Saturday, February 17, 2018

Zoonotic Tuberculosis and straw men

When people have little to add to a debate, they often stand up a 'straw man' and then spend a huge amount of time and oxygen knocking him down. And so it is with the eradication of this insidious disease, which we call bovine TB - or more accurately, zoonotic Tuberculosis.

It is fourteen long years since we asked our 500 Parliamentary questions of the then Minister of a Labour administration. Most of the answers were logged on the site, in 2004.

The crucial one was efficacy of the intradermal skin test, used as a herd test, and how effective it was at clearing TB from cattle herds. The answer was given in this list - Column 540 [150492] [link]
"All countries that have either eradicated, or have a programme to control, bovine tuberculosis use one or more forms of the skin test. The Government have close links with a number of countries in various stages of eradication and exchanges information and experiences on the use of the tests in the context of these programmes."
So why has the straw man of how rubbish the skin test is, been allowed to gain traction?

The answer to that is money [link] Plain and simple. Research is followed by the begging bowl for more research. Why? Those PQs in 2003/4 told us all that Defra already knew about how infectious badgers were, how they were an ideal maintenance reservoir of this zoonotic disease, and how they passed the bacteria between themselves and on to cattle and other mammals. We explored how much bacteria was excreted by these creatures and how little it took to infect a cow. How long m.bovis survived under various conditions, and what killed it. At one point we were accused of backing the badger lobby, when our PQs explored how much badgers suffered from this disease.

We back the eradication of a Grade 3 zoonotic pathogen, nothing else.

Nothing has changed, except that after twenty years of ultimate protection, there are now many more badgers and hundreds more infected / infectious ones spreading a lethal load into the environment.

 But still those straw men keep coming. The latest being Cath Rees's Phage test - [link] turned down for use in human pulmonary tuberculosis, its use is being proposed for our cattle. No matter that phage screening is not, and never has been used as a diagnostic test. The research has been done, and now must be sold to recoup laboratory costs. Ker-ching.

 And then there is politics. And an election looming, with an opposition determined to hug fluffy things and pander to minority groups - at any cost. That's Corbyn, but the echo chamber that is Michael Gove is looking to his next job, and holding hands with a super-annuated rock star, for inspiration. - [link]

So once again we'll end this posting with another PQ which explained why the Thornbury badger clearance had been so successful.
" The fundamental difference between the Thornbury area and other areas [] where bovine tuberculosis was a problem, was the systematic removal of badgers from the Thornbury area. No other species was similarly removed. No other contemporaneous change was identified that could have accounted for the reduction in TB incidence within the area" [157949]

Here is the result, compared with other less successful badger culls. Especially that charade with passed for 'science' a decade ago, where 8 nights of culling with cage traps, splintered an infectious population and then the operators walked away.

So while Brian May quotes John Bourne's well edited Final Report, he would do better to read that odious little man's evidence to EFRAcom in 2007, where he boasted that at the end of his trial, culling badgers was not to be part of the solution.
And those were his instructions at the beginning. -[link]

Stick to the basics, keep it simple. Everything else is just so many straw men.  

Tuesday, January 16, 2018

Strange bedfellows


We hear on Instagram that yesterday a high level meeting took place at DEFRA headquarters - link (pic above) to discuss zoonotic Tuberculosis and the UK plan to eradicate it. Attendees included the great and the good from the NFU, Secretary of State Michael Gove several 'ologists of various hues and...



 a superannuated, guitar playing star-gazer. Dr. Brian May

 

Now, as we are 5 years in to a 25 year eradication plan, which involves farmers coughing up cash to mop up two decades of Defra's negligence in tackling the disease in wildlife, one would have thought there would not be too much to discuss. Especially as the NFU are circulating the screen shots which we aired in this posting - [link] to illustrate the size of the historic problem in herds, compared with new outbreaks post badger cull.

 But we could be wrong. Or maybe Gove is just starstruck - link.

Tuesday, January 09, 2018

Before .... and after.

The NFU have circulated some screen grabs of the interactive TB map - [link] - so beloved of Camel Ebola and his friends - which show a startling drop in herds under restriction in the two pilot badger cull areas. Produced as a power point presentation, the slides start with a potted history of how to clear TB in cattle herds.




