Medical Microbiology Commons^™

Validation Of A Real-Time Pcr Laboratory Developed Test For The Detection Of Pneumocystis Jirovecii In Bronchoalveolar Lavage Samples, Caitlyn Moon

Honors Scholar Theses

Pneumocystis jirovecii is an opportunistic, host-obligate fungal pathogen responsible for causing P. jirovecii pneumonia (PJP) in humans. PJP is treated with trimethoprim-sulfamethoxazole (TMP-SMX), a strong broad-spectrum antibiotic that carries risk of renal and hepatotoxicity. Therefore, rapid diagnosis or exclusion of PJP is crucial to ensure PJP-positive patients receive effective treatment and PJP-negative patients avoid unnecessary antibiotics. Unlike most microorganisms, P. jirovecii cannot be cultured, presenting complications for the typical methods of diagnosing fungal pathogens. Historically, the gold standard for diagnosis was direct microscopic examination with stains such as methenamine silver and calcofluor white, but this diagnostic technique requires highly skilled …

Hyperglycemia And Mycoplasma Pneumoniae Cards Toxin Impacts On Lung Epithelial And Fibroblast Injury And Recovery, Alejandra Y. Delgado, Naila Villagomez, Shuri Magdalene

Posters - 2026

Mycoplasma pneumoniae CARDS toxin induces cytotoxicity and inflammation in lung epithelial cells²·¹⁰·¹¹, while hyperglycemia independently elevates ROS and disrupts fibroblast repair¹·⁵·⁸, contributing to the heightened respiratory infection severity seen in diabetic patients¹. However, the interaction between hyperglycemic conditions and CARDS toxin-induced lung injury remains unexplored.

This study investigates how increasing high-glucose (HG) pre-conditioning modifies CARDS toxin-induced injury and recovery in A549⁶ and IMR-90⁷ cells compared to normal glucose (NG ≈ 5mM) controls. We hypothesized that increasing glucose pre-conditioning concentrations would produce a dose-dependent increase in CARDS toxin-induced oxidative stress¹² and inflammatory cytokine production¹⁵ in IMR-90 and A549 compared with normal …

Investigating Corollaries Between Streptococcus Gallolyticus Subsp. Gallolyticus Virulence And Colorectal Cancer, Tyler G. Myers

Pursuit - The Journal of Undergraduate Research at The University of Tennessee

Streptococcus gallolyticus subsp. gallolyticus (Sgg) is a gram-positive, non-beta-hemolytic bacterium that belongs to the Lancefield group D of streptococcal pathogens. For the past several decades, associations between Sgg bacteremia and colorectal cancer (CRC) have been apparent, with gastroenterologists routinely recommending colonoscopies for positive cases of Sgg in either blood or stool samples. However, current research has not wholly established whether Sgg acts as a causative agent of CRC or if pre-existing cancers make the lumen of the colon more hospitable to its colonization. Regardless, Sgg has been implicated in the modulation of host inflammatory pathways and subsequent remodeling …

Investigating Bacterial Vaginosis Pathogenesis Using Peptide Nucleic Acid-Fluorescence In Situ Hybridization With A Focus On The Roles Of Gardnerella Species, Prevotella Bivia, And Fannyhessea Vaginae, Sheridan D. George, Megan H. Amerson-Brown, Lúcia G.V. Sousa, Tyler M. Carter, Alexa H. Rinehart, Ashleigh N. Riegler, Sixto M. Leal, Kristal J. Aaron, Jiaying Hao, Ashutosh Tamhane, Chaoling Dong, John W. Lammons, Jacob H. Elnaggar, Keonte J. Graves, Paweł Łaniewski, Melissa M. Herbst-Kralovetz, Christopher M. Taylor, Nuno Cerca, Christina A. Muzny

