Read cloud and short read metagenomic sequencing of stool samples from a human HCT patient

We applied metagenomic read cloud sequencing to four longitudinal stool samples collected from an HCT patient before and after heavy antibiotic exposure. During this time period, the patient experienced Escherichia coli gut domination and an E. coli bloodstream infection. Read clouds improve the completeness and contiguity of genome assemblies for individual organisms, enabling the placement of multiple copies of antibiotic resistance genes both within and across genomes. The presence of resistance genes is shown to correlate with the timing of antibiotics administered to the patient, and comparative genomic analysis of the various E. coli strains across time indicates that the E. coli bloodstream infection likely originated from the gut.