Assaying the Microbiome During Critical Illness

Critical illness is associated with large-scale perturbations in the gut microbiota. We compared four sample types in intensive care unit patients – rectal, nares, and antecubital swabs, and stool – using 16S rRNA gene sequencing. Stool was obtained in 31% of attempts, while swabs were reliably obtained (≥97% of attempts). Although not compositionally identical, rectal swabs captured microbiota perturbations in critically ill patients similar to those previously described using stool. Additionally, potentially informative changes in the gut microbiome occurring during late-onset sepsis in an ICU were captured using shotgun metagenomic sequencing of rectal swabs. Initiation of empiric antibiotic therapy was associated with compositional collapse of the gut microbiome within 24 hours, with Pseudomonas aeruginosa becoming the dominant community member and acquiring genomic variants in resistance-associated loci. Overall, rectal swabs were easily obtained and captured compositional and metagenomic perturbations common during critical illness, demonstrating their potential utility for microbiome analysis in this population.M.Sc