School of Graduate Studies Faculty Publications

Background. Bacterial vaginosis (BV) is a vaginal dysbiosis characterized by polymicrobial communities of BV-associated bacteria (BVAB) adhered to the vaginal epithelium. Despite decades of research, its etiology remains unknown. We aimed to investigate BV biofilm formation over time among women who developed incident BV (iBV) using peptide nucleic acid-fluorescence in situ hybridization (PNA-FISH), focusing on 3 key BVAB (Gardnerella species, Prevotella bivia, and Fannyhessea vaginae). Methods. Heterosexual, nonpregnant women ages 18–45 with optimal vaginal microbiota were enrolled to self-collect twice-daily vaginal specimens for 60 days. iBV was defined as a Nugent score of 7–10 on ≥ 4 consecutive specimens. For …

Enhancing Preparedness: A Genetic Study Of Sar-Cov-2 And Other Microbial Public Health Threats In Wastewater From A College Town, Christian N. Hutchinson

Master's Theses

Problem

The SARS-CoV-2 (COVID-19) pandemic revealed both the systemic vulnerabilities of our healthcare system as well as the importance of timely, localized data for informing public health responses. Traditional testing approaches were essential but often failed to capture the full extent of viral spread, especially in those with mild or asymptomatic conditions that relied on at home testing. This underreporting hindered effective allocation of resources and made developing effective intervention strategies difficult. We also realized the potential for wastewater surveillance to be applied to tracking antimicrobial resistance gene markers. Taken together, this approach should have important implications for improving public …

The Swib Domain-Containing Dna Topoisomerase I Of Chlamydia Trachomatis Mediates Dna Relaxation, Li Shen, Abigail R. Swoboda, Caitlynn Diggs, Shomita Ferdous, Andrew Terrebonne, Amanda Santos, Noel Wolf, Luis Lorenzo Carvajal, Guangming Zhong, Scot P. Ouellette, Yuk Ching Tse-Dinh

School of Graduate Studies Faculty Publications

Chlamydia trachomatis has a DNA topoisomerase I with a unique C-terminal domain (CTD) homologous to eukaryotic SWIB domains. This study focused on determining the function of the SWIB domain-containing TopA from C. trachomatis (CtTopA). We demonstrated that, despite the lack of sequence similarity at the CTDs between CtTopA and TopA from Escherichia coli (EcTopA), full-length CtTopA removed negative DNA supercoils in vitro and complemented the growth defect of a topA mutant of E. coli. CtTopA is less processive in DNA relaxation than EcTopA in dose-response and time course studies. An antibody generated against the SWIB domain of CtTopA specifically recognized …

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 …

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 …

Houston, We Have A Problem: Diagnostic Difficulties In The Aids Patient With Tuberculosis Infection, Hector D. Preciado, Maria E. Torres, Muhammad A. Siddiqui, Liza Salloum, Lee Gelpi, Jose E. Campo Maldonado

Research Colloquium

Background: Tuberculosis (TB) is the leading cause of infectious death worldwide with 1.5 million deaths annually and nearly 1/4th of the world’s population (1.7 billion) infected with latent tuberculosis infection (LTBI) in 2014. Its diagnosis conventionally relies on tuberculin skin testing (TST), and Interferon-Gamma Release Assay (IGRA) which relies on the production of Interferon Gamma (IFN-y) in response to Mycobacterium tuberculosis (MTB) specific antigens. IGRA is a useful tool for detecting latent TB disease, and can be used as an adjunct for the diagnosis of active TB cases. Increases in IFN-y levels might support the diagnosis of a new TB …

Medmicromaps, A Novel Decision-Tree Guide For Infectious Diseases Differential Diagnoses, And Evaluation Of Pre- And Post-Pandemic User Engagement By Preclinical Medical Students, Jason Ceballos, Tavsimran Luthra, Lucia Garces-Torres, Valerie Lentz, Jack Nelson, Claudia Carceles-Roman, Ian Holyoak, Jane Harrington

International Journal of Emerging and Disruptive Innovation in Education : VISIONARIUM

Background: Medical education has undergone major changes in the past 5 years to adapt to the digital-centered student population with diverse learning preferences. To address the challenges of shifting delivery modalities, multimedia resources were created to provide interactive e-learning material on infectious diseases for year 2 medical students.

