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Letter To The Editor: Evidence For A Two-Step Species-Level Pulmonary Nocardiosis Diagnostic Approach, John Halphen, Mohadese Ahmadzade, Babith Mankidy, Ashkan Berenji, Mohammad Ghasemi-Rad

Faculty, Staff and Students Publications

Pulmonary nocardiosis, a rare and diagnostically challenging infection, usually presents with heterogeneous radiographic findings, compounded by the low sensitivity of traditional confirmatory cultures. In their most recent work, Wang et al analyzed 102 patients with pulmonary nocardiosis to address these concerns, investigating species-characteristic imaging patterns, pathological associations, and the role of metagenomic next-generation sequencing (mNGS) in the diagnostic approach. High-resolution computed tomography (CT) in adult patients with pulmonary infections caused by Nocardia wallacei was demonstrated to have a sensitive (85.71%) and specific (83.34%) presentation of bronchopneumonia in relation to the five Nocardia species in the sample with CT data. The …

Incidence Of Autoimmune Diseases In Children With Atopy Treated With Dupilumab, Stanislaw J Gabryszewski, Kathryn Hirabayashi, Morgan Botdorf, Mitchell Maltenfort, Christopher B Forrest, Theresa W Guilbert, Madeline Schutt, Hiroki Morizono, Gerardo Vazquez Garcia, Anna Cristina Garza-Mayers, Joseph Demetrius Hernandez, Sara Anvari, Suchitra Rao, Jonathan M Spergel

Faculty, Staff and Students Publications

Background: The type 2 inflammation-blocking agent dupilumab has gained traction as an effective treatment of multiple atopic diseases. New-onset autoimmune manifestations have been infrequently reported in dupilumab-treated atopic patients, primarily among adults. Autoimmune outcomes in atopic children on dupilumab are less clear.

Objective: We aimed to determine if dupilumab treatment of atopic children is associated with increased autoimmune or autoinflammatory disease diagnosis risk.

Methods: Using a multi-institutional electronic health record database composed of 10 PEDSnet academic health systems, we performed a retrospective cohort study of children aged 6-17 with atopy (ie, moderate-to-severe atopic dermatitis and/or persistent asthma, as defined by …

2026 Clinical Practice Guideline Update By The Infectious Diseases Society Of America And The Pediatric Infectious Diseases Society On The Management Of Community-Acquired Pneumonia In Infants And Children Older Than 3 Months Of Age: The Choice Of Chest Tube Size, Shawn D St Peter, Krow Ampofo, Thomas Brogan, Michael D Cabana, Claudia Espinosa, Todd A Florin, Jeffrey S Gerber, Michelle Gill, Debra L Palazzi, Mark Sawyer, Angela Statile, Derek J Williams, Sheena Patel, Mark I Neuman, Samir S Shah

Faculty, Staff and Students Publications

This paper is part of a larger clinical practice guideline on the diagnosis and management of parapneumonic effusion and empyema in children, developed by the Infectious Diseases Society of America. In this paper, the panel provides recommendations on the appropriate size of thoracostomy tube for drainage. The panel's recommendations are based upon evidence derived from systematic literature reviews and adhere to a standardized methodology for rating the certainty of evidence and strength of recommendation according to the GRADE (Grading of Recommendations Assessment, Development, and Evaluation) approach.

2026 Clinical Practice Guideline Update By The Infectious Diseases Society Of America And The Pediatric Infectious Diseases Society On The Management Of Community-Acquired Pneumonia In Infants And Children Older Than 3 Months Of Age: The Use Of Tpa And Dnase Or Tpa Alone For Fibrinolysis, Shawn D St Peter, Krow Ampofo, Thomas Brogan, Michael D Cabana, Claudia Espinosa, Todd A Florin, Jeffrey S Gerber, Michelle Gill, Debra L Palazzi, Mark Sawyer, Angela M Statile, Derek J Williams, Sheena Patel, Mark I Neuman, Samir S Shah

