DAFM Laboratories

Quarterly

Surveillance Report

Quarter 4 2015

DAFM surveillance reports available at http://www.agriculture.gov.ie/rvlreport/

Introduction The laboratories operated by the Department of Agriculture, Food and Marine (DAFM) provide

data on the patterns and frequency of occurrence of non-regulated diseases in farmed animal

populations in Ireland. This disease surveillance role is fulfilled through routine diagnostic, post-

mortem and targeted surveillance activities. Data from these activities is published collectively on a

monthly, quarterly and annual basis. This quarterly report and other surveillance reports can be

accessed at: http://www.agriculture.gov.ie/rvlreport/.

The surveillance role of the laboratories compliments the broader remit of DAFM in surveillance

and control of diseases of animals. In addition to annual reports, periodical reports are published to

ensure the timely feedback of accurate data to the relevant industry stakeholders to inform

husbandry practices and disease control measures.

The quarterly surveillance reports are designed to provide a brief overview of disease trends in a

given quarter. Further, and more detailed, commentary on individual cases or individual outbreaks

can be accessed through monthly reports published in the Veterinary Ireland Journal and also

available at: http://www.agriculture.gov.ie/rvlreport/.

This Quarter The data presented in this report refers to the fourth quarter of 2015 (October to December). This

is a period in which an increase in respiratory disease outbreaks is typically recorded in cattle

leading to increased submissions to DAFM laboratories. Dry weather from September leading into

October however resulted in delayed housing of many animals, an event which often heralds the

onset of respiratory disease in weanlings. Nevertheless, a wetter than average November and

extremely wet, yet mild, December contributed to a late onset of many of these cases. Cases of

hoose pneumonia (Dictyocaulus viviparus) were still prominent among respiratory disease cases in

this quarter but their relative importance diminished as herd owners came to grips with the heavy

lungworm larval burden which favourable weather conditions earlier in the autumn appear to have

promoted.

Sheep carcase submissions increased almost three fold in this quarter compared to the third

quarter with a notable increase recorded in fatal cases of both acute (16 cases) and chronic fluke (5

cases). The annual fluke forecast had highlighted the increased risk posed to sheep flocks this year

and many cases were also recorded in early January 2016. Parasitic disease prevalence is

influenced by favourable mild and wet weather conditions and this contributed to parasitic

gastroenteritis also being recorded as the cause of death in 17 sheep this quarter.

Ruminal acidosis is occasionally recorded in animals introduced rapidly to heavy concentrate

feeding at this time of year and was recorded as the cause of death in 12 sheep, mostly 6 to 8

month old lambs, in 8 different flocks. The measured introduction of concentrates to the diet of

animals with appropriate availability of roughage is important in preventing fatal ruminal acidosis

cases.

DAFM surveillance reports available at http://www.agriculture.gov.ie/rvlreport/

The weather in Quarter 4 2015

Rainfall

Figure 1: The average monthly rainfall (in millimetres) recorded for Quarter 4 2015 compared to the three previous years and the 30-year mean monthly rainfall (trend line). (Source: Met Eireann, www.met.ie).

Temperature

Figure 2: The mean monthly temperature (in degrees Celsius) for Quarter 4 2015 compared to the previous three years and the 30-year mean monthly temperature (trend line). (Source: Met Eireann www.met.ie).

DAFM surveillance reports available at http://www.agriculture.gov.ie/rvlreport/

Soil temperature

Figure 3: The mean monthly soil temperature (in degrees Celsius) for Quarter 4 2015 compared to the previous three years. (Source: Met Eireann www.met.ie).

Submission numbers to the RVLs in Quarter 4 2015

SPECIES Carcass Diagnostic Foetus

Avian 70 72

Bovine 499 9025 1051

Canine 12 70

Cervine 30 2

Equine 5 51 1

Ovine 542 1171 31

Porcine 185 70 1

Feline 3 2

Badger 36

Caprine 12 17 3

Exotic 8 5

Vulpine 439

Lagomorph 22 5

Piscine 2

Murine 1

Broiler 4

Grand Total 1865 10495 1087

Table 1: The submission numbers of carcases, diagnostic samples and foetuses to the RVLs during Quarter 4 2015. Note that figures refer to sample numbers – one carcase or foetus counts as one sample under the carcase or foetus headings, one blood sample or faecal sample counts as one sample under the diagnostic heading. Any disparity between submission numbers and numbers of diagnoses below is due to submitted carcases in which a final diagnosis has not been assigned at the time of analysis.

DAFM surveillance reports available at http://www.agriculture.gov.ie/rvlreport/

Bovine disease surveillance

The causes of bovine mortality (all ages)

Figure 4: The causes of bovine mortality recorded on post-mortem examination in cattle of all ages by the RVLs, categorised by system or cause, during Quarter 4 2015 (n=378).

Figure 5: The frequency of the ten most common individual diagnosed causes of death in cattle of all ages, recorded on post-mortem examination by the RVLs during Quarter 4 2015 (n=378).

DAFM surveillance reports available at http://www.agriculture.gov.ie/rvlreport/

Figure 6: The relative frequency of the most common individual bovine respiratory disease diagnoses, in cattle of all ages, recorded on post-mortem examination by the RVLs during Quarter 4 2015 (n=113).

Figure 7: The relative frequency of the most common individual bovine alimentary tract disease diagnoses, in cattle of all ages, recorded on post-mortem examination by the RVLs during Quarter 4 2015 (n=102).

Figure 8: The relative frequency of bovine clostridial disease diagnoses, in cattle of all ages, recorded on post-mortem examination by the RVLs during Quarter 4 2015 (n=13).

