Microbiology Commons^™

Advancing The Virus Diagnostic Toolkit: Development Of Accurate And Reliable Artificial Virus-Mimicking Positive Controls And Crispr-Based Detection, Habeeb Yinka Atanda

Graduate Theses and Dissertations

Accurate and reliable detection of plant viruses is critical for protecting berries and other economically important crops. Yet diagnostic programs face persistent challenges with positive control availability, biosafety concerns, and specificity limitations. This thesis advances the diagnostic toolkit for berry viruses through three complementary innovations that address fundamental gaps in current detection methodologies. First, this research developed and validated virus-mimicking artificial positive controls (ViMAPCs) for diverse viruses affecting berry crops for endpoint PCR applications. ViMAPCs incorporate size differentiation, which enables immediate visual gel band discrimination between control and natural infection signals. Amplification efficiency analysis demonstrated close correspondence with true-positive controls …

Evaluation Of Tracheal And Cecal Microbial Composition In Heat Stressed Broilers Supplemented With Phytogenic Additives, Andressa Silveira Stein

Graduate Theses and Dissertations

The rise in global temperatures has become a concern due to its significant impact on the agricultural sector, including poultry production. Heat stress caused by high temperatures directly affects animal welfare, health and productivity, leading to major losses in the poultry sector. In broilers, heat stress affects feed consumption, weight gain, mortality and may also lead to changes in the microbiome, which can increase the predisposition to disease and impact the overall performance of these animals. The aim of this thesis was to reproduce field conditions, simulating an increase in temperature, and to evaluate possible changes in the respiratory and …

Identifying Microbial Complexities And Control Strategies At Pre-Harvest Poultry Production, Tolulope Tiwa Ogundipe

Graduate Theses and Dissertations

While significant progress has been made in post-harvest control of Salmonella in the poultry industry, the development of effective pre-harvest intervention strategies remains critical for reducing foodborne pathogens. Environmental reservoirs such as poultry litter and drinking water systems (DWS) are potential harborage sites for Salmonella and other microbial communities. Understanding the microbiota of these environments, including biofilms within water lines, is essential to identifying factors contributing to Salmonella colonization and improving pre-harvest control approaches. This study aimed to evaluate the incidence and quantity of Salmonella in poultry litter and water lines, characterize the microbial populations in these environments, and assess …

Bacterial Chondronecrosis With Osteomyelitis In Broilers: Etiology And Selected Mitigation Measures, Khawla Saud Alharbi

Graduate Theses and Dissertations

Bacterial chondronecrosis with osteomyelitis (BCO) is the predominant cause of lameness in broiler chickens. It mainly impacts broiler production and animal welfare, causing substantial financial losses accounting for 1- 2% due to bird condemnations at the marketing age. Remediating BCO lameness disease demands investigating its causes using appropriate models and evaluating preventive measures, such as enhancing epithelial tissue health and tight junction integrity in the digestive and respiratory tract, strengthening immune functions, and improving bone strength. Therefore, the objectives of this dissertation were to 1) study predisposing factors for BCO lameness by investigating the effects of deoxynivalenol (DON) and fumonisin …

Characterization Of Streptococcus Gallolyticus: An Emerging Pathogen Causing Turkey Streptococcosis, Latasha S. Gray

Graduate Theses and Dissertations

During the past five years, there has been an increased occurrence of Streptococcus gallolyticus in young turkey poults. This emerging pathogen previously affected turkey flocks without any indication of disease prior to acute mortality. However, recently there has been two cases of neurological presentation associated with S. gallolyticus subsp. pasteurianus that are unique to traditional disease presentation in turkey poults. The objectives of the present dissertation were to compile data associated with the two neurological cases and compare different S. gallolyticus strains as well as pathogenic Enterococcus cecorum to the neurological strains. The two neurological cases occurred between July and …

Bactericidal Mechanism Of Peracetic Acid Against Salmonella Mediated By Reactive Oxygen Species, Mohammed Khalid Wheib Al-Doury

Graduate Theses and Dissertations

Peracetic acid (PAA) is extensively used as a bactericidal agent in poultry processing to reduce foodborne pathogens, including Salmonella enterica serotype Typhimurium (S. Typhimurium). Despite its widespread application, the exact mechanisms underlying its bactericidal effects, particularly the role of reactive oxygen species (ROS), remain incompletely understood. This dissertation examines the role of ROS in PAA-mediated bacterial killing and explores both genetic and metabolic factors that influence bacterial susceptibility to PAA. Findings from these studies have implications for enhancing the efficacy of PAA, thereby improving food safety practices in the industry.

