Monday, June 25, 2012

Losing sight of the plot

Today, June 25th 2012, saw the beginning of the Badger Trust's challenge in the High Court; they are objecting to a couple of pilot badger culls. And the chattering classes are out in force, all with a view on something which affects very few.

Damian Carrington from the Guardian leads the pack with his report, which has attracted 130 comments so far. Very few show any awareness of the reason why tuberculosis in any species needs to be tackled and the risk to themselves and their pets, even in inner cities, is conveniently airbrushed. Leaving aside the grammatical niceties within its title, one sentence in the Guardian report has generated not a little hot air in itself, and it's nothing to do with a badger cull.
Cull opponents are also attacking the "undue influence" of the National Farmers' Union (NFU) in the decision to go ahead with the shooting of badgers across England. In a February letter to the Badger Trust, seen by the Guardian, officials at the environment department (Defra) argued that "advice from the NFU was so integral to the development of the cull policy" that it considered the NFU to be a part of the government in this instance, and would therefore not release its "internal" communications with the lobby group.
The incestuous relationship between Defra and the 'Guardian' newspaper which is also mentioned in the piece, is obviously seen as a different sort of 'relationship' by Guardian readers, as it escapes their comment. But the NFU part of government? We call it a revolving door. Government says jump, NFU replies 'on whom?' Why else is the moratorium on Section 10 of the Protection of Badgers Act still in place, a full 6 years after the end the RBCT? Why else have cattle farmers born the brunt of endless futile cattle measures in exchange for.... what? Deals which never materialise, promises never kept.

 So what have we really got here for barristers to squabble over? An untried policy to take pot shots at badgers, cobbled together from snippets of a political prevarication   ' trial ' which from its outset was designed to fail , with permissive licenses overseen by a quango which has made no secret of its discomfort over culling any badger, let alone one with tuberculosis. Some appear surprised to see Rosie Woodroffe (ex ISG) perching amongst the Badger Trust supporters, having given them a statement.
We are not surprised; it is a position she has always held.

When badger tuberculosis is eventually sorted out, and it will be, all these people will need another cause to support them in the manner to which they have become accustomed. The wider this polemic gets, the more hangers-on it attracts. And the excuses for doing nothing, become quite remarkable.

Thursday, June 14, 2012

We like this...

Searching for something else can sometimes turn up solid gold. And a search today has done just that.
PCR (Polymerase Chain Reaction) has been around for decades now, and  the most logical use of it with bTB would be to identify infected badger setts as opposed to those used by groups relatively clean and healthy. Ex WLU staff tell us that much of the resistance to culling badgers across wide areas using mathematical models could be negated if more confidence could be given to the disease status of the badgers themselves.

So it is with our apologies that we have to say, we missed this one, submitted for publication in August 2011, and published November 14th 2011 as a validated, peer reviewed piece in PlosOne. It is attributed to Travis E.R et al (2011) and entitled;

"An inter-laboratory validation of a real time PCR assay to measure host excretion of bacterial pathogens, particularly of mycobacterium bovis".

The Abstract from the paper :
Advances in the diagnosis of Mycobacterium bovis infection in wildlife hosts may benefit the development of sustainable approaches to the management of bovine tuberculosis in cattle. In the present study, three laboratories from two different countries participated in a validation trial to evaluate the reliability and reproducibility of a real time PCR assay in the detection and quantification of M. bovis from environmental samples.
The sample panels consisted of negative badger faeces spiked with a dilution series of M. bovis BCG Pasteur and of field samples of faeces from badgers of unknown infection status taken from badger latrines in areas with high and low incidence of bovine TB (bTB) in cattle. Samples were tested with a previously optimised methodology. The experimental design involved rigorous testing which highlighted a number of potential pitfalls in the analysis of environmental samples using real time PCR. Despite minor variation between operators and laboratories, the validation study demonstrated good concordance between the three laboratories: on the spiked panels, the test showed high levels of agreement in terms of positive/negative detection, with high specificity (100%)and high sensitivity (97%) at levels of 105 cells g21 and above.
Quantitative analysis of the data revealed low variability in recovery of BCG cells between laboratories and operators. On the field samples, the test showed high reproducibility both in terms of positive/negative detection and in the number of cells detected, despite low numbers of samples identified as positive by any laboratory. Use of a parallel PCR inhibition control assay revealed negligible PCR-interfering chemicals coextracted with the DNA.
This is the first example of a multi-laboratory validation of a real time PCR assay for the detection of mycobacteria in environmental samples. Field studies are now required to determine how best to apply the assay for population-level bTB surveillance in wildlife.
So, what are we waiting for? The field trial could be done at Badger Heaven  Woodchester Park, where not only is the disease status of every social group known and has been logged for decades, but no doubt individual badgers have Christian names too. This is from where some of  the 300 field samples mentioned in this study were matched to epidemiological information already held. Will someone please contact Brian May, the RSPCA, Jack Reedy and Secret World. In no particular order of course, but perhaps include Jim Paice too - as his department co-funded this project, he may be interested. Or not.

Tuesday, June 12, 2012

Haven't we done well?

As we approach the first Judicial Review on whether or not to cull badgers by taking pot shots at them, in Farmers Guardian, Alistair Driver examines how this country arrived at such a position.

Defra's graph shows that in 2011, despite ongoing problems with the ability of the new IT system to count correctly, we culled 34,175 cattle (compared with 31,965 in 2010)

Almost 3,000 herds (2,965) had their TB free status officially Withdrawn, meaning that TB had been confirmed in the slaughtered cattle. This represents 4.95 per cent of tests on TB free herds.

