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Host/niche adaptation and specificity in Escherichia coli Open Access


Other title
host specificity
Escherichia coli
logic regression
Type of item
Degree grantor
University of Alberta
Author or creator
Zhi, Shuai
Supervisor and department
Norman Neumann (School of Public Health)
Examining committee member and department
Linda Chui (Laboratory Medicine and Pathology)
Patrick Hanington (School of Public Health, University of Alberta)
Yutaka Yasui (School of Public Health, University of Alberta)
Paul Stothard (Department of Agricultural, Food and Nutritional Science )
Christopher Yost (Department of Biology at University of Regina)
School of Public Health
Public Health
Date accepted
Graduation date
2016-06:Fall 2016
Doctor of Philosophy
Degree level
Patterns of microbial host specificity have been observed at all host-related taxonomic levels, and several studies have demonstrated that Escherichia coli (E. coli) appears to display some level of host adaptation and specificity. Colonization of the gastrointestinal tract by E. coli largely depends on its ability to sense and respond to the physiological conditions of the gut - biological processes governed by the regulome. Consequently, it was hypothesized that genetic polymorphisms in the intergenic regions of the regulome may represent a unique target for assessing DNA sequence polymorphisms associated with host specificity. Supervised learning logic-regression-based analysis of DNA sequence variability in E. coli intergenic regions (ITGR) was used to identify single nucleotide polymorphism (SNP) biomarker patterns correlated with host origin. The results demonstrate that a significant proportion of the E. coli population found in a human/animal host appear to be host-specific. Various levels of host-specific information, as determined by sensitivity and specificity analysis, were encoded in different ITGRs, and not all ITGRs were informative across all animals examined. Whole genome discovery analysis revealed that certain ITGRs encode extremely high levels of host-specific information, reinforcing the finding that the majority of the E. coli populations from a particular animal are host-specialists. Moreover, an analysis of the genes regulated by these host-specific ITGRs revealed the selection forces potentially driving evolution of host-specificity. In E. coli derived from humans, many of the host-specific ITGRs regulated antibiotic resistant genes, whereas in cattle, ITGRs regulating environmental survival/stress genes were dominant. These bioinformatics tools were also used to assess whether certain populations of E. coli may have evolved to live outside their vertebrate host (i.e., water). To evaluate this, E. coli was isolated from chlorine-treated wastewater and subjected to ITGR logic regression-based biomarker analysis. Interestingly, wastewater E. coli was found to be genetically distinct from human and animal strains. Moreover, these strains were infrequently observed in other water matrices (i.e., groundwater, surface water), suggesting that these strains were specifically adapted to survive in a wastewater environment and not a ‘water-based’ environment. Many of these wastewater strains (~59%) possessed a genetic insertion element (IS30) located within the uspC-flhDC intergenic region, and for which a PCR assay was developed to identify these strains in environmental samples. The occurrence of these wastewater strains in the environment correlated with other known markers of sewage/wastewater pollution (i.e., Bacteroides). The identification of naturalized wastewater E. coli strains offered an excellent opportunity to further explore the adaptive phenotype/genotype characteristics that allow for survival of these strains in a non-host environment. This was important to address in the thesis since it is well known that the majority of DNA sequence variability in biological systems is non-adaptive. To provide evidence of adaptive evolution, wastewater strains were characterized for phenotypic/genotypic characteristics that might reveal life history strategies for survival in this unique matrix. Naturalized wastewater strains were shown to: i) be chlorine-tolerant, ii) be capable of robust biofilm production, iii) possessed a vigorous generalized stress response (RopS), iv) possessed universal stress protein genes (usp), and v) carried the locus of heat resistance – elements known to be important for survival of E. coli in the non-host environment. These strains were also shown to differentially survive through the wastewater treatment process. The findings presented in this thesis advance our knowledge regarding microbial evolution and host specificity, and the approaches developed can also be used to characterize sources of microbial contamination and protect public health from contaminated water and food.
This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for the purpose of private, scholarly or scientific research. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.
Citation for previous publication
Zhi S, Banting G, Li Q, Edge TA, Topp E, Sokurenko M, Scott C, Braithwaite S, Ruecker NJ, Yasui Y, McAllister T, Chui L, Neumann NF. 2016. Evidence of Naturalized Stress-Tolerant Strains of Escherichia coli in Municipal Wastewater Treatment Plants. Appl Environ Microbiol 82:5505-5518.Zhi S, Li Q, Yasui Y, Banting G, Edge TA, Topp E, McAllister TA, Neumann NF. 2016. An evaluation of logic regression-based biomarker discovery across multiple intergenic regions for predicting host specificity in Escherichia coli. Mol Phylogenet Evol 103:133-142.Zhi S, Li Q, Yasui Y, Edge T, Topp E, Neumann NF. 2015. Assessing host-specificity of Escherichia coli using a supervised learning logic-regression-based analysis of single nucleotide polymorphisms in intergenic regions. Mol Phylogenet Evol 92:72-81.

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