Copyright is owned by the Author of the thesis. Permission is given for a copy to be downloaded by an individual for the purpose of research and private study only. The thesis may not be reproduced elsewhere without the permission of the Author. MASSEY UNIVERSITY – INSTITUTE OF VETERINARY, ANIMAL AND BIOMEDICAL SCIENCES Antimicrobial Resistance in Young New Zealand Horses A thesis submitted in fulfilment of the requirements for the degree of a Master of Veterinary Science Submitted 12th December 2014 Toombs-Ruane, Leah Jo 12/15/2014 December 2014 Abstract The emergence of bacteria that are resistant to antibiotics used in horses has been reported worldwide, including in Australia, the USA and United Kingdom. There is a lack of published comparative scientific information on the New Zealand equine population. However, recent individual cases of multi-drug resistant (MDR) bacterial infections reported by veterinarians have raised concerns about the situation in New Zealand. The use of antimicrobials coupled with less than ideal prescription practice in the horse industry may have led to inadvertent selection for MDR bacteria. An initial perspective on antimicrobial resistance in NZ is gleaned through a retrospective description of laboratory submissions in the form of a database analysis from 2004 to 2013/2014. In neonates (foals less than three weeks of age), the presence of MDR bacteria was identified in 37.5% (24/64) of foals; although 81.6% (102/125) of bacteria cultured from foals included in the study were sensitive to either penicillin or gentamicin. Of the respiratory samples from horses three-years-old and younger, the most commonly cultured bacteria were Staphylococcus species accounting for 40.1% (310/774) of isolates. These bacteria were sensitive to penicillin, ceftiofur and gentamicin for > 90% of isolates. Of all respiratory equine submissions, MDR bacteria were recovered from 39.2% (93/237) of horses. Using multiple correspondence analysis, MDR was associated with submissions from 2009-2014 and two-year-old horses from the Waikato region. These two population groups were targeted specifically for examination due to the potentially severe consequences of bacterial disease in neonates (Chapter 3), and the anecdotal experience of high clinical use of antimicrobials in young horses, especially in the treatment of clinically apparent respiratory disease (Chapter 4). Multi-drug resistance was assessed as part of this work, and is presented in the systematic literature review (Chapter 2), and in both descriptive studies (Chapters 3 and 4). The results of the two retrospective descriptive studies presented show that there is a substantial proportion of submissions from young horses in New Zealand that grow multi-resistant bacterial isolates, and that there is decreased efficacy of commercially available antimicrobials in this country. The antimicrobial resistance reported in this study has potential clinical implications, and reflects the first step in a multifactorial approach to improve and maintain horse and human health. Acknowledgements I owe an eternal debt of gratitude to my generous and wise supervisors Sarah Rosanowski, Jackie Benschop and Chris Riley (the dream team!). Special thanks to Sarah, who was always quick and astute in her critiques and advice (even from afar): I absolutely could not have done this without your help! Big and grateful thanks to Anna Kendall, Joe Mayhew and Kate Hill for their bright and shiny brains, which they allowed me to pick from time to time! For her statistical wisdom, and grace in agreeing to help me with the MCA, I owe Charlotte Bolwell a cake that I never quite got around to baking. Thanks to the McGeorge Research Fund and the New Zealand Equine Research Foundation for providing funding for this project. Thanks also to NZVP and especially Isobel Gibson for her time and database expertise. And finally, a special thank you to all veterinarians in practice who have submitted samples for bacterial culture and sensitivity, as well as to those who will do so into the future. And of course, thank you to my mum! Abbreviations ACVIM American college of veterinary internal medicine AMR Antimicrobial resistance CC Clonal complex CI Confidence interval CIA Critically important antimicrobial ESBL Extended-spectrum beta-lactamase OR Odds ratio MCA Multiple correspondence analysis MDR Multi-drug resistance MIC Minimum inhibitory concentration MLST Multi-locus sequence typing MPI Ministry for primary industries MRCoNS Methicillin resistant coagulase-negative Staphylococcus species MRS Methicillin resistant Staphylococcus species MRSA Methicillin resistant Staphylococcus aureus NZ New Zealand OIE World organiation for animal health (office international des epizooties) PCR Polymerase-chain reaction PFGE Pulse-field gel electrophoresis PMQR Plasmid-mediated quinolone resistance PRISMA Preferred reporting items for systematic reviews and meta-analysis SVARM Swedish veterinary antimicrobial resistance monitoring TMPS Trimethoprim-sulfonamide combination (i.e. trimethoprim-sulfamethoxazole, trimethoprim-sulphadiazine) VRE Vancomycin resistant Enterococcus WHO World health organisation Contents 1 INTRODUCTION........................................................................................................... 1 1.1 Overview ....................................................................................................................... 1 1.2 Motivation for this study: a clinical perspective ....................................................... 2 1.3 A brief review of antimicrobial resistance in horse populations ............................. 3 1.3.1 General results of equine culture and sensitivity ................................................................................ 3 1.3.2 Antimicrobial use and stewardship .................................................................................................... 7 1.3.3 Selected research into equine bacterial resistance .............................................................................. 9 1.4 Summary of objectives .............................................................................................. 13 2. SYSTEMATIC REVIEW: HOW IS MULTI-DRUG RESISTANCE REPORTED IN EQUINE POPULATIONS? ...................................................................................... 15 2.1 Abstract ....................................................................................................................... 15 2.2 Introduction ................................................................................................................ 15 2.3 Methodology ............................................................................................................... 17 2.4 Results ......................................................................................................................... 19 2.5 Discussion.................................................................................................................... 36 2.6 Conclusions ................................................................................................................. 38 3. ANTIMICROBIAL SENSITIVITY OF BACTERIA ISOLATED FROM NEONATAL FOAL SAMPLES SUBMITTED TO A NEW ZEALAND VETERINARY PATHOLOGY LABORATORY. ....................................................... 39 3.1 Abstract ....................................................................................................................... 39 3.2 Introduction ................................................................................................................ 40 3.3 Materials and Methods .............................................................................................. 41 3.3.1 Data collection.................................................................................................................................. 41 3.3.2 Case selection ................................................................................................................................... 41 3.3.4 Culture and sensitivity, identification and classification .................................................................. 42 3.3.5 Antimicrobial sensitivity and multi-drug resistance definition ........................................................ 42 3.3.6 Data analysis .................................................................................................................................... 42 3.4 Results ......................................................................................................................... 43 3.4.1 Overall submissions ......................................................................................................................... 43 3.4.2 Specimens ........................................................................................................................................ 45