Date of Award


Document Type

Doctoral Thesis

Degree Name

Doctor of Philosophy


Biological Sciences

First Advisor

Dr. Séamus Fanning


This study was undertaken to evaluate various molecular techniques for the analysis of Gram negative bacterial associated epidemics. The first investigation dealt with bovine mastitis outbreaks, where the causative agent was identified as Pseudomonas aeruginosa. Epidemiological findings, suggested that all herds were infected from teat wipes that were contaminated with this organism. Initial investigations using the polymerase chain reaction (PCR), indicated a possible clonal relationship between all outbreak linked strains, with one exception. This finding was confirmed following pulsed-field gel electrophoresis (PFGE) and ribotype analysis. PCR was again employed to study a rather unusual epidemic, involving Salmonella tel-el-kebir over a six-month period. All patients were owners of, or in close contact with, pet terrapins. DNA amplification fingerprinting of organisms isolated from patients and terrapins, confirmed the clonality of all isolates involved.

Recently Salmonella enterica serotype Typhimurium, phage type definitive type (DT) 104, has emerged as an epidemic strain world-wide. In this study 226 randomly collected strains of S. Typhimurium from the Cork region of southern Ireland, were analysed based on their phenotypic and genotypic characteristics. The majority of these isolates were phage typed as DTI 04 and were resistant to five or more antimicrobials, including ampicillin, chloramphenicol, streptoymycin, sulphonamide and tetracycline. Antibiotic resistance is often disseminated on R- plasmids and transposons. Recently a third mechanism was described involving a novel group of naturally occurring mobile genetic element, integrons. Gene cassettes form part of the latter structure containing one or more open reading frames (ORF) encoding antimicrobial resistance genes. Several gene cassettes were characterised by automated DNA sequencing methods. These data were then used to generate specific DNA probes to map the corresponding resistance genes to regions of the S. Typhimurium genome. Macrorestriction enzyme analysis using Xbal identified a conserved 10 kbp multiresistance gene cluster or “resistance island” in DTI 04 isolates of R-type ACSSuT. Larger clusters were detected in DT104 and non-DT104s additionally resistant to other antimicrobials.

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