The first study investigates ROS as a central component …

The Impact Of Reactive Oxygen Species On Bactericidal Activity And Drug Resistance In Salmonella Typhimurium Upon Chlorine And Eugenol Exposure, Mohammed Aljuwayd

Graduate Theses and Dissertations

Salmonella Typhimurium (S.T) is a foodborne pathogenic bacterium which causes salmonellosis in human beings. Chicken is the most common source of S.T contamination. In chapter I, I discuss the growth of the poultry industry, the role chickens play as Salmonella reservoirs, the spread of drug-resistant strains caused by chicken husbandry and antibiotic use, and how eugenol can be used in poultry feed to decrease Salmonella infections and improve intestinal health. In chapter Ⅱ, I summarize the role of reactive oxygen species (ROS) in bactericidal activity. In chapter Ⅲ, I describe the killing mechanism of sodium hypochlorite (NaOCl) and identify the …

The Effect Of Microbial Bile Acid Metabolism On Clostridium Perfringens Virulence, Tahrir Jatli Alenezi

Graduate Theses and Dissertations

Clostridium perfringens is a predominant intestinal pathogen affecting both humans and animals, including chickens resulting in significant economic losses. In chapter I, I have overviewed the dynamics of the intestinal immune system, the composition of the intestinal microbiome, and how the microbiome influences inflammation in the development of Clostridium infection. The intricate interplay between immunity, microbiota, and their metabolites is likely critical in the pathogenesis of C. perfringens and uncovering these interactions may unveil new avenues for prevention and treatment. The objective of this chapter is to provide updated insights into the role of host-microbe interactions and their potential therapeutic …

Securing Rice Safety Through Innovative Radiative Heat Treatment And Proper Storage, Faith Achieng Ouma

Graduate Theses and Dissertations

Securing the microbial safety of rice is a rising priority within the food industry, especially when used as an ingredient to manufacture ready-to-eat, minimally-processed products. Mold contamination is typically the most problematic for rice because certain species of Aspergillus produce toxic secondary metabolites known as aflatoxins, rendering the grain unfit for human and animal consumption. The objectives of this study are to: (1) investigate the effectiveness of using high-power (915 MHz frequency), short-duration microwaves (MWs) to inactivate microbes on rough rice; (2) use a three-level screening design to determine which storage factors, such as temperature, relative humidity (RH), storage duration, …

Radiofrequency And Gaseous Technologies For Enhancing The Microbiological Safety Of Low Moisture Food Ingredients, Surabhi Wason

Graduate Theses and Dissertations

High heat resistance and long survival of Salmonella in low moisture food ingredients (LMFIs) such as spices and seeds are concerning as they are typically consumed without cooking. Therefore, it is challenging to effectively inactivate pathogenic bacteria without negatively impacting the quality of the treated product. This dissertation aimed to develop and evaluate novel intervention technologies: in-package radiofrequency steaming and non-thermal gaseous technologies to improve the microbial safety of LMFIs. The dissertation can be divided into three parts. The first part of this dissertation on the thermal inactivation kinetics of Salmonella and a surrogate, Enterococcus faecium NRRL B-2354on black pepper …

An Ecological Perspective Of American Rodent-Borne Orthohantavirus Surveillance, Nathaniel Mull

