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List of focus molecules in gene networks and upstream analysis. Gene symbols, full gene name and fold change values were displayed for the illustrations of network and upstream analyses. (XLSX 14 kb

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Additional file 5: of RNA sequencing for global gene expression associated with muscle growth in a single male modern broiler line compared to a foundational Barred Plymouth Rock chicken line

O'Keeffe, James

Crowley, Michael J.

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Title Single animal breakdown situations (sabs) - application of a modelAuthors(s) O'Keeffe, James, Crowley, Michael J.Publication date 1996-07Publication information O’Keeffe, James, and Michael J. Crowley. Single Animal Breakdown Situations (Sabs) - Application of a Model. University College Dublin. Centre for Veterinary Epidemiology and Risk Analysis, July, 1996.Series Selected Papers, 1995Publisher University College Dublin. Centre for Veterinary Epidemiology and Risk AnalysisItem record/more informationhttp://hdl.handle.net/10197/8973Downloaded 2024-01-25T04:02:17ZThe UCD community has made this article openly available. Please share how this accessbenefits you. Your story matters! (@ucd_oa)© Some rights reserved. For more informationSingle Animal Breakdown Situations (SABS) -Application of a Model J. J. O'Keeffe and M. J. Crowley1 Introduction A sizeable number of "false positive" animals are unavoidable in the late stages of an eradication scheme the basis of which is a screening test. The screening test used here is the Single Intradermal Comparative Tuberculin Test (SICTT). Estimates of the specificity of this test in Irish conditions vary from 99.8 per cent to 99.9 per cent (O'Reilly, 1992, Monaghan and others, 1994) and up to 99.95 per cent in Round tests (O'Keeffe, 1993). On the l 0 million animal tests carried out each year in Ireland this would result in an expected range of "false positives" from 20,000 down to 5,000. With approximately 30,000 animals deemed reactor annually, the number of false positives each year is most likely to be within the lower estimates of 5,000 -10,000. The number of herds placed under movement control due to a "false positive" animal is more difficult to estimate. A simplistic analysis might suggest the number to be between 5,000 and l 0,000, that is, a 1: 1 ratio between "false positive" animals and "false positive" herds. With less than 8,000 herds expected to be placed under movement dontrol any year since 1990, the simple hypothesis of a 1: 1 ratio is clearly not supported by the facts. Furthermore of the herd episodes fully matched 1989 - 19942, 48.1 per cent have either had tuberculosis laboratory confirmed, or a tuberculous lesion found at gross post-mortem examination of animals deemed "reactor". The overall lesion rate in animals deemed "reactor" for this period was 31.6 per cent3. A lesion rate of 31.6 per cent, following the post-mortem examination procedure followed in Irish export plants is an underestimate of the true rate. Using the matched episode data, a fictional year with 8,000 herds identified with one or more animals positive to the SICTT would result in tuberculosis being confirmed at routine post-mortem examination in animals from approximately 4,000 herds. It is unlikely, therefore, that the "false-positive" animal:herd ratio is less than 2: 1. Given that some false positives would concurrently be identified in herds with tuberculosis, due to random distribution ' the expected "false-positive" animal to herd ratio might be 3: 1 or higher. Further analysis of data available in relation to animals removed as reactors since 1989 planned at the TIU will result in a more accurate-estimate of this important ratio. If one assumes that included in the 8,000 fictional herds, identified with one or more test positive animals, are 1,000-2,000 herds with only one false-positive animal then these herds are, in fact, clear of tuberculosis and probably have a high animal health status. The inclusion of 1 Statistics Laboratory, University College, Cork. 2 See "Episode classification: in the Eradication of Bovine Tuberculosis:A Different Perspective" this volume 3 S "F ffi . · ee actors a ectmg the rate of disclosure of tuberculous lesions in tuberculin reactor cattle at slaughter" th is volume. ERAD/TEAGASC 34 Tuberculosis Investigation Unit, UCO these herds in the Annual Statistics of "herds placed under movement control" would be reasonable and a statement of fact for the information of customers, both domestic and international. To continue to include these data in the Annual Statistics of herds "restricted for tuberculosis", along with herds with tuberculosis de facto is incorrect, however. In April, 1996, the Department of Agriculture, Food