Insight into the epidemiology of swine dysentery by analyzing treatment records and using ...

152 Pages·2016·2.01 MB·English

by  Krysia Walczak

Insight into the epidemiology of swine dysentery by analyzing treatment
records and using simulation modelling
by
Krysia Walczak

A Thesis
presented to
The University of Guelph

In partial fulfillment of requirements
for the degree of
Master of Science
in
Population Medicine

Guelph, Ontario, Canada
© Krysia Walczak, December, 2015
ABSTRACT
INSIGHT INTO THE EPIDEMIOLOGY OF SWINE ANALYZING TREATMENT
RECORDS AND USING SIMULATION MODELLING
Krysia Walczak Advisor:
University of Guelph, 2015 Dr. Zvonimir Poljak

This thesis describes Brachyspira species infection dynamics in a population of growing pigs,
including the clinical manifestation of the infection known as swine dysentery (SD). Using
production data from a clinically infected herd, intramuscular treatments with tiamulin and
lincomycin were considered to be indicative of swine dysentery. Risk factors for the treatment
rates were determined. In addition, important parameters were extracted from the literature and
the treatment data and were used to replicate SD progression in a herd through deterministic
modelling. Parameters that are most associated with mortality due to clinical SD were identified
using sensitivity analysis. Finally, a stochastic compartmental model was developed to describe
Brachyspira infection and SD clinical disease within a herd. Treatment and production costs
were also incorporated into the model to identify the most cost-effective treatment protocol for
this disease.
iii

DEDICATION
This thesis is dedicated to my mother and father
Deborah Yip Chuck and Jerzy Walczak
Thank you for your complete and unwavering support in me and for teaching me the values that
define who I am today.
iv

ACKNOWLEDGEMENTS
I would like to sincerely thank my advisor, Dr. Zvonimr Poljak, for his unwavering
encouragement and support throughout this experience. I gained invaluable epidemiological and
statistical skills during my time as his student through his guidance and confidence in me. I
would also like to extend my gratitude to my advisory committee, Dr. Bob Friendship, Dr. Amy
Greer, and Dr. Alfons Weersink for their contributions and time to support and guide me
throughout my thesis. I would also like to thank Dr. Egan Brockoff and the producer who were
involved in this project through their invaluable contribution of production data.

I would like to thank my graduate peers and friends for their support and for the
opportunity to discuss ideas and challenges. I would also like to thank the Swine Group, for the
chances to present my progress and provide me with helpful feedback, as well as allowing me to
learn more about others’ research.

Thank you to my parents, Jerzy and Deborah, and to my sisters, Gillian and Asia. Thank
you for your love and strength throughout this journey, it means the world to me.
v

STATEMENT OF WORK
Krysia Walczak created the thesis draft. Manuscript editing was contributed by Drs. Zvonimir
Poljak, Robert Friendship, Amy Greer, and Alfons Weersink. This committee also provided
support throughout the research process. Funding for this project was provided by OMAFRA and
NSERC.

Dr. Egan Brockoff provided the field production data used for the analysis of treatment rates.
These data were analyzed and the results were interpreted by Krysia Walczak. Dr. Zvonimir
Poljak supervised the analysis of these data and the interpretation of results.

Deterministic models were developed by Krysia Walczak with the guidance of Dr. Zvonimir
Poljak. Analysis and interpretation of the results were done by Krysia Walczak under the
supervision of Dr. Zvonimir Poljak.

The stochastic model was developed by Krysia Walczak under the supervision of Dr. Zvonimir
Poljak. Expert opinion and suggestions of the various model aspects were used under the advice
of Drs. Robert Friendship and Zvonimir Poljak. Analysis of the model and the interpretation of
the results were done by Krysia Walczak with the guidance of Dr. Zvonimir Poljak.
vi

TABLE OF CONTENTS
ABSTRACT ......................................................................................................................................... ii
DEDICATION .................................................................................................................................... iii
ACKNOWLEDGEMENTS ................................................................................................................ iv
STATEMENT OF WORK .................................................................................................................. v
LIST OF FIGURES ............................................................................................................................ ix
LIST OF TABLES ............................................................................................................................... x
CHAPTER ONE:
INTRODUCTION, LITERATURE REVIEW AND OBJECTIVES ........................................... 1
INTRODUCTION ............................................................................................................................... 1
LITERATURE REVIEW .................................................................................................................... 2
Description of the pathogen ................................................................................................................. 2
Pathogenicity and natural history of disease ........................................................................................ 5
Prevalence of infection or colonization, description of outbreaks, risk factors ................................. 11
Frequency of clinical disease and impact on production ................................................................... 13
Treatment and control options ........................................................................................................... 14
Transmission models ......................................................................................................................... 19
OBJECTIVES .................................................................................................................................... 22
REFERENCES .................................................................................................................................. 23
CHAPTER TWO:
DESCRIPTIVE STUDY OF TREATMENT RATES FOR TIAMULIN AND
LINCOMYCIN IN SWINE DYSENTERY AFFECTED GROWING PIGS ............................ 32
ABSTRACT ....................................................................................................................................... 32
INTRODUCTION ............................................................................................................................. 32
METHODS ........................................................................................................................................ 33
Farm description ................................................................................................................................ 33
Records .............................................................................................................................................. 34
Statistical analysis .............................................................................................................................. 36
Disease transmission parameters ....................................................................................................... 38
RESULTS .......................................................................................................................................... 39
Intramuscular treatments .................................................................................................................... 40
vii

