Characterization of Escherichia coli diversity in a freshwater environment

Escherichia coli (E. coli) is an indicator of faecal contamination as it is assumed that faecal contamination is the main source of these bacteria in the environment. Recent studies have, however, shown that E. coli can be found in the environment without any apparent link to faecal contamination. These environmental E. coli isolates multiply and survive in niches including soil, sand, sediment and water. Environmental E. coli are usually associated with phylogroups A and B1, two of the 7 phylogroups (A, B1, B2, C, D, E and F) typically used to group E. coli isolates. Some environmental isolates have also been linked to Clades III-V, which are novel undescribed Escherichia species. In this study E. coli was isolated from different niches within various freshwater dams. To represent the E. coli circulating in the human population, E. coli was isolated from sewage samples. To determine the diversity within the Escherichia coli population and to identify possible environmental E. coli, the sigma factor S (rpoS), β-D-glucuronidase (uidA), methyl-directed mismatch repair (mutS) and fatty acyl-CoA synthetase (fadD) genes were sequenced and Maximum Likelihood trees were drawn using the individual and concatenated datasets. The phylogenetic trees were also used to determine which phylogroup the isolates are associated with and if any of the isolates belonged to the undescribed species or clades. The population dynamics was determined using TCS and SplitsTree analysis. The phylogenetic trees showed that the diversity amongst these isolates was high. None of the isolates were part of the clades and most of the isolates group with phylogroups A and B1 as expected. Three possible unique clusters of environmental isolates were observed which respectively formed part of phylogroups B2, D and no specific phylogroup. Phylogroups B2 and D are usually associated with isolates that cause extra-intestinal infection and was not expected to be represented by environmental isolates. Population structure analyses indicated that these clusters could be part of sub-populations within the larger E. coli population and may be genetically separate from the rest of the isolates.Dissertation (MSc)--University of Pretoria, 2014.Microbiology and Plant PathologyMScUnrestricte