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

AMR pathogen surveillance methods often fail to address within-species diversity, which is essential to link transmission of AMR bacteria between different sources. Emerging metagenomic approaches have shown promise to resolve within-species variation, however, the most appropriate method is unclear. Our DECODE project (Defining E. coli Diversity in Complex Samples: Methods for Surveillance & Transmission) will determine the most accurate and cost-effective method at scale to define intraspecies diversity of Escherichia coli from complex samples with a resolution of epidemiologically informative single nucleotide variants to support One Health AMR surveillance and transmission modelling. To achieve this, we will create well-defined and proportion-controlled mixtures of E. coli mimicking within-human gut diversity as in vitro models and will spike stool and sewage to validate and refine laboratory and bioinformatic workflows. Concurrently, we will establish bioinformatic pipelines initially using synthetic data to determine the influence of different subtypes of E. coli on performance. Next, we will demonstrate the applicability of our methods in different complex samples (stool, sewage effluent and freshwater) in a One Health context and from different locations in sub-Saharan Africa and Europe and will create a catalogue of setting-specific E. coli diversity. Ultimately, knowledge of intraspecies diversity is key to understanding transmission and in turn designing novel interventions to interrupt transmission of AMR bacteria and thereby reduce the number of infections.