Naturalized Escherichia coli from New Zealand wetland and stream environments.

This research investigates the presence of a naturalized clade of Escherichia coli in wetland and stream biofilms. Escherichia coli is used as a faecal indicator in water quality monitoring programmes worldwide, with the assumption that this bacterium is exclusively a commensal of the vertebrate gut. However, recent findings indicate growth and multiplication of E. coli in water and soils. This study seeks to clarify the relationships between environmental and commensal E. coli strains retrieved from New Zealand streams by evaluating fundamental genetic differences using the multilocus sequence typing (MLST) method. Environmental and commensal strains showed a high diversity of MLST profiles. Genetic analyses of linkage disequilibrium, index of association and rates of synonymous and nonsynonymous substitutions were used to investigate sequence variability and nature of change. Phylogenetic trees based on the concatenated sequences of the seven MLST housekeeping genes displayed distinct clustering of environmental strains. Comparison of the New Zealand sequences with worldwide E. coli strains retrieved from the Shigatox MLST database online did not allow the identification of a clear environmental genotype. However, some New Zealand aquatic E. coli isolates showed close relationships with strains from human and bovine origins, suggesting that environmental isolates were originally derived from subpopulations of commensal E. coli from these sources.