Infectious Disease For further volumes: http://www.springer.com/series/7646 Ivano de Filippis Marian L. McKee ● Editors Molecular Typing in Bacterial Infections Editors Ivano de Filippis Marian L. McKee Instituto Nacional de Controle de BioReliance Corporation Qualidade em Saúde Rockville, MD Fundação Oswaldo Cruz (FIOCRUZ) USA Rio de Janeiro Brazil ISBN 978-1-62703-184-4 ISBN 978-1-62703-185-1 (eBook) DOI 10.1007/978-1-62703-185-1 Springer NewYork Heidelberg Dordrecht London Library of Congress Control Number: 2012950050 © Springer Science+Business Media New York 2013 This work is subject to copyright. 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Printed on acid-free paper Humana Press is a brand of Springer Springer is part of Springer Science+Business Media (www.springer.com) Contents Part I General Consideration on Microorganism Typing Methods 1 Molecular Epidemiology ....................................................................... 3 Amy E. Seitz and D. Rebecca Prevots Part II Gastrointestinal Pathogens 2 Enterococcus ........................................................................................... 17 Lucia Martins Teixeira and Vânia Lúcia Carreira Merquior 3 Listeria monocytogenes........................................................................... 27 Todd J. Ward 4 Enterobacteriaceae................................................................................. 39 Steven L. Foley, Aaron M. Lynne, and Rajesh Nayak 5 Molecular Typing of Vibrio cholerae: Imprints in the Epidemiology of Cholera ............................................................ 53 T. Ramamurthy, A.K. Mukhopadhyay, R.K. Nandy, and G. Balakrish Nair 6 Molecular Typing of Clostridium dif fi cile ............................................. 73 Andrej Weintraub and Carl Erik Nord 7 Oral and Intestinal Bacteroidetes ......................................................... 87 Marina C. Claros and Georg Conrads Part III Oral and Respiratory Pathogens 8 Streptococci............................................................................................. 109 Lesley McGee and Bernard Beall v vi Contents 9 Molecular Typing of Streptococcus mutans ......................................... 127 Kazuhiko Nakano, Ichiro Nakagawa, Satu Alaluusua, and Takashi Ooshima 10 Genotyping of Periodontal Anaerobic Bacteria in Relationship to Pathogenesis ............................................................ 149 Masae Kuboniwa and Atsuo Amano 11 Molecular Typing of Nontuberculous Mycobacteria .......................... 167 Jakko van Ingen and Dick van Soolingen 12 Molecular Typing of Neisseria meningitidis ......................................... 179 Muhamed-Kheir Taha and Ala-Eddine Deghmane 13 Molecular Typing in Bacterial Infections Haemophilus spp. ............ 193 Marina Cerquetti 14 Moraxella ................................................................................................ 211 Nevada M. Pingault and Thomas V. Riley 15 Legionella pneumophila Typing ............................................................ 221 Christophe Ginevra 16 Mycoplasma and Ureaplasma ............................................................... 229 Ken B. Waites, Li Xiao, Vanya Paralanov, Rose M. Viscardi, and John I. Glass 17 Corynebacterium diphtheriae ................................................................. 283 Igor Mokrousov 18 Burkholderia ........................................................................................... 301 Pavel Drevinek and Eshwar Mahenthiralingam Part IV Urogenital Pathogens 19 Treponema ............................................................................................... 311 Allan Pillay 20 Chlamydiaceae ....................................................................................... 327 Troy Skwor and Deborah Dean Part V Vector Borne Pathogens 21 Borreliae .................................................................................................. 353 Dionysios Liveris, Klára Hanincová, and Ira Schwartz 22 Erysipelothrix .......................................................................................... 