This is followed with screen shots from APHA's iTB map. The first taken to show historic TB restrictions in the years leading up to the culls,(Closed cases)  the second after four years of culling.(Open or ongoing on the day the map was printed)

This is a snap shot of herds which had been historically been under restriction in the Gloucestershire pilot cull area. Single dots are single outbreaks. Turquoise dots indicate clusters of up to 20 farms under restriction.




And now, herds currently under TB restriction after 4 years culling.




In Somerset, historic outbreaks in the years before the cull started:





And a snapshot after four years culling:





( ** Please note that the iTBmap charts show different time scales and are not comparable. The historic data shows several years of closed breakdowns - and illustrates the need for a cull?
While the second screen grab, shows holdings currently under restricton, after four years of culling.)

And remember, this was culling for 42 nights only, complete with intense scrutiny, huge publicity, (most of it bad) and much interference.

 The results are stunning.

The editors and contributors to this site have always supported a targeted cull of infectious badgers, encouraging the developers of non invasive testing in their work. The shock waves which followed the announcement that they did not wish 'their' test to be used to cull badgers, are still reverberating.

So as we wish readers a happy new year, we extend grateful thanks to the farmers of Gloucestershire and Somerset for piloting the alternative strategy. The fact that more badgers and not necessarily the infected ones will be killed, seems to have escaped the gravy train which follows this disease around.

Nevertheless the results of even a partial cull, are beyond expectations.

So a Happy New Year to all.

Friday, December 22, 2017

Defra's Christmas presents.



A few months ago Defra held yet another 'consultation' -[link] on the way forward to its ambition of TB free status for England in 25 years time. As usual this included a lot of buck passing cost cutting dressed up as  a 'benefit' for disease control. The phrase 'earned recognition' appeared many times.

 And yesterday Defra's plans were released, pretty much unchanged despite objections. This department does have a nasty habit of lobbing a hand grenade into your in-box on the eve of a holiday and yesterday was no exception. 

So here is our 2017 Christmas blog post:

 On the first day of Christmas, Defra brought to me: another pile of guff for my filing cabinet.

 On the second day of Christmas, Defra brought to me: two herd tests a year and another pile of guff for my filing cabinet.

 On the third day of Christmas, Defra brought to me: a 90 day SI test interval, two herd tests per year and another pile of guff for my filing cabinet.

 On the fourth day of Christmas, Defra brought to me: reduced cash if reactors are presented dirty, a 90 day SI test interval, two herd tests per year and another pile of guff for my filing cabinet.

On the fifth day of Christmas, Defra brought to me: more TB advice on biosecurity, reduced cash if reactors are dirty, a 90 day SI test interval, two herd tests a year and another pile of guff for my filing cabinet.

 On the sixth day of Christmas, Defra brought to me: a new compensation table for pigs, sheep, deer and camelids, more TB advice on biosecurity, reduced cash if reactors are dirty, a 90 day SI test interval, two herd tests a year and another pile of guff for my filing cabinet.

 On the seventh day of Christmas, Defra brought to me: grants to vaccinate badgers, a new compensation table for pigs, sheep, deer and camelids, more TB advice on biosecurity, reduced cash if reactors are dirty, a 90 day SI test interval, two herd tests a year and another pile of guff for my filing cabinet.

 On the eight day of Christmas, Defra brought to me: delayed slaughter for pregnant cattle, grants to vaccinate badgers, a new compensation table for pigs, sheep, deer and camelids, more TB advice on biosecurity, reduced cash if reactors are dirty, a 90 day SI test interval, two herd tests a year and another pile of guff for my filing cabinet.

 On the ninth day of Christmas, Defra brought to me: no live movement of  Inconclusive reactors, delayed slaughter for pregnant cattle, grants to vaccinate badgers, a new compensation table for pigs, sheep, deer and camelids, more TB advice on biosecurity, reduced cash if reactors are dirty, a 90 day SI test interval, two herd tests a year and another pile of guff for my filing cabinet.

 On the tenth day of Christmas, Defra brought to me: more gamma testing, no live movement of Inconclusive reactors, delayed slaughter for pregnant cattle, grants to vaccinate badgers, a new compensation table for pigs, sheep, deer and camelids, more TB advice on biosecurity, reduced cash if reactors are dirty, a 90 day SI test interval, two herd tests a year and another pile of guff for my filing cabinet.