Faculty, Staff and Students Publications

This paper is part of a larger clinical practice guideline on the diagnosis and management of parapneumonic effusion and empyema in children, developed by the Pediatric Infectious Diseases Society and the Infectious Diseases Society of America. In this report, the panel provides recommendations for intrapleural fibrinolysis with tissue plasminogen activator (tPA) alone over tPA and dornase alfa (DNase) in children (3 months to 18 years) with complicated parapneumonic effusion and empyema. The panel's recommendations are based upon evidence derived from systematic literature reviews and adhere to a standardized methodology for rating the certainty of evidence and strength of recommendation according …

Clinical Practice Guideline By The Infectious Diseases Society Of America And The Pediatric Infectious Diseases Society: 2026 Guideline Update On The Management Of Community-Acquired Pneumonia In Infants And Children Older Than 3 Months Of Age, Shawn D St Peter, Krow Ampofo, Thomas Brogan, Michael D Cabana, Claudia Espinosa, Todd A Florin, Jeffrey S Gerber, Michelle Gill, Debra L Palazzi, Mark Sawyer, Angela M Statile, Derek J Williams, Sheena Patel, Mark I Neuman, Samir S Shah

Faculty, Staff and Students Publications

As the first part of an update to the clinical practice guideline on the management of community-acquired pneumonia in infants and children older than 3 months of age, we present six updated recommendations. The updated recommendations span the characterization and management of pneumonia with parapneumonic effusion. The panel's recommendations are based on evidence derived from systematic literature reviews and adhere to a standardized methodology for rating the certainty of evidence and strength of recommendation according to the GRADE (Grading of Recommendations Assessment, Development, and Evaluation) approach.

2026 Clinical Practice Guideline Update By The Infectious Diseases Society Of America And The Pediatric Infectious Diseases Society On The Management Of Community-Acquired Pneumonia In Infants And Children Older Than 3 Months Of Age: The Use Of Chest Ultrasound In Children With Parapneumonic Effusion, Shawn D St Peter, Krow Ampofo, Thomas Brogan, Michael D Cabana, Claudia Espinosa, Todd A Florin, Jeffrey S Gerber, Michelle Gill, Debra L Palazzi, Mark Sawyer, Angela M Statile, Derek J Williams, Sheena Patel, Samir S Shah, Mark I Neuman

Faculty, Staff and Students Publications

This paper is part of a larger clinical practice guideline on the diagnosis and management of parapneumonic effusion and empyema in children, developed by the Pediatric Infectious Diseases Society and the Infectious Diseases Society of America. In this paper, the panel provides recommendations for the role of chest ultrasound to evaluate parapneumonic effusion and empyema. The panel's recommendations are based upon evidence derived from systematic literature reviews and adhere to a standardized methodology for rating the certainty of evidence and strength of recommendation according to the GRADE (Grading of Recommendations Assessment, Development, and Evaluation) approach.

2026 Clinical Practice Guideline Update By The Infectious Diseases Society Of America And The Pediatric Infectious Diseases Society On The Management Of Community-Acquired Pneumonia In Infants And Children Older Than 3 Months Of Age: The Use Of Pleural Fluid Drainage Compared To Surgical Debridement, Shawn D St Peter, Krow Ampofo, Thomas Brogan, Michael D Cabana, Claudia Espinosa, Todd A Florin, Jeffrey S Gerber, Michelle Gill, Debra L Palazzi, Mark Sawyer, Angela M Statile, Derek J Williams, Sheena Patel, Samir S Shah, Mark I Neuman

Faculty, Staff and Students Publications

This paper is part of a larger clinical practice guideline on the diagnosis and management of parapneumonic effusion and empyema in children, developed by the Infectious Diseases Society of America. In this paper, the panel provides recommendations on the choice of pleural fluid drainage by chest tube with fibrinolysis versus mechanical debridement. The panel's recommendations are based upon evidence derived from systematic literature reviews and adhere to a standardized methodology for rating the certainty of evidence and strength of recommendation according to the GRADE (Grading of Recommendations Assessment, Development, and Evaluation) approach.

