Publications by authors named "Vaughn Cooper"

The field of microbial ecology, evolution, and biodiversity (EEB) is at the leading edge of understanding how microbes shape our biosphere and influence the well-being of humankind and Earth. To that end, EEB is developing new transdisciplinary tools to analyze these ecologically critical, complex microbial communities. The American Society for Microbiology's Council on Microbial Sciences hosted a virtual retreat in 2023 to discuss the trajectory of EEB both within the Society and microbiology writ large.

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  • Elexacaftor/tezacaftor/ivacaftor (ETI) therapy has significantly improved cystic fibrosis (CF) treatment, yet its impact on sinus microbiota remains unknown.
  • A study involving 38 adults with CF and chronic rhinosinusitis examined sinus samples pre- and post-ETI using advanced sequencing methods.
  • Results showed that while total bacterial load and diversity didn't significantly change after ETI, certain bacterial species, including methicillin-resistant Staphylococcus aureus (MRSA), persisted, indicating the need for ongoing management of these pathogens in CF care.
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A Pacific native lineage of ST36 serotype O4:K12 was introduced into the Atlantic, which increased local source illnesses. To identify genetic determinants of virulence and ecological resiliency and track their transfer into endemic populations, we constructed a complete genome of a 2013 Atlantic-traced clinical isolate by hybrid assembly.

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  • Understanding bacterial movement from human feces may help diagnose and treat inflammatory bowel disease.
  • The text outlines a method for conducting a microbial swarming assay to isolate and identify these bacteria using techniques like MALDI-TOF mass spectrometry and whole-genome sequencing.
  • It emphasizes the importance of validating results by repeating the swarming assay to confirm the observed behavior of the bacteria.
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Unlabelled: Today, more than 90% of people with cystic fibrosis (pwCF) are eligible for the highly effective cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapy called elexacaftor/tezacaftor/ivacaftor (ETI) and its use is widespread. Given the drastic respiratory symptom improvement experienced by many post-ETI, clinical studies are already underway to reduce the number of respiratory therapies, including antibiotic regimens, that pwCF historically relied on to combat lung disease progression. Early studies suggest that bacterial burden in the lungs is reduced post-ETI, yet it is unknown how chronic populations are impacted by ETI.

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spp. are often resistant to antibiotics, and infections with these organisms are difficult to treat. A potential alternative treatment for spp.

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Background: While the widespread initiation of elexacaftor/tezacaftor/ivacaftor (ETI) has led to dramatic clinical improvements among persons with cystic fibrosis (pwCF), little is known about how ETI affects the respiratory mucosal inflammatory and physiochemical environment, or how these changes relate to lung function.

Methods: We performed a prospective, longitudinal study of adults with CF and chronic rhinosinusitis (CF-CRS) followed at our CF center (n = 18). Endoscopic upper respiratory tract (paranasal sinus) aspirates from multiple visit dates, both pre- and post-ETI initiation, were collected and tested for cytokines, metals, pH, and lactate levels.

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spp. are often resistant to antibiotics, and infections with these organisms are difficult to treat. A potential alternative treatment for spp.

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Background: Sepsis is a common and deadly syndrome, accounting for more than 11 million deaths annually. To mature a deeper understanding of the host and pathogen mechanisms contributing to poor outcomes in sepsis, and thereby possibly inform new therapeutic targets, sophisticated, and expensive biorepositories are typically required. We propose that remnant biospecimens are an alternative for mechanistic sepsis research, although the viability and scientific value of such remnants are unknown.

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  • Antibiotic resistance is a big problem for global health, and fluoroquinolone resistance is rare even though the drug is often used.
  • * Research found that some bacteria can adapt to survive antibiotics by changing how they use energy, without actually becoming resistant.
  • * This study helps us understand why fluoroquinolone resistance is uncommon, showing that it comes with some disadvantages for bacteria during infections.
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  • Scientists need to understand how germs (pathogens) from the environment change and grow, especially because of climate change.
  • Researchers studied how certain bacteria and their viruses (phages) affected the spread of a specific type of bacteria that caused problems in the Atlantic Ocean.
  • They found that when these viruses were lost, the bacteria changed quickly, suggesting that these viruses might help germs adapt and evolve in nature.
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We report here seven draft genomes of bacterial strains from two Danish wastewater facilities, two of which might be characterized as a new group within the and genera, respectively. These genomes will provide useful references for understanding bacterial interactions and horizontal gene transfer within bacterial communities.

