Overview of sample collections and analytical purposes
| Sample | Type | Timing | Analysis | Readouts |
| Nasopharynx | eNAT (Copan) | Enrollment, 3x weekly, exacerbation | Amplicon sequencing (16S rRNA and ITS) | Diversity estimation and relative abundances of bacterial (bacteriome) and fungal (mycobiome) taxa |
| WMTS | Identification of RNA viruses and host transcripts | |||
| Venous blood | PAXgene DNA (BD) | Enrolment | Genomic sequencing | SNP identification associated with increased risk of COPD, exacerbations and microbial infection |
| PPT (BD) | Enrolment, exacerbation, outcome assessment | WMTS | Plasma derived ECV assessment to identify circulating host transcripts | |
| Cell-free DNA (Streck) | WMTS | Assessment of circulating microbial DNA | ||
| SST (BD) | Enrollment, 3x weekly, exacerbation, outcome assessment | ELISA-based multiplex analysis | Assessment of broad multiplex cytokine panel | |
| MSD | Anti-bacterial titers | |||
| Metabolomics | Host and microbiome derived metabolites | |||
| Proteomics | Host protein characterisation | |||
| PAXgene RNA (BD) | WMTS | RNA virus and host transcript identification | ||
| Spontaneous sputum | N.A. | Enrollment, 3x weekly, exacerbation | Amplicon sequencing (16S rRNA and ITS and qPCR for NTHi) | Diversity estimation and relative abundances of bacterial (bacteriome) and fungal (mycobiome) taxa |
| WMTS | RNA virus and host transcript identification | |||
| Proteomics | Host protein characterisation | |||
| Metabolomics | Host and microbiome derived metabolites | |||
| Enrollment, exacerbation | Traditional bacterial culture* | Bacterial taxa identification | ||
| Cytospin | Cell differentials | |||
| Stool | OMNIgene Gut | Enrolment, exacerbation, outcome assessment | Whole metagenomic shotgun sequencing | Microbial taxa characterisation at species level, and functional profiling |
| OMNImet Gut | Metabolomics | Host and microbiome derived metabolites |
*Supporting both routine clinical care and study specific measurements at exacerbation.
BD, Becton Dickinson; ECV, extracellular vesicle; ELISA, enzyme-linked immunosorbent assay; ITS, internal transcribed spacer; MSD, Meso Scale Discovery Electrochemiluminescence; NTHi, Nontypeable Haemophilus influenzae; qPCR, quantitative PCRs; rRNA, ribosomal ribonucleic acid; SNP, single nucleotide polymorphism; WMTS, whole metatranscriptomic sequencing.