Methods: Medical students at a USA-accredited Caribbean medical school were provided with supplemental e-learning materials including animations, illustrations, diagnostic algorithms aka MedMicroMaps, and Case-Based tutorials. Participants were classified by semester and lecture delivery: In-person: Cohort 1 (n=526); Virtual: Cohort 2 (n=651); and Hybrid: Cohort 3 ( …

Typhlitis In A Neutropenic Patient, Alice He Bs, Wern Lynn Ng Md, Lay She Ng Md, Si Yuan Khor Md, Chandi Garg Md

Tower Health Research Day

No abstract provided.

Rare Case Of Mycobacterium Avium Complex Peritonitis In A Patient With Multiple Myeloma Undergoing Peritoneal Dialysis, Sacide S. Ozgur, Nida Ansari, Dhruv Patel, Ryan Rahman, Raymond Shih

Journal of Community Hospital Internal Medicine Perspectives

Mycobacterium avium complex (MAC) infections can present as a variety of severe diseases. While it has a predilection for immunocompromised patients such as those with Human immunodeficiency virus (HIV), it can also affect immunocompetent patients as well. One of the rare yet severe diseases that MAC infections can present is MAC peritonitis. Often hard to distinguish from other causes of peritonitis, high clinical suspicion should be maintained for those who are susceptible. Here we present an 85-year-old female with a past medical history of end-stage renal disease on peritoneal dialysis who presented with nausea and vomiting. She was found to …

Clostridioides Difficile: Identification Of Rival Organisms & Evaluation Of Non-Antibiotic Treatment Implementation, Justin Davis

Honors Undergraduate Theses

Clostrioides difficile is a common cause of nosocomial (hospital-acquired) infections. Patients receiving antibiotic treatment experience dysbiosis of gut microbiota, and C. difficile, normally held in check by the various other organisms, takes this opportunity to propagate. Symptoms of infection generally include diarrhea, colitis, dehydration, and fever. Understanding that C. difficile generally only causes illness when it is the dominant bacterium (i.e. when growth is relatively unchecked by other microbes), it is appropriate to investigate potential competitive organisms that may be introduced after antibiotic courses or during active C. difficile infection to effectively displace it. Fecal samples from the University …

Advancing Clinical Bacterial Diagnosis: Gram-Stained Whole-Slide Image Classification With Attention-Based Deep Learning, Jack Mcmahon

Computer Science Senior Theses

We introduce a new method for the classification of Gram-stained WSIs. As a test for the diagnosis of blood infections, Gram stains are highly relevant to informing patient treatment. Rapid analysis of Gram stains has been shown to be positively associated with better clinical outcomes, indicating the need for better tools to aid in automatic Gram stain analysis. To date, this area of research has been underexplored, with previous studies relying on the manual patch-level annotation of WSIs to generate training data. This is the first application of a transformer-based model to Gram-stain WSI classification, an approach that is far …

Ftsk Regulates The Assembly Of The Division Machinery In The Ftsz-Less Chlamydia Trachomatis, Mckenna Katherine Harpring

Theses and Dissertations (ETD)

In evolving to obligate intracellular dependence, Chlamydia trachomatis serovar L2 (Ct), has eliminated several gene products essential for cell division in most other bacteria, including FtsZ, the central coordinator of divisome assembly. In the absence of FtsZ, we show that divisome assembly in Ct is initiated by FtsK, a chromosomal translocase. Chlamydial FtsK forms discrete foci at the septum and at the base of the progenitor mother cell, and our data indicate that FtsK foci at the base of the mother cell mark the location of nascent divisome complexes that form at the site where a daughter cell will emerge …

Examining How Non-Antifungal Medications Impact Host-Fungal Interactions, Parker Ryan Reitler

