E. coliphylogeny drives co-amoxiclav resistance through variable expression ofblaTEM-1

Abstract

AbstractCo-amoxiclav resistance inE. coliis a clinically important phenotype associated with increased mortality. The class A beta-lactamaseblaTEM-1is often carried by co-amoxiclav-resistant pathogens, but exhibits high phenotypic heterogeneity, making genotype-phenotype predictions challenging. We present a curated dataset ofn=377E. coliisolates representing all 8 known phylogroups, where the only acquired beta-lactamase isblaTEM-1. For all isolates, we generate hybrid assemblies and co-amoxiclav MICs, and for a subset (n=67/377),blaTEM-1qPCR expression data. First, we test whether certainE. colilineages are intrinsically better or worse at expressingblaTEM-1, for example, due to lineage differences in regulatory systems, which are challenging to directly quantify. Using genotypic features of the isolates (blaTEM-1promoter variants and copy number), we develop a hierarchical Bayesian model forblaTEM-1expression that controls for phylogeny. We establish thatblaTEM-1expression intrinsically varies across the phylogeny, with some lineages (e.g. phylogroups B1 and C, ST12) better at expression than others (e.g. phylogroups E and F, ST372). Next, we test whether phylogenetic variation in expression influences the resistance of the isolates. With a second model, we use genotypic features (blaTEM-1promoter variants, copy number, duplications;ampCpromoter variants; efflux pump AcrF presence) to predict isolate MIC, again controlling for phylogeny. Lastly, we use a third model to demonstrate that the phylogenetic influence onblaTEM-1expression causally drives the variation in co-amoxiclav MIC. This underscores the importance of incorporating phylogeny into genotype-phenotype predictions, and the study of resistance more generally.