Bacterial ribosomal RNA detection in cerebrospinal fluid using a viromics approach

Table 1 Diagnostic performance per pathogen

Pathogen	Pathogen specific reads^a	Total sample read depth (N)^b	Sensitivity	Specificity
H. influenzae	≥ 1 read	All (18)	56%	100%
H. influenzae	≥ 1 read	≥ 10,000 reads (14)	71%	100%
K. pneumoniae	≥ 10 reads	All (1)	100%	100%
K. pneumoniae	≥ 10 reads	≥ 10,000 reads (1)	100%	100%
N. meningitidis	≥ 10 reads	All (23)	64%	100%
N. meningitidis	≥ 10 reads	≥ 10,000 reads (22)	67%	100%
S. pneumoniae	≥ 10 reads	All (24)	67%	92%
S. pneumoniae	≥ 10 reads	≥ 10,000 reads (16)	88%	90%
L. monocytogenes	≥ 1 read	All (24)	21%	100%
L. monocytogenes	≥ 1 read	≥ 10,000 reads (15)	27%	100%

^aFor each pathogen, the minimum pathogen read count with the best diagnostic performance is reported. ^bPerformance was compared between all samples and the subset with total read count ≥ 10,000. The 97% read identity dataset was used. See Additional file 2: Table S2 for performance at alternative threshold parameters

ISSN: 2045-8118