DAFM surveillance reports available at http://www.agriculture.gov.ie/rvlreport/

The causes of bovine mortality (age-specific)

Figure 9: The causes of bovine mortality in neonatal calves (calves aged less than one month) recorded on post-mortem examination by the RVLs, categorised by system or cause, during Quarter 4 2015 (n=90).

Figure 10: The causes of bovine mortality in calves (calves aged greater than one month but less than three months) recorded on post-mortem examination by the RVLs, categorised by system or cause, during Quarter 4 2015 (n=30).

DAFM surveillance reports available at http://www.agriculture.gov.ie/rvlreport/

Figure 11: : The causes of bovine mortality in weanlings (bovine animals aged greater than three months but less than twelve months) recorded on post-mortem examination by the RVLs, categorised by system or cause, during Quarter 4 2015 (n=151).

Figure 12: The causes of bovine mortality in adults (bovine animals aged greater than or equal to twelve months) recorded on post-mortem examination by the RVLs, categorised by system or cause, during Quarter 4 2015 (n=105).

DAFM surveillance reports available at http://www.agriculture.gov.ie/rvlreport/

The relative frequency of pathogens identified in specific post-mortem examination

diagnostic categories

Figure 13: The relative frequency of specific respiratory pathogens identified in bovine carcases examined on post-mortem examination by the RVLs, in which a diagnosis of respiratory disease was made during Quarter 4 2015 (n=116).

Figure 14: The relative frequency of specific alimentary tract disease pathogens identified in bovine carcases examined on post-mortem examination by the RVLs, in which a diagnosis of ‘enteritis’ or ‘gastro-enteritis’ was made during Quarter 4 2015 (n=76).

DAFM surveillance reports available at http://www.agriculture.gov.ie/rvlreport/

Figure 15: The frequency of identification of Clostridium species as a significant pathogen contributing to death on post-mortem examination of bovine animal carcases of all ages by the RVLs during Quarter 4 2015 (n=24).

The frequency of detection of enteric pathogens in neonatal bovine enteritis cases

Enteric pathogen Negative Positive %Positive

Rotavirus 167 60 26.4%

Cryptosporidium parvum 175 53 23.2%

E.coli K99 165 11 6.3%

Coronavirus 227 1 0.4%

Salmonella culture 230 1 0.4%

Table 2: The relative frequency of detection of enteric pathogens in the faecal samples of neonatal calves (aged less than one month of age) harvested during Quarter 4 2015 from both clinically ill animals by veterinary practitioners in the field and from bovine carcases during post-mortem examination by the RVLs (n=230).

DAFM surveillance reports available at http://www.agriculture.gov.ie/rvlreport/

Results of the zinc sulphate turbidity (ZST) test in neonatal calves

Figure 16: The results of the ZST tests performed on both clinically ill animals and on carcases submitted for post-mortem examination by the RVLs during Quarter 4 2015 (n=125). The ZST test is used to determine the immunoglobulin status of the calf which can reflect the extent to which maternal colostral immunity has been transferred to the calf via the colostrum. A value of greater than or equal to 20 units is considered indicative of adequate immunoglobulin levels in the calf.

Results of milk samples submitted for mastitis culture

Figure 17: The relative frequency of isolation of specific mastitis pathogens in milk sample submissions (n=646) for bacteriological culture by the RVLs during Quarter 4 2015.

DAFM surveillance reports available at http://www.agriculture.gov.ie/rvlreport/

Bovine abortion and perinatal death

Foetal diagnosis Number Percentage

Abortion 643 90.1%

Anoxia/Hypoxia 6 0.8%

Hereditary and developmental anomalies 9 1.3%

Mummification 4 0.6%

Stillbirth 0 0.0%

Perinatal mortality 10 1.4%

Placentitis 6 0.8%

Goitre 1 0.1%

Dystocia 0 0.0%

Bacteraemia/Septicaemia 1 0.1%

Weak calf syndrome 7 1.0%

Aspiration pneumonia 2 0.3%

Haemorrhage 0 0.0%

Miscellaneous causes 10 1.4%

No Diagnosis 15 2.1%

Table 3: The causes of foetal (calves in utero up to 260 days gestation) or perinatal (calves from 260 days gestation to 48 hours post-delivery) death diagnosed on post-mortem examination (n=714) by the RVLs during Quarter 4 2015.

Figure 18: The relative frequency of detection of infectious agents in foetuses submitted to the RVLs for post-mortem examination during Quarter 4 2015 in which abortion, stillbirth or placentitis was diagnosed (n=649).

DAFM surveillance reports available at http://www.agriculture.gov.ie/rvlreport/

Ovine disease surveillance

Causes of ovine mortality

Figure 19: The causes of mortality in sheep carcases recorded on post-mortem examination by the RVLs during Quarter 4 2015, categorised by the system affected or by cause (n=140).

Figure 20: The ten most common individual diagnoses recorded in sheep carcases on post-mortem examination by the RVLs during Quarter 4 2015 (n=140).

DAFM surveillance reports available at http://www.agriculture.gov.ie/rvlreport/

Figure 21: The relative frequency of respiratory disease diagnoses in sheep as recorded on post-mortem examination by the RVLs during Quarter 4 2015 (n=22).

Figure 22: The relative frequency of alimentary tract disease diagnoses in sheep as recorded on post-mortem examination by the RVLs during Quarter 4 2015 (n=27).

Figure 23: The relative frequency of clostridial disease diagnoses in sheep as recorded on post-mortem examination by the RVLs during Quarter 4 2015 (n=7).

DAFM surveillance reports available at http://www.agriculture.gov.ie/rvlreport/

Ovine abortion

Figure 24: The frequency of detection of abortifacients in ovine foetus during Quarter 4 2015 (n=22).