Wednesday 25 January 2017 - Improving the diagnosis and management of serious infection using nanopore metagenomic sequencing
Rapid and accurate diagnosis is critical for the effective treatment of life threatening infections, such as bloodstream, respiratory tract and complicated urinary tract infections. These clinical syndromes have complex aetiology and require the recognition of pathogens within challenging sample matrices. The “gold standard” culture techniques are labour intensive, slow (≥2 days) and often offer poor clinical sensitivity. In the absence of rapidly available pathogen and antimicrobial susceptibility information, the patient is treated empirically with broad-spectrum therapy. This empirical therapy is often inappropriate.
A paradigm shift in diagnostics technology is required, moving to methods capable of detecting any pathogen or resistance within hours. Shotgun metagenomics sequencing has the potential to be the technology of choice, combining rapidity with comprehensiveness beyond that of culture or PCR. Nanopore real-time sequencing technology has, for the first time, made it feasible to apply metagenomic sequencing to acute infection diagnosis.
By providing rapid pathogen identification and resistance profiling, metagenomic sequencing will afford clinicians with a timely and accurate diagnosis, reducing empiric treatment to a single dose and enabling tailored antimicrobial therapy. I will present data from the nanopore metagenomics sequencing pipelines we are developing for the diagnosis of sepsis, pneumonia and UTIs.
I gained my Ph.D. in the molecular diagnosis of foodborne pathogens at the National University of Ireland, Galway (NUIG) followed by a two-year post-doc at NUIG and a two year stint in industry with Beckman Coulter. In 2010 I returned to academia, taking up a Senior Research Associate position at University College London. In 2013 I was appointed Lecturer in Medical Microbiology at UEA (Norwich Medical School) and I was promoted to Senior Lecturer in 2016. My research focuses on the molecular diagnosis of pathogens and associated antimicrobial resistance in complex clinical syndromes such as sepsis, respiratory tract infections and urinary tract infections.