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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>
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<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="johnes-disease" class="section level1">
<h1><span class="header-section-number">Section 2</span> Johne’s Disease</h1>
<hr />
<p><br><br></p>
<blockquote>
<ul>
<li>Aideen Kennedy
<ul>
<li>Research Officer, Kilkenny Regional Veterinary Laboratory, DAFM, Leggatsrath, Hebron Road, Kilkenny, Ireland</li>
</ul></li>
</ul>
</blockquote>
<hr />
<p><br><br></p>
<p>Johne’s disease (JD) is a chronic granulomatous enteritis of ruminants caused by <em>Mycobacterium avium subspecies paratuberculosis</em> (MAP). Clinical JD is characterised by diarrhoea and progressive cachexia and ultimately results in death.</p>
<p>In total, seventy seven positive MAP faecal cultures, from 53 different herds, were recorded in 2018 (Figure <a href="johnes-disease.html#fig:jdmap">2.2</a>). Ten herds had more than one positive culture, with seven being the highest number of MAP faecal positive cultures in one single farm. Over 90 <em>per cent</em> of positive animals were female. A mixture of dairy and beef breeds recorded positive results. However, almost 30 <em>per cent</em> of positive samples were from Holstein Friesians (Table <a href="johnes-disease.html#tab:jdtabuno">2.1</a>).</p>
<table class="table table-striped table-hover table-condensed" style="width: auto !important; margin-left: auto; margin-right: auto;">
<caption>
<span id="tab:jdtabuno">Table 2.1: </span>Summary of 2018 MAP positive faecal cultures by breed and gender
</caption>
<thead>
<tr>
<th style="text-align:left;color: pnasbluetext;">
Breed
</th>
<th style="text-align:left;color: pnasbluetext;">
Female
</th>
<th style="text-align:left;color: pnasbluetext;">
Male
</th>
<th style="text-align:left;color: pnasbluetext;">
Total
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
Holstein Friesian
</td>
<td style="text-align:left;">
22 (31.0)
</td>
<td style="text-align:left;">
1 (16.7)
</td>
<td style="text-align:left;font-weight: bold;">
23 (29.9)
</td>
</tr>
<tr>
<td style="text-align:left;">
Limousin
</td>
<td style="text-align:left;">
12 (16.9)
</td>
<td style="text-align:left;">
1 (16.7)
</td>
<td style="text-align:left;font-weight: bold;">
13 (16.9)
</td>
</tr>
<tr>
<td style="text-align:left;">
Charolais
</td>
<td style="text-align:left;">
9 (12.7)
</td>
<td style="text-align:left;">
0 (0.0)
</td>
<td style="text-align:left;font-weight: bold;">
9 (11.7)
</td>
</tr>
<tr>
<td style="text-align:left;">
Friesian
</td>
<td style="text-align:left;">
8 (11.3)
</td>
<td style="text-align:left;">
0 (0.0)
</td>
<td style="text-align:left;font-weight: bold;">
8 (10.4)
</td>
</tr>
<tr>
<td style="text-align:left;">
Jersey
</td>
<td style="text-align:left;">
8 (11.3)
</td>
<td style="text-align:left;">
0 (0.0)
</td>
<td style="text-align:left;font-weight: bold;">
8 (10.4)
</td>
</tr>
<tr>
<td style="text-align:left;">
Aberdeen Angus
</td>
<td style="text-align:left;">
4 (5.6)
</td>
<td style="text-align:left;">
3 (50.0)
</td>
<td style="text-align:left;font-weight: bold;">
7 (9.1)
</td>
</tr>
<tr>
<td style="text-align:left;">
Belgian Blue
</td>
<td style="text-align:left;">
3 (4.2)
</td>
<td style="text-align:left;">
0 (0.0)
</td>
<td style="text-align:left;font-weight: bold;">
3 (3.9)
</td>
</tr>
<tr>
<td style="text-align:left;">
Shorthorn
</td>
<td style="text-align:left;">
1 (1.4)
</td>
<td style="text-align:left;">
1 (16.7)
</td>
<td style="text-align:left;font-weight: bold;">
2 (2.6)
</td>
</tr>
<tr>
<td style="text-align:left;">
Blonde D’Aquitaine
</td>
<td style="text-align:left;">
1 (1.4)
</td>
<td style="text-align:left;">
0 (0.0)
</td>
<td style="text-align:left;font-weight: bold;">
1 (1.3)
</td>
</tr>
<tr>
<td style="text-align:left;">
Hereford
</td>
<td style="text-align:left;">
1 (1.4)
</td>
<td style="text-align:left;">
0 (0.0)
</td>
<td style="text-align:left;font-weight: bold;">
1 (1.3)
</td>
</tr>
<tr>
<td style="text-align:left;">
Norwegian Red
</td>
<td style="text-align:left;">
1 (1.4)
</td>
<td style="text-align:left;">
0 (0.0)
</td>
<td style="text-align:left;font-weight: bold;">
1 (1.3)
</td>
</tr>
<tr>
<td style="text-align:left;">
Partanaise Cross
</td>
<td style="text-align:left;">
1 (1.4)
</td>
<td style="text-align:left;">
0 (0.0)
</td>
<td style="text-align:left;font-weight: bold;">
1 (1.3)
</td>
</tr>
</tbody>
</table>
<p>Latency is a common feature of mycobacterial diseases, animals can remain sub-clinically infected without showing any clinical signs of the disease for many years. Clinical disease is reported to occur most frequently in cattle aged 2–5 <em>years</em>. In line with this, based on a number of assumptions, it is estimated that 50 <em>per cent</em> of animals that tested positive in 2018 were displaying symptoms of JD by four years of age (Figure <a href="johnes-disease.html#fig:jdfiguno">2.3</a>). At time of analysis, all male animals that had a positive result in 2018 were no longer alive and only 24 <em>per cent</em> of positive female animals were still alive (Figure <a href="johnes-disease.html#fig:jdfgstatus">2.4</a>).</p>
