Organisms Commons^™

A Microbiome Analysis Of The Relationship Among Crayfish Ectosymbionts And Their Environment, John Hoverson

Senior Honors Theses

The purpose of this project was to determine if there are differences present between the α-diversities of the crayfish microbiome and its surrounding water and sediment. Furthermore, this project sought to discover if these differences hold when microbiomes are evaluated between crayfish of first and second stream orders. Finally, this project sought to determine if the presence of branchiobdellidan ectosymbionts on the crayfish caused further differences in the crayfish microbiome. While the hypothesized patterns between crayfish, ectosymbionts, and stream order were not found to exist, a significantly different microbiome was observed between water, sediment, and crayfish, and the α-diversity of …

Increasing Antibiotic Resistance In Shigella Bacteria In The United States, William J. Pharr

The Corinthian

Shigella bacteria cause half a million infections, 6,000 hospitalizations, and 70 deaths annually in the United States. These bacteria are of particular concern due to their high survivability, low infectious dose, and high adaptability. Cases of shigellosis from Shigella sonnei are becoming a more prevalent issue in the U.S. as the bacteria continues to develop higher resistance to today’s strongest antibiotics. Much of this resistance is connected to the exchange of genes between strains of Shigella due to insertion sequences (IS), intercontinental travel, and men who have sex with men (MSM). As a result of increased resistance, the use of …

Author Correction: Roadmap For Naming Uncultivated Archaea And Bacteria (Nature Microbiology, (2020), 5, 8, (987-994), 10.1038/S41564-020-0733-X), Alison E. Murray, John Freudenstein, Simonetta Gribaldo, Roland Hatzenpichler, Philip Hugenholtz, Peter Kämpfer, Konstantinos T. Konstantinidis, Christopher E. Lane, R. Thane Papke, Donovan H. Parks, Ramon Rossello-Mora, Matthew B. Stott, Iain C. Sutcliffe, J. Cameron Thrash, Stephanus N. Venter, William B. Whitman, Silvia G. Acinas, Rudolf I. Amann, Karthik Anantharaman, Jean Armengaud, Brett J. Baker, Roman A. Barco, Helge B. Bode, Eric S. Boyd, Carrie L. Brady, Paul Carini, Patrick S.G. Chain, Daniel R. Colman, Kristen M. Deangelis, Maria Asuncion De Los Rios, Paulina Estrada-De Los Santos

Life Sciences Faculty Research

No abstract provided.

Investigating Microbial And Host Factors That Modulate Severity Of Clostridioides Difficile Associated Disease, Armando Lerma

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Clostridioides difficile is recognized as one of the most important pathogens in hospital and community healthcare settings. The clinical outcome of infection of toxigenic C. difficile infection (CDI) ranges from asymptomatic colonization to fulminant pseudomembranous colitis and death. In recent studies, it has been suggested that a high proportion of nosocomial CDI cases are transmitted from asymptomatic carriers which might be acting as infection reservoirs. Understanding what causes the different responses to infection could lead to the development of novel prevention and treatment strategies. Although several explanations have been proposed to explain variations in susceptibility, understanding of the exact mechanisms …

Response Of Extensively Drug Resistant Salmonella Typhi To Treatment With Meropenem And Azithromycin, In Pakistan, Sonia Qureshi, Abdullah B. Naveed, Mohammad Tahir Yousafzai, Khalil Ahmad, Sarwat Ansari, Heeramani Lohana, Aiman Mukhtar, Farah Naz Qamar

Department of Paediatrics and Child Health

Introduction: Salmonella Typhi is one of the leading health problems in Pakistan. With the emergence of extensively drug resistant (XDR) Salmonella Typhi, treatment options are limited. Here we report the clinical manifestations and the response to treatment of patients with XDR Typhoid fever. The patients were treated with either Meropenem or Azithromycin or a combination of both.
Methods: We reviewed the records of culture confirmed XDR typhoid who visited Aga Khan University Hospital (AKUH), Karachi and Aga Khan Secondary Care Hospital, Hyderabad from April 2017 to June 2018. Symptoms developed during disease, unplanned treatment extension and complications developed while on …

Stutzman, Kelsi - Covid-19 Journal, Kelsi Stutzman

Personal Journals

Personal journal of Kelsi Stutzman, a student in Dr. Laughlin-Schultz's HIS3810 History of Illinois course during Fall, 2020

Vitamin D In Covid-19 Pneumonia: High Yield With Low Risk, Shahan Waheed, Emaduddin Siddiqui

Department of Emergency Medicine

No abstract provided.

