Date of Award

Spring 5-10-2019

Document Type


Degree Name

Master of Biological Science (MBioSci)



First Advisor

Dr. Anuradha Ghosh

Second Advisor

Dr. James Whitney

Third Advisor

Dr. Duane Whitback


The goals of this study is two-fold. The first part investigates bacterial isolates from commercial poultry feed and the second part deals with bacterial isolates recovered from retail food. In order to reduce pathogen contamination in poultry products identification of overall microbial populations in poultry production processing steps have always been considered an important monitoring tool for assessing sanitizer effectiveness and the corresponding responses of bacteria load levels on poultry carcasses. Bacterial isolates recovered from corn-based chicken feed were purified on aerobic plate count agar and eleven morphologically different colonies were selected for whole genome sequencing. In this part, the objectives were to: 1. sequence, assemble, and annotate the whole genome of these isolates, 2. compare the genomic profile among these isolates. Whole genome sequencing (WGS) was performed using Illumina MiSeq platform. Genome assembly was carried out via SPADeS; quality was checked via Quast; and annotation was achieved via PROKKA. The isolates were identified as Kosakonia cowanii (3), Enterococcus gallinarum (2), Klebsiella variicola (2), and Pantoea vagans (2), and Stenotrophomonas spp. (2) The total %GC content of these bacteria ranged between 53 and 57; whole genome length was calculated as 4.8-5.7 X 106 bases; number of rRNA molecules were found to be 8-14; and total protein coding sequences were up to 5500. The data obtained from this study would help in identifying characteristics of a hygeinic indicator organism in the poultry processing pipeline and thus reinforce applciaitonnof WGS in food safety. For the other part of the study, potential pathogenic bacterial isolates were recovered from retail food. An array of biochemical tests were performed to characterize a total of twenty isolates: set of Gram positive (E. coli and Salmonella) and gram negative (Enterococcus faecalis/faecium and Staphylococcus aureus) strains. The objective of this part was to identify combination of biochemical tests that will effectively differentiate potential food-borne pathogens at the strain level. For the tests, catalase, lactose fermentation, bile esculin hydrolysis, and nitrate reduction, statistically significant differences were noticed among these two groups. A handful of tests were found to differential between strains of E. coli: hemolysis on phenylethyl blood agar, Mueller tellurite reduction, Salmonella: maltose and mannose fermentation, Enterococcus faecium/faecalis: sucrose fermentation and Staphylococcus aureus: bile esculin. The outcome from this part of the study will help in combining specific biochemical tests with molecular diagnostic tools for rapid identification of foodborne pathogens.



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