Associations between health, management and antimicrobial use in Danish swine and veal calves

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Associations between health, management and antimicrobial use in Danish swine and
veal calves
Fertner, Mette Ely
Publication date:
2016
Document Version
Publisher's PDF, also known as Version of record
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Citation (APA):
Fertner, M. E. (2016). Associations between health, management and antimicrobial use in Danish swine and
veal calves. National Veterinary Institute, Technical University of Denmark.

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Associations between health,
management and antimicrobial use
in Danish swine and veal calves
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Mette Fertner
DTU Vet
Ph.D. Thesis
July 2016

Associations between health,
management and antimicrobial use in
Danish swine and veal calves
PhD Thesis
Mette Fertner

July 2016
Associations between health,
management and antimicrobial use in
Danish swine and veal calves

PhD Thesis
Mette Fertner
2016

Supervisors Professor Nils Toft, Section for Epidemiology, National Veterinary
Institute, Technical University of Denmark
Senior Advisor Anette Boklund, Section for Epidemiology, National
Veterinary Institute, Technical University of Denmark
Associate Professor Helle Stege, Section for Production and Health,
Department of Large Animal Sciences, University of Copenhagen
Associate Professor Lasse Engbo Christiansen, Department of
Applied Mathematics and Computer Science, Technical University
of Denmark
Assessment Researcher Vibeke Frøkjær Jensen,
committee Section for Epidemiology, National Veterinary Institute,
Technical University of Denmark
Chief Executive Officer Ken Steen Pedersen, PhD,
Ø‐Vet A/S, Denmark
Professor Jeroen Dewulf,
Department of Obstetrics, Reproduction and Herd Health,
Ghent University, Belgium
Cover photos Mette Fertner
Published by National Veterinary Institute
Bülowsvej 27, 1870 Frederiksberg, Denmark
Request report from www.vet.dtu.dk
Not everything that can be counted counts, and not everything that counts can be counted.
Albert Einstein

Preface
This thesis was funded by the National Veterinary Institute, Technical University of
Denmark, where I was enrolled at the Section of Epidemiology from December 2011 to
July 2016, including three months research visit at the Department of Health Management,
Prince Edward Island, Canada. I would like to thank all people helping me through. Thanks
to all the farmers and practicing veterinarians showing me practical life and what is
actually behind the excessive amounts of Danish register data. Thanks to the data
providers (the Classification Authority, SEGES and DVFA). Without data, this thesis would
not have been feasible!
Thanks to my supervisors Anette Boklund, Nils Toft, Claes Enøe, Helle Stege and Lasse
Engbo Christiansen for sharing your knowledge, for input and discussions… Nils, thanks
for your outspoken instant opinion clearing things out on what is actually important.
Anette, thanks for your always open door, patience and endless feedback on papers with
hints on how to move on. Although it wasn’t planned from the beginning – the two of you
made up quite a good main supervision team. It truly has been an educational journey
which I wouldn’t be without! Thanks to Claes, my main supervisor the first year, for giving
me the chance to work on this project and to take ownership of it. And of course, thanks to
Javier Sanchez and Henrik Stryhn which in my mind, are my Canadian supervisors and
definitely the best hosts I could ever imagine. Thanks for your hospitality and engagement
in my project.
And then, I would like to thank Nana Dupont, with whom I had the most VetStat‐
conversations, defeated the most data challenges and shared the most ideas and code
during the last years. You were always there when needed. Thanks!
Thanks to the VetStat study group (Amanda Brinch Kruse, Camilla Birkegård, Leonardo de
Knegt, Vibe Dalhoff Andersen, Gitte Blach Nielsen, Nana Dupont). Great discussions once
we started. I would have wished you had been there at the time I started the PhD. Thanks
to the advisory group (Anders Elvstrøm, Andreas Birch, Erik Jacobsen, Poul Bækbo,
Elisabeth Okholm Nielsen) for your interest in the study, input and discussions. A special
thanks to Erik (and his successor Laura Mie Jensen) for your readiness to talk about
VetStat‐issues whenever needed.
Former and present colleagues in the Epi‐group at DTU Vet: Thanks for the laughs. You are
awesome!
And last but not least, thanks to my husband, Chris, for the unconditional support and for
holding our family together these last intensive months. Thanks to Frida and Iben for
supplying life with joy! And to my mom for support in daily life whenever needed.

Mette Frederiksberg, July 2016
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Content
List of original publications ............................................................................. 9 
Summary .......................................................................................................... 11 
Sammendrag ................................................................................................... 13 
Abbreviations .................................................................................................. 15 
1.  Introduction ............................................................................................. 17 
1.1  Background .......................................................................................................... 17 
1.2  Historical outline of antimicrobial use in production animals from a Danish
perspective .......................................................................................................... 18 
1.3  Production animals and clinical indications for treatment .................................... 20 
1.4  Administration of antimicrobials ........................................................................... 22 
1.5  Registers .............................................................................................................. 24 
2.  Aim of the thesis ..................................................................................... 27 
3.  Materials and definitions ........................................................................ 29 
3.1  Quantification of antimicrobials at herd-level ....................................................... 29 
3.2  Definition of health ............................................................................................... 31 
3.3  Definition of management .................................................................................... 31 
3.4  Databases ............................................................................................................ 32 
3.4.1  VetStat .......................................................................................................... 32 
3.4.2  CHR .............................................................................................................. 32 
3.4.3  SPF .............................................................................................................. 32 
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