The Inhibitory Effects Of An Antimicrobial Gel On The Staphylococcus Species, Mara Trinkle

Undergraduate Honors Theses

The prevalence of antibiotic resistant bacteria has made the choices for topical treatments for patients who experience burns wounds extremely limited. The Staphylococcus genus is naturally occurring in and on the human body but can become harmful once it enters the bloodstream. A novel antimicrobial gel has been shown by our laboratory to inhibit both the planktonic growth and biofilm formation of Staphylococcus aureus in previous studies. The antimicrobial gel is made of seven natural compounds including antioxidants (vitamin C and E). We wanted to examine the effects of the antimicrobial gel on numerous other Staphylococcal species because it is …

Plasmodium Impairs Antibacterial Innate Immunity To Systemic Infections In Part Through Hemozoin-Bound Bioactive Molecules., Christopher Lynn Harding

Electronic Theses and Dissertations

Despite efforts to decrease the global health burden of malaria, infections with Plasmodium species continue to cause over 200 million episodes of malaria each year which resulted in 405,000 deaths in 2018 [1]. One complication of malaria is increased susceptibility to invasive bacterial infections. Plasmodium infections impair host immunity to non-Typhoid Salmonella (NTS) through activities of heme oxygenase I (HO-I) )-induced release of immature granulocytes and myeloid cell-derived IL-10. Yet, it is not known if these mechanisms are specific to NTS. We show here, that Plasmodium yoelii 17XNL (Py) infected mice had impaired clearance of systemic Listeria monocytogenes (Lm) during …

Utility Of Molecular Tools For The Identification And Characterization Of Infectious Agents, Shih Keng Loong

Student Works (2020-2029)

Molecular tools involving nucleic acid sequence-based detection offer rapid, sensitive and specific identification of bacterial infections, all together instrumental in timely patient management and infection control. Analyses of DNA sequences played a pivotal role in the discovery of novel or uncommon bacterial pathogens. This method can be applied to detect and identify rare and potentially pathogenic bacterial infectious diseases emerging from the interactions between human, animal and the environment. In this study, the 16S rDNA sequencing demonstrated superior utility against the conventional phenotypic identification systems for the identification of rare pathogenic bacteria. Its inability to differentiate between certain bacterial species …

The Use Of Animal-Assisted Therapeutic Interventions In The Hospital Setting During The Covid-19 Pandemic, Alicia Cesare

Graduate Theses/Dissertations

Handlers of therapy and/or facility dogs working within hospital settings have experienced various barriers and challenges within their practice during the COVID-19 pandemic. Animal-assisted interventions, specifically therapeutic working dogs, are a valued source of support to individuals, communities, hospital settings, and disaster sites during times of community distress. The purpose of this study was to identify barriers and solutions to the continued use of animal-assisted therapeutic interventions in support of patients and families within the hospital setting during the COVID-19 pandemic. This researcher’s position within the research is the knowledge and experience of being a facility dog handler within the …

Invasive Pulmonary Infection By Syncephalastrum Species: Two Case Reports And Review Of Literature, Memoona Irshad, Nosheen Nasir, Urooj Haider Hashmi, Joveria Farooqi, Syed Faisal Mahmood