2026 Clinical Practice Guideline Update By The Infectious Diseases Society Of America And The Pediatric Infectious Diseases Society On The Management Of Community-Acquired Pneumonia In Infants And Children Older Than 3 Months Of Age: The Use Of Pleural Fluid Drainage Versus Observation, Shawn D St Peter, Krow Ampofo, Thomas Brogan, Michael D Cabana, Claudia Espinosa, Todd A Florin, Jeffrey S Gerber, Michelle Gill, Debra L Palazzi, Mark Sawyer, Angela M Statile, Derek J Williams, Sheena Patel, Mark I Neuman, Samir S Shah

Faculty, Staff and Students Publications

This paper is part of a larger clinical practice guideline on the diagnosis and management of parapneumonic effusion and empyema in children, developed by the Infectious Diseases Society of America. In this paper, the panel provides recommendations for pleural fluid drainage in children (3 months to 18 years) with parapneumonic effusion and empyema. The panel's recommendations are based upon evidence derived from systematic literature reviews and adhere to a standardized methodology for rating the certainty of evidence and strength of recommendation according to the GRADE (Grading of Recommendations Assessment, Development, and Evaluation) approach.

Bacterial Fecal Microbiome Composition Associated With Hiv Stage Among Rural And Peri-Urban Adults Living With Hiv In Uganda, Bożena M Morawski, Elise R Morton, Miya Yunus, Claudia Muñoz-Zanzi, Rojelio Mejia, Ran Blekhman, David R Boulware, Sarah M Lofgren

Faculty, Staff and Students Publications

Background

Gut microbiome composition in HIV-infection provides insight into HIV pathogenesis and potentially offers avenues to adjunctive HIV therapies. Although two-thirds of people living with HIV (PLHIV) are in Africa, studies of the gut microbiome PLHIV have focused on non-African populations. Additionally, social, cultural, and environmental factors influence the gut microbiome and differ substantially between African and Western and urban and rural communities. Here, we quantify the relationships between immune status and fecal microbiome composition in 175 rural Ugandan PLHIV.

Methods

In 2013, 175 Ugandan PLHIV contributed a single fecal sample as part of a cohort study of 202 participants. …

Underexplored Maternal Microbiomes: Immune, Metabolic, And Microbial Pathways Shaping Pregnancy Outcomes, Rafael Tomoya Michita, Nicole Jimenez, Melissa M Herbst-Kralovetz, Indira U Mysorekar

Faculty, Staff and Students Publications

Maternal microbial ecosystems play critical roles in shaping reproductive physiology and pregnancy outcomes. During the pre-conception and prenatal periods, these communities modulate maternal physiology by regulating immune tolerance, nutrient metabolism, and susceptibility to pregnancy complications such as preterm birth, hypertensive disorders, and gestational diabetes. While the gut microbiota has been extensively studied, the roles of cervicovaginal, urinary, respiratory, oral, and upper reproductive tract microbiomes remain less clear. In this minireview, we synthesize current knowledge on these underexplored maternal microbiomes, with an emphasis on the cervicovaginal and urinary microbiota and their interactions with the placenta and fetus. We discuss cross-niche microbial …

Defining The Society Of Pediatric Liver Transplantation (Split) Research Agenda: A Delphi Consensus Project, Sharad I Wadhwani, Pooja Reddy Spector, Amy G Feldman, Katryn N Furuya, Kayla Hartjes, Chaowapong Jarasvaraparn, Beau Kelly, Stacee M Lerret, Krupa Mysore, Arti Pawaria, Philip Rosenthal, Amy Shui, Voytek Slowik, Sarah Taylor, Jennifer Vittorio, Pamela L Valentino

Faculty, Staff and Students Publications

Background: Despite major advances in surgical and medical management, only one-third of pediatric liver transplant (LT) recipients remain morbidity-free at 10 years. The Society of Pediatric Liver Transplantation (SPLIT) published a research agenda over 10 years ago, and much progress has been made since then. An updated consensus-driven SPLIT research agenda could guide future research and funding priorities. We aimed to identify and prioritize key research needs across the continuum of pediatric LT care using a modified Delphi consensus approach.

Methods: We conducted a three-round modified Delphi process among SPLIT members. In round 1, participants submitted open-ended research priorities. In …

Comparing Observed With Self-Reported Hand Hygiene Adherence Among Bedside Nurses And Physicians At Two Hospitals In The United States, Prathit A Kulkarni, M Todd Greene, Sanjay Saint, Karen E Fowler, Serene Jacob, Laura Dillon, Michelle Espiritu, Nathan Houchens, Huberta T Cozart, Barbara W Trautner

Faculty, Staff and Students Publications

Background: Hand hygiene is a core component of infection prevention in healthcare settings. One potential reason for lack of adherence to recommended hand hygiene practices is erroneous self-perception. We aimed to compare perceptions about hand hygiene compliance with objective data.

