<!DOCTYPE html> <html > <head> <meta charset="UTF-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <title>Section 9 Antimicrobial Resistance | Animal Disease Surveillance</title> <meta name="description" content="This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook."> <meta name="generator" content="bookdown and GitBook 2.6.7"> <meta property="og:title" content="Section 9 Antimicrobial Resistance | Animal Disease Surveillance" /> <meta property="og:type" content="book" /> <meta property="og:description" content="This is a minimal example of using the bookdown package to write a book. 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The output format for this example is bookdown::gitbook." /> <meta name="author" content="Department of Agriculture, Food and the Marine"> <meta name="viewport" content="width=device-width, initial-scale=1"> <meta name="apple-mobile-web-app-capable" content="yes"> <meta name="apple-mobile-web-app-status-bar-style" content="black"> <link rel="prev" href="bovine-respiratory-disease-brd.html"> <link rel="next" href="bovine-parasitic-diseases.html"> <script src="libs/jquery-2.2.3/jquery.min.js"></script> <link href="libs/gitbook-2.6.7/css/style.css" rel="stylesheet" /> <link href="libs/gitbook-2.6.7/css/plugin-table.css" rel="stylesheet" /> <link href="libs/gitbook-2.6.7/css/plugin-bookdown.css" rel="stylesheet" /> <link href="libs/gitbook-2.6.7/css/plugin-highlight.css" rel="stylesheet" /> <link href="libs/gitbook-2.6.7/css/plugin-search.css" rel="stylesheet" /> <link href="libs/gitbook-2.6.7/css/plugin-fontsettings.css" rel="stylesheet" /> <script 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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> <li class="divider"></li> <li><a href="https://www.agriculture.gov.ie" target="blank"> DAFM webpage</a></li> </ul> </nav> </div> <div class="book-body"> <div class="body-inner"> <div class="book-header" role="navigation"> <h1> <i class="fa fa-circle-o-notch fa-spin"></i><a href="./">Animal Disease Surveillance</a> </h1> </div> <div class="page-wrapper" tabindex="-1" role="main"> <div class="page-inner"> <section class="normal" id="section-"> <img src="images/logo.png" align="right" height="130"> <br><br><br><br> <div id="antimicrobial-resistance" class="section level1"> <h1><span class="header-section-number">Section 9</span> Antimicrobial Resistance</h1> <hr /> <p><br><br></p> <blockquote> <ul> <li>William Fitzgerald <ul> <li>Research Officer, Limerick Regional Veterinary Laboratory, Knockalisheen,Limerick, Ireland</li> </ul></li> </ul> </blockquote> <hr /> <p><br><br></p> <p>Antimicrobial Resistance (AMR) is defined by the Office International des Epizooties (OIE) as the emergence of resistance amongst bacteria, viruses, fungi and parasites to products known as antimicrobials that are designed to treat them. The OIE has also stated that ‘the overuse and misuse of antimicrobials in human, animal and plant sectors has dramatically accelerated the emergence of AMR. Consequently, minimising the emergence and spread of AMR requires a co-ordinated, focused, multi-sectoral and multinational effort’.</p> <p>The World Health Organisation (WHO) categorises antimicrobials used in human health as <em>critically important</em>, <em>highly important</em> and <em>important</em> to human health. Critically important antimicrobials (CIAs) should NOT be used as first line of treatment in animals –they should only be used when there is no effective alternative antimicrobials available for target species and indication–.