Herdowners User Guide for the ICBF March 2020 FINAL

Johne’s disease leaflet series

ANIMAL HEALTH IRELAND Contributing to a profitable and sustainable farming and agri-food sector through improved animal health

Herdowner’s User Guide for the Johne’s Disease Screen on ICBF

Johne's Control AnimalHealthIreland.ie

JOHNE’S DISEASE CONTROL PROGRAMME Animal Health Ireland, 2-5 The Archways, Carrick-on-Shannon, Co. Leitrim, N41WN27

CONTENTS

ABOUT THE USER GUIDE .................................................................................................................3

GUIDE TO THE JOHNE’S DISEASE SCREEN

A. COMMON QUESTIONS . ..............................................................................................................4 A1. Animal testing.................................................................................................................................. 5 A2. Results.............................................................................................................................................. 5 A3. VRAMP............................................................................................................................................. 6 B. GENERAL ............................................................................................................................................7 B1. Accessing the ICBF website. ............................................................................................................ 7 B2. Accessing the Johne’s disease Screen.............................................................................................8 C. THE JOHNE’S DISEASE SCREEN ................................................................................................9 C1. Introduction..................................................................................................................................... 9 C2. Herd details section.......................................................................................................................12 C3. Test results (summary table and graph) section...........................................................................14 C4. Reports section..............................................................................................................................17 View laboratory results by herd test (batch) date....................................................................17 View status of every animal currently on the farm. .................................................................18 View status of every animal that has left the farm since the date of enrolment.....................19

ABOUT THE USER GUIDE

The purpose of this User Guide is to assist herdowners who are registered in the Irish Johne’s Control Programme (IJCP) to access and use their herds’ Johne’s disease Screens on the Irish Cattle Breeding Federation (ICBF) website. The Johne’s disease Screen presents each herd’s history for Johne’s disease (JD) testing and VRAMPs. This information is useful to herdowners for monitoring and planning their activities and outcomes under the IJCP for the prevention, management and control of Johne’s disease. For ease of use this guide is arranged into the following sections:

A. Common questions B. General C. Johne’s disease Screens

a. Herd details b. Test results c. Reports

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HERDOWNER’S USER GUIDE FOR THE JOHNE’S DISEASE SCREEN ON ICBF

A. COMMON QUESTIONS | B. General | C. Johne’s disease Screen

A. COMMON QUESTIONS

This section provides quick and simple answers for users who already have a basic understanding of the AHI Screens. Other users may need to refer to more detailed information in sections B and C. These sections provide more information about the Johne’s disease Screen.

Figure 1. Key information for herdowners

❶ Select year ❷ Summary test results ❸ Date of last VRAMP ❹ View all results in selected year

❺ Whole herd test completed ❻ Filter field for animal tag number ❼ Animal tag number

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HERDOWNER’S USER GUIDE FOR THE JOHNE’S DISEASE SCREEN ON ICBF

A. COMMON QUESTIONS | B. General | C. Johne’s disease Screen

A1. ANIMAL TESTING

NOTE: The red-spot references below refer to Figure 1 showing the location on the Johne’s disease Screen of key information. Q1. What animals do I need to test this year (before I commence testing)? A whole herd test (WHT) requires that all eligible animals are sampled i.e. those aged two years and above in the herd on the date that sampling begins (defined as date on which results for 10 or more animals are submitted to the ICBF database). This date is not available to ICBF until the first test has been conducted. Where only some of the animals in the herd have been sampled, a list of remaining eligible animals can be accessed (see Q3). Q2. Has my Whole Herd Test been completed this year? In the Herd Details section to the left of the screen, the item Whole herd test completed❺ shows whether the WHT is completed Yes , Not yet complete , or Not yet started. Q3. To complete my Whole Herd Test this year, what animals do I still have to test? If the WHT has started, the number of animals which have been tested and those that have not been tested are shown as a bar-chart by clicking on the text of Yes , or Not yet complete. ❺ This will display details of the WHT status, and a horizontal bar chart of the proportion of eligible animals tested, eligible untested animals still on the farm, and eligible untested animals that have left the farm. Clicking on any one of these sections of the bar chart will display a list of the eligible animals in that section and their test status. If eligible untested animals are shown, contact your approved veterinary practitioner to either complete your WHT or excuse non-breeding separate animals from testing. A2. RESULTS Q4. What are the results of testing? Test results are prominently displayed in the centre of the Johne’s disease Screen. ❷ You can select whether you see these as a table or as a graph, and you can see further details of each cell of information by clicking on it. Take care to select the correct year (top of screen) that you want to display. Also take care that in the graph view, relatively small bars may be difficult to discern.

