Tag Archives: bovineTB

Cattle testing with Gamma interferon

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On 19th August, Defra sent an email to ‘stakeholders’ announcing that as part of the work to refresh the bTB strategy, it will be “enhancing test sensitivity in cattle herds”. This is “to help identify infected cattle which may not have been detected by the skin test.” This news doesn’t seem to have been reported very widely, but has been covered by South West Farmer.

Defra say:

“At present, mandatory interferon-gamma (‘gamma’) blood testing applies to certain TB breakdown herds in the High Risk Area (HRA) and six-monthly surveillance testing parts of the Edge Area of England.  We are working to extend gamma testing to all herds experiencing a new breakdown with Officially Tuberculosis Free Withdrawn (OTFW) status in the HRA and six-monthly parts of the Edge Area. ”

“Therefore, farmers with eligible herds in these areas will be able to apply to APHA from 01 September 2025 for government-funded gamma testing as a voluntary option. All cattle with a positive gamma test result will be removed and usual valuation and compensation procedures will apply.”

“Using the skin and gamma tests together is proven to increase test sensitivity, particularly in herds where Bovine Tuberculosis has already been identified.  This means infected animals can be detected and removed from the herd earlier, reducing the spread of the disease within the affected herd and the risk of future breakdowns after the herd has regained its Officially TB Free (OTF) status.”      

This change is a voluntary one. If you don’t want to know whether your cattle have bTB using Gamma, you’re not obliged to find out. While the option for extra testing is welcome, it raises some interesting questions.

Strange Timing?

Government’s updated bTB control strategy is scheduled for spring 2026. It is to take its lead from a  ‘Godfray Group’  review of new science published since the 2018 review, and this new review is expected shortly.

So why the urgency to push Gamma now?  Could it be that APHA’s ‘Year End Descriptive Epidemiology Reports’ show that their long-term objective of reducing OTF-W (Officially TB Free Withdrawn) incidence to less than 1% has absolutely no hope of success & they really can’t afford to delay any longer?

Might Godfray have decided that OTF-S (Officially TB Free Suspended) is in reality a sufficiently accurate measure of new infection (see explainer), and the implication of this is that any fall in bTB has been modest and is levelling off to reflect the inadequate capacity of the flawed current approaches. Could the very high profile bTB breakdown at Clarkson’s Diddly Squat Farm have had some influence in this decision? (See Farmers Weekly take on this). Clarkson did say he would be speaking to officials at Defra…. It appears, incidentally, that he has bought from herds that have been in breakdown over the last five years or so.

It was use of Gamma that has reduced bTB since 2013

APHA’s scientific paper analysing the results of the Badger Culling Policy (BCP) (Birch et al 2024) claimed a 56% bTB reduction benefit over the period of badger culling. What it failed to articulate with clarity was that BCP  was really a mixture of culling, increased frequency SICCT cattle testing and the introduction of Gamma testing in badger cull areas, and much earlier than indicated in that report.

Mis-describing the extent and timing of use of Gamma, that paper implied, with muddled wording, that badger culling was responsible for the disease benefit measured. The reality is that declines in bTB most closely mirror the introduction of enhanced cattle measures. Analysis of competing models in Langton et al 2022 suggested that the best random effects model was the one without badger culling as a co-variate; all the random effects models which included ‘cull’ failed to identify an effect of culling. Perhaps this is beginning to sink in at Defra.

What about the other cattle tests?

Anybody who has watched the BBC’s “Brian May: the Badgers, the farmers and me” will know that extensive efforts using a suite of cattle tests have been trialed for 10 years by vet Dick Sibley at Gatcome Farm in Devon. Working around Defra’s strict and problematic rules about the use of cattle testing, this groundbreaking work has shown not only how different tests can be used to identify the disease at different times in the life of cattle, but also how to use such a process to effectively manage infected animals to minimize spread. Where then, is the plan to utilize the full range of cattle tests that could be used to drive down disease?

So, is the new introduction of optional Gamma testing a token response to the clear failure of badger culling and recognition of a need for change?  Alone, it will simply find more disease, delay OTF declaration and drive up OTF-S and OTF-W figures.  An increase that misguided commentators will then no doubt claim is ‘due to badger culling being stopped’.

It’s too little too late; whether or not Defra attempt to cling to the flawed RBCT publications and  badger blame game is about to be revealed. Their problem is that they surely won’t want to admit they wasted  £100’s of millions and killed 250,000 badgers for nothing, so they may well be reluctant to accept what has become obvious to the world of science and statistics; badgers have not been shown to be a significant factor in the control of bovine TB in cattle herds.

RBCT uncertainties debate gains momentum

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On December 13th 2022, a preprint was put up on the ResearchSquare platform. Entitled ‘Absence of effects of widespread badger culling on tuberculosis in cattle’ [1], it was a reanalysis of the Randomized Badger Culling Trials (RBCT). Following a protracted period of review, with a number of very long silences, and relatively few revisions, it was published in Nature Scientific Reports on July 15th 2024 (Torgerson et al 2024) [2]. Finding a major anomaly, it uses a range of statistical models to re-examine the RBCT data  and concludes that most standard analytical options did not show any evidence to support an effect of badger culling on bovine TB in cattle.