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Pathogenic bacteria must evolve various mechanisms in order to evade the host immune response that they are infecting. One aspect of the primary host immune response to an infection is the production of an inflammatory effector component, nitric oxide (NO⋅). has uniquely evolved a diverse array of strategies to circumvent the inhibitory activity of nitric oxide.

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Background: Chronic rhinosinusitis (CRS) is common in individuals with cystic fibrosis (CF) and is marked by chronic inflammation and episodes of infection that negatively impact quality of life. Several studies have shown that elexacaftor-tezacaftor-ivacaftor (ETI) improves symptoms and examination findings in CF-CRS. The current study determines the effect of ETI on the sinonasal microbiota in CF.

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Introduction: The Cardiovascular Disease (CVD) Prevention project is a VA-DoD initiative, supported by the Joint Incentive Fund. The goal of the project is to create an innovative, 3D virtual space within the VA-Virtual Medical Center (VA-VMC) platform that provides Veterans and Active Duty Service Members with educational resources on the prevention of CVD.

Materials And Methods: The Performance Health and Wellness Center is a new center within the VA-VMC.

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Background: Healthcare-associated bacterial pathogens frequently carry plasmids that contribute to antibiotic resistance and virulence. The horizontal transfer of plasmids in healthcare settings has been previously documented, but genomic and epidemiologic methods to study this phenomenon remain underdeveloped. The objectives of this study were to apply whole-genome sequencing to systematically resolve and track plasmids carried by nosocomial pathogens in a single hospital, and to identify epidemiologic links that indicated likely horizontal plasmid transfer.

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  • High sugar diets in high-income countries may negatively impact the function of intestinal stem cells (ISCs) and transit-amplifying (TA) cells, which are crucial for maintaining the colonic epithelium and repairing damage.
  • Research using colonoids and a mouse model showed that excess sugar limits the development and proliferation of these cells by reducing the expression of growth-related genes and altering their metabolic pathways.
  • Findings suggest that short-term high-sucrose intake can inhibit the regenerative capabilities of ISCs and TA cells, potentially guiding dietary choices for better recovery from intestinal injuries.
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Background: There is increased interest in bacteriophage (phage) therapy to treat infections caused by antibiotic-resistant bacteria. A lung transplant recipient with cystic fibrosis and Burkholderia multivorans infection was treated with inhaled phage therapy for 7 days before she died.

Methods: Phages were given via nebulization through the mechanical ventilation circuit.

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When microbes grow in foreign nutritional environments, selection may enrich mutations in unexpected pathways connecting growth and homeostasis. An evolution experiment designed to identify beneficial mutations in Burkholderia cenocepacia captured six independent nonsynonymous substitutions in the essential gene , which modifies tRNA by adding a lysine to the anticodon for faithful AUA recognition. Further, five additional mutants acquired mutations in tRNA, which strongly suggests that disrupting the TilS-tRNA interaction was subject to strong positive selection.

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We performed whole genome sequencing on SARS-CoV-2 from 59 vaccinated individuals from southwest Pennsylvania who tested positive between February and September, 2021. A comparison of mutations among vaccine breakthrough cases to a time-matched control group identified potential adaptive responses of SARS-CoV-2 to vaccination.

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  • Staphylococcus aureus can worsen outcomes when it causes pneumonia following viral infections, like influenza, leading to a complex situation known as superinfection.
  • Research has investigated how cell wall-anchored proteins (CWAs) in S. aureus affect its virulence during single and superinfections, revealing that these proteins are critical for bacterial survival and lung damage.
  • A specific CWA, known as SasD, has been identified as a novel factor that reduces inflammation and bacterial burden in superinfections, providing insights into how S. aureus interacts with the immune system in the lungs.
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Background And Objectives: A key strategy for resolving the antibiotic resistance crisis is the development of new drugs with antimicrobial properties. The engineered cationic antimicrobial peptide WLBU2 (also known as PLG0206) is a promising broad-spectrum antimicrobial compound that has completed Phase I clinical studies. It has activity against Gram-negative and Gram-positive bacteria including infections associated with biofilm.

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Healthcare-associated infections (HAIs) cause mortality, morbidity, and waste of health care resources. HAIs are also an important driver of antimicrobial resistance, which is increasing around the world. Beginning in November 2016, we instituted an initiative to detect outbreaks of HAIs using prospective whole-genome sequencing-based surveillance of bacterial pathogens collected from hospitalized patients.

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