A more complete picture: capturing single nucleotide variant diversity in extended-spectrum beta-lactamase producing Escherichia coli using post-enrichment metagenomics.

cefotaxime. Seven single colonies were picked, and the remaining biomass of all colonies was collected from each plate, sequenced and analysed using the mSWEEP/mGEMS pipeline. We created a custom SNV calling workflow that allows heterozygous SNVs in a bacterial population and found that the choice of reference changed the number of measurable SNV distances between the sc-WGS and pe-MGS. Using our custom workflow with a core-gene reference captured 99% of all the SNV calls from multiple sc-WGS data in the pe-MGS data of the same culture. The plate sweep method offers a feasible, cost-effective alternative to multiple single colony picks for describing within-host ESBL-EC diversity. The workflow we developed allows for effective SNV calling from pe-MGS data that were comparable to SNV calls from multiple sc-WGS data from the same sample.