Of 80,454 herds registered on the VetNet system with Defra, a staggering 10.07 percent (8,108) had TB problems and herd restrictions due to a 'TB incident' during the year 2011.

For our readers' comparison, International TB free trading status demands 99.99per cent of herds test clear, and 99.98 per cent of cattle.

Haven't we done well?

Sunday, June 03, 2012

The silly season

They keep coming and sometimes it seems as if they come in bundles of ten. What are 'they'? Half cocked theories published in journals which really should do some checking before giving them credence and from people whose pedigrees suggest they should know better. Wild assumptions do not a theory prove. Especially when sooooo many other so called facts in the published papers are just downright wrong.

But then a judicial review is on the horizon, and true to form the beneficiaries of the badger v. cattle polemic are rising to the occasion. This time, trying (once again) to prove this huge undiscovered reservoir of bTB in cattle, researchers from Liverpool made some pretty wild leaps of faith and connected incidence of liver fluke with an alleged failure of the skin test. The 'science' journal  Nature published this, obviously without checking the detail. Jumping off the page was the assertion that preMT began in 2001. It did not, that was 2006 - but let that pass.

Lumping New Zealand with the UK and Ireland, as a country with a wildlife reservoir and bTB problems in cattle is also overstating the facts. After a twenty year blitz on its TB infected  possums, by 2013 NZ hopes to achieve TB free trading status, while ignoring our wildlfe reservoirs has ensured that the heap of sentinel slaughtered cattle in the UK and Ireland, continues to grow. For the record, NZ has achieved 0.35 per cent incidence in its cattle herds in 2010/11; but herd restrictions were applied in around 24 per cent of cattle herds in the west of England and Wales, with a GB average of 10 per cent. Hardly comparable.

But the assumption of specificity of the intradermal skin test with a mean average of 80 percent is the core of the paper. Thus it is missing shed loads of cattle - all with liver fluke? But the specificity of the skin test need not be 'assumed' at all. From a F O I request, Defra answered this question recently thus:
"... the SICCT test specificity in GB would be at least 995.9 per 1000 or 99.59%. Given that the majority of skin test reactors detected in GB originated from endemic TB areas of England and Wales and were likely to be infected (regardless of post-mortem findings), a better estimator of the true test specificity would be the converse of the proportion of test reactors observed in a very low TB incidence area such as Scotland, where the majority (but not all) of the test reactors could be expected to constitute false positive test results. Since we had a rate of 0.8 tuberculin skin test reactors per 1,000 animal tests in Scotland in the first nine months of 2010, this means that the test specificity was about 999.2 per 1,000 (or 99.92%). Therefore, in addition to the field trials carried out by Lesslie et al. in the mid-1970s, the current field data continues to indicate a very high specificity of the SICCT test ... "
And for once, Defra's answer to this paper's publication was spot on. If the skin test was missing millions of cattle - up to 20 % the paper asserts - then not only would this happen in all other countries using the test (unless Faciola hepatica is unique to the UK as well) but eventually all these infectious cattle would end up with gross lesions in the abattoir. A Defra spokesperson told Farmers Guardian that:
"..... research showed that ‘cattle that have both liver fluke and bTB still test positive for bovine TB, and would be culled to control the disease. The absence of positive cases of bovine TB in some areas coinciding with large amounts of liver fluke cannot be used to claim liver fluke is hiding cases, as cattle carcases are inspected in abattoirs and we would see evidence of TB in the slaughtered animals if this was the case."
Assuming this paper is correct in its many 'assumptions' that would mean about 20 per cent of all cattle slaughtered in the UK were riddled with liver fluke and also bTB would it not?
The UK cattle herd is around 9.6 million animals. Annual slaughterings involve about 3.5 million cattle so 700,000 or thereabouts should have lesions? Yes? No?
Just 1013 were confirmed with bTB at abattoir inspections in 2011.
That is the huge 'reservoir' which attracts so much hot air.

 And this week, Nature ran another paper, this time from Donnelly and Woodroffe, claiming that no one could really count badgers and thus the 70 percent clearance in the proposed pilot culls may be breached, leading to compliance problems with the Bern Convention. As one comment on this story pointed out, Bern has yet to have grasped the ecological impact of too many badgers - particularly on hedgehogs.

 Northen Ireland too has the begging bowl out. In this oral presentation, the Oliver syndrome is much in evidence. Please may we have some more porridge research cash? On top of the £3.5 million already spent of course.

And again some repeated wild assumptions about the skin test sensitivity (see above) and mathematical models based on mathematical models based on ... And Rosie Woodroffe's assertion seems to have gathered credence with the telling. Did you know that dead cattle spread TB?

Felling a single tree needs an 'ecological impact' assessment, so how much more 'impact' was there when these modellers cleared 11 million animals from the landscape in 2001? Thousands of acres were barren with altered cropping, long grass, funeral pyres and noise. And vitally for badgers, no grazing cattle or sheep. There was nothing for badgers to eat and so they moved. Woodroffe opined that delayed cattle tests 'were the only explanantion' for the spike in badger TB and thus cattle had given the disease to badgers. Rubbish. The whole ecology changed for that year, and the badgers moved out to find the nearest live cattle. They met resident badgers and fought. Result? Perturbation and TB, which they brought back with them when they returned back to restocked farms in the heartlands of this bloody carnage.

As well it being the silly season, on 25th June there's a Judicial Review coming up, and jobs to protect. These people need another cause.