Theses and Dissertations (ETD)

Invasive fungal infections (IFIs) are estimated to kill 1.5 million people each year with mortality rates remaining high (around 30-70%), despite the availability of three major classes of antifungal drugs. Furthermore, millions more suffer debilitating infections of the mucosal membranes or destructive subcutaneous mycoses. One of the most common IFIs is invasive candidiasis, mostly commonly caused by Candida albicans infections, with mortality rates of approximately 30%. In addition, the population of susceptible individuals and the incidences of both mucosal and systemic mycoses continue to rise due to the widespread use of broad-spectrum antibacterial agents, cancer chemotherapies, and the immune suppressive …

The Implications Of Ferroptosis In Antibiotic Resistance, Marysol Hohl

Senior Honors Theses

Bacterial infections in the United States are becoming increasingly resistant to existing antibiotic treatments. Due to projected increases in resistance and the recent decrease in novel antibacterials, experts have determined that the United States is in the “post-antibiotic era.” The scientific community has failed to resolve resistance despite the continual discovery of new antibiotic compounds. In the past decade, a novel form of cell death called ferroptosis has been implicated in antibiotic treatment by employing the use of nanotechnology. This literature review will describe the problem of bacterial resistance and demonstrate how current research is pioneering a new age of …

Rare Case Of Prosthetic Joint Infection Caused By Salmonella Enterica - A Case Report, Carlos Ramos, Shyama Appareddy, Peter J. Gonzalez

Research Colloquium

Introduction: Collectively, over 1 million total knee arthroplasties (TKA) and total hip arthroplasties (THA) are performed in the United States each year. In 2010 it was estimated that 1.58% of the United States general population has received a TKA. Prosthetic joint infections (PJI) are the most common indication for a TKA revision1 . In total, S. aureus is responsible for about 50% of all prosthetic joint infections, and about 15% are caused by gram negative pathogens2 .

Objective: This is a case report which describes the presentation and clinical course of a 59-yearold female with Salmonella enterica septic arthritis of …

Catheter-Associated Urinary Tract Infections: Patient Characteristics, Treatment, And Clinical Outcomes In One South Texas Acute Care Hospital, Kimberly A. Ambrosini, Jose Campo Maldonado

Research Colloquium

Background: Catheter-associated urinary tract infections (CA-UTIs) account for 40 percent of nosocomial infections worldwide. Their elimination is at the forefront of quality improvement in one South Texas acute care hospital.

Methods: Over a period of 6 months, five CA-UTIs occurred in one South Texas acute care hospital. These cases were identified via regular surveillance by Infection Prevention staff and the Laboratory Department of the hospital. This research reviews patient age, sex, length of stay, bacteria contracted, appropriate antibiotic use, patient characteristics, and overall outcomes.

Results: Between the months of July and December 2021, 5 CAUTIs were contracted. Patients ranged in …

A Qualitative Analysis Of Candida Auris Laboratory Surveillance In Nebraska, Lissa M. Young

Capstone Experience: Master of Public Health

Objectives: Candida auris is an emerging pathogenic yeast that was first identified in Japan in 2009 and detected in the United States in 2015. As of 2020, C. auris has been reported in cases throughout 41 countries, including the United States. The ability of this species of yeast to spread rapidly and survive for long periods of time on surfaces, the high mortality rate of those infected, and its multidrug resistant phenotype, have rendered it a urgent public health threat (the highest threat level) by the United States Centers for Disease Control and Prevention beginning in 2019 (CDC, 2019). Since …

A Novel Gardnerella, Prevotella, And Lactobacillus Standard That Improves Accuracy In Quantifying Bacterial Burden In Vaginal Microbial Communities, Jacob H. Elnaggar, Caleb M. Ardizzone, Nuno Cerca, Evelyn Toh, Paweł Łaniewski, Rebecca A. Lillis, Melissa M. Herbst-Kralovetz, Alison J. Quayle, Christina A. Muzny, Christopher M. Taylor

