Assessment of antimicrobial treatment strategies in pig production

169 Pages·2017·5.67 MB·English

university of copenhagen
Assessment of Antimicrobial Treatment Strategies in Pig Production Using
Mathematical Models
Ahmad, Amais
Publication date:
2014
Document version
Early version, also known as pre-print
Citation for published version (APA):
Ahmad, A. (2014). Assessment of Antimicrobial Treatment Strategies in Pig Production Using Mathematical
Models. Faculty of Health and Medical Sciences, University of Copenhagen.
Download date: 31. Dec. 2022
FACULTY OF HEALTH AND MEDICAL SCIENCES
UNIVERSITY OF COPENHAGEN

AMAIS AHMAD | PHD THESIS 2014

Assessment of antimicrobial treatment strategies in pig
production using mathematical models

Assessment of antimicrobial treatment strategies in pig
production using mathematical models

Amais Ahmad
PhD thesis 2014

This thesis has been submitted to the Graduate School of the Faculty of Health and Medical
Sciences, University of Copenhagen
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SUPERVISORS
Principal supervisor
Professor Søren Saxmose Nielsen
Department of Large Animal Sciences, Faculty of Health and Medical Sciences
University of Copenhagen, Denmark
Associate supervisors
Professor Nils Toft
National Veterinary Institute
Technical University of Denmark, Denmark
Associate Professor Lasse Engbo Christiansen
Department of Applied Mathematics and Computer Science
Technical University of Denmark, Denmark

ASSESSMENT COMMITTEE
Associate Professor Matthew James Denwood (Chairperson)
Department of Large Animal Sciences, Faculty and Health and Medical Sciences
University of Copenhagen, Denmark
Dr Charlotte Sonne Kristensen
Danish Agriculture and Food Council-Pig Research Centre, Denmark
Dr Alison E. Mather
Wellcome Trust Sanger Institute, Pathogen Genomics Group, Hinxton, UK

Assessment of antimicrobial treatment strategies in pig production using mathematical models
Amais Ahmad, PhD thesis 2014 © Amais Ahmad
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TABLE OF CONTENTS
ACKNOWLEDGMENTS….………………………………………………………………… 5
SUMMARY…………………………………………………………………………………. 7
SAMMENDRAG…………………………………………………………………….………. 9
CHAPTER1: GENERAL INTRODUCTION……………………………………………….. 13
1.1 Antimicrobial use and antimicrobial resistance………………………………..……… 14
1.1.1 Antimicrobial resistance………………………………….………….………… 14
1.1.2 Public health impact…………………………………….………….………….. 15
1.1.3 Danish pig production…………………………………………….…………… 16
1.1.4 Antimicrobial use in Danish pig production……………………..……………. 16
1.1.5 Escherichia coli as indicator bacteria…………………………..……………... 17
1.1.6 Surveillance and control methods……………………………..………………. 18
1.1.6.1 The Danish Integrated Antimicrobial Resistance Monitoring and 18
Research Program (DANMAP)…………………………………..…
1.2 Designing treatment strategies……………………………………………………...…. 19
1.2.1 Background……………………………………………………………..……… 19
1.2.2 Pharmacokinetics (PK)……………………………………………….….…….. 20
1.2.3 Pharmacodynamics (PD)…………………………………………….………… 21
1.2.4 Pharmacokinetics-pharmacodynamics (PK-PD)…………………….………… 23
1.2.4.1 PK-PD indices………………………………………….…………… 23
1.2.4.2 PK-PD modeling (in vitro)……………………………..…………… 23
1.2.4.3 Mathematical models for in vivo growth…………….….………….. 24
1.3 Aims and research questions……………………………………………….……….…. 27
CHAPTER 2: MATERIALS AND METHODS……………………………………….……. 29
2.1 In vitro growth experiments……………………………………………………..…….. 31
2.1.1 Strains selection………………………………………………………..………. 31
2.1.2 Single antimicrobial exposure (tetracycline, ampicillin, gentamicin)……....….. 32
2.1.3 Multi-drug exposure (tetracycline + ampicillin)………………..……………… 32
2.2 Growth rate estimations……………………………………………….………………. 33
2.3 In vitro pharmacodynamics ……………………………………………………………. 34
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2.3.1 Single antimicrobial.……………………………………………………………. 34
2.3.2 Antimicrobials in combination….………………………………………………. 35
2.4 In vivo pharmacokinetics……………………………………………………………….. 36
2.5 Model structure…………………………………………………………………………. 36
2.6 Model inputs…………………………………………………………………………….. 38
2.6.1 Single antimicrobial treatment…………………………………………………... 38
2.6.2 Multidrug antimicrobial treatment…………………………………………….… 39
CHAPTER 3: RESULTS………………………………………………………………………. 41
3.1 Pharmacodynamics of antimicrobials…………………………………………….…….. 42
3.1.1 Single drug PD parameters…………………………………………...…………. 42
3.1.2 Combined drugs PD parameters (tetracycline + ampicillin)………….………… 44
3.2 Pharmacokinetics………………………………………………………….…..………… 45
3.3 In vivo growth models……………………………………………………..….………… 46
3.3.1 Single drug treatment strategies……………………………………….………… 47
3.3.2 Multidrug treatment strategies………………………………..……….………… 49
CHAPTER 4: DISCUSSION………………….……………………………………………… 53
4.1 In vitro growth response…………………………………………...……………………. 54
4.2 In vivo pharmacokinetics………………………………………..….…………………… 55
4.3 In vivo growth…………………..……………………………………………………….. 56
CHAPTER 5: CONCLUSIONS AND FUTURE PERSPECTIVES………………………….. 59
References……………………………….………………………….…………………………. 63
ACCOMPANYING MANUSCRIPTS…..………………………….………………………… 69

