European Manual of Clinical Microbiology
Transcription
European Manual of Clinical Microbiology
European Manual of Clinical Microbiology 1st Edition EMCM The Editors thank the financial support of Companies to allow the achievement of this manual. However, the members of the editorial board have disclosed any potentially relevant conflicts of interest likely to prejudice the data published in this book or inconsistent with the objectives of the ESCMID and the SFM. 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 or otherwise, without the prior permission of the Publishers, the European Society for Clinical Microbiology and Infectious Diseases (Basel) or the Société Française de Microbiologie (Paris). No responsibility is assumed by the Publishers for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions or ideas contained in the material herein. Because of the rapid advances in the medical sciences, the Publishers recommend that independent verification of diagnoses and drug should be made. La Loi du 11 mars 1957 interdit les copies ou reproductions destinées à une utilisation collective. Toute représentation ou reproduction intégrale ou partielle faite par quelque procédé que ce soit, sans le consentement de l’auteur ou ses ayants droits, est illicite et constitue une contrefaçon sanctionnée par les articles 425 et suivants du Code Pénal. ISBN: 978-2-87805-026-4 Editorial Let’s go European! Giuseppe Cornaglia René J. Courcol From a French handbook to a European manual: This was the challenge met (and won) in less than one year by the Editorial Board of and all those contributing to the European Manual of Clinical Microbiology. Early in 2011, the Presidents of the European Society for Clinical Microbiology and Infectious Diseases and of the Société Française de Microbiologie, decided to publish a text of clinical microbiology. The template for this would be the widely popular French REMIC, which non-French authors would adapt and integrate in accordance with ‘European’ practices and the European body of knowledge. A number of microbiologists gathered at the ECCMID in Milano agreed to take on this challenge. This new book, contains contributions by nearly one hundred experienced medical microbiologists, and is mainly intended for all those involved in medical microbiology. However, its style makes it suitable for clinicians, too, and as a reference test for residents and students. Diagnostic schemes and recommendations spring from the professional experience of internationally-recognised authors, and make large use of guidelines and consensus documents published by several international societies. This is but the first edition of the Manual, and, like all books, it is incomplete and not sufficiently up-to-date at the time of going to press. Future editions - possibly available in electronic format as well - will draw on an even broader participation of microbiologists from all over Europe, as well as on precious feedbacks of readers throughout Europe and beyond. Editors Giuseppe Cornaglia Professor of Microbiology Department of Pathology and Diagnostics; University of Verona Verona, Italy [email protected] René Courcol Professor of Bacteriology Laboratoire de Bactériologie-Hygiène, Institut de Microbiologie, Centre Hospitalier Universitaire; Université de Lille 2 Lille, France [email protected] Jean-Louis Herrmann Professor of Bacteriology Laboratoire de Microbiologie, Hôpital Raymond Poincaré, Assistance Publique-Hôpitaux de Paris; Université Versailles-St Quentin Garches, France [email protected] Gunnar Kahlmeter Professor of Microbiology Clinical Microbiology, Central Hospital Växjö, Sweden [email protected] Hélène Peigue-Lafeuille Professor of Virology Centre Hospitalier Universitaire, Laboratoire de Virologie ; Université d’Auvergne Clermont-Ferrand, France [email protected] Jordi Vila Professor of Microbiology Department of Clinical Microbiology Hospital Clinic, School of Medicine, University of Barcelona, Barcelona Centre for International Health Research, CRESIB Villarroel Barcelona, Spain [email protected] Contributors M. Aigner Department of Hygiene, Microbiology and Social Medicine, Division of Hygiene and Medical Microbiology Innsbruck, Austria Guido Antonelli Laboratory of Virology - Department of Molecular Medicine – Sapienza University Roma, Italy [email protected] Javier Ariza Infectious Diseases Department, Hospital Universitari de Bellvitge, IDIBELL Barcelona; Spain [email protected] Bertille de Barbeyrac Centre National de Référence des Chlamydiae; Université Victor Ségalen Bordeaux II Bordeaux, France [email protected] Fernando Baquero Department of Microbiology, Ramón y Cajal University Hospital (SERMAS), Ramón y Cajal Institute