Infectious Disease Commons^™

Genome-Wide Approaches To Bacterial Strain Typing: A History And Review Of Recent Methodological Advances, William C Shropshire, Blake M Hanson, Samuel A Shelburne

Faculty, Staff and Student Publications

Purpose of review: Whole genome sequencing (WGS) has transformed bacterial strain typing, an essential tool for outbreak detection, antimicrobial resistance surveillance, and tracking clonal emergence across clinical, research, and public health settings. Herein, we will review recent advances in WGS-based bacterial strain typing methods for purposes of comparison and classification with a focus on improvements in variant identification, strain classification, and transmission assessment.

Recent findings: Advances in sequencing technologies as well as variant calling methodologies and parameter optimization have enhanced the precision and accuracy of single nucleotide variant identification. Hierarchical clustering of gene-by-gene strain typing, combined with novel data management …

Indoor Air Quality Conditions And Respiratory Virus Detections In Elementary Schools—Kansas City, Missouri, February–March 2023, Olivia M. Almendares, Jasmine D. Ruffin, Luke Gard, Rangaraj Selvarangan, Anjana Sasidharan, Dithi Banerjee, Nibha Sagar, Amanda Hayes, Sydnie Petty, Brian R. Lee, Chris T. Young, Janelle Potter, Shannon Tilsworth, Jennifer Goldman, Jennifer E. Schuster, Hannah L. Kirking

Manuscripts, Articles, Book Chapters and Other Papers

Background/Objectives: Respiratory viruses circulate year-round and can spread indoors via inhalation of airborne particles. Effective ventilation and filtration may reduce transmission, particularly in school settings where children and staff spend significant time. This study examines the impact of indoor air quality (IAQ) and ventilation in schools on respiratory virus detection.

Methods: During February 27 to March 30, 2023, we assessed the relationship between IAQ and respiratory viruses in two Kansas City, Missouri, elementary schools by collecting bioaerosol samples, student and staff nasal swabs, and monitoring IAQ across 10 rooms (six classrooms, two common spaces, and two nurses’ offices). We calculated …

Intention To Take Pre-Exposure Prophylaxis (Prep) As An Hiv Preventive Medication: An Application Of The Health Belief Model And Theory Planned Behavior, Besuthu Nakekelwa Nkambule

Graduate Theses and Dissertations

South Africa (SA) has 7.7 million citizens (12.6% of its 2023 population) living with human immunodeficiency virus (HIV). The use of pre-exposure prophylaxis (PrEP) as an antiretroviral medication for HIV-negative individuals is a promising HIV prevention strategy in SA that can help the attainment of an HIV free generation. PrEP offers greater than 90% protection against HIV acquisition. Despite SA’s efforts in increasing PrEP coverage for its citizens, primarily to those at substantial risk, its adoption remains relatively low. Structural barriers related to access, costs, lack of awareness, and, more recently, US funding cuts exacerbate the challenges of PrEP’s potential …

Effects Of Long Covid On Healthcare Utilization, Michael Gottlieb, Erica S. Spatz, Huihui Yu, Imtiaz Ebna Mannan, Michelle Santangelo, Caitlin Malicki, Nicole L. Gentile, Rachel E. Geyer, Alex Charlton, Jonathan W. Dyal, Joann G. Elmore, Kristyn Gatling, Mandy J. Hill, Juan Carlos C. Montoy, Kelli N. O'Laughlin, Kristin L. Rising, Sharon Saydah, Kari A. Stephens, Ralph C. Wang, Lauren E. Wisk, Arjun K. Venkatesh, Robert A. Weinstein

Jefferson Center for Connected Care Faculty Papers

BACKGROUND: While most research on Long COVID (LC) has focused on symptoms and quality of life, there remains a critical need to better understand the effect of LC on resource utilization. This study sought to determine the type and amount of healthcare utilization among participants with versus without LC.

