Medical Microbiology Commons^™

Mucosa-Associated Microbiota In Barrett’S Esophagus, Dysplasia, And Esophageal Adenocarcinoma Differ Similarly Compared With Healthy Controls, Shajan Peter, Amanda Pendergraft,, William Vanderpol, Mel Wilcox, Kondal R. Kyanam Kabir Baig, Casey Morrow, Jacques Izard, Peter J. Mannon

Department of Food Science and Technology: Faculty Publications

Introduction: Alterations in the composition of the human gut microbiome and its metabolites have been linked to gut epithelial neoplasia. We hypothesized that differences in mucosa-adherent Barrett’s microbiota could link to risk factors, providing risk of progression to neoplasia.

Methods: Paired biopsies from both diseased and nonaffected esophagus (as well as gastric cardia and gastric juice for comparison) from patients with intestinal metaplasia (n = 10), low grade dysplasia (n = 10), high grade dysplasia (n = 10), esophageal adenocarcinoma (n = 12), and controls (n = 10) were processed for mucosa-associated bacteria …

The Influence Of Polycyclic Aromatic Hydrocarbons In Fcgriib -/- Lupus Mice, Kanyarat Udompornpitak

Chulalongkorn University Theses and Dissertations (Chula ETD)

The activation of aryl hydrocarbon receptor (Ahr) through polycyclic aromatic hydrocarbons (PAHs), the major components of particulate matter at 2.5 micron (PM2.5) in the polluted air, might aggravate inflammation and lupus activity. Hence, 1,4-chrysenequinone (1,4-CQ), a substance in the PAHs group, was tested in a lupus model from FcgRIIb deficiency (FcgRIIb-/-) using macrophages and mice. Although the activation by 1,4-CQ alone was unable to induce inflammation, the pre-conditioning by lipopolysaccharide (LPS), a representative inflammatory-activator, before 1,4-CQ (LPS/1,4-CQ) induced more predominant inflammation in macrophages when compared with LPS or 1,4-CQ activation alone as determined by supernatant cytokines (TNF-α, IL-6 and IL-10). …

Molecular Detection Of Viable Mycobacterium Tuberculosis Complex In Clinical Specimens, Suthidee Petsong

Chulalongkorn University Theses and Dissertations (Chula ETD)

Tuberculosis (TB) is the global health concern because of the rising incidence and mortality. TB is caused by Mycobacterium tuberculosis complex (MTBC) and transmitted via inhalation of infectious droplet nuclei circulating in the air. The World Health Organization (WHO) recommends the use of Acid-fast (AFB) smear microscopy, MTBC culture, and molecular detection of MTBC DNA for diagnosis of TB. The response to treatment should be acquired as soon as possible to reduce disease transmission and drug resistance. Although MTBC culture is a gold standard, it is laborious, expensive, and may take up to 8 weeks. The AFB staining and molecular …

Understanding The Host Immune Response Against Pseudomonas Aeruginosa To Develop Novel Therapeutics And Vaccines, Emel Sen Kilic

Graduate Theses, Dissertations, and Problem Reports (ETD)

Pseudomonas aeruginosa is a Gram-negative opportunistic bacterium that causes a broad range of acute and chronic infections. The high adaptability and emergence of multidrug-resistant strains of this bacterium pose a significant threat to human health. Particularly, pneumonia caused by this pathogen is associated with high morbidity and mortality in immunocompromised patients. To prevent these infections, we aimed to develop novel vaccine strategies by characterizing the host immune response against P. aeruginosa. During respiratory infections, P. aeruginosa first contacts with epithelial cells along the respiratory tract. Using RNA-sequencing, we were able to characterize transcriptional changes of the epithelial cells in …

Evaluation Of The Diagnostic Accuracy And Utility Of A New Dengue Rapid Diagnostic Test In Malaysia, Zhuo Lin Chong

Student Works (2020-2029)

Dengue is an emerging arboviral disease endemic to many tropical countries including Malaysia. Due to its unspecific symptoms, dengue diagnosis can only be confirmed through diagnostic tests. Existing laboratory-based dengue diagnostics like enzyme linked immunosorbent assay (ELISA) is accurate in detecting dengue non-structural protein-1 (NS1), and anti-dengue immunoglobulin M (IgM) and G (IgG); but is also more complicated and time-consuming. Commercially available dengue rapid immunochromatographic test (RIT) is efficient but less sensitive. A new dengue rapid diagnostic rest (RDT) using biosensors may be both efficient and accurate in diagnosing acute dengue. This study evaluated this new dengue NS1-based RDT and …

Microbiotyping The Sinonasal Microbiome, Ahmed Bassiouni, Sathish Paramasivan, Arron Shiffer, Matthew R Dillon, Emily K Cope, Clare Cooksley, Mahnaz Ramezanpour, Sophia Moraitis, Mohammad Javed Ali, Benjamin S Bleier, Claudio Callejas, Marjolein E Cornet, Richard G Douglas, Daniel Dutra, Christos Georgalas, Richard J Harvey, Peter H Hwang, Amber U Luong, Rodney J Schlosser, Pongsakorn Tantilipikorn, Marc A Tewfik, Sarah Vreugde, Peter-John Wormald, J Gregory Caporaso, Alkis J Psaltis