Methods: Direct observations of hand hygiene performance by nurses and physicians during typical workflow in inpatient general medicine wards were conducted from 12 September 2022 to 27 October 2022 at two academic Veterans Affairs medical centers. Participants were surveyed regarding perceptions about their hand hygiene performance relative to recommended practices.

Results: Among nurses, hand hygiene was performed in 1,397/3,690 (37.9%) …

Rounding Styles On Inpatient Infectious Disease Consult Services: Impact On Education And Patient-Care Delivery, Melanie Kiener, Vanessa Ku, Prathit A Kulkarni

Faculty, Staff and Students Publications

Inpatient infectious disease (ID) consult services have recently been experiencing increased patient volumes due to a variety of factors, including higher patient complexity, increased patient turnover, growing rates of antimicrobial resistant infections, population aging, and ID outbreaks. As a result, increased time and resources have been required to continue to deliver high-quality medical care to patients. At academic teaching hospitals, providing patient care in the context of increased volumes must be balanced with the educational mission for trainees. Rounding is a central component of ID clinical work which brings together patient care and education. In this narrative review, we aim …

Statistical Methods In Aging Research: Improving Current Practices And Embracing Emerging Approaches, Deependra K Thapa, Erik S Parker, Mounika Kandukuri, Xi Rita Wang, Thirupathi R Mokalla, Olivia C Robertson, Wasiuddin Najam, Andrew E Teschendorff, Andrew W Brown, John R Speakman, Yisheng Peng, Bernard S Gorman, Heping Zhang, Luis-Enrique Becerra-Garcia, Colby J Vorland, David B Allison

Faculty, Staff and Students Publications

Aging research relies on varied statistical methods, and applying these methods appropriately is important for scientific rigor. However, proper use of these statistical techniques is a challenge. We discuss two categories of statistical methods in aging research: (a) emerging methods requiring further validation, including techniques to examine compression of morbidity, maximum lifespan, immortal time bias, molecular aging clocks, and treatment response heterogeneity, and (b) classic and existing methods needing reconsideration and improvement, such as stepwise regression, generalized linear models, methods for accounting for clustering and nesting effects, methods for testing for group differences, methods for mediation …

Predicting Mortality And Costs After Emergency Department Visits By People With Dementia: Timing And Location Matter, Jason K Bowman, Christine S Ritchie, Kei Ouchi, Kyler M Godwin, James A Tulsky, Joan M Teno

Faculty, Staff and Students Publications

Background: People with dementia have high rates of emergency department (ED) and hospital utilization, high mortality and costs, and other poor outcomes. To successfully impact the care trajectories of these patients, health care systems must pragmatically identify the correct target population. This study described patterns of ED utilization by people with dementia and explored the accuracy of administrative data models to predict mortality and costs.

Methods: Retrospective cohort study of a 20% random sample of Traditional Medicare (TM) beneficiaries with dementia, age ≥ 66 years, and an index ED visit in 2018. One-year mortality and high costs were described, and …

Incidence Of Cancers Among Children Living With Hiv In Malawi After Widespread Availability Of Antiretroviral Therapy: A Population-Based Study, Casey L Mcatee, Fatsani Manase, William Kamiyango, Jimmy Villiera, Mark Zobeck, Joseph Mhango, Allison Silverstein, Samuel Maloya, Apatsa Matatiyo, Eluness Simwela, Honour Mhango, Desire Hellings, Brigid O'Brien, Claudia Wallrauch, Tom Heller, Matthew Painschab, Kate Westmoreland, Atupele Mpasa, Rizine Mzikamanda, Nmazuo Ozuah, Joseph Lubega, Nader Kim El-Mallawany, Carl E Allen, Michael E Scheurer

Faculty, Staff and Students Publications

Purpose: Few data describe the modern epidemiology of pediatric HIV-associated cancers in sub-Saharan Africa, home to over 80% of the world's children living with HIV. This study evaluated the incidence of cancers among these children over 15 years after widespread antiretroviral therapy (ART) adoption in Malawi.

