[Applications of PCR techniques for molecular epidemiology of infectious diseases]

The development of new PCR-based typing methods in the last years have supposed an important advance in the study of infectious diseases. Arbitrarily primed PCR (AP-PCR) and repetitive element sequence-based PCR (rep-PCR) are the most widely used PCR-based fingerprinting methods for bacteria and fungi. Major advantages of these methods are flexibility, technical simplicity and high discriminatory power. The AP-PCR presents problems of low inter-run and inter-laboratory reproducibility which make necessary the optimization of the protocol and reagents. PCR-RFLP is based in the enzymatic digestion of polymorphic genes amplified by PCR. This method is easy to perform and discriminatory, although less than AP-PCR or rep-PCR. Amplified fragment length polymorphism (AFLP) is a highly reproducible and discriminatory typing method based on the amplification by PCR of restriction fragments obtained from chromosomic DNA. This method is more discriminative and reproducible than AP-PCR, rep-PCR and PCR-RFLP, but it is more time-consuming and expensive, and requires specialised personnel. Most of these PCR-based typing methods are less time-consuming, rapid and easy to perform and of interpretation than pulsed-field gel electrophoresis (PFGE; gold standard method for typing most bacterium and fungi), but they usually are less discriminative and reproducible than PFGE, depending on the species studied and the method of PCR used. In summary, there are several PCR-based methods which are useful as a primary approach to the study of the clonal relationship among microbial isolates. The selection of the method to be used depend on technical (rapid, low time-consuming, easy to perform and to interpret, reproducible and discriminatory) and economical (low cost) factors.