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HERDOWNER’S USER GUIDE FOR THE JOHNE’S DISEASE SCREEN ON ICBF

A. COMMON QUESTIONS | B. General | C. Johne’s disease Screen

Q5. How do I view the test results of a single animal in my herd? Under Herd Details , click on View all results in selected year ❹ to load a list of animals tested in the current year. This will display the seven most recent test results, up to the year selected, for each animal. Find the desired animal in the list either by scrolling down the page or by typing the tag number of the desired animal in the Tag filter❻ above the list of animals. (If the desired animal is not shown, you may need to select a different year (at the top of the screen) ❶ to match when the animal was tested.) Further test results and other relevant information about the animal may be seen by clicking on the Tag number ❼ to display a drop-down screen. A3. VRAMP Q6. When was my most recent VRAMP done? The Date of last VRAMP❸ is displayed in the Herd Details section to the left of the screen. Q7. What were the contents of my VRAMP? This information is not currently available on the Johne’s disease Screen. Contact your Approved Veterinary Practitioner.

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HERDOWNER’S USER GUIDE FOR THE JOHNE’S DISEASE SCREEN ON ICBF

A. Common Questions | B. GENERAL | C. Johne’s disease Screen

B. GENERAL

B1. ACCESSING THE ICBF WEBSITE

1. Access the ICBF database by typing www.icbf.com into your Web browser (Figure 1a). NOTE: Google Chrome is preferred, but other browsers such as Microsoft Edge, Firefox, Sierra for Mac, etc. should also work without problems, but are not officially supported. 2. Log in to the ICBF database using the login obtained from ICBF (Figure 1b).

Figure 1a. Landing page for ICBF

Figure 1b. ICBF log-in page

Your Username is your Herd number or unique Identifier and your password is a minimum of 6 characters. If you have forgotten your password, contact ICBF by either: • Email to query@icbf.com • Phone 023 882 0452 [9am – 5.30pm], or • Text the word PASS to 089 457 7663 to receive your password. NOTE : Your mobile number needs to be stored on ICBF for this option. For security, do not share your log-in details. Once you have logged in to the ICBF website, you will see a menu bar running along the top of the screen, useful links on the right, and tabs to herd information in the middle of the screen (Figure 1c). The menu bar across the top is retained in all ICBF herd screens.

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HERDOWNER’S USER GUIDE FOR THE JOHNE’S DISEASE SCREEN ON ICBF

A. Common Questions | B. GENERAL | C. Johne’s disease Screen

Figure 1c. Herdowner’s homepage on ICBF

B2. ACCESSING THE JOHNE’S DISEASE SCREEN To access the Johne’s disease Screen, hover your cursor over SERVICES in the menu bar at the top of the screen, then click on AHI Animal Health (Figure 1d).

Figure 1d. Select AHI Animal Health

Click on the icon for Johne’s Control (Figure 1e) to launch the Johne’s disease Screen for your herd.

Figure 1e. Launching the Johne’s disease Screen

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HERDOWNER’S USER GUIDE FOR THE JOHNE’S DISEASE SCREEN ON ICBF

A. Common Questions | B. GENERAL | C. JOHNE’S DISEASE SCREEN

C. JOHNE’S DISEASE SCREEN

C1. INTRODUCTION

The Current Johne’s Herd Status screen (Figure 2a) provides data on the testing of the herd in any selected year and the current VRAMP status.

Figure 2a. Johne’s disease Screen

Immediately under the menu bar, you can select the year for the the test data you wish to view. You can only select one year at a time. The selection defaults to the current year. There are three sections in the middle of the screen, for Herd Details, Test results for the selected year, and various reports. These sections are described below. Test results are colour-coded to assist with the quick identification of animals and results. Test-positive results are colour-coded red, test-inconclusive are coloured yellow and test-negative results are coloured green. Untested animals have a results field which is empty and un-coloured. It is important to check the test type (ELISA on milk or blood, or PCR or culture on faeces) associated with a positive (red) or inconclusive (yellow) result.