<div class="figure" style="text-align: center"><span id="fig:jd"></span>
<img src="images/JD.jpg" alt="Thickened and wrinkled intestinal mucosa (granulomatous enteritis) in the ileum of a cow with Johne's disease (Mycobacterium avium ssp. paratuberculosis). Photo: Cosme Sánchez-Miguel." width="60%" />
<p class="caption">
Figure 2.1: Thickened and wrinkled intestinal mucosa (granulomatous enteritis) in the ileum of a cow with Johne’s disease (Mycobacterium avium ssp. paratuberculosis). Photo: Cosme Sánchez-Miguel.
</p>
</div>
<div class="figure" style="text-align: center"><span id="fig:jdmap"></span>
<img src="Surveillance_files/figure-html/jdmap-1.png" alt="Number of herds by county with at least one animal diagnosed with JD by faecal mycobacterial culture in 2018." width="576" />
<p class="caption">
Figure 2.2: Number of herds by county with at least one animal diagnosed with JD by faecal mycobacterial culture in 2018.
</p>
</div>
<div id="jd-transmission" class="section level2">
<h2><span class="header-section-number">2.1</span> JD transmission</h2>
<p>In many herds, initial introduction of MAP usually occurs as result of acquiring an infected but clinically normal animal. In 2018, a number of animals that subsequently recorded MAP faecal culture positive results underwent multiple herd movements throughout their lifetime, potentially allowing spread of the disease. Five was the greatest number of herd movements recorded by a positive animal, excluding movements to factory or knackery (Table <a href="johnes-disease.html#tab:jdtbdos">2.2</a>).</p>
<table class="table table-striped table-hover table-condensed" style="width: auto !important; margin-left: auto; margin-right: auto;">
<caption>
<span id="tab:jdtbdos">Table 2.2: </span>Movement statistics excluding movements to factory or knackery.
</caption>
<thead>
<tr>
<th style="text-align:right;color: pnasbluetext;">
Minimun
</th>
<th style="text-align:right;color: pnasbluetext;">
Median
</th>
<th style="text-align:right;color: pnasbluetext;">
Maximun
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:right;">
0
</td>
<td style="text-align:right;">
1
</td>
<td style="text-align:right;">
5
</td>
</tr>
</tbody>
</table>
<p>Once MAP is introduced to a herd, infection with MAP is understood to occur, primarily, as a calf. Animals younger than six months are believed to be the most susceptible. Neonates are considered to be at highest risk of acquiring MAP infection due to increased permeability of intestines during the first 24 <em>hours</em> of life and an immature immune system. Older animals are believed to be less susceptible; however, infection can still occur <span class="citation">(Windsor and Whittington <a href="#ref-Windsor201037">2010</a>)</span>.</p>
<p>Severity and rate of JD progression in individual animals are dependent on MAP exposure dose and age at time of infection. Infection usually occurs via the faecal-oral route, although in-utero transmission can also occur. Exposure of calves to adult faeces is the most important risk factor in MAP transmission <span class="citation">(Doré et al. <a href="#ref-Dore2012">2012</a>)</span>. Faecal-oral transmission is facilitated by faecal contamination of feedstuff and calf’s environment, with highest environmental risk factors for neonatal infection being faecal contamination of udders and calving pens. Colostrum and milk from infected cows can also contain quantities of MAP capable of infecting calves. Feeding pooled colostrum or milk from multiple cows of unknown MAP status is considered to increase risk of infection within a herd.</p>
<div class="figure" style="text-align: center"><span id="fig:jdfiguno"></span>
<img src="Surveillance_files/figure-html/jdfiguno-1.png" alt="Survival curves measure how much time elapsed before a certain event occurred. In this case, the event is represented by submission of a faecal sample to an RVL. An assumption is made that faecal samples are submitted soon after the animal displays diarrheoa unresponsive to treatment. 50 \% of animals may have displayed symptoms consistent with the disease by four years of age. The graph on the bottom represents number of animals at risk of developing symptoms over time." width="80%" />
<p class="caption">
Figure 2.3: Survival curves measure how much time elapsed before a certain event occurred. In this case, the event is represented by submission of a faecal sample to an RVL. An assumption is made that faecal samples are submitted soon after the animal displays diarrheoa unresponsive to treatment. 50 % of animals may have displayed symptoms consistent with the disease by four years of age. The graph on the bottom represents number of animals at risk of developing symptoms over time.
