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<li><a href="./">Disease Surveillance</a></li>
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<li><a href="index.html#section"></a></li>
<li class="chapter" data-level="" data-path="introduction.html"><a href="introduction.html"><i class="fa fa-check"></i>Introduction</a><ul>
<li class="chapter" data-level="0.1" data-path="introduction.html"><a href="introduction.html#passive-surveillance"><i class="fa fa-check"></i><b>0.1</b> Passive surveillance</a></li>
<li class="chapter" data-level="0.2" data-path="introduction.html"><a href="introduction.html#climate-change"><i class="fa fa-check"></i><b>0.2</b> Climate change</a></li>
<li class="chapter" data-level="0.3" data-path="introduction.html"><a href="introduction.html#the-report"><i class="fa fa-check"></i><b>0.3</b> The report</a></li>
</ul></li>
<li class="chapter" data-level="1" data-path="diseases-of-cattle-overview.html"><a href="diseases-of-cattle-overview.html"><i class="fa fa-check"></i><b>1</b> Diseases of Cattle Overview</a><ul>
<li class="chapter" data-level="1.1" data-path="diseases-of-cattle-overview.html"><a href="diseases-of-cattle-overview.html#neonatal-calves-birth-to-one-month-of-age"><i class="fa fa-check"></i><b>1.1</b> Neonatal Calves (birth to one month of age)</a></li>
<li class="chapter" data-level="1.2" data-path="diseases-of-cattle-overview.html"><a href="diseases-of-cattle-overview.html#calves-one-to-five-months-of-age"><i class="fa fa-check"></i><b>1.2</b> Calves (one to five months of age)</a></li>
<li class="chapter" data-level="1.3" data-path="diseases-of-cattle-overview.html"><a href="diseases-of-cattle-overview.html#weanlings-six-months-to-one-year-of-age"><i class="fa fa-check"></i><b>1.3</b> Weanlings (six months to one year of age)</a></li>
<li class="chapter" data-level="1.4" data-path="diseases-of-cattle-overview.html"><a href="diseases-of-cattle-overview.html#adult-cattle-over-12-months-of-age"><i class="fa fa-check"></i><b>1.4</b> Adult Cattle (over 12 months of age)</a></li>
</ul></li>
<li class="chapter" data-level="2" data-path="johnes-disease.html"><a href="johnes-disease.html"><i class="fa fa-check"></i><b>2</b> Johne’s Disease</a><ul>
<li class="chapter" data-level="2.1" data-path="johnes-disease.html"><a href="johnes-disease.html#jd-transmission"><i class="fa fa-check"></i><b>2.1</b> JD transmission</a></li>
<li class="chapter" data-level="2.2" data-path="johnes-disease.html"><a href="johnes-disease.html#jd-diagnostics"><i class="fa fa-check"></i><b>2.2</b> JD Diagnostics</a></li>
<li class="chapter" data-level="2.3" data-path="johnes-disease.html"><a href="johnes-disease.html#post-mortem-examination"><i class="fa fa-check"></i><b>2.3</b> Post mortem examination</a></li>
<li class="chapter" data-level="2.4" data-path="johnes-disease.html"><a href="johnes-disease.html#control-programme"><i class="fa fa-check"></i><b>2.4</b> Control Programme</a><ul>
<li class="chapter" data-level="2.4.1" data-path="johnes-disease.html"><a href="johnes-disease.html#acknowledgement"><i class="fa fa-check"></i><b>2.4.1</b> Acknowledgement</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="3" data-path="clostridial-disease.html"><a href="clostridial-disease.html"><i class="fa fa-check"></i><b>3</b> Clostridial disease</a><ul>
<li class="chapter" data-level="3.1" data-path="clostridial-disease.html"><a href="clostridial-disease.html#blackleg"><i class="fa fa-check"></i><b>3.1</b> Blackleg</a></li>
<li class="chapter" data-level="3.2" data-path="clostridial-disease.html"><a href="clostridial-disease.html#botulism"><i class="fa fa-check"></i><b>3.2</b> Botulism</a></li>
<li class="chapter" data-level="3.3" data-path="clostridial-disease.html"><a href="clostridial-disease.html#malignant-oedema"><i class="fa fa-check"></i><b>3.3</b> Malignant Oedema</a></li>
<li class="chapter" data-level="3.4" data-path="clostridial-disease.html"><a href="clostridial-disease.html#enterotoxaemia"><i class="fa fa-check"></i><b>3.4</b> Enterotoxaemia</a></li>
<li class="chapter" data-level="3.5" data-path="clostridial-disease.html"><a href="clostridial-disease.html#black-disease"><i class="fa fa-check"></i><b>3.5</b> Black Disease</a></li>
<li class="chapter" data-level="3.6" data-path="clostridial-disease.html"><a href="clostridial-disease.html#braxy"><i class="fa fa-check"></i><b>3.6</b> Braxy</a></li>
<li class="chapter" data-level="3.7" data-path="clostridial-disease.html"><a href="clostridial-disease.html#clostridial-abomasitis"><i class="fa fa-check"></i><b>3.7</b> Clostridial abomasitis</a></li>
<li class="chapter" data-level="3.8" data-path="clostridial-disease.html"><a href="clostridial-disease.html#clostridial-vaccination"><i class="fa fa-check"></i><b>3.8</b> Clostridial Vaccination</a></li>
</ul></li>
<li class="chapter" data-level="4" data-path="bovine-neonatal-enteritis.html"><a href="bovine-neonatal-enteritis.html"><i class="fa fa-check"></i><b>4</b> Bovine Neonatal Enteritis</a><ul>
