Professor Judy Breuer at UCL leads the PATHSEEK consortium, which generates whole genome sequencing data directly from clinical specimens for use in diagnostic microbiology.The consortium is focused on pathogens with an unmet clinical and public health need or for which the threat is of global importance, including HIV, influenza, Hepititis B/C, TB and Chlamydia. Professor Breuer’s molecular epidemiology work using Norovirus sequences led to the dissection of hospital transmission chains and defines a new paradigm for the application of the next generation sequencing technologies in a clinical setting. Professor Breuer’s work on Varicella zoster viral transmission highlighted the molecular details of the VZV host-virus interaction and provided insight into viral requirements for replication and spread.

Pathogen sequencing for identification, detection of resistance mutations, and documenting transmission, outbreaks and epidemics, is increasingly important in diagnostic microbiology. While current methods generate consensus sequence, deep sequencing is able to detect resistance mutations present at low frequencies, for example in HIV, thereby providing important additional data for personalizing management of infected patients. PATHSEEK consortium will benefit from this background knowledge and, by using this method, will prove the concept of high throughput diagnostic pathogen sequencing, providing data within one working day for diagnostic use.

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