Escherichia coli has been delineated into phylogroups (A, B1, B2, C, D, E, F). Strains of different phylogroups vary in their ecological niche, and propensity to cause disease.  Of all the phylogroups, B2 is the most abundant phylogroup in developed countries and is clinically significant, as strains belonging to this phylogroup are often the cause of extra-intestinal infections. Although phylogroup B2 are highly diverse, relatively few B2 lineages represent the great majority of B2 strains isolated from humans. Although B2 strains are usually a small fraction of the E. coli recovered from water samples, their presence may be indicative of human faecal contamination and represent human health risk.

The aim of this study was to determine what fraction of phylogroup B2 strains isolated from water samples belonged to human associated B2 lineages and their survival ability in different types of water. 

Over 10,000 isolates of E. coli from more than 900 water samples collected in the Sydney and Gold Coast regions were characterised for their phylogroup membership.  A total of 825 strains belonging to phylogroup B2 were assigned to one of the human associated B2 lineages using a recently developed allele-specific PCR method for lineage assignment. A subset (291) of the Gold Coast isolates were sequenced type using the CH typing scheme (fimH, fumC). 

Overall, the allele specific PCR method identified 40% of the isolates as potentially belonging to one of the human associated lineages.  However, confirmation of subgroup I isolates (putative St131) and subgroup IX isolates (putative ST95) using ST specific PCR based methods revealed that less than 5% of subgroup I and IX isolates actually represented human associated lineages.

The results of this study demonstrate that human associated phylogroup B2 strains represent a small fraction of the E. coli strains present and persist in Australian waters.