Babies and bath water

In our posting below we added a little padding to how a very selective cull of badgers infected with tuberculosis might be framed. But concentrating entirely on PCR, in a can't do, won't do piece, Badger Trust person David Williams, explains why the Trust don't support question this approach.
Mr. William's points are in quote boxes, with our answers below:

Did the sample come from cattle, badgers, foxes or other wildlife that could have walked through a farmyard, field or cow pat, any of them carrying infection?

We have the 'canaries' Mr. Williams. The sentinels. Try 34,000 cattle last year, a shed load of alpacas, sheep, pigs and even domestic pets. Thus the initial Risk Assessment and field maps of reactor location (any sort) gives AHVLA case managers the location of the problem(s.) And if badger groups (the animals, not their protectors, but ... ?) were baited with small (different) coloured beads or fluoresced powder, tracking from individual setts would show which group or individual was occupying the same land.
Prof. Krebs proposed following 'badger boundaries' in 1996, and he was quite correct. Only then would this be followed up by sett test on latrines, bedding or even air from a sett so identified.

Did the sample come from a live badger or a long-dead one?

If it was a long dead badger, he would hardly be likely to be leaving fresh deposits in latrines or changing his bed regularly (unless they are ghostly deposits)

If taken from soil did it come from a badger?

Again it is not just soil, but say soil in sett entrance, fresh latrines or any material associated with the group. So cross contamination unlikely.

If a positive sample was found in a sett, would you catch and kill all the badgers in that sett?

Yes because it would show that the TB bacteria was present in the sett so even if some badgers were not yet infectious it is very likely they would become so in time. The presence of m.bovis bacteria in the sett (humid, dark and most) offers the ideal situation for survival of this bacterium, and transmission. See PQs:  

"Mr. Paterson: To ask [] what evidence there is that viable M. bovis bacilli remaining in badger setts?
Mr. Bradshaw: M. bovis survival is promoted by low levels of sunlight, low to moderate temperatures and high relative humidity. A typical badger sett experiences 100 per cent. relative humidity at all times of year, a fairly constant temperature, which is always higher than ambient temperature and almost total darkness. Hence, although no quantitative studies have been carried out, it seems possible that M. bovis bacilli could remain viable in badger setts long enough to infect badgers during recolonisation."

Would you catch and then test beside setts where an infected sample was found?

No. Testing of individual badgers (with only the positive ones culled) would cause perturbation by breaking up the social group. And see PQ answer above, the uninfected ones would become infectious via their sett or latent infection, over time.

A positive sample from inside a sett could be from a badger not normally living in that sett or a fox using it temporarily.

PCR would not be used as a stand alone tool, but in connection with tracing reactor (cattle, pig, alpaca, sheep, buffalo) movements. This after AHVLA risk assessment to rule out movement on to farm or confirm a wildlife source for the reactor. See point 1.
PCR could then pinpoint infection after the first two stages. There is no need to take samples from every sett, just those flagged up by such mapping and bait marking. If the positive samples were gathered either from a 'disperser' badger (one not normally living in that sett and excluded from its normal group) or a fox,  if they are carrying m.bovis then they are a risk to all other mammals and should be culled.
 The target of eradication is not any particular species, but b.Tuberculosis.

If you don't identify and test all the social group, a massive task, selective removal becomes impossible.

Quite. Selective removal is impractical as stated before and for the reasons given. But the same applies to the 'selective' vaccination of badgers as promoted by the Badger Trust as the way forward. By not assessing population density prior to vaccination, thus not vaccinating all the social group, makes it pointless, even without taking into consideration the weaknesses of the vaccine or pre screening badgers for existing disease status.

Infected badgers do not necessarily excrete the TB bacillus.

This may be the case in individual badgers but at some point, infected badgers will excrete TB bacillus. PCR detects the DNA of m.bovis, rather than a candidate's immune response to it, thus bacteria will have to be present for it to flag up a positive sample. It is quite likely that if the social group is infected some will be shedding bacteria while others might not be doing so at the time of testing. But any sort of stress, and that could include cage trapping to vaccinate, is likely to push those badgers 'infected' but not 'infectious' into shedding status, with inevitable results.

For a selective cull expensive trapping is going to be required unless you gas or poison the sett indiscriminately.

'Indiscriminate' in the context of an positively identified underground midden of bacteria, (see above) is not a word we would use. It is extremely 'discriminate' having undergone a three part screen. And as explained, the survival of m.bovis in the confines of a badger sett, could keep infection going for years, infecting more and more occupants.
So ideally whole sett culling using daytime anaesthesia (not poison and not a material where a sub lethal dose harms) to cull the whole social group at one go and so avoiding perturbation. And incidentally, avoiding the cost and bureaucratic trappings of disposing of Class 1 Hazardous Waste, as a 'dead' badger is classified.
 It is worth remembering that Lord Krebs proposed the use of PCR and efficient whole social group removal in his original design for the RBCT in 1996. (See our posting below) He and fellow author Dr. Rosie Woodroffe, also wanted such setts unoccupied for at least two years, to prevent onwards transmission of disease to incoming badgers. They referred to this as 'prevention of recolonisation'. So we support this; such setts should be destroyed to prevent recolonisation by other badgers, thus preventing the onward transmission of disease to healthy badgers.

Conversely, the location of the 70 per cent of cattle herd sentinels testing clear, together withe negative PCR screens, could allow a much more targeted vaccination programme, should the Badger Trust wish to pursue this?