Methods: We conducted a retrospective population-based cohort study leveraging multiple independent data sources comprehensive of all cancer diagnoses among children living with HIV in Northern and Central Malawi between 2010 and 2024. HIV-associated cancers were defined as those cancers with well-established epidemiologic associations with HIV. Cumulative incidence and average annual percent change were estimated …

Adenovirus Disease Following Pediatric Liver Transplantation: 10-Year Experience From A Large Pediatric Transplant Program, Anna M Banc-Husu, Sara Hassan, N Thao N Galvan, Elizabeth A Moulton, Jeremy M Schraw, Kathleen Hosek, Dana Cerminara, Flor M Munoz, Krupa Mysore

Faculty, Staff and Students Publications

Background: Human adenovirus in immunocompromised patients can be life-threatening. We describe the prevalence, clinical presentation, and treatment of adenovirus after pediatric liver transplantation at a large transplant center.

Methods: We performed a retrospective cohort study of adenovirus infection in children from 2013 to 2022. We compared incidence, clinical characteristics, and outcomes of post-transplant children by adenovirus treatment status.

Results: Adenovirus disease developed in 26% (84/320) children after liver transplant. Median age at liver transplant was 17.5 months, 48% were female; 50% had biliary atresia. Fever (53%), gastrointestinal symptoms (48%), and hepatitis (41%) were the most common clinical presentations at diagnosis. …

Respiratory Syncytial Virus Co-Detection With Other Respiratory Viruses Is Not Significantly Associated With Worse Clinical Outcomes Among Children Aged <2 Years: New Vaccine Surveillance Network, 2016-2020, Justin Z Amarin, Ariana P Toepfer, Andrew J Spieker, Haya Hayek, Tess Stopczynski, Yasmeen Z Qwaider, Laura S Stewart, James D Chappell, Mary Allen Staat, Elizabeth P Schlaudecker, Geoffrey A Weinberg, Peter G Szilagyi, Janet A Englund, Eileen J Klein, Marian G Michaels, John V Williams, Rangaraj Selvarangan, Christopher J Harrison, Leila C Sahni, Vasanthi Avadhanula, Meredith L Mcmorrow, Heidi L Moline, Natasha B Halasa

Faculty, Staff and Students Publications

Background: Risk factors for severe respiratory syncytial virus (RSV) illness include early infancy, premature birth, and underlying medical conditions. However, the clinical significance of respiratory viral co-detection is unclear. We compared the clinical outcomes of young children with RSV-only detection and those with RSV viral co-detection.

Methods: We conducted active, population-based surveillance of children with medically attended fever or respiratory symptoms at 7 US medical centers (1 December 2016-31 March 2020). Demographic and clinical data were collected through parental interviews and chart abstractions. Nasal swabs, with or without throat swabs, were systematically tested for RSV and 6 other common respiratory …

Online Decision Support For Implementing Evidence-Based Hpv Vaccination Strategies In Texas Safety-Net Pediatric Clinics: Impact On Hpv, Mcv, And Tdap Initiation, Ross Shegog, Hanxiao Sun, Erica L Frost, Laura C Thormaehlen, Travis A Teague, Catherine Mary Healy, Hina Azam, Aadeel Khawaja, Laura Aubree Shay, Dale S Mantey, Sally W Vernon, Lara S Savas

Faculty, Staff and Students Publications

Introduction: HPV vaccination rates for adolescents in the United States are below recommended levels. The Adolescent Vaccination Program (AVP) guides pediatric clinics on how to implement evidence-based strategies to increase HPV vaccination rates. These strategies comprise the adoption of (1) immunization champions, (2) provider assessment and feedback, (3) continuing education, and (4) prompts, (5) parent reminders, and (6) parent education. The AVP systems-based intervention has demonstrated increased HPV vaccination rates in large urban pediatric clinic networks. The purpose of this study was to assess the feasibility of using an online decision support tool, the AVP Implementation Tool (AVP-IT), to …

Discovery And Characterization Of A Novel Pseudomonas Phage Of A New Genus, Paul Nicholls, Justin R Clark, Anthony Maresso

Faculty, Staff and Students Publications

Background: Bacteriophages exhibit great diversity and are classically divided into lytic and temperate lifestyles. Commonly, bioinformatics is used to predict the temperate lifestyle. As the nosocomial pathogen Pseudomonas aeruginosa is common in freshwater, this biome represents an ideal location for the discovery of Pseudomonas phages.