Graduate Theses and Dissertations

Orthohantaviruses are a global group of viruses found primarily in rodents, though several viruses have also been found in shrews and moles. Many rodent-borne orthohantaviruses are capable of causing one of several diseases in humans, and the mortality associated with these diseases ranges from < 0.1% - 50% depending on the specific etiological virus. In North and South America, orthohantavirus research was ignited by an outbreak of severe disease in the Four Corners region of the United States in 1993. However, despite the discovery of over 20 orthohantaviruses in the Americas, our understanding of orthohantavirus ecology and virus-host dynamics in this region is still limited, and orthohantavirus surveillance is generally restricted in scope to select regions and small portions of host distributional ranges. In Chapter I, I present a literature review on the current understanding of American rodent-borne orthohantavirus ecology. This review focused on under-studied orthohantaviruses, addressing gaps in knowledge by extrapolating information from well-studied orthohantaviruses, general rodent ecology, and occassionally from Eurasian orthohantavirus-host ecology. There were several key conclusions generated from this review that warrant further research: 1) the large number of putative orthohantaviruses and gaps in orthohantavirus evolution necessitate further surveillance and characterization, 2) orthohantavirus traits differ and are more generalizable based on host taxonomy rather than geography, and 3) orthohantavirus host species are disproportionately found in grasslands and disturbed habitats. In Chapter II, I present a prioritized list of rodent species to target for orthohantavirus surveillance based on predictive modeling using machine learning. Probable orthohantavirus hosts were predicted based on traits of known orthohantavirus hosts using two different types of evidence: RT-PCR and virus isolation. Predicted host distributions were also mapped to identify geographic hotspots to spatially guide future surveillance efforts. In Chapter III, I present a framework for understanding and predicting orthohantavirus traits based on reservoir host phylogeny, as opposed to the traditional geographic dichotomy used to group orthohantaviruses. This framework establishes three distinct orthohantavirus groups: murid-borne orthohantaviruses, arvicoline-borne orthohantaviruses, and non-arvicoline cricetid-borne orthohantaviruses, which differ in several key traits, including the human disease they cause, transmission routes, and virus-host fidelity. In Chapter IV, I compare rodent communities and orthohantavirus prevalence among grassland management regimes. Sites that were periodically burned had high rodent diversity and a high proportion of grassland species. However, rodent seroprevalence for orthohantavirus was also highest in burned sites, representing a trade-off in habitat management outcomes. The high seroprevalence in burned sites is likely due to the robust populations supported by the high quality habitat resulting from prescribed burning. In Chapters V and VI, I describe Ozark virus and Sager Creek virus, two novel orthohantaviruses discovered from specimens collected during Chapter IV. Both chapters report full genome sequences of the respective viruses and compare both nucleotide and protein phylogenies with related orthohantaviruses. Additionally in Chapter VI, I support the genetic analyses with molecular and ecological characterizations, including seasonal fluctuations in host abundance, correlates of prevalence, evidence of virus shedding, and information on host cell susceptibility to Sager Creek virus.

Fulfilling Koch’S Postulates And Evaluation Of Different Administration Routes In Poults Challenged With Streptococcus Gallolyticus, Latasha Gray

Graduate Theses and Dissertations

Streptococcus gallolyticus (SG) is a Gram-positive found as commensal gut flora in animals and humans. SG has been associated with acute mortality in poults 2 to 3 weeks of age, with lesions mainly consisting of splenomegaly, hepatomegaly, and pericarditis. The objective of this thesis was to reproduce disease in poults caused by SG recovered from clinical field isolates and evaluate different routes of administration. Three field isolates from geographically disparate areas in Arkansas and Missouri were used for the experiments contained in this thesis. Antibiotic sensitives of the three field isolates revealed sensitivity to penicillin as well as a wide …

The Role Of Microbiota-Biotransformed Bile Acid Metabolites On Campylobacter Jejuni- And Clostridium Perfringens-Infection, Ying Fu

Graduate Theses and Dissertations

Campylobacter jejuni (C. jejuni) and Clostridium perfringens (C. perfringens) are two leading pathogenic bacteria responsible for both human and animal diseases. In chapters Ⅱ to Ⅳ, I presented an overview of current knowledge on the role of immune response, microbiota, bile acids and their microbial metabolites on campylobacteriosis, and C. perfringens induced necrotic diseases.In chapter Ⅴ, I investigated effects of deoxycholic acid-modulated anaerobes (DCA-Anaero) on attenuating chicken transmission-exacerbated campylobacteriosis. SPF Il10-/- mice were gavaged with clindamycin for 7 days followed by infected with three C. jejuni strains, Cj-P0 (C. jejuni AR101), Cj-P1 (from chicken pre-infected with C. jejuni AR101), and …

The Antimicrobial Resistance Plasmid Mobilome Of Salmonella Enterica And Related Enteric Species And Factors That Influence The Transfer Efficiency., Suad Algarni