 On the eleventh day of Christmas, Defra brought to me: extra testing for certain types of enterprises, which they pay for, more gamma testing, no live movement of  Inconclusive reactors, delayed slaughter for pregnant cattle, grants to vaccinate badgers, a new compensation table for pigs, sheep, deer and camelids, more TB advice on biosecurity, reduced cash if reactors are dirty, a 90 day SI test interval, two herd tests a year and another pile of guff for my filing cabinet.

 On the twelfth day of Christmas, Defra brought to me: employment opportunities for private vets, extra testing for certain types of enterprises, which they pay for, more gamma testing, no live movement of  Inconclusive reactors, delayed slaughter for pregnant cattle, grants to vaccinate badgers, a new compensation table for pigs, sheep, deer and camelids, more TB advice on biosecurity, reduced cash if reactors are dirty, a 90 day SI test interval, two herd tests a year and another pile of guff for my filing cabinet.

 It's all, and more, in this pdf - [link]

The thought to hang on to here, is the answer to our PQ way back in the mists of 2004, when we asked why the Thornbury badger clearance had been so successful. Following that there combined with test / slaughter of any reactors, were no cases of TB in cattle for the following decade or more. 

The answer was unequivocal. And all of the above, just so much guff. A sop to the Treasury and Brian May's groupie's but completely unnecessary.

" The fundamental difference between the Thornbury area and other areas [] where bovine tuberculosis was a problem, was the systematic removal of badgers from the Thornbury area. No other species was similarly removed. No other contemporaneous change was identified that could have accounted for the reduction in TB incidence within the area" [157949]

A very happy Christmas to all our readers, farmers and vets.

Friday, December 15, 2017

Singing from the same hymn sheet

It seemed a simple enough question. But drew a raft of answers, many totally incorrect, from people who should know the answer.

 After cattle have tested clear, and providing that the herd is not under restriction for TB, then in many areas of England, farmers have just 60 days in which to trade them. But when does the clock start ticking?

 One of our contributors had occasion to ascertain this date recently. And he received some surprising answers.

 From an NFU spokeman, '60 days from reading day' : so 60 days after the test is read?

This marked a change from past practise, so our contributor then phoned the newly hatched TB Advisory service - [link] and was given the same answer by telephone. 60 days from the reading of the test.

Not content with this answer either, the facts were requested in writing, and an APHA booklet -[link] appeared in his in-box. Page 5 is the relevant information to answer the question, and it states:

 "Pre movement tests are valid for 60 days (from the date of the injection, which is day zero of the 60 day period)".
So the 60 days starts from jab day, but begins the day after the tuberculin antigen is given?

 Not according the blumph on the TB Hub - [link] advisory service website. This states:

 "Clear pre-movement test results are valid for 60 days from the date of injection (day one of the test)".

Being charitable that 'day one' mention may be construed as the first part of a two part test. But it may also be construed as the day the 60 day movement window begins. It's a fudge.


 Farmers' BPS payments depend upon having clear knowledge of their responsibilities for testing of cattle and following these to the letter, with threats of substantial deductions for non-compliance.
So, it is a damned disgrace disappointing that the verbal information sought was so very wrong, and two NFU or Government backed websites contradictory.


It would be helpful if all these advisers were singing from the same hymn sheet, but the paucity of correct information on this very basic question, indicates the people offering it are not even in the same choir.



Sunday, November 26, 2017

Hiding in plain sight

Published in September was a string of mathematically modeled figures from the original pilot culls in Gloucestershre and Somerset. Or at least the first two years of them.

Pinned out, dissected and calculated into figures that a laymen can understand, Roger Blowey MRCVS has explained to the Veterinary Record, that when the modeled figures are closely examined, the drop in cattle incidents in the two pilot areas is quite startling.

58 per cent in Gloucestershire, and 21 per cent in Somerset. 



Published by the Wiley Online Library, the paper is headed "Assessing the first 2 years of industry led badger culling in England on the incidence of bovine tuberculosis in cattle 2013 - 15"

It can be viewed on this link. - [link] The modelers compared several non cull areas of both counties, as similar in size and cattle density as was possible, and then extruded the results.
Screen grab from the paper.