Torgerson et al 2024 [2] noted that the statistical model selected for use in the original study in 2006 [5] was one of the few models that did show an effect from badger culling. However, various model assessment criteria suggest that the original model was not an optimal model compared to other options available. You can read a short blog on the new Torgerson et al paper here, and the full paper is available here. Essentially, the more appropriate models in the latest study strongly suggest that badger culling does not bring about the disease reduction reported.

Following publication, the new analysis [2] was mentioned in an article in Vet Times on July 24th, and in Vet Record in their 3/10 August edition. Neither publication noted its major significance. No other mainstream media reported on it at all. This is perhaps surprising since the government badger cull policy rests all but entirely on the conclusions from the RBCT. It is the science that DEFRA has used in court to defend their decisions to experiment with culling. It is the science that has resulted in 11 (12 including 2024) years of intensive and supplementary badger culling across huge areas of England, and around 230,000 dead badgers. In other words it is the pivotal piece of work for the decision-making around badger culling policy.

The reluctance of the media to report further on Torgerson et al. is a prelude to work by two of the authors of the original 2006 analysis (Christl Donnelly and Rosie Woodroffe) together with a DPhil Statistics student at Oxford University (Cathal Mills), who had, at the time of publication, two rebuttal papers in press with Royal Society Open Science [3,4]. Unusually, the abstracts and supplementary information for these new papers were posted online and available to view before publication without the main text. Enquiries regarding the posted information and the main papers resulted in in press versions being helpfully forwarded. The new analyses from Mills et al. are entitled An extensive re-evaluation of evidence and  analyses of the Randomised Badger Culling Trial (RBCT) I: Within proactive culling areas [3], and  An extensive re-evaluation of evidence and analyses of the Randomised Badger Culling Trial II: In neighbouring areas [4].

Published on August 21st, the two new papers largely duplicate the analyses in Torgerson et al 2024, but use different model assessment criterion to come to a different conclusion. In fact they double-down on the conclusions of the original 2006 analysis: “…we estimate substantial beneficial effects of proactive culling within culling areas, consistent with separate, existing, peer-reviewed analyses of the RBCT data.”

So in the year and a half since the posting of the Torgerson pre-print [1], Mills, Woodroffe and Donnelly have been working on their rebuttal to it. Torgerson and his team have looked through the in press versions of the Mills et al (2024) publications [3,4] for a few days and multiple problems stand out. In particular:

  1. Incorrect statements regarding disease control outcomes since 2010
  2. Use of a non-peer reviewed publication
  3. Confusion between the offset and overdispersion leading to incorrect calculation of disease exposure
  4. Incorrect and confused statements regarding model comparisons
  5. Exaggerated claims during use of new modelling.
  6. Failure to address the modern interpretation of SICCT test reactors
  7. Failure to recognise the onward effect of the analytical failure on multiple subsequent publications and policy outcomes.

Somewhat unusually, the new Mills et al papers do not refer to or cite the published Torgerson et al paper [2], only the first pre-printed version of Torgerson et al. from 2022 [1]. So in essence, the new Mills et al papers [3,4] are out of date at the time of publication, failing to refer to the updated 2023 preprint or the final version in  Scientific Reports published 15th July 2024 [2]. Following contact with the Royal Society, a response raising concerns with the newly published papers is being written and will be submitted shortly. An interim report has been put together by Torgerson and Langton with brief observations on the new papers (see here).

The Royal Society says it is committed to reproducibility. Reproducibility is the ability of independent investigators to draw the same conclusions from an experiment by following the documentation shared by the original investigators [6]. The issues identified in [2] and “rebutted” in [3,4] illustrate one of the major issues of the reproducibility crisis: poor statistical inference. It is hoped that the conclusions of this exchange will inform future bovine TB intervention policy this autumn.

References

[1] Torgerson P, Hartnack S, Rasmusen P, Lewis F, Langton T. 2022 Absence of effects of widespread badger culling on tuberculosis in cattle. In Review. (doi:10.21203/rs.3.rs-2362912/v1)

[2] Torgerson, P.R., Hartnack, S., Rasmussen, P. et al. Absence of effects of widespread badger culling on tuberculosis in cattle. Sci Rep 14, 16326 (2024). https://doi.org/10.1038/s41598-024-67160 (available: https://www.nature.com/articles/s41598-024-67160-0)

[3] Mills CL, Woodroffe R, Donnelly CA. 2024,  An extensive re-evaluation of evidence and analyses of the Randomised Badger Culling Trial (RBCT) I: Within proactive culling areas. R. Soc. Open Sci. (doi:10.1098/rsos.240385)

[4] Mills CL, Woodroffe R, Donnelly CA. 2024, An extensive re-evaluation of evidence and analyses of the Randomised Badger Culling Trial II: In neighbouring areas. R. Soc. Open Sci. 11:240386.

[5] Donnelly CA, Woodroffe R, Cox DR, Bourne FJ, Cheeseman CL, Clifton-Hadley RS, Wei G, Gettinby G, Gilks P, Jenkins H, Johnston WT. Positive and negative effects of widespread badger culling on tuberculosis in cattle. Nature. 2006 Feb 16;439(7078):843-6.

[6] Gundersen Odd Erik 2021The fundamental principles of reproducibility. Phil. Trans. R. Soc. A. 37920200210