</p> <p>Additionally, some CIAs are further classified as Highest Priority Critically Important Antibiotics (HPCIAs). WHO Highest Priority CIA group contains antimicrobials licensed for use in veterinary medicine including 3<sup>rd</sup> and 4<sup>th</sup> generation cephalosporins, fluoroquinolones, macrolides, and polymyxins. Further information is available in the DAFM webpage <span class="citation">(Department of Agriculture, Food and the Marine <a href="#ref-AIDSR2016">2018</a>)</span>.</p> <p>Every year, the Veterinary Laboratory Service (VLS) handles between 1500–2000 bacterial isolates from multiple species; in 2018, there were 1,826 isolates. As part of DAFM plan to monitor AMR within the Irish animal health sector, VLS focuses on particular patterns of AMR, outlined in Figure <a href="antimicrobial-resistance.html#fig:amrfigdos">9.2</a>.</p> <div class="figure" style="text-align: center"><span id="fig:sensitivity"></span> <img src="images/sensitivity2.jpg" alt="Antibiotic sensitivity test illustrating thin paper disks containing antibiotic placed on an agar plate with growing bacteria. Note the clear zone of inhibition, where bacteria growth around antibiotic disk has been inhibited. Photo: Pat Sheehan." width="50%" /> <p class="caption"> Figure 9.1: Antibiotic sensitivity test illustrating thin paper disks containing antibiotic placed on an agar plate with growing bacteria. Note the clear zone of inhibition, where bacteria growth around antibiotic disk has been inhibited. Photo: Pat Sheehan. </p> </div> <p>A number of antibiotic panels are used across VLS to initially assess levels of AMR nationally, the Respiratory, Enteric, Gram-positive and the Mastitis causing Gram-negative panels (Figure ). Statuary surveillance of AMR in zoonotic and commensal bacteria is carried out by CVRL as part of an EU- wide harmonised monitoring programme , details of which can be found <a href="https://www.agriculture.gov.ie/media/migration/animalhealthwelfare/amr/nationalinterdepartmentalamrconsultativecommittee/OneHealthRptAntimicrobialUseResistance010219.pdf">here</a>.</p> <p><br><br></p> <style> div.blue { background-color:#e6f0ff; border-radius: 5px; padding: 20px;} </style> <div class="blue"> <p>Disk Diffusion Test</p> <p>The Kirby-Bauer test or disk diffusion test, is a standard tool for measuring the effectiveness of antimicrobials against pathogenic microorganisms (Figure <a href="antimicrobial-resistance.html#fig:sensitivity">9.1</a>). Antimicrobial-impregnated paper disks are placed on on a plate that is inoculated to allow growth of the bacteria and time for the agent to diffuse into the agar. As the drug moves through the agar, it establishes a concentration gradient. If the organism is susceptible to it, a clear zone will appear around the disk where growth has been inhibited.</p> <p>The size of this <em>zone of inhibition</em> depends pon the sensitivity of the bacteria to the specific antimicrobial agent and the point at which the chemical’s <em>minimum inhibitory concentration</em> (MIC) is reached.</p> </div> <p><br><br></p> <div class="figure" style="text-align: center"><span id="fig:amrfigdos"></span> <img src="images/AMR2.png" alt="The significant AMR patterns that Veterinary Laboratory Service (VLS) monitors." width="60%" /> <p class="caption"> Figure 9.2: The significant AMR patterns that Veterinary Laboratory Service (VLS) monitors. </p> </div> <div id="staphylococcus-aureus-1" class="section level2"> <h2><span class="header-section-number">9.1</span> <em>Staphylococcus aureus</em></h2> <p>In 2018, there were 407 isolates of <em>Staphylococcus aureus</em> in the VLS. Of these, 392 (96.3 <em>per cent</em>) were susceptible to Tetracycline, 407 (100 <em>per cent</em>) were susceptible to Trimethroprim-Sulphonamide, 403 (99 <em>per cent</em>) were susceptible to Amoxycillin-Clavulanate (Table <a href="antimicrobial-resistance.html#tab:tres">9.1</a>).