<li class="chapter" data-level="4.1" data-path="bovine-neonatal-enteritis.html"><a href="bovine-neonatal-enteritis.html#neonatal-enteritis"><i class="fa fa-check"></i><b>4.1</b> Neonatal enteritis</a><ul>
<li class="chapter" data-level="4.1.1" data-path="bovine-neonatal-enteritis.html"><a href="bovine-neonatal-enteritis.html#rotavirus-enteritis"><i class="fa fa-check"></i><b>4.1.1</b> Rotavirus enteritis</a></li>
<li class="chapter" data-level="4.1.2" data-path="bovine-neonatal-enteritis.html"><a href="bovine-neonatal-enteritis.html#cryptosporidiosis"><i class="fa fa-check"></i><b>4.1.2</b> <em>Cryptosporidiosis</em></a></li>
<li class="chapter" data-level="4.1.3" data-path="bovine-neonatal-enteritis.html"><a href="bovine-neonatal-enteritis.html#coronavirus-enteritis"><i class="fa fa-check"></i><b>4.1.3</b> Coronavirus enteritis</a></li>
<li class="chapter" data-level="4.1.4" data-path="bovine-neonatal-enteritis.html"><a href="bovine-neonatal-enteritis.html#escherichia-coli-k99"><i class="fa fa-check"></i><b>4.1.4</b> <em>Escherichia coli</em> K99</a></li>
<li class="chapter" data-level="4.1.5" data-path="bovine-neonatal-enteritis.html"><a href="bovine-neonatal-enteritis.html#salmonella-dublin"><i class="fa fa-check"></i><b>4.1.5</b> <em>Salmonella</em> Dublin</a></li>
<li class="chapter" data-level="4.1.6" data-path="bovine-neonatal-enteritis.html"><a href="bovine-neonatal-enteritis.html#campylobacter-jejuni"><i class="fa fa-check"></i><b>4.1.6</b> <em>Campylobacter jejuni</em></a></li>
<li class="chapter" data-level="4.1.7" data-path="bovine-neonatal-enteritis.html"><a href="bovine-neonatal-enteritis.html#giardia-spp."><i class="fa fa-check"></i><b>4.1.7</b> <em>Giardia spp.</em></a></li>
<li class="chapter" data-level="4.1.8" data-path="bovine-neonatal-enteritis.html"><a href="bovine-neonatal-enteritis.html#coccidiosis"><i class="fa fa-check"></i><b>4.1.8</b> Coccidiosis</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="5" data-path="zinc-sulphate-turbidity-zst-test.html"><a href="zinc-sulphate-turbidity-zst-test.html"><i class="fa fa-check"></i><b>5</b> Zinc Sulphate Turbidity (ZST) Test</a><ul>
<li class="chapter" data-level="5.1" data-path="zinc-sulphate-turbidity-zst-test.html"><a href="zinc-sulphate-turbidity-zst-test.html#zst-test-and-the-importance-of-colostrum"><i class="fa fa-check"></i><b>5.1</b> ZST test and the importance of colostrum</a></li>
<li class="chapter" data-level="5.2" data-path="zinc-sulphate-turbidity-zst-test.html"><a href="zinc-sulphate-turbidity-zst-test.html#outline-of-2018-figures"><i class="fa fa-check"></i><b>5.2</b> Outline of 2018 figures</a></li>
<li class="chapter" data-level="5.3" data-path="zinc-sulphate-turbidity-zst-test.html"><a href="zinc-sulphate-turbidity-zst-test.html#shortcomings-in-submission-practices"><i class="fa fa-check"></i><b>5.3</b> Shortcomings in submission practices</a></li>
<li class="chapter" data-level="5.4" data-path="zinc-sulphate-turbidity-zst-test.html"><a href="zinc-sulphate-turbidity-zst-test.html#zst-and-immunoglobulin-classes"><i class="fa fa-check"></i><b>5.4</b> ZST and immunoglobulin classes</a></li>
<li class="chapter" data-level="5.5" data-path="zinc-sulphate-turbidity-zst-test.html"><a href="zinc-sulphate-turbidity-zst-test.html#post-mortem-samples"><i class="fa fa-check"></i><b>5.5</b> <em>Post mortem</em> samples</a></li>
<li class="chapter" data-level="5.6" data-path="zinc-sulphate-turbidity-zst-test.html"><a href="zinc-sulphate-turbidity-zst-test.html#ovine-submissions"><i class="fa fa-check"></i><b>5.6</b> Ovine submissions</a></li>
</ul></li>
<li class="chapter" data-level="6" data-path="bovine-abortion.html"><a href="bovine-abortion.html"><i class="fa fa-check"></i><b>6</b> Bovine Abortion</a><ul>
<li class="chapter" data-level="6.1" data-path="bovine-abortion.html"><a href="bovine-abortion.html#primary-pathogens"><i class="fa fa-check"></i><b>6.1</b> Primary Pathogens</a></li>
<li class="chapter" data-level="6.2" data-path="bovine-abortion.html"><a href="bovine-abortion.html#salmonella-dublin-abortion"><i class="fa fa-check"></i><b>6.2</b> <em>Salmonella Dublin</em> abortion</a><ul>
<li class="chapter" data-level="6.2.1" data-path="bovine-abortion.html"><a href="bovine-abortion.html#listerial-abortion"><i class="fa fa-check"></i><b>6.2.1</b> Listerial abortion</a></li>
<li class="chapter" data-level="6.2.2" data-path="bovine-abortion.html"><a href="bovine-abortion.html#leptospiral-abortion"><i class="fa fa-check"></i><b>6.2.2</b> Leptospiral abortion</a></li>
<li class="chapter" data-level="6.2.3" data-path="bovine-abortion.html"><a href="bovine-abortion.html#minor-primary-abortifacients-sporadic-abortions"><i class="fa fa-check"></i><b>6.2.3</b> Minor Primary Abortifacients (sporadic abortions)</a></li>
</ul></li>
