Escherichia colihas been proposed to have two habitats—the intestines of mammals/birds and the nonhost environment. Our goal was to assess whether certain strains ofE. colihave evolved toward adaptation and survival in wastewater. Raw sewage samples from different treatment plants were subjected to chlorine stress, and ∼59% of the survivingE. colistrains were found to contain a genetic insertion element (IS30) located within theuspC-flhDCintergenic region. The positional location of the IS30element was not observed across a library of 845E. coliisolates collected from various animal hosts or within GenBank or whole-genome reference databases for human and animalE. coliisolates (n= 1,177). Phylogenetics clustered the IS30element-containing wastewaterE. coliisolates into a distinct clade, and biomarker analysis revealed that these wastewater isolates contained a single nucleotide polymorphism (SNP) biomarker pattern that was specific for wastewater. These isolates belonged to phylogroup A, possessed generalized stress response (RpoS) activity, and carried the locus of heat resistance, features likely relevant to nonhost environmental survival. Isolates were screened for 28 virulence genes but carried only thefimHmarker. Our data suggest that wastewater contains a naturalized resident population ofE. coli. We developed an endpoint PCR targeting the IS30element within theuspC-flhDCintergenic region, and all raw sewage samples (n= 21) were positive for this marker. Conversely, the prevalence of this marker inE. coli-positive surface and groundwater samples was low (≤5%). This simple PCR assay may represent a convenient microbial source-tracking tool for identification of water samples affected by municipal wastewater.
IMPORTANCEThe results of this study demonstrate that some strains ofE. coliappear to have evolved to become naturalized populations in the wastewater environment and possess a number of stress-related genetic elements likely important for survival in this nonhost environment. The presence of non-host-adapted strains in wastewater challenges our understanding of usingE. colias a microbial indicator of wastewater treatment performance, suggesting that theE. colistrains present in human and animal feces may be very different from those found in treated wastewater.