Oxford nanopore next generation sequencing in a front-line clinical microbiology laboratory without on-site bioinformaticians

Next generation sequencing (NGS) technologies have previously been out of reach for most front-line diagnostic microbiology laboratories due to high costs, significant space requirements, and the need for expert bioinformaticians. However, this is rapidly changing, and these technologies are increasingly becoming feasible for front-line laboratories. We have integrated a routine weekly NGS run into our laboratory workflow at low cost and low additional staffing requirement using the MinION device [Oxford Nanopore Technologies (ONT), UK]. This workflow is run entirely by our staff without input from bioinformaticians. It produces a rapid, local in silico multilocus sequence type (MLST), and data that are suitable for a variety of other applications, including reference laboratory phylogenetic analysis.