RSV testing: PCR Overkill?

Fri Jan 19 14:54:34 EST 1996

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

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