Document Type


Degree Name

Master of Science (MSc)



Program Name/Specialization

Integrative Biology


Faculty of Science

First Advisor

Dr. Robin M. Slawson

Advisor Role



Recent studies suggest the potential exists for enteric microorganisms to become “naturalized” to the complex natural environment through maintenance of their populations via replication and adaptation to the stress imposed by their external surroundings. The aim of this research was to better understand the potential for antimicrobial resistant (AMR) Salmonella to become “naturalized” and the physiological adaptations that allow for non-host survivability as reflected by AMR and community profiling. To better elucidate the prominent factors leading to a “naturalized” condition, two approaches were taken: 1) survey-based field research to gain perspective on the prevalence of AMR Salmonella isolated from variously impacted water sources; a local watershed, a constructed wetland for the treatment of human waste, and a wastewater treatment facility, and 2) bench-scale batch microcosm systems to monitor Salmonella survival in environmentally-relevant conditions including three temperatures 4oC, 12oC and 22oC. An integrative approach to phenotypic (culture-based) and genotypic (molecular-based) analysis was taken to profile test microorganisms at multiple levels. Specifically, quantitative PCR (qPCR) was used to enumerate pathogen removals from the environment and AMR analysis was conducted for resistance profiling against 12 antibiotics. The functional and structural fingerprints of the communities harbouring Salmonella were investigated by community-level physiological profiling (CLPP) and denaturing gradient gel electrophoresis (DGGE), respectively. The relative abundance of Salmonella was comparable to concentrations of E. coli within all impacted water sources (on average ranging from 103 to 105 gene copies/ 100 mL) and did not appear to be influenced by seasonality. The natural hardiness of environmental Salmonella was exemplified by high percent resistance occurrence levels (average between 20% and 40%) observed in these same waters. Microcosm study results indicated that Salmonella persistence was not dependent on temperature when interspecies diversity was a factor and that changes in Salmonella AMR levels in the absence of antimicrobial exposure were likely stress-induced. From both field study and microcosm results, functional and structural fingerprinting of microbial communities revealed that AMR Salmonella was harboured in both genetically and metabolically diverse communities, including communities demonstrating high metabolic versatility but low genetic diversity. Therefore, AMR levels of Salmonella derived from different community situations may be a consequence of both increased opportunities for the exchange of genetic material in healthy communities, and a stress response within low-integrity communities. Collectively, these findings suggest that the response of Salmonella to environmental stress not only dictates its ability to survive in non-host environments, but also impacts its phenotypic expression of AMR. This information is important with regard to the “naturalization” potential of Salmonella upon dissemination into the open environment following release from a host and the risk implications to public health.

Convocation Year


Convocation Season