Slush-ice chilling has been applied to catfish fillets by processors for several years. However, little is known about the effect of this system on fillets’ safety and quality. Salmonella counts were reduced (P≤0.05) between 0.55 - 0.83 log CFU/g by slush ice treatments (0% - 4.5% salt), regardless of salt concentration. Salmonella counts for slush ice treated fillets were less (P≤0.05) than for untreated fillets during refrigerated storage. However, Salmonella reduction was similar (P>0.05) among all treatments after 12 days of storage. Sensory evaluation showed that a 24 h-slush-ice treatment negatively affected (P≤0.05) the texture, drip, and odor of fillets during storage at 2 ± 2°C. Lightness (61.7), hue (80.6), and chroma (10.1) values were similar (P>0.05) between slush-ice fillets and water-chilled fillets. Psychotrophs, coliforms, and E. coli counts (5.1, 1.6 and /g, respectively) were similar (P>0.05) among fillets collected before and after 24 h in slush ice.

The prevalence of Salmonella within poultry environments and on poultry products has been well documented. However, there has not been a study documenting the effect of utilizing used litter in newly constructed commercial broiler houses on Salmonella status or on the rate and source of Salmonella contamination within new houses. Objectives of this study are to 1) determine environmental source and rate of Salmonella spp. colonization in two newly constructed broiler houses 2) to evaluate the effect of mixing used broiler litter with clean litter in a new broiler house. Results of this study suggest that Salmonella contamination of the poultry house environment occurred within the first 2-4 weeks of bird placement and that the source of contamination may have been the chicks themselves. Litter inoculation may be beneficial in reducing Salmonella levels within the first flock if it is known that the chicks are already contaminated with Salmonella spp.

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Bacteriophage Felix O1, also known as enterobacteria phage O1, has been used to type Salmonella Typhi and is an excellent candidate for use in bioremedial and therapeutic applications. It has extremely high intra-species specificity and is strictly virulent in nature, unable to undergo lysogeny. To facilitate the development of the bacteriophage for use in these areas, the full sequence of the genome had been elucidated previously. In this work, identification and classification of functional coding sequences via reverse transcriptase-polymerase chain reaction was performed. All of the 115 putative open reading frames (ORFs) studied were found to be functional. 53.0%, 9.6%, and 18.3% of the ORFs investigated were found to initiate expression early, middle or late in the lytic cycle, respectively. Expression of the remaining 19.1% ORFs was evident when the amount of total RNA was increased and when samples were taken at a later time point. Comparisons between bacteriophage Felix O1 and the phage with the most shared homologs, phage T4, revealed many similarities in times of gene expression. / Master of Science

Tomato fruit have been associated with numerous outbreaks of salmonellosis in recent years. Trace back suggests tomato fruit may become contaminated during pre-harvest, however exact routes are unclear. The objective of this study was to determine the potential for Salmonella enterica serotype Newport to be associated with the roots, leaves, stems, and ultimately fruit of red round tomato plants through contaminated irrigation water, at various stages of plant development, when grown under controlled environmental conditions. Tomato plants were individually root irrigated with 250 or 350 ml (depending on growth stage) of 7 log CFU/ml S. Newport contaminated irrigation water every seven days. Presence of the pathogen in plant tissue was evaluated at five growth stages; 14 days post transplant, early fruit, mid fruit, full fruit, and terminal stages. At each stage, roots, stems, leaves, and two tomato fruit, if present, from four S. Newport and four water irrigated (negative control) tomato plants were sampled for S. Newport contamination. Association of S. Newport was detected in tomato roots and stems using both conventional plating and molecular techniques. Twenty-four samples were confirmed positive for S. enterica using PCR. Sixty-five percent of the roots, 40% of the stems, 5% of the leaves and 5% of the fruit sampled were confirmed to contain S. enterica. Overall, there was significant difference in the presence of S. Newport according to tissue sampled (roots > stems > leaves and fruit) (P > 0.05). There was no correlation between growth stage and presence of S. Newport in tissues (P > 0.05). Ultimately, irrigation with S. Newport has a low probability of contaminating tomato fruit. / Master of Science

