Low cost nanopore sequencing in a front-line clinical microbiology laboratory without on-site bioinformaticians

Abstract

Next-generation sequencing (NGS) technologies have previously been out of reach for most front-line diagnostic microbiology laboratories due to high costs and the need for expert bioinformaticians. However, this is rapidly changing and these technologies are increasingly becoming feasible in the clinical setting. Our facility is a typical mid-sized clinical microbiology laboratory: non-university affiliated with well-established molecular testing capability, but no pre-existing NGS experience. With a limited budget and minimal additional staffing requirement we have integrated a routine weekly MinION run into our standard laboratory workflow. This is run entirely by our staff without input from bioinformaticians or others with prior NGS expertise, and leverages existing equipment to perform tasks such as nucleic acid extraction. With the aid of GPU-enhanced base calling the workflow produces a rapid, local in silico Multi Locus Sequence Type (MLST), and data that are suitable for a variety of other applications, including cloud transfer to a reference laboratory for phylogenetic analysis. These data form our recently established hospital genomic surveillance program, which supports local infection prevention and control (IPC) teams. Since the beginning of 2022 we have sequenced over 1000 hospital bacteria using this workflow, have detected and controlled a significant ward-based outbreak of Clostridioides difficile, and provided useful data to local IPC teams on many occasions. We are currently assisting other clinical laboratories in New Zealand to set up similar workflows.

Meet the speaker

Dr Max Bloomfield is a clinical microbiologist and infectious diseases physician based in Wellington, New Zealand. His interests include hospital infection control, epidemiology, and antimicrobial resistance. He is chair of the Genomics Special Interest Group of the New Zealand Microbiology Network, which aims to improve access to NGS in clinical laboratories across the country and promote a nationally consistent approach to the clinical use of sequencing.