Pathogenic Microbiology Commons^™

Development Of A Multi-Epitope Peptide Vaccine Against Monkeypox Virus: Immunoinformatics Analysis For South East Asian Hla Alleles, Nelson Chandra, Mochammad Aqilah Herdiansyah, Viol Dhea Kharisma, Arif Nur Muhammad Ansori, Arli Aditya Parikesit

Makara Journal of Science

The monkeypox virus (MPXV), a DNA virus causing zoonotic disease, poses major global public health challenges, with mortality rates between 3%–6%. Although smallpox vaccines provide partial cross-protection, there is a critical need for a dedicated, effective monkeypox (mpox) vaccine. This study aimed to design a multi-epitope peptide-based vaccine specifically adapted to the HLA allele profiles common in Southeast Asian populations, where MPXV cases are rising. Using immunoinformatics, we screened for and detected B and T cell epitopes from the MPXV cell surface antigen and IFN-alpha/beta receptor proteins. The vaccine design was validated through a rigorous evaluation of its antigenicity, immunogenicity, …

Virulence Analysis, Characterization Of Integron, And Antimicrobial Resistance Genes In Strains Of Acinetobacter Baumannii Recovered From The Hydrological Sub-Region Of Soto La Marina, Tamaulipas, Tunde Olarinde Olaniyan, Ana Verónica Martínez Vázquez, Susana Silvia Fernández Dávila, Cesar Marcial Escobedo Bonilla, Virgilio Bocanegra Garcia

Research Symposium

Background: Acinetobacter baumannii (A. baumannii) is an important bacterium due to its frequent recovery as a multidrug-resistant pathogen in hospital settings. Its antimicrobial resistance capacities made it an important challenge to health care. Colistin has been adopted as the last resort drug for managing infections associated with A. baumannii and many other multidrug-resistant Gram-negative bacteria (MDR-GNB). Because of the rise in the use of colistin for the treatment of MDR-GNB, the evolution and spread of colistin-resistant bacteria is possible thus raising a potential threat to public health. However, we have chosen to focus on A. baumannii, a …

Transcription Factor Binding And Discovery Of Novel Gene In The Opportunistic Human Pathogen, Pseudomonas Aeruginosa, Alaina Westee

Symposium of Student Scholars

Pseudomonas aeruginosa (PA) is a gram-negative, ubiquitously-found bacterium that primarily causes nosocomial, or hospital-borne, infections within immunocompromised patients. Therefore, it has been deemed a critical priority pathogen by the World Health Organization (WHO) and the Center for Disease Control (CDC), generating a need for research on its fundamental biology. The Van Dyke laboratory focuses on proteins called transcription factors, which promote or repress gene expression to regulate an organism’s functioning. We are specifically studying the cadmium-responsive transcription factor, CadR, due to the importance of metals in virulence and the lack of information on PA’s response to metal fluctuations. We intend …

Immuno-Bioinformatics Study Of Secondary Metabolites From Watercress Nasturtium Officinale As Immunostimulant In Whiteleg Shrimp Litopenaeus Vannamei By Targeting Peroxinectin And Scavenger Receptor Class B, Qurrota A’Yunin, Muhaimin Rifa’I, Maftuch Maftuch, Yoga Dwi Jatmiko, Muhammad Hermawan Widyananda, Triyanto Triyanto, Muhammad Tegar Handrianto

Karbala International Journal of Modern Science

The viral disease affects the whiteleg shrimp (Litopenaeus vannamei) and causes losses. Immunostimulants are recognized as a more environmentally friendly approach to disease management and antimicrobial properties of aquatic organisms. Watercress (Nasturtium officinale) is an aquatic plant species that contains antioxidant properties that can protect the organism from disease and boost the immune system. Shrimp rely heavily on innate immunity to combat infectious agents due to their absence of adaptive immunity. Peroxinectin and scavenger receptor class B (SRB) play essential roles in the shrimp defense system. This research employs a bioinformatic to assess the immunostimulatory potential …

Novel Infection By Mucor Hiemalis Kills Caenorhabditis Hosts Through Intestinal Perforation, Jay Ni

