Antimicrobial resistance in companion animal pathogens in Australia and assessment of pradofloxacin on the gut microbiota Sugiyono Saputra A thesis submitted in fulfilment of the requirements of the degree of Doctor of Philosophy School of Animal and Veterinary Sciences The University of Adelaide February 2018 Table of Contents Thesis Declaration ...................................................................................................................... iii Dedication ................................................................................................................................. iv Acknowledgement ...................................................................................................................... v Preamble .................................................................................................................................... vi List of Publications ..................................................................................................................... vii Abstract .......................................................................................................................................ix Chapter 1 General Introduction ................................................................................................. 1 1.1. Antimicrobials and their consequences ............................................................................ 2 1.2. The emergence and monitoring AMR................................................................................ 2 1.3. Effect of pradofloxacin on dysbiosis of normal microbiota in rabbits as an animal model .................................................................................................................................................. 5 1.4. Aims and objectives of the present study ......................................................................... 8 1.5. References ....................................................................................................................... 10 Chapter 2 Antimicrobial resistance in coagulase-positive staphylococci isolated from companion animals in Australia: A one year study................................................................... 14 Statement of authorship ........................................................................................................ 15 Original article ........................................................................................................................ 17 Supplementary information .................................................................................................. 35 Chapter 3 Antimicrobial resistance in clinical Escherichia coli isolated from companion animals in Australia ................................................................................................................... 38 Statement of authorship ........................................................................................................ 39 Original article ........................................................................................................................ 41 Chapter 4 Antimicrobial resistance in companion animal pathogens in Australia: a current perspective................................................................................................................................ 50 Statement of authorship ........................................................................................................ 51 Original article ........................................................................................................................ 53 Chapter 5 Metagenomic studies of gut microbial diversity and structure changes after antibiotic treatment .................................................................................................................. 75 Statement of authorship ........................................................................................................ 76 Original article ........................................................................................................................ 78 Chapter 6 Faecal microbiota profiling in rabbits following single and multiple doses of oral pradofloxacin .......................................................................................................................... 105 Statement of authorship ...................................................................................................... 106 Original article ...................................................................................................................... 108 Supplementary information ................................................................................................ 125 Chapter 7 Oral pradofloxacin has limited impact on the gastric and caecal microbiota of rabbits ..................................................................................................................................... 132 Statement of authorship ...................................................................................................... 133 Original article ...................................................................................................................... 136 Supplementary information ................................................................................................ 147 i Chapter 8 General Discussion ................................................................................................. 151 8.1. General summary ......................................................................................................... 152 8.2. Major findings .............................................................................................................. 153 8.2.1. Comparative rates of AMR in Australia is low for Gram-negative pathogens but moderately high for Gram-positive pathogens ................................................................ 153 8.2.2. High levels of AMR among bacterial isolates from veterinary healthcare-associated infections .......................................................................................................................... 154 8.2.3. Resistance to antimicrobials that are critical to human care remains either undetected or low among companion animal isolates from Australia ............................ 156 8.2.4. Oral pradofloxacin has different effects on gastric, caecal and faecal microbial diversity ............................................................................................................................ 157 8.2.5. Pradofloxacin is safe for use in rabbits ................................................................... 158 8.3. Implication of findings and future works ....................................................................... 159 8.4. Conclusions .................................................................................................................... 160 8.5. References ..................................................................................................................... 162 ii Acknowledgements In the name of Allah, the Most Gracious and the Most Merciful. Alhamdulillah, I praise and thank Allah SWT for giving me the strength and courage to complete my study. I would like to offer my sincerest gratitude to my principal supervisor, Professor Darren J. Trott, who has supported me throughout my study with his knowledge, patience, encouragement and superb supervision. Without him, I won’t be able to finish my journey as a PhD student. Sincere thanks to Professor Gordon Howarth for his valuable advice, consultation and encouragement; Professor David Jordan for his wonderful support, kindness, helping me with statistical analysis and writing; Dr Sam Abraham for the guide during my first year of study and for the opportunity to finish AMR survey project, Assoc. Professor Jacqueline Norris and Dr Kate Worthing for brilliant research collaboration and valuable comments on the paper, Prof. John Turnidge and Ms Jan Bell for valuable advice on antimicrobial resistance. Special thanks to koala, rabbit and microbiome-research group, Dr Natasha Speight, Dr Esmaeil Ebrahimie and Dr Manijeh Mohammadi-Dehcheshmeh which I have been involved in and got more knowledge in the field. I would like to express my appreciation to Ms Niranjala Seimon from International Sponsored Student Advisor/Australia Awards Liaison Officer, for continuous support over the years. Special thanks to Lesley Menzel, Rebecca Dunbar, and David Purdie for the support during my first years stay at Roseworthy Residential College. To all of my friends, Saad Gilani (with Anne Marie and Haiqa) and Noor Haliza Hasan, thank you for the inspiration, you were brilliant students. Pardeep Sharma, Abd and Bedur, Wei Yee Chan, Nadia Zulkifli, Entesar Shuhaib, Farida Mazumder, Sri Dwi Hastuti, Janet Pandi, Sangay Tenzin, Alex, Vivek Pande, Vaibhav Gole, Consuela Estrella, thank you for the friendship and wonderful moment during my study. Special thanks to my colleague, Neil Griffiths, Shangzhe Xie, Jessica Fabijan, Amanda Kidsley, Elizabeth Hickey, Vanessa Tamlin, Mandy Bowling, Mohinder Singh, Oliver Wilkins, Shewli Mukerjee, Arthur Mason, Richelle Butcher, Nicola Woodward, Caitlyn Page and other DVM students. Finally, I would like to extend my thanks to my family, I can never say enough thanks to my parents, Ibu Siti Sugiarti and Bapak Daryono who always pray for me and support me anytime, anywhere, throughout