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ACKNOWLEDGMENTS
This PhD project was a part of MINIRESIST project funded by the Danish Strategic Research Council
and carried out at the Department of Large Animal Sciences, Faculty of Health and Medical Sciences,
University of Copenhagen.
I would like to express my warm thanks to my main supervisor, Søren Saxmose Nielsen, for the
continuous support, constructive advice and aspiring guidance. Thank you for always pushing me, for
having regular status meetings, for having an open door for discussion, and last but not least thank you
for having patience with my slow speed. I would like to thank my co-supervisors, Lasse Engbo
Christiansen, Nils Toft, and Kaare Græsbøll for always providing me with good ideas, comments and
insights to the manuscripts. I would also like to thank everyone who has contributed to this PhD thesis,
and provided great support and encouragement for the duration of the project.
Thanks to my mother for her enormous support, and my late father, to whom I dedicate this work.
Finally, thanks to my lovely wife Tayyaba, for supporting and encouraging me. Thanks for giving birth
to two cute babies who have created a source of happiness in stressful conditions throughout the time of
my research.

Frederiksberg C, October, 2014
Amais Ahmad
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SUMMARY
The phenomenon of antimicrobial resistance (AMR) is well established, but its persistent increase and
alarming proportions threaten the ability of antimicrobials to treat infections. AMR has become a major
issue in veterinary antimicrobial use, specifically in food production animals, due to the potential
consequences for human health. Danish pig production accounted for 76% of the total veterinary use of
antimicrobials in 2012 with 79% of pig production used in weaning pigs. Escherichia coli (E. coli) are
the predominant bacteria in the gastrointestinal flora of humans and animals, and can serve as a reservoir
of AMR. Furthermore, around 40% of E. coli isolates from healthy pigs throughout the Denmark over
the past five years were found to be resistant to tetracycline and ampicillin. There is, therefore, a need to
reduce the levels of resistance in the pig production system using improved treatment strategies. Dosing
factors, along with the in vivo epidemiological parameters, govern the relation between resistance and
antimicrobial use. Mathematical modeling and simulation techniques have been used over the past two
decades to evaluate the effect of these factors on the development of resistance, and are considered to be
powerful tools in designing treatment strategies.
The overall aim of the thesis was to develop an in vivo bacterial growth model to predict and assess the
effect of dosing factor on resistance growth in order to optimize treatment strategies. Specific aims were
to a) estimate pharmacodynamic (PD) parameters of E. coli strains representative of the Danish porcine
E. coli strains, when these are exposed to tetracycline and ampicillin, b) characterize the PD effect of
combined concentrations of tetracycline and ampicillin, and c) evaluate the treatment strategies that
better suppress the growth of resistant strains both under single and multidrug treatments.
Fifty E. coli strains were randomly selected from 160 collected isolates from pigs as a part of
DANMAP, and were considered to be representative of the Danish pig population. In vitro growth
experiments were performed using BioScreen under exposure of tetracycline and ampicillin, both
independently and in combination. PD parameters of strains were estimated for these exposures.
Differential equation model use developed for continuous changes in bacterial counts over time in pig
intestine both with and without antimicrobial treatment. A total period of 35 days after first day of
treatment was simulated in the model. Antimicrobial treatments were introduced in the model based on
different combinations of dosing frequency and treatment durations. In addition, the effect of different
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