Table 3 Species detected after read classification and reference genome alignment in CRuMPIT
From: Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices
Sample | ONT minion species | TaxID | Mapped reads (% of identified bacterial) | Mapped bases (% of identified bacterial) | Sonication species | Tissue culture species | MiSeq reads (% of bacterial) |
|---|---|---|---|---|---|---|---|
229a | Staphylococcus aureus | 1280 | 815 (89) | 1,912,820 (113) | S. aureus | S. aureus | 6038 (98) |
249a | Cutibacterium acnes | 1747 | 23,500 (68) | 29,443,269 (66) | P. acnes | P. acnes | 108,940 (100) |
259a | Staphylococcus epidermidis | 1282 | 155 (50) | 223,611 (44) | S. epidermidis | S. epidermidis | 749 (86) |
312a | Citrobacter koseri | 545 | 11,629 (78) | 24,631,203 (81) | C. koseri | C. koseri | 221,516 (95) |
335a | Morganella morganii | 582 | 613 (62) | 515,991 (37) | M. morganii | M. morganii | 3555 (94) |
352a | Bacillus thuringiensis | 1428 | 41 (7) | 27,026 (6) | Bacillus species | Bacillus species | 1109 (86*) |
Bacillus cereus | 1396 | 119 (21) | 85,627 (19) | ||||
354a | Arcanobacterium haemolyticum | 28,264 | 584 (24) | 547,413 (25) | A. haemolyticum | Â | 11,182 (72) |
Fusobacterium nucleatum | 851 | 529 (22) | 493,717 (23) | Â | Â | 1156 (7) | |
Enterococcus faecalis | 1351 | 225 (9) | 223,665 (10) | E. faecalis | E. faecalis | 1173 (8) | |
506a | Non detected | Â | Â | Â | No growth | No growth | Non detected |
509a | Non detected | Â | Â | Â | No growth | No growth | Non detected |