</p>
</div>
<div class="figure" style="text-align: center"><span id="fig:jdfgstatus"></span>
<div id="htmlwidget-4353e50f33a37cf82d3a" style="width:60%;height:480px;" class="grViz html-widget"></div>
<script type="application/json" data-for="htmlwidget-4353e50f33a37cf82d3a">{"x":{"diagram":"digraph vtree {\ngraph [layout = dot, compound=true, nodesep=0.1, ranksep=0.5, fontsize=12]\nnode [fontname = Helvetica, fontcolor = black,shape = rectangle, color = black,margin=0.1]\n\nedge[style=solid]\nNode_1->Node_2 Node_1->Node_3\nNode_2->Node_4 Node_2->Node_5\nNode_3->Node_6\n\nNode_1[label=<Total No. of animals<BR/>77> color=black style=\"rounded,filled\" fillcolor=<#EFF3FF>]\nNode_2[label=<Female<BR/>71 (92%)> color=black style=\"rounded,filled\" fillcolor=<#FEE0D2>]\nNode_1[label=<Total No. of animals<BR/>77> color=black style=\"rounded,filled\" fillcolor=<#EFF3FF>]\nNode_3[label=<Male<BR/>6 (8%)> color=black style=\"rounded,filled\" fillcolor=<#DE2D26>]\nNode_4[label=<ALIVE<BR/>17 (24%)> color=black style=\"rounded,filled\" fillcolor=<#DEEBF7>]\nNode_5[label=<Dead<BR/>54 (76%)> color=black style=\"rounded,filled\" fillcolor=<#3182BD>]\nNode_6[label=<Dead<BR/>6 (100%)> color=black style=\"rounded,filled\" fillcolor=<#3182BD>]\n\n}\n","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
<p class="caption">
Figure 2.4: Status of animals diagnosed in 2018 with Johne’s disease as per the 25 of April, 2019
</p>
</div>
<div class="figure" style="text-align: center"><span id="fig:jd2"></span>
<img src="images/Langhans2.jpg" alt="Microphotography of Langhan's-type giant cells (arrows) occasionally observed in tuberculoid granulomas seen in the lamina propia of the small intestine in animals with Johne's disease. Inset: Ziehl-Neelsen stained section showing acid-fast (Mycobacterium avium ssp. paratuberculosis bacilli). Photo: Cosme Sánchez-Miguel." width="60%" />
<p class="caption">
Figure 2.5: Microphotography of Langhan’s-type giant cells (arrows) occasionally observed in tuberculoid granulomas seen in the lamina propia of the small intestine in animals with Johne’s disease. Inset: Ziehl-Neelsen stained section showing acid-fast (Mycobacterium avium ssp. paratuberculosis bacilli). Photo: Cosme Sánchez-Miguel.
