Table 1.
Contributions of 16S rRNA gene-targeted NGS from heart valve tissue specimens to the diagnosis of infective endocarditis for the 27 patients of this study.
| Patient ID | Initial Microbiological Diagnosis before 16S rRNA Gene-Targeted NGS |
Identification Technique(s) for Diagnosis |
Bacterial Taxa with the Highest Relative Abundance and Minority Findings Suspicious of Being Clinically Important by 16S rRNA Gene-Targeted NGS |
|
|---|---|---|---|---|
| High confident consistent group |
#1 | Staphylococcus aureus 1 | PCR, WEC 1 | Staphylococcus spp. (99.9%) |
| #2 | Staphylococcus epidermidis | BC, PCR | Staphylococcus spp. (99.8%) | |
| #3 | Staphylococcus lugdunensis | BC, PCR | Staphylococcus spp. (99.9%) | |
| #4 | Streptococcus bovis group | BC, PCR | Streptococcus spp. (99.1%) | |
| #5 | S. bovis group | BC, PCR | Streptococcus spp. (99.1%) | |
| #6 | Streptococcus milleri | BC | Streptococcus spp. (99.6%) | |
| #7 | Streptococcus mitis | BC, PCR | Streptococcus spp. (99.8%) | |
| #8 | Streptococus sanguinis | BC, PCR | Streptococcus spp. (99.8%) | |
| #9 | S. mitis | BC, PCR | Streptococcus spp. (99.9%) | |
| #10 | Streptococcus oralis | BC, PCR | Streptococcus spp. (99.9%) | |
| #11 | Coxiella burnetii | PCR | C. burnetii (99.5%) | |
| #12 | Enterococcus faecalis | BC, PCR | E. faecalis (99.9%) | |
| #13 | E. faecalis | BC, PCR | E. faecalis (99.8%) | |
| #14 | E. faecalis | BC, PCR | E. faecalis (99.9%) | |
| #15 | E. faecalis | BC, PCR | E. faecalis (99.7%) | |
| #16 | Haemophylus parainfluenzae | BC, PCR | H. parainfluenzae (99.5%) | |
| #17 | Streptococcus agalactiae | BC, PCR | S. agalactiae (99.9%), Coxiellaceae (<1%) | |
| #18 |
Streptococcus anginosus group (Streptococcus intermedius 2, S. anginosus 3) |
BC 2, PCR 3 | S. anginosus (99.7%), Streptococcus spp. (<1%) | |
| Corroborated mixed infections |
#19 |
Brucella melitensis,
C. burnetii 4 |
BC, PCR, IFA 4, htpAB PCR 4 | Brucellaceae (99.7%), C. burnetii (<1%) |
| #20 | E. faecalis, S. epidermidis 5 | BC, PCR, CTC 5 | E. faecalis (99.6%), Staphylococcus spp. (<1%) | |
| #21 | S. aureus, Escherichia coli 6 , E. faecalis 7 | BC, PCR, VC 6, BC 7† | S. aureus (99.6%), E. faecalis (<1%) | |
| Reclassified as mixed infection |
#22 | Tropheryma whipplei | PCR | T. whipplei (99.8%), C. burnetii (<1%) |
| Low confident consistent group |
#23 | E. faecalis | BC, PCR | E. faecalis (68.8%), H. parainfluenzae (29.7%) |
| #24 | Streptococcus mutans | BC, PCR | S. mutans (69.5%), E. faecalis (28.6%) | |
| New diagnosis | #25 | No etiology | BC, PCR | S. aureus (95.1%) |
| Discordant diagnosis | #26 | E. faecalis | BC, PCR | Streptococcus spp. (26.4%), E. faecalis (15.9%) * |
| #27 | H. parainfluenzae | BC | Streptococcus spp. (99.2%), H. parainfluenzae (<1%) |
ID, identification number; 1, 2, 3, 4, 5, 6 and 7, technique by which the microorganism was detected; PCR, polymerase chain reaction (targeting 16S rRNA gene from heart valve tissues); WEC, wound exudate culture; BC, blood culture; IFA, immunofluorescence assay; htpAB PCR, PCR targeting the htpAB gene for C. burnetii; CTC, catheter tip culture; VC, heart valve culture; †, after surgery. *, a total of 11 bacterial taxa were detected at relative abundance > 1% (See Supplementary Table S1).