PCR - used on everything but badgers?

Two pieces of research which were completed around 2005, and published in 2006 may be of interest. They both deal with 'bovine' TB in species other than badgers, and the risk to cattle from these mammals in a farm environment.

We found these papers in a huge pdf file on the Defra website, which if nothing else shows just how much 'research' a coughing badger generates. Scroll down to P. 336 for the work on SE 3010 (The risk to cattle from Wildlife species other than Badgers, in areas of high herd breakdowns.)
The conclusion, after a £754K spend was that locally, some species of deer could prove problematic, but that common farmland wildlife, other than badgers, are relatively unimportant to the control of bTB in cattle:

Most species exhibited a relatively low risk to cattle. The highest risks were associated with fallow and red deer. Given these results, the paucity of data on interactions between deer and cattle and their rapidly expanding numbers and distribution in southern England, deer may be a potential source of infection for cattle.

But for us, more interesting was a parallel study using live sampling, costing £1.2 million and known as SE 3009 which can be found on p 324. (The risk to cattle from Mycobacterium bovis infection in Wildlife species other than Badgers.) The conclusion of this one:

The same strain of M. bovis can infect bank voles, badgers and cattle on the same farm. However, the prevalence of infectious individuals is extremely low in this, and in other abundant farmland wildlife. Mathematical modelling suggests it is unlikely that the wildlife species we studied represent a significant reservoir of infection for cattle, though occasional spill-overs from badgers and cattle may occur. Our additional case-control study supports the view that small mammals are unlikely to contribute to the risk of bTB in cattle.

So far so good. Of  4,180 samples, only badgers and single bank vole tested positive. And what method was used 10 -12 years ago to sample bits from these16 species of  mammal which  included foxes, rabbits, rats, squirrels and many varieties of mice?

Confirmatory testing of presumptive positives was by growth onto selective media by the TB Reference Laboratory, Weybridge and/or confirmation by polymerase chain reaction (PCR).

No, you did not mis-read that; the paper goes on the describe:

Four PCR-based methods were used. These were PCR for IS1081, a multi-copy element generally present in 6 copies in members of the Mycobacterium tuberculosis (MTB) complex; PCRs to detect and distinguish between M. microti and classical M. bovis on the basis of deletion regions (known as RD7 and RD4); and Spacer-OLIGOnucleotide TYPING – ‘spoligotyping’.

So why after a spend of £1.2m and a published paper which concluded that " the modelling of risks was not possible due to the very low infection rates found" (using PCR) is this technology, now a decade more advanced and available from AHVLA on a commercial basis for some m.tuberculosis complex bacteria, being so sidelined for badgers?

 We could say 'more research?' but we will resist the temptation. This time.