WGS of foodbourne pathogens: River catchments in Devon UK
Up to ten presumptive Listeria colonies were selected and up to three presumptive E.coli and Salmonella colonies per plate. Methods adapted from Qiagen Blood and Tissue DNeasy kit was used to lyse sleceted colonies. Listeria colonies were resuspended into 90 l of Enzymatic Lysis Buffer containing lysozyme (Qiagens Blood and Tissue kit instructions) and this was incubated for 30 minutes as 37C before adding 110 of ATL buffer containing Proteinase K (Qiagens Blood and Tissue kit instructions) and resulting suspension was incubated at 56C for two hours. E. coli and Salmonella colonies were resuspended in  ATL buffer containing Proteinase K buffer and incubated for two hours at 56C. The QiaAmp HT DNA extraction kit with the QiaCube device was used to purify the DNA. DNA concentrations were measured using the One-DNA kit with the GloMax fluorimeter device. DNA extracts were repeated until 2ng/l concentration was reached. The Illumina Nextera XT DNA Library Preparation Kit and Nextera Index Kit v2 were used to prepare the DNA for sequencing with the NextSeq550 platform, following the manufacturers instructions.