METHODS: This was a secondary analysis of a prospective, longitudinal, multicenter U.S. study of adult participants with symptomatic COVID-19, confirmed with testing, who completed 3-month post-infection surveys and had electronic health record data for at least 180 days pre- and post-index testing. We excluded participants with any COVID-19 infections within the …

A Cancer Education Needs Assessment: Informing Middle-Aged Female Patients About The Relationships Between Obesity And Women’S Health Concerns In The Reproductive System, Breast, And Endometrial Health, Batul Mirza

MUSC Theses and Dissertations

Obesity significantly impacts women’s health, particularly among middle-aged women, by increasing the risk of hormone-sensitive cancers such as breast, endometrial, and reproductive system cancers. This study examines the educational needs of this demographic group regarding obesity-related cancer risks and explores effective intervention strategies. Obesity-induced mechanisms – hormonal imbalances, chronic inflammation, and insulin resistance – drive cancer susceptibility, emphasizing the need for targeted health education. The study employs a qualitative design, which includes interviews with subject matter experts (SMEs) and surveys of middle-aged women. The goal is to assess awareness, perceived barriers, and preferred learning methods. Findings suggest that with many …

Patient Information Needs During Ambulatory Medication Changes: A Qualitative Study, Elaine Giletta, Vanessa B. Hurley, Yushi Yang, Jessica L. Schwartz, Rabia Jalalzai, Nicole L. Mollenkopf, Raquel Mayne, Samantha I. Pitts

Journal of Patient-Centered Research and Reviews

Purpose: We performed interviews with patients and caregivers to explore whole-person, whole-regimen information needs at times of routine outpatient medication changes. We categorized information needs in this relatively unstudied context and identified which needs were commonly recognized as insufficiently met.

Methods: We explored the content of the semi-structured interviews, which involved nine patients and two caregivers of pediatric patients, all of whom experienced a recent medication change in the outpatient setting of a large urban academic healthcare system. We used inductive thematic analysis to organize information needs into categories to identify key information gaps.

Results: We identified five categories of …

Commentary On Blaser's "Antibiotic Use And Its Consequences For The Normal Microbiome", Fred C. Tenover

AMR Commentary

If you have not read this eye-opening commentary by Dr. Martin Blaser about the negative impact of the widespread use of antibiotics in children, you should. The goal of giving antibiotics to children usually is to treat an infection — an earache, a respiratory tract infection, or perhaps a potentially deadly bloodstream infection. Those antibiotics, however, will often kill more than just the bacteria that are causing the infection. Humans have large quantities of “good bacteria” in our intestinal tracts, on our skin, and elsewhere on our body that play an important role in keeping us healthy.

The Effect Of Individual Variation On Epidemiological Dynamics: From Super-Spreaders To Landscapes Of Risk, Alexis Shannon Beagle

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Individuals that make up a population always display some level of variation between members. At the smallest scale, individuals always maintain genetic variation, but variation continues to arise at other scales of biological organization from physiological or immunological variation within individuals to variation in behavior between individuals that can be both genetically and environmentally mediated. The role of individual variation is particularly important in the context of infectious diseases because there is strong evidence that infections are highly heterogenous, indicating that patterns of individual variation drive a significant portion of the epidemiological patterns we observe. Individual variation leads to heterogeneity …

Implementing A Team-Based Approach To Reduce Blood Culture Contamination Rates In The Emergency Department: A Quality Improvement Initiative, Melissa Lockhart

Doctor of Nursing Practice Projects

Background: Blood culture contaminations (BCC) present significant risks to patients, including adverse drug reactions and the exacerbation of antibiotic resistance. BCC can also result in millions of dollars in financial burdens for hospitals due to the need for follow-up testing, treatment complications, and antibiotic stewardship efforts. At this facility, the contamination rate in the emergency department (ED) consistently exceeds the national benchmark of 3%. Contributing factors include high patient turnover and increased nursing workloads, which can lead to shortcuts in essential practices such as hand hygiene and skin disinfection before collection.

Purpose: This project aimed to evaluate whether implementing a …

Variation A Blood Culture Testing For Three Common Infections, Smit Shah, Jennifer Goldman, Matt Hall, Jillian Cotter, Samantha A. House, Matthew J. Molloy, Michelle Polich, Michael J. Steiner, John R. Stephens, Michael J. Tchou, Ronald J. Teufel Ii, Irma Ugalde, Andrew Yu, Jessica Markham

Presentations

Background: Routine blood culture (BC) testing in uncomplicated community-acquired pneumonia (CAP), skin and soft tissue infections (SSTI), and urinary tract infections (UTI) has demonstrated low clinical utility. Objectives: To evaluate hospital-level BC testing trends and their association with clinical outcome differences for children hospitalized with CAP, SSTI, and UTI. Methods: This retrospective cohort study used the Pediatric Health Information System database to identify hospitalizations of children aged 3 months-18 years admitted with CAP, SSTI, or UTI from 2016-2023. We excluded patients with complicated infections, medical complexity, ICU admission, or length of stay (LOS) >7 days. Hospital-level BC testing rates were …

