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.
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".

Sunday, October 29, 2017

Infectivity of vaccinated badgers

Last week, UCD Centre for Veterinary Epidemiology and Risk Analysis, UCD School of Veterinary Medicine, University College Dublin, and the Quantitative Veterinary Epidemiology group, Wageningen Institute of Animal Sciences, Wageningen University & Research, Netherlands published a paper -[link] on the vaccination of badgers.

 Over four years, groups of badgers were jabbed with either BCG or a placebo and then tested for results. The paper describes:
In this manuscript, we present the results of a badger field trial conducted in Ireland and discuss how the novel trial design and analytical methods allowed the effects of vaccination on protection against infection and, more importantly, on transmission to be estimated.
Cutting through all the guff, we pick out the following paragraphs:
Over the study period, 55 new infections occurred in non-vaccinated (out of 239 = 23.0%) and 40 in vaccinated (out of 201 = 19.9%) badgers.
This is 'protection against infection'  part. So after vaccinating, a difference of  just 3 per cent? But then the modelers got to work, and "Statistical analysis showed that susceptibility to natural exposure with M. bovis was reduced in vaccinated compared to placebo treated badgers: vaccine efficacy for susceptibility, VES, was 59% (95% CI = 6.5%-82%)." But crucially:
However, a complete lack of effect from BCG vaccination on the infectivity of vaccinated badgers was observed, i.e. vaccine efficacy for infectiousness (VEI) was 0%.
Infectivity of badgers is the amount of detritus left behind for any other mammal to fall over. That's the 'transmission' bit. Especially important for our sentinel, tested cattle, and described in the paper as " extremely important in the case of vaccination in badgers, as the ultimate goal is to help in the control or eradication of M. bovis infection in cattle."

 Not just in Ireland either. Our lot have been playing with BCG (at 10x the rate for humans) for several years. We discussed their results here - [link] and veterinary professionals gave their view here - [link]
And we also remember poor old badger D313 - [link] who had his dose of BCG and developed zoonotic Tuberculosis in pretty much every organ, during the Lesellier trial. -[link]

So the paper's 'stand out' paragraph for us is this blinder:
A reduction in the total infectivity of vaccinated and subsequently infected badgers in the field had been anticipated based on the reduction in disease progression observed in vaccinated compared to non vaccinated badgers in experimental studies (Chambers et al., 2011).

However, no reduction of infectivity was found in our study. The lack of effect of BCG vaccination on infectivity in the general badger population is thus at odds with the hypothesis that vaccination, by reducing disease progression, reduces the infectivity of vaccinated and subsequently infected badgers.

From this study, we cannot determine whether a similar reduction in disease progression to that observed in experimental studies was found in the field as no post-mortem data were available. Nevertheless, if that reduction in disease progression does exist, we did not find a concurrent reduction in infectivity. The lack of effect of vaccination on infectivity has implications in terms of the effectiveness of BCG badger vaccination in Ireland (or how much reduction of transmission is achieved by vaccination).
Post mortem data was available to Lesellier, and those vaccinated badgers all had lesions and all were shedding. (Link above)

The Farmers Union of Wales understands only too well, how ineffective faffing about with vaccinating badgers is. In an an article - [link] published by the Institute for Welsh Affairs earlier this year, Dr. Nick Fenwick describes the result of four years of vaccinating:
So it comes as little surprise that the latest official report on the badger vaccination programme in north Pembrokeshire, which cost £3.7 million, concludes that “Consistent trends in indicators of bTB incidence have not yet been seen…”
Perhaps someone should tell The Badger Trust, Rosie Woodroffe,  Brian May, and even the Secretary of State - link] And also ask, with these results echoing those of Lessellier in 2011, why on earth anyone is still promoting and funding this?  

Wednesday, October 25, 2017


Would you choose a veterinary professional to tune your guitar? Probably not.

But today our Secretary of State for Agriculture tweeted about his meeting with superannuated star gazer, Dr. Brian May - he of Save Me fame - to discuss a way forward on the thorny question (at least for an upwardly mobile politician) of zoonotic Tuberculosis.

This was the Tweet from Save Me, updating Gove on the way forward. Improved cattle testing, vaccination and stupid farmers. Nice one.

Now Gove is not the sharpest knife in the box, having (according to Private Eye) attempted to unblock his lavatory with a vacuum cleaner - until he was stopped. We understand that he is however well known for echoing the thoughts of those to whom he spoke most recently.

So perhaps some refreshing factoids better make their way into his shell like.

 For instance, in our PQs over a decade ago now, we asked the reason why certain areas of the UK, which had undergone a thorough cull of badgers, had achieved such success.

The answer was unequivocal and needs to be inscribed over the door of every building occupied by this most political of government departments, and especially the office of the Secretary of State:
" 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 - Hansard]
Other areas too had spectacular success, including East Offaly, Steeple Lees and Hartland, but also the four area trial - [link] in Ireland with a reduction in cattle TB of around 96 per cent.

 And two decades or more ago, these areas had no bolt on cattle measures at all. Particularly of the sort Dr. May and his cohorts propose.

Just, as the PQ said 'a systematic removal of badgers from the area'.

Keep it simple.


Wednesday, October 18, 2017

RSPCA and the cull

From The Times - link] this morning: (The Times is paywall protected)

 "The RSPCA has softened its stance on badger culling by dropping a promise to publicly shame or investigate farmers who take part.
After years of threatening farmers with public disgrace and expulsion from its animal welfare schemes, it said it had accepted advice from “external auditors” that culling badgers was not an “automatic breach” of its ethical farming rules.

