Sunday, February 07, 2016

Strategy? what strategy?

In today's Sunday Telegraph - [link] columnist Christopher Booker examines the rationale behind Defra's road block on its own research into a DNA test which will identify infectious badgers.

And a road block of some proportions it certainly is, with spurious misinformation freely offered, despite this test, as we remarked in this posting - [link] passing 4 out of 5 strict criteria (when offered genuine positively infected samples, not 'putative') And it achieved this even when the 'blind' testers used half the optimum samples required, one tenth of the bacteria and a third of background prevalence it needed for the best results.

What was left was 'specificity' (false positives) at group level which was described as 'borderline'..

But the samples were singles, were they not? And the group level specificity was 'calculated' from 1 animal out of 10. We think what Defra's apparatchiks did, was to take a single sample / badger? at say 99 per cent specificity and model it back to a group, thereby creating a heap of falsely accused, but very dead badgers.

But qPCR cannot to be modeled. It is DNA. So a simple answer - Yes or No, but not the milkman.
It is also a group test, not a single animal test.

These are the results chart for  Warwick University's Test B in Defra's 'blinded' trial.

The reason for this rejection and all the hubris surrounding it, is we think, that once zTB is found in an animal - any animal - then under International Statute, responsibility for its eradication commensurate with dealing with a grade 3 zoonotic pathogen, passes to Defra. It cannot be shafted onto farmer funded population reductions. Thus a battle is raging, as Booker explains:
" The truth is, I learn on very good authority, that a battle is raging, with officials still too much under the influence of the animal rights lobby, who are stopping further research needed to perfect the test. If they win, it would be a scandal not only to those thousands of cattle farmers for whom TB has been an appalling tragedy.
This is a tragedy for all the healthy badgers too. Badgerists please take note.

Thinking about this 25 year strategy which Defra are ratting on about, (21 now as the first four years have elapsed - but let that pass) designed apparently to eradicate zTuberculosis from our shores, we have come to the conclusion that it is not a 'strategy' at all.

What this country has is a reactive, annual, farmer funded cull, over very few of the affected areas, repeated in 4 year bites, 25 times plus a shed load of cattle measures. And then what? When areas deemed to have jumped through enough of Natural England's hoops have completed their 4 years, there is nothing at all to put in place afterwards. No 'management' at all.

And the so called, but ever moving 'Edge' area with its expanding number of TB restricted herds and slaughtered sentinel cattle? That mobile buffer between the High Risk area, steeped in cattle measures and infected badgers, and the far North, North East and Eastern counties, for whom zTB is a distant problem. For those farming cattle in the Edge, with an ever increasing, bubbling  infection, there is nothing at all.

 So when we speak of using qPCR to locate infectious badgers, we do not mean as an alternative to an initial population reductions in the areas where badgers are so abundant - [link]  and their infection rates extend to half the population.

We see this technique of DNA matching as a long term tool, to screen and manage infected groups of badgers (and wild boar or deer) over the whole country as and when they occur. Disease driven. And certainly to give the pilot cull areas some sort of safety net after their 4 year stints.

 The alternative is to leave infection to build up to the extent which is seen now in Wales, the West and South West, and then apply for a four year wipe out cull. Which is no strategy at all.

Sunday, January 31, 2016

Never trust an authority figure..

... and definitely don't follow one. This cartoon reflects the position of our industry in 2016.

If we do not learn from history, then sadly for our cattle, our industry and the emotional and financial health of our livestock farmers, we are condemned to repeat it.

 Over the last twenty years we have listened in disbelief and increasing anger, to the prattling of those inhabiting their setts in the Westminster bubble, hell bent on finding that huge hidden reservoir of cattle TB which is driving the epidemic in this country, while ignoring the blindingly obvious.

Having trousered £1m in 1997, they employed one of the most 'political' scientists - [link] on the planet to prevaricate for another decade. And have wrapped the UK's primary wildlife reservoir of zoonotic Tuberculosis up in its grade 1 listed Ancestral home with ultimate protection. So, as they busily skip towards their protected pensions,  what can we remind them of as another new year breaks?

Here's a few points for starters.
We are hearing some alarming 'factoids' about the universally applied intradermal skin test. But apparently only applicable in certain areas of England, Wales and Ireland it seems. In the rest of the world, it works just fine. Now if this internationally used skin test was missing X per cent of infected cattle in parts of Great Britain (take your pick on what figure is doing the rounds) but let's settle on 20 per cent, then eventually, all these disease riddled animals would end up in abattoirs. That's what happens. And they would go down the line past a Meat Hygiene operative, trained to look for evidence of - tuberculosis.
So how many do they find? Defra reported in 2014:
Between 2009 and 2013, over 11.1 million cattle were recorded as slaughtered in 313 slaughterhouses in GB. During this period 7,370 samples with lesions suspicious of bTB were submitted to AHVLA by meat inspection teams of the Food Standards Agency (FSA) leading to an overall rate of 0.66 submissions per 1,000 animals slaughtered.

