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Clinical Infectious Diseases Emerging Concepts and Strategies in Clinical Microbiology and Infectious Diseases Guest Editors: Didier Raoult, MD, PhD Fernando Baquero, MD, PhD This supplement was sponsored by the Fondation Méditerranée Infection (FMI). Cover Image: View of the new Méditerranée Infection building in Marseille, France. Photograph by Oleg Mediannikov © Oleg Mediannikov. The opinions expressed in this publication are those of the authors and are not attributable to the sponsors or to the publisher, editor, or editorial board of Clinical Infectious Diseases. Articles may refer to uses of drugs or dosages for periods of time, for indication, or in combinations not included in the current prescribing information. The reader is therefore urged to check the full prescribing information for each drug for the recommended indications, dosage, and precautions and to use clinical judgment in weighing benefits against risk of toxicity. MARCH20176513 15 August 2017 Volume 65 Clinical Infectious Diseases Supplement 1 The title Clinical Infectious Diseases is a registered trademark of the IDSA EMERGING CONCEPTS AND STRATEGIES IN CLINICAL MICROBIOLOGY AND INFECTIOUS DISEASES S1 Rewiring Microbiology and Infection S55 A Hospital-Based Committee of Moral Philosophy Didier Raoult and Fernando Baquero to Revive Ethics Margaux Illy, Pierre Le Coz, and Jean-Louis Mege S4 Building an Intelligent Hospital to Fight Contagion S58 Evaluating the Clinical Burden and Mortality Jérôme Bataille and Philippe Brouqui Attributable to Antibiotic Resistance: The Disparity of Empirical Data and Simple Model S12 From Expert Protocols to Standardized Estimations Management of Infectious Diseases Cédric Abat, Jean-Marc Rolain, Grégory Dubourg, Jean-Christophe Lagier, Camille Aubry, Marion Delord, Pierre Michelet, Pierre-Edouard Fournier, Hervé Chaudet, and Didier Raoult Hervé Tissot-Dupont, Matthieu Million, Philippe Brouqui, Didier Raoult, and Philippe Parola S64 Developing Research in Infectious and Tropical Diseases in Africa: The Paradigm of Senegal S20 Many More Microbes in Humans: Enlarging the Cheikh Sokhna, Oumar Gaye, and Ogobara Doumbo Microbiome Repertoire Jean-Christophe Lagier, Michel Drancourt, Rémi Charrel, Fadi Bittar, S70 Place of International Congresses in the Diffusion Bernard La Scola, Stéphane Ranque, and Didier Raoult of Knowledge in Infectious Diseases Britta Lassmann and Giuseppe Cornaglia S30 Medical Entomology: A Reemerging Field of Research to Better Understand Vector-Borne S74 Viruses in the 21st Century: From the Infectious Diseases Curiosity-Driven Discovery of Giant Viruses to Maureen Laroche, Jean-Michel Bérenger, Pascal Delaunay, Remi Charrel, Bruno Pradines, Franck Berger, Stéphane Ranque, Idir Bitam, New Concepts and Definition of Life Bernard Davoust, Didier Raoult, and Philippe Parola Patrick Forterre S39 New Laboratory Tools for Emerging Bacterial S80 Basic Sciences Fertilizing Clinical Microbiology Challenges and Infection Management Pierre-Edouard Fournier, Michel Drancourt, and Didier Raoult Fernando Baquero S50 New Approaches to Prevent Healthcare-Associated S84 Data Science Priorities for a University Infection Hospital–Based Institute of Infectious Diseases: Philippe Brouqui, Sophia Boudjema, Alberto Soto Aladro, Eric Chabrière, A Viewpoint Olga Florea, Hoa Nguyen, and Jean Charles Dufour Alain-Jacques Valleron Clinical Infectious Diseases academic.oup.com/cid An Official Publication of the Infectious Diseases Society of America and the HIV Medicine Association EDITOR STATISTICAL EDITORS In the Literature Robert T. Schooley Norma Terrin, Senior Editor Stan Deresinski Steven Cohen DEPUTY EDITOR Farzad Noubary News Ferric C. Fang Donald Kaye ASSISTANT DEPUTY EDITOR HISTOPATHOLOGY EDITORS Photo Quiz/Arcanum Barbara D. Alexander