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John Fell Study (JFS) 

The John Fell Fund project is an internally funded project looking at different proof-of-priniciple methods to optimise rapid direct-from-sample infection diagnostics using nanopore sequencing including:

  • Looking at cell sorting (i.e. bacterial enrichment strategies) prior to sequencing
  • Looking at different bacterial DNA amplification approaches 
  • Using RNA nanopore sequencing
  • Using on-sequencer enrichment for bacterial/AMR gene targets, known as adaptive sampling
  • We will be exploring these methods in parallel an in combination.

    The John Fell fund study aims to improve direct-from-sample diagnostic workflows for bacterial infections using nanopore sequencing, encompassing both rapid pathogen identification and prediction of antibiotic susceptibility phenotypes from genotype.

    We want to try some different approaches to improve the yield of bacterial DNA that is available for sequencing, including cell sorting and enrichment by genome amplification, and also try RNA sequencing and bacterial sequence enrichment/human sequence depletion by applying Read Until (Adaptive Sampling).

    It’s 2 years of funding that was awarded to Nicole Stoesser and David Eyre,