West Chester University Graduate Theses, Dissertations, and Final Projects

The nematode Caenorhabditis elegans has emerged as a popular model system to investigate cell biology and host-pathogen interactions. Presently, C. elegans is studied as a natural host of intracellular pathogens such as microsporidia and Orsay virus along with extracellular bacterial and fungal pathogens. The use of C. elegans as a model in host-pathogen research is limited by the number of naturally occurring pathogens to the organism. Through a sampling project to identify new pathogens of C. elegans, we identified the fungus Mucor hiemalis as a pathogen of Caenorhabditis species. We observed the fungus in the intestinal lumen of wild-caught …

Clonal Variation In Effector Gene Expression As A Mechanism For Pathogenic Adaptation In Magnaporthe Oryzae, Rebekah J. Ellsworth

Theses and Dissertations--Plant Pathology

Magnaporthe oryzae is a filamentous fungal pathogen that causes destructive diseases in cereals, including rice blast, wheat blast, and gray leaf spot. It is responsible for 10–30% annual yield losses in rice (Nalley et al., 2016) and up to 100% loss in wheat under favorable conditions (Kohli et al., 2011). Disease management typically relies on the use of resistant cultivars, but M. oryzae rapidly overcomes host resistance by mutating or deleting avirulence (AVR) genes recognized by host immune receptors. This rapid adaptation, often occurring within one to two growing seasons, presents a major challenge to breeding for durable resistance.

The …

Genetic Analysis Of Methionine Restriction-Associated Mitochondrial Unfolded Protein Response Signaling., Josh D. Dodge

Biology Dissertations - Archive

The lifespan of an organism is dictated by various genetic and environmental factors. One such determinant is the health of mitochondria which are organelles that mediate various critical cell functions including a significant role in generating the vast supply of cellular energy. Indeed, the gradual decline of mitochondrial function is believed to be a hallmark and possible cause of aging. Paradoxically, mild mitochondrial dysfunction early in life extends lifespan in various model organisms. Cells use diverse approaches to promote mitochondrial homeostasis, including the transcriptional reprogramming of cells by mitochondrial unfolded protein response (UPRmt) to mitigate mitochondrial stress. Consistently, UPRmt activation …

The Role Of Horizontal Gene Transfer In Antibiotic Resistance Amidst Prevalent Community And Healthcare-Associated Mrsa Rates, Gabrielle Nascimento

Honors College Theses

In recent decades, cases of community-acquired MRSA (CA-MRSA) and healthcare-associated MRSA (HA-MRSA) have been on the rise. The ability of antibiotic resistance to transfer between microorganisms greatly expands its threat to the effective treatment and containment of bacterial infections. The mecA gene is found on a mobile cassette within the Staphylococcal cell and encodes for PBP2a, an alternate version of penicillin-binding protein (PBP) with less binding affinity for β-lactam antibiotics, increasing resistance to the effects of antibiotics. The goal of this research is to investigate the horizontal transfer of the mecA gene between various Staphylococcus species as well as to …

Wasting Disease Of A Marine Foundation Species Links Community Interactions To Disease Dynamics, Lillian R. Aoki, Olivia J. Graham, Reyn M. Yoshioka, Rebecca Maher, Lindsay Alma, Eileen E. Hofmann, Colleen A. Burge, Drew Harvell, Maya L. Groner

CCPO Publications

Infectious disease plays a key role in shaping marine communities, including in seagrass meadows, which form biodiverse coastal habitats. Eelgrass (Zostera marina) is the most widespread seagrass species and is susceptible to seagrass wasting disease, caused by the protist Labyrinthula zosterae. As a foundation species, eelgrass strongly influences ecosystem structure, function and services; recent work has begun to explore the links between critical community interactions and seagrass wasting disease. Here, we highlight recent advances about how the eelgrass community regulates and responds to seagrass wasting disease, from the microbiome to herbivores and filter feeders. We further show …

Nucleotide-Derived Bacterial Alarmones Attenuate The Induction Of Type-I Interferon Responses In A Murine Macrophage Reporter Cell Line, Ryan P. Kilduff, Erin B. Purcell, Lisa M. Shollenberger

Chemistry & Biochemistry Faculty Publications

The stringent response is a well-studied phenomenon in many bacterial systems and regulates resource-consuming activities such as transcription, translation, and replication. The stringent response is a well-conserved signaling framework, as are the nucleotide-derived signaling mediators, collectively referred to as (p)ppGpp or as alarmones. There is a wealth of research evaluating nucleotide-derived alarmone signaling in bacterial models, however, their potential to modulate innate immune signaling has not yet been evaluated. Several common pathogen-synthesized molecules, such as lipopolysaccharide (LPS) and cyclic-di-AMP (c-di-AMP), act as pathogen-associated molecular patterns (PAMPs), which are common patterns that alert the innate immune system of bacterial infection. The …