Materials and methods: We characterized a genetically distinct species of Pseudomonas phage using next-generation sequencing and conventional microbiological methods. We characterized its lifestyle by purifying infected colonies and identifying persistent phage production.

Results: Genetics revealed a phage of a novel genus. Characterization showed a narrow host range and bioinformatics suggested a lytic lifestyle. Experimental data …

Utilization Of Intensive Care Interventions In Critically Ill Patients With Candidemia Versus Bacteremia: A Multicenter Retrospective Cohort Study, Mary North Jones, Masayuki Nigo, Stefano Casarin, James Kurian, Aarjav Sanghvi, Enshuo Hsu, Stephen L Jones, Ashton Connor, David B Corry, Cesar A Arias, Max W Adelman

Faculty, Staff and Students Publications

Objectives: Candida species are one of the most common causes of ICU-onset bloodstream infection (BSI). Yet, there is no robust guidance on when to initiate empiric antifungals for ICU patients suspected of BSI. We compared patients with ICU-onset candidemia vs. ICU-onset bacteremia to determine which patients may benefit from empiric antifungals.

Design: We compared characteristics between patients with bacteremia vs. candidemia at time of culture. We determined risk factors for death and constructed a multivariable regression to determine if candidemia is an independent risk factor for death.

Setting/patients: We included ICU patients from a hospital system in Houston, Texas (n …

Diagnostic Evaluation And Treatment Of Utis In Children With Neurogenic Bladder, Jacqueline G Holden, Sowdhamini Wallace, Pearl W Chang, Stephanie Davis-Rodriguez, Rana F Hamdy, John M Morrison, Michael J Tchou, Victor Trevisanut, Vijaya Vemulakonda, Catherine S Forster

Faculty, Staff and Students Publications

Objective: Children with neurogenic bladder (NGB) are at increased risk for urinary tract infections (UTIs), but there is a lack of guidelines to assist clinicians in diagnosing and treating these children. Our objective was to describe the presentation and treatment of provider diagnosed UTIs in children with NGB compared to children with vesicoureteral reflux (VUR) and to assess the proportion of children with NGB who met a consortium definition of UTI.

Study design: We included children < 18 years old with either VUR or NGB who were diagnosed in the emergency department with a febrile UTI in our multicenter retrospective cohort study. We extracted and compared UTI symptoms and urinalysis results specific to children with NGB to children with VUR. We measured the proportion of UTI diagnoses concordant with the Urologic Management to Preserve Initial Renal Function (UMPIRE) consensus definition of UTI, defined as ≥ 100,000 CFU/mL of 1 or 2 organisms, pyuria, and ≥ two symptoms of UTI.

Results: The most common symptom among all children in the cohort was vomiting (38.8 %). Of the 215 children with NGB, 41.3 % met …

A Scalable Organoid Model Of Urothelial Aging For Metabolic Interrogation, Infection Modeling, And Reversal Of Age-Associated Changes, Adwaita R Parab, Arnold M Salazar, Steven J Bark, Margarita Divenko, Vasanta Putluri, D'Feau J Lieu, Aadya S Singh, Nagireddy Putluri, Indira U Mysorekar

Faculty, Staff and Students Publications

Aging leads to a progressive decline in overall bladder function resulting in lower urinary tract symptoms and increased susceptibility to infections. However, tissue-specific mechanisms of aging, specifically the contributions of the urothelium, remain elusive. Here, we introduce mouse bladder epithelium-derived organoids (mBEDOs) as a scalable platform to model urothelial aging. mBEDOs from aged mice recapitulate key features of age-associated cellular reprogramming, including oxidative stress, senescence, and DNA damage. We demonstrate the utility of mBEDOs for modeling Uropathogenic Escherichia coli (UPEC) infection, generating assembloids between mBEDOs and macrophages to model epithelial-immune interactions, and genetic perturbation. Using the mBEDO platform, we also …

Nasal Microbiome And Phageome Profiles Are Associated With Prospective Respiratory Viral Infection Risk In School-Age Children, Michael S Kelly, Ching-Ying Huang, Minsik Kim, Dastan Haghnazari, Aribah Baig, Ye Sun, Bryan R Lenneman, Michael J Tisza, Amparito Cunningham, Diane Gold, Wanda Phipatanakul, Peggy S Lai

Faculty, Staff and Students Publications

Background: Respiratory viral infections are common and can trigger asthma exacerbations in children. The roles of the nasal microbiome and phageome (viruses that infect microbes) are not well understood.

