Automated sample-to-answer workflows for whole-genome sequencing to investigate hospital-acquired infections | LC 25

Biography

Dr Michael Wiley is an Associate Professor at the University of Nebraska Medical Center and Director of Genomic Epidemiology for the Nebraska Public Health Laboratory. He is also a co-founder of PathoSeq Bio — a small business focused on developing hybrid-capture assays for detecting pathogens. Michael’s focus is on bringing sequencing for pathogen characterization to any laboratory in the world.

Abstract

Whole-genome sequencing (WGS) has become an important component of hospital infection control programs. Evidence shows that WGS can help detect outbreaks within hospitals more quickly, resulting in improved patient care and a reduction in the cost of hospital-acquired infections (HAIs). Public health laboratories and hospitals have been increasingly implementing WGS. In part, this is due to an increased interest in generating and analyzing data on site for rapid results rather than sending it to a third party. This report describes a process we used to compare two automated sample-to-answer workflows to provide real-time data to address HAIs. For this comparison, the Nebraska Public Health Laboratory (NPHL) shares a campus with the University of Nebraska Medical Center and Nebraska Medicine, the state's largest hospital system for access to isolates for testing. NPHL is thus uniquely positioned to evaluate two commercially available sample-to-answer systems, the Clear DX (Clear Labs, USA) and the ElysION (Oxford Nanopore Technologies, UK). Since 2022, the Clear DX instrument has been used by NPHL for WGS of SARS-CoV-2 and the CDC's PulseNet program for the evaluation of foodborne pathogens. In December 2024, NPHL acquired an ElysION. In evaluating these two platforms, consideration will be given to their cost, response time, quality of results, and ability to analyze HAI outbreaks associated with organisms, including the sequencing of plasmids.