Browsing by Author "Hanlon, Keelyn E."
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Item Evaluation of the fresh beef bacterial community through processing retail display conditions using 16S rRNA gene amplification sequencing(2019-12) Hanlon, Keelyn E.; Miller, Markus F.; Brashears, Mindy M.; Legako, Jerrad F.; Presley, Steven M.; Sánchez-Plata, Marcos X.; McCann, Joshua C.Microorganisms are ubiquitous and provide challenges in the food production system. Beyond monitoring for pathogens or food safety hazards, there is a need for understanding and controlling spoilage organisms, and indicators of potential spoilage especially with products that have a more limited shelf-life, such as fresh meat. Arguably, just as important, yet less widely studied is the presence and behavior of the natural product microbial community. This project was composed of two phases, one with whole muscle steaks, and another with ground beef. Both employed 16S rRNA sequencing to better understand the bacterial community in fresh beef. The overall objective was to characterize the microbial community in fresh beef from the U.S. and understand how packaging environment and retail display influence changes or shifts in the community. The first project evaluated the microbial community of beef steaks subjected to four different packaging environments widely used in the beef industry and to one of three different retail display conditions. The second project evaluated the bacterial community present in commercially ground beef that either had or had not been exposed to lactic acid as beef trim, after three chub storage aging periods and retail display. For the microbial community evaluation DNA extractions were performed prior to 16S rRNA sequencing on the V3-V4 region. Data processing and filtering were performed with the DADA2 package in R. Analysis was performed on relative abundance, alpha diversity, and beta diversity values. Dominant phyla in both studies were Proteobacteria and Firmicutes. Commonly identified genera at end of retail display of fresh beef steaks included Carnobacterium, Pseudomonas, and Lactobacillus. At the phyla level, lighting and packaging type did not have a significant effect on relative abundance. There were, however, some indications that lighting had an effect on some of the genera. With retail steaks, this study provided some evidence that light exposure of packages may have an impact on the genera found on fresh beef steaks. Ground beef, from untreated trim, bacterial richness was found to decrease with retail display time. From this study it was determined that an antimicrobial dip, in combination with chub storage age and retail display, can influence the microbial community of ground beef.Item Presence of salmonella, escherichia coli O157 and campylobacter in small-ruminants(2015-12) Hanlon, Keelyn E.; Miller, Markus F.; Brashears, Mindy M.; Brooks, J. ChanceMeat derived from goats and lambs is an important and often underappreciated protein source in the U.S., but it is especially important in developing countries challenged with food insecurity. While extensive studies have been conducted examining pathogen prevalence in beef, pork and poultry species, less research is available about pathogen presence in small-ruminants. In developing countries, small-ruminants often co-exist with humans in living and work conditions, making cross contamination and frequent contact with fecal matter a common occurrence. In the U.S., the popularity of small ruminants as a protein source is growing. Additionally, many small-ruminants are considered pets presenting potential pathogen exposure to family members. Salmonella, Campylobacter and Escherichia coli O157 are all pathogens of concern known to be found in livestock. Understanding the presence of these pathogens in small-ruminants can influence processing method improvements for these species to minimize food safety risks. This study had three main objectives: 1) To determine pathogen prevalence in small-ruminants on hide and fecal samples collected from U.S. and international sources; 2) Salmonella prevalence in small-ruminant carcass surface and retail samples from the U.S. and international sources; and 3) Salmonella prevalence found in lymph nodes from sheep and goats. Samples were collected at abattoirs and farms located in California, New Mexico, Texas, the Bahamas and Mexico over a 14 month period. Samples were processed using a combination of traditional culturing methods and real-time PCR. All presumptive positive samples were confirmed by isolation and biochemical analysis. Campylobacter, E. coli O157 and Salmonella were detected in samples collected from both sheep and goats. Salmonella was detected in 17.11% of hide samples, 13.91% of fecal samples, 16.82% of retail samples, and 1.94% - 9.62% of lymph nodes and up to 5.20% on carcass surfaces. E. coli O157 was present in 1.50% of hide samples and 15.30% of fecal samples. Campylobacter was found in 80.68% of fecal samples. The results indicate the presence of potential pathogens from small-ruminant sources. Further study of the trends of these pathogens through season, geographical location and management conditions, as well as control measures, are important to better understand the risks associated with these pathogens present in small-ruminants.