Table 2 Biomaterials and laboratory parameters collected in pedCAPNETZ
Source | Specimen | Direct analysis | Biobank sampling (planned analyses) |
|---|---|---|---|
Upper airway tract | Nasopharyngeal aspirate or swab | PCR pathogen screen, microbiome analysis, culture (optional) | No |
Lower airway tract | Sputum (± inhalation with NaCl 3%) | PCR pathogen screen, microbiome analysis, culture | Yes |
Lower airway tract | Deep throat swab (± inhalation with NaCl 3%) | PCR pathogen screen, microbiome analysis, culture | Yes |
Urogenital tract | Urine | Antigen screening: legionella, pneumococcus | Yes |
Blood | EDTA | Diff blood count | Yes (genomics, epigenomics) |
Blood | Serum | CRP, Creatinin, sodium, urea, procalcitonin (optional), interleukin-6 (optional), blood gas (optional), chlamydia and mycoplasma serology (optional) | Yes (proteomics, metabolomics, antibody-screening) |
Blood | Plasma | Yes (microRNA) | |
Lavage | BAL (optional) | Differential cell count, culture | Yes (microRNA, biomarker analyses) |
Others | Pleural effusion (optional), nasal secretions (planned) | Lactate, pH, protein, culture | Yes (biomarker analyses) |