Taxonomic Utility of PCR-Restriction Pattern Analysis for Rapid Identification of Clinical Isolates of aerobic Actinomycetes to the Genus Level

PCR-restriction pattern analysis (PRA), a previously described method for the identification of aerobic actinomycetes was evaluated for potential use with clinically significant aerobic actinomycetes. In this method, Amplified 16S rDNA of actinomycetes was restricted with selected endonucleases and electrophoresed on agarose gels. The restriction patterns of the unknown isolates were compared to the established patterns. This study included 93 cultures. PRA identification using an amplified 16S rDNA (amplicon) was compared to identification by traditional methods, including growth characteristics, susceptibility patterns and biochemical testing. Microbiological examination of five cultures ruled out aerobic actinomycetes, and they were omitted from the study. The identification method allowed 88 clinical actinomycete isolates to be identified to the genus level. The 88 isolates produced PRA patterns matched to those in the current PRA database which lead to their differentiation into four major genera, Nocardia, Streptomyces, Gordonia and Actinomadura. Significantly, the genus Streptomyces could be differentiated from all other actinomycete clinical isolates by using four restriction endonucleases, Sau3AI, AsnI, KpnI and SphI. The predominant genus of actinomycetes identified in this study was Nocardia which comprised 40 isolate out of 88 (45%). Thirty two isolates (32) out of 88 (36%) were identified as Streptomyces, 8 isolates (9%) were identified as Gordonia while 8 isolates (9%) were identified as Actinomadura. PRA results were reportable within 2 to 5 working days and were accurate, faster and less expensive than those of traditional methods