Graduate Theses and Dissertations

The dynamic distribution of antimicrobial resistance genes in Salmonella enterica is considered a public health risk. S. enterica is one of the most important etiological agents of foodborne illness and has a critical impact on global human health. In S. enterica and related species, mobile genetic elements (MGEs) serve as primary vehicles for the dissemination of antibiotic resistance genes in the bacterial evolution. This dissemination can be impacted by different selective pressures that leads to diverse antibiotic response phenotypes. This project focusses on the dynamics of antimicrobial resistance genes, particularly exploring the transfer efficiency of multidrug resistance plasmids in S. …

Optimization Of Clostridium Septicum Antigen Production And Evaluation Of Vaccine Administration Parameters For A Candidate Bacterin-Toxoid To Prevent Dermatitis In Commercial Turkeys, Aaron Forga

Graduate Theses and Dissertations

The objective of this thesis was to optimize the hemolytic activity of two isolates of Clostridium septicum to evaluate if hemolytic titer of C. septicum antigen at time of formalin inactivation corresponded to increased serum antibody titer to the C. septicum alpha-toxin of turkeys immunized with an experimental formalin inactivated bacterin-toxoid vaccine. Chapter 1 provides a brief overview of the thesis. Chapter 2 consists of a literature review focused on clostridial dermatitis, specifically C. septicum-associated dermatitis (cellulitis) that affects commercial turkeys. Chapter 3 outlines our attempts to optimize an experimental autogenous bacterin-toxoid vaccine as a potential strategy to mitigate clostridial …

Molecular Characterization Of Nitrogenase Regulation In Methanosarcina Acetivorans, Melissa Chanderban

Graduate Theses and Dissertations

Nitrogenase is the metalloenzyme only found in bacteria and archaea that is essential for biological nitrogen fixation (diazotrophy), but it can also serve as a catalyst in biofuel production. All diazotrophs contain a molybdenum (Mo) nitrogenase, while some species contain additional alternative nitrogenases where either vanadium (V) or iron (Fe) replace Mo in the active site cofactor. Nitrogen fixation by bacteria has been extensively studied. The limited investigation of nitrogen fixation in methanogenic archaea (methanogens) indicates production of nitrogenase is simpler than in bacteria and methanogen nitrogenase has different biochemical properties. Thus, methanogen nitrogenases provide a promising alternative for genetic …

A Cross-Scale Nexus: Microbial Functional Genes In Tandem With Molecular-Level Nitrogen Fluxes And Implications For Field-Scale Biogeochemical Processes, Srusti Maddala

Graduate Theses and Dissertations

Nitrogen (N) biogeochemical cycling entails close networking between soil nutrients, plant species and resulting microbial communities, and abiotic factors such as temperature, moisture, and pH. To better understand transformations of N in soil microsites, which are known to be rich in N-cycling behavior, the microdialysis technique was employed to generate in situ data on temporal alterations of N during wetting-drying conditions in both the field and laboratory. The objectives were to 1) determine the lifespan of the microdialysis technique in field conditions, 2) evaluate the ability of the method to yield N fluxes that would be differential between the two …

Characterization Of Genetic Pathways Involved In Resistance To A Novel Antifungal Peptide, Kayla L. Haberman

Graduate Theses and Dissertations

Antibiotic resistance is increasing prevalence, particularly in Candida glabrata. This opportunistic pathogen is closely phylogenetically related to Saccharomyces cerevisiae; however, its characterization is limited. C. glabrata is only second to Candida albicans as a fungal pathogen in immunocompromised patients. Commonly resistant to azoles, the most common fungal therapy, it has become costly and challenging to treat. A histatin 5 derived antifungal peptide, KM29, has a high degree of efficacy in Candida species and S. cerevisiae. The objective of this work is to advance our understanding of the mechanism of action of KM29 against C. glabrata. Previous work in the lab …

Habitability, And Evolution Of Microorganisms Under Extreme Conditions, Azarin Yazdani

Graduate Theses and Dissertations

The choice of a solvent determines the possible biochemistry of life. Life on Earth is based on carbon biochemistry and has evolved in an environment with water as a solvent. As a polar solvent abundant on Earth, water has unique physical properties, including a large range of liquidity and low viscosity, making it a very good solvent for terrestrial life. Liquids other than water are abundant in the universe, and the chemical nature of these liquids might lead to different chemistries of life. In the first chapter, we review the main characteristics of a good solvent, and then we use …

