A 5 ' nuclease PCR (TaqMan) high-throughput assay for detection of the mecA gene in staphylococci

In an effort to find a rapid, efficient, and reliable method of screening l arge numbers of bacterial isolates for specific antimicrobial resistance ge nes, we compared conventional PCR results to the results generated using th e TaqMan 5' nuclease PCR kit in conjunction with an ABI Prism 7700 Sequence Detector for detecting the mecA gene in various species of staphylococci. DNA was extracted using two techniques. The first used a high-salt extracti on method suitable for conventional PCR but resulted in a 7.2% rate of PCR inhibition with the TaqMan technique. PCR inhibition could be overcome by d iluting samples 1:5 prior to testing. The second method used the Qiagen QIA amp Tissue Kit; no instances of PCR inhibition were encountered with this m ethod. A total of 197 (96%) of the 206 samples with no inhibition showed ag reement between the two methods. Eight of the nine disagreements were likel y the result of low-level DNA cross contamination caused by frequent specim en handling. Target DNA in all eight of these samples was first detected in the initial tests only after >30 PCR cycles, and all were negative upon re peat testing even after 30 PCR cycles using freshly extracted DNA. Among th ose positive samples in agreement, target DNA was invariably detected befor e 30 PCR cycles, The TaqMan assay eliminated the need to load, run, stain, and read agarose gels and provided the advantage of instant detection of PC R product by laser-activated fluorescence. Thus, final results were obtaine d 2 h after PCR was initiated, as opposed to a requirement of 2 days to exa mine 96 samples by agarose gel electrophoresis.