Professor Mark Pallen on outwitting microbial pathogens

Posted on Friday 21st January 2011

Hospital infections are of serious concern to the public, to policy-makers and to the press. There has even been talk of an imminent post-antibiotic apocalypse, in which we run out of treatment options for some pathogens.

Fundamental to the problem of infection control in trauma patients, including returning military personnel, is a lack of medical intelligence about the nature, spread and evolution of microbial pathogens. Just as a soldier needs to know who the enemy is, where he is and how he got there, healthcare professionals need not only to identify the organisms that cause infection, but to track their spread from patient to patient and in the hospital environment.

Molecular fingerprinting has been used for many years to document the spread of microbial pathogens, but has generally lacked the resolution to reveal chains of transmission within hospital outbreaks. A new technology - high-throughput sequencing - means we can now determine the entire genetic blueprint of individual bacterial isolates relatively quickly, easily and cheaply. This enables us to distinguish bacteria that differ by as little as a millionth of a genome.

The University of Birmingham already has a high-throughput sequencing capability on campus, but with the arrival of the SRM Centre, we are poised to use it to make a decisive practical impact on our understanding of the spread of pathogenic bacteria. Rapid bacterial genome sequencing will help infection control staff to direct finite resources into infection control, both in individual patients and in formulating policies for detecting and containing outbreaks.

Professor Mark Pallen and Dr Nick Loman have collaborated with UHBFT microbiology staff to show how these approaches can be applied to the fine-grained epidemiology of hospital outbreaks. With funding from the Hospital Infection Society, they targeted a local outbreak of a multi-drug-resistant bacterium (Acinetobacter baumannii) spanning military and civilian patients. They showed that genome sequencing was able to shed light on chains of transmission involving otherwise indistinguishable isolates. Professor Pallen has subsequently received MRC funding to genome-sequence nearly 200 more Acinetobacter isolates, which will encompass isolates from military personnel.

‘All significant bacterial isolates from military or civilian trauma patients can now be genome-sequenced as a matter of routine (around 200 isolates per year),’ says Professor Pallen ‘High-throughput sequencing of molecular barcodes will also be used to profile the mixed populations of microorganisms that colonise infected wounds and tissues allowing us to detect previously unrecognised pathogens. Clinical specimens from approximately 100 trauma patients each year will also be subject to sophisticated community profiling to uncover the full diversity of the microbial populations infecting trauma patients and determine how these populations respond to therapeutic interventions, including antibiotics and novel therapeutic dressings.’

* For more information or to arrange an interview please contact Jenni Ameghino, University of Birmingham Press Office, Tel: 0121 415 8134. Mobile: 07768 924156.