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.