Mapping stool reads against BSI whole genome sequences (WGS).

Each available BSI isolate was subjected to whole genome shotgun sequencing and then assembly into WGS (mean 97.49% coverage; mean 78.81X depth). Stool short reads were then aligned with multiple genomes (indicated on the left of the graph), which included the cognate BSI WGS (“subject”), the WGS of other subjects’ BSI organisms of the same species if any (“cohort”), and unrelated species-matched WGS downloaded from Genbank (“database”). Sequence similarity was calculated based on mismatches defined as single nucleotide variant per megabase pair (SNV/Mbp), reflected along the X axis for each stool sample compared with multiple genomes. (A) Results for six BSI episodes where stool and BSI WGS showed sequence-based strain identity. The SNV/Mbp is indicated along the X axis for each alignment; for clarity, the value is shown for those less than 1000 SNV/Mbp followed by the proportion genome aligned. The red arrow indicates the cognate BSI WGS matched to the stool sample. Each bar is colored to indicate the proportion of genome aligned with stool short reads (because of the short bar, the proportion of genome aligned is shown as a fraction next to the SNVs for the low-SNV matched sample. (B) Representative example of a stool/BSI WGS that did not match. Stool alignment with the cognate Achromobacter BSI WGS showed SNV/Mbp that was no lower than when compared with unrelated WGS of Achromobacter (which was identified only at the genus level by the clinical microbiology lab) downloaded from GenBank.