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The Fish Pathogen Francisella Orientalis: Characterisation and Vaccine Development

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The fish pathogen Francisella orientalis: characterisation and vaccine development A thesis submitted to the University of Stirling for the degree of: Doctor of Philosophy in Aquatic Veterinary Studies By D.V.M. José Gustavo Ramírez Paredes Institute of Aquaculture University of Stirling, Stirling, Scotland, United Kingdom April 2015 Declaration Declaration This thesis has been composed in its entirety by me, the candidate. Except where specifically acknowledged, the work described in this thesis has been conducted independently and has not been submitted for any other degree. José Gustavo Ramírez Paredes Candidate’s signature: _________________________________________ Supervisor’s signature: _________________________________________ Supervisor’s signature: _________________________________________ Date: _________________________________________ I Supervisors and external advisors Supervisors and external advisors …………………………….. Professor Randolph Richards Institute of Aquaculture Stirling, United Kingdom …………………………….. Professor Sandra Adams Institute of Aquaculture Stirling, United Kingdom Dr. Duncan Colquhoun Dr. Esteban Soto Section for Bacteriology School of Veterinary Medicine Norwegian Veterinary Institute University of California-Davis Oslo, Norway California, United States Dr. Pär Larsson Dr. Cristian Gallardo Umeå University Hospital and Interdisciplinary Centre for Aquaculture Swedish Defence Research Agency Research and University of Concepcion Umeå, Sweden Concepcion, Chile Dr. Kim Thompson Dr. David Penman Aquaculture Research Group Institute of Aquaculture Moredun Research Institute University of Stirling Edinburgh, United Kingdom Stirling, United Kingdom II To my ever supportive parents Gloria Paredes & Gustavo Ramírez y a la memoria de mi abuelita Clotilde Coty Pérez III Acknowledgments Acknowledgements The studies of this thesis were conducted at the Aquatic Vaccine Unit, Institute of Aquaculture, University of Stirling and were partially financed by the National Council for Science and Technology in Mexico (CONACyT) with a scholarship that covered most of my tuition fees and some of my personal expenses. First of all I am truly grateful to my supervisors at the Institute of Aquaculture (IoA), Professor Alexandra Adams and Professor Randolph Richards, Dr. Kim Thompson and Dr. David Penman for giving me the opportunity to undertake a PhD, encouraging my research and allowing me to grow as a scientist. My sincere gratitude and appreciation are also given to Dr. Duncan Colquhoun and Dr. Pär Larsson for their expert advice and help during the course of the work. I will never forget your keenness, guidance and contributions to my project. I am without doubt in “life-debt” with both of you for being a cornerstone for this study and trusting my ideas. My acknowledgments also to Mr. Warren Turner at Nam Sai Farms, DVM Khan Kledmanee at the Faculty of Veterinary Medicine in Mahidol University, family Krajangwong and Dr. David Little for facilitating my visit to Thailand. The “chapter zero” “chasing Francisella in Thailand” was the baseline of this thesis! I am also grateful to Dr. Cristian Gallardo at Universidad de Concepcion and the “INCAR crew” for your hospitality while visiting the lab in Chile and to Dr. Esteban Soto for your invaluable advices, long hours on the phone and interest on my proposals. I really hope this is the beginning of many more collaborations with both of you. I am truly indebted to my friends Dr. Phuoc Nguyen Ngoc and Dr. Dilok Wongsathein for their help in the bacteriology and molecular labs when I had just arrived to Stirling. I will always remember those “Francisella hunting” days in the pangasius fish with Dr. Phuoc. A huge thanks also to Dr. Keith Jolley and Dr. Martin Maiden at Oxford University for allowing me to use their rMLST platform for my genomic analyses and to Hans-Jürgen Busse at the University of Veterinary Medicine in Vienna Austria for kindly contributing with the chemotaxonomical analyses of some of the strains. Many thanks to Caroline Öhrman and Mats Forsman at the Swedish Defence Research Agency for their contribution to the bacterial genome sequencing. I am furthermore grateful to James Dick at the IoA Nutrition Group for his support with the bacterial fatty acid analysis. Thanks also to Dr. Mansour El-Matbouli at the University of Veterinary Medicine in Vienna Austria and Dr. Cesar Ortega Santana at the Faculty of Veterinary Medicine Universidad Autónoma del Estado de México for their contribution with bacterial isolates. Special credits to DVM Miguel Mendoza for his astounding performance during his MSc project which enormously contributed to Chapter 5. Thanks patron for trusting this