Table 2.
Comparison of Subjects for Whom CSF Testing Was Positive by Any Method
| Subject | CSF Culture | HSV PCR | EV PCR | CSF Multiplex PCR | CSF Other Test (Positive Result) | CSF mNGS | Total Sequencing Reads | Number of Reads for Identified Organism |
|---|---|---|---|---|---|---|---|---|
| Concordant CSF mNGS and CSF Usual Care Results | ||||||||
| 1001 | Haemophilus influenzae | negative | not done | not done | H influenzae | 2.85E + 07 | 5.17E + 04 | |
| 1003 | no organisms | positive | not done | HSV | HSV | 2.38E + 07 | 9.80E + 01 | |
| 1007 | Enterococcus faecalis | not done | not done | not done | E faecalis | 2.63E + 07 | 2.05E + 04 | |
| 1017 | Streptococcus agalactiae | not done | not done | S agalactiae | S agalactiae | 1.81E + 07 | 5.61E + 05 | |
| 1019 | no organisms | not done | positive | not done | Enterovirus | 1.54E + 07 | 2.26E + 02 | |
| 1020 | no organisms | negative | positive | Enterovirus | Enterovirus | 1.84E + 07 | 1.43E + 03 | |
| 1023 | no organisms | negative | positive | not done | Enterovirus | 2.27E + 07 | 3.34E + 02 | |
| 1025 | no organisms | not done | positive | Enterovirus | Enterovirus | 1.60E + 07 | 9.90E + 01 | |
| 1026 | no organisms | negative | positive | Enterovirus | Enterovirus | 1.72E + 07 | 8.70E + 01 | |
| 1027 | no organisms | negative | positive | not done | Enterovirus | 1.60E + 07 | 1.27E + 04 | |
| 1028 | no organisms | not done | positive | not done | Enterovirus | 1.67E + 07 | 1.30E + 01 | |
| 1030 | Streptococcus pneumoniae | negative | not done | S pneumoniae | S pneumoniae | 2.22E + 07 | 5.53E + 03 | |
| 2001 | S agalactiae | not done | not done | not done | S agalactiae | 2.26E + 07 | 1.58E + 05 | |
| 2005 | S pneumoniae | not done | negative | S pneumoniae | S pneumoniae | 3.17E + 07 | 5.73E + 05 | |
| 2006 | no organisms | not done | not done | Enterovirus | Enterovirus | 2.41E + 07 | 1.98E + 03 | |
| 3001 | Neisseria meningitidis | not done | not done | N meningitidis | N meningitidis | 2.11E + 07 | 3.71E + 02 | |
| 3002 | no organisms | not done | not done | Enterovirus | Enterovirus | 1.48E + 07 | 3.40E + 01 | |
| 3012 | no organisms | not done | not done | negative | 16S PCR Streptococcus dysgalactiae | S dysgalactiae | 2.11E + 07 | 8.29E + 05 |
| 3013 | S agalactiae | not done | not done | negative | S agalactiae | 1.16E + 07 | 8.44E + 02 | |
| 3015 | S pneumoniae | not done | not done | S pneumoniae | S pneumoniae | 1.34E + 07 | 1.19E + 05 | |
| False-Positive CSF mNGS Results | ||||||||
| 1009 | no organisms | not done | not done | not done | Cryptococcus spp | 2.25E + 07 | 5.54E + 02 | |
| 2003 | no organisms | not done | not done | not done | Staphylococcus warneri | 3.06E + 07 | 1.17E + 03 | |
| 2011 | no organisms | not done | not done | not done | Mucor circinelloides | 2.27E + 07 | 6.77E + 04 | |
| 2022 | no organisms | not done | not done | negative | Streptococcus bovis | 2.20E + 07 | 1.41E + 02 | |
| False-Negative CSF mNGS Results | ||||||||
| 1016 | Cryptococcus neoformans | not done | not done | negative | no pathogens detected | 2.37E+07 | - | |
| 2015 | no organisms | not done | not done | HHV-6 | no pathogens detected | 1.33E + 07 | - | |
| 2016 | Staphylococcus aureus | not done | not done | HHV-6 | no pathogens detected | 1.83E + 07 | - | |
| 3010 | no organisms | not done | not done | negative | EBV (PCR) | no pathogens detected | 1.85E + 07 | - |
| 3014 | Staphylococcus epidermidis | not done | not done | Negative | no pathogens detected | 1.25E + 07 | - |
Abbreviations: CSF, cerebrospinal fluid; EBV, Epstein-Barr virus; EV, enterovirus; HHV-6, human herpes virus 6; HSV, herpes simplex virus; mNGS, metagenomic next-generation sequencing; PCR, polymerase chain reaction.