</p>
</div>
</div>
<div id="jd-diagnostics" class="section level2">
<h2><span class="header-section-number">2.2</span> JD Diagnostics</h2>
<p>As treatment of MAP is generally regarded as ineffective, diagnostic testing is often used to direct subsequent management decisions (e.g. calf in separate area, cull, etc.) and allow preventative management messures of non-infected herd mates. As MAP is a slow growing bacterium, infection can remain latent for many years making diagnosis difficult. Diagnostic tests currently in use involve either identification of MAP itself (culture), identification of MAP genetic elements (PCR), or detection of the immune response MAP infection elicits (ELISA) <span class="citation">(Behr and Collins <a href="#ref-Behr2010">2010</a>)</span>.</p>
<p>Faecal culture is generally taken as the reference test for MAP. An advantage of culture is that detection of MAP in faecal samples confirms presence of viable MAP in an animal. Due to absent or intermittent shedding of bacteria early in the disease process, sensitivity of culture can be low. Specificity, however, is almost 100 <em>per cent</em>. Due to the fastidious nature of MAP, culture takes a number of weeks. Polymerase Chain Reaction (PCR) is another faecal based test used to detect DNA of MAP, it offers a rapid method of detecting MAP status.</p>
<p>Enzyme Linked Immune Sorbent Assay (ELISA) examines the host’s immune response to MAP and is extensively used for routine diagnosis. ELISA is favoured as a screening test due to its relatively low cost, compared to faecal culture or PCR. ELISAs also provide faster results when compared to culture methods. ELISA relies on identifying serum antibodies to a particular antigen as an indicator of infection. It is important to note that a positive ELISA reaction is NOT confirmation of JD. The specificity of MAP ELISA tests can be influenced by tuberculin testing and by exposure to non-MAP environmental mycobacteria (giving rise to false positive results). The sensitivity of MAP ELISA tests is influenced by stage of infection, high in animals with clinical disease but low in infected animals that are shedding few MAP organisms (where false negative results may arise).</p>
</div>
<div id="post-mortem-examination" class="section level2">
<h2><span class="header-section-number">2.3</span> Post mortem examination</h2>
<p>On post mortem, gross and microscopic lesions associated with JD are primarily confined to the intestine and mesenteric and ileo-caecal lymph nodes. Gross lesions are characterised by thickening and corrugation of intestinal mucosa, most prominent in distal ileum and ileo-caecal valve. Histological lesions associated with JD can vary widely; villi are frequently fused and mucosa is invariably thickened, infiltration of macrophages -including giant cells- is commonly identified in the submucosa and acid fast bacilli are commonly present. JD cannot be diagnosed solely on post mortem, diagnosis needs to be confirmed by faecal culture and/or histology (intestine/lymph nodes).</p>
</div>
<div id="control-programme" class="section level2">
<h2><span class="header-section-number">2.4</span> Control Programme</h2>
<p>A voluntary national JD control programme is on-going in Ireland under the guidance of <a href="http://animalhealthireland.ie/?page_id=340">Animal Health Ireland</a>. The aim is to provide pathways for test-negative and test-positive herds to demonstrate progress towards an improved herd assurance for JD. Primary aspects of this programme involve identification of potentially infected animals via either milk or blood ELISA testing, confirmation relying on faecal based testing. Highlighting on farm management practices using veterinary risk assessment and management plans (VRAMP) is commonly used as a tool in a number of control programmes, including AHI’s JD control programme. VRAMP is a combined work between a farmer and a trained local vet familiar with his/her farm which facilitates identifying specific high risk management practices occurring in such farm that may facilitate spread of JD. Repeat visits allow monitoring of successful implementation of management changes.</p>
<div id="acknowledgement" class="section level3">
<h3><span class="header-section-number">2.4.1</span> Acknowledgement</h3>
<p>Dr Kevin Kenny (TB Section, DAFM) for providing the JD dataset and Alma Wilson (Cork RVL, DAFM) for sorting out this data for analysis.</p>
</div>
</div>
</div>
<h3>References</h3>
<div id="refs" class="references">
<div id="ref-Windsor201037">
<p>Windsor, Peter A., and Richard J. Whittington. 2010. “Evidence for Age Susceptibility of Cattle to Johne’s Disease.” <em>The Veterinary Journal</em> 184 (1): 37–44. doi:<a href="https://doi.org/https://doi.org/10.1016/j.tvjl.2009.01.007">https://doi.org/10.1016/j.tvjl.2009.01.007</a>.</p>
</div>
<div id="ref-Dore2012">
<p>Doré, E., J. Paré, G. Côté, S. Buczinski, O. Labrecque, J.P. Roy, and G. Fecteau. 2012. “Risk Factors Associated with Transmission of Mycobacterium Avium Subsp. Paratuberculosis to Calves Within Dairy Herd: A Systematic Review.” <em>Journal of Veterinary Internal Medicine</em> 26 (1): 32–45. doi:<a href="https://doi.org/10.1111/j.1939-1676.2011.00854.x">10.1111/j.1939-1676.2011.00854.x</a>.</p>
</div>
<div id="ref-Behr2010">
<p>Behr, Marcel A, and Desmond M Collins. 2010. <em>Paratuberculosis: Organism, Disease, Control</em>. CABI.</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>
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