Sharpening the hospital infection control toolset with front-line Oxford Nanopore sequencing | LC26

Abstract
One of the key functions of hospital infection prevention and control (IPC) is to prevent the transmission of important pathogens between patients. Traditional pathogen surveillance in hospitals involves monitoring the incidence of key organisms, grouped by species and antibiotic resistance phenotype. This approach is still in widespread use globally, but is imprecise and prone to both under- and over-calling true transmission events. This can negatively impact healthcare by allowing outbreaks to grow to a large size before detection, or by imposing draconian control measures when they were not required. In early 2022 our on-site hospital laboratory, which had no prior next-generation sequencing (NGS) experience, established a genomic pathogen surveillance program using Oxford Nanopore sequencing. This transformed our pathogen surveillance from low- to high-resolution and has detected several hospital outbreaks that would have either been missed entirely or detected at a much later stage by traditional surveillance methods. Importantly, sequencing has also enabled several suspected outbreaks to be refuted in the context of apparent increases in the incidence of certain organisms, meaning disruptive control measures could be avoided. Nanopore sequencing is now well integrated into the IPC processes at our hospital, enabling highly agile data-driven responses to situations of concern. In this talk I will discuss our journey with nanopore sequencing and explain how this can serve as a model for other healthcare systems, including those without prior NGS experience.

Biography
Dr Max Bloomfield is a clinical microbiologist and infectious diseases physician working in Wellington, New Zealand. He is actively involved with hospital infection control, epidemiology, and antimicrobial resistance from both a clinical and research standpoint. A key interest of his relates to the practical translation of technologies, such as Oxford Nanopore sequencing, to enable effective, pragmatic, and sustainable use in the clinical space.