Allelopathic Effect Of Cereal Straw Extracts On Growth Of Raphidocelis Subcapitata And Microcystis Aeruginosa, Holly Wren

Graduate Theses and Dissertations

Harmful algal blooms are increasing in size, duration, and intensity around the globe. For several decades, cereal straws have been recognized as a viable algal control method, though the mechanisms by which cereal straws inhibit algae remain a topic of research. The objectives of this study were to evaluate the effectiveness of decomposing cereal straw extract, particularly rice (Oryza sativa) and barley (Hordeum vulgare) straw extract, to inhibit the green alga Raphidocelis subcapitata or cyanobacteria Microcystis aeruginosa in bioassays and to determine if the effectiveness of decomposing rice straw extract is altered by the presence of natural organic matter or …

Chondronecrosis With Osteomyelitis In Broilers: Bacterial Species Involvement And Influence Of Probiotics And Synbiotics, Amer Abdullah Hasan

Graduate Theses and Dissertations

Since 1945, the market for broiler production has evolved from a collection of smallholder poultry farms into an industry worth billions of dollars. Poultry production has not gone without challenges. Lameness in young broilers is presently a serious issue in the poultry industry for reasons of animal health and welfare, as well as significant lost production and revenue. Bacterial chondronecrosis with osteomyelitis (BCO) is a major form of lameness in broilers. This dissertation contains information about (i) the influence of Staphylococcus agnetis, Staphylococcus saprophyticus, Staphylococcus epidermidis and Enterococcus faecalis on inducing BCO lameness, (ii) evaluation of of probiotics for reducing …

Bacterial Chondronecrosis With Osteomyelitis In Broilers: Genomics, Phylogenomics, And Methods To Detect Specific Pathogens During Outbreaks., Abdulkarim Abdulaziz A. Shwani

Graduate Theses and Dissertations

Lameness is a major issue in animal welfare and the broiler industry. Bacterial chondronecrosis with osteomyelitis (BCO) is one of the main causes of lameness. Many staphylococcal species, including Staphylococcus agnetis isolate 908, have been isolated from the bones and blood of lame broilers at the University of Arkansas. Staphylococcus agnetis is a coagulase-variable, Gram-positive bacterial species that has been previously associated with subclinical or mild clinical cases of mastitis in dairy cattle. The annotated complete genome of hypervirulent strain 908 was published at NCBI. In this study, it has been compared to nine genomes we assembled for hypervirulent isolates …

Diffusive Dynamics Of Biological Macromolecules In The Cytoplasm Of Live Bacteria, Asmaa Ali Sadoon

Graduate Theses and Dissertations

Bacteria are small organisms that play important roles in our bodies and in maintaining our surrounding environment. However, bacterial infections are considered as one of the health diseases that threatens the lives of humans. Resistance of bacteria to antibiotics has made treating bacterial infections more challenging. With the emergence of many developed optical techniques, it has become possible to study various biological mechanisms of molecules inside these small organisms with high resolution and precise localization. In this research, single particle tracking photoactivation localization microscopy (sptPALM) technique was used to investigate the dynamics of fluorescent histonelike nucleoid-structuring proteins (H-NS) in live …

Enzymatic Degradation Of Microcystin-Lr By Microcystinase (Mlra), Faisal Alqhtani

Graduate Theses and Dissertations

Microcystin-LR (MC-LR) is affecting the water supply worldwide. Hence, a way to eliminate this toxin is an essential target. In this study, successful cloning of the mlrA gene and producing MlrA enzyme that can degrade the cyclic MC-LR to linearized MC-LR was done. MlrA protein was expressed in Escherichia coli BL-21 (E. coli). Also, enhancing the MlrA yield by adding nickel to LB media was a success in producing more MlrA enzyme from the same volume. Even though the enzyme showed no activity after adding Ni, the enzyme was expressed at a higher yield. Furthermore, it was to investigate adding …

Development And Evaluation Of Models For Hatchery-Mediated Infection Of Neonatal Broiler Chicks, Brittany Danielle Graham