Salmonella enterica serovar Typhimurium (S. Typhimurium) is an important human pathogen. The Centers for Disease Control and Prevention (CDC) estimates that 1,027,561 people become ill with nontyphoidal Salmonellosis annually, and S. Typhimurium is one of the most common disease causing serovars. Quantification of the true number of cases of salmonellosis is hampered by the presence of a carrier state. These carriers are animals and humans that carry the pathogens for a variable period of time without showing any clinical signs. One of the biggest barriers to controlling and preventing salmonellosis in a population is identification of these carriers. Identifying these latent carriers of chronic infections is vital to preventing such disease transmission and creating avenues for novel control and treatments. In my dissertation research, we developed a cell culture model to study latent Salmonella infections. By activating human monocytes with retinoic acid and vitamin D3, we were able to isolate Salmonella from such cells 45 days after inoculation. We subsequently used this model to identify genes that were upregulated in this chronic infection model. We found that aceA, a gene that codes for isocitrate lyase, is significantly upregulated on days 10 and 30 post infection. Isocitrate lyase is part of the glyloxylate cycle. Some bacterial species have developed a mechanism to utilize acetone as a carbon source to synthesize tricarboxylic acid (TCA) cycle intermediates. This anaplerotic reaction allows organisms to conserve carbon and use alternative carbon sources. This cycle is one way in which bacteria can adapt and survive in an intracellular environment. This intracellular survival is key to latent infections persisting within a host. It is biologically plausible that, in order to survive in a latent state, S. Typhimurium would up-regulate genes that would facilitate intracellular survival. After establishing the cell culture model, we tested the hypothesis that aceA is upregulated in latent infections of S. Typhimurium in a mouse model. We orally challenged mice that were resistant to Salmonella infection, collected their feces, and collected tissue specimens at several time points up to 135 days post-challenge. These samples were cultured and tested using quantitative polymerase chain reaction (qPCR). The qPCR results showed that tissue samples from inoculated mice had increased aceA expression 95 days after challenge. Finally, we examined whether aceA expression could be detected in cattle lymph node samples. Supra-mammary lymph nodes from 40 dairy cattle and mesenteric lymph nodes from 100 culled cattle were sampled and submitted for culture and qPCR. None of the supra-mammary lymph nodes were positive for Salmonella via culture or aceA qPCR; however, 11 mesenteric lymph nodes showed increased aceA expression in qPCR compared to 5 culture positive lymph nodes. Further research is necessary, but these results demonstrate some of the advantages of using genetic primers to identify latent Salmonella infections in clinically normal cattle. In addition, the assay may be able to differentiate between latent and active salmonellosis, and could be used to provide targeted drug delivery. / Doctor of Philosophy / Salmonella enterica serovar Typhimurium (S. Typhimurium) is an important human pathogen. Determining the true number of cases of salmonellosis is made more difficult because of the presence of a carrier state. These carriers are animals and humans that carry the pathogens for a variable period of time without showing any clinical signs. Identifying these latent carriers of chronic infections is vital to preventing such disease transmission and creating avenues for novel control and treatments. In my dissertation research, we looked at genetic markers from an offshoot of the TCA cycle, the glyoxylate pathway. We used these markers to test the hypothesis that these glyoxylate pathway genes would be upregulated in latent S. Typhimurium infections. Our research involved developing a cell culture model, then using the results from the cell culture model to inform a mouse model, and then a cattle lymph node diagnostic study. The cell culture model indicated that the gene for isocitrate lyase, aceA, is significantly upregulated compared to housekeeping genes. We found the presence of aceA in chronically infected mice, as well as cattle lymph node samples. Further research is necessary, but these results demonstrate some of the advantages of using genetic primers to identify latent Salmonella infections in clinically normal cattle.

Current detection methods require at least one 24-48 hour enrichment step for the detection of Salmonella. This poses a problem because product often needs to be shipped before microbial contamination levels can be adequately ascertained. Therefore, the need for more rapid methods of Salmonella detection becomes apparent. The purpose of this thesis was to determine if an immunologically-based method, Immunomagnetic Capture(IMC) -ELISA and molecular-based detection methods, PCR and Taqman® PCR employing IMC without enrichment, could detect at least 102 cfu/ml of S. Typhimurium in broiler carcass rinse fluid (CRF) samples. IMC-ELISA, IMC-PCR, and IMC-Taqman® PCR were initially tested using 0 to 106 cfu/ml of pure culture S. Typhimurium. Each detection method was tested using artificially contaminated CRF samples. Finally, standardized IMC-ELISA, IMC-PCR, and IMC-Taqman® PCR methods were tested using commercial CRF samples. Salmonella concentrations were verified using a traditional plate method. IMC-ELISA produced consistent results when detecting at least 104 to 106 cfu/mL of pure culture S. Typhimurium. IMC-ELISA was not able to produce repeatable results when testing artificially contaminated CRF samples. S. Typhimurium was not detected in commercial CRF samples which by virtue of direct plating on XLT-4 were found to contain essentially no Salmonella (<1 cfu/ml). IMC-PCR was able to consistently detect 102 cfu/ml, whereas IMC-Taqman® PCR was able to detect 101 cfu/ml of pure culture S. Typhimurium. IMC-PCR, required four hours to complete, and it consistently detected 104 cfu/ml of S. Typhimurium in artificially contaminated CRF samples. IMC-Taqman® PCR took 3 hours to perform and was able to detect 103 cfu/ml S. Typhimurium in artificially contaminated CRF samples. The sensitivity, as well as the decreased time requirements of these detection methods, would suggest their usefulness in a commercial processing setting. / Master of Science