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HERDOWNER’S USER GUIDE FOR THE JOHNE’S DISEASE SCREEN ON ICBF

A. Common Questions | B. GENERAL | C. JOHNE’S DISEASE SCREEN

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Figure 2b. Rows of animal tests displayed at the bottom of the screen

There are many displays in the Johne’s disease Screen that present lists of animals as a table at the bottom of the screen, such as in Figure 2b. Sometimes you may need to scroll down to see these tables. These tables may be downloaded readily to print, or as a PDF document, or to a spreadsheet file, by clicking on the appropriate button to the top-right of the table. Note that once downloaded they still need to be opened to view, by clicking on the downloaded file (usually at the bottom of the screen), the spreadsheet file which has been downloaded and opened should be converted from the CSV format to Excel or similar for saving. The table may also be manipulated on-screen without being downloaded. Use the arrows in the header row to sort the rows (e.g. clicking on the arrow in the DOB column will sort the column from oldest to youngest; clicking again will re-sort from youngest to oldest). Use the filtering row above the table to search and to filter. To simplify the screen, the filtering row may be simply hidden (and retrieved) by using the button labelled either Hide filters or Show filters . Click on an animal’s tag number to display a drop-down screen (Figure 2c) of further ICBF information relevant to JD about that animal. This individual animal information includes details of the animal’s pedigree, including dam, sire, date of birth and complete testing history, as well as animal’s current status regarding date of entry and how long it has been in the herd (or date of departure). This display of individual animal details is available on all screens where individual animals are listed.

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HERDOWNER’S USER GUIDE FOR THE JOHNE’S DISEASE SCREEN ON ICBF

A. Common Questions | B. GENERAL | C. JOHNE’S DISEASE SCREEN

Figure 2c. Drop-down screen of individual animal details

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HERDOWNER’S USER GUIDE FOR THE JOHNE’S DISEASE SCREEN ON ICBF

A. Common Questions | B. GENERAL | C. JOHNE’S DISEASE SCREEN

C2. HERD DETAILS SECTION

The left-hand section on this screen provides a summary of herd information and includes several hyperlinks.

Figure 2d. Herd Details screen The Date of most recent enrolment in the IJCP is the date the herd was enrolled in the current year of the Programme. For herds that were enrolled prior to the current year, this date will be 1-Jan- of the current year, and the Date of initial enrolment in the IJCP displays the herd’s commencement date in the preceding Pilot Programme, Phase I or Phase 2. The Date of last positive faecal culture or PCR is a quick reference to whether the herd has a prior confirmation by ancillary test of Johne’s disease. The Date of last VRAMP displays the date of upload of the most recent VRAMP. The contents of the VRAMP are not accessible from the Johne’s disease Screen; you must contact your AVP to obtain or view a copy of a VRAMP. By clicking the View all results in selected year hyperlink, you can see the results for all animals which were tested in the year selected. The results are displayed below the middle section of the Current Johne’s Herd Status screen (Figure 2e). Use the scroll bar to view the data. It should be noted that this list may include test results which occurred in the selected year for animals which have since left the herd. It may also include test results for animals which were not eligible for testing under the IJCP because they were under two years of age, but were tested anyway.

Figure 2e. Display of View all results in selected year

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HERDOWNER’S USER GUIDE FOR THE JOHNE’S DISEASE SCREEN ON ICBF

A. Common Questions | B. GENERAL | C. JOHNE’S DISEASE SCREEN

The list of individual animals displays current and previous JD test results. The Herd Details also displays the dates of the last TB test and the next scheduled TB test. A TB test may interfere during the following 90 days with an ELISA test for Johne’s disease. Displaying these TB test dates enables appropriate interpretation and follow up of ELISA test results for samples taken during the 90 days after a TB test and to plan blood or milk sampling to avoid interference. The item Whole Herd Test Completed shows the status of the WHT for the selected year, and displays as Yes for WHT Completed, Not Yet Started , or Not Yet Complete . Clicking on Yes or Not Yet Complete displays details of the WHT status, and a horizontal bar chart and list of eligible animals and their test status is displayed at the bottom of the screen (Figure 2f). The descriptor of untested animals refers to eligible animals that were in the herd on the date that the WHT for the current year commenced but have not yet been tested in that year. This bar chart and the list are particularly useful to identify untested eligible animals. Some of these animals may have left the herd.

