A Polyphasic Perspective on Escherichia coli Niche-Specificity: The Characterization of Naturalized, Wastewater-Specific E. coli and the Emergence of Wastewater Treatment Resistance in the Microbial World
Creators: Yu, Daniel
Publisher: name: University of Alberta Library
Year: 2024

<p>Although typically considered to be capable of colonizing and transiting between several different niches, evidence suggests that the Escherichia coli species exhibits a significant degree of host- and niche-specificity. This has led to the hypothesis that E. coli taxonomy may be more appropriately described using a ‘species-complex’ model, consisting of several distinct niche-specific groups known as ‘ecotypes’. While various microbial taxonomic schemes have been developed to date, current conventional microbial diagnostic and classification methods appear to be unsuitable for reliably identifying and differentiating between microbial ecotypic groups. <br>
Herein, we describe the application of a logic regression-based workflow for the discovery of putative E. coli ecotypes, and the subsequent polyphasic characterization of the specific genotypic, phenotypic, and ecotypic adaptations underlying their niche-specificity. Building on previous studies in our laboratory, logic regression was used to analyse the sequence variation contained within intergenic regions (ITGRs) across the E. coli genome. Reinforcing previous findings, logic regression modelling was found to generate highly niche-specific single nucleotide polymorphism (SNP) biomarkers across a wide range of host and environmental niches that not only appeared to demarcate putative E. coli ecotypes, but also could be used for the source (i.e., ecotype) attribution of unknown environmental strains. Interestingly, in addition to being effective for differentiating between host-associated E. coli ecotypes, logic regression also consistently distinguished wastewater-derived strains from their host-associated counterparts, suggesting they may represent a unique E. coli ecotype adapted to engineered environments as primary niches. <br>
Through a polyphasic approach, various characteristics underlying this ‘naturalized-engineered’ ecotype were identified. Wastewater- and meat plant-derived strains were found to group into naturalized-engineered-associated sequence types (ST635 and ST399) and several serotypes, representing distinct lineages that may have independently emerged across food- and water-associated engineered environments. Strains belonging to these naturalized-engineered ecotypic groups were characterized by unique genetic traits, as they were enriched in genes and genetic markers associated with biofilm formation, microbial defense, and stress resistance (i.e., against DNA-damaging stimuli, oxidizing agents, heat, heavy metals), but lacked host-adaptive genes related to colonization and virulence. Recapitulating these genotypic findings, wastewater-specific (WWS) E. coli strains were also characterized by various phenotypic adaptations that could promote their survival across the wastewater treatment train, including enhanced resistance to heat, slower growth kinetics, and enhanced biofilm formation under nutrient-limiting and low temperature conditions. <br>
As such, with the WWS strains as a model system, we were able to demonstrate the utility of our logic regression-based, polyphasic workflow for the exploration of putative ecotypes within the E. coli species. While these findings have important conceptual implications for prokaryotic taxonomy, especially in how bacterial species may be defined, the characterization of a wastewater treatment resistant ecotype implies that other E. coli populations could also be evolving resistance to wastewater disinfection. Reflecting this, comprehensive comparative genomic approaches revealed that other, non-naturalized wastewater-derived E. coli strains surviving wastewater treatment were virtually identical to clinically relevant extraintestinal pathogenic E. coli (ExPEC) strains. Our findings, therefore, also point to a concerning public health prospect – that pathogenic microbes could similarly be evolving resistance to wastewater treatment and disinfection. </p>