Date of Award

12-2014

Degree Type

Dissertation

Degree Name

Doctor of Philosophy

Major

Food Science and Technology

Major Professor

Irene B. Hanning

Committee Members

Jun Lin, David Golden, P. Michael Davidson

Abstract

Whole genome sequencing (WGS) is the most discriminatory of typing methods and can provide additional information including virulence, antigen targets for vaccine development, and antimicrobial resistance profiles. The first part of this study aimed to determine the application of WGS as a genotyping method for Campylobacter by comparing WGS to two commonly used genotyping methods, Pulsed-field gel electrophoresis (PFGE) and flaA typing. Five Campylobacter strains isolated from conventional and organic poultry, and five additional isolates with published genomes were compared using the three methods. A total of 8 PFGE patterns and 8 flaA alleles were identified from the 10 strains. Not surprisingly, WGS was more discriminatory than the other two methods and identified distinct differences among all ten isolates including genome size, G-C% content, and distribution of genes. Additionally, WGS revealed a number of virulence factors, including antibiotic and heavy metal resistance. Interestingly, genes coding for resistance to antibiotics were present in both conventional and organic isolates, but only conventional isolates possessed resistance to arsenic. The second part of this study aimed to understand the differences in resistance in organic and conventional isolates and determine if roxarsone, an organoarsenical coccidiostat used in poultry production, selected for arsenic resistance in Campylobacter. Eighty-two isolates of Campylobacter were collected from 246 retail organic and conventional chickens from 2009 to 2010 prior to the roxarsone withdrawal. In 2013 and 2014, an additional 65 isolates were collected from 120 retail organic and conventional chickens, after the roxarsone withdrawal. PCR determined the presence of arsenic resistance (ars) genes arsC, acr3, arsB, arsP, and arsR and agar dilution MICs were conducted to determine levels of resistance. Presence of arsP, arsC, and acr3 were significantly correlated to isolates from conventional chickens pre-roxarsone withdrawal (Pre-RW) and these isolates had higher resistance to all arsenic compounds tested, compared to those from organic. Post-RW isolates retained arsenic resistance genes, but an overall reduction in arsenate and roxarsone MICs was observed. It appears that despite the removal of the selective pressure of roxarsone, Campylobacter retains genes that confer arsenic resistance.

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