Section of Internal Medicine

Background: Syncephalastrum species belong to the class Zygomycetes and order Mucorale. These are found in the environment and tropical soil, usually presenting as colonizers and rarely cause human infection. Syncephalastrum racemosum is a species of the genus Syncephalastrum and is the most commonly identified pathogen. Most cases are reported in immunocompromised individuals, such as patients on long term steroids, poorly controlled diabetes, or patients with malignancy.
Case presentation: We are describing two cases of rare fungal infection by Syncephalastrum species causing invasive pulmonary manifestation. Both patients had compromised immune status and presented with worsening dyspnea to the emergency room. Both …

Wild Mice With Different Social Network Sizes Vary In Brain Gene Expression, Patricia C. Lopes, Barbara König

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Background

Appropriate social interactions influence animal fitness by impacting several processes, such as mating, territory defense, and offspring care. Many studies shedding light on the neurobiological underpinnings of social behavior have focused on nonapeptides (vasopressin, oxytocin, and homologues) and on sexual or parent-offspring interactions. Furthermore, animals have been studied under artificial laboratory conditions, where the consequences of behavioral responses may not be as critical as when expressed under natural environments, therefore obscuring certain physiological responses. We used automated recording of social interactions of wild house mice outside of the breeding season to detect individuals at both tails of a distribution …

A Race Against Time: Reduced Azithromycin Susceptibility In Salmonella Enterica Serovar Typhi In Pakistan, Junaid Iqbal, Irum Fatima Dehraj, Megan E. Carey, Zoe A. Dyson, Denise Garrett, Jessica C. Seidman, Furqan Kabir, Senjuti Saha, Stephen Baker, Farah Naz Qamar

Department of Paediatrics and Child Health

Antimicrobial resistance is an ongoing issue in the treatment of typhoid fever. Resistance to first-line antimicrobials and extensively drug resistant (XDR) Salmonella Typhi isolates in Pakistan have left azithromycin as the only remaining effective oral treatment. Here, we report the emergence of organisms with a single point mutation in acrB gene, implicated in azithromycin resistance, in a S. Typhi isolate from Pakistan. The isolation of this organism is worrisome and highlights the significance of the introduction of typhoid conjugate vaccine in South Asia.
Importance: The emergence of XDR Salmonella Typhi in Pakistan has left azithromycin as the only viable oral …

Do Plant Secondary Metabolite‐Containing Forages Influence Soil Processes In Pasture Systems?, Andrea K. Clemensen, Juan J. Villalba, George E. Rottinghaus, Stephen T. Lee, Frederick D. Provenza, Jennifer R. Reeve

Wildland Resources Faculty Publications

Grazed pastures are susceptible to N loss from urine/manure additions, which increases eutrophication, affecting the global N cycle. Plant secondary metabolites (PSM), such as condensed tannins (CT) and terpenes, influence silviculture soil dynamics by generally decreasing N mineralization. We investigated whether cattle‐grazed pastures of non‐traditional grass and legume forage monoculture strips including CT‐containing sainfoin (Onobrychis viciifolia Scop.) and tall fescue (TF) [Schedonorus arundinaceus (Schreb.) Dumort.] influenced soil dynamics compared with traditional grass and legume forage monoculture strips of alfalfa (Medicago sativa L.), without tannins, and TF. Throughout the study, CT in sainfoin averaged 58.9 g kg^{−1 …}

Uplc-Ms/Ms Analysis Of Cyp1a-Mediated Ethoxyresorufin-O-Deethylation Activity In The Rat Kidney Microsomes, Devaraj Venkatapura Chandrashekar, Reza Mehvar

Pharmacy Faculty Articles and Research

Ethoxyresorufin (ER)-O-deethylation (EROD) activity has been widely used to assess cytochrome P450 1A (CYP1A) activity. The kinetics of CYP1A activity have been well characterized in the liver microsomes. However, studies in kidney microsomes are limited due to the much lower EROD activity in this organ. Here, we developed and validated a sensitive UPLC-MS/MS assay for the characterization of the EROD activity in the rat kidney microsomes. In a 50 µL reaction mixture, rat kidney microsomes (0.25 mg/mL) were incubated with ER (0.1–5 µM) and NADPH (1 mM) for 10 min. Acidic solvents, such as trichloroacetic acid or formic …