Impacts Of Tick Parasitism On The Rodent Gut Microbiome, Robert J. Brinkerhoff, Joshua Pandian, Meghan Leber, Isabella D. Hauser, Holly D. Gaff

Biological Sciences Faculty Publications

Host microbiota may impact disease vector behavior and pathogen transmission, but little is known about associations between ectoparasites and microbial communities in wildlife reservoir species. We used Illumina metagenomic sequencing to explore the impacts of tick parasitism on the rodent fecal microbiome in both a field and laboratory setting. We found that tick parasitism on wild hosts was associated with variation in the fecal microbiota of both the white-footed deermouse, Peromyscus leucopus, and the southern cotton rat, Sigmodon hispidus. In a lab experiment, we detected significant changes to the fecal microbiome after experimental exposure to immature ticks in …

Elucidation Of The Post-Transcriptional Regulation And Role In Iron Homeostasis Of The Outer Membrane Vesicle Protein Ynce In Salmonella, Mira J. Schmidt

Honors Undergraduate Theses

Iron is an essential element for most bacteria as it is a crucial cofactor for enzymes involved in fundamental reactions such as DNA synthesis. Despite being the fourth most abundant element on Earth, bacteria face challenges acquiring iron under aerobic conditions due to the poor solubility of its oxidized form (Fe³⁺). To overcome this, bacteria have developed various strategies of iron acquisition, such as the production of siderophores. Siderophores are small molecules that scavenge free Fe³⁺ in iron-deprived environments. Iron acquisition is tightly regulated due to its capability of promoting hydrogen peroxide formation via the Fenton reaction. In Salmonella Typhimurium, …

Development Of A Proposed Selective Medium For The Isolation And Differentiation Of P. Sordellii, Dimyana Bottros

Honors Undergraduate Theses

Clostridium, a genus of anaerobic, spore-forming bacteria, includes clinically and ecologically significant species like Clostridium difficile and Paeniclostridium sordellii. C. difficile causes antibiotic-associated colitis, while P. sordellii is linked to fatal infections and spontaneous abortions. Recent studies found both species in marine sediments, suggesting their role in environmental and wildlife health disturbances, including the 2013 mass mortality of over 300 manatees in the Indian River Lagoon. However, isolating and differentiating P. sordellii is challenging due to the lack of selective media optimized for its growth. This thesis proposes a novel selective medium tailored to P. sordellii’s physiological …

Caveolin-Mediated Endocytosis: Bacterial Pathogen Exploitation And Host-Pathogen Interaction, Dibyasri Barman, Rishi Drolia

Biological Sciences Faculty Publications

Within mammalian cells, diverse endocytic mechanisms, including phagocytosis, pinocytosis, and receptor-mediated endocytosis, serve as gateways exploited by many bacterial pathogens and toxins. Among these, caveolae-mediated endocytosis is characterized by lipid-rich caveolae and dimeric caveolin proteins. Caveolae are specialized microdomains on cell surfaces that impact cell signaling. Caveolin proteins facilitate the creation of caveolae and have three members in vertebrates: caveolin-1, caveolin-2, and caveolin-3. Many bacterial pathogens hijack caveolin machinery to invade host cells. For example, the Gram-positive facultative model intracellular bacterial pathogen Listeria monocytogenes exploits caveolin-mediated endocytosis for efficient cellular entry, translocation across the intestinal barrier, and cell–cell spread. Caveolin …

Interactions Between Lipopolysaccharide And Capsule Retention In Klebsiella Pneumoniae And The Resultant Effects On Macrophages, Juliane Leigh Nguy

UNF Graduate Theses and Dissertations

Klebsiella pneumoniae is the third most common cause of nosocomial infections in the United States. The capsular polysaccharides (CPS) are virulence factors allowing K. pneumoniae to evade host immune systems. The current model of capsule structure indicates that CPS fibrils interact with the external O-antigen of lipopolysaccharide molecules to enhance retention to the bacterial outer membrane. These interactions may influence pathogenicity in clinically relevant strains. This study characterized alterations to LPS and CPS structure, the impact of these changes on capsule retention, membrane permeability, biofilm formation, and macrophage interactions. LPS and CPS were quantified and visualized in four strains of …