Objective: We sought to characterize the epidemiology of respiratory viral infections and the interplay between the nasal microbiome, phageome, and viral infections in school-age children with asthma.

Methods: We performed metagenomic sequencing and quantitative RT-PCR detection of respiratory viruses on 375 nasal samples from 227 school-age children with asthma collected routinely 3 times over a year. Surveys on parent-reported cold and asthma symptoms were administered routinely every 2 months. We evaluated …

Cressent: A Bioinformatics Toolkit To Explore And Improve Ssdna Virus Annotation, Ricardo R Pavan, Matthew B Sullivan, Michael J Tisza

Faculty, Staff and Students Publications

ssDNA viruses are important components of diverse ecosystems; however, it remains challenging to systematically identify and classify them. This is partly due to their broad host range and resulting genomic diversity, structure and rapid evolutionary rates. In addition, distinguishing genuine ssDNA genomes from contaminating sequences in metagenomic datasets (e.g. from commercial kits) has been an unresolved issue for years. Here, we present CRESSENT (CRESS-DNA Extended aNnotation Toolkit), a comprehensive and modular bioinformatic pipeline focused on ssDNA virus 'genome-to-analysis' and annotation. The pipeline integrates multiple functionalities organized into several modules: sequence dereplication, decontamination, phylogenetic analysis, …

The Evolution Of Public Health Statistical Modeling Approaches And How To Advance Their Incorporation Into Modern Arboviral Surveillance, Maggie Mccarter, Stella C W Self, Alex Ewing, Mufaro Kanyangarara, Sarah M Gunter, Melissa S Nolan

Faculty, Staff and Students Publications

Statistical modeling of infectious disease transmission patterns has been in existence since the mid-1700s, evolving in their utility as the scientific and technological revolutions progressed. Despite the expansion of emerging mathematical and statistical methodologies over the past 250 yr, their usage has largely remained restricted to academic settings. This forum article will discuss the evolution of disease modeling techniques, the most common types of models in use today, and recommendations on how key archetypes can be incorporated into future public health practice. With the recent global impetus to predict and forecast novel pathogens, this article raises the question: Why are …

The Use Of Artificial Intelligence In Decreasing Vaccine Skepticism And Hesitancy, Nathaniel Wolf, Nhan Nguyen, Rojelio Mejia

Faculty, Staff and Students Publications

Purpose of review: Recent advances in artificial intelligence (AI) coincide with decreases in confidence in vaccines. This review examines studies that analyze and mitigate vaccine skepticism by implementing artificial intelligence strategies in various ways.

Recent findings: Studies have explored public attitudes towards vaccines using AI to analyze language in social media postings and interactions, scrutinize AI responses to vaccine-related queries, and attempt to use AI to directly influence vaccine hesitancy. Findings show that AI can be effective in addressing vaccine hesitancy in various ways, including, but not limited to, directly interacting with vaccine-hesitant groups, identifying reasons for vaccine hesitancy, and …

Maternal Immunization With Vp8* Mrna Vaccine Yields Superior Passive Transfer Of Rotavirus-Neutralizing Antibodies To Foals, Karin E R Borba, Rebecca M Legere, Nathan M Canaday, Jill W Skrobarczyk, Zachary W T Arnold, Elena Cotton-Betteridge, Cristina Poveda, Michael F Criscitiello, Angela I Bordin, Luc R Berghman, Jeroen B K Pollet, Noah D Cohen

Faculty, Staff and Students Publications

Background: Despite the availability of a killed whole-virus (KV) vaccine, diarrhea caused by equine rotavirus group A (ERVA) remains a significant health concern for foals in the United States. The vaccine is administered to pregnant mares, with foals protected by passive transfer of colostral antibodies. However, KV-induced immunity is only partially protective and maternal antibody levels in foals are often low and wane rapidly. To address these limitations, we developed a mRNA-based ERVA vaccine encoding the highly conserved VP8* protein to evaluate whether it can provide improved immune protection.

