Genotypic and survival characteristics of Escherichia coli phylogroup B2 from water

Abstract

Water is the most essential substance for life on earth. Hence, strict drinking water guidelines are framed to ensure the safety of drinking water supplies. For over a century, Escherichia coli has been used as the primary indicator of recent faecal contamination in water. E. coli is used as a faecal indicator bacteria (FIB) due to its high prevalence in the gut and faeces of humans, its ease of detection, and the assumption that E. coli cells quickly die once they leave the host. Recent population genetic studies are challenging these assumptions and suggest that E. coli is a versatile species and that some strains have adapted to the external environment or may even have become free-living without any association with the human host. As such, E. coli as FIB is increasingly questioned. Additionally, water industry has been trying to find methods to identify the source of faecal inputs to waterways, including typing of E. coli that have been isolated from the water. For this purpose, first, the prevalence of human associated E. coli strains in water samples from various catchments across Sydney and southeast Queensland regions was investigated. Genotypic characterisation of this study revealed that the four predominantly human associated Sequence Types (ST)s (73, 95, 131, and ST69) represent less than 1% of the total E. coli isolates evaluated. This indicates that the E. coli in these drinking water sources are either non-human in origin or not recently contaminated with human activities. Second, a comparative genomics approach was used to contrast host and environmental isolates of E. coli to determine the extent to which the variable gene content of isolates from these two environments differed. This study showed two distinct clusters, one predominantly human associated and another native vertebrate animal associated. The environmental water isolates were equally distributed between the two clusters. The results hence suggest that not all E. coli from environment are human associated but may originate from animals as well. Third, an experiment was conducted to compare the survival pattern of both host and environmental isolates of E. coli in different water treatment types such as heat sterilisation and filter sterilisation and investigated on the variable gene content of these isolates to better understand the variation in survival with respect to each treatment. This study results suggested that contrary to the expectations that E. coli has poor survival in water, some went dormant achieving viable but non-culturable state (VBNC), exclusively in heat sterilised water, and some E. coli strains survived for extended periods in both water treatments. Further evaluation showed that the among strain variation observed has an underlying genetic component. Hence, to best consider E. coli as a FIB, all the investigations indicate that the difference within E. coli need to be considered and further characterised to differentiate true human E. coli and E. coli from other non-human sources. Overall, the results of these studies contribute towards understanding the limitations of using E. coli as an indicator of recent faecal pollution in water.