<li class="chapter" data-level="6.3" data-path="bovine-abortion.html"><a href="bovine-abortion.html#protoozoal-abortion"><i class="fa fa-check"></i><b>6.3</b> Protoozoal abortion</a></li>
<li class="chapter" data-level="6.4" data-path="bovine-abortion.html"><a href="bovine-abortion.html#secondary-pathogens"><i class="fa fa-check"></i><b>6.4</b> Secondary Pathogens</a><ul>
<li class="chapter" data-level="6.4.1" data-path="bovine-abortion.html"><a href="bovine-abortion.html#mycotic-abortions"><i class="fa fa-check"></i><b>6.4.1</b> Mycotic abortions</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="7" data-path="bovine-mastitis.html"><a href="bovine-mastitis.html"><i class="fa fa-check"></i><b>7</b> Bovine Mastitis</a><ul>
<li class="chapter" data-level="7.1" data-path="bovine-mastitis.html"><a href="bovine-mastitis.html#milk-culture-in-rvls"><i class="fa fa-check"></i><b>7.1</b> Milk Culture in RVLs</a><ul>
<li class="chapter" data-level="7.1.1" data-path="bovine-mastitis.html"><a href="bovine-mastitis.html#staphylococcus-aureus"><i class="fa fa-check"></i><b>7.1.1</b> <em>Staphylococcus aureus</em></a></li>
<li class="chapter" data-level="7.1.2" data-path="bovine-mastitis.html"><a href="bovine-mastitis.html#streptococcus-uberis"><i class="fa fa-check"></i><b>7.1.2</b> <em>Streptococcus uberis</em></a></li>
<li class="chapter" data-level="7.1.3" data-path="bovine-mastitis.html"><a href="bovine-mastitis.html#truperella-pyogenes"><i class="fa fa-check"></i><b>7.1.3</b> <em>Truperella pyogenes</em></a></li>
</ul></li>
<li class="chapter" data-level="7.2" data-path="bovine-mastitis.html"><a href="bovine-mastitis.html#contaminated-samples"><i class="fa fa-check"></i><b>7.2</b> Contaminated samples</a></li>
</ul></li>
<li class="chapter" data-level="8" data-path="bovine-respiratory-disease-brd.html"><a href="bovine-respiratory-disease-brd.html"><i class="fa fa-check"></i><b>8</b> Bovine Respiratory Disease (BRD)</a><ul>
<li class="chapter" data-level="8.1" data-path="bovine-respiratory-disease-brd.html"><a href="bovine-respiratory-disease-brd.html#bacterial-bovine-respiratory-disease"><i class="fa fa-check"></i><b>8.1</b> Bacterial Bovine Respiratory Disease</a></li>
<li class="chapter" data-level="8.2" data-path="bovine-respiratory-disease-brd.html"><a href="bovine-respiratory-disease-brd.html#viral-bovine-respiratory-disease"><i class="fa fa-check"></i><b>8.2</b> Viral Bovine Respiratory Disease</a></li>
<li class="chapter" data-level="8.3" data-path="bovine-respiratory-disease-brd.html"><a href="bovine-respiratory-disease-brd.html#trends"><i class="fa fa-check"></i><b>8.3</b> Trends</a></li>
<li class="chapter" data-level="8.4" data-path="bovine-respiratory-disease-brd.html"><a href="bovine-respiratory-disease-brd.html#parasitic-bovine-respiratory-disease"><i class="fa fa-check"></i><b>8.4</b> Parasitic Bovine Respiratory Disease</a></li>
</ul></li>
<li class="chapter" data-level="9" data-path="antimicrobial-resistance.html"><a href="antimicrobial-resistance.html"><i class="fa fa-check"></i><b>9</b> Antimicrobial Resistance</a><ul>
<li class="chapter" data-level="9.1" data-path="antimicrobial-resistance.html"><a href="antimicrobial-resistance.html#staphylococcus-aureus-1"><i class="fa fa-check"></i><b>9.1</b> <em>Staphylococcus aureus</em></a></li>
<li class="chapter" data-level="9.2" data-path="antimicrobial-resistance.html"><a href="antimicrobial-resistance.html#streptococcus-uberis-1"><i class="fa fa-check"></i><b>9.2</b> <em>Streptococcus uberis</em></a></li>
<li class="chapter" data-level="9.3" data-path="antimicrobial-resistance.html"><a href="antimicrobial-resistance.html#pasteurella-multocida"><i class="fa fa-check"></i><b>9.3</b> <em>Pasteurella multocida</em></a></li>
<li class="chapter" data-level="9.4" data-path="antimicrobial-resistance.html"><a href="antimicrobial-resistance.html#mannheimia-haemolytica"><i class="fa fa-check"></i><b>9.4</b> <em>Mannheimia haemolytica</em></a></li>
<li class="chapter" data-level="9.5" data-path="antimicrobial-resistance.html"><a href="antimicrobial-resistance.html#escherichia-coli"><i class="fa fa-check"></i><b>9.5</b> <em>Escherichia coli</em></a><ul>
<li class="chapter" data-level="9.5.1" data-path="antimicrobial-resistance.html"><a href="antimicrobial-resistance.html#maldi-tof"><i class="fa fa-check"></i><b>9.5.1</b> Maldi-ToF</a></li>
<li class="chapter" data-level="9.5.2" data-path="antimicrobial-resistance.html"><a href="antimicrobial-resistance.html#whole-genome-sequencing"><i class="fa fa-check"></i><b>9.5.2</b> Whole Genome Sequencing</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="10" data-path="bovine-parasitic-diseases.html"><a href="bovine-parasitic-diseases.html"><i class="fa fa-check"></i><b>10</b> Bovine Parasitic Diseases</a><ul>
<li class="chapter" data-level="10.1" data-path="bovine-parasitic-diseases.html"><a href="bovine-parasitic-diseases.html#trichostrongylidae"><i class="fa fa-check"></i><b>10.1</b> Trichostrongylidae</a><ul>
