Genome_sequencing_of_individual_clones_of_eight_ETECs_and_K12_MG1655. Genome_sequencing_of_individual_clones_of_eight_ETECs_and_K12_MG1655

Summary: Genome sequencing of individual clones of human Enterotoxigenic Escherichia coli and laboratory-adapted K12 MG1655; checking for any genomic diversity prior to phenotyping. Project background: Enterotoxigenic Escherichia coli (ETEC) is the cause of over 80 million episodes of human diarrhoea globally per year, associated with nearly 50,000 deaths, particularly in children under five in low and middle-income countries. ETEC isolates are genetically highly variable, but by definition all carry plasmids encoding toxins (heat labile (LT) and/or heat stable (ST) toxins), which enable them to cause watery diarrhoea, and a variety of colonization factors that allow them to adhere to the gut. Despite genetic variation in the ETEC core genome Astrid Von Mentzer showed that ten clades of human ETEC isolates are stably associated with particular virulence factors [Von Mentzer et al. (2014) Nature Genetics. 46:1321] and identified 8 ETEC strains that represent the major phylogenetic diversity of clinical ETEC [Von Mentzer et al (2021) Scientific Reports 11:9256]. Project outline: We aim to understand how ETEC virulence plasmids influence gene expression in representatives of the major clades compared to each other and to a laboratory-adapted E. coli control, K12 MG1655. We plan to investigate a number of laboratory phenotypes. The master stock for each ETEC isolate has already been sequenced [Von Mentzer et al (2021) Scientific Reports 11:9256]. Our stock of MG1655 K12 has not been sequenced and different mutations are known to have appeared in different global stocks of this K12 sub-clone [Soupene et al (2003) J. Bact. 185:5611]. Here we plan to sequence, by Illumina and PacBio, three single colony-purified clones from each for eight ETECs (E36, E562, E925, E1373, E1441, E1649, E1779 and E2980) plus our stock of MG1655 K12. We wil use these data to check for genomic variation between clones, compare to reference genomes for each strain, prior to phenotypic analysis. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/