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Trends in Microbiology Vol. 10 No. 10 (Suppl.), 2002 A TRENDS Guide to Infectious Diseases | Review Molecular detection and genotyping of pathogens:: more accurate and rapid answers James Versalovic and James R. Lupski Rapid molecular methods have enhanced the capabilities of laboratories to identify and characterize microbial pathogens in greater detail. Nucleic acid amplification strategies and advances in amplicon detection have been key aspects in the progress of molecular microbiology. Sophisticated new amplification–detection combinations are resulting in many applications in laboratory testing for infectious diseases. These applications include qualitative detection, sub-species-level DNA fingerprinting, molecular resistance testing and genotyping, and quantitative (viral load) testing. When applied selectively in the laboratory, these applications can enhance diagnostic approaches and clinical management and will probably evolve into standard laboratory and point-of-care testing protocols. Microbial genomes are being sequenced at a staggering rate; studies, but these methods are limited in sensitivity in there were 81 publicly available bacterial genome sequences comparison with in vitro nucleic acid amplification. as of June 1, 2002 (/ In the 1980s, molecular probes were applied in clinical PMGifs/Genomes/micr.html). Our understanding of sub- microbiology for the first time. Researchers were quick to species-level or strain-level differences in bacterial and viral appreciate the conserved nature of the ribosomal RNA genomes has sharpened our appreciation of the differences (rRNA) operon and Carl Woese began using these between clones or quasi-species of microbial pathogens. sequences to establish the field of bacterial phylogenetics Elevated