School of Graduate Studies Faculty Publications

Bacterial vaginosis (BV) is the most common vaginal dysbiosis. In this condition, a polymicrobial biofilm develops on vaginal epithelial cells. Accurately quantifying the bacterial burden of the BV biofilm is necessary to further our understanding of BV pathogenesis. Historically, the standard for calculating total bacterial burden of the BV biofilm has been based on quantifying Escherichia coli 16S rRNA gene copy number. However, E. coli is improper for measuring the bacterial burden of this unique micro-environment. Here, we propose a novel qPCR standard to quantify bacterial burden in vaginal microbial communities, from an optimal state to a mature BV biofilm. …

Stewardship Opportunities For Cervical Lymphadenitis And Deep Neck Space Abscesses, Aaron Shaw, Brian R. Lee, Lauren Kazmaier, Emily Baker, Tina Dao, Sandra Arnold, Angela Myers

Research Days

Background: Cervical lymphadenitis (LAD) and deep neck space abscesses (DNSA) are common pediatric infections caused by similar bacteria. We sought to determine differences in presentation, diagnosis, and treatment between LAD and DNSA to identify antimicrobial and diagnostic stewardship opportunities.

Methods: Charts were obtained using ICD9/10 codes for retropharyngeal and parapharyngeal abscessed (DNSA), and LAD between 1/1/10-12/31/20 from two pediatric centers. 1981 charts were identified. Charts were excluded if the diagnosis was not a bacterial infection (e.g. Kawasaki disease), if the LAD was not in the neck, or if caused by less common bacteria (e.g. tuberculosis). Data on presenting signs, symptoms, …

Elucidating The Impact Of Sos-Response Timing In On Escherichia Coli Survival Following Treatment With Fluoroquinolone Topoisomerase Inhibitors, Stephanie Schofield

Honors Scholar Theses

Antibiotic treatment failure is a public health crisis, with a 2019 report stating that roughly 35,000 deaths occur in the United States yearly due to bacterial infections that are unresponsive to antibiotics (1). One complication in the treatment of bacterial infection is antibiotic persistence which further compromises our battle to effectively treat infection. Bacterial persisters can exist in clonal bacterial cultures and can tolerate antibiotic treatment by undergoing reversible phenotypic changes. They can survive drug concentrations that their genetically identical kin cannot. Some persisters remain in a slow growing state and are difficult to target with current antibiotics. A specific …

Effect Of Temperature On The Microbiome Of A Laboratory Reared Colony Of Haemaphysalis Longicornis Ticks, Brianna Mitchell

Poster Presentations

Honors research poster.

Haemaphysalis longicornis is a species of tick native to eastern Asia, including eastern China, Japan, eastern Russia, and Korea. To date, it has invaded and has now established its existence in Australia, New Zealand, and several of the Pacific Islands. This species of tick has recently been introduced to the United States, having a confirmed sighting in November 2017 on a sheep farm in New Jersey and since establishing populations in 18 states along the east coast and Appalachia. Based on the existing locations of H. longicornis in its native regions, as well as in the United …

Diagnosis Of Urinary Tract Infections And Rapid Molecular Characterization Of Antibiotic Resistance, Mohammed Harris

All Dissertations

Urinary tract infections (UTIs) are one of the most common infectious clinical entities in both community and hospital settings. They have a broad range of clinical severity yet inflict large epidemiological burden of morbidity and mortality on patients and the healthcare system with billions of dollars in cost of treatment. Understanding what methods are optimal for diagnosing UTIs are critical to mitigate the marked impact and cost of these infections.

