REARRANGEMENT HOT SPOT (rhs) GENES ARE POTENTIAL MARKERS FOR MULTILOCUS SEQUENCE TYPING OF ESCHERICHIA COLI O157:H7 STRAINS

Open Access
Author:
Liu, Kuanqing
Graduate Program:
Food Science
Degree:
Master of Science
Document Type:
Master Thesis
Date of Defense:
June 05, 2009
Committee Members:
  • D Edward G Dudley And Dr Stephen J Knabel, Thesis Advisor
  • Edward G Dudley, Thesis Advisor
  • Stephen John Knabel, Thesis Advisor
Keywords:
  • multilocus sequence typing
  • E. coli O157:H7
  • rearrangement hot spot (rhs)
  • phylogeny
  • molecular subtyping
Abstract:
Escherichia coli O157:H7 is an important foodborne pathogen, notorious for its low infectious dose and its capacity to cause severe diseases such as hemorrhagic colitis and hemolytic uremic syndrome. Molecular subtyping methods are powerful tools for microbial source tracking during outbreaks. Pulsed-field gel electrophoresis is currently the “gold standard” molecular method for subtyping E. coli O157:H7, however, a sequence-based scheme such as multilocus sequence typing would provide a less ambiguous and more rapid, cost-effective, and portable method. Previous publications reported that the genomes of E. coli O157:H7 contain genes that are highly conserved between strains. This hindered the development of an effective MLST scheme for subtyping E. coli O157:H7. In this study, several rhs genes were targeted, which were recently shown to be under the strongest positive selection of genes encoded within the E. coli genome. Eighteen E. coli O157:H7 strains from Lineage I and II, and 15 E. coli O157:H7 strains from 8 clades were included. Examination of these rhs genes revealed 44 polymorphic loci (PL) and 10 sequence types (STs) among the 18 lineage-strains, and 280 PL and 12 STs among the 15 clade-strains. Phylogenetic analysis using rhs genes generally agreed with the Lineage I and II classification defined previously. This study also showed E. coli O157:H7 strains from Clade 8 fall into Lineage I/II. Additionally, unique markers were found in rhsA and rhsJ that might be used to define Clade 8 and Clade 6. Therefore, rhs genes may be useful in discriminating strains and determining the phylogeny of E. coli O157:H7.