M.bovis was identified in 5,366 [of those] samples.
Full report on this link - [link]
But 5,366 out of 11.1 million cattle with culture positive evidence of zTB is not 20 per cent missed, or even 2 per cent. Its just under 0.05 per cent. Some reservoir. Some lie.

And don't mention the Isle of Man - [link] a lump of rock in the Irish sea, from which you can see if not touch, parts of Ireland, Wales and England: enjoying the same weather, geology, cattle husbandry and testing. But no TB and no badgers. Maybe it is the TT races? But then correlation is not causation, is it?

So as more severe cattle measures rain down on herds unfortunate to live in the areas of England frequented by endemically infected badgers, will they work? Will testing all breakdown herds twice under severe interpretation, using more GammaIFN (with a specificity of around 65 per cent) and very little movements except direct to an abattoir, work?

So a message to all you bright young things, who think this is a new idea, it is not. -[link] It was done with bells on in Cornwall in the 1970s by a DVM called William Tait who operated  fierce and brutal cattle carnage. And repeated from 1988 - 1992 by Liam Downie - [link] in the Republic of Ireland.

 Predictably, the results of both were a futile and expensive embarrassment. Except that our lot seem hell bent on repeating them. Why?

Which brings us around to the latest guff to hit the cattle industry. The Berlin wall which Defra have erected around the best piece of pure science to be available to us for a long while.
A screening test to find infected badgers - [link] something which we have always been assured wouldn't happen.

But having accepted this validated test in 2011, repeated it to find its best operational protocol in 2014, Defra then proceeded to ignore that protocol in a blinded trial commissioned in 2015.
And still one test passed 4 out of 5 strict criteria with flying colours, when offered genuinely positive (spiked) samples. So what was left? Professor Wellington's PCR test was said to be 'borderline' on group specificity.

And would thus leave a possible heap of falsely accused, but very dead badgers.

We could remind readers that gammaIFN has a specificity around 65 per cent when used on cattle, leading to many  false positives, but let that pass.

The blinded trial used single samples, so how did they arrive at a group figure? We suspect that they 'modeled' it back from a single sample / badger. But PCR is not a test which can be 'modeled'. It is DNA.

Think paternity tests and Forensic Science. No interpretation, just a yes or a no - but not the milkman.

Now being the cynical lot that we are at blogger headquarters, we see this as an evasion of responsibility.

Because if a Grade 3 zoonotic pathogen is found, then the responsibility for its removal and eradication is not that of farmers, running around the countryside within a mythical boundary, trying to shoot 70 per cent of the possible carriers. That responsibility is Defra's, and must be operated under strict bio hazard conditions.

And that is a responsibility they would rather not accept.

Our co-editor has succinctly offered a quote by Upton Sinclair which fits the bill quite neatly;
"It is difficult to get a man to understand something, when his salary depends upon him not understanding it."

Saturday, January 16, 2016

TB free

On January 12th 2016, Defra applied to the European Union for TB free status for the Isle of Man.

Apart from hosting races where motor bikes take over the island for a few days, the Isle of Man has many similarities with its geographic neighbours.
Sitting half way between Ireland and North Wales, with an amazing view of both those regions and Scotland, the island shares the same weather, geological features, cattle husbandry, cattle breeds, husbandry and veterinary TB testing regime. But there the similarity ends.

The chart shows their success and the basis for this application - [link]

The Badger Trust have used the Isle of Man to make mischief before - [link] as we described in 2007.
In 2012, they announced that the Isle of Man was 'rife with TB'. Nothing has changed. The chart taken from the application, tells a different story.

Animals imported into the island are post movement tested, and any breakdown not associated with a bought in animals, is dealt with swiftly by action on wildlife in the location. In this case, feral ferrets, polecats and wallabies. This was statement from the Isle of Man authorities, given to us in 2007:
"We can clear up our outbreaks without further breakdown because we don’t have a large reservoir of infected badgers.

We think it may be circulating to a minor extent outside cattle and are looking for a wildlife reservoir – suspects at the moment are feral wallabies, feral cats, polecats and rats. If and when we find proof of an infected wildlife reservoir, we will take action to control/eradicate.

