Table 3.
Bacterial identification results from 21 clinical orthopedic samples based on culture and NGS of 16S-23S rRNA region.
| Sample | Patient | Material | Culture | NGS of 16–23S rRNA region (% of total reads) |
|---|---|---|---|---|
| KM1 | Patient A | biopsy (tissue) | Negative | Propionibacterium acnes (9.1%)A, Haemophilus parainfluenzae (2.3%), eukaryotic DNA (88.6%) |
| KM2 | Patient A | punctate (fluid) | Negative | eukaryotic DNA (100%) |
| KM3 | Patient A | punctate (fluid) | Negative | Sediminibacterium salmoneum (0.3%), eukaryotic DNA (99.7%) |
| KM4 | Patient A | punctate (fluid) | Negative | Gemella sanguinis (1.3%), Haemophilus parainfluenzae (1.0%), eukaryotic DNA (97.7%) |
| KM5 | Patient A | punctate (fluid) | Negative | Herminiimonas sp. (10.5%), Propionibacterium acnes (9.7%)A, Moraxella catarrhalis (7.5%), eukaryotic DNA (72.3%) |
| KM6 | Patient B | pus | Negative | Streptococcus intermedius (100%) |
| KM7 | Patient C | biopsy (tissue) | Negative | eukaryotic DNA (100%) |
| KM8 | Patient C | biopsy (tissue) | Negative | No identification |
| KM9 | Patient D | joint puncture (fluid) | Negative | Enhydrobacter aerosaccus (49.8%)B, Acinetobacter septicus (18.1%)B, Moraxella osloensis (14.0%), Staphylococcus sp. (5.8%), Rheinheimera soli (3.1%), Staphylococcus epidermidis (2.6%), Psychrobacter sp. (2.4%)B, Propionibacterium acnes (1.3%)A, Alkanindiges sp. (0.6%), Acinetobacter sp. (0.4%)B, Chryseobacterium sp. (0.3%)B |
| KM10 | Patient D | joint puncture (fluid) | Negative | No identification. |
| KM11 | Patient D | biopsy (tissue) | Negative | Propionibacterium acnes (9.8%)A, Bacillus nealsonii (6.7%)B, Pseudomonas fluorescens (0.6%)A, eukaryotic DNA (82.9%) |
| KM12 | Patient D | biopsy (tissue) | Negative | eukaryotic DNA (100%) |
| KM13 | Patient D | biopsy (tissue) | Negative | Undibacterium oligocarboniphilum (3.5%)B, Propionibacterium acnes (0.7%)A, eukaryotic DNA (95.9%) |
| KM14 | Patient D | biopsy (tissue) | Negative | Propionibacterium acnes (1.4%)A, eukaryotic DNA (98.6%) |
| KM15 | Patient D | biopsy (tissue) | Negative | Veillonella parvula (0.9%), eukaryotic DNA (99.1%) |
| KM16 | Patient D | biopsy (tissue) | Negative | eukaryotic DNA (100%) |
| KM17 | Patient E | blood | n.d. | Bacillus cereus (0.5%)B, eukaryotic DNA (99.5%) |
| KM18 | Obduction material A | formaline captured, biopt (tissue) | n.d. | Propionibacterium acnes (64.4%)A, Staphylococcus epidermidis (25.4%), Paracoccus sanguinis (10.1%)B |
| KM19 | Obduction material B | formaline captured, lung biopt (tissue) | n.d. | Staphylococcus epidermidis (36.0%), Propionibacterium acnes (34.6%)A, Pseudomonas fluorescens (29.4%)A |
| KM20 | Patient F | joint puncture (fluid) | Negative | eukaryotic DNA (100%) |
| KM21 | Patient F | biopsy (tissue) | Negative | Acinetobacter sp. (18.6%)B, Paucibacter sp. (12.8%), Herminiimonas arsenicoxydans (5.2%), eukaryotic DNA (63.4%) |
ASpecies present in negative control(s) and regarded as contamination introduced during sample preparation. BGenus absent in negative controls but previously reported as contamination of DNA extraction kits, PCR and other laboratory reagents10.