371 Yumiko Imada Contents vii Part VI Pathogens Causing Healthcare-Associated Infection 23 Staphylococci .......................................................................................... 385 Jodi A. Lindsay 24 Molecular Typing Methods for the Genus Pseudomonas ................... 407 Balázs Libisch Part VII Emerging and Re-emerging Pathogens 25 Acinetobacter baumannii ........................................................................ 433 Lenie Dijkshoorn 26 Molecular Typing of Coxiella burnetii: A Review of Available Methods with Major Focus on PCR-Based Techniques ..................... 457 V. Boldis, E. Spitalska, and R. Toman Index ................................................................................................................ 471 Contributors Satu Alaluusua Department of Pediatric and Preventive Dentistry, Institute of Dentistry , University of Helsinki and Department of Oral and Maxillofacial Diseases , Helsinki University Central Hospital , Helsinki, Finland Atsuo Amano Department of Preventive Dentistry , Osaka University Graduate School of Dentistry , Suita , Osaka , Japan Bernard Beall Respiratory Diseases Branch , Division Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention , Atlanta , GA , USA V. Boldis HPL Medical Laboratories, Bratislava, Slovak Republic Marina Cerquetti Department of Infectious, Parasitic and Immune-mediated Diseases , Istituto Superiore di Sanità , Rome , Italy Marina C. Claros Institute of Medical Microbiology and Infectious Epidemiology (at time of experiments) , University of Leipzig , Leipzig , Germany Georg Conrads Division of Oral Microbiology and Immunology, Department of Operative and Preventive Dentistry & Periodontology , RWTH Aachen University Hospital , Aachen , Germany Department of Medical Microbiology , RWTH Aachen University Hospital , Aachen , Germany Deborah Dean Children’s Hospital Oakland Research Institute , Oakland , CA , USA University of California at San Francisco School of Medicine , San Francisco , CA , USA University of California at Berkeley , Berkeley , CA , USA ix x Contributors Ala-Eddine Deghmane Unit of Invasive Bacterial Infection and National Reference Centre for Meningococci, Institut Pasteur, Paris, France Lenie Dijkshoorn Department of Infectious Diseases C5-P , Leiden University Medical Center , Leiden , The Netherlands Pavel Drevinek Department of Medical Microbiology and Department of Pediatrics , 2nd Faculty of Medicine , Charles University , Prague, Czech Republic Steven L. Foley Division of Microbiology , National Center for Toxicological Research, U.S. Food and Drug Administration , Jefferson , AR , USA Christophe Ginevra Laboratoire pathogénie bactérienne et immunité innée, Université Lyon 1, Faculté de médecine Lyon est , INSERM U851, Centre national de référence des légionelles , Hospices civils de Lyon , Lyon, France John I. Glass J. Craig Venter Institute , Rockville , MD , USA Klára Hanincová Department of Microbiology and Immunology , New York Medical College , Valhalla , NY , USA Yumiko Imada Center for Animal Disease Control and Prevention, National Institute of Animal Health , Tsukuba , Ibaraki , Japan Jakko van Ingen Department of Clinical Microbiology , Radboud University Nijmegen Medical Center , Nijmegen , The Netherlands Masae Kuboniwa Department of Preventive Dentistry , Osaka University Graduate School of Dentistry , Suita , Osaka , Japan Balázs Libisch Laboratory of Microbiology , Research Institute for Soil Science of the Hungarian Academy of Sciences , Budapest , Hungary Jodi A. Lindsay Infection and Immunity , Division of Clinical Sciences , St George’s, University of London, London , UK Dionysios Liveris Department of Microbiology and Immunology , New York Medical College , Valhalla , NY , USA Aaron M. Lynne Department of Biological Sciences , Sam Houston State University , Huntsville , TX , USA Eshwar Mahenthiralingam Cardiff School of Bioscience, Cardiff University , Cardiff , UK Lesley McGee Respiratory Diseases Branch, Division Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention , Atlanta , GA , USA Vânia Lúcia Carreira Merquior Departamento Microbiologia, Imunologia e Parasitologia , Universidade do Estado do Rio de Janeiro , Rio de Janeiro , RJ , Brazil