Figure 2f. Display of details of progress towards completion of Whole Herd Test

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HERDOWNER’S USER GUIDE FOR THE JOHNE’S DISEASE SCREEN ON ICBF

A. Common Questions | B. GENERAL | C. JOHNE’S DISEASE SCREEN

C3. TEST RESULTS (SUMMARY TABLE AND GRAPH) SECTION

The central section of the Dashboard/Current Johne’s Herd Status screen provides a summary of the testing history of the herd for the year that has been selected. This summary may be viewed as either a table (default view, or select the tab, Summary Table ) (Figure 3a), or as a graph (select Summary Graph ) (Figure 3b).

Figure 3a. Summary table of test results

Figure 3b. Summary table of test results

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HERDOWNER’S USER GUIDE FOR THE JOHNE’S DISEASE SCREEN ON ICBF

A. Common Questions | B. GENERAL | C. JOHNE’S DISEASE SCREEN

The table and graph display the results of testing for the selected year. The results are reported as positive, inconclusive or negative for ELISA, and positive or negative for culture and PCR. The test date is the date that samples are received in the laboratory; this may be some days after the date that samples were collected from the farm. All animals tested for Johne’s disease at a particular event, including those that may have since left the herd and those which may have been ineligible (tested, but not required by the programme) under the IJCP, are reported. The summary test information does not display untested eligible animals; they are displayed in the item Whole Herd Test Completed in the Herd Details section, as explained above. The summary test information is displayed as the number of animals in a result category reported for each specific test event (date). It is easy to see how many positive, negative or inconclusive results there are for any test event. Within this Summary Table , click on any reported result to load a listing of those individual animals and their test details (scroll down the screen to view) (Figure 3c).

Figure 3c. Display of all individual animals in a single test cell in the test results table

In the Summary Graph view, hovering over a particular coloured result within a given column of the graph brings up the descriptor of that colour (e.g. ELISA Negative), the number of animals assigned that result and the proportion of all tests on that date which this represents. To see further details of these animals, click on the relevant colour within a column to load a listing (Figure 3d) of those individual animals and their test details; this is similar to displaying all individual animals from a single test cell in the test results table, as described above.

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HERDOWNER’S USER GUIDE FOR THE JOHNE’S DISEASE SCREEN ON ICBF

A. Common Questions | B. GENERAL | C. JOHNE’S DISEASE SCREEN

Figure 3d. Display of all individual animals in a single result in the test results graph

Users are cautioned that a relatively small group of test results may be difficult to detect, especially in the context of a large group of results on a graph. This risk of overlooking small numbers of animals can be addressed by referring to the default display of the data as a table before displaying the graph, or by de- selecting large groups such as ELISA Negative (Figure 3e).

Figure 3e. Graphical display, using same data as Figure 3b but with ELISA Negative results de-selected from the data

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HERDOWNER’S USER GUIDE FOR THE JOHNE’S DISEASE SCREEN ON ICBF

A. Common Questions | B. GENERAL | C. JOHNE’S DISEASE SCREEN

C4. REPORTS SECTION

The right-hand section of the Current Johne’s disease Herd Status Screen (Figure 4a) contains a list of herd-level reports.

Figure 4a. Display of options for reports

VIEW LABORATORY RESULTS BY HERD TEST (BATCH) DATE This screen provides a summary of herd test results by date and laboratory (Figure 4b). It provides information on the sample and test, the total number of samples tested, and the number that were positive, negative, inconclusive or empty. This is a useful report to confirm that all the samples that were sent to a laboratory have been tested and the results uploaded.

Figure4b. View Lab Results By Batch screen

Click on the hyperlinked Date field within this report, to view a list of the animals whose test results are recorded as part of this ‘ batch ’ (Figure 4c).

Figure 4c. View Lab Results By Batch screen - Individual animal contributors to the batch

As described previously, further information on each individual animal is available by clicking on its Animal Number .

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HERDOWNER’S USER GUIDE FOR THE JOHNE’S DISEASE SCREEN ON ICBF

A. Common Questions | B. GENERAL | C. JOHNE’S DISEASE SCREEN

VIEW STATUS OF EVERY ANIMAL CURRENTLY ON THE FARM The report, View status of every animal currently on the farm , lists all animals in the herd, irrespective of age or testing status on the date the report is viewed (Figure 5a). It includes detailed information about the most recent test results for an animal, along with a summary of the testing history for an animal. The test results are presented in chronological order, with the most recent result shown on the left hand side. The report opens as a table below the View Johne’s Herd Status main screen and may require the use of a scroll bar to be viewable. This report refreshes each time you open the report.