Placental Transfer Of Sars-Cov-2 Antibodies In Mother-Neonate Pairs: A Prospective Nested Cohort Study, Alex Mugo, Angela Koech, Liberty Cantrell, Moses Mukhanya, Isaac Mwaniki, Joseph Mutunga, Merryn Voysey, Rachel Craik, Marleen Temmerman, Geoffrey Omuse

Centre of Excellence in Women and Child Health

Background: Newborns depend on the transfer of IgG across the placenta to acquire protection against pathogens. We assessed the placental transfer of SARS-CoV-2 antibodies, primarily derived from infection, from seropositive pregnant women enrolled in a pregnancy cohort in Kilifi, Kenya.

Methods :The study was nested within a prospective observational multi-country cohort study. All available paired maternal delivery and cord blood samples were selected. Maternal sera were tested for SARS-CoV-2 receptor binding domain (RBD) IgM/IgG total antibodies using the Wantai assay. For positive samples, maternal and corresponding cord blood samples were tested for SARS-CoV-2 IgG antibodies against the spike (anti-spike) and …

Covid-19 Vaccine-Induced Rhabdomyolysis In A 53-Year-Old Woman, Akash Hazari, Jack Chien, Daniel Nunez

HCA Healthcare Journal of Medicine

Introduction

COVID-19-induced rhabdomyolysis is a common complication in COVID-19 infection. However, only a handful of cases have been reported showing links between COVID-19 vaccine and rhabdomyolysis.

Case Presentation

We present the case of a 53-year-old woman, who recently received COVID-19 vaccine and presented to the hospital with progressive extremity weakness. Common reasons for rhabdomyolysis were ruled out as possibility and the patient was found to have rhabdomyolysis induced from COVID-19 vaccine.

Conclusion

Even though COVID-19 vaccine-induced rhabdomyolysis is rare, it should be considered in the differential diagnosis with patients presenting with neuromuscular complaints and a recent COVID-19 vaccine.

Efficacy And Safety Of Lotilaner Ophthalmic Solution 0.25% In Demodex Blepharitis: A Systematic Review, Stephanie P. Fabara, Thalia Fabara, Akankcha Alok, Nausheen Khuddus

HCA Healthcare Journal of Medicine

Demodex blepharitis is a chronic eyelid inflammation caused by Demodex mites, which are ubiquitous skin parasites. Lotilaner, a newly United States Food and Drug Administration (FDA)-approved drug, is an antiparasitic agent that selectively inhibits parasite-specific γ-aminobutyric acid chloride channels, inducing spastic paralysis and death of Demodex mites. It is applied as an ophthalmic solution, 0.25%, twice a day for 6 weeks, and it has a long half-life and high lipophilicity, facilitating the penetration of the drug into the eyelash follicles and meibomian glands where the mites reside. This study systematically reviewed 6 clinical trials that compared lotilaner with placebo for …

Gejala Neuropsikiatri Pasien Hiv Setelah Menjalani Transisi Antiretrovirus Nevirapin Ke Dolutegravir Di Rumah Sakit Cipto Mangunkusumo, Jakarta, Metra Adi Pratama, Rudi Putranto, Herqutanto Herqutanto, Aisyah Syahrani, Aljira Fitya Hapsari, Veritea Natali, Meivina Ramadhani Pane, Evy Yunihastuti

Jurnal Penyakit Dalam Indonesia

Introduction. Dolutegravir (DTG) is one of the effective antiretroviral therapies (ART) for suppressing HIV replication and has a favorable safety profile. However, reports regarding neuropsychiatric side effects, especially in patients transitioning from a nevirapine (NVP) regimen to dolutegravir, have started to emerge. This study aimed to describe the changes in neuropsychiatric symptoms before and after the transition from a NVP-based ARV regimen to DTG in HIV patients at Cipto Mangunkusumo Hospital (RSCM), Jakarta.

