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Whole genome sequencing (WGS) has revolutionised routine microbiology investigations and infection prevention and control (IPC) by enabling precise pathogen identification, tracking transmission routes, and facilitating faster susceptibility testing, particularly for Mycobacterium tuberculosis. Over the past decade - especially in the wake of the pandemic - sequencing capabilities have expanded significantly, with commercial software also making data analysis more accessible. However, despite these remarkable research advancements, their integration into routine clinical practice has not been seamless. Many diagnostic laboratories in the UK and beyond continue to face challenges in delivering sequencing services, hindered by various practical and logistical barriers.
Beyond traditional sequencing platforms that require complex laboratory settings, portable sequencing devices, some as small as a mobile phone, can now be deployed virtually anywhere, making genomic surveillance more accessible. Recent developments in WGS have significantly improved our ability to study microbial genomes with greater accuracy and speed. Long-read sequencing technologies enhance the resolution of complex bacterial genomes, allowing for better characterisation of resistance genes and virulence factors. Additionally, real-time sequencing enables rapid pathogen identification, which is crucial for outbreak response and infection control measures.
Furthermore, metagenomic sequencing, which analyses all genetic material in a sample, is increasingly used to identify potential sources of infection or multiple infections occurring simultaneously in highly immunocompromised patients and critically ill individuals, for which traditional culture methods have failed to provide any positive result. Recognising its potential, the UK government has recently funded an ambitious initiative to expand respiratory metagenomic capabilities across a consortium of NHS hospital sites.
These advancements are paving the way for more effective infection control strategies, ensuring that genomic technologies continue to play a vital role in public health and clinical microbiology.
Despite its potential, WGS presents several challenges in IPC, with data interpretation and standardisation remaining complex. Specialised expertise and computational resources are required, though commercial software has made analysis more accessible. Traditional typing methods, once easily visualised on paper, have been replaced by more intricate phylogenetic trees and single nucleotide polymorphism (SNP) analyses, which vary depending on the bacterial species. While there is some international consensus on threshold levels for well-preserved genomes such as Mycobacterium tuberculosis, uncertainty persists regarding appropriate thresholds for other bacteria, including Gram-positive and Gram-negative species. This shift means that genomic interpretation is no longer a simple black-and-white process but rather a dynamic and evolving framework.
The cost of sequencing and analysis remains a barrier to routine healthcare implementation. Despite large-scale pathology consolidation, most sequencing is still handled by national reference labs, causing delays due to sample transport. Strained NHS budgets further limit in-house sequencing, though the COVID-19 pandemic briefly changed this, with government funding enabling real-time sequencing of transmission events and variants. However, that financial support has now vanished, making sustained investment crucial to ensure sequencing remains a core tool in infection prevention, rather than an underutilised resource constrained by funding limitations.
Another critical issue is that sequencing training is not yet incorporated into IPC education, limiting the ability of frontline healthcare workers to fully leverage the benefits of genomic surveillance. Given the growing role of sequencing in infection control, there is a pressing need to make WGS training more common for IPC professionals, ensuring that they are equipped to interpret genomic data and apply sequencing insights in real-time clinical settings. Expanding educational programs and professional development initiatives could help bridge this gap, ultimately improving infection prevention strategies across healthcare facilities.
These challenges highlight the need for greater standardisation, funding, and infrastructure development to ensure that WGS can be effectively integrated into IPC strategies, improving patient outcomes and healthcare efficiency.
Interested in exploring this topic further? Attend our annual conference, HISCON, where WGS's growing role in IPC and healthcare will be explored in greater depth. More information including full programme can be found in the link below.