Graduate Theses and Dissertations

Formaldehyde fumigation has been used to control the microbial load in commercial hatch cabinets. The hatch cabinet environment promotes replication and dissemination of both apathogenic and pathogenic microorganisms. As the microbial load increases during the hatching phase, formaldehyde eliminates airborne microorganisms circulating in the hatch cabinet environment. Due to the hazardous properties of formaldehyde, non-toxic alternatives to formaldehyde fumigation to control the microbial bloom in hatch cabinets are needed. The objectives of the present dissertation were to develop challenge models using singular or multiple microorganisms associated with the microbial bloom to simulate contamination that occurs in commercial hatch cabinets. Initially, …

Directed Genome Evolution To Identify Genes For Macrophage Survival By Staphylococcus Agnetis, Sonali Lakshika Anne Lenaduwe Lokuge

Graduate Theses and Dissertations

Bacterial Chondronecrosis with Osteomyelitis (BCO) is a debilitating infection that negatively impacts animal welfare and costs the broiler industry billions of dollars annually. We have previously isolated Staphylococcus agnetis 908 from BCO samples obtained from broilers at the University of Arkansas research farm. This isolate can induce BCO lameness at greater than 50% in broilers exposed to the pathogen in drinking water. We found that S. agnetis 908 is capable of surviving and escaping macrophages compared to a closely related cattle isolate,1379. Through Directed Genome Evolution (DGE) we identified that this difference is at least partially associated with an alanine …

The Persistence Of Human Norovirus Surrogate In Leafy Greens Production System, Wenjun Deng

Graduate Theses and Dissertations

Since mostly consumed raw, foodborne pathogen contamination of leafy greens has led to a large number of foodborne disease outbreaks and illnesses each year in the United States. Human noroviruses (hNoV) are the most common viral pathogen transmitted by leafy greens. In this dissertation, the persistence of the hNoV surrogate Tulane virus (TV) on pre-harvest lettuce and microgreens was investigated. Lettuces are the most studied leafy green model, while previous hNoV research has mainly focused on the post-harvest stage of production. Here, pre-harvest hydroponically grown lettuce were used to determine TV persistence on leafy greens. After inoculation on leaves at …

Developing A Microdialysis Sampling-Based Biofilm/Macrophage Co-Culture Model, Alda Diaz Perez

Graduate Theses and Dissertations

The host immune system and bacterial cells are known to interact during the human lifetime. Bacteria secrete a wide variety of signaling molecules, known as quorum sensing (QSC) molecules, that modulate the host immune system. While immune-biofilm interactions involve this chemical signaling network, the mechanisms through which this occurs are not well understood. This work aimed to develop a new method that can be used not only in vitro settings but also in vivo. The microdialysis sampling technique has widely been used in in vitro and in vivo settings in humans, mice, and rats for the collection of neuropeptides, cytokines, …

Pathogenicity Of Staphylococcus Agnetis Associated With Lame Broilers With Osteomyelitis, Sura Faris Salih Zaki

Graduate Theses and Dissertations

We developed High Resolution Melt Analysis (HERMA) as a rapid and reliable molecular diagnostic assay for the detection and identification of the main bacterial species recovered from the blood and lesions of bacterial chondronecrosis with osteomyelitis (BCO) from the lame broilers at the University of Arkansas poultry research farm. Also, the present study confirms that raising young birds on suspended wire flooring has been proved to successfully induce lameness attributable to BCO with birds being more susceptible to bacteraemia than those that were raised on litter flooring. The newly described pathogen, Staphylococcus agnetis, has been reported to be overrepresented in …

An Impedimetric Aptasensing System For The Rapid Detection Of Salmonella Typhimurium, America Sotero

Graduate Theses and Dissertations

Salmonella Typhimurium is a foodborne pathogen associated with raw and undercooked eggs, poultry, beef, fruits, and vegetables. In the United States, Salmonella is responsible for approximately 1.2 million illnesses, 23,000 hospitalizations, and 450 deaths annually. For many years, conventional detection methods such as culture-dependent and PCR-based methods have been the “golden standards” for the detection of this pathogen due to their high sensitivity and reliability. However, they still have some disadvantages such as long enrichment steps and high costs that need to be overcome. The development of a rapid and reliable method for the detection of S. Typhimurium is needed …