and Forestry (DAFF) introduced a new policy for "Singleton Herds", i.e. herds in which a breakdown had been initiated by a single animal being deemed "reactor". Assuming certain criteria are fulfilled, movement control is eased if the first reactor retest is clear. Previously, such herds were required to pass two consecutive reactor retests at 60-day intervals before movement control was relaxed. This policy addresses the issue directly. The criteria in Table 1 differentiate "false-positive reactors" situations from "true infection". Background A risk assessment based on future testing outcome on a sample of herds which had a single animal deemed "reactor" at the index herd 7 test was carried out by O'Keeffe (1994). In that study the sample was limited to herds from ten counties identified during one year, 1990. The database presently being assembled contains fully matched details of 45,385 (90.1 %) of the 50,387 episodes of tuberculosis which occurred during the period, 1989 1994. This paper demonstrates one potential use of the database, using data from the "Single Animal Breakdown Situations (1989-1994)" as an example. Methodology All 45,385 episodes, for which test and animal data have been validated and fully matched, were analysed. Those episodes with a single animal deemed "reactor" at Table 1. Inclusion Criteria: DAFF policy for "Singleton Herds" Herd Category Skin Difference of animal deemed reactor using SICTT6 Post-mortem examination of animal deemed reactor Area adjacent to herd The criteria represent a prudent attempt to identify herds placed under movement control which are the result of a "false-positive" animal on the SICTT. Category C herds were restricted at some point in the preceeding year because, on trace-back, an animal with laboratory confirmed tuberculosis or an animal with tuberculosis-like lesions on gross post-mortem examination following slaughter was identified from these herds. 5 Category D herds have been clear of tuberculosis for at least a year. 6(Bovine 72 hr skin measurement - Initial bovine measurement) minus (Avian 72hr meas. - Initial avian meas.) 7The sample was drawn from herds which had a single reactor animal on the fo llowing test types:Round tests (RND), Special Check tests (SCT), Six Month Check tests (SMC) and Contiguous tests (CD. ERAD/TEAGASC Limited to C'I or D) Bovine difference - avian difference< 13mm No tuberculous lesions disclosed at slaughter, confirmed by Central Veterinary Laboratory. (including use of Bactec ). No tuberculosis problem present 35 the precipitating test and which had passed their first reactor retest were identified. The model used assumes that all these herds would have qualified for the present DAFF policy in relation to "Singleton Herds". This ignores the limiting criteria described in Table 1. The model, therefore, is a worst case scenario test of the DAFF policy. Tuberculosis Investigation Unit, UCD Table 2. Matched Breakdown Episodes under study, 1989 - 1994. Year No. of Episodes % Episodes 1989 10,435 23.0 1990 10,098 22.2 1991 6,818 15.0 1992 7,882 17.4 1993 7,098 15.6 1994 3,054* 6.7 Total 45,385 100.0 *This represents only those episodes initiated and concluded in 1994. Many of the episodes initiated in 1994 would not have been concluded until 1995. The herds which, having had a single animal deemed "reactor", and had passed their first reactor retest (RR) were followed to their next RR. The herds which failed this second RR are the population targeted by the limiting criteria (Table 1 ). Because the development of the database is not yet fully complete, only two of the limiting criteria are incorporated in the model at this stage. These are (i) herds with a lesion confirmed in the index reactor animal and (ii) herds with a single "reactor" whose SICTT skin difference is greater than 12mm. When fully complete, the database will allow the inclusion of all the criteria in the final model. The herds which would have been excluded by the limiting criteria are identified and quantified in relation to their frequency and also qualitatively, in relation to the number of " reactor" animals they contributed at the second R/R. The residue of herds and "reactors" remaining after including the criteria at (i) and (ii) above, will be further reduced when the limiting criteria based on herd category and area testing history are added to the model. Results The distribution per year of the episodes analysed is given in Table 2. Of the 45,385 episodes, 26,288 (57.9%) had a single animal only deemed " reactor" at the index test. Table 3. Frequency of reactors in herds which failed the second reactor retest (R/R) having passed the first R/R following disclosure of a single reactor at the index test. No of reactors at 2nd R/R No. of herds % of herds 0 22197 95.9 1 539 2.3 2 191 .8 3 101 .4 4 41 .2 5 30 .1 6 12 .1 7 or more 41 .2 Total 23,152 100.0 ERAD/TEAGASC 36 Tuberculosis Investigation Unit, UCO Table 4. Frequency of subsequent reactor disclosure in 508 episodes in which herds failed the second reactor retest having passed the first reactor retest following a single reactor disclosed at the index test, excluding those herds which failed the limiting criteria in respect of lesions and skin difference measurements as set out in Table 1. No of reactors at 2nd R/R No. of episodes % of episodes 1 289 2 107 3 52 4 25 5 10 6 6 7 or more 19 Of the 26,288 episodes initiated by a single animal deemed reactor, 23,152 (88. 