Skip to main content

Table 3 Clinical PathoScope performance on the 16S amplimer dataset

From: Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data

   Clinical PathoScope Results
Accession Sample type Species identified Reads assigned (%)
SRR949994 S. aureus ATCC No. 25923 MSSA S. aureus 3,479 (98.0)
   P. aeruginosa 36 (1.0)
SRR949995 E. faecalis ATCC No. 51299 E. faecalis 2,351 (89.8)
   S. aureus 139 (5.3)
   E. hirae 44 (1.7)
   P. aeruginosa 42 (1.6)
SRR949996 P. aeruginosa ATCC No. 27853 P. aeruginosa 5,661(82.3)
   E. coli 1,021 (14.9)
SRR949997 E. coli ATCC No. 25922 E. coli 4,169 (94.7)
   S. enterica 66 (1.6)
SRR949998 Mixture of E. coli, E. faecalis, P. aeruginosa, S. aureus (above) E. coli 14,280 (31.9)
  E. faecalis 14,306 (31.9)
   P. aeruginosa 8,771 (19.6)
   S. aureus 6,594 (14.8)
SRR950015 Clinical Sample (F1) A. baumannii 4,889 (59.4)
   P. aeruginosa 3,177 (38.7)
SRR950024 Clinical Sample (G1) P. aeruginosa 1,131 (94.5)
   E. coli 45 (3.8)
SRR950025 Clinical Sample (H1) E. aerogenes 587 (85.9)
   P. aeruginosa 18 (2.6)
   Erwinia sp. Ejp617 19 (2.8)
   E. coli 18 (2.6)
   S. enterica 9 (1.3)
   E. asburiae 10 (1.5)
   S. intermedius 8 (1.2)