</p> </div> <div id="streptococcus-uberis-1" class="section level2"> <h2><span class="header-section-number">9.2</span> <em>Streptococcus uberis</em></h2> <p>In 2018, there were 291 <em>Streptococcus uberis</em> isolates in the VLS. Of these, 228 (78.3 <em>per cent</em>) were susceptible to Tetracyclines, 273 (93.8 <em>per cent</em>) were susceptible to Trimethoprim-Sulphonamide, 286 (98.2 <em>per cent</em>) was susceptible to Penicillin, 280 (96.2 <em>per cent</em>) susceptible to Ampicillin and 289 (99.3 <em>per cent</em>) were susceptible to Amoxycillin-Clavulanate (Table <a href="antimicrobial-resistance.html#tab:tres">9.1</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:tres">Table 9.1: </span>Common bacterial isolates detected in the VLS and the level of sensitivity to first-line antibiotics </caption> <thead> <tr> <th style="text-align:left;font-weight: bold;color: pnasbluetext;"> </th> <th style="text-align:left;font-weight: bold;color: pnasbluetext;"> S. aureus (n=407) </th> <th style="text-align:left;font-weight: bold;color: pnasbluetext;"> S. uberis (n=291) </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;font-weight: bold;"> Ampicillin </td> <td style="text-align:left;"> 190 (46.6%) </td> <td style="text-align:left;"> 280 (96.2%) </td> </tr> <tr> <td style="text-align:left;font-weight: bold;"> Tetracycline </td> <td style="text-align:left;"> 392 (96.3%) </td> <td style="text-align:left;"> 228 (78.3%) </td> </tr> <tr> <td style="text-align:left;font-weight: bold;"> Trimethoprim-Sulphonamide </td> <td style="text-align:left;"> 407 (100%) </td> <td style="text-align:left;"> 273 (93.8%) </td> </tr> <tr> <td style="text-align:left;font-weight: bold;"> Florfenicol </td> <td style="text-align:left;"> Not Tested </td> <td style="text-align:left;"> Not tested </td> </tr> <tr> <td style="text-align:left;font-weight: bold;"> Amoxycillin-Clavulanate </td> <td style="text-align:left;"> 403 (99%) </td> <td style="text-align:left;"> 289 (99.3%) </td> </tr> </tbody> </table> <p><br><br></p> <style> div.blue { background-color:#e6f0ff; border-radius: 5px; padding: 20px;} </style> <div class="blue"> <p><strong>Case Study</strong></p> <p><strong>Vancomycin resistant <em>Enterococcus spp.</em> (VRE) in a calf:</strong></p> <p>A single isolate of Vancomycin resistant <em>Enterococcus faecium</em> was confirmed in a calf using WGS. <em>Enterococci</em> are commensal Gram-positive bacteria that form part of the normal gut flora of animals and humans. Vancomycin is a member of the glycopeptide antimicrobial class and is of critical importance in the treatment of infections, caused by drug resistant organisms, such as <em>Staphylococcus aureus</em>. The use of the glycopeptide avoparicin, as a growth promoter in animals, was linked to the emergence of VRE in pigs and poultry and as a result, its use for this purpose was banned in 1996.</p> <p>The level of VRE infection in Irish hospitals is one of the highest in Europe. Hospital outbreaks tend to be associated with a distinct, adapted subpopulation, which are often Ampicillin and Ciprofloxacin resistant. The latter is an unusual finding in animal derived isolates and the role of animals as a potential reservoir of resistance for human epidemic <em>Enterococcus</em> strains remains unclear.</p> </div> <p><br><br></p> </div> <div id="pasteurella-multocida" class="section level2"> <h2><span class="header-section-number">9.3</span> <em>Pasteurella multocida</em></h2> <p>In 2018, there were 181 isolates of <em>Pasteurella multocida</em> in the VLS. Of these, 173 (99.5 <em>per cent</em>) were susceptible to Tetracycline, 177 (97.7 <em>per cent</em>) was susceptible to Trimethoprim-Sulphonamide, 159 (87.8 <em>per cent</em>) were susceptible to Florfenicol, 179 (98.9 <em>per cent</em>) were susceptible to Amoxycillin-Clavulanate (Table <a href="antimicrobial-resistance.html#tab:dos">9.2</a>).