for Health Research (IRYCIS), and Network Research Centre for Epidemiology and Public Health (CIBERESP). Madrid, Spain [email protected] Paul Bates Chair in Biomedicine, Faculty of Health and Medicine, Lancaster University Lancaster, United Kingdom [email protected] Patrick Boiron Centre d’Ecologie Microbienne, bactéries opportunistes, Observatoire des Nocardioses ; Faculté de Pharmacie, Université de Lyon Lyon, France [email protected] Stéphane Bonacorsi Laboratoire de Microbiologie, Hôpital Robert Debré, Assistance Publique-Hôpitaux de Paris; Université Paris Diderot Paris, France [email protected] Richard Bonnet Laboratoire de Bactériologie, Centre Hospitalier Universitaire; Université d’Auvergne Clermont-Ferrand, France [email protected] Tristan Bourcier Service d’Opthalmologie, Nouvel Hôpital Civil ; Université de Strasbourg Strasbourg, France [email protected] Emilio Bouza Dept. of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Universidad Complutense Madrid, Spain [email protected] Françoise Brun-Vezinet Département de Microbiologie, Laboratoire de Virologie, Hôpital Bichat, Assistance PubliqueHôpitaux de Paris ; Université Paris 7 Paris, France [email protected] Almudena Burillo Dept. of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Universidad Complutense Madrid, Spain [email protected] Christophe Burucoa Laboratoire de Bactériologie, Centre Hospitalier Universitaire; Université de Poitiers Poitiers, France [email protected] Dominique de Briel Département de Microbiologie, Hôpitaux Civils de Colmar Colmar, France [email protected] Rafael Canton Servicio de Microbiologıa and CIBERESP, Hospital Universitario Ramon y Cajal, Instituto Ramon y Cajal de Investigacion Sanitaria Madrid, Spain [email protected] Maria R. Capobianchi National Institute for Infectious Diseases “L. Spallanzani” Roma, Italy [email protected] Etienne Carbonnelle Service de Microbiologie, Hôpital Européen Georges Pompidou, Assistance PubliqueHôpitaux de Paris ; Université Pierre et Marie Curie Paris, France [email protected] Francesco Castelli Chair of Infectious Diseases, University of Brescia Brescia, Italy [email protected] Concetta Castilletti Laboratory of Virology, National Institute for Infectious Diseases “L. Spallanzani” Roma, Italy [email protected] Jean-Didier Cavallo Service de Santé des Armées Ecole du Val-de-Grâce Paris, France [email protected] Stéphane Chevaliez Centre National de Référence Coordonnateur des hépatites des virus B, C et Delta. Service de bactériologie-virologie-hygiène, Groupe Hospitalier Henri Mondor ; Assistance PubliqueHôpitaux de Paris. Université Paris Est. Créteil, France. [email protected] Massimo Clementi Laboratory of Microbiology and Virology, Università Vita-Salute San Raffaele, Milano. Milano, Italy. [email protected] Jan Clerinx Department of Clinical Sciences, Institute of Tropical Medicine Antwerp (ITMA) Antwerp, Belgium [email protected] Stéphane Corvec Service de Bactériologie-Hygiène, Institut de Biologie des Hôpitaux de Nantes, Centre Hospitalier Universitaire ; Université de Nantes Nantes, France [email protected] Giovanni Delogu Istituto di Microbiologica, Università Cattolica del Sacro Cuore Roma, Italy [email protected] Emmanuel Dutoit Laboratoire de Parasitologie-Mycologie, Institut de Microbiologie, Centre Hospitalier Universitaire; Université de Lille 2 Lille, France [email protected] Matthew Dryden Royal Hampshire Hospital Winchester, United Kingdom [email protected] Luc Dubreuil Laboratoire de Bactériologie, Faculté de Pharmacie, Université de Lille 2 Lille, France [email protected] Johan van Eldere Laboratory of Experimental Bacteriology, Department of Medical Diagnostics, University Hospital Leuven Leuven, Belgium [email protected] Heinz Ellerbrok Robert Koch-Institute, Centre for Biological Safety Berlin, Germany [email protected] Önder Ergönül Department of Clinical Microbiology and Infectious Disease, Ankara University, School of Medicine Ankara, Turkey [email protected] Birgitta Evengard Dept. Clinical Microbiology, Umeå University Umeå, Sweden [email protected] Pieter LA Fraaij Department of Virology, Erasmus Medical Center Rotterdam, The Netherlands [email protected] François Freymuth Laboratoire de Virologie, Centre Hospitalier Universitaire Côte de Nacre ; Université de Caen Caen, France [email protected] Antoine Garbarg-Chenon Service de Microbiologie, Hôpital ArmandTrousseau, Assistance Publique-Hôpitaux de Paris; Université Pierre et Marie Curie Paris, France [email protected] Christian Giske Clinical Microbiology, Karolinska Institutet–MTC, Karolinska University Hospital, Solna, Stockholm,Sweden [email protected] Gilbert Greub Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, University Hospital