<li class="chapter" data-level="10.1.1" data-path="bovine-parasitic-diseases.html"><a href="bovine-parasitic-diseases.html#nematodirus-spp."><i class="fa fa-check"></i><b>10.1.1</b> Nematodirus spp.</a></li>
</ul></li>
<li class="chapter" data-level="10.2" data-path="bovine-parasitic-diseases.html"><a href="bovine-parasitic-diseases.html#coccidia"><i class="fa fa-check"></i><b>10.2</b> Coccidia</a><ul>
<li class="chapter" data-level="10.2.1" data-path="bovine-parasitic-diseases.html"><a href="bovine-parasitic-diseases.html#treatment-and-control"><i class="fa fa-check"></i><b>10.2.1</b> Treatment and control</a></li>
</ul></li>
<li class="chapter" data-level="10.3" data-path="bovine-parasitic-diseases.html"><a href="bovine-parasitic-diseases.html#rumen-and-liver-fluke"><i class="fa fa-check"></i><b>10.3</b> Rumen and Liver Fluke</a><ul>
<li class="chapter" data-level="10.3.1" data-path="bovine-parasitic-diseases.html"><a href="bovine-parasitic-diseases.html#treatment-and-control-1"><i class="fa fa-check"></i><b>10.3.1</b> Treatment and Control</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="11" data-path="bovine-viral-diarrhoea-bvd-eradication-programme-and-infectious-bovine-rhinotracheitis.html"><a href="bovine-viral-diarrhoea-bvd-eradication-programme-and-infectious-bovine-rhinotracheitis.html"><i class="fa fa-check"></i><b>11</b> Bovine Viral Diarrhoea (BVD) Eradication Programme and Infectious Bovine Rhinotracheitis</a><ul>
<li class="chapter" data-level="11.1" data-path="bovine-viral-diarrhoea-bvd-eradication-programme-and-infectious-bovine-rhinotracheitis.html"><a href="bovine-viral-diarrhoea-bvd-eradication-programme-and-infectious-bovine-rhinotracheitis.html#bovine-viral-diarrhoea-bvd-eradication-programme"><i class="fa fa-check"></i><b>11.1</b> Bovine viral diarrhoea (BVD) eradication programme</a><ul>
<li class="chapter" data-level="11.1.1" data-path="bovine-viral-diarrhoea-bvd-eradication-programme-and-infectious-bovine-rhinotracheitis.html"><a href="bovine-viral-diarrhoea-bvd-eradication-programme-and-infectious-bovine-rhinotracheitis.html#negative-herd-status-nhs"><i class="fa fa-check"></i><b>11.1.1</b> Negative herd status (NHS)</a></li>
<li class="chapter" data-level="11.1.2" data-path="bovine-viral-diarrhoea-bvd-eradication-programme-and-infectious-bovine-rhinotracheitis.html"><a href="bovine-viral-diarrhoea-bvd-eradication-programme-and-infectious-bovine-rhinotracheitis.html#targeted-advisory-service-on-animal-health-tasah"><i class="fa fa-check"></i><b>11.1.2</b> Targeted Advisory Service on Animal Health (TASAH)</a></li>
</ul></li>
<li class="chapter" data-level="11.2" data-path="bovine-viral-diarrhoea-bvd-eradication-programme-and-infectious-bovine-rhinotracheitis.html"><a href="bovine-viral-diarrhoea-bvd-eradication-programme-and-infectious-bovine-rhinotracheitis.html#infectious-bovine-rhinotracheitis-eradication-programme"><i class="fa fa-check"></i><b>11.2</b> Infectious bovine rhinotracheitis eradication programme</a></li>
</ul></li>
<li class="chapter" data-level="12" data-path="sheep-diseases-overview.html"><a href="sheep-diseases-overview.html"><i class="fa fa-check"></i><b>12</b> Sheep Diseases Overview</a><ul>
<li class="chapter" data-level="12.1" data-path="sheep-diseases-overview.html"><a href="sheep-diseases-overview.html#diseases-of-sheep"><i class="fa fa-check"></i><b>12.1</b> Diseases of Sheep</a></li>
<li class="chapter" data-level="12.2" data-path="sheep-diseases-overview.html"><a href="sheep-diseases-overview.html#lambs-birth-to-12-months-of-age"><i class="fa fa-check"></i><b>12.2</b> Lambs (birth to 12 months of age)</a></li>
<li class="chapter" data-level="12.3" data-path="sheep-diseases-overview.html"><a href="sheep-diseases-overview.html#adult-sheep-over-12-months-of-age"><i class="fa fa-check"></i><b>12.3</b> Adult Sheep (over 12 months of age)</a></li>
</ul></li>
<li class="chapter" data-level="13" data-path="ovine-parasitic-diseases.html"><a href="ovine-parasitic-diseases.html"><i class="fa fa-check"></i><b>13</b> Ovine Parasitic Diseases</a><ul>
<li class="chapter" data-level="13.1" data-path="ovine-parasitic-diseases.html"><a href="ovine-parasitic-diseases.html#agents-of-parasitic-gastroenteritis"><i class="fa fa-check"></i><b>13.1</b> Agents of Parasitic Gastroenteritis</a></li>
<li class="chapter" data-level="13.2" data-path="ovine-parasitic-diseases.html"><a href="ovine-parasitic-diseases.html#trichostrongylidae-1"><i class="fa fa-check"></i><b>13.2</b> Trichostrongylidae</a></li>
<li class="chapter" data-level="13.3" data-path="ovine-parasitic-diseases.html"><a href="ovine-parasitic-diseases.html#nematodirus"><i class="fa fa-check"></i><b>13.3</b> Nematodirus</a></li>
<li class="chapter" data-level="13.4" data-path="ovine-parasitic-diseases.html"><a href="ovine-parasitic-diseases.html#coccidia-1"><i class="fa fa-check"></i><b>13.4</b> Coccidia</a></li>
