Evidence of Naturalized Stress-Tolerant Strains of Escherichia coli in Municipal Wastewater Treatment Plants
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abstract
ABSTRACTEscherichia coli
has been proposed to have two habitats—the intestines of mammals/birds and the nonhost environment. Our goal was to assess whether certain strains of
E. coli
have evolved toward adaptation and survival in wastewater. Raw sewage samples from different treatment plants were subjected to chlorine stress, and ∼59% of the surviving
E. coli
strains were found to contain a genetic insertion element (IS
30
) located within the
uspC-flhDC
intergenic region. The positional location of the IS
30
element was not observed across a library of 845
E. coli
isolates collected from various animal hosts or within GenBank or whole-genome reference databases for human and animal
E. coli
isolates (
n
= 1,177). Phylogenetics clustered the IS
30
element-containing wastewater
E. coli
isolates 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 the
fimH
marker. Our data suggest that wastewater contains a naturalized resident population of
E. coli
. We developed an endpoint PCR targeting the IS
30
element within the
uspC-flhDC
intergenic region, and all raw sewage samples (
n
= 21) were positive for this marker. Conversely, the prevalence of this marker in
E. 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.
IMPORTANCE
The results of this study demonstrate that some strains of
E. coli
appear 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 using
E. coli
as a microbial indicator of wastewater treatment performance, suggesting that the
E. coli
strains present in human and animal feces may be very different from those found in treated wastewater.
