Proactive whole genome sequencing for IPC - is it worth it?

In preparation for tomorrow's journal club (which you can register for here), we’ve written a blog on this paper
which will be covered by Dr James Price.

Whole genome sequencing (WGS) shows a tremendous amount of promise for Infection Prevention and Control
(IPC), from understanding and modelling transmission of infections through to outbreak detection and management. However, may questions remain over whether WGS can be implemented as a cost-effective solution.

Evaluating the Economic Impact of SARS-CoV-2 Genome Sequencing in Hospital Infection Control

The study by Panca et al. (2023) within the COG-UK Hospital-Onset COVID-19 Infection (HOCI) trial
provides one of the most comprehensive economic evaluations to date of integrating WGS into IPC practice.

Study Overview

Conducted across 14 UK hospitals, the study assessed the cost implications of using WGS data, delivered through a Sequence Reporting Tool (SRT), to inform IPC investigations. Researchers applied a micro-costing approach, gathering detailed data from laboratories and IPC teams. Costs were analysed from the hospital perspective and included both sequencing expenditure and IPC resource use.

Key Findings

The average per-sample cost for SARS-CoV-2 sequencing was £77.10 for rapid turnaround (24–48 hours) and £66.94 for longer turnaround (5–10 days). Consumables, rather than staffing or equipment, were the primary cost drivers, representing approximately two-thirds of total sequencing costs.

Across all participating sites, total IPC management costs during the three-month intervention phases were
estimated at £225,070 for individual HCAIs and £416,447 for outbreak events. The most significant contributors were lost bed-days from ward closures and cohorting, followed by outbreak meetings and cleaning requirements.

When SRT outputs were acted upon, the economic picture shifted slightly. Sequencing data identified previously
unrecognised hospital-acquired cases, increasing HCAI management costs by around £5,000, but simultaneously excluded certain false-positive outbreaks, reducing outbreak management costs by over £11,000.

Implications

While WGS undoubtedly adds to immediate IPC expenditure, the benefits extend beyond short-term costs.
Accurate identification of transmission pathways can prevent unnecessary ward closures, reduce redundant testing, and enhance staff confidence in outbreak management.

Importantly, the study was conducted during peak pandemic pressures, when staffing shortages and high infection volumes limited the full implementation of sequencing feedback. The authors suggest that under less strained conditions and with faster turnaround times WGS could offer even greater value to hospitals.

What this means for IPC

The paper concludes that WGS represents a promising, though initially costly, enhancement to hospital IPC strategies. Continued technological advancements and economies of scale are expected to reduce per-sample costs. Moreover, linking WGS data with electronic health records could streamline its integration into clinical
workflows, minimising the need for separate interpretation meetings and specialised training.

WGS may soon be a cost-effective necessity for safe and efficient hospital care but more work is needed to understand how the technology can be implemented day to day in healthcare settings.

Join us for the discussion at tomorrow's Journal Club here!