Infectious diseases cause millions of deaths each year and resistance to treatment (where antibiotics stop working) is a global problem. Fortunately, the way we study infections has been radically transformed over the past 15 years. We now examine the genes within infection-causing bacteria, viruses and other types of microorganisms (termed “pathogens”) to identify which ones play roles in causing disease and whether the pathogens are resistant to the treatments we can provide. We call this “genome sequencing” – where scientists “read” the specific sequence of DNA or RNA that make up a pathogen’s genetic code.

A specific type of genome sequencing called “metagenomics” is becoming viable for studying infectious diseases. Metagenomics allows us to study all the potential pathogens in a sample simultaneously, instead of having to look just for ones we suspect. This technique is vital for identifying infectious outbreaks caused by new or unexpected pathogens. This was how the SARS-CoV-2 virus that causes COVID-19 was detected in early 2020.

Genomic sequencing can also help control infections, through understanding where they come from (locally, from international sources, from animals or the environment) and help governments make better policies about how to protect our communities from outbreaks.

However, these techniques are not mainstream in public health due to lack of training and the costs and complexity of implementation, meaning we are not yet using genomics and metagenomics fully to tackle infectious diseases.

The vision of our Public Health Genomics HPRU is to harness genome sequencing to enable the UK to use genetic data from pathogens routinely in clinical care and in public health policies across a wide range of infectious disease threats.

We will explore new approaches to genome sequencing, including metagenomics. Assessing all the possible pathogens contained in a patient sample will help better understand how pathogens interact with each other, and how resistance to antibiotics occurs.

The HPRU will help develop standard ways for sequencing genomes, as well as new approaches to combining data about the pathogen and the person with the infection to better understand which people are at greater risk of catching an infection, or having poor outcomes due to that infection. We will also explore exciting new ways to sequence genomes directly from the environment, for example water and wastewater, which can provide useful information about how pathogens spread throughout the country.

We will expand our knowledge of how pathogens change over time to cause disease and how pathogens can become more or less dangerous over time, as they gain or lose genetic factors which change how they infect people. This will also help to understand how pathogens can become resistant to treatments.

We will also use modern methods to look at these complex issues including artificial intelligence (where computers can identify patterns from complex data to make predictions).

Finally, because pathogens do not respect international borders, our methods will help build a toolkit for others to use these technologies internationally, improving the global response to infectious diseases.

In collaboration with the University of Birmingham.