Ann Marie Nelson Anthony Amoroso Mary Klassen-Fischer ASSOCIATE EDITORS Reviews of Anti-infective Agents Constance A. Benson EDITORIAL OFFICE STAFF Louis D. Saravolatz Carlos del Rio Carlos M. Terra, Vaccines Kathryn M. Edwards Managing Editor Stanley Plotkin Vance G. Fowler Claire R. Neumann, David N. Fredricks Acquisitions Editor Barbara E. Murray Blake Campbell, PAST EDITORS Peter G. Pappas Editorial Office Assistant Reviews of Infectious Diseases Robin Patel Edward H. Kass, 1979–1989 David L. Paterson SPECIAL SECTION EDITORS (vols. 1–11) David A. Pegues Sydney M. Finegold, 1990–1991 William A. Petri Book Reviews (vols. 12 and 13) Stephanie N. Taylor Gary P. Wormser David L. Thomas Clinical Infectious Diseases Clinical Practice Sydney M. Finegold, 1992–1999 COVER ART EDITORS Ellie J. C. Goldstein (vols. 14–29) Michael Grizzard Sherwood L. Gorbach, 2000-2016 Healthcare Epidemiology Mary Grizzard (vols. 30-63) Robert A. Weinstein STATISTICAL ASSOCIATE EDITOR Immunocompromised Hosts Victor De Gruttola David R. Snydman 13001300 WilsonWilson Blvd.,Blvd., SuiteSuite 300 Diana L.1300 Olson Wilson (Vice President, Blvd., Suite Communications) 300 Arlington,Arlington, VAVA 2220922209 1300Arlington, Wilson VABlvd., 22209 Suite 300 Telephone:Telephone: (703)(703) 299-0200 Telephone:Arlington, (703) VA 299-1215 22209 Fax:Fax: (703)(703) 299-0204299-0204 Telephone:Fax: (703) (703) 299-8766 299-1215 E-mail:E-mail: [email protected]@idsociety.org E-mail:Fax: [email protected] (703) 299-8766 URL:URL: http://www.idsociety.orghttp://www.idsociety.org URL:E-mail: http://www.hivma.org [email protected] URL: http://www.hivma.org BOARDBOARD OFOF DIRECTORS BOARD OF DIRECTORS BOARD OF DIRECTORS EXECUTIVE COMMITTEECOMMITTEE EXECUTIVE COMMITTEE EXECUTIVE COMMITTEE WilliamJohan S.G. Bakken, Powderly, President President Carlos del Rio, Chair WilliamPaul G. G. Auwaerter, Powderly, President-Elect President-Elect WendyWendy Armstrong, Armstrong, Chair-Elect Chair PaulCynthia G. Auwaerter, L. Sears, Vice Vice President President MelanieRafael Campo, Thompson, Vice-Chair Chair-Elect PenelopeLarry K. H. Pickering, Dennehy, Secretary Secretary Adaora Adimora,W. David ImmediateHardy, Vice Past Chair Chair HelenHelen W.W. Boucher,Boucher, Treasurer Carlos del Rio, Immediate Past Chair StephenJohan B. S. Calderwood, Bakken, Immediate Immediate Past Past President President DIRECTORSDIRECTORS DIRECTORS DIRECTORS BarbaraAngela D.M. AlexanderCaliendo Joel Ang Henry F. Chambers Henry F. Chambers StephenJoel Boswell Ang Janet A. Englund Janet A. Englund MichelleJudith Feinberg S. Cespedes Thomas Fekete Thomas Fekete LisaJudith K. Fitzpatrick Feinberg Lawrence P. Martinelli Lawrence P. Martinelli DonnaLisa K. Futterman Fitzpatrick Thomas A. Moore Thomas A. Moore RajeshDonna T. Dutterman Gandhi Trish M. Perl Daniel P. McQuillen SallyRajesh L. Hodder T. Gandhi Steven K. Schmitt Trish M. Perl CaroleLori A. Gordon Hohl Judith A. Aberg (HIVMA Representative) Joel E. Gallant (HIVMA Representative) JeanneCarole Keruly A. Hohl Anthony Harris (SHEA Liaison) Sarah E. Cosgrove (SHEA Liaison) MichelleRenslow Collins Sherer Ogle David W. Kimberlin (PIDS Liaison) David W. Kemberlin (PIDS Liaison) WilliamJames M. Towner Sosman Mark A. Leasure (Chief Executive Officer) Chris Busky (Chief Executive Officer) RochelleWilliam Walensky Towner Judith A. Aberg (IDSA Representative) PUBLICATIONS COMMITTEE Rochelle Walensky PUBLICATIONS COMMITTEE Andrea WeddleIra (Executive Wilson Director) LouisSusan D. L. Saravolatz, Koletar, Chair Chair Joel Gallant (IDSA Representative) AdeelMark Ajwad DiNubile Butt Andrea Weddle (Executive Director) HanaMark DiNubile El-Sahly MathiasLarry S. LichterfeldMcDaniel IrvingAaron Nachamkin Milstone MicheleJennifer I. S. Morris Read CindyCindy TamingaTaminga Yi-WeiYi-Wei TangTang HarrysHarrys TorresTorres RichardRichard