Genetic analysis of strain differences in the fish pathogen Yersinia ruckeri

This thesis is an investigation of molecular typing techniques to assess variation among different strains of Y. ruckeri. Analysis of the 16S rRNA, glnA, and gyrB partial genes using denaturing gradient gel electrophoresis (DGGE), demonstrated that these housekeeping genes were too conserved to be useful targets for differentiation. Different positions of the 16S rRNA genes in Y. ruckeri were detected by use of Southern blots, and the different patterns generated were used to group strains. Targeting the 16S-23S internal transcribed spacer (ITS) yielded differentiation in product size when seen on agarose and DGGE gels, but DNA sequences among these strains were also too uniform to be useful for differentiation. PCR-amplification of Enterobacterial repetitive intergenic consensus (ERIC) and repetitive extragenic consensus (REP) sequences showed variations in both agarose and DGGE gels. For ERIC sequences, 6 different banding patterns were obtained on agarose gels, which were further differentiated into a total of 11 patterns by DGGE analysis. The REP sequences provided 4 different banding patterns on agarose gels, and 8 patterns on DGGE. When analyzed, the patterns did not group strains based on any known phenotypic trait, with the exception of some similarities between serotypes.