Chapter 1 and 2 in this work surveys the broad array of diagnostic modalities for UTIs and highlights their advantages and limitations in the context of the current standard of …

A Review Of Staphylococcus Aureus Pathogenesis, Global Impact, And The Rise Of Antibiotic-Resistant Clones, Anders Kleinbeck

Honors Scholar Theses

Staphylococcus aureus is a pathogen of grave concern to global public health. The pathogen has shown an unrivaled propensity to obtain resistance to nearly every antibiotic drug approved and prescribed for its treatment. This review will provide an overview of the history and evolution of S. aureus, including an analysis of its transition from the nosocomial setting to the community and the factors contributing to the species’ innate pathogenicity. This paper will also discuss the molecular mechanisms by which resistance to a wide range of popular antibiotic substances was obtained and will provide insight into the evolutionary patterns exhibited by …

Topical Anesthetic Gel Interferes With Antibacterial Efficacy Of Povidone-Iodine Both In Vitro And In Vivo, Cecilly Kelleher Bs, Jacob Im Md, Linda Kang Bs, Aleksey Mishulin Md, Sukhvinder Singh Phd, Ashok Kumar Phd

Medical Student Research Symposium

Purpose: To evaluate the effects of viscous lidocaine gel on the antimicrobial efficacy of povidone-iodine (PI) and their order of application in both in vitro and in vivo models.

Methods: In vitro antibacterial effects were tested against Staphylococcus aureus (S. aureus) with disc diffusion methods for application of lidocaine alone, PI alone, PI before lidocaine, and lidocaine before PI. Zones of inhibition were measured after incubation at 37°C overnight. Mouse eyes were colonized with S. aureus for in vivo study to which PI and/or lidocaine were applied in various combinations. Eyes were then rinsed with saline, and …

Chlamydia Trachomatis Subverts Alpha-Actinins To Stabilize Its Inclusion, A. Haines, J. Wesolowski, F. Paumet

Department of Microbiology and Immunology Faculty Papers

Chlamydia trachomatis is the leading cause of sexually transmitted bacterial disease and a global health burden. As an obligate intracellular pathogen, Chlamydia has evolved many strategies to manipulate its host and establish its intracellular niche called the inclusion. C. trachomatis reorganizes the host actin cytoskeleton to form scaffolds around the inclusion and reinforce the growing inclusion membrane. To control the kinetics and formation of actin scaffolds, Chlamydia expresses the effector InaC/CT813, which activates the host GTPase RhoA. Here, we have discovered that InaC stabilizes actin scaffolds through the host actin cross-linking proteins α-actinins 1 and 4. We demonstrate that α-actinins …

Combatting Bacterial Infections: The Efficacy Of Poly-Gamma-Glutamic Acid On The Prevention Of Nasopharyngeal Infections Among Individuals With Cleft Lip And Palate, Florence Pun

Scripps Senior Theses

Cleft lip and palate (CLP) is a medical condition where children are born with an unfused lip and palate. While surgery is required to fuse the lip and palate, there are other conditions that children with CLP face after surgeries, such as otitis media (OM), speech impediments, and difficulty breathing. Particularly, OM occurs frequently in individuals with CLP because the tensor veli palatini muscles cannot open the Eustachian tube frequently and ventilate the middle ear properly, even after surgery. This thesis is a research proposal to evaluate whether γ-PGA can be used in nasal washes to safely prevent nasopharyngeal infections …

Follow-Up Blood Cultures In Gram-Negative Bacteremia: How Do They Impact Outcomes?, Azza Elamin, Faisal Khan, Rajasekhar Jagarlamudi

Journal of Community Hospital Internal Medicine Perspectives

Introduction: Several studies have questioned the utility of obtaining follow-up blood cultures in Gram-negative bacteremia, but the impact of this practice on clinical outcomes is not fully understood. Methods: A retrospective cohort study of adult patients admitted with Gram-negative bacteremia over a two year period, to compare outcomes in those with and without follow-up blood cultures obtained. Data collected included demographics, comorbidities and presumed source of bacteremia. White blood cell count and presence of fever or hemodynamic compromise on the day of follow-up blood culture were recorded. The primary objective was to compare 30-day mortality between the two groups. Secondary …