Abstract

BALBIN, MICHELLE MACUGAY. Surveillance and Development of Detection Platform for Antimicrobial Resistance and Pathogenic Bacteria. (Under the direction of Dr. Siddhartha Thakur). The study aimed to identify the antimicrobial resistance (AMR) determinants and virulence factors in Salmonella spp. and Escherichia coli from different anthropogenic areas in North Carolina. Soil samples were collected from different anthropogenic areas: urban and natural. Minimum inhibitory concentration (MIC) was determined by using the broth microdilution method. Whole genome sequencing and analysis were done to identify the AMR determinants and virulence factors among the isolates. The urban environment was observed to have a higher prevalence of Salmonella spp. and E. coli. The Salmonella spp. isolates showed resistance to Sulfisoxazole and Streptomycin, while E. coli was resistant to Sulfisoxazole, Cefoxitin, and Ampicillin. The WGS analysis identified Salmonella serotypes Schwarzengrund and Mississippi. Aminoglycoside resistance genes and IncFIB and IncFIC(FII) plasmids were detected among Salmonella spp. In general, E. coli was predominated by isolates from phylogroup B1, B2, and D. Multidrug transporter mdfA gene was detected in most of the E. coli from the natural and in all isolates from the urban environment. FosA7 gene was detected in an isolate from a residential yard. The pCoo and pB171 plasmids were detected in urban, while col 156 and pHN7A8 plasmids were detected in natural environments. The detection of AMR determinants and virulence factors in these bacteria is significant in understanding the occurrence and even the development of AMR. The presence of these determinants in different anthropogenic areas only suggests that there is still more in the environment and the need for continuous AMR surveillance. There are several laboratory techniques used in the research and surveillance of bacterial pathogens such as Salmonella spp. and antimicrobial resistance (AMR). However, these techniques require expensive laboratory facilities and highly trained individuals, creating a gap in surveillance and research especially in developing counties. Therefore, there is a need to develop a simple, rapid, specific, sensitive, and low-cost detection platform that can be used in field testing or laboratories with lesser capabilities. Gold nanoparticles (AuNPs) are widely used in nanosensors due to their tunability, biocompatibility, and optical properties, particularly surface plasmon resonance. We designed and performed a simple, rapid, sensitive, specific, and cost-effective detection platform using functionalized AuNPs based on colorimetric assay. In this study, we describe an enzyme-free detection method of bacterial pathogen using DNA functionalized AuNPs. Our method directly detected the Salmonella spp. extracted genomic DNA without prior amplification or the use of enzymes. Moreover, each step in the described method does not require expensive instruments. This detection method can be easily performed in a water bath or heat block and the results can be observed by the naked eye, eliminating the need to perform gel electrophoresis. This method can be completed within 45