Table 1.
Identified organisms by culture, smear and gene sequencing in each case
| Case (Sample) | Culture | Smear | Gene sequencing | Reads (%) |
| 1 (Vitreous) |
Staphylococcus epidermidis | – | Staphylococcus epidermidis | 672 (58.8) |
| Staphylococcus saccharolyticus | 329 (28.8) | |||
| Staphylococcus capitis | 50 (4.4) | |||
| Staphylococcus hominis | 22 (1.9) | |||
| Staphylococcus caprae | 16 (1.4) | |||
| 2(Cornea) | Moraxella spp | GNR | Moraxella nonliquefaciens | 1662 (95.5) |
| Moraxella catarrhalis | 40 (2.3) | |||
| Moraxella lacunata | 18 (1.0) | |||
| 3 (Cornea) | Staphylococcus aureus | – | Staphylococcus aureus | 4496 (92.3) |
| Staphylococcus petrasii | 81 (1.7) | |||
| 4 (Cyst) | Haemophilus influenzae | GNR | Haemophilus influenzae | 3261 (85.1) |
| Haemophilus aegyptius | 431 (11.2) | |||
| Cutibacterium acnes | 42 (1.1) | |||
| 5 (Cornea) | Pseudomonas aeruginosa | GNR | Pseudomonas aeruginosa | 2659 (48.6) |
| Peptoniphilus lacydonensis | 362 (6.6) | |||
| Cutibacterium acnes | 347 (6.3) | |||
| Staphylococcus epidermidis | 274 (5.0) | |||
| Ralstonia pickettii | 248 (4.5) | |||
| Streptococcus pneumoniae | 244 (4.5) | |||
| Streptococcus dysgalactiae | 224 (4.1) | |||
| Finegoldia magna | 209 (3.8) | |||
| Staphylococcus saccharolyticus | 148 (2.7) | |||
| Staphylococcus aureus | 136 (2.5) | |||
| Streptococcus mitis | 100 (1.8) | |||
| 6 (Cornea) | Pseudomonas aeruginosa | GNR | Pseudomonas aeruginosa | 17 (44.7) |
| Candida | Ralstonia pickettii | 14 (36.8) | ||
| Sphingomonas leidyi | 2 (5.3) | |||
| NC | – | – | Ralstonia pickettii | 10 (83.3) |
In the 16S rRNA gene analysis, low-abundance taxa with less than 1% of classified reads were discarded to minimise potential misidentification. Spurious classification results with a single mapped read were also eliminated.
GNR, gram-negative rods; NC, negative control; 16S rRNA, 16S ribosomal RNA.