Escherichia coli is widely used as an indicator of faecal contamination in water, as it is easily identified, a ubiquitous inhabitant of the intestinal tract of humans and other mammals, and believed to persist for only a few days once outside the host.

Strains of E. coli can be partitioned into subgroups that have been denoted as A, B1, B2, D, C, E, F and clade I-V.  The clonal composition of E. coli inhabiting most host populations does not reflect the clonal composition of E. coli isolated from water bodies.  In water bodies, strains belonging to phylogroup B1 predominate.  Previous studies have suggested that some B1 strains may have enhanced persistence in water (>12 days) relative to other E. coli strains.  Although B1 strains are uncommonly detected in human faeces, they are very common in some host groups, such as carnivorous mammals and birds.

A recent study demonstrated that at least one lineage of B1 strains (clonal complex 87) represents a predominately host associated lineage.  However, the relative abundance of this lineage in water is unknown, nor is it known if there are B1 strains predominately associated with non-host environments.  Consequently whole genome sequencing was under taken on a collection of 116 B1 strains that had been repeatedly isolated from water bodies across eastern Australia, together with 76 diverse faecal B1 strains. Phylogenetic analysis revealed two distinct lineages of B1 strains that predominately consisted of environment isolates.  These lineages lack antibiotic resistance determinants and harbour very few virulence factors associated with either intestinal or extra-intestinal disease. Consequently, these strains appear to be members of autochthonous populations of E. coli that inhabit diverse water bodies.

This study enhances our understanding of persistent B1 E. coli strains in water and demonstrates that their existence further confounds E. coli’s use as a water quality indicator of faecal contamination..