Molecular techniques in clinical microbiology: praxies and limitations

Molecular biology has revolutionized many areas of clinical microbiology in the past decade. Although conventional culture and biochemical testing remain the gold standard in most situations, molecular techniques are increasingly being utilized because of their rapid turnaround time and versatility. For identification of micro-organisms, nucleic acid amplification methods like polymerase chain reaction (PCR) are most popular due to their high sensitivity and specificity. Some of these have even been commercialized recently. Detection of antimicrobial resistance is greatly facilitated by PCR of the resistance genes, especially in problematic organisms such as Mycobacterium tuberculosis and cytomegalovirus. Molecular typing techniques including restriction fragment length polymorphism, ribotyping, and pulse field gel electrophoresis play an important role in the investigation of outbreaks, offering additional information on the clonality of incriminated organisms. Some diseases previously suspected to be infective in origin, e.g. Whipple's disease, are now proven to have a microbial aetiology using nucleic acid analysis. Despite this explosive proliferation of knowledge and techniques, the use of molecular techniques must be judicially evaluated. The high sensitivity of these techniques inevitably creates the problem of false positivity and cross-contamination. Information generated from molecular typing must be interpreted in the light of available epidemiological data. In a number of cases, universally accepted standardization is not available and correlation of results from different laboratories is difficult. The current cost and degree of expertise required in the running of these tests still precludes their application in smaller institutions. Further evaluation is essential to ensure cost-effective utilization of these promising techniques