What was probably more amusing, was the that bastion of Badger Protection, the BBC gave this story a whirl on their flagship Countryfile -[link] programme.

But as the figures in Lucy Brunton's paper contain no mention of a 58 per cent drop in cattle incidence of zTB in Gloucestershre after two years with a Gatling gun, one may assume that in some quarters, their  results may prove a tad embarrassing.

Nevertheless, with a new battery in his calculator, Mr. Blowey has done the donkey work, and there it is. A good result. Hidden in plain sight.

Tuesday, November 21, 2017

A new test or 'dangerous nonsense'?

Bacteriophage technology has been around for almost 100 years - [link]

It is well understood and in simple terms is a bacterial virus which attacks bacteria and replicates within the cells. Work has been done over decades to see if this could replace drugs in the treatment of antibiotic resistant strains of TB.

 From 1999, a paper which explains the background to phage exploration and despite high hopes, how it failed to act as a 'cure' for Tuberculosis - [link]

And from 2004, the Journal of Clinical Microbiology - [link] concluded that:
"The small increase in sensitivity over that of direct microscopy does not justify the introduction of this technique for routine diagnosis of pulmonary tuberculosis at this time."
Meanwhile Biotec Laboratories in the UK were also investigating the use of phage technology to diagnose human Tuberculosis - [link] with their FASTPlaque TB tm screen.

 The results of this project were not outstanding, with many false positives and also false negatives leading us to question whether the test is species or type specific?

 A comment - [link] from a 2006 paper, exploring new methods of detecting TB in humans (m tuberculosis) describes Biotec's phage technology as follows:
"The results demonstrated that, when performed on culture isolates, phage assays have relatively high accuracy. A total of 11 out of 19 (58%) studies included in the review reported sensitivity and specificity estimates of at least 95%.Specificity estimates were slightly lower and more variable than sensitivity; five out of 19 (26%) studies reported specificity under 90%.

Only two studies performed phage assays directly on sputum specimens, with inconsistent results."
So the results were described as 'inconsistent' with specificity (false positives ) under 90%..

So what has this to do with m.bovis (a close cousin of m.tuberculosis) in our cattle?

A great deal when the company pioneering it offers opportunist interviews - [link] while guesstimating its sensitivity / specificity. The Times covered the story with an attention grabbing headline earlier this month, and this was picked up by the farming press.:
"When the veterinary surgeon arrived at a dairy farm in Devon yesterday, he already knew at least 30 cows were infected with tuberculosis. Their blood had tested positive using a new kind of TB test that is being pioneered by researchers at Nottingham University."
A skin test followed, and the cattle tested clear. The herd owner is quoted:
"He also knows that the 30 cows that tested positive using the blood test, known as phage, could infect the rest of his herd but he can’t afford to slaughter them."

The government only compensates farmers for animals that have failed their standard, approved tests. Those 30 cows have passed more than 30 skin tests each."

“If we knew getting rid of them would clear the TB immediately we would do it,” the farmer said. “But if it didn’t, I would go bust.”

There is a risk that the phage test hasn’t identified every animal with TB. There is also a risk that the cows could pick up new infections from the environment.
There is also a big risk that the phage test misdiagnosed those positives. In other words, a bundle of hopeful certainty, from a test not validated as a diagnostic test at all and with dubious specificity.

And then this cruncher:
Dick Sibley, a vet who is leading the farm trial, said a survey of badger setts in the fields around the farm had shown 30 per cent of the animals had TB.
and:
Young cows share the fields with those badgers before they are brought inside to calve. “Even if we slaughtered 50 cows out of 500 there might be an infection remaining in the herd that we hadn’t found,” he said. “We can’t ask the farmer to do all this to get rid of the disease, only to let the animals get reinfected from the environment.”
So, using a test not cleared for diagnostics, and with a dubious pedigree, Sibley has decided that in spite of his remarks about the infectivity of local badgers, that the Biotec phage test is the next Big Thing. And more cattle must be killed?

 Our microbiologist co-editor has the following comments:
"Phages are well understood,  old technology. They cannot be used as a diagnostic tool.  End of.

To use bacteriophages thus is an abuse of the test and dangerous nonsense".