Table 1.
Laboratory procedures for each pathogen included in the Biofire FilmArray ME panel are listed (X = performed regularly). Primary culture included cultivation of CSF samples at 35–37 °C with 5% CO2, all samples were plated on blood agar plates (BAB), chocolate agar (CHOC) and sabouraud agar, and were incubated in fluid thioglycollate medium (thioglycollate broth), respectively. In case of CSF-samples sent for detection of yeast and bacterial pathogens, gram stain and primary culture are performed routinely, NAT analysis is performed if mandatory (e.g. verification of bacteria seen in gram stain). Additionally, bacterial 16S rRNA genes and mycotic 18S rRNA sequences are detected via commercially available SepsiTest™-UMD (Molzym) upon request. For all viral pathogens, primarily quantitative real-time PCR was performed. In these samples, gram stain was only performed upon request (*1). For Human herpesvirus 1 and human herpesvirus 2, commercially available RealStar®-PCRs (Altona Diagnostics) were performed for confirmation if indicated. Diagnostic PCRs for CSF diagnostic in our laboratory are laboratory developed tests (“LDTs”), all LDTs are quantitative real-time PCRs using specific primers and probes. Design of LDTs is based on references given into parentheses
| Pathogen | Gram stain | Primary culture | NAT | |
|---|---|---|---|---|
| Bacteria | Escherichia coli K1 | X | X | LDT (Diaz, Waller [21]/ SepsiTest™-UMD |
| Haemophilus influenzae | X | X | LDT (Abdeldaim, Stralin [18])/SepsiTest™-UMD | |
| Listeria monocytogenes | X | X | LDT (Le Monnier, Abachin [25])/SepsiTest™-UMD | |
| Neisseria meningitidis | X | X | LDT (Abdeldaim, Stralin [18])/SepsiTest™-UMD | |
| Streptococcus agalactiae | X | X | LDT (Diaz, Waller [21])/SepsiTest™-UMD | |
| Streptococcus pneumoniae | X | X | LDT (Stralin, Herrmann [30])/SepsiTest™-UMD | |
| Viruses | Cytomegalovirus | X*1 | LDT (Khansarinejad, Soleimanjahi [24]) | |
| Enterovirus | X*1 | LDT (Dierssen, Rehren [22]) | ||
| Herpes simplex virus 1 | X*1 | LDT (Meylan, Robert [26])/RealStar® HSV | ||
| Herpes simplex virus 2 | X*1 | LDT (Meylan, Robert [26])/RealStar® HSV | ||
| Human herpesvirus 6 | X*1 | LDT (Cassina, Russo [20]) | ||
| Human parechovirus | X*1 | LDT (Benschop, Molenkamp [19]) | ||
| Varizella zoster virus | X*1 | LDT (Pollak, Dovrat [27]) | ||
| Yeast | Cryptococus neoformans/gattii | X | X | LDT (Veron, Simon [31])/SepsiTest™-UMD |