Center and University of Lausanne Lausanne, Switzerland [email protected] Margareta Ieven Department of Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp Antwerp, Belgium. [email protected] Benoît Jaulhac Laboratoire de Bactériologie, Hôpital Universitaire ; Centre National de Référence des Borrelia ; Université Louis Pasteur Strasbourg, France [email protected] Per Juto Clinic Clinical Virology, Umeå University Umeå, Sweden. Yamina Kabrane [email protected] Ingegerd Kallings Department of Bacteriology, Swedish Institute for Infectious Disease Control Stockholm, Sweden [email protected] Laetitia M. Kortbeek Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment Bilthoven, The Netherlands [email protected] Brigitte Lamy Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier ; Université de Montpellier Montpellier, France [email protected] Philippe Lanotte Université François-Rabelais de Tours, UFR de Médecine Tours, France [email protected] Cornelia Lass-Flörl Department of Hygiene, Microbiology and Social Medicine, Division of Hygiene and Medical Microbiology, Innsbruck Medical University. Innsbruck, Austria [email protected] Patrice Laudat Laboratoire Arnaud Tours, France [email protected] Jean-Philippe Lavigne Laboratoire de Bactériologie, Groupe HospitaloUniversitaire de Carémeau; Université Montpellier 1 Nîmes, France [email protected] Christine Lawrence Laboratoire de Microbiologie, Hôpital Raymond Poincaré, Assistance Publique-Hôpitaux de Paris [email protected] Jacques Le Bras Laboratoire de Parasitologie, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris ; Université Paris Descartes Paris, France [email protected] Roland Leclercq Laboratoire de Microbiologie, Centre Hospitalier Universitaire Côte de Nacre ; Université de Caen Caen, France [email protected] Veerle Lejon Department of Clinical Sciences, Institute of Tropical Medicine Antwerp (ITMA) Antwerp, Belgium [email protected] Alban Le Monnier Centre National de Référence des Listeria, Institut Pasteur Paris, France [email protected] Isabelle Leparc-Goffart Institut de Recherches Biomédicales des Armées – Antenne de Marseille Centre National de Référence des Arbovirus Marseille, France [email protected] Audrey Mérens Service de biologie médicale, Hôpital d’instruction des Armées-Bégin Saint-Mandé, France [email protected] Marcelle Mounier Pôle de Biologie-Hygiène, Centre Hospitalier Universitaire, Limoges; Université de Limoges Limoges, France [email protected] Elisabeth Nagy Institute of Clinical Microbiology, University of Szeged Szeged, Hungary [email protected] Gérard Lina Centre National de Référence des Staphylocoques, Hospices Civils de Lyon; Université Lyon 1 Lyon, France [email protected] Olav B Natås Department of Medical Microbiology, Stavanger University Hospital Stavanger, Norway [email protected] Caroline Loïez Laboratoire de Bactériologie-Hygiène, Institut de Microbiologie, Centre Hospitalier Universitaire Lille, France [email protected] Maria-Mercedes Nogueras Mas [email protected] Anton van Loon Department of Virology, Medical Microbiology, University Medical Center Utrecht, The Netherlands [email protected] Nino Manca Institute of Microbiology and Virology, Spedali Civili, University of Brescia Brescia, Italy Luis Martinez-Martinez Department of Molecular Biology, University of Cantabria and University Hospital Marqués de Valdecilla-IFIMAV Santander, Spain [email protected] Max Maurin Département de Microbiologie Clinique, Centre Hospitalier Universitaire; Université Joseph Fourier Grenoble, France [email protected] Francis Mégraud Centre National de Référence des Campylobacter et Helicobacter; Université Victor Ségalen Bordeaux II Bordeaux, France [email protected] Albert D.M.E. Osterhaus Department of Virology, Erasmus Medical Center Rotterdam, The Netherlands [email protected] Tibor Pal Department of Medical Microbiology, Faculty of Medicine and Health Sciences, United Arab Emirates University Al-Ain, United Arab Emirates [email protected] Alvaro Pascual Department of Microbiology, University Hospital Virgen Macarena, and University of Seville Seville, Spain [email protected] Jean-Michel Pawlotsky Centre National de Référence Coordonnateur des hépatites des virus B, C et Delta. Service de bactériologie-virologie-hygiène, Groupe Hospitalier Henri Mondor ; Assistance PubliqueHôpitaux de Paris. Université Paris Est. Créteil, France [email protected] Agnès Perrin Service de Gestion du Risque Infectieux et des Vigilances, Centre Hospitalier Universitaire Lille, France [email protected] Mathieu Picardeau Institut Pasteur, Unité de Biologie des Spirochètes, Centre de Référence des Leptospires, Centre Collaborateur OMS pour l’Epidémiologie des Leptospires Paris, France [email protected] Mario Poljak Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia [email protected] Maria Eugenia Portillo Microbiology Laboratory, Reference Laboratory of Catalunya Barcelona, Spain [email protected] Claire Poyart Centre National de Référence des Streptocoques, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris ; Université Paris Descartes Paris, France [email protected] Tomàs Pumarola Service of Microbiology, Hospital Clinic, Barcelona-CRESIB Barcelona, Spain [email protected] Caroline Rambaud Service de Médecine Légale, Hôpital Raymond Poincaré, Assistance Publique-Hôpitaux de Paris; Université Versailles-St Quentin Garches, France [email protected] Didier Raoult Laboratoire de Bactériologie, Unité des Rickettsies, Assistance Publique-Hôpitaux de Marseille ; Université de la Méditerranée Marseille, France [email protected] Philippe Riegel Laboratoire de Bactériologie, Centre Hospitalier Universitaire; Université Louis Pasteur Strasbourg, France [email protected] Jérôme Robert Laboratoire de Bactériologie-Hygiène, Hôpital La Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris; Université Pierre et Marie Curie Paris, France [email protected] Anne-Laure Roux Laboratoire de Microbiologie, Hôpital Raymond Poincaré, Assistance Publique-Hôpitaux de Paris; Université Versailles-St Quentin Garches, France [email protected] Martin Rottman Laboratoire de Microbiologie, Hôpital Raymond Poincaré, Assistance Publique-Hôpitaux de Paris ; Université Versailles-St Quentin Garches, France [email protected] Eva Ružić-Sabljić Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia [email protected] Veroniek Saegeman Department of Laboratory Medicine, UH-KULeuven, Leuven, Belgium [email protected] Christine Segonds Laboratoire de Bactériologie-Hygiène, Institut Fédératif de Biologie, Hôpital Purpan, Centre Hospitalier Universitaire Toulouse, France [email protected] Ferran Segura Porta Infectious Diseases Healthcare Programme, Corporació Sanitaria Parc Taulí, Sabadell Barcelona, Spain [email protected] Harald Seifert Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany [email protected] Jean-Marie Seigneurin Département de Microbiologie Clinique, Centre Hospitalier Universitaire ; Université Joseph Fourier Grenoble, France [email protected] Katja Seme Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia [email protected] Boualem Sendid Laboratoire de Parasitologie-Mycologie, Institut de Microbiologie, Centre Hospitalier Universitaire; Université de Lille 2 Lille, France [email protected] Kathrine Summermatter Institute of Virology and Immunoprophylaxis (IVI) Mittelhaeusern, Switzerland [email protected] Peter Tenke Department of Urology, South-Pest Hospital Budapest, Hungary [email protected] Andrej Trampuz Infectious Diseases Service, Department of Internal Medicine, University Hospital of Lausanne Lausanne, Switzerland [email protected] Riccardo Utili Unita di Medicina Infettivologica e dei Trapianti, Seconda Universita degli studi di Napoli, Ospedale Monaldi Napoli, Italy [email protected] Martin Schutten Erasmus Medical Center, Department of Virology Rotterdam, The Netherlands [email protected] Jorgen Skov-Jensen Statens Serum Institute, Mycoplasma Laboratory Copenhagen, Denmark [email protected] Hoang Vu-Thien Service de Microbiologie, Hôpital ArmandTrousseau, Assistance Publique-Hôpitaux de Paris; Université Pierre et Marie Curie Paris, France [email protected] Anne Bianchi Centre National de Référence de la Syphilis Paris, France [email protected] Anne Bouvet Centre National de Référence des Streptocoques, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris ; Université Paris Descartes Paris, France [email protected] Emmanuelle Cambau Laboratoire de Bactériologie, Groupe Hospitalier Saint Louis-Lariboisière-Fernand Widal, Assistance Publique-Hôpitaux de Paris; Université Paris Diderot [email protected] Christine Chaumeil Laboratoire de Microbiologie, Fédération des Maladies infectieuses oculaires, Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts Paris, France [email protected] Jean-Marie Delarbre Laboratoire de Microbiologie, Centre Hospitalier Mulhouse, France [email protected] Agnès Ferroni Laboratoire de Microbiologie, Hôpital Necker, Assistance Publique-Hôpitaux de Paris; Université Paris Descartes Paris, France [email protected] Frédéric Wallet Laboratoire de Bactériologie-Hygiène, Institut de Microbiologie, Centre Hospitalier Universitaire Lille, France [email protected] Jean-Louis Gaillard Laboratoire de Microbiologie-Hygiène, Hôpital Ambroise Paré, Assistance Publique-Hôpitaux de Paris; Université Versailles-St Quentin Boulogne-sur-Seine, France [email protected] Wolfgang Witte Robert Koch Institute, Wernigerode Branch