<li class="chapter" data-level="13.5" data-path="ovine-parasitic-diseases.html"><a href="ovine-parasitic-diseases.html#liver-and-rumen-fluke"><i class="fa fa-check"></i><b>13.5</b> Liver and rumen fluke</a></li>
<li class="chapter" data-level="13.6" data-path="ovine-parasitic-diseases.html"><a href="ovine-parasitic-diseases.html#sarcocystosis-cysticercosis"><i class="fa fa-check"></i><b>13.6</b> Sarcocystosis & Cysticercosis</a></li>
</ul></li>
<li class="chapter" data-level="14" data-path="disease-of-pigs.html"><a href="disease-of-pigs.html"><i class="fa fa-check"></i><b>14</b> Disease of Pigs</a><ul>
<li class="chapter" data-level="14.1" data-path="disease-of-pigs.html"><a href="disease-of-pigs.html#post-mortem-diagnoses"><i class="fa fa-check"></i><b>14.1</b> Post mortem diagnoses</a><ul>
<li class="chapter" data-level="14.1.1" data-path="disease-of-pigs.html"><a href="disease-of-pigs.html#gastrointestinal-disease"><i class="fa fa-check"></i><b>14.1.1</b> Gastrointestinal disease</a></li>
<li class="chapter" data-level="14.1.2" data-path="disease-of-pigs.html"><a href="disease-of-pigs.html#systemic-disease"><i class="fa fa-check"></i><b>14.1.2</b> Systemic disease</a></li>
<li class="chapter" data-level="14.1.3" data-path="disease-of-pigs.html"><a href="disease-of-pigs.html#respiratory-disease"><i class="fa fa-check"></i><b>14.1.3</b> Respiratory disease</a></li>
</ul></li>
<li class="chapter" data-level="14.2" data-path="disease-of-pigs.html"><a href="disease-of-pigs.html#notifiable-disease"><i class="fa fa-check"></i><b>14.2</b> Notifiable disease</a><ul>
<li class="chapter" data-level="14.2.1" data-path="disease-of-pigs.html"><a href="disease-of-pigs.html#african-swine-fever-awareness"><i class="fa fa-check"></i><b>14.2.1</b> African swine fever awareness</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="15" data-path="poultry.html"><a href="poultry.html"><i class="fa fa-check"></i><b>15</b> Poultry</a><ul>
<li class="chapter" data-level="15.1" data-path="poultry.html"><a href="poultry.html#avian-influenza-surveillance"><i class="fa fa-check"></i><b>15.1</b> Avian Influenza Surveillance</a><ul>
<li class="chapter" data-level="15.1.1" data-path="poultry.html"><a href="poultry.html#active-surveillance"><i class="fa fa-check"></i><b>15.1.1</b> Active surveillance</a></li>
<li class="chapter" data-level="15.1.2" data-path="poultry.html"><a href="poultry.html#passive-surveillance-1"><i class="fa fa-check"></i><b>15.1.2</b> Passive surveillance</a></li>
</ul></li>
<li class="chapter" data-level="15.2" data-path="poultry.html"><a href="poultry.html#avian-mycoplasma-surveillance"><i class="fa fa-check"></i><b>15.2</b> Avian Mycoplasma Surveillance</a><ul>
<li class="chapter" data-level="15.2.1" data-path="poultry.html"><a href="poultry.html#active-surveillance-1"><i class="fa fa-check"></i><b>15.2.1</b> Active surveillance</a></li>
<li class="chapter" data-level="15.2.2" data-path="poultry.html"><a href="poultry.html#passive-surveillance-2"><i class="fa fa-check"></i><b>15.2.2</b> Passive surveillance</a></li>
</ul></li>
<li class="chapter" data-level="15.3" data-path="poultry.html"><a href="poultry.html#avian-salmonella-surveillance"><i class="fa fa-check"></i><b>15.3</b> Avian Salmonella surveillance</a></li>
<li class="chapter" data-level="15.4" data-path="poultry.html"><a href="poultry.html#newcastle-disease"><i class="fa fa-check"></i><b>15.4</b> Newcastle Disease</a></li>
<li class="chapter" data-level="15.5" data-path="poultry.html"><a href="poultry.html#disease-diagnostics"><i class="fa fa-check"></i><b>15.5</b> DISEASE DIAGNOSTICS</a></li>
<li class="chapter" data-level="15.6" data-path="poultry.html"><a href="poultry.html#case-reports-in-poultry"><i class="fa fa-check"></i><b>15.6</b> Case reports in poultry</a><ul>
<li class="chapter" data-level="15.6.1" data-path="poultry.html"><a href="poultry.html#tetratrichomonas-gallinarum"><i class="fa fa-check"></i><b>15.6.1</b> <em>Tetratrichomonas gallinarum</em></a></li>
<li class="chapter" data-level="15.6.2" data-path="poultry.html"><a href="poultry.html#gallibacterium-anatis"><i class="fa fa-check"></i><b>15.6.2</b> <em>Gallibacterium anatis</em></a></li>
<li class="chapter" data-level="15.6.3" data-path="poultry.html"><a href="poultry.html#enterococcus-caecorum"><i class="fa fa-check"></i><b>15.6.3</b> <em>Enterococcus caecorum</em></a></li>
<li class="chapter" data-level="15.6.4" data-path="poultry.html"><a href="poultry.html#chronic-cholera"><i class="fa fa-check"></i><b>15.6.4</b> Chronic cholera</a></li>
<li class="chapter" data-level="15.6.5" data-path="poultry.html"><a href="poultry.html#ornithobacterium-rhinotracheale"><i class="fa fa-check"></i><b>15.6.5</b> Ornithobacterium rhinotracheale</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="16" data-path="tb-and-deer-in-ireland.html"><a href="tb-and-deer-in-ireland.html"><i class="fa fa-check"></i><b>16</b> TB and Deer in Ireland</a></li>
<li class="chapter" data-level="17" data-path="r-packages.html"><a href="r-packages.html"><i class="fa fa-check"></i><b>17</b> R packages</a></li>
