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test for detecting enteric disease as a cause of death in cattle. Based on data in Table 24. Se= sensitivity; Sp=specificity; PPV = positive predictive value; NPV = negative predictive value;
App Prev = apparent prevalence; True Prev = true prevalence; CI = Confidence Interval.
Parameter Estimate
95 CI Lower
Upper Se
0.5 0.24
0.7
Sp
0.98 0.94
0.99
PPV
0.5 0.24
0.76
NPV
0.98 0.94
0.99
App Prev
0.05 0.03
0.08
True Prev
0.05 0.03
0.08 While the NPV is very high, the PPV for a gross necropsy diagnosis of enteric disease was
relatively poor. This is likely to be the result of a relatively poor Se as well as the low prevalence of the condition. Enteric conditions include diseases such as salmonellosis and
under favourable conditions shedding animals, rough voyage with associated stress and presence of concurrent disease it is possible that multiple cases of enteric disease could
occur.
If Se and Sp are held at the values above and prevalence is increased to 0.1 and 0.2, the PPV does rise to 0.74 and 0.86, respectively.
7.10.7 Other diagnostic classifications
Clinical categories of recumbency andor weakness and ill thrift andor shy feeder accounted for 31 and 23 animals, respectively Section 7.5 and Table 11 but there was very little
relationship between animals in either of these two clinical categories and either gross necropsy diagnosis Table 11 or final cause of death Table 12. The information suggests
that these two clinical categories are non-specific, descriptive terms that are not associated with particular diseases.
There were a range of other conditions that were listed either as clinical categories or as gross necropsy diagnoses, however the number of animals recorded against each of these
other conditions was so small as to preclude effective assessment of the diagnostic performance of these conditions association between clinical category or gross necropsy
diagnosis and the gold standard of final cause of death.
7.11 Discussion
The project design called for enrolling 40 voyages and completing necropsies at three broad levels: 75 necropsies with detailed examination of all collected tissues, 75 necropsies with
some tissues collected and with limited pathology testing and up to 100 necropsies without any collection of samples gross necropsy only. These figures assumed a total of 250
necropsies but of these only about 150 were expected to result in samples being imported for pathology testing.
Very early in Stage 3 the project team saw that voyage enrolment rates were likely to result in fewer than 40 voyages and as a result an effort was made to encourage necropsy and
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collection of biological samples from as many dead animals as possible. The project ended with necropsy forms being submitted for 215 deaths and necropsies and collection of
samples were achieved on 197 of these. All samples were processed and examined for histology and molecular testing where ever possible.
The final result was that we collected pathology data and information from more animals than we had planned to while enrolling fewer voyages than we had planned to.
Since the purpose of the necropsies was to establish and describe common causes of death, the project team felt that the project had collected sufficient samples to be confident
that we had achieved this goal.
Respiratory disease was the most common cause of mortality identified in the current study, accounting for about 50 of the 215 deaths for which information was obtained and 59.1
of the deaths for which a final diagnosis could be made.
Estimates of the proportion of deaths attributed to respiratory disease in feedlot studies in Canada range from 46-55
20
and in the United States from 55 –75.
21
A recent survey of Australian cattle feedlots reported that respiratory disease and musculoskeletal conditions
were the two most common causes of death, accounting for 53 and 15 of all mortalities, respectively.
22
These findings are consistent with the results from the current project. Histological evidence of concurrent respiratory disease was also present in an average of
33 of animals for which respiratory disease was not considered the primary cause of death.
There were two important differences between our findings and those of an earlier study of causes of death in four cattle export voyages to the Middle East.
23
The most important cause of death in cattle reported in the Norris et al study was heat stroke, followed by trauma
or musculoskeletal disease and injury and respiratory disease. The two key differences were that we found respiratory disease accounted for a higher proportion of mortalities and
our findings suggested that heat stroke was a very uncommon cause of death in the population of export cattle we followed.