Figure 5a. Display of the test status of all animals currently on the farm

The column header line contains sort arrows which enable you to re-order the data. (Figure 5a). The information in any of the columns may be sorted by clicking on the up/down arrow beside each column header. For a numerical list, clicking once will sort the data lowest to highest (e.g. for Birth year one click will show animals listed as oldest to youngest). On an alphanumeric list, clicking once will sort A to Z, and a second time Z to A (e.g. on the Results column, this will present all of the positive results together). These elements of functionality are common to many of the screens. Additionally, a filter is built into the screen (click on the Show filters button) by which means the user can find data. Where a specific tag number is known press Ctrl+F and enter the tag number, the table will automatically find it. The report is downloadable to Excel, saveable as a PDF document or printable by selecting the appropriate option at the top of the listing.

A QUICK WAY TO FIND INFORMATION ABOUT A PARTICULAR TAG NUMBER IS TO PRESS CTRL+F AND ENTER THE TAG NUMBER.

There is a hyperlink from the Animal Tag number which if clicked, opens to a newwindow to provide information about the animal and its pedigree along with a list of the tests carried out, test dates, test laboratory, test value and interpreted result. This window is the same as that accessed from the View Lab Results By Batch screen.

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HERDOWNER’S USER GUIDE FOR THE JOHNE’S DISEASE SCREEN ON ICBF

A. Common Questions | B. GENERAL | C. JOHNE’S DISEASE SCREEN

VIEW STATUS OF EVERY ANIMAL THAT HAS LEFT THE FARM SINCE THE DATE OF ENROLMENT (DATE OF REGISTRATION WITH THE IJCP IS INSERTED) This report is a list of all animals that have left the herd since the date of registration in the IJCP (Figure 6a). The report opens as a table below the View Johne’s Herd Status main screen and may require the use of a scroll bar to be viewable.

Figure 6a. Display of View status of every animal that has left the farm since date of enrolment

This report refreshes each time the user opens the report. You can select a year (top of screen) and refresh the View status of every animal that has left the farm since.. . report to change the reporting period. The report is not limited to eligible animals and includes all age groups. The test history of each animal is listed up to the date it left the herd. This report includes detailed information about the most recent test results for each animal, along with a summary of their testing history. The test results are presented in chronological order, most recent first. The data may be sorted using a filter and also downloaded as described above. As with the report View status of every animal currently on the farm , the test results in this report are colour- coded to assist with the quick identification of test-positive (results field is red), test-negative (green), test- inconclusive (yellow), and untested (empty and un-coloured results field) animals. There is a hyperlink from the Animal Tag number field, which if clicked, opens to a new window to provide information about the animal and its pedigree, along with a list of the tests carried out, test date, test laboratory, test values and interpreted result.

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INTELLECTUAL PROPERTY All images contained in this leaflet are the property of AHI, or have been included with the permission of the owner. Please seek permission from AHI if you wish to use these images and provide the correct attribution of ownership when reproducing them. If reusing any other material in this leaflet, please attribute AHI as the source. IMPORTANT NOTICE - DISCLAIMER This leaflet is issued and shall be read only on the basis that it will not relied upon by any person as a basis for any act or omission or otherwise without obtaining professional veterinary and health and safety verification and advice and that no liability or responsibility to any person is accepted or shall be incurred, and no recourse or claim by any person will be made, by or against AHI, any stakeholder, collaborator, officer, agent, subcontractor or employee of AHI, any member of the Technical Working Group, any contributor to, author, publisher, distributor, reviewer, compiler or promoter of or any other person in respect of or in connection with the leaflet or the contents thereof or any matter omitted therefrom.

No representation or guarantee is given, whether by AHI or any other such person, that the contents of this information leaflet are comprehensive, up to date, or free from error or omissions, nor that the advice provided is appropriate in every particular circumstance. The contents of this information leaflet are not intended to be a substitute for appropriate direct advice from your veterinary practitioner. Appropriate veterinary and health and safety advice should be taken before taking or refraining from taking action in relation to the animal disease dealt with in this information leaflet. The contents of this leaflet may be updated, corrected, varied or superseded from to time by later publications or material on the AHI website and reference should be made to that website accordingly. Any references in this booklet or links in the AHI website to external websites or other resources are provided for convenience only and the contents thereof are not to be considered as endorsed thereby.

Johne's Control AnimalHealthIreland.ie

JOHNE’S DISEASE CONTROL PROGRAMME Animal Health Ireland, 2-5 The Archways, Carrick-on-Shannon, Co. Leitrim, N41WN27

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