Multisociety Guidance For Infection Prevention And Control In Nursing Homes, Lona Mody, Sonali D. Advani, Muhammad Salman Ashraf, Allison H. Bartlett, Suzanne F. Bradley, Deborah P. Burdsall, Jennifer A. Hanrahan, Susan S. Huang, Robert L.P. Jump, Lindsay Nicolle, Mary-Claire Roghmann, Patricia Stone, Rekha K. Murthy

Department of Medicine Faculty Publications

This multisociety guidance was endorsed by SHEA, APIC, IDSA, PALTmed, and AGS. It provides recommendations for infection prevention and control (IPC) in the context of the complexity of nursing home care in the United States: increased medical acuity of residents, the spread of multidrug-resistant organisms, and the threat of emerging pathogens. Recommendations and implementation suggestions address IPC leadership, staffing, and resources, healthcare personnel and residents‘ adherence to precautions and effective hand hygiene, outbreak preparedness, training, occupational health, cleaning and disinfection in the care environment, and the involvement of IPC in the facility. The guidance also addresses the challenges of maintaining …

Cultures For Acid-Fast Bacilli: Are We Being Good Stewards?, Jennifer Hanrahan, Julie D. Sill, Patricia Ver Schneider, Jessica F. Copeland, Elsie Frimpongmaa Amoako-Kissi, Ogochukwu O. Ilobi, Angela J. Toepp

Department of Medicine Faculty Publications

Objective: To describe the use of cultures for acid-fast bacilli (AFB) and situations in which AFB cultures are unlikely to be of clinical benefit.

Design: Retrospective descriptive study of AFB cultures submitted to Sentara Health microbiology laboratory from December 1, 2021, to December 1, 2023. Data were collected from the electronic medical record and included patient demographics, the service line that ordered the culture, specimen source, and culture results.

Setting: Sentara Healthcare System.

Patients: All patients who had specimens submitted to the microbiology laboratory during the study period were included.

Results: A total of 13,944 AFB cultures from 8,243 …

Oral Microbiome And Inflammatory Bowel Disease: New Understanding And Call To Action, Michael Saadeh, Sydney Donohue, Shaina Ailawadi, Gordon Hong, David A. Johnson

Department of Medicine Faculty Publications

The oral microbiome is the second largest microbial community in the human body after the gut microbiome. It includes an array of fungi, bacteria, amoebae, flagellates, archaea, and viruses, all of which are potential pathogens. This microbiome can act as a facilitator not only for protection but also for aggravation when dysbiosis occurs. Although conventional thought is this is primarily in terms of oral health issues, such as dental caries and gingival disease. The systemic effects of the oral microbiome however, are relevant to both gastrointestinal (GI) disease and non-GI disease. These systemic risks occur for several reasons, including upregulation …

Biochemical And Molecular Analysis Of Anr-Dependent Microoxic Fitness Factors In Pseudomonas Aeruginosa, Stacie E. Balsam

Dartmouth College Ph.D Dissertations

Pseudomonas aeruginosa is a prominent opportunistic pathogen that is often found in microoxic environments like sites of infection and colony biofilms. P. aeruginosa can grow at oxygen (O2) at concentrations as little as 3 μM and also grows anaerobically by generating energy using nitrate as an alternate electron acceptor. An important way P. aeruginosa adapts to low O2 is through Anr, a transcription factor that upregulates many genes important for microoxic and anoxic fitness.

Specifically, Anr regulates mhr which encodes a hemerythrin protein (Mhr) that binds O2 with affinities relevant to microoxia and is also necessary for full fitness of …

The Effects Of Salinity On The Cutaneous Microbiome And Pathogen Infection On The Pacific Tree Frog (Pseudacris Regilla) In Monterey Bay, California, Usa, Hannah Eunhae Kim

EWU Masters Thesis Collection

Global climate change and infectious diseases are considered a leading cause of amphibian population declines worldwide. Changes in precipitation and salinity have altered watershed systems and microbial communities, reducing habitat availability and physiological performances for amphibian survival. The salt refuge hypothesis, however, is a proposed explanation that higher saline environments may reduce susceptibility to pathogens such as Batrachochytrium dendrobatidis (Bd). The Moro Cojo Slough State Marine Reserve (MCSSMR) (California, USA) is known as an abundant breeding ground for endangered/threatened amphibian species. To test and expand the salt refuge hypothesis, I evaluated Bd prevalence and intensity and the cutaneous microbiome of …