</p> <p><br><br></p> <style> div.blue { background-color:#e6f0ff; border-radius: 5px; padding: 20px;} </style> <div class="blue"> <p><strong>Case Study</strong></p> <p><strong>AMR in Pasteurella multocida</strong></p> <p><em>Pasteurella multocida</em> frequently exists as a commensal bacterium of the respiratory tract in animals but it may act also as a primary or secondary pathogen. In 2018, almost 90 <em>per cent of </em>P. multocida* isolates were susceptible to all of the antimicrobials in the respiratory panel (Ampicillin, Amoxicillin-Clavulanate, Ceftiofur, Tetracycline, Sulfamethoxazole-Trimethoprim, Enrofloxacin, Florfenicol, Tulathromycin and Tilmicosin).</p> <p>To date, 1 multi-drug resistant isolate of <em>P. multocida</em> from 2018 has undergone WGS. Resistance genes for Aminglycoside, Macrolide, Sulphonamide, and Tetracycline resistance were identified in the strain, which originated from the lung tissue of a weanling calf. The calf was one of at least seven that died during a large outbreak of respiratory disease and it had concurrent lungworm infestation. It is planned to continue with the genotypic characterisation of resistant <em>P. multocida</em> in 2019.</p> </div> <p><br><br></p> </div> <div id="mannheimia-haemolytica" class="section level2"> <h2><span class="header-section-number">9.4</span> <em>Mannheimia haemolytica</em></h2> <p>In 2018, there were 150 isolates of <em>Mannheimia haemolytica</em>. Of these, 135 (90 <em>per cent</em>) was susceptible to Tetracycline, 146 (97.3 <em>per cent</em>) were susceptible to Trimethoprim-Sulphonamide and 149 (99.3 <em>per cent</em>) were susceptible to Amoxycillin-Clavulanate and Florfenicol (Table <a href="antimicrobial-resistance.html#tab:dos">9.2</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:dos">Table 9.2: </span>Common bacterial isolates detected in the VLS and the level of sensitivity to first-line antibiotics (continued) </caption> <thead> <tr> <th style="text-align:left;font-weight: bold;color: pnasbluetext;"> </th> <th style="text-align:left;font-weight: bold;color: pnasbluetext;"> M. haemolytica (n=150) </th> <th style="text-align:left;font-weight: bold;color: pnasbluetext;"> P. multocida (n=181) </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;font-weight: bold;"> Ampicillin </td> <td style="text-align:left;"> 143 (95.3%) </td> <td style="text-align:left;"> 169 (93.4%) </td> </tr> <tr> <td style="text-align:left;font-weight: bold;"> Tetracycline </td> <td style="text-align:left;"> 135 (90%) </td> <td style="text-align:left;"> 173 (95.6%) </td> </tr> <tr> <td style="text-align:left;font-weight: bold;"> Trimethoprim-Sulphonamide </td> <td style="text-align:left;"> 146 (97.3%) </td> <td style="text-align:left;"> 177 (97.8%) </td> </tr> <tr> <td style="text-align:left;font-weight: bold;"> Florfenicol </td> <td style="text-align:left;"> 149 (99.3%) </td> <td style="text-align:left;"> 159 (87.8%) </td> </tr> <tr> <td style="text-align:left;font-weight: bold;"> Amoxycillin-Clavulanate </td> <td style="text-align:left;"> 149 (99.3%) </td> <td style="text-align:left;"> 179 (98.9%) </td> </tr> </tbody> </table> </div> <div id="escherichia-coli" class="section level2"> <h2><span class="header-section-number">9.5</span> <em>Escherichia coli</em></h2> <p>In 2018, there were 268 isolates of <em>Escherichia coli</em> in the VLS. Of these, 191 (71.2%) were susceptible to Tetracycline, 230 (85.8%) were susceptible to Trimethoprim-Sulphonamide and 229 (85.4%) were susceptible to Amoxycillin-Clavulanate (Table <a href="antimicrobial-resistance.html#tab:uno">9.3</a>).