Investigating causes of mortality in live export cattle

244 Pages·2014·3.56 MB·English

Investigating causes of mortality in live export cattle

This thesis is presented for the degree of
Doctor of Philosophy at Murdoch University

By

Sarah Jo Moore
BVSc (Hons) MSc (Bioinf)
May 2014

1
2
Declaration

I declare that this thesis is my own account of my research and contains as its main content
work which has not previously been submitted for a degree at any tertiary education
institution.

....................................
(Sarah Jo Moore)

3
4
“Sure, the big events attract a lot of attention,
but what really matters is what goes on every single day.”
Michael Tilson Thomas

5
6
Abstract
This research project was initiated to provide industry with current, credible, scientific data
on causes of death and risk factors for mortality in Australian live export cattle on long-haul
voyages.
Animal data and necropsy samples were collected from animals that died on 20 research
voyages during the study period March 2010 to September 2012. The average voyage
mortality percentage was 0.37%. Respiratory disease was the most commonly diagnosed
cause of death, accounting for 107/215 (49.8%) of deaths overall, and 107/181 (59.1%) of
deaths for which a diagnosis could be made. In addition, pneumonia was identified in 33%
of animals for which respiratory disease was not considered the primary cause of death.
Other common causes of death included lameness (n = 22/181, 12.2%), ketosis (n = 12,
6.6%), septicemia (n = 11, 6.1%), and enteric disease (n = 10, 5.5%).
Quantitative polymerase chain reaction (qPCR) assays were developed to detect viruses
and bacteria known to be associated with bovine respiratory disease (BRD) in necropsy and
nasal swab samples: Bovine coronavirus (BCoV, Betacoronavirus 1), Bovine herpesvirus 1
(BoHV-1), Bovine viral diarrhoea virus (BVDV), Bovine respiratory syncytial virus (BRSV),
Bovine parainfluenza virus 3 (BPIV-3), Histophilus somni, Mycoplasma bovis, Mannheimia
haemolytica and Pasteurella multocida
Two-thirds (130/195) of animals from which lung samples were collected had histological
changes and/or positive qPCR results suggestive of infectious lung disease: 93/130 (72%)
had evidence of primary bacterial infection, 4 (3%) with primary viral infection, 29 (22%)
with concurrent bacterial and viral infections, and for 4 (3%) the causative organism could
not be indentified. M. bovis, H. somni, P. multocida, M. haemolytica and BCoV were
significantly associated with respiratory disease during voyages.
7
Results from nasal swab and serological samples collected at entry to the pre-export
assembly depot indicated that there were significant differences in nasal and
seroprevalence between animals sourced from different properties. Combined nasal swab
and serum results suggest that BCoV and BVDV are likely to be important infectious agents
in the development of BRD in live export cattle while BPIV-3 is unlikely to play a major role.
The contribution of BoHV-1, BRSV and bacteria of interest is difficult to determine.
Analysis of animal and voyage data collected by industry between January 1995 and
December 2012 revealed that while there has been an overall reduction in voyage
mortality rates since 2000, there remain significant differences in mortality rate between
load and discharge regions. Examination of daily mortality data available for research
voyages revealed that peak daily mortality risk occurs at 3-4 weeks post-departure. The
development of methods for spatial analyses coupled with data available in the National
Livestock Identification System database allowed the description of patterns of animal
movement prior to export.
This study has improved our understanding of causes of death and risk factors for mortality
in Australian live export cattle. We now have baseline data on the prevalence of BRD
organisms in live export cattle that could be used to develop strategies for BRD prevention
and control prior to loading and during voyages.

8
Table of Contents
Declaration ............................................................................................................................... 3
Abstract .................................................................................................................................... 7
Acknowledgements ................................................................................................................ 13
Communications arising from this thesis ............................................................................... 15
Scientific papers ................................................................................................................. 15
Presented at conferences .................................................................................................. 15
Public media ....................................................................................................................... 15
Abbreviations ......................................................................................................................... 16
Chapter 1: General Introduction ............................................................................................ 19
Chapter 2: Literature review .................................................................................................. 23
2.1 Transport of live animals by sea ............................................................................ 23
2.2 Management of cattle prior to being loaded onto the vessel ............................... 25
2.3 Risk factors affecting mortality during voyages ..................................................... 29
2.3.1 Voyage length ................................................................................................ 29
2.3.2 Class of cattle (feeder, slaughter, breeder) ................................................... 30
2.3.3 Type of cattle (Bos taurus, Bos indicus) ......................................................... 30
2.3.4 Importing country .......................................................................................... 32
2.3.5 Season ............................................................................................................ 32
2.4 Causes of mortality in live export cattle ................................................................ 33
2.4.1 Heat stroke ..................................................................................................... 34
2.4.2 Lameness ........................................................................................................ 35
2.4.3 Respiratory disease ........................................................................................ 38
2.5 Conclusion .............................................................................................................. 55
Chapter 3: Development of quantitative PCR assays for the detection of viruses and
bacteria known to be associated with bovine respiratory disease ....................................... 57
3.1 Summary ................................................................................................................ 57
3.2 Introduction ........................................................................................................... 57
3.3 Materials and Methods .......................................................................................... 59
3.3.1 Samples .......................................................................................................... 59
3.3.2 DNA/RNA extraction ...................................................................................... 59
3.3.3 Quantitative PCR development ..................................................................... 60
3.3.4 Construction of plasmid controls ................................................................... 62
3.3.5 Test validation ................................................................................................ 67
9
3.4 Results .................................................................................................................... 68
3.5 Discussion ............................................................................................................... 72
Chapter 4: Mortality of live export cattle on long-haul voyages: pathological changes and
pathogens .............................................................................................................................. 77
4.1 Summary ................................................................................................................ 78
4.2 Introduction ........................................................................................................... 79
4.3 Materials and methods .......................................................................................... 81
4.3.1 Data and sample collection ............................................................................ 81
4.3.2 Processing of fixed tissues ............................................................................. 82
4.3.3 Processing of samples in VTM ........................................................................ 83
4.3.4 Detection of microbial nucleic acids .............................................................. 83
4.3.5 Interpretation of qPCR results ....................................................................... 84
4.3.6 Determining the cause of death .................................................................... 85
4.3.7 Statistical analysis .......................................................................................... 85
4.4 Results .................................................................................................................... 86
4.4.1 Voyage data ................................................................................................... 86
4.4.2 Mortality ........................................................................................................ 89
4.4.3 Clinical presentation ...................................................................................... 90
4.4.4 Gross pathology ............................................................................................. 91
4.4.5 Histology ........................................................................................................ 93
4.4.6 Molecular results ........................................................................................... 94
4.4.7 Final diagnosis ................................................................................................ 98
4.5 Discussion ............................................................................................................. 101
4.6 Author’s contributions ......................................................................................... 110
4.7 Acknowledgements .............................................................................................. 111
4.8 Supplementary Tables ......................................................................................... 112
4.9 Additional Material .............................................................................................. 113
Chapter 5: Estimation of nasal shedding and seroprevalence of organisms known to be
associated with bovine respiratory disease in Australian live export cattle ....................... 115
5.1 Summary .............................................................................................................. 116
5.2 Introduction ......................................................................................................... 116
5.3 Materials and Methods ........................................................................................ 119
5.3.1 Study population .......................................................................................... 119
5.3.2 Nasal swab samples ..................................................................................... 122
10