Assessing host-specificity of Escherichia coli using a supervised learning logic-regression-based analysis of single nucleotide polymorphisms in intergenic regions

Zhi, Shuai; Li, Qiaozhi; Yasui, Yutaka; Edge, Thomas A.; Topp, Edward; Neumann, Norman F.

doi:10.1016/j.ympev.2015.06.007

Cited by 22 publications

(48 citation statements)

References 45 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…coli isolates were sourced from three bacterial libraries originally established from the following geographically disparate areas of Canada: (i) the Hamilton/Toronto region of Ontario, as described by Edge and Hill (23); (ii) Ottawa (Ontario), Lennoxville (Quebec), and Brandon (Manitoba), as described by Lyautey et al (24); and (iii) Alberta, as described by White et al (25) (bovine isolates) and Zhi et al (20) (human isolates). For further details regarding bacterial libraries, please refer to the work of Zhi et al (20). …”

Section: Methodsmentioning

confidence: 99%

“…coli isolates, we used a maximum likelihood phylogenetic analysis of the following three intergenic regions: (i) uspC-flhDC , (ii) csgBAC-csgDEFG , and (iii) asnS-ompF . The selection of these regions was based on our previous publications, in which host-specific SNP biomarkers were identified in these three intergenic regions across 15 animal species (20) and these intergenic sequences correlated with adaptive phenotypes in E. coli (25).…”

Section: Methodsmentioning

confidence: 99%

“…coli isolates, we used a novel logic regression-based biomarker approach described by Zhi et al (20) to identify SNP patterns in intergenic regions ( csgBAC-csgDEFG and asnS-ompF ) that were highly specific to wastewater E. coli isolates.…”

Section: Methodsmentioning

confidence: 99%

“…Recently, we identified single nucleotide polymorphic (SNP) biomarkers of host specificity in E. coli isolates from 15 different human and animal species by using logic regression modeling of intergenic DNA sequences (20). In preliminary experiments evaluating these host-specific biomarkers of E.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Evidence of Naturalized Stress-Tolerant Strains of Escherichia coli in Municipal Wastewater Treatment Plants

Zhi

Banting

et al. 2016

Appl Environ Microbiol

Self Cite

View full text Add to dashboard Cite

Escherichia 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 (IS30) located within the uspC-flhDC intergenic region. The positional location of the IS30 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 IS30 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 IS30 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.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Evidence of Naturalized Stress-Tolerant Strains of Escherichia coli in Municipal Wastewater Treatment Plants

Zhi

Banting

et al. 2016

Appl Environ Microbiol

Self Cite

View full text Add to dashboard Cite

show abstract

“…Previously, the authors characterised the occurrence of host-specific strains of E. coli in a variety of human and animal isolates by using logic regression analysis of intergenic deoxyribonucleic acid (DNA) sequences (Zhi et al, 2015(Zhi et al, , 2016a. The authors applied these novel bioinformatic tools to understand E. coli population genetics better in non-host environments, such as waste water, leading to the discovery of naturalised strains of E. coli in municipal waste water (Zhi et al, 2016b).…”

Section: Introductionmentioning

confidence: 99%

Stress resistance in naturalised waste water E. coli strains

Zhi

BantingGraham

RueckerNorma³

et al. 2017

Journal of Environmental Engineering and Science

Self Cite

View full text Add to dashboard Cite

The authors recently demonstrated that naturalised strains of Escherichia coli exist in municipal waste water, characterised by (a) biomarker patterns in intergenic regions distinct from human and animal E. coli strains and (b) an insertion element (IS30) located in the uspC-flhDC intergenic region of the genome. Remarkably, these strains are naturally adapted to survival and growth in waste water and differentially survive the treatment process. The authors sought to explore the adaptive mechanisms used by these strains for survival. A serial stress experiment (nutrient deprivation and osmotic stress followed by chlorine treatment) was performed and survival was measured using culture. Waste water strains were shown to be approximately 100 times more resistant to chlorine treatment than a wild-type human faecal strain. Naturalised waste water strains were also more robust at producing biofilmsan adaptive strategy for surviving environmental stressors. Since biofilm formation has been linked to increased motility, the authors examined the expression of the flagellar regulator gene, flhDC, under serial stress conditions. Chlorine was a potent inducer of flhDC expression in waste water strains. The results demonstrate that waste water strains possess adaptive genotypic/phenotypic properties related to their survival in waste water and challenge the understanding of treatment reduction based on E. coli as an indicator of treatment performance.

show abstract

Identification of interactions of binary variables associated with survival time using survivalFS

et al. 2019

View full text Add to dashboard Cite

Assessing host-specificity of Escherichia coli using a supervised learning logic-regression-based analysis of single nucleotide polymorphisms in intergenic regions

Cited by 22 publications

References 45 publications

Evidence of Naturalized Stress-Tolerant Strains of Escherichia coli in Municipal Wastewater Treatment Plants

Evidence of Naturalized Stress-Tolerant Strains of Escherichia coli in Municipal Wastewater Treatment Plants

Stress resistance in naturalised waste water E. coli strains

Identification of interactions of binary variables associated with survival time using survivalFS

Contact Info

Product

Resources

About