Tracing the source of BSI. (A) Scheme describing the BSI source detection pipeline: collection of relevant biological samples for shotgun sequencing (patient’s positive blood cultures, stool samples, and donor-derived fecal microbiota transplant capsules) (i); construction of the reference genomes using sequences of the positive blood culture strains (genome assembly and gene classification into species core genes and strain gene groups) (ii); and identification of BSI strains in the metagenomic samples (searching for species and strain genes identified in the reference genome) (iii). (B) Detection of blood culture strains in fecal samples. Rows are grouped by patients and correspond with bacterial strains detected in the blood cultures. Using the metagenomic bioinformatic pipeline, we searched for BSI-causing strains within donor and recipient stool samples. Offending bacterial strains were absent from fecal microbiota transplant donor capsules. However, they could be detected in a portion of recipients’ stool samples at various time points before and after the FMT and BSI event. Source data for the figure are available in the data supplement. aGVHD, acute GVHD. Reproduced with permission, copyright © Elvire Thouvenot.