Impact of selective digestive decontamination on the pangenome composition of ESBL-E. coli

Selective digestive decontamination (SDD) is routinely applied in Dutch ICUs to prevent colonization by potentially pathogenic microorganisms. In the R-GNOSIS ICU study, conducted outside of the Netherlands, SDD consisted of a mix of an oropharyngeal paste and a gastric suspension containing colistin, tobramycin and nystatin. Although SDD improves patient outcomes, its impact on the pangenome and resistome of colonizing Escherichia coli remains poorly understood. This study aimed to determine whether SDD influences the genomic composition and resistance repertoire of E. coli isolates from ICU patients.

We compared 129 genomes of E. coli isolates from patients that received SDD and patients that did not receive SDD, but standard care only (baseline patients) in five ICUs located across three European countries (R-GNOSIS ICU study). Comparative analyses were performed to assess differences in the pangenome, plasmidome and antibiotic resistance gene content between groups.

The overall pangenome compositions of E. coli isolates from SDD-treated and baseline patients were highly similar. Accessory genome variation was strongly associated with phylogeny, but not with SDD exposure. Plasmidome differences were explained by the interaction of ICU location and phylogroup. A tobramycin resistance gene, flanked by IS26 elements and frequently co-occurring with blaCTX-M-15, was more prevalent in isolates from SDD patients. No mcr genes associated with transferable colistin resistance were detected.

SDD did not significantly alter the overall pangenome or plasmidome composition of colonizing E. coli in ICU patients. However, a potentially mobile tobramycin resistance gene was more prevalent in E. coli from SDD patients.