Rapid metagenomics analysis of EMS vehicles for monitoring pathogen load using nanopore DNA sequencing

Pathogen monitoring and detection are important challenges faced by the public sector, as the transmission of harmful pathogens presents a serious threat to global health security. While in most hospitals, programs are in place for the mitigation of pathogen spread, no equivalent practice is in place for the emergency medical service (EMS) vehicles transporting individuals at risk for colonization and infection by opportunistic pathogens. It is difficult to fully, and without bias, characterize the microbiome of an ambulance using standard cell-culturing techniques. Therefore, we report a third-generation sequencing approach to characterize the microbial community of EMS vehicles. We describe a streamlined MinION® sequencing based approach to investigate the microbiome of EMS vehicles. As a proof of concept and to demonstrate the sensitivity of the reported approach, we performed EMS vehicle sampling over the course of a three-week period using three separate ambulances collecting samples from three different locations in each vehicle to characterize the spatial and temporal microbiome diversity. The data reported demonstrates for the first time that using a nanopore-based approach it is possible to make comparisons between locations and to assess the microbial profile of vehicles, providing EMS and others with a critical tool to mitigate disease transmission and spread.