Defining E. coli Diversity in Complex Samples: Methods for Surveillance & Transmission

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Escherichia coli is a ubiquitous bacteria that is ordinarily harmlessly carried by humans. E. coli can also, however, cause serious infection and be complicated by resistance to antibiotics. The first step in causing infection is for the bacteria to colonise the gut of individuals. For this to happen they must be swallowed. Where more dangerous and/or drug-resistant E. coli are acquired most commonly is not clear, but follows a breakdown in personal hygiene often due to a lack of functional hygiene infrastructure whether in hospitals or the community. It is anticipated that well-designed interventions to interrupt E. coli transmission will lead to fewer infections and less antibiotics being used. Due to the complexity and expense of potential interventions to prevent transmission of these bacteria, an improved understanding of where and how E. coli are acquired is critical.Demonstrating a person has acquired an E. coli from a specific source requires confirmation of indistinguishable E. coli from two epidemiologically connected samples. Distinguishing bacteria of the same species in complex samples is very challenging and there is currently no gold standard approach to describing the within-species diversity of E. coli in a sample at scale. We will develop genomic methods for accurately identifying the diversity and abundance of E. coli in complex samples at scale that can be used for transmission modelling. Subsequently, we will investigate its applicability to diverse samples from different countries to create a catalogue of E. coli diversity in different settings.