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UNIVERSITAT ROVIRA I VIRGILI SANITARY IMPORTANCE OF ARCOBACTE Arturo Levican Asenjo Dipòsit Legal: T.1425-2013 Arturo Alberto Levican Asenjo Sanitary importance of Arcobacter Doctoral Thesis Directed by Dr. Maria José Figueras Dr. Luis Collado González Departament de Ciències Mèdiques Bàsiques Unitat de Biologia i Microbiologia Reus 2013 UNIVERSITAT ROVIRA I VIRGILI SANITARY IMPORTANCE OF ARCOBACTE Arturo Levican Asenjo Dipòsit Legal: T.1425-2013 Maria José Figueras Salvat professor of Microbiology of the Department of Basic Health Sciences, Faculty of Medicine and Health Sciences of the University Rovira i Virgili and Luis Collado González researcher and teacher of the Institute of Biochemistry and Microbiology, Faculty of Sciences of the University Austral of Chile. CERTIFY THAT: The present work entitled: ”Sanitary importance of Arcobacter” prepared by Arturo Levican Asenjo to obtain the degree of doctor by the University Rovira i Virgili, have been carried out under our supervision at the Unit of Microbiology of the Department of Basic Health Sciences, and that it fulfils the requirements to obtain the International Doctorate mention. Reus, May 14, 2013. Dra. Maria José Figueras Salvat Dr. Luís Collado González UNIVERSITAT ROVIRA I VIRGILI SANITARY IMPORTANCE OF ARCOBACTE Arturo Levican Asenjo Dipòsit Legal: T.1425-2013 To Karin, Fabian and Gabriela UNIVERSITAT ROVIRA I VIRGILI SANITARY IMPORTANCE OF ARCOBACTE Arturo Levican Asenjo Dipòsit Legal: T.1425-2013 Acknowledgments I express my sincere gratitude to my advisor Prof. Maria José Figueras for her continuous support of my PhD study and research, for her patience, motivation, enthusiasm, and also for encouraging me to give the best of myself. I also thank her for giving so much of her valuable time over recent months to help me finish this thesis in time. I also thank Dr. Luis Collado, co-Director of this work, for helping me get started on this PhD and for his guidance and support from the beginning. I thank Prof. Josep Guarro for his advice, support and friendship during my years in the Microbiology Unit in Reus. My sincere appreciation goes to all other Professors in the Unit for everything I have learned from them and for their continuous help and support. And I thank sincerely Prof. Luis Zaror (Universidad Austral de Chile) for trusting me and for his help in starting my PhD studies. I’m grateful to the team of technicians for their help in my everyday life and to my lab mates for the stimulating discussions and for all the fun we have had in the last four years. In particular, to Luis, Eduardo and Valentina for their support during my first years here in Reus and to Katiuska for her unconditional friendship. I also thank Phil for his help in correcting my writings in English and for his useful advice. I’m very grateful to Prof. Stephen Forsythe of the School of Science and Technology, Nottingham Trent University, for giving me the opportunity to conduct the tissue culture study in his laboratory. Furthermore, I thank to all other teachers and lab mates, in special to Aldwkali Alkeskas for teaching me, to Susan Joseph for her support and for her friendship during my time in Britain. I'm also grateful to my house-mates there in Clifton, Nottingham, Cèlie and Mert, for the enriching conversations, for the shared time and for their friendship. I thank the Laboratori de Salut Pública, Agencia de Protecció de la Salut, Tarragona, Spain, and IRTA (Research and Technology Food and Agriculture) of Sant Carles de la Ràpita, Spain for providing me with shellfish samples and to Jaume Cabré at the WWTP in Reus, Spain, for his help in providing us the access to sampling points. This acknowledgement extends to all who have participated as co-authors in the studies included in this thesis. My sincere thanks also goes to the external reviewers, Dr. Sarah de Smet and Dr. Dang Duong Bang, who agreed to review this thesis and whose comments improved it significantly. UNIVERSITAT ROVIRA I VIRGILI SANITARY IMPORTANCE OF ARCOBACTE Arturo Levican Asenjo Dipòsit Legal: T.1425-2013 I am deeply and forever indebted to my family: My parents José and Norma, my sister Monica and my brother José for their guidance and love, which made it possible for me to finish my undergraduate studies; especially to my brother Jorge who motivated me to follow this career. To my family-in-law who welcomed me: to Eliana and Sergio, and Felipe and Vivian, who raised my loved wife, and are always there to support us. To Mabel, Cristian and Colomba for their love and support. Also to all uncles and cousins who were always encouraging me to keep going, especially to Aunt Tere and Maly, who surely are somewhere taking care of us. Words could never adequately express my gratitude to my loving wife Karin and our precious children Fabian and Gabriela, who had to leave family, friends and part of their lives behind in Chile, to supporting me in this adventure. I’m proud of your fortitude because I know that this change was not an easy one. Certainly, this success is also yours because without your love and support I'd never have finished this thesis. I love you all so much !!!. Last but not least, I acknowledge the Universitat Rovira i Virgili for my doctoral grant, as well as to Conicyt, Chile for their financial support through Becas Chile. Some of the studies included in this thesis were supported by project AGL2011-30461-C02-02 of the Ministerio de Ciencia e Innovación (MICINN), Spain and/or by funding from the European Union Seventh Framework Programme ([FP7/2007-2013] under grant agreement n° 311846). I also acknowledge the travel grant obtained to participate in the 16th International Workshop on Campylobacter, Helicobacter and Related Microorganisms, Vancouver, Canada. UNIVERSITAT ROVIRA I VIRGILI SANITARY IMPORTANCE OF ARCOBACTE Arturo Levican Asenjo Dipòsit Legal: T.1425-2013 EXAMINATION COMMITTEE Dr. Jesús López Romalde Centro de Investigaciones Biológicas (CIBUS), Departament of Microbiology and Parasitology University of Santiago de Compostela, Spain Dr. Josepa Gené Departament of Basic Health Sciences, Universitat Rovira i Virgili Reus, Spain Dr. Sandra McLellan Great Lakes Water Institute, School of Freshwater Sciences University of Wisconsin, Milwaukee, USA SUBSTITUTES Dr. Dolors Furones Nozal Institut de Recerca i Tecnologia Agroalimentària (IRTA) Sant Carles de la Ràpita, Spain. Dr. Josep Cano Departament of Basic Health Sciences, Universitat Rovira i Virgili Reus, Spain Dr. Andrea Serraino Department of Veterinary Medical Sciences University of Bologna, Italy EXTERNAL EVALUATORS Dr. Sarah De Smet Het Varkensloket, Institute for Agricultural and Fisheries Research (ILVO) Melle, Belgium Dr. Dang Duong Bang Laboratory of Applied Micro and Nanotechnology (LAMINATE), Diagnosis Technology, Division of Food Microbiology National Food Institute, Teknical University of Denmark Søborg, Denmark UNIVERSITAT ROVIRA I VIRGILI SANITARY IMPORTANCE OF ARCOBACTE Arturo Levican Asenjo Dipòsit Legal: T.1425-2013 CONTENTS Page 1 INTRODUCTION 1.1 The genus Arcobacter……………………………………………………………………… 3 1.1.1 Methods for the characterization of new species 1.1.1.1 16S rRNA gene……………………………………………………………….