The Gastrointestinal Bacteria Reference Unit at Public Health England (PHE) implemented whole genome sequencing (WGS) for outbreak detection and routine surveillance using the Illumina HiSeq in 2014. Recently, they explored ways of integrating the use of the Oxford Nanopore Technologies (ONT) MinION into their routine service for typing Shiga Toxin producing E. coli (STEC) and to see if the data generated can be used in outbreak investigations.

The long read lengths produced by the ONT MinION are allowing for the characterization of prophage regions of the genome, which are taken up by the bacteria from the environment. The uncovering of geographical clues provided by these regions, is helping to identify the source and mode of transmission of the bacteria and allowing for accurate tracking of the outbreak. These prophage regions are incredibly hard to differentiate using short read sequencing due to their repetitive sequences and require explicit consideration during phylogenetic analysis. SNPs in the regions have been masked in the Illumina data but discrepant bases were highlighted in the ONT data. ONT’s MinION can be used to generate genomic data that can be incorporated into PHE’s routine service and to a point where the genomes will fall within the same branch of a phylogenetic tree when compared to Illumina data, but the ONT data is providing more information than ever before.

Register

When: Wednesday, April 18th, 2018
Time: 8:00am PDT/ 11:00am EDT/ 4:00pm BST
The webinar will be available on-demand after this date. 

 

David Grieg
Bioinformatician,
Public Health England

David completed an undergraduate degree in Biomedical Science at the University of Bedfordshire in 2014 and then completed a Masters degree in Biomedical Sciences specialising in Medical Microbiology the following year. He then went on to work in the Gastrointestinal Bacteria Reference Unit (GBRU) at Public Health England starting at the start of 2016 and have remained there since. During his time in GBRU, he has worked on both the laboratory and bioinformatics sides of the department. David’s current research is based around the application of single-molecule sequencers from Oxford Nanopore Technologies for public health microbiology and the characterisation of gastrointestinal pathogens, in particular Shiga-toxin producing E. coli (STEC).