Genomic and growth fitness study of extended spectrum β-lactamase-producing Escherichia coli from bloodstream infections after introduction of a national 4C antimicrobial stewardship policy in Scotland.

Background: Extended spectrum β-lactamase-producing Escherichia coli remains a major cause of hospital-acquired bloodstream infections in countries with high antimicrobial stewardship compliance.

Methods: Isolates from bloodstream infections that occurred between 2010 and 2020 in a tertiary level hospital in North-East Scotland soon after introduction of the "4C" antimicrobial stewardship policy were analysed for phylogenetic structure, antimicrobial resistance, plasmid and virulence gene carriage. Growth fitness was measured in kinetic assays. Non-metric-multidimensional-scaling was used to evaluate clonal relationships, antimicrobial resistance, and virulence profiles in early and later years after the 4C policy introduction. Clonal and fitness trends over the study period were determined by generalized additive modelling. The relationship between clonal type, antimicrobial resistance, and fitness was evaluated by linear regression.

Results: Three hierarchical phylogenetic clusters were identified, with the most dominant cluster (O25:H4/fimH30) including all, and nearly exclusively, Clade C ST131 isolates as well as minor non-ST131 sequence types. The prevalence of ST131 was largely stable over the study period. Resistance to aminoglycosides and aztreonam in ST131 was lower (p=0.019 and p=0.004, respectively) during later years (2016-2020) by 28% on average compared to early years soon after 4C policy implementation (2010-2014). Carriage of virulence factors involved in bacterial adaptation was higher in ST131 compared to non-ST131 but mostly stable in early vs later years. Growth fitness of ST131 was lower than non-ST131 and declined steadily in later years (p<0.0001).

Conclusion: Despite stable virulence factor carriage, population structure and resistance to cephalosporins, we show increased susceptibility of ST131 to aminoglycosides and aztreonam and concurrent fitness decline years after the introduction of the 4C policy.