It is not clear why respiratory disease accounted for a lower proportion of mortalities in the Norris et al study in comparison to the current project. There were differences in design with
the earlier study involving designated research personnel accompanying each selected voyage, conducting necropsies and generally assuming responsibility for all sample and data
collection. The Norris et al study was conducted about a decade prior to this study and there have been changes in management of shipboard conditions and animal selection since that
time including implementation of heat stress management associated with HotStuff. Our project involved regular AAVs doing the data collection and performing necropsies on board
ship. Our project involved pathologists examining all tissues collected during voyages and the results from these examinations indicated a high level of agreement with the AAV
classifications of causes of death based on gross necropsy alone. In addition, our project included one voyage where a research team member accompanied the voyage and
20
Edwards 1996; Gagea et al. 2006
21
Loneragan et al. 2001
22
Perkins 2013
23
Norris et al. 2003
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conducted necropsies and the results from this voyage were consistent with results from all other voyages. As a result we are generally confident in the findings from this project. This
suggests that the differences between the earlier paper
24
, and the current project were due to changes in the interplay of various causal factors animal, ship, climate, pathogen,
management etc that may influence mortality risk. Quantitative PCR assay was used in the present study to detect potential respiratory
pathogens in samples collected from the nose and lungs of cattle on board export vessels. The prevalence of viruses of interest BCoV, BoHV-1, BRSV, BVDV, BPIV-3 was less than
15 in both nasal and lung samples. The prevalence of these viruses was higher in animals with clinical or histological evidence of respiratory disease than those without, with the
exception of BRSV in lung samples.
In the pathogenesis of BRD, viruses play a primary role, causing damage to the respiratory tract and facilitating secondary invasion by bacteria that may go on to cause a fatal bacterial
pneumonia. It is possible that by the time that an animal develops severe disease and dies from a secondary bacterial pneumonia, that much of the evidence to document an initial or
primary viral infection and the ability to detect specific primary viruses may be obscured.
As a result our findings are considered consistent with the general understanding of respiratory disease in cattle where primary viral infection is often followed by secondary
bacterial infection.
We have reported a molecular diagnosis of BCoV in association with respiratory disease in Western Australian and South Australian cattle that were sampled during this study.
In a separate publication, BCoV was recently reported in association with respiratory disease in cattle on a property on the south coast of New South Wales, Australia.
25
BCoV appears to be emerging as a potential cause of respiratory disease in cattle and more work is required
to determine whether there are strain differences between enteric and respiratory syndromes associated with BCoV infection and to assess relative importance of BCoV compared to
other respiratory viruses and also potential control and prevention strategies.
We reported a tendency for a statistical association between BVDV and respiratory disease. A number of animals that tested positive for BVDV came from consignments in which acutely
or persistently infected animals had been previously identified and removed from the consignment prior to loading, using the pestivirus antigen capture ELISA or PACE test. Our
findings suggest that current pre-export testing strategies for BVDV will not eliminate the risk of BVDV circulation amongst cattle being assembled for export.
We found significant associations between a diagnosis of BRD as a cause of death and detection of each of the four bacterial pathogens of interest in lung tissue. Animals with
histologic pneumonia were more likely to have a positive qPCR result for each of the four bacteria than animals without pneumonia. The strongest statistical association was reported
for Mycoplasma bovis but associations for all four bacteria were statistically significant.
In addition, animals with histologic pneumonia were more likely to have three of the four bacteria detected in nasal swabs compared to animals without pneumonia M. bovis, M.
24
Ibid.
25
Hick et al. 2012
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haemolytica, and P. multocida. All of these bacteria are known to be important causes of BRD in cattle.
We did not find an association between M. bovis detection and musculoskeletal conditions though M. bovis is well described as a cause of arthritis and tenosynovitis in cattle in addition
to BRD. Relatively few samples from musculoskeletal lesions were collected during our study in comparison to the collection of respiratory disease samples and the lack of
association in our study may have been due to sampling constraints.
We also reported a small number of cases with histologic changes consistent with myocarditis, pneumonia or thrombotic meningoencephalitis associated with H. somni
infection. Myocarditis, BRD, polyarthritis and thrombotic meningoencephalomyelitis are described as common clinical manifestations of H. somni infection in feedlot cattle.