<li class="chapter" data-level="" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i>References</a></li>
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<li><a href="https://www.agriculture.gov.ie" target="blank"> DAFM webpage</a></li>
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<div id="bovine-neonatal-enteritis" class="section level1">
<h1><span class="header-section-number">Section 4</span> Bovine Neonatal Enteritis</h1>
<p><br><br></p>
<blockquote>
<ul>
<li>Denis Murphy
<ul>
<li>Research Officer, Athlone Reginal Veterinary Laboratory, Coosan, Athlone, Co. Meath</li>
</ul></li>
</ul>
</blockquote>
<hr />
<p><br><br></p>
<blockquote>
<p>Neonatal enteritis is consistently the most frequently diagnosed cause of mortality in calves less than one month old in the Republic of Ireland. It is generally caused by the interaction of one or more infectious enteric pathogens and several predisposing factors.</p>
</blockquote>
<div id="neonatal-enteritis" class="section level2">
<h2><span class="header-section-number">4.1</span> Neonatal enteritis</h2>
<p>The most common clinical presentation in neonatal enteritis is watery diarrhoea (occasionally containing blood) usually leading to dehydration and, in severe cases, progressing to profound weakness and death. In order to identify the enteric pathogens involved in cases of neonatal calf diarrhoea, a series of tests are performed on faecal samples collected at <em>post mortem</em> from affected calf carcases or submitted by veterinary practitioners from clinical cases.</p>
<p>Approximately 1800 such faecal samples were examined in DAFM laboratories in 2018 (Table <a href="bovine-neonatal-enteritis.html#tab:neotabuno">4.1</a>). This section shows the most common infectious agents diagnosed in calves less than one month old. The relative frequency of identification of pathogens in calf faecal samples in the Republic of Ireland in 2018 is plotted in Figure <a href="bovine-neonatal-enteritis.html#fig:neofiguno">4.2</a>. Rotavirus and <em>Cryptosporidium spp.</em> were the most common pathogens identified while <em>E coli</em> K99, coronavirus and <em>Salmonella</em> Dublin were recorded relatively infrequently. <br><br></p>
<table class="table table-striped table-hover table-condensed" style="width: auto !important; margin-left: auto; margin-right: auto;">
<caption>
<span id="tab:neotabuno">Table 4.1: </span>Number of tests and relative frequency of enteropathogenic agents identified in faecal samples of calves up to one month of age in 2018.
</caption>
<thead>
<tr>
<th style="text-align:left;font-weight: bold;color: pnasbluetext;">
Organism
</th>
<th style="text-align:right;font-weight: bold;color: pnasbluetext;">
No. of Tests
</th>
<th style="text-align:right;font-weight: bold;color: pnasbluetext;">
Positive
</th>
<th style="text-align:right;font-weight: bold;color: pnasbluetext;">
Percentage
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;font-style: italic;">
Rotavirus
</td>
<td style="text-align:right;">
1757
</td>
<td style="text-align:right;">
599
</td>
<td style="text-align:right;font-weight: bold;">
34.1
</td>
</tr>
<tr>
<td style="text-align:left;font-style: italic;">
Cryptosporidia
</td>
<td style="text-align:right;">
1871
</td>
<td style="text-align:right;">
413
</td>
<td style="text-align:right;font-weight: bold;">
22.1
</td>
</tr>
<tr>
<td style="text-align:left;font-style: italic;">
Campylobacter Jejuni
</td>
<td style="text-align:right;">
1644
</td>
<td style="text-align:right;">
146
</td>
<td style="text-align:right;font-weight: bold;">
8.9
</td>
</tr>
<tr>
<td style="text-align:left;font-style: italic;">
Giardia
</td>
<td style="text-align:right;">
1080
</td>
<td style="text-align:right;">
87
</td>
<td style="text-align:right;font-weight: bold;">
8.1
</td>
</tr>
<tr>
<td style="text-align:left;font-style: italic;">
Coronavirus
</td>
<td style="text-align:right;">
1763
</td>
<td style="text-align:right;">
23
</td>
<td style="text-align:right;font-weight: bold;">
1.3
</td>
</tr>
<tr>
<td style="text-align:left;font-style: italic;">
E.Coli K99
</td>
<td style="text-align:right;">
1299
</td>
<td style="text-align:right;">
15
</td>
<td style="text-align:right;font-weight: bold;">
1.2
</td>
</tr>
<tr>
<td style="text-align:left;font-style: italic;">
Salmonella Dublin
</td>
<td style="text-align:right;">
1756
</td>
<td style="text-align:right;">
16
</td>
<td style="text-align:right;font-weight: bold;">
0.9
</td>
</tr>
</tbody>
</table>
<p><br><br></p>
<div class="figure" style="text-align: center"><span id="fig:crypto"></span>
<img src="images/crypto.jpg" alt="Cryptosporidial oocysts in a faecal smear, modified Ziehl-Neelsen (ZN) stain. Photo: Cosme Sanchez-Miguel." width="50%" />
<p class="caption">
Figure 4.1: Cryptosporidial oocysts in a faecal smear, modified Ziehl-Neelsen (ZN) stain. Photo: Cosme Sanchez-Miguel.
