Claire Jenkins - Application of Oxford Nanopore Technology in the E. coli Reference Laboratory at Public Health England
Nanopore Community Meeting 2017
The Gastrointestinal Bacteria Reference Unit at Public Health England (PHE) implemented whole genome sequencing (WGS) for outbreak detection and routine surveillance using the HiSeq Illumina platform in 2014. Recently, we explored ways of integrating Oxford Nanopore Minion Technology into our routine service for typing Shiga Toxin producing E. coli (STEC). A pilot study showed that outputs from the Minion platform could be incorporated into the existing PHE bioinformatics pipelines, and integrated with Illumina data. STEC outbreak clusters were successfully identified and investigated using a combination of Illumina and Minion data. Furthermore, analysis of the Minion WGS data facilitated the analysis of the prophage and plasmid content of the STEC isolates, and may provide important clues to the source and transmission of this clinically significant zoonotic, foodborne pathogen.