What is the enhanced hospital hygiene impact of sequencing data in tracking nosocomial transmissions?A genomic study utilizing long- and short-read technologies

Introduction
Carbapenem-resistant Enterobacterales (CPE) pose great concerns in healthcare. Prevention efforts focus on patients with spatiotemporal connections carrying the same bacterial species of CPE. However, the extent of transmissions through environmental reservoirs and cross-species plasmid transfer in hospitals remains unknown. Whole genomic sequencing (WGS) offers a more in-depth insight into the genomic relationship on core-genome and plasmid levels (1). But this technology is not yet part of routine workflows.

Goals
Using VIM-CPE as an example, we investigated the benefit of WGS in analyzing plasmids and exploring bacterial relationships outside of hospital outbreak events.

Materials & Methods
We included inpatient episodes from 2018 to 2021 involving patients who tested positive for blaVIM CPE anytime during their admission. Employing short- and long-read technology, we combined WGS data on core-genome and plasmid levels with epidemiological and patient movement data, to analyze genomically related cases of VIM-CPE and detect potential transmission routes.

Results
We included 43 cases from 38 patients. The core-genome analysis identified 26 cases belonging to four clusters of highly related isolates, indicating clonal spread. Two plasmids were present in multiple isolates of different species. Putative transmission events on both genetic levels were mainly indirect and occurred over a long period with the ICU being a key location. Nearly half of the transmission events were plasmid-mediated.

Summary
Our findings challenge the dogma of spatiotemporal connection and urge a broader investigation into temporal connections when genomic data suggests relatedness. We emphasize considering plasmid transfer alongside bacterial relatedness in infection prevention efforts concerning CPE. By understanding these factors, we can enhance infection prevention strategies and effectively combat the spread of CPE in the hospital.

Orlek A, Stoesser N, Anjum MF, Doumith M, Ellington MJ, Peto T, et al. Plasmid Classification in an Era of Whole-Genome Sequencing: Application in Studies of Antibiotic Resistance Epidemiology. Front Microbiol. 2017;8:182.