Advantages and Limitations of Direct PCR Amplification of Bacterial 16S-rDNA from Resected Heart Tissue or Swabs Followed by Direct Sequencing for Diagnosing Infective Endocarditis: A Retrospective Analysis in the Routine Clinical Setting

Table 3

Overview of species identification obtained with PCR and sequencing methods and comparison to the results of preoperative blood cultures (preBC).

PCR positive , species identification
Concordance (PCR/preBC)		Discordance (on genus and/or species level)		Additional information (no preBC data available)
		PCR	Result of preBC
Enterococcus faecalis	5	Enterococcus faecalis	Streptococcus gordonii	Enterococcus faecalis	1
Staphylococcus aureus	1	Enterococcus faecium	Enterococcus faecalis	Staphylococcus aureus	2
Streptococcus agalactiae	1	Staphylococcus aureus	Staphylococcus auricularis	Staphylococcus epidermidis	1
Aerococcus urinae	1	Staphylococcus epidermidis	Streptococcus oralis	Staphylococcus lugdunensis	1
Gemella haemolysans	1	Streptococcus gallolyticus subsp. pasteurianus	Streptococcus alactolyticus	Streptococcus mitis	1
		Streptococcus gordonii	Streptococcus pneumoniae	Streptococcus pneumoniae	1
		Streptococcus gordonii	Streptococcus viridans	Streptococcus sanguinis	1
		Streptococcus mitis	Streptococcus intermedius	Anoxybacillus spp.	1
		Bartonella quintana	Staphylococcus epidermidis	Propionibacterium acnes	1
		Granulicatella adiacens	Streptococcus viridans
		Streptococcus oralis	Streptococcus viridans
		Enterococcus faecium	Gram-positive cocci
		Staphylococcus epidermidis	Gram-positive cocci
		Propionibacterium acnes	Negative preBC

In 7 patients with positive PCR amplicon, direct sequencing failed due to a bacterial mixture or low DNA concentrations .
Results of preBC were taken and analyzed in hospitals of primary care according to local standard microbiological laboratory procedures.