Fig. 1: Overview of the methods, data generated, and clinical features of this sample set.
From: Rare transmission of commensal and pathogenic bacteria in the gut microbiome of hospitalized adults
a Overview of the experimental and computational workflow used to generate sequencing datasets, bin metagenome-assembled genomes (MAGs), and compare strains between patients. b Number of stool samples sequenced per patient. c Percentage of MAGs meeting each quality level40, stratified by sequencing method. d Of patients who have the given organism detected (≥50% coverage breadth) in a time course sample, percentage of patients where the organism was below the detection threshold (<50% coverage breadth) in the first sample. e Percentage of patients with at least one sample positive with (≥1% relative abundance) or dominated by (≥30% relative abundance) hospital-acquired infection (HAI) organisms, as identified by Kraken2- and Bracken-based classification. f Percentage of bloodstream infections (BSIs) identified with each organism or group in HCT patients and hospital-wide. Source data for this figure are provided in Supplementary data 2–4 and Supplementary Table 1.