If any badgers were to be imported and released illegally, we would take immediate steps to eradicate on the grounds that they are non-indigenous species and a threat to our national herd.
So while we in England and Wales prattle on about vaccinating badgers (and in Brian May's case, cattle) while vets and breed societies take their collective eye off the ball by producing genetic indices, and our Ministry ducks out of its collective responsibility for eradication of zTB in wildlife, by using the same basic tools of test and slaughter, the Isle of Man has succeeded in becoming TB free. The difference is that they also eradicate TB from their wildlife.

 As we said in 2007, we should be so lucky - or our cattle should. - [link]

We are reminded that annually, in order to receive the lion's share of the EU's TB budget, this country has to submit an eradication plan. And more importantly, the results of previous largesse. We reported the 2014 presentation in this post - [link] together with a screen grab of the twee back page which accompanied it.

We also remarked that cattle domiciled in mainland Britain have nothing to thank our ministry for.
Nothing at all.

Monday, January 11, 2016

A Happy New Year - not.

For a couple of Devon farmers, the last few weeks have been anything but happy. A couple of weeks before Christmas, farmer Michael Ashton's lovely jersey herd - [link] was reduced by a quarter, after 45 cattle were revealed as reactors. The reports carried an extraordinary comment attributed to the NFU, that:
" ...a fox may have dragged a dead, infected badger across pasture land and passed on the disease."
Whaaaat? Why bring a bloody fox into the equation? A half dead badger crawling around can easily infect a herd of cattle with no help at all from anything else. He's a mobile WMD. (Weapon of Mass Destruction)

(Picture credit - North Devon Journal.)

And the news this week is no better, with Crediton farmer, Malcolm Huxtable inviting Dr. Brian May to watch, as his cattle were condemned - [link] as reactors.

May's reaction was to once again push for cattle to vaccinated. That is the answer, he said, with all the confidence of the totally uninformed. And this posting, after his last foray into vaccination, explains why it won't work. Ever. [link]

And he forgets of course, the WHO's (World Health Organisation) rationing of BCG base vaccines to try and cover a 30 percent shortfall in supply. - [link]

He also chooses to ignore  the continuing upspill of badger TB into many mammals other than tested cattle, including domestic pets, their owners and vets. Or is Dr. May suggesting we vaccinate every mammal which may cross the path of a badger riddled with a Grade 3 zoonotic pathogen? And boost it annually, of course.

Come to think of it, what on earth are we doing even entertaining such obscure idealists?
The only people who should be dealing with the eradication of zoonotic Tuberculosis - where ever it is found - are Public Health, Defra and owners of animals which by International Statute have to be tested in an approved zTB eradication programme.

The opinions of anyone else, no matter how famous, are distractions. Fudge.

Thursday, December 24, 2015

Merry Christmas to all our readers.

We wish you all a merry Christmas and a peaceful, prosperous New Year. And we hope that none of your plans are derailed by any small, black and white critters with a persistent cough and severe incontinence.

Monday, December 21, 2015

The end of another year.

It's now 12 years since we posted most of the 538 Parliamentary questions, which formed the basis of this site in 2004. It is also over 100 years since Professor Koch did his experiments with m.bovis, and instigated the first postulates of disease transmission, which relied on a set of principles, rather than absolute proof.

In between then and now, this country had almost eradicated zTB from its cattle herds, only to see a resurgence in the mid 1980s from a wildlife reservoir it seems soooo reluctant to touch. And hasn't touched at all since a £1m bung to the Labour government in 1997.

Not unsurprisingly,  in the last couple of decades, main setts in England have increased by 103 per cent. How do we know? Because almost two years ago now, this article - [link] was published by Fera, which told us. Fera have also confirmed that in areas of endemic TB, about 50 per cent of the badgers are infected.

Apparently, we have a 25 year plan, but from where we stand, that seems long on cattle measures and short on anything to do with a wildlife reservoir of disease. But then, it's what Professor Bourne manipulated - [link] his team to deliver, almost 20 years ago. His idea was to let farmers knock off a few (a very few ) badgers to get them to accept cattle measures. Most of which, by next year, will be in place.

Meanwhile the Chinese whispers surrounding a DNA screening test for infected badgers get louder. Who has the megaphone we have yet to find out, but they are dead wrong. - [link]

Even when offered half the optimum number of samples, one tenth of the optimum number of bacteria and using a third of the background prevalence of disease, this test performed very well, meeting 4 out of 5 of Defra's criteria. The one on which it was 'borderline' was Specificity. That is the number of false positives any test gives;  which while not upsetting many people when it comes to tests used for cattle, appears to give Defra's mandarins indigestion when applied to badgers.

