Impact of selective digestive decontamination on patient gut microbiome

To study the effect of antibiotic therapy during patient hospitalization on the antibiotic resistance gene (ARG) reservoir (‘the resistome’) formed by the human microbiota, conventional clinical culturing methods are insufficient. Here, we apply functional metagenomics (using large-insert fosmid libraries in Escherichia coli) and metagenomic shotgun sequencing to examine resistome dynamics in a patient admitted to an Intensive Care Unit, throughout hospital stay and nine months after hospital discharge. Our data indicate that selection for antibiotic resistance, specifically among anaerobic gut commensals, occurs during hospital stay. Functional metagenomics provided data on the genetic context of the resistance genes, which are frequently associated with putative mobile genetic elements. Metagenomic sequencing allowed the identification and relative quantification of many ARGs (between one and eleven for each antibiotic family) per sampled time-point. We suggest that metagenomic shotgun sequencing may be applied as a monitoring tool to detect and quantify ARGs in patient microbiota.