Risk factors for tiamulin and adjusted lincomycin usage .................................................................. 41
Disease transmission parameters ....................................................................................................... 43
Estimates of incubation time .............................................................................................................. 43
DISCUSSION .................................................................................................................................... 43
REFERENCES .................................................................................................................................. 49
CHAPTER THREE:
ASSESSMENT OF DETERMINANTS OF MORTALITY DUE TO BRACHYSPIRA
HYODYSENTERIAE INFECTION IN A POPULATION OF GROWER-FINISHER PIGS:
DISEASE SIMULATION APPROACH ....................................................................................... 58
ABSTRACT ....................................................................................................................................... 58
BACKGROUND ............................................................................................................................... 59
METHODS ........................................................................................................................................ 60
General descriptions of the model dynamics ..................................................................................... 60
General parameters for all models ..................................................................................................... 60
Model 1 .............................................................................................................................................. 62
Parameters for Model 1 ...................................................................................................................... 63
Model 2 .............................................................................................................................................. 64
Parameters for Model 2 ...................................................................................................................... 64
Model 3 .............................................................................................................................................. 66
Parameters for Model 3 ...................................................................................................................... 66
One way sensitivity analysis .............................................................................................................. 67
RESULTS .......................................................................................................................................... 68
DISCUSSION .................................................................................................................................... 69
CONCLUSION .................................................................................................................................. 72
REFERENCES .................................................................................................................................. 73
CHAPTER FOUR:
BIOECONOMIC MODELLING OF TREATMENTS WITH INJECTABLE
ANTIBIOTICS AGAINST SWINE DYSENTERY DUE TO BRACHYSPIRA
HYODYSENTERIAE ....................................................................................................................... 85
ABSTRACT ....................................................................................................................................... 85
INTRODUCTION ............................................................................................................................. 86
viii

MATERIALS AND METHODS ....................................................................................................... 86
General description ............................................................................................................................ 86
Model description .............................................................................................................................. 87
General assumptions .......................................................................................................................... 88
Treatment effects ............................................................................................................................... 89
Economic model ................................................................................................................................ 92
RESULTS .......................................................................................................................................... 94
DISCUSSION AND CONCLUSION ............................................................................................... 98
REFERENCES ................................................................................................................................ 103
CHAPTER FIVE:
CONCLUSIONS, LIMITATIONS, FUTURE RESEARCH RECOMMENDATIONS, AND
IMPLICATIONS ........................................................................................................................... 122
CONCLUSIONS.............................................................................................................................. 122
LIMITATIONS ................................................................................................................................ 125
FUTURE RESEARCH RECOMMENDATIONS .......................................................................... 126
IMPLICATIONS ............................................................................................................................. 128
REFERENCES ................................................................................................................................ 129
Appendix 2.1 .................................................................................................................................... 130
Appendix 2.2 .................................................................................................................................... 131
Appendix 2.3 .................................................................................................................................... 132
Appendix 2.4 .................................................................................................................................... 133
Appendix 3.1 .................................................................................................................................... 137
Appendix 4.1 .................................................................................................................................... 140
ix

LIST OF FIGURES
Figure 1.1: Average incubation period obtained from the literature using meta-analysis ................ 28
Figure 1.2: Minimum incubation time obtained from the literature ................................................. 29
Figure 1.3: Average duration of clinical signs from the literature.................................................... 30
Figure 1.4: Proportion of animals that develop clinical signs after Brachyspira infection .............. 31
Figure 2.1: Boxplot of total count of intramuscular treatments (start of the season) ....................... 51
Figure 2.2: Boxplot of total count of intramuscular treatments (season of growth) ......................... 52
Figure 2.3: Histogram representing a series of serial intervals extracted from the early growing
phase on the basis of treatments with tiamulin .................................................................................. 53
Figure 2.4: Effective reproductive number (R ) for each batch approximated using intramuscular
e
tiamulin treatments............................................................................................................................. 54
Figure 3.1: Schematic diagram of Model 1 ...................................................................................... 75
Figure 3.2: Schematic diagram of Model 2 ...................................................................................... 76
Figure 3.3: Schematic diagram of Model 3 ...................................................................................... 77
Figure 3.4: Results from Model 1 uncertainty analysis .................................................................... 78
Figure 3.5: Results from Model 2 uncertainty analysis .................................................................... 79
Figure 3.6: Results from Model 3 uncertainty analysis .................................................................... 80
Figure 4.1: Schematic diagram for a Brachyspira infection in an individual animal ..................... 105
Figure 4.2: Lincomycin model, Model 1 ........................................................................................ 106
Figure 4.3: Baseline model, Model 2a with 5% clinical cases ....................................................... 107
Figure 4.4: Baseline model, Model 2b displaying the disease from a historical perspective ......... 108
Figure 4.5: Tiamulin treatment model, Model 3 ............................................................................. 109
Figure 4.6: Tylosin treatment model, Model 4 ............................................................................... 110
Figure 4.7: Boxplots of expected total net losses and expected net losses per pig ......................... 111
x

LIST OF TABLES
Table 2.1: Risk factors considered for mixed Poisson univariable analysis ..................................... 55
Table 2.2: Mixed Poisson regression univariable analysis of factors associated with
intramuscular treatment rates ............................................................................................................. 56
Table 2.3: Final mixed Poisson multivariable models ...................................................................... 57
Table 3.1: Initial conditions for deterministic models ...................................................................... 81
Table 3.2: Parameters used for deterministic modelling................................................................... 83
Table 4.1: Initial conditions for stochastic modelling..................................................................... 112
Table 4.2: Parameters and flows used for stochastic modelling ..................................................... 113
Table 4.3: Economic parameters for modelling .............................................................................. 116
Table 4.4: Descriptive statistics for all stochastic model variations ............................................... 118
Table 4.5: Economic descriptive statistics ...................................................................................... 120