But how do they calculate DNA? Obviously the acronym PCR (Polymerase Chain Reaction) fuddles their collective brain, so we'll stick to Deoxyribonucleic Acid which is the long word for DNA. An acronym most people have heard of and trust.
Think paternity tests, forensic science, Silent Witness and TV murder mysteries.

And the only way a DNA sample (PCR is DNA fragments) can give a false positive is if the sample (or those playing with it?) is corrupt or contaminated. It's a straight 'Yes' or 'No'. But what you cannot do is 'model' it to give stupid results, if you want to trash the whole idea. Neither can you take specificity of one test on one badger and model it back to a group. Warwick's badger DNA test is a group test, relying on 20 samples taken from a group latrine - the one nearest the sett. And used as instructed and validated, it works.

So as this year draws to a close, what have we achieved? Just three small pilot cull areas with some dubious input data on existing herd breakdowns - [link] which are proving difficult to substantiate - one way or the other. Two of these pilots end next year, with nothing in place after that. Meanwhile, we have several mini cull areas awaiting Natural England's attention. They'll have to move quickly to catch up on Fera's 103 per cent increase in main sett populations.
And, we hear, possibly some mini T-Bags. Local discussion groups which are to feed 'information' - as yet unspecified - up to the big TBEAG and thus to government.Who can then file it.

 Inevitably, we also have another raft of cattle measures to look forward to. Two tests at severe interpretation for any herd in the high risk area which has a breakdown, regardless of the cattle post mortem results. And a post movement test for cattle moving out of that area and not slaughtered within 120 days.

The one good thing which happened this year, is that the daft idea of vaccinating badgers - [link] has hit the buffers. But with cynicism born of years of practice, we expect some other inventive  prevarication to replace it - bio-garbage security being one possibility.

Meanwhile zoonotic Tuberculosis marches eastwards and north on four small paws, at a rate of knots. And there is nothing at all in the way of targeted wildlife management for these areas, only a nervous wait until they achieve High Risk status. And then they can try to comply with Natural England's mathematical carnage of a 70 percent cull on 90 per cent of land, in 6 short weeks. And pay for it..

Our grateful thanks to all our contributors around the world, and a very merry Christmas from us all at blogger headquarters.

Sunday, December 06, 2015

BCG for badgers, while babies go short,

As the worldwide shortage of BCG vaccine for human beings hits the headlines, we hear that Wales has abandoned its trial of using the drug for badgers. Farmers guardian - [link] has the story of the Welsh Assembly Government's second U turn affecting the cattle farmers in this area.

Their first was to abandon plans for a cull of badgers, in favour of jabbing them.

There was no head count, no pre screening for existing health status and using a drug which had no efficacy data presented. Just trap and jab - as many as you can. And the cost? a staggering £2.8m in the first 3 years, and around 5,500 doses delivered in four years; with no certainty that they were given to the 'right' badger, or one who just put up with a needle in its bum, for the sake of a reward of peanuts.

We say this after hearing of a Devon badger which arrived on a local autopsy table, with numerous puncture wounds in its derriere. It appeared to have been 'vaccinated' numerous times.

Shortages of BCG first hit the headlines in 2012, when The Telegraph - [link] reported the closure of the plant operated by Canadian company, Sanofi Pasteur. This story was updated in 2014 by the Daily Mail - [link] which reported 'thousands of people' were left without the drug, which was now being used for bladder and bowel cancer.
Thousands of bladder cancer patients face an uncertain future because stocks of a drug that prevents the disease progressing are running perilously low.

The crisis means patients may be soon given a stark choice: surgical removal of the entire organ, or risk the cancer returning. Up to 12,000 people are to be left without the crucial medication, called BCG, as British hospitals run out of supplies.
And earlier this summer, the World Health Organisation (WHO) issued a rationing system for supplies of BCG. Their new recommendations are on this WHO paper [link] with their explanation for the rationing:
In 2015, 180 million doses were needed, and only 107 million were available."
That is a 30 per cent shortfall.

Just one badger vaccination offered to a candidate of unknown health status and due to be repeated for at least 5 years - if the badger volunteered for his jab, is 10x the strength of a 'normal' dose for a adult human being and 20x that needed for a baby.

Excellent PR for the farming industry isn't it? Particularly as the drug itself, as predicted, seems to be having no effect on cattle TB in the area whatsoever.

But that was never the intention. What did Defra say in 2011? "Pump-prime farmers to accept the concept of vaccination"? We discussed it in this post - [link] And it gets no more palatable with re-reading it.

Patronising guff. And if Defra want to carry on vaccinating badgers, as one veterinary pathologist wryly commented, they could " use saline: it will have just the same effect".

* Grateful thanks to Ken Wignall for the use of his cartoon, first shown in Farmers Guardian.