Additional file 1 of Evaluating the potential for respiratory metagenomics to improve treatment of secondary infection and detection of nosocomial transmission on expanded COVID-19 intensive care units

Additional file 1: Supplementary Methods and Tables S1-S8. Table S1. List of pre-defined pathogen and reference source for each pathogen. Table S2. All non-pathogenic organisms identified in all respiratory samples processed with clinical metagenomics (above pre-defined thresholds). Table S3. Clinical characteristics and results of routine microbiological tests performed on intubated COVID-19 patients across 7 linked dedicated COVID-19 intensive care units on Guy’s and St Thomas’ hospital sites during the first wave of the COVID-19 pandemic. Table S4A. Sequencing metadata for all respiratory samples processed with clinical metagenomics. Table S4B. Negative controls run with each batch of samples sequenced. Table S5. Phenotypic resistance reported by culture and resistance genes reported by clinical metagenomics in all culture-positive samples after 2 hours of sequencing. Table S6. Microbiology, PCR and clinical metagenomics results for all samples processed in this study for the identification of Aspergillus fumigatus. Table S7A-D. Klebsiella pneumoniae and Corynebacterium striatum alignment for outbreak analysis. Table S8A-E. Performance reported after testing different parameters on training set for pathogen identification. The number of True Positive (TP), False Positive (FP), True Negative and False Negative (TN) samples as well as sensitivity, specificity along and calculated Youden’s Index ((sensitivity+specificity)-1) are presented.