1%) were clear at the first reactor retest. Of the latter, 22, 197 (95. 9%) had no further reactors at the second reactor retest. The frequency of reactors at the second reactor retest for herds whose episode was precipitated by a single animal deemed reactor and which passed_ their first reactor retest is presented in Table 3. When the 22, 197 herds which did not disclose a reactor at the second R/R are excluded, a total of 955 herd episodes remain which had one or more reactors at this R/R having passed the ·first R/R, where the precipitating test resulted in only a single animal being deemed "reactor". These 955 episodes resulted in 1,945 animals deemed "reactor" at the second RIR. Were (i) no limiting criteria applied to these episodes, and (ii) were movement controls lifted on these herds following the first clear reactor retest, then the above outcome, adjusted for reactor animals subsequently sold, would represent the best predictor of the results of the next herd test in these herds. This estimate is based on a test carried out 60 days following the first RIR, whereas the first test after the lifting ERAD/TEAGASC 37 56.9 21.1 10.2 4.9 2.0 1.2 3.7 of movement controls would normally be a Six-Month Check test. The outcome of the test at six months post-derestriction would be at least that observed at two months post derestriction. Animal to animal transmission (from other infected cattle or infected wildlife ) would add to the number of additional test positives identified following the additional 120-day interval. Of these 955 episodes, 305 (31.9%) had a lesion identified on gross post-mortem examination of the index animal deemed " reactor". These 305 herds did not meet the criterion on lesion result and were, therefore, excluded. Of the 650 episodes remaining, 142 (21.8%) were episodes where the initial animal deemed reactor had a skin difference (bovine - avian) greater than 12mm., thus failing the criteria on skin difference. These 142 episodes were similarly excluded. The remaining 508 episodes, of which 289 (56.9%) had a single animal deemed reactor at the second R/R, disclosed 1091 reactors in total. The frequency of reactors in these episodes is detailed in Table 4. Tuberculosis Investigation Unit, UCO Conclusions This analysis demonstrates how a policy initiative might be modelled based upon historkal data organised in a relational database. The projected outcome is based on the actual test results of herds. Modelling allows managers to generate expected outcome scenarios to a range of policy proposals. The outcome scenarios could be further analysed using advanced statistical and econometric tools, e.g. risk analysis and cost benefit analysis. Analysis based on these principles will result in policies which will maximise the future efficiency and effectiveness of the operation of the Bovine Tuberculosis Eradication Scheme. References Monaghan, M. L., Doherty, M. L., Collins, J. D., Kazda, J. F., and P. J. Quinn (1994). The tuberculin test. Veterinary Microbiology, 40 : 111 - 124 O'Reilly, L. M. (1992). Specificity and sensitivity of tuberculin tests. In: Proceedings of the ERAD/TEAGASC 38 International Conference on Animal Tuberculosis in Africa and the Middle East, 28-30 April 1992, Cairo. Moussa A. A. M., Lofti 0, Mahir S. et al. eds. General Organisation for Veterinary Services, 1992: 87-139. O'Keeffe, J. J., (1993). A model of the effect of herd size on the outcome of the tuberculin test. Tuberculosis Investigation Unit, University College Dublin, Selected Papers 1992, 39-44. O'Keeffe, J. J. (1994). Bovine tuberculosis: Risk assessment on single animal breakdown situations (SABS). Tuberculosis Investigation Unit, University College Dublin, Selected Papers 1993, 8-22. Acknowledgements We wish to acknowledge the valued assistance of Ms. Claire Devereaux and Mr. Paul O'Leary of the Statistics Laboratory, University College, Cork, for their invaluable contribution to this work. Tuberculosis Investigation Unit, UCD 

Single animal breakdown situations (sabs) - application of a model

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Single animal breakdown situations (sabs) - application of a model

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