Methods. This study employed a prospective cohort design involving 292 HIV patients at Cipto Mangunkusumo Hospital who were transitioning from NVP to DTG regimen. Participants …

Immune Thrombocytopenic Purpura Association With Epstein-Barr Virus, Amer Aldamouk, Bachr Masri, Ali Khan, Pulkita Uppal

Graduate Medical Education Research Journal

Immune thrombocytopenia (ITP), also referred to as idiopathic thrombocytopenic purpura, is an acquired form of thrombocytopenia caused by antibodies directed against platelet glycoproteins, particularly anti-GpIIb/IIIa antibodies. Epstein-Barr virus (EBV), a herpes virus infecting a large majority of the population before adulthood, has been implicated in various immune-mediated disorders, including ITP. In this report, we present a case of a young adult female with a history of thrombocytopenia who was found to have severe thrombocytopenia attributed to chronic EBV infection. Despite initial treatment with corticosteroids and intravenous immunoglobulin (IVIG), the patient's condition necessitated second-line therapies, including rituximab and thrombopoietin receptor agonists. …

Pneumococcal Colonization Dynamics Among Young Children With And Without Respiratory Symptoms During The First Year Of The Sars-Cov-2 Pandemic., Liset Olarte, Brian R. Lee, Dithi Banerjee, Douglas Swanson, Christopher J. Harrison, Rangaraj Selvarangan

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: Non-pharmaceutical interventions to mitigate the spread of SARS-CoV-2 were implemented across the United States in 2020. These public health measures might influence pneumococcal colonization in younger children and their subsequent risk of invasive pneumococcal disease. Our objective was to evaluate pneumococcal colonization rates in children ≤ 5 years of age with and without respiratory symptoms during the first 12 months of SARS-CoV-2 pandemic (April 2020 - March 2021).

STUDY DESIGN: This is a retrospective cross-sectional study evaluating pneumococcal colonization rates, density and serotype distribution across three study periods (April-July [Period 1], August-November [Period 2] and December-March [Period 3]) after …

A Tubo-Ovarian Abscess In Aplastic Anemia Presenting As Fever Of Unknown Origin, Rashi Mittal, Saurabh Kumar Gautam, Prasan Kumar Panda, Latika Chawla

Chulalongkorn Medical Journal

This report describes a complex case of a tubo-ovarian abscess (TOA) presenting atypically as fever of unknown origin (FUO) in a young woman initially diagnosed with severe aplastic anemia. The case involved protracted febrile illness, heavy menstrual bleeding, and pancytopenia. Identification of an Escherichia coli tubo-ovarian abscess, rather than tuberculosis, emphasized the need for a thorough evaluation in atypical presentations of TOA. Negative tuberculosis tests highlighted the variety of possible microbial etiologies. The resolution of fever following drainage and tailored antibiotic therapy, along with timely surgical intervention, demonstrated the importance of specific management strategies in such cases. Awareness of the …

Building Models, Building Capacity: A Review Of Participatory Machine Learning For Hiv Prevention, Mark Sendak, Meg Young, Jee Young Kim, Alifia Hasan, Clare Kelsey, Catherine O’Neal, Tonya Jagneaux, Wayne Wilbright, John Couk, Stephen Lim, Tamachia Davenport, Shirley Lolis, Jennifer Thomas, Shannon Widman, Suresh Balu, Meredith Clement, Lance Okeke

School of Medicine Faculty Publications

A growing number of researchers and practitioners are embracing a “participatory turn” in machine learning (ML) to improve model development, prevent harm, and provide communities more influence over systems that impact them. In this paper, we explore the intersection of participatory practices in healthcare and the emerging focus on responsible AI with a focus on human immunodeficiency virus (HIV) care. We review the historical context of participation in HIV treatment and prevention, emphasizing how patient activism has shaped practices in this field. We then review participatory ML in HIV prevention and present a brief case study of a project designed …

Early Versus Late Vasopressor Initiation In Septic Shock – Elviss Study, Nathan Crawford, Brittanii Prahl, Jordan Amaro, Barbara Branneman, Jack Huber

2025 Swedish FISH (Fostering Interdisciplinary Solutions in Healthcare) Conference

No abstract provided.

Once-Daily Versus Twice-Daily Oral Vancomycin For Secondary Prevention Of Clostridioides Difficile Infection In Patients Treated With Systemic Antibiotics, Catherine Palmer

2025 Swedish FISH (Fostering Interdisciplinary Solutions in Healthcare) Conference

No abstract provided.