In spite of limitations including the potential presence of PCR inhibitors in clinical samples and the possibility of sample-to-sample contamination, molecular amplification methods can be useful in establishing the cause of IE. To date, PCR methods have been applied with most success to surgically excised valve tissues.
Because several possible etiologic agents are normally being considered in cases of culture-negative IE, the most commonly applied approach involves the use of "universal" PCR primers. These primers are directed against highly conserved sequences that are common to all bacteria, thereby allowing amplification of genetic material from virtually any species of bacteria. The segment to be amplified (most often genes encoding for 16S rRNA) is chosen based on the presence of intervening regions with sequence variability, allowing identification of organisms by sequencing of the PCR product with subsequent comparison of the result to a sequence database. Podglajen et al.  evaluated 16S rDNA PCR/sequencing of valve tissues resected from 36 patients with clinically definite IE by the modified Duke criteria. PCR identification was possible in 26 of 30 cases with positive blood cultures prior to surgery, and in 5 of 6 blood culture-negative cases (four Bartonella species, one S. gallolyticus).
When a particular diagnosis is suspected, species-specific PCR assays can also be employed. Protocols have been developed for many of the agents of culture-negative IE including C. burnetti, Bartonella spp., Brucella spp., Tropheryma whipplei, Chlamydia spp. and Legionella spp. .
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