Kevin O'Donnel asks:
> Are there many cases where PCR is not overkill? Or to put the
> question another way, aside from screening for mutations, for which
> applications in the clinical or plant pathology fields is PCR now the
> method of choice?
This is a very good question. Here is my personal answer - and I'd be most
interested in any other views.
There does seem to be a feeling in some quarters that PCR will replace all of
current diagnostic microbiology. That could be true, but I do remember similar
promises being made for antigen detection kits about 10 years ago. They were
going to convert all of microbiology into bedside tests - it was just a matter
of making the right monoclonals.
Another impresion I come across is that any lab which cannot do PCR at the drop
of a hat must be living in the dark ages. In my opinion there are just being
cautious, and not jumping on the bandwagon.
PCR does have a place now for diagnosis and management of hepatitis C.
It probably has a place in diagnosis of TB, though it is not yet clear quite
where. It is not sensitive enough to screen out negative specimen prior to
culture, and does not (yet) give sensitivity results. It may be used as a
quick test to confirm that a smear-positive specimen does indeed contain
Mycobacterium tuberculosis, but that is an expensive approach and not really
much faster than "conventional" Bactec culture followed by probe-based species
identification. It is useful in pathology for dealing with fixed tissue.
There are some other specific organisms that are hard to recover by
conventional methods, and may be detected better by PCR, but I don't think that
PCR is established as the best diagnostic method for any of these. In many
cases these organisms are not common, or not commonly looked for.
There are some "high-volume" examples where PCR (and other amplification
methods) are being investigated annd promoted by large companies to replace
current technologies. Chlamydia and gonococcus testing come to mind. I don't
think that amplification technology offers a huge advantage in these cases,
though there are some benefits. (The biggest benefit will perhaps be to the
company that comes out with a really good system - or is that being too
cynical?) Benefits include the ability to test urine rather than cervical
swabs for Chlamydia, for example.
There are some disadvantages to PCR over culture for any of these organisms.
Lack of antibiotic sensitivity tests is one, and lack of a whole genome for
PFGE etc is another. These are potentially soluble problems. The basic
problems of false-positive results has not yet been answered however. The
automated systems may well get round it, but for any "home-made" PCR system
there is a very real potential problem. There is a very good paper on this
point in J Clin Micro (Feb 1994, vol 32, p 277-84) showing that some apparently
well-organised labs had large numbers of false positives in doing PCR for TB.
No diagnostic microbiology lab which hopes to survive can afford to ignore PCR
etc. We need to study it, and we need to get some expertise. But I don't
think we need feel obliged to actually do much of it right now, with the
exception of Hep C.
Paddy Gibb MB, PhD
Foothills Hospital & Provincial Public Health Laboratory