Methods: Pregnant mares (n = 12 per group) were …

Pathways, Outputs And Impact Of Nih-Supported Bioinformatics And Genomics Graduate Trainees In Africa, Daudi Jjingo, Andrew Walakira, Suhaila Hashim, Cisse Cheickna, Ronald Galiwango, Caleb Kibet, Florence N Kivunike, Gerald Mboowa, Fredrick Elishama Kakembo, Babajide Ayodele, Jean-Baka Domelevo Entfellner, Santie De Villiers, Karen Wambui, Segun Fatumo, Tinashe Chikowore, John Mukisa, Alfred Ssekagiri, Nicholas Bbosa, Julius Mulindwa, Samuel Kyobe, Mike Nsubuga, Grace Kebirungi, Eric Katagirya, Savannah Mwesigwa, Ibra Lujumba, Rogers Kamulegeya, Samuel Kirimunda, Stephen Kanyerezi, Shahiid Kiyaga, Ivan Sserwadda, Davis Kiberu, Bernard S Bagaya, Julius Okwir, Patricia Nabisubi, Grace Nabakooza, Mugume Twinamatsiko Atwine, Ricard Sserunjogi, Rolanda Julius, Mariam Quiñones, Meghan Mccarthy, Phillip Cruz, Karlynn Noble, Christopher J Whalen, Darrell Hurt, Maria Y Giovanni, Michael Tartakovsky, Deogratius Ssemwanga, John M Kitayimbwa, Steven J Reynolds, Christopher C Whalen, Andrew Kambugu, Neil A Hanchard, Li Jian, Peter Amoako-Yirenkyi, Graeme Mardon, I King Jordan, Samson Pandam Salifu, Mamadou Wele, Ezekiel Adebiyi, Jeffrey G Shaffer, Seydou Doumbia, David Patrick Kateete, Michelle Skelton, Nicola Mulder, Jonathan K Kayondo, Daniel Masiga, H3africa Consortium

Faculty, Staff and Students Publications

Global biomedical and health research is increasingly relying on genomic and computational approaches, largely driven by the increasing volumes of nucleic acid sequencing. Concurrently, epidemiological studies and clinical records are generating enormous amounts of data amenable to disease modeling, machine learning, and artificial intelligence techniques. Bioinformatics and data science expertise is therefore essential for improved population health. Accordingly, in 2012, the US National Institutes of Health (NIH) in partnership with the Wellcome Trust, and with support from the African Society for Human Genetics, initiated the H3Africa (Human Heredity and Health in Africa) consortium. One of its key goals was to …

A Systematic Literature Review Of Cvid Reveals Pervasive Detrimental Noninfectious Manifestations, G Michelle Ducasa, Rebecca A Marsh, Ali Mojebi, Hsi-En Ho, Charlotte Cunningham-Rundles, Lisa Forbes Satter, Elena W Y Hsieh, Sinisa Savic, Marta Dafne Cabañero-Navalón, Hector Balastegui-Martin, Joud Hajjar, Gulbu Uzel, Kevin S Thorneloe, Jocelyn R Farmer

Faculty, Staff and Students Publications

Noninfectious manifestations of common variable immunodeficiency (CVID) are not formally summarized. We performed a systematic literature review to generate a comprehensive reference for the field. Splenomegaly was the most reported manifestation across 53 publications, occurring in a median of 35.2% of patients. Frequently reported digestive system manifestations included diarrhea (median 27.8%; 21 publications), hepato(spleno)megaly (median, 21.0%; 19 publications), portal hypertension (median 21.0%; 3 publications), nodular lymphoid hyperplasia (median, 17.0%; 9 publications), and enteropathy (median, 16.0%; 34 publications). Other notable manifestations included interstitial lung disease (median, 8.7%; 32 publications) and autoimmune cytopenias (median 18.0%; 21 publications). Steroids and rituximab were the …