Despite the plethora of strategies used to oppose antimicrobial resistance (AMR) in hospitals, no successful policies have been implemented to tackle AMR in the environment. Efforts to develop the latter are crucial to minimising transmission of AMR genes and organisms between hospitals, agricultural, water and wastewater systems. To create such environmental anti-AMR policies, it is important to understand how bacteria persist in the environment, given that long survival times correspond to greater opportunities for bacteria to spread AMR genes. As environmental survival is a complex process involving several abiotic factors and biological processes, many uncharacterised environmental survival mechanisms are likely to exist.
To identify such novel mechanisms, we used an environmental Escherichia coli isolate (Ec19) collected from a creek near a Victorian private hospital. This isolate belongs to the sequence type 73 cluster, a lineage commonly associated with urinary tract infections, and possesses several AMR genes. E. coli Ec19 was exposed to a creek water microcosm for 24 hours, followed by RNA extraction and sequencing. We also performed transposon insertion sequencing of E. coli Ec19 following incubation in creek water for five days.
The combined gene expression and genome-scale fitness datasets revealed many genes implicated in creek water survival. These include genes that encode zinc and potassium ion transporters, and enzymes involved in metabolism of glycerol, lipopolysaccharide, amino acids and nucleotides. Notable hits across both microcosm experiments were genes encoding the curli fimbriae, an amyloid fibre adhesin well characterised in virulence. These novel findings significantly contribute to our understanding of bacterial environmental persistence, which can be used as a foundation for further research.