</p>
</div>
<p><br><br></p>
<div id="rotavirus-enteritis" class="section level3">
<h3><span class="header-section-number">4.1.1</span> Rotavirus enteritis</h3>
<p>Rotavirus (34.09 <em>per cent</em>) has consistently been the most frequently identified pathogen in calf faecal samples in the Republic of Ireland in recent years, its frequency ranging from 30–35 <em>per cent</em> between 2010 and 2018 (Figure <a href="bovine-neonatal-enteritis.html#fig:neofigdos">4.4</a>). Calves are most susceptible to rotavirus enteritis up to three weeks of age. Adult animals are the primary source of rotavirus infection for neonatal calves. The severity of clinical signs depends on several factors including the age of the animal and the immune status of the calf, the latter depends on the absorption of colostral antibodies immediately after birth. Rotavirus targets villi in the upper small intestine causing shortening and fusion of such villi, this results in malabsorption and leads to diarrhoea. Death may ensue due to acidosis, dehydration and starvation.</p>
<div class="figure" style="text-align: center"><span id="fig:neofiguno"></span>
<img src="Surveillance_files/figure-html/neofiguno-1.png" alt="Bovine Neonatal Enteritis. Relative frequency of enteropathogenic agents identified in calf faecal samples tested in 2018." width="576" />
<p class="caption">
Figure 4.2: Bovine Neonatal Enteritis. Relative frequency of enteropathogenic agents identified in calf faecal samples tested in 2018.
</p>
</div>
<p><br><br></p>
</div>
<div id="cryptosporidiosis" class="section level3">
<h3><span class="header-section-number">4.1.2</span> <em>Cryptosporidiosis</em></h3>
<p><em>Cryptosporidium parvum</em> is a small single-cell parasite which causes damage to intestinal epithelial cells of the lower small intestine resulting in mild to severe enteritis, typically affecting calves during their second week of life. Affected calves excrete large numbers of oocysts which are highly resistant and can survive in the environment up to several months under favourable conditions. Transmission between animals is by faecal-oral route, often via a contaminated environment. Control of the parasite is best achieved by strict maintenance of good calf housing hygiene practices and avoiding mixing animals of different ages. Ammonia-based disinfectants are most effective. The prophylactic use of drugs such as halofuginone lactate may also be useful. In addition to causing disease in animals, <em>Cryptosporidium spp.</em> has the potential to cause zoonotic disease especially in immunocompromised humans; therefore farm workers should take appropriate hygiene precautions when handling calves.</p>
<p><br><br></p>
</div>
<div id="coronavirus-enteritis" class="section level3">
<h3><span class="header-section-number">4.1.3</span> Coronavirus enteritis</h3>
<p>Calves are most susceptible to coronavirus enteritis between one and three weeks of age. Coronavirus preferentially infects enterocytes in the lower small intestines and colon, typically resulting in blunting and fusion of villi and mild enterocolitis.</p>
<p><br><br></p>
</div>
<div id="escherichia-coli-k99" class="section level3">
<h3><span class="header-section-number">4.1.4</span> <em>Escherichia coli</em> K99</h3>
<p><em>E. coli</em> K99 is an enterotoxigenic <em>E. coli</em> (ETEC) and an important cause of neonatal enteritis in very young calves, typically less than three days of age. These strains of E. coli preferentially colonise the lower small intestine and produce toxins that cause secretion of water and electrolytes from the intestinal mucosa, resulting in rapid dehydration. The percentage prevalence of <em>E. coli</em> K99 would likely be higher if testing for this enteric pathogen was restricted to animals younger than one week old.</p>
<p><br><br></p>
</div>
<div id="salmonella-dublin" class="section level3">
<h3><span class="header-section-number">4.1.5</span> <em>Salmonella</em> Dublin</h3>
<p><em>Salmonella enterica</em> subsp.<em>enterica</em> serovar Dublin (<em>Salmonella</em> Dublin) is the most common <em>Salmonella</em> serotype that affects calves in the Republic of Ireland and was isolated in 0.91 <em>per cent</em> of neonatal faecal samples cultured in 2018. The relative frequency of detection of <em>Salmonella</em> Dublin from such cases has fallen significantly over the past decade from 3.4 <em>per cent</em> in 2011 to 0.9 <em>per cent</em> in 2018 (Figure <a href="bovine-neonatal-enteritis.html#fig:neofigdos">4.4</a>). It is not clear why this has occurred. <em>Salmonella</em> Dublin infection has a number of clinical presentations in neonatal calves including acute enteritis, osteomyelitis and septicaemia/systemic disease. <em>Salmonella</em> enteritis is characterised by watery mucoid diarrhoea with presence of fibrin and blood. While Salmonella can cause diarrhoea in both adult cattle and calves, infection is more common and often more severe in calves from 10 days to 3 months old. In addition, calves can shed the organism for variable periods of time and/or intermittently depending on the degree of infection (carrier state).</p>
<p><br><br></p>
<style>
div.blue { background-color:#e6f0ff; border-radius: 5px; padding: 20px;}
</style>
<div class="blue">
<p>The basic principles for the prevention and control of neonatal enteritis are enhancing host immunity and reducing the load of enteric pathogens in the environment. The importance of good colostrum management, leading to an adequate passive immunity transfer, in the prevention of calf diarrhoea is a given.</p>