The audit was launched last year by its former chief executive, Jeremy Cooper. His predecessor, Gavin Grant, had threatened to “name and shame” farmers involved in the cull and said people would boycott milk “from farms soaked in badgers’ blood”.

 That's big of them isn't it?

 A previous headline could have been 'RSPCA promotes zoonotic Tuberculosis throughout it supplying farms'.

Sunday, October 08, 2017

Beneficial crisis?

Most crises create casualties by the lorry load, but also beneficiaries - if you are cute enough to jump onto that particular bandwagon.  'Bovine' TB or zoonotic Tuberculosis as we prefer to label it, is no exception.
Hard on the heels of those reams of 'research' which we spoke about in this post - [link] comes a new initiative from animal health screening lab, BioBest.

 With a little help from Danielle Gunn-Moore, BioBest now advertise a screening test - [link] for Canine and Feline TB. Their sales sheet explains:
The interferon gamma test is intended to assist in the diagnosis of suspected canine and feline TB cases. The interferon gamma test can be useful in categorising cats and dogs with suggestive lesions. This in turn can inform decisions as to whether treatment is appropriate and whether it is necessary to report the case to AHVLA (Suspected Bovine TB is a notifiable disease in all mammals).

There is also some evidence that the test can be used to monitor treatment, with responses falling in cats in remission. The test has been developed in collaboration with Professor Danielle Gunn-Moore of the University of Edinburgh and with the technical support of colleagues from AHVLA.
It is to be hoped that the use of GammaIfn is somewhat more specific to zTB when used on cats and dogs, than its use has proved to be in cattle. False positives in that species are well documented.
And is 'treatment' of zTB, an often fatal zoonotic pathogen, in a companion animal, likely to be sharing air space, if not its owner's bed, a good idea?

But we digress..

We came across Professor Gunn-Moore in 2013, when she published articles giving a link to infected badgers and an increase in felines with TB. - [link] We remarked then, that with a veterinary post mortem on a cat costing in the region of £100, digging a hole may be cheaper.

 And we are also reminded of the genetic predictions made concerning feline encepalopothies in the 90s, when it was thought that Siamese / Burmese cats may be more susceptible. Until it was realised that the value of these animals made veterinary investigations more likely.

 BioBest say:
The test will initially be performed on the 1st and 3rd Thursdays of each month at a cost of £200 per sample.
That £200 per sample, would buy a truck load of cats. And it is unlikely that many owners taking up BioBest's offer of screening, will have offered unpasteurised milk to their pets..

Friday, September 29, 2017

Ker -ching.

If there's one thing we've learned over the last two decades gathering information about the UK's epidemic of zTuberculosis, it is that salary and pensions are way ahead of any principles - scientific or otherwise.

 We first came across this phenomenon with the diminutive professor, John Bourne. He headed the ISG (Independent Scientific Group, who were actually neither of those adjectives) and conducted the farce of the Randomised Badger Culling Trial (RBCT) 1997 - 2005. This was a debacle in which he was proud to explain to the EFRA committee that his trial's conclusion - [link] was predetermined before it started. Ker-ching.

 Then we have Warwick University, happily trousering at least £1m to develop their qPCR test for use in non-invasive screening and identifying infectious badgers. Building on the validation in 2011, Liz Wellington's team - [link] were provided with a substantial sum of taxpayer's cash to bring this test into field use. Only to fly in the face of a farmer contributor, when asked to endorse the method for culling badgers. That, Warwick staff stated unequivocally, they would not do - [link] 
We have yet to ascertain whether Warwick retain Intellectual Property Rights over a taxpayer funded test. But although they do not wish it used to identify infected badger groups, they seem very happy to play with it in the 'environment'. - Ker-ching.

And then there is the fragrant Rosie: Professor Bourne's sidekick on the RBCT, he taught her well.

Presently, together with a few political vets and Wellington's team, Rosie Woodroffe is playing around with a grossly infected group of badgers in West Cornwall.
Farmers involved are telling us that they wish they'd never agreed to let these people on to their farms. The drip feed of 'results' while making good copy, bear no relation to reality - [link] at farm level. Farmers who regularly lost just one of two cattle per test, now report lorry loads going, after Rosie's lot had cage trapped them.
But following TB infected badgers, the cash keeps rolling. Ker-ching.

Wales too has its benficiaries of this crisis. In 2010, their chief veterinary officer, Christianne Glossop (picture above)  gave a stunning overview -[video link] of her plans to eradicate TB in Wales.
(Apologies - blogger didn't like the video link, so it's added as a URL link. Click to view)
What Glossop said in 2010 was spot on when she speaks of 'tackling all sources of infection' and that 'we must deal with infection in badgers'. And crucially, culling badgers 'makes a big difference to the level of infection in the countryside' and that 'directly reduces infection in cattle herds'. All correct.

But with a little arm twisting from an incoming Labour administration, seven years and heap of dead cattle later, Glossop now attempts to defend Wales's appalling record on eradicating TB without touching badgers. Record numbers of cattle slaughterings, the Welsh four year vaccination debacle, (much cash, but no effect on cattle TB at all) and the Intensive Action Area (where tried and failed cattle measures were repeated) leading to many cattle farmers giving up the struggle.
All this after the Welsh badger cull was cancelled.  Glossop is still in her position. Ker-ching.

 As we have said many times, it is difficult to get someone to understand something, when his salary depends upon him not understanding. Ker-ching.