Phenotypic and Genotypic Characteristics for Escherichia coli strains responsible for bacterial bloom events in Australia

Abstract

Escherichia coli is widely used as an indicator of recent faecal contamination of drinking and recreational waters. However, evidence suggests that E. coli can proliferate in the environment outside a host, confounding its use as a faecal indicator. E. coli strains that produce significantly elevated counts of 10,000 - 100,000 cells/100 ml of water (bloom events) are reported from freshwater reservoirs and recreational lakes in Australia. Bloom strains are not faecal associated and may represent free-living E. coli. A limited number of strains are responsible for bloom events and all belong to E. coli phylogroups A and B1. Bloom strains have acquired a capsule originating from Klebsiella. Diversity and distribution of Klebsiella capsules in E. coli overall and in bloom strains were investigated. A PCR-based protocol was developed to detect capsule-positive E. coli and discriminate strains that harbour bloom strain-associated capsule types. Bloom strain attributes that could lead to the elevated cell densities observed in bloom events were experimented. The B1 bloom strain from the east coast (termed B1-001) which is numerically dominant and always present in bloom events was further characterised, and why B1-001 strain has not been detected in recent bloom events assessed using the Colilert-18 system was investigated. Frequency of Klebsiella capsules in E. coli was only 7% and 23 different Klebsiella capsule types were detected. All bloom strains were encapsulated and seven Klebsiella capsule types were detected among the eight bloom strains isolated to date. Capsules were observed only in strains from E. coli phylogroups A, B1, and C, and all encapsulated strains were of O-serogroups O8, O9, and O89. Capsule gene region and the adjacent O-antigen gene region in encapsulated E. coli are a result of a horizontal gene transfer event that occurred between E. coli and Klebsiella. The PCR accurately detected known bloom, non-bloom encapsulated, and capsule-negative strains. A pan genome comparison of phylogroup A E. coli revealed that the iron uptake system encoded by fecIRABCDE operon was over-represented among bloom strains (100%) compared to non-bloom E. coli (<39%). Growth assays however showed that the fec operon is unlikely to contribute to the elevated cell densities. In contrast, strains that were encapsulated had a growth rate advantage compared to capsule-negative strains. B1-001 bloom strain was closely related to Shigella but its closest relatives were lactose-positive E. coli. Several features that are beneficial for a free-living lifestyle such as flagella and curli were disrupted in B1-001. In Colilert-18, B1-001 was heavily outcompeted by the two phylogroup A bloom strains from the east coast, explaining why B1-001 was not detected in recent bloom events assessed using Colilert-18. The current study suggests that any E. coli strain that harbours a Klebsiella capsule may be able to produce elevated counts under conducive environmental conditions. The recurrence of bloom events across Australia confounds the use of E. coli as a water quality indicator and urges a shift to alternative indicators. Show more