<p>An average 40 <em>Kg</em> calf requires 3 <em>litres</em> of colostrum within 2–4 <em>hours</em> of birth. Thereafter, appropriate nutrition of young calves, including diarrhoeic calves, is essential. Calves should be grouped according to age on dry clean bedding and avoiding high stocking density. There should be good hygiene practices including appropriate disinfection between batches and rapid isolation and treatment of sick calves.</p>
<p>Colostral and milk antibodies against certain bacterial and viral enteric agents can be enhanced by vaccination of the cows during the dry period (passive immunisation).</p>
</div>
<p><br><br></p>
</div>
<div id="campylobacter-jejuni" class="section level3">
<h3><span class="header-section-number">4.1.6</span> <em>Campylobacter jejuni</em></h3>
<p><em>C. jejuni</em> was found in almost 8.88 <em>per cent</em> of neonatal calf faecal samples tested in 2018. It is not considered pathogenic for cattle. However, it is routinely surveyed in neonatal faecal samples because it is a zoonosis and a major cause of gastroenteritis in humans. Therefore, appropriate hygiene precautions should be taken by personnel handling stock.</p>
<p><br><br></p>
</div>
<div id="giardia-spp." class="section level3">
<h3><span class="header-section-number">4.1.7</span> <em>Giardia spp.</em></h3>
<p><em>Giardia spp.</em> is one of the most prevalent and widespread intestinal protozoan parasite in humans and several vertebrate animal species worldwide. The clinical significance of <em>Giardia spp.</em> as enteric pathogen in calves is questionable. While eight strains are recognized, only two strains are thought to be transferable to humans (A&B) and thus potentially zoonotic <span class="citation">(Thompson <a href="#ref-Thompson2004">2004</a>)</span>. Appropriate precautions should be taken by calf handlers.</p>
<p><br><br></p>
<p><br><br></p>
</div>
<div id="coccidiosis" class="section level3">
<h3><span class="header-section-number">4.1.8</span> Coccidiosis</h3>
<p>Coccidiosis is caused by protozoan parasites of the genus <em>Eimeria spp.</em> Only three (<em>Eimeria bovis</em>, <em>Eimeria alabamensis</em> and <em>Eimeria zuernii</em>) out of twelve bovine coocidia species are pathogenic. Some of the non-pathogenic or weakly pathogenic species are capable of producing massive numbers of oocysts, therefore faecal coccidial occyst counts need to be interpreted in conjunction with history and clinical findings. Coccidia damage the epithelial cells lining of the gut causing diarrhoea and possibly dysentery.</p>
<p><br><br></p>
<table class="table table-striped table-hover table-condensed" style="width: auto !important; margin-left: auto; margin-right: auto;">
<caption>
<span id="tab:neotabdos">Table 4.2: </span>Number of tests and relative frequency of coccidiosis in faecal samples of calves up to one month of age in 2018.
</caption>
<thead>
<tr>
<th style="text-align:right;font-weight: bold;color: pnasbluetext;">
No. of Tests
</th>
<th style="text-align:right;font-weight: bold;color: pnasbluetext;">
Positive
</th>
<th style="text-align:right;font-weight: bold;color: pnasbluetext;">
Percentage
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:right;">
610
</td>
<td style="text-align:right;">
107
</td>
<td style="text-align:right;font-weight: bold;">
18
</td>
</tr>
</tbody>
</table>
<p><br><br></p>
<p>Coccidiosis is particularly common in calves between three weeks and six months of age but it can occur in older animals also. Calves become infected when placed in environments contaminated by older cattle or other infected calves, e.g. indoors on bedding, outdoors around drinking and feeding troughs. Poor hygiene, high stocking density and poor health and nutrition will all contribute to a calf becoming infected. The frequency of detection of coccidiosis in neonatal calves less than 1 month old in the Republic of Ireland in 2018 was 18 <em>per cent</em> (Table <a href="bovine-neonatal-enteritis.html#tab:neotabdos">4.2</a>).</p>
<p><br><br></p>
<style>
div.blue { background-color:#e6f0ff; border-radius: 5px; padding: 20px;}
</style>
<div class="blue">
<p>Often, peak coccidia oocyst-shedding does not correlate with the onset of diarrhoea in calves. Detection of <em>Coccidia spp.</em> in faecal samples is facilitated by sampling pre-clinical comrade animals as well as those showing clinical signs.</p>
</div>
<p><br><br></p>
<p><br><br></p>
<div class="figure" style="text-align: center"><span id="fig:cocci"></span>
<img src="images/coccidiosis.jpg" alt="Microphotography of coccidial oocysts in a faecal smear (faecal flotation). Photo: Cosme Sanchez-Miguel." width="50%" />
<p class="caption">
Figure 4.3: Microphotography of coccidial oocysts in a faecal smear (faecal flotation). Photo: Cosme Sanchez-Miguel.
</p>
</div>
<p><br><br></p>
<div class="figure" style="text-align: center"><span id="fig:neofigdos"></span>
<img src="Surveillance_files/figure-html/neofigdos-1.png" alt="Trends in the incidence of Rotavirus, Cryptoporidia and Salmonella Dublin in calves less than one month old with neonatal enteritis." width="576" />
<p class="caption">
Figure 4.4: Trends in the incidence of Rotavirus, Cryptoporidia and Salmonella Dublin in calves less than one month old with neonatal enteritis.
</p>
</div>
<p><br><br></p>
<hr />
</div>
</div>
</div>
<h3>References</h3>
<div id="refs" class="references">
<div id="ref-Thompson2004">
<p>Thompson, RC Andrew. 2004. “The Zoonotic Significance and Molecular Epidemiology of Giardia and Giardiasis.” <em>Veterinary Parasitology</em> 126 (1-2). Elsevier: 15–35.</p>
</div>
</div>
<hr />
<p style="text-align: center;font-size: medium">A cooperative effort between the VLS and the SAT Section of the <a href="https://www.agriculture.gov.ie/">DAFM</a></p>
</section>
</div>
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