Reference genomes used for pangenome analysis.

BackgroundThe gut microbiome is believed to contribute to bloodstream infection (BSI) via translocation of dominant gut bacteria in vulnerable patient populations. However, conclusively linking gut and blood organisms requires stringent approaches to establish strain-level identity.MethodsWe enrolled a convenience cohort of critically ill patients and investigated 86 bloodstream infection episodes that occurred in 57 patients. Shotgun metagenomic sequencing was used to define constituents of their gut microbiomes, and whole genome sequencing and assembly was done on 23 unique bloodstream isolates that were available from 21 patients. Whole genome sequences were downloaded from public databases and used to establish sequence-identity distribution and define thresholds for unrelated genomes of BSI species. Gut microbiome reads were then aligned to whole genome sequences of the cognate bloodstream isolate and unrelated database isolates to assess identity.ResultsGut microbiome constituents matching the bloodstream infection species were present in half of BSI episodes, and represented >30% relative abundance of gut sequences in 10% of episodes. Among the 23 unique bloodstream organisms that were available for whole genome sequencing, 14 were present in gut at the species level. Sequence alignment applying defined thresholds for identity revealed that 6 met criteria for identical strains in blood and gut, but 8 did not. Sequence identity between BSI isolates and gut microbiome reads was more likely when the species was present at higher relative abundance in gut.ConclusionIn assessing potential gut source for BSI, stringent sequence-based approaches are essential to determine if organisms responsible for BSI are identical to those in gut: of 14 evaluable patients in which the same species was present in both sites, they were identical in 6/14, but were non-identical in 8/14 and thus inconsistent with gut source. This report demonstrates application of sequencing as a key tool to investigate infection tracking within patients.</div

Clinical characteristics of enrolled patients.

Major diagnosis refers to most common principal acute and underlying reasons for ICU stay; full details are in S1 Table. Numbers add to greater than 100% due to concomitant processes. There are no significant differences in any clinical characteristics between BSI-positive subjects and BSI-negative subjects or between BSI-positive subjects and BC-available subjects (chi-square test if categorical, t-test if continuous; applying 0.05 significance threshold).</p

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.</p

Clinical features associated with BSI episodes where BSI species was detected in gut microbiome (≥0.01%).

Clinical features associated with BSI episodes where BSI species was detected in gut microbiome (≥0.01%).</p

BSI episodes where species were detected in gut.

Subjects are ordered by the relative abundance of BSI species in highest abundance stool sample, and grouped into those with dominant (≥30%), 2.5–30%, and 0.1–2.5% relative abundances. The last column indicates whether the stool reads matched the BSI isolate WGS for those episodes where the BSI isolate was available for sequencing.</p

S1 File -

BackgroundThe gut microbiome is believed to contribute to bloodstream infection (BSI) via translocation of dominant gut bacteria in vulnerable patient populations. However, conclusively linking gut and blood organisms requires stringent approaches to establish strain-level identity.MethodsWe enrolled a convenience cohort of critically ill patients and investigated 86 bloodstream infection episodes that occurred in 57 patients. Shotgun metagenomic sequencing was used to define constituents of their gut microbiomes, and whole genome sequencing and assembly was done on 23 unique bloodstream isolates that were available from 21 patients. Whole genome sequences were downloaded from public databases and used to establish sequence-identity distribution and define thresholds for unrelated genomes of BSI species. Gut microbiome reads were then aligned to whole genome sequences of the cognate bloodstream isolate and unrelated database isolates to assess identity.ResultsGut microbiome constituents matching the bloodstream infection species were present in half of BSI episodes, and represented >30% relative abundance of gut sequences in 10% of episodes. Among the 23 unique bloodstream organisms that were available for whole genome sequencing, 14 were present in gut at the species level. Sequence alignment applying defined thresholds for identity revealed that 6 met criteria for identical strains in blood and gut, but 8 did not. Sequence identity between BSI isolates and gut microbiome reads was more likely when the species was present at higher relative abundance in gut.ConclusionIn assessing potential gut source for BSI, stringent sequence-based approaches are essential to determine if organisms responsible for BSI are identical to those in gut: of 14 evaluable patients in which the same species was present in both sites, they were identical in 6/14, but were non-identical in 8/14 and thus inconsistent with gut source. This report demonstrates application of sequencing as a key tool to investigate infection tracking within patients.</div

Pair-wise comparisons between purportedly unrelated strains within species.

Pair-wise comparisons between purportedly unrelated strains within species.</p

Distribution of within-species pairwise comparisons.

Distribution of within-species pairwise comparisons.</p

Whole genome sequence assembled from blood culture isolates.

Whole genome sequence assembled from blood culture isolates.</p

Species-level detection of BSI isolates in gut microbiome.

BSI organism species-level representation in the gut microbiome. Data reflect the number of episodes in which the gut microbiome specimen with highest relative abundance of the BSI species was detected at the indicated relative abundance threshold.</p