</p> <p><br><br></p> <style> div.blue { background-color:#e6f0ff; border-radius: 5px; padding: 20px;} </style> <div class="blue"> <p><strong>Case Study</strong></p> <p><strong>Multiple Drug Resistant <em>Escherichia coli</em> on a suckler farm:</strong></p> <p><em>Escherichia coli</em> was isolated from the organs and faeces of animals from a farm that was experiencing high mortality rates due to cases of enteritis and unresponsive post- operative infections. Evaluation of the bacterial genome confirmed that the strain was pathogenic to cattle and that its virulence genes were not targeted by commercially available vaccines.</p> <p>Genes encoding resistance to beta lactam antimicrobials, included extended spectrum Beta-lactams, Fluoroquinolones, Phenicols, Aminoglycosides, Sulphonamides and Tetracyclines were identified.</p> </div> <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:uno">Table 9.3: </span>Common bacterial isolates detected in the VLS and the level of sensitivity to first-line antibiotics (continued) </caption> <thead> <tr> <th style="text-align:left;font-weight: bold;color: pnasbluetext;"> </th> <th style="text-align:left;font-weight: bold;color: pnasbluetext;"> E. coli (n=268) </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;font-weight: bold;"> Ampicillin </td> <td style="text-align:left;"> Not tested </td> </tr> <tr> <td style="text-align:left;font-weight: bold;"> Tetracycline </td> <td style="text-align:left;"> 191 (71.2%) </td> </tr> <tr> <td style="text-align:left;font-weight: bold;"> Trimethoprim-Sulphonamide </td> <td style="text-align:left;"> 230 (85.8%) </td> </tr> <tr> <td style="text-align:left;font-weight: bold;"> Florfenicol </td> <td style="text-align:left;"> Not Tested </td> </tr> <tr> <td style="text-align:left;font-weight: bold;"> Amoxycillin-Clavulanate </td> <td style="text-align:left;"> 229 (85.4%) </td> </tr> </tbody> </table> <p>Figure 3: Antibiotic panels used in the VLS and their constituent antibiotics</p> <br><br> <style> div.blue { background-color:#e6f0ff; border-radius: 5px; padding: 20px;} </style> <div class="blue"> <p><em>Respiratory Panel</em></p> <ul> <li>Ampicillin</li> <li>Amoxicillin Clavulanate</li> <li>Ceftiofur</li> <li>Tetracycline</li> <li>Sulfamethoxazole & Trimethoprim</li> <li>Enrofloxacin</li> <li>Florfenicol</li> <li>Tulathromycin</li> <li>Timlicosin</li> </ul> </div> <p><br><br></p> <br><br> <style> div.blue { background-color:#e6f0ff; border-radius: 5px; padding: 20px;} </style> <div class="blue"> <p><strong>Enteric Panel</strong></p> <ul> <li>Ampicillin</li> <li>Amoxicillin Clavulanate</li> <li>Ceftiofur</li> <li>Tetracycline</li> <li>Sulfamethoxazole & Trimethoprim</li> <li>Enrofloxacin</li> <li>Neomycin</li> <li>Cefpodoxime</li> <li>Streptomycin</li> </ul> </div> <p><br><br></p> <br><br> <style> div.blue { background-color:#e6f0ff; border-radius: 5px; padding: 20px;} </style> <div class="blue"> <p><strong>Gram-Positive</strong></p> <ul> <li>Ampicillin</li> <li>Amoxicillin Clavulanate</li> <li>Ceftiofur</li> <li>Tetracycline</li> <li>Sulfamethoxazole & Trimethoprim</li> <li>Cephalothin</li> <li>Cefoxitin</li> <li>Pirlimycin</li> <li>Kanamycin</li> <li>Erythromycin</li> <li>Cephalexin & Kanamycin</li> </ul> </div> <p><br><br></p> <br><br> <style> div.blue { background-color:#e6f0ff; border-radius: 5px; padding: 20px;} </style> <div class="blue"> <p><strong>Mastitis Causing Gram-Negative Panel</strong></p> <ul> <li>Ampicillin</li> <li>Amoxicillin Clavulanate</li> <li>Ceftiofur</li> <li>Tetracycline</li> <li>Sulfamethoxazole & Trimethoprim</li> <li>Enrofloxacin</li> <li>Neomycin</li> <li>Streptomycin</li> <li>Kanamycin</li> <li>Cefpodoxime</li> <li>Cephalexin & Kanamycin</li> </ul> </div> <p><br><br></p> <div id="maldi-tof" class="section level3"> <h3><span class="header-section-number">9.5.1</span> Maldi-ToF</h3> <p>One