A role for portable single-molecule nanopore sequencing in the management of a hospital Salmonella outbreak

Foodborne outbreaks of Salmonella remain a pressing public health concern. We recently detected a large outbreak of Salmonella enterica serovar Enteritidis phage type 14b affecting over 30 patients in our hospital. This outbreak was linked to community cases as well as cases detected nationally and Europe-wide. The potential risk posed to hospital patients with Salmonella is high and demands rapid action. We investigated, for the first time, the potential of the Oxford Nanopore MinION™, a portable, laptop-driven, real-time single-molecule whole-genome sequencer for the rapid detection of outbreak strains. We integrated data from this platform with a thorough outbreak investigation undertaken prospectively on the Illumina MiSeq platform. This outbreak was placed into national context by integration with whole-genome data from surveillance genome data produced by Public Health England. Our results show the MinION™ can identify the bacterial species and serotype of a sample within 30 minutes, and determine to single nucleotide level if a sample is part of the outbreak within 2 hours. This novel, multi-tiered approach using genome sequencing and integration of digital datasets represents a possible technological paradigm for future outbreaks and may have impact on infection control practices.