Trichosporon Species And Fusarium Species As A Cause Of Empyema Thoracis In A Diabetic Patient, Nousheen Iqbal, Muhammad Ammar, Muhammad Irfan, Kauser Jabeen

Section of Pulmonary & Critical Care

Of late, fungal infections are increasingly being recognized in diabetic patients. Here we present a case of polymicrobial fungal empyema due to Trichosporon species and Fusarium species developed after community-acquired pneumonia in a diabetic patient. Trichosporon species are basidiomycetous yeast and Fusarium species are soil saprophytes with a worldwide distribution. Fungal empyema cases are rare and are mostly caused by Aspergillus and Candida species. Polymicrobial fungal empyema with Trichosporon species and Fusarium species has not been reported previously. Our patient was successfully treated with antifungal therapy. This case highlights that fungal empyema should be considered in diabetic patients especially if …

Genomic Diversity Of Bacteriophages Infecting Microbacterium Spp, Deborah Jacobs-Sera, Lawrence A. Abad, Richard M. Alvey, Kirk R. Anders, Haley G. Aull, Suparna S. Bhalla, Lawrence S. Blumer, David W. Bollivar, J. Alfred Bonilla, Kristen A. Butela, Roy J. Coomans, Steven G. Cresawn, Tom D'Elia, Arturo Diaz, Ashley M. Divens, Nicholas P. Edgington, Gregory D. Frederick, Maria D. Gainey, Rebecca A. Garlena, Kenneth W. Grant, Susan M.R. Gurney, Heather L. Hendrickson, Lee E. Hughes, Margaret A. Kenna, Karen K. Klyczek, Hari Kotturi, Travis Mavrich, Angela L. Mckinney, Evan C. Merkhofer, Jordan Moberg Parker, Sally D. Molloy

Life Sciences Faculty Research

The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also pervasively mosaic, and replete with genes of unknown function. To further explore this broad group of bacteriophages, we describe here the isolation and genomic characterization of 116 phages that infect Microbacterium spp. Most of the phages are lytic, and can be grouped into twelve clusters according to their overall relatedness; seven of the phages are singletons with no close relatives. Genome sizes vary from 17.3 kbp to 97.7 kbp, …

Fecal Microbiota Transplantation And Gut Microbiome Effects On Psychiatric Illnesses, Mona Seresht

Physician Assistant Studies | Student Authored Articles

Despite the medical advances that have been made in regards to mental health, psychiatric medications, and alternative therapies, many patients continue to suffer day in and day out, unable to live the type of life they desire. Many times, the medication route includes many episodes of trial and error, side effects, and no significant improvement in actual symptoms. Therapy, although effective, typically necessitates a supplemental medication for the best results. Fecal microbiota transplantation (FMT) is a method where feces from a healthy donor is transferred to an affected patient, typically via colonoscopy. Theoretically, this alters the gut microbiome in a …

Multicenter Clinical Evaluation Of The Revogene Strep A Molecular Assay For Detection Of Streptococcus Pyogenes From Throat Swab Specimens, Dithi Banerjee, Jeff Michael, B. Schmitt, H. Salimnia, N. Mhaissen, D. M. Goldfarb, P. Lachance, M. L. Faron, T. Aufderheide, N. Ledeboer, A. Weissfeld, Rangaraj Selvarangan

Manuscripts, Articles, Book Chapters and Other Papers

Copyright © 2020 Banerjee et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license Group A streptococcus (GAS) species cause bacterial pharyngitis in both adults and children. Early and accurate diagnosis of GAS is important for appropriate antibiotic therapy to prevent GAS sequalae. The Revogene Strep A molecular assay (Meridian Bioscience Canada Inc, Quebec City, QC, Canada) is an automated real-time PCR assay for GAS detection from throat swab specimens within approximately 70 min. This multicenter prospective study evaluated the performance of the Revogene Strep A molecular assay compared to that …