of the more recent advancements in clinical veterinary bacteriology which has helped immensely in relation to identification of pathogens is the use of Maldi-ToF Mass Spectrometry. MALDI is the abbreviation for Matrix Assisted Laser Desorption/Ionization, TOF is Time of Flight. A portion of a colony of the microbe in question is placed onto the sample target and overlaid with matrix. The mass spectra generated are analyzed by dedicated software and compared with stored profiles. Species identification by this procedure is much faster, more accurate and cheaper than other procedures based on immunological or biochemical tests. Maldi ToF can also be used to predict the antibiotic susceptibility of a bacterial species. In 2018, this technique was used to confirm the identity of 588 isolates within DAFMs Veterinary Laboratory Service.</p> <div class="figure" style="text-align: center"><span id="fig:unnamed-chunk-82"></span> <img src="images/Malditof.jpg" alt="Sequencing platform for the generation of whole genome sequences. Photo: Rosemarie Slowey." width="60%" /> <p class="caption"> Figure 9.3: Sequencing platform for the generation of whole genome sequences. Photo: Rosemarie Slowey. </p> </div> </div> <div id="whole-genome-sequencing" class="section level3"> <h3><span class="header-section-number">9.5.2</span> Whole Genome Sequencing</h3> <p>Sequencing of bacterial DNA sequences (whole genome sequencing, WGS) has been undertaken in the VLS since 2016. These sequences can be screened for antimicrobial resistance and virulence genes and sequences compared to evaluate the relatedness of the strains, which is particularly important in outbreak investigations. WGS has been used to confirm unusual resistance patterns initially detected in the RVLs.</p> </div> </div> </div> <h3>References</h3> <div id="refs" class="references"> <div id="ref-AIDSR2016"> <p>Department of Agriculture, Food and the Marine. 2018. “Policy on Highest Priority Critically Important Antimicrobials.” Dept. of Agriculture, Food; the Marine. <a href="https://www.agriculture.gov.ie/media/migration/animalhealthwelfare/amr/PolicyHighestPriorityCriticallyImpAntimicrobials191118.pdf" class="uri">https://www.agriculture.gov.ie/media/migration/animalhealthwelfare/amr/PolicyHighestPriorityCriticallyImpAntimicrobials191118.pdf</a>.</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> </div> </div> <a href="bovine-respiratory-disease-brd.html" class="navigation navigation-prev " aria-label="Previous page"><i class="fa fa-angle-left"></i></a> <a href="bovine-parasitic-diseases.html" class="navigation navigation-next " aria-label="Next page"><i class="fa fa-angle-right"></i></a> </div> </div> <script src="libs/gitbook-2.6.7/js/app.min.js"></script> <script src="libs/gitbook-2.6.7/js/lunr.js"></script> <script src="libs/gitbook-2.6.7/js/plugin-search.js"></script> <script src="libs/gitbook-2.6.7/js/plugin-sharing.js"></script> <script src="libs/gitbook-2.6.7/js/plugin-fontsettings.js"></script> <script src="libs/gitbook-2.6.7/js/plugin-bookdown.js"></script> <script src="libs/gitbook-2.6.7/js/jquery.highlight.js"></script> <script> gitbook.require(["gitbook"], function(gitbook) { gitbook.start({ "sharing": { "github": false, "facebook": true, "twitter": true, "google": false, "linkedin": false, "weibo": false, "instapaper": false, "vk": false, "all": ["facebook", "google", "twitter", "linkedin", "weibo", "instapaper"] }, "fontsettings": { "theme": "white", "family": "sans", "size": 2 }, "edit": { "link": null, "text": null }, "history": { "link": null, "text": null }, "download": [["ADSR_2018_Compressed_29_7_2019.v2.pdf", "ADSR-2018"]], "toc": { "collapse": "section", "scroll_highlight": true } }); }); </script> </body> </html>