A more complete picture: Capturing single nucleotide variant diversity in ESBL-producing Escherichia coli using post-enrichment metagenomics

Inferring transmission relies on modelling high-quality genomic data to accurately distinguish between isolates from the same source and those from different sources. The post-enrichment metagenome sequencing (pe-MGS) method uses a culture-based sequencing approach to analyse the diversity of a target pathogen and has been effectively used to analyse the transmission of nosocomial infections. However, a direct comparison of single nucleotide variant (SNV) call accuracy, cost and feasibility of the single colony whole genome sequence (sc-WGS) data and the post-enrichment metagenome sequencing (pe-MGS) for an antimicrobial resistant bacteria of clinical importance, extended-spectrum beta-lactamase producing E. coli (ESBL-EC), was required. A spiked stool sample and rectal swabs from six study participants were pre-enriched and cultured on selective agar. Seven single colonies were picked, and the remaining biomass was collected from each plate and sequenced. All the sequence data was characterised using the mSWEEP/ mGEMS pipeline. The sc-WGS and the pe-MGS from the spiked stool sample was used to validate the custom pipeline by directly comparing SNV calls.