Title
Comparative genomics and phylogenetic assignment of Extraintestinal Pathogenic Escherichia coli
Degree Type
Dissertation
Date of Award
2018
Degree Name
Doctor of Philosophy
Department
Veterinary Microbiology and Preventive Medicine
Major
Microbiology
First Advisor
Catherine M. Logue
Second Advisor
Qijing Zhang
Abstract
Extraintestinal Pathogenic Escherichia coli (ExPEC) are a group of E. coli associated with disease outside the intestinal tract of the host. These organisms are known to cause a diversity of disease states in humans and animals. ExPEC are often divided into subpathotypes including Neonatal Meningitis E. coli (NMEC), associated with neonatal bacterial meningitis (NBM) in humans; uropathogenic E. coli (UPEC), associated with urinary tract infections in both humans and animals; and Avian Pathogenic E. coli (APEC), which causes colibacillosis in poultry. However, in vivo studies have demonstrated that the subpathotypes are more fluid than their names recognize. This work compares ExPEC subpathotypes to assess phenotypic and genomic differences amongst them. Specifically, differences between the subpathotypes are assessed via a phenotypic biofilm assay and polymorphisms in a known virulence factor, outer membrane protein A (OmpA). The results indicate that statistically significant similarities and differences were found between subpathotypes in their polymorphisms of OmpA and ability to form biofilms in certain media. Statistically significant differences were observed when the chromosomal differences of these E. coli are assessed via Clermont’s phylogenetic typing scheme. Both OmpA polymorphisms and biofilm formation results suggest that the phylogenetic groups are important when attempting to make generalizations about ExPEC subpathotypes. To examine an ExPEC subpathotype in greater resolution than traditional typing schemes allow, NMEC was chosen for a large sequencing study as NBM is a devastating disease that affects newborns resulting in sepsis and meningitis and mortality rate ranging from 15-40%. An examination of 58 NMEC genomic sequences found that NMEC had no conserved chromosomal type, as indicated via their serogroups, sequence types, phylogenetic groups, or identification of four NMEC clades based on the presence of conserved genes for each clade. Nineteen completed or nearly completed NMEC chromosomes concurred with this conclusion. An examination of NMEC plasmids revealed significant diversity among the Inc replicon types including the presence of Col replicons, yet IncFIB replicons were prevalent in most NMEC genomes. The NMEC sequencing data suggests that the NMEC subpathotype has considerable variation and that no strain should be considered prototypical.
Copyright Owner
Daniel Ward Nielsen
Copyright Date
2018-12
Language
en
File Format
application/pdf
File Size
204 pages
Recommended Citation
Nielsen, Daniel Ward, "Comparative genomics and phylogenetic assignment of Extraintestinal Pathogenic Escherichia coli" (2018). Graduate Theses and Dissertations. 17278.
https://lib.dr.iastate.edu/etd/17278
