Genetic diversity and population structure ofEscherichia coliisolated from freshwater beaches

Abstract

Escherichia coli is an important member of the gastrointestinal tract of humans and warm-blooded animals (primary habitat). In the external environment outside the host (secondary habitat), it is often considered to be only a transient member of the microbiota found in water and soil, although recent evidence suggests that some strains can persist in temperate soils and freshwater beaches. Here we quantified the population genetic structure of E. coli from a longitudinal collection of environmental strains isolated from six freshwater beaches along Lake Huron and the St. Clair River in Michigan. Multilocus enzyme electrophoresis (MLEE) and multilocus sequence typing (MLST) revealed extensive genetic diversity among 185 E. coli isolates with an average of 40 alleles per locus. Despite evidence for extensive recombination generating new alleles and genotypic diversity, several genotypes marked by distinct MLEE and MLST profiles were repeatedly recovered from separate sites at different times. A PCR-based phylogrouping technique showed that the persistent, naturalized E. coli belonged to the B1 group. These results support the hypothesis that persistent genotypes have an adaptive advantage in the secondary habitat outside the host.

Type II toxin–antitoxin systems are unevenly distributed among Escherichia coli phylogroups

“…Moreover, the latter predominate among E. coli strains with the ability to survive in the environment (Walk et al, 2007). By contrast, group B2 are more likely to be host-adapted, 'specialists' (Gordon & Cowling, 2003;Nowrouzian et al, 2005;White et al, 2011), and at least some B2 strains appear to be regular human commensals (Clermont et al, 2008;Carlos et al, 2010).…”

“…enterohaemorrhagic, enteroinvasive and enterotoxigenic E. coli pathovars, belong to groups A, B1 or D (Chaudhuri & Henderson, 2012). Furthermore, the E. coli phylogroups also differ with regard to growth rate (Gordon & Cowling, 2003;Walk et al, 2007;Carlos et al, 2010), genome size (Bergthorsson & Ochman, 1998), metabolic networks (Vieira et al, 2011) and antibiotic resistance profiles (Bukh et al, 2009). Therefore, we assumed the existence of a potential link between TAs and E. coli phylogeny, as these genetic elements are ubiquitous in E. coli genomes, and appear to be implicated in the cell physiology at various levels.…”

A comparison of homologous recombination rates in bacteria and archaea

“…It is a ubiquitous commensal in the intestine of mammals and birds, but certain types are also known to persist in the environment (Walk et al, 2007). Although usually harmless, E. coli also encompasses several important pathogenic lineages.…”

“…Although usually harmless, E. coli also encompasses several important pathogenic lineages. Strains belonging to well-defined clade ET-1 are prevalent in freshwater environments (Walk et al, 2007) and have low HRR. The intestinal g-proteobacterium Salmonella enterica on the other hand was found to have very high HRR.…”

Variation of an indicator ofEscherichia colipersistence from surface waters of mixed-use watersheds, and relationship with environmental factors

“…Stepwise multiple regression results and coefficients using parameters described in Table 2 better in secondary habitats. Confirmation of this hypothesis would require that E. coli in the more pristine water samples be found to be distinct from those in the more heavily contaminated, using for example Multilocus Sequence Typing or Repetitive Extragenic Palindromic PCR (Ishii et al, 2006;Walk et al, 2007). A second possibility is that the E. coli concentrations in the range examined here did not saturate prey density with respect to (for example) planktonic grazing or viral lysis.…”