Assessment and implementation of a whole genome sequencing scheme for rapid resolution of Legionella pneumophila outbreaks in Canada to better protect vulnerable populations

Funding period: 2023–2025
Lead: Jennifer Tanner
Total GRDI funding: $250,400

Legionella pneumophila (Lp) is a bacterial pathogen endemic in waterways worldwide that causes a serious form of pneumonia called Legionnaires’ Disease (LD). LD disproportionately affects the elderly and immunocompromised, often requiring hospitalization and can be fatal. The source of infections are often contaminated human-made water systems that release small droplets of water (aerosols), such as whirlpool spas, showerheads and air-cooling systems. The disease appears to be increasing in incidence over time. With the environmental nature of the infection, large numbers of individuals over large geographical areas can be infected, and for long periods, due to confounding factors like wind and multiple sources to investigate. Having efficient methods available to genetically fingerprint (subtype) Lp and subsequently link clinical and environmental samples is key to identifying the source(s) of infection and resolving LD outbreaks. Currently, the standard subtyping method in place for Lp is of limited resolution, requiring Canadian public health laboratories to submit the genetic data for 7 genetic loci from isolates in question to an international database at Public Health England, via email, where analysis occurs and subtype results returned. With this service being subject to availability, and at times lengthy, it is not amenable to high throughput response and ultimately impedes rapid investigations of outbreaks.

What? The proposal intends to develop and implement a workflow for high-resolution subtyping and disease cluster determination (outbreaks) of Lp using computational analysis of whole genome sequence data that can be performed in-house by public health laboratories across Canada. The developed workflow will be amenable to commonly used sequencing platforms (Illumina and Nanopore), stakeholder training provided for implementation and multicentre validated. Additionally, to support high volumes of samples, methods for automatic extraction of genomic material from Lp will be developed and validated.

So What? The direct outputs of this project will be a validated workflow for rapidly subtyping and clustering Lp as well as methodology for high-throughput processing of Lp isolates for emergency preparedness. The outcomes of the project will equip Canada to rapidly detect and inform potential LD outbreaks, and to provide greater support to LD outbreak investigations.