26
We reported heat stroke as the primary cause of death in only two of 215 animals less than 1 though hyperthermia secondary to other disease conditions pneumonia and
septicaemia was described in a further 9 animals. The reduced occurrence of heat stroke as a cause of death in comparison to earlier studies
27
, may be due to factors such as misclassification, changes in selection and management of cattle both prior to and during the
voyage, and changes in airflow and climatic management on-board export vessels. Musculoskeletal conditions including lameness and injury, was the second most common
cause of death in the current project. The proportion of deaths attributed to musculoskeletal conditions and injury in our study 15.3 was lower than previous estimates of 23
28
, and 25.
29
This is likely due to a combination of factors including things such as animal selection, change in type of cattle being exported and improved conditions and management
during the voyage. Lameness may occur at any stage during the export supply chain, often occurring as a result
of a combination of injury and abrasive or rough flooring. During the voyage, injuries are more common during rough weather particularly in combination with heavier animals and
reduced stocking density more opportunity for animal movement or falls.
30
Difficulty in separating and treating individual animals during the voyage and ongoing movement of the
vessel and local conditions wet bedding, abrasive flooring mean that musculoskeletal injuries that may heal relatively well in a land-based environment may develop into serious
and potentially life-threatening conditions on-board an export ship. A number of cattle with musculoskeletal conditions were euthanased because they were not able to recover in time
to be unloaded at a destination port, reflecting the difficulty in managing these conditions on board a ship. Recommendations for best practice for cattle selection and bedding
management to reduce the incidence of lameness have been made in previous industry reports
31
, and in Commonwealth mortality investigation reports as described in Shiell et al.
32
26
Van Donkersgoed et al. 1994
27
Norris et al. 2003
28
Hedlefs 1988
29
Norris et al. 2003
30
Banney, Henderson, and Caston 2009; Hedlefs 1988
31
Banney, Henderson, and Caston 2009
32
Shiell, Perkins, and Hewitt 2014
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This project involved AAVs performing routine clinical work during the voyage including conducting necropsies and collecting samples. Samples were imported back into Australia
and examined by veterinary pathologists to establish cause of death. An important outcome for this project was to use the findings to assess and improve the ability of AAVs to
accurately classify causes of death without having to import biological samples back into Australia and have them examined by a pathologist.
Our findings confirm that AAVs are very capable of accurately assigning deaths to the appropriate primary cause using gross necropsy alone.
Our findings suggest that ante-mortem clinical observations on animals are not an effective way to classify or identify the cause of death for animals that subsequently die, with the
possible exception of musculoskeletal and injury conditions. Between 40-50 of deaths in our study had no ante-mortem clinical disease information recorded suggesting that many
deaths occur without any prior information on likely diseases. For those animals that died and that had any ante-mortem information recorded, ante-mortem clinical records were not
useful in identifying the cause of death except for musculoskeletal conditions such as trauma and lameness.
Lameness and musculoskeletal injury severe enough to result in euthanasia or death, was most effectively detected using ante-mortem clinical information, followed by gross necropsy.
Our findings also suggest that a number of animals with severe lameness conditions may develop secondary diseases perhaps as a result of being compromised by lameness.
In contrast, respiratory disease is only poorly detected by ante-mortem clinical information, however it is well detected using gross necropsy.
Other important causes of death inappetence, enteric disease had very high negative predictive values with gross necropsy but lower positive predictive values, indicating that
gross necropsy can confidently be used to rule these conditions out and less confidently to diagnose them as the primary cause of death.
The important practical application of this information is that AAVs can confidently classify deaths according to the most important likely causes of death in export cattle and that this
will require a combination of ante-mortem records focussing particularly on lameness conditions and gross necropsy for other conditions, most particularly respiratory disease.
8 Results - Stage 4 – Nasal shedding and seroprevalence
of potential pathogens
Stage 4 objectives were designed to incorporate sampling of animals during the assembly feedlot stage of the export supply chain in order to understand possible levels of exposure to
potential respiratory disease pathogens as animals are sourced and assembled, and where possible to relate these findings to subsequent disease occurrence during export.
The general purpose was to investigate the contribution of pre-existing or concurrent disease, management practices, seasonality or other factors to development of clinical
disease once animals were on-board. In addition we wanted to describe processes for handling and health management at assembly depots.
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8.1 Description of management of cattle in assembly depots
