Additional file 1 of Implementation of the FilmArray ME panel in laboratory routine using a simple sample selection strategy for diagnosis of meningitis and encephalitis

Additional file 1: Table S1. Overview of analytical methods performed and detection rates in n = 4623 CSF samples received

Additional file 2 of Implementation of the FilmArray ME panel in laboratory routine using a simple sample selection strategy for diagnosis of meningitis and encephalitis

Additional file 2: Table S2. Overview of pathogens detected by different methods. Numbers of pathogens detected by routine diagnostic procedures, numbers detected by Film Array ME Panel as well as confirmatory results are given

Percent categorical agreement (CA) between comparator methods for colistin MIC determination and the reference broth microdilution method.

Percent categorical agreement (CA) between comparator methods for colistin MIC determination and the reference broth microdilution method.</p

Colistin AST methods compared in this study.

VITEK 2 cards were incubated and evaluated automatically by the device, all other tests were incubated at 36 ± 2°C for 16–20 hours in ambient air. McF, McFarland standard; CAMHB, cation-adjusted Muller-Hinton II broth; QC, quality control; MHA, Muller-Hinton agar; BMD, broth microdilution; FSCA, Field Safety Corrective Action.</p

Characteristics of the isolates used in this study.

Susceptibility and resistance to colistin is reported as observed in the reference in-house broth microdilution method.</p

Percent essential agreement (EA) between comparator methods for colistin MIC determination and the reference broth microdilution method.

Percent essential agreement (EA) between comparator methods for colistin MIC determination and the reference broth microdilution method.</p

Mixing cells during irradiation increases inactivation efficiency.

Vero B4 cells were infected with HSV-1 and irradiated in tissue vials. Cells were treated with the indicated irradiation dose in a single interval (No Mixing, black line) or were treated repeatedly with a fluence of 2,500 mJ/cm2 followed by mixing for the total dose stated (With Mixing, green line). Sample inactivation was evaluated by plaque assay with a limit of detection (LoD) of 5x102 PFU/mL. Each dose curve was performed with n = 1.</p

Protocol.io version of UV inactivation protocol.

Protocol describing UV inactivation of infected cells. Also available at https://doi.org/10.17504/protocols.io.81wgb676qlpk/v1. (PDF)</p

Schematic of validation procedure of UV inactivation protocol for SARS-CoV-2.

Samples were generated with 3 biological replicates under the conditions that lead to no detectable virus. Fresh cells were treated with the UV irradiated samples, and these treated cells were passaged for three weeks to test for viral replication. The inactivation protocol is the same for HSV-1 and HCMV, except for differences in the number of cells and passaging times, which are described in the Materials and Methods section.</p

Inactivation of SARS-CoV-2 infected cells.

Vero E6 cells infected with SARS-CoV-2 were UV-inactivated. (A) The virus titres of samples taken during inactivation validation were determined with a limit of detection (LoD) of 5 PFU/mL. The before inactivation and UV inactivated samples were performed with biological replicates, n = 3, and the standard deviation is shown. The untreated control sample was performed with n = 1. (B) Immunofluorescence imaging of cells treated with the UV-inactivated infected cells was performed with biological replicates, n = 3. Cells were stained for the SARS-CoV-2 protein N and with DAPI. The scale bar represents 100 μm.</p