project and me as a supervisor. IV Acknowledgments Also thanks to Dr. Matt Metselaar (Fish Vet Group UK) for believing in my ideas. A major part of this project would not have been possible without the financial support from the FVG in Chapters 2 and 5. I would like to collectively acknowledge all the staff at the IoA but especially to Keith Ranson at the Tropical Aquarium, Niall Auchinachie at the challenge aquarium, Hillary McEwan and Karen Snedden at the Aquatic Vaccine Lab, Linton Brown at the Electron Microscope, Debbie Faichney at the Bacteriology Lab, Jacquie Ireland in Genetics and Denny Conway in Parasitology. I am also thankful to my friend DVM Sandra Schlittenhardt for her contribution with the histopathological interpretations. I also gratefully acknowledge Dr. Mario Garduño Lugo and Biol. Germán Muñoz- Córdova at the Faculty of Veterinary Medicine, National Autonomous University of Mexico for broadening my academic horizons and setting me up on track to pursue this degree in the field of the Aquatic Veterinary Medicine. Important part of this quest were the friends and colleagues with whom I shared many scientific and les serious discussions, moments of happiness and stress: Claudia Mansilla, Nilantha Jayasuriya, Stuart McMillan, Thao Ngo, Carsten Krome, Jomer Bo Lucanas, Carina Duarte, Phil Lyons, Benjamin Lopez, Jan Heumann, Sara Picon, Eric Leclercq, Rasina Rasid, Mathew Sprague, Nancy Xu, La Licenciada Berta Rivera, Polyana Silva, Ploy Krajangwong, Lislie Solis, Rogelio Sierra, Winarti Sarmin and Khalid Shahin and also a huge apology in advance for all those that I maybe forgetting at this time in the morning (27/5/15 5:05 am). I should also say thank you to the members of the Aquaculture Students Association (ASA) my good friends: Antonis Chalaris, Hazel McDonald and Lynn Chalmers, It’s been nice working with you towards the benefit of our community. A very special recognition to Dr. Sean Monaghan who more than a friend has been like a brother to me over these years in Scotland. Million thanks for your patience and advices. I am deeply thankful and indebted to my dearest Marie for your love, support and encouragement during the completion of this thesis. I will never forget the nice days together and the many ways you helped me to pass through the toughest moments of my project. Finally and most importantly I’d like to express my deepest gratitude to my loving family back in Mexico who have always been there to support me. Words cannot express how grateful I am, especially to my beloved parents Goya y Pedro. This work is dedicated to both of you as well as to my sister Gabby Ramirez-Paredes, my dearly loved nephew Ångel his father Guillermo and my grandma Maria de Jesus Ledesma whom I am looking forward to meet again at the end of the summer, thanks again for your prayers and blessings abue. This thesis is also dedicated to my other grandmothers Clotilde Perez Onofre who passed away last December while I was writing it. Te quiero muchísimo abuela Cota Pérez y espero que orgullosa desde el cielo me estés mirando. V Abstract Abstract Piscine francisellosis in an infectious emerging bacterial disease that affects several marine and fresh water fish species worldwide, including farmed salmon, wild and farmed cod, farmed tilapia and several ornamental species, for which no commercial treatment or vaccine exists. During 2011 and the first semester of 2012, chronic episodes of moderate to high levels of mortality with nonspecific clinical signs, and widespread multifocal white nodules as the most consistent gross pathological lesion were experienced by farmed tilapia fingerlings at two different locations in Northern Europe. In this study such outbreaks of granulomatous disease were diagnosed as francisellosis with a genus-specific PCR, and 10 new isolates of the bacterium including the one named STIR-GUS-F2f7, were recovered on a new selective “cysteine blood-tilapia” agar and cysteine heart agar with bovine haemoglobin. Ultrastructural observations of the pathogen in Nile tilapia (O. niloticus) tissues suggested the secretion of outer membrane vesicles (OMVs) by the bacterial cells during infection in these fish. This represented the first documented report of isolation of pathogenic Francisella strains from tilapia in Europe. The phenotypic characterisation indicated that isolates recovered were able to metabolise dextrin, N-acetyl-D glucosamine, D-fructose, α-D-glucose, D-mannose, methyl pyruvate, acetic acid, α-keto butyric acid, L-alaninamide, L-alanine, L- alanylglycine, L-asparagine, L-glutamic acid, L-proline, L-serine, L-threonine, inosine, uridine, glycerol, D L-α-glycerol phosphate, glucose-1-phosphate and glucose-6- phosphate. The predominant structural fatty acids of the isolates were 24:1 (20.3%), 18:1n-9 (16.9%), 24:0 (13.1%) 14:0 (10.9%), 22:0 (7.8%),
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