Microbiology

Theme Leads:

Prof Tim Mitchell | Prof Robin May

What’s it all about?

Hospital infections are of serious concern to the public, to policy-makers and the media. Infections, whether isolated or as outbreaks, continue to pose significant challenges for military trauma patients.

Why is it so important to understand infections?

A multi-drug-resistant pathogen called Acinetobacter has been a particular problem among injured soldiers returning from Iraq and Afghanistan. Acinetobacter is a bacteria which is very common in many different environments and is normally not harmful to healthy humans. However, patients are more vulnerable because they are already ill or have injuries which have weakened their body’s ability to fight infection.

In Birmingham, we also see many military patients with eye infections which are difficult to diagnose and manage.

Cutting Edge Technology

We have used a method called high-throughput genome sequencing (HTS) to diagnose and understand transmission of bacteria (Pseudomonas, Acinetobacter) and fungi (Candida).

This method has allowed us to identify the source of infection and subsequently prevent its transmission in the hospital. As a result, we were awarded further funding from DoH to evaluate transmission at 3 additional hospital sites nationally.

A significant advancement in the use of this method has been the development, last year, by Oxford Nanopore, of the MinION, a USB-stick whole-genome sequencer, which runs off a laptop and makes it possible to determine whether a person is infected with a particular infection within a matter of minutes.

Dr Nick Loman’s team were the first early access testers and the first to publish in peer-reviewed journals using this technology. A significant impact of this work in the military setting was the use of this technology by our bioinformatician (Josh Quick), who travelled to Guinea and set up the MinIOn for sequencing Ebola strains in a field hospital, with results transmitted back to Birmingham for data analysis.

Sequencing has continued in the field with local technicians and visiting epidemiologists being trained in the use of the platform and to date some 130 strains have now been sequenced with an average turnaround time to providing results of less than 3 days. This information has proved invaluable in assisting epidemiologists with contact tracing and defining the likely sources of ongoing cases, particularly where links between cases seem uncertain.

In addition to providing useful information for this current outbreak, this work also provides proof of principle that sequencing can be carried out in the field for a variety of pathogens, reducing the difficulties with needing to transport samples across borders and providing rapid information for action.

This approach is highly relevant to the idea of a light-weight military medical laboratory and could allow both rapid diagnosis and examination of potential sources and spread of infective agents and mitigate against operational consequences.

What is the impact of this research?

A key problem when controlling infection in trauma patients is that clinicians still do not fully understand the nature, spread and evolution of bacteria like Acinetobacter and other microbes.

Medical microbiology, even in the 21st Century, still relies on techniques devised in the 19th Century, such as microscopy and the growing of cultures to identify pathogens within clinical samples.

By developing new techniques we hope to be able to make the diagnosis, tracking and treatment of infections more effective.