R.R. WatkinsWatkins SherwoodRobert T. L. Schooley, Gorbach, Editor, Editor, CIDCID MartinMartin S.S. Hirsch,Hirsch, Editor,Editor, JID PaulPaul E. Sax, E. Sax, Editor, OFIDOFID PenelopeJanet A. H. Englund Dennehy (Board (Board Liaison) Liaison) Diana L. Olson (Vice President, Communications) Clinical Infectious Diseases SUPPLEMENT ARTICLE Rewiring Microbiology and Infection Didier Raoult1 and Fernando Baquero2 1Aix Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales émergentes, INSERM 1095, IRD 198, IHU Méditerranée Infection, Marseille, France; and 2Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Madrid, Spain Keywords. microbiological research; modern tools; systematic questioning; University Hospital Institute (IHU) Méditerranée Infection; single site. The emergence of microbiology in the 19th century was made was associated with great freedom for these early researchers possible by the use of new tools: first, the popularization of the in microbiology. The creation of a single site, which was then microscope, then the development of culture techniques, then implemented in all French-speaking countries, in association the discovery that some bacteria could not be grown in pres- with the Army Health Service, played an essential role in the ence of oxygen, and, finally, the development of the techniques fight against infectious and parasitic diseases, both in the devel- of staining and gelification of culture media. Microbiology was oped world and shortly after in the southern and eastern under- initially intended to understand the processes of fermentation developed colonial regions and countries. by Pasteur [1] and then, microbial diseases of humans, ani- The success of this form of research was made possible by mals, and plants. To demonstrate that Bacillus anthracis and the integration of all elements acting as a source of signifi- Mycobacterium
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  • Diversity of Spotted Fever Group Rickettsiae and Their Association

    Diversity of Spotted Fever Group Rickettsiae and Their Association

    www.nature.com/scientificreports OPEN Diversity of spotted fever group rickettsiae and their association with host ticks in Japan Received: 31 July 2018 May June Thu1,2, Yongjin Qiu3, Keita Matsuno 4,5, Masahiro Kajihara6, Akina Mori-Kajihara6, Accepted: 14 December 2018 Ryosuke Omori7,8, Naota Monma9, Kazuki Chiba10, Junji Seto11, Mutsuyo Gokuden12, Published: xx xx xxxx Masako Andoh13, Hideo Oosako14, Ken Katakura2, Ayato Takada5,6, Chihiro Sugimoto5,15, Norikazu Isoda1,5 & Ryo Nakao2 Spotted fever group (SFG) rickettsiae are obligate intracellular Gram-negative bacteria mainly associated with ticks. In Japan, several hundred cases of Japanese spotted fever, caused by Rickettsia japonica, are reported annually. Other Rickettsia species are also known to exist in ixodid ticks; however, their phylogenetic position and pathogenic potential are poorly understood. We conducted a nationwide cross-sectional survey on questing ticks to understand the overall diversity of SFG rickettsiae in Japan. Out of 2,189 individuals (19 tick species in 4 genera), 373 (17.0%) samples were positive for Rickettsia spp. as ascertained by real-time PCR amplifcation of the citrate synthase gene (gltA). Conventional PCR and sequencing analyses of gltA indicated the presence of 15 diferent genotypes of SFG rickettsiae. Based on the analysis of fve additional genes, we characterised fve Rickettsia species; R. asiatica, R. helvetica, R. monacensis (formerly reported as Rickettsia sp. In56 in Japan), R. tamurae, and Candidatus R. tarasevichiae and several unclassifed SFG rickettsiae. We also found a strong association between rickettsial genotypes and their host tick species, while there was little association between rickettsial genotypes and their geographical origins.