 187 Tuberculides 157 INDEX Tuberculosis 159–67 antibiotic era 164 antibiotic resistance 164–5 control 166–7 directly observed therapy of short course (DOTS) strategy 164 drug-resistant 165 drug toxicity 165 endocrine consequences 161–2 epidemiology 160 histopathology 160 hospital infection control 166 incidence 159 initial assessment 166 integrated conventional and molecular diagnostic service 164 national infection control 166 pre-antibiotic era 164 smear-negative pulmonary 165–6 therapeutic regimen 164 treatment 164–6 vaccination in 166 see also Mycobacterium tuberculosis Tuberculosis lymphadenitis 161 Tuberculosis meningitis 161 Tularemia 281 glandular 282 infection 282 pneumonic 282 typhoidal 282 ulceroglandular 281 Tumour necrosis factor (TNF) 44, 349 Tumour necrosis factor-α (TNF-α) 4, 42, 44, 210, 319, 368 TWAR (Taiwan acute respiratory) strains 318 Typhoid clinical features 370–1 complications 370–1 differential diagnosis 370 incidence 368–9 laboratory diagnosis 371 Widal test for 372 Typhus 285 Uncomplicated gonococcal infection (UGI) 223 Ureaplasma 305, 306–14 Ureaplasma parvum 305–7 Ureaplasma urealyticum 305–7, 321 Ureibacillus 139–40 Ureidopenicillins in P aeruginosa 433 Urethritis 321 Urinary tract infection (UTI) 61, 99, 107, 231, 347–8, 431 Urogenital tract infections 308–9 Vaccination B anthracis 151, 154 β-haemolytic streptococcal disease 15–16 C difficile 563 Chlamydia 326 cholera 409–10 H pylori 473 leptospirosis 463 Lyme disease 511–13 M catarrhalis 193 meningococcal 210–11 P aeruginosa 428–9 pneumococcal 53 S aureus 88 S typhi 367 shigellosis 356 tuberculosis 166–7 Valinomycin 146 Vancomycin in B cereus 153 in C difficile 557 in Campylobacter 485 in CONS 99, 106–8 in Enterococcus 59, 61–2, 65, 154 in infective endocarditis 24–30 in K kingae 191 in S aureus 86–7 in S bovis 35 in S pneumoniae 41 in Veillonellae 538 Variable-number tandem repeat (VNTR) analysis 86 Vascular endothelial growth factor (VEGF) 297 VDRL test 507–8 Veillonella 537–8 Verocytotoxins (VT) 353–4 Verotoxins 353–4 Vibrio 407–16 definition 407–8 description of organism 407–8 disease syndromes associated with 407 identification 413–14 species found in human clinical specimens 413 taxonomy 407 see also Cholera Vibrio alginolyticus 407–8, 413 Vibrio carchariae 413 Vibrio cholerae 351, 407–16 colonisation 409, 411–12 detection 412 environmental control of virulence 410 human challenge studies 409 infective dose 409 isolation 412–13 non-O 413 non-O1 413 non-cholera 408 rapid identification 414 serotyping 414 transmission 408–9 typing 414 Vibrio cincinnatiensis 412–13 Vibrio damsela 407–8 Vibrio danisela 413 Vibrio fluvialis 408, 413 Vibrio furnissii 413 Vibrio hollisae 412, 413 Vibrio metschnikovii 407–8, 412–13 Vibrio mimicus 407, 411, 414 Vibrio parahaemolyticus 408, 411, 413–14 Vibrio subtilis 139 Vibrio vulnificus 407–8, 413 Vibrionaceae 407, 424 Vibriostatic test 424 Virgibacillus 139, 145 Virgibacillus pantothenticus 139 Viridans streptococci, differentiation from Gram-positive organisms 59 VITEK2 system 342 Weeksella virosa 234 Weeksella zoohelcum 234 Weil-Felix serologic test 287, 289 Whipple’s disease 329–37 antibiotic therapy 334 blood 335 cell cultures 336 cellular immunity 333 clinical features 334–5 diagnosis 335–7 electron microscopy diagnosis 335 epidemiology 333 ... crista S infantis S peroris S orisratti Sanguis groupb S sanguis S parasanguis S gordonii Salivarius group S salivarius S vestibularis S thermophilus Mutans group S mutans S sobrinus S rattus S. .. β-Haemolysis by Principles and Practice of Clinical Bacteriology Second Edition © 2006 John Wiley & Sons, Ltd Anginosus group S anginosus S constellatus S intermedius Mitis group S mitis S oralis S. .. dysgalactiae subsp equisimilis is considered a less pathogenic species than GAS but is a relatively common cause of similar superficial disease and may also be associated with invasive disease of the