Document Type


Degree Name

Master of Science (MSc)



Program Name/Specialization

Integrative Biology


Faculty of Science

First Advisor

Dr. Gabriel Moreno-Hagelsieb

Advisor Role



Bacterial human pathogens are among the leading causes of death around the world, especially in low income and developing countries. One important element in a bacterium’s ability to cause disease are genes that directly contribute to pathogenicity called virulence factors. A second significant aspect are antimicrobial resistance genes which allow microorganisms to persist in the presence of antimicrobial agents. In this project I aimed to determine if Salmonella isolated from different sources differed in pathogenicity profiles based on the complement of genes identified through genomic analysis. Accordingly, Salmonella genomes were organized into 8 groups: animal, clinical, human, environmental, food, water source, plant, and nut. A negative control, consisting primarily of non-pathogenic E. coli, was also included. To determine disease-causing potential, the proteins encoded by these genomes were compared against the Virulence Factor Database (VFDB), the PathFam database, and the Comprehensive Antimicrobial Database (CARD). The negative controls coded for significantly fewer proteins matching the VFDB and PathFams, but significantly more matching the CARD, than all other groups. Though visibly overlapping, most isolation sources were found to be significantly different to each other (p value < 0.05), aside from the very small nut and plant groups. When clustered by their specific matches to the VFDB and CARD, genomes from the same environmental groups did not cluster together. Therefore, while the groups were statistically different from each other in number of matches, those differences were not due to group-specific virulence factors. Though most isolation source groups were found to be significantly different in VFDB, CARD and PathFam matches, further analyses are needed to determine if that difference is large enough to influence Salmonella’s disease-causing potential. Methods and results from this analysis can be built upon in the future to better identify potential pathogens isolated from different environments.

Convocation Year


Convocation Season