Wernigerode, Germany [email protected] Daniel Garin Institut de Recherche Biomédicales des Armées Grenoble, France [email protected] Bengt Wretlind Dept of Clinical Microbiology, Karolinska Institutet at Karolinska University Hospital Huddinge Stockholm, Sweden [email protected] Associate Contributors Henri Agut Laboratoire de Virologie, Hôpital La PitiéSalpêtrière, Assistance Publique- Hôpitaux de Paris ; Université Pierre et Marie Curie Paris, France [email protected] Vinent Jarlier Laboratoire de Bactériologie-Hygiène, Hôpital La Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris; Université Pierre et Marie Curie Paris, France [email protected] Bernard La Scola Laboratoire de Bactériologie, Unité des Rickettsies, Assistance Publique-Hôpitaux de Marseille ; Université de la Méditerranée Marseille, France [email protected] Jean-Christophe Lucet Hôpital Bichat, Assistance Publique-Hôpitaux de Paris; Université Pierre et Marie Curie Paris, France [email protected] Jean-Luc Mainardi Service de Microbiologie, Hôpital Européen Georges Pompidou, Assistance PubliqueHôpitaux de Paris; Université Pierre et Marie Curie Paris, France [email protected] Catherine Neuwirth Laboratoire de Bactériologie, Centre Hospitalier Universitaire; Université de Dijon Dijon, France [email protected] Béatrice Pangon Laboratoire de Microbiologie, Centre Hospitalier de Versailles Le Chesnay, France [email protected] Michèle Pérouse de Montclos Laboratoire de Bactériologie, Centre Hospitalier Lyon Sud Pierre-Bénite, France [email protected] Michel Simonet Laboratoire de Bactériologie-Hygiène, Institut de Microbiologie, Centre Hospitalier Universitaire; Université de Lille 2 Lille, France [email protected] Ousmane Traore Service d’Hygiène Hospitalière, Centre Hospitalier Universitaire; Université d’Auvergne Clermont-Ferrand, France [email protected] Table of contents GENERAL CLINICAL MICROBIOLOGY Gastroenteritis.....................................171 Clinical microbiology: a future based on tradition.............................................17 Sexually transmitted infections............181 The principles of microbiological: work and good laboratory practices.....21 Ocular infections.................................203 MALDI-TOF in microbiology..................31 Molecular methods in microbiology......37 Beyond culturing in microbiology..........49 Bacteria in purulent and serous fluids...197 Cutaneous infections...........................215 Dermatophytes in skin, nails and hair...223 Bone and joint infections.....................227 The diabetic foot..................................235 Quality management in microbiology....59 Perinatal infections..............................241 Round-the-clock services in microbiology......................................69 Infections in burn patients...................251 Antimicrobial susceptibility testing........77 Microbiological examination of postmortem samples.......................255 Transportation of biological samples - International regulations......................87 SPECIFIC MICROORGANISMS MICROBIOLOGICAL DIAGNOSIS Septicemia...........................................101 Endocarditis........................................111 Catheter-related infections..................115 Anaerobes...........................................261 Borrelia burgdorferi sensu lato............271 Brucella species..................................277 Helicobacter pylori..............................283 Leptospira species..............................287 Central nervous system infections......123 Listeria monocytogenes......................291 Urinary tract infections........................133 Mycobacterium species......................297 Upper respiratory tract infections........145 Rickettsia and related bacteria...........309 Lower respiratory tract infections........153 Arboviruses.........................................315 Pulmonary infections in cystic fibrosis...163 Hepatitis virus.........................................327 Human Immunodeficiency Virus (HIV)...343 Influenza virus.....................................363 Viruses in hemorragic fevers...............369 Leishmania species.............................381 Plasmodium species...........................389 Trypanosoma species.........................399 EPIDEMIOLOGY AND INFECTION CONTROL Antimicrobial resistance surveillance..411 Screening for multidrug-resistant bacteria in health care setting...........................421 Laboratory hygiene and safety...........427 Microbiology of the health care environment............437 Molecular tools for epidemiology........445 Public health microbiology..................455 The risk of bioterrorism and class 3 microorganisms...............461