Faculty, Staff and Student Publications

This study offers a novel description of the sinonasal microbiome, through an unsupervised machine learning approach combining dimensionality reduction and clustering. We apply our method to the International Sinonasal Microbiome Study (ISMS) dataset of 410 sinus swab samples. We propose three main sinonasal “microbiotypes” or “states”: the first is Corynebacterium-dominated, the second is Staphylococcus-dominated, and the third dominated by the other core genera of the sinonasal microbiome (Streptococcus, Haemophilus, Moraxella, and Pseudomonas). The prevalence of the three microbiotypes studied did not differ between healthy and diseased sinuses, but differences in their distribution were evident based …

Synergistic Activities Of Antibiotic Combinations Against Carbapenem-Resistant Klebsiella Pneumoniae And Mechanisms Of Carbapenem Resistance In Klebsiella Pneumoniae Clinical Isolates., Netchanok Muhummudaree

Chulalongkorn University Theses and Dissertations (Chula ETD)

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has been increasing reported worldwide. The aims of this study were to investigate the mechanisms of carbapenem resistance in K. pneumoniae Thai isolates and study the synergistic activities of antibiotic combinations against CRKP isolates. Two-hundred and forty CRKP clinical isolates were obtained from patients at King Chulalongkorn Memorial Hospital between September 2016 and April 2020. The antibiotic susceptibility testing was determined by agar dilution to imipenem, meropenem, amikacin, fosfomycin, ciprofloxacin and by broth microdilution to colistin. The prevalence rates of resistance to imipenem, meropenem, ciprofloxacin, fosfomycin, amikacin, and colistin were 90.42%, 91.67%, 95.84%, 41.25%, 20%, and …

Application Of Phage Display Technology For The Production Of Antibodies Againststreptococcus Suis Serotype 2, Pattarawadee Sulong

Chulalongkorn University Theses and Dissertations (Chula ETD)

Streptococcus suis (S. suis) serotype 2 infection is problematic in the swine industry and responsible for most cases of human infection worldwide. Since current multiplex PCR cannot differentiate between serotypes 2 and 1/2, then serotype-specific antibodies (Abs) are required for serotype identification to confirm S. suis serotype 2 infection. This study aimed to generate Abs specific to S. suis serotype 2 by phage display from a human heavy chain variable domain (VH) antibody library. For biopanning, whole cells of S. suis serotype 2 were used as the target antigen. With increasing selection stringency, we could select the VH Abs that …

Characterization Of Carbon Storage Regulator A (Csra) Homolog As A Global Gene Regulator In Leptospira Spp., Theerapat Phoka

Chulalongkorn University Theses and Dissertations (Chula ETD)

Leptospira spp. consist of non-pathogenic and pathogenic species. The bacteria can survive in diverse environments and therefore need mechanisms of rapid adaptation to environmental changes. However, molecular mechanisms of stress response in Leptospira are not fully understood. Carbon Storage Regulator A (CsrA) is a well-characterized, conserved, post-transcriptional global regulator that plays a critical role in response to environmental changes in many bacteria. CsrA has been reported to regulate several pathways such as glycogen metabolism, motility, biofilm formation, and virulence-associated genes. Based on available genomics data of Leptospira spp., we found putative csrA homolog, approximately 50% similarity with csrA of E. …

The Differential Dendritic Cell Properties In Response To Candida Albicans And Non-Albican Candida Β-Glucan, Truc Thi Huong Dinh

Chulalongkorn University Theses and Dissertations (Chula ETD)

Increased mortality and antifungal drug resistance of non-albicans Candidiasis patients have become an alarming in health problems nowadays, whereas profound knowledge of their pathogenesis mechanisms is still limited. The immune responses of innate and adaptive immunity play a crucial role in protecting from Candida infections. Dendritic cells (DCs) are the most notable because of their roles in bridging an innate immunity and specific adaptive immunity to eliminate fungal invasion. It is little known about DC functions in non-albicans Candida (NACs) infections. Besides, there is less study on evaluating the DC properties upon the interaction between DCs and NACs-derived ß-glucans. Therefore, …

Neutrophil Extracellular Traps (Nets) Formation Of Fcgr2b Deficient Mice In Lupus Mouse Model With Ischemic Reperfusion Injury, Wilasinee Saisorn

Chulalongkorn University Theses and Dissertations (Chula ETD)

Acute kidney injury (AKI) caused by renal ischemic reperfusion (I/R) is the most prevalent cause of morbidity and mortality in patients. Neutrophil extracellular traps (NETs) are important for the progression of lupus nephritis after renal I/R injury. Because neutrophils are the first immune cell that respond to tissue damage, neutrophils might be an important cell that determines renal I/R injury. Additionally, NET components, including cell-free DNA, histone, nucleosome, and cytoplasmic protein compartment release the auto-antigens that accelerate lupus disease activity. Therefore, this project aimed to compare NETs formation in several internal organs following renal I/R injury in Fcgr2b deficient (Fcgr2b-/-) …

Detection Of Leptospires By Rpa-Nalfia And Crispr-Cas12a, Sirawit Jirawannaporn

Chulalongkorn University Theses and Dissertations (Chula ETD)

The key barrier in leptospirosis diagnosis is a lack of available sensitive point-of-care testing. Therefore, we aimed to develop and validate nucleic acid lateral flow immunoassay (NALFIA) and clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 12a (CRISPR/Cas12a) platform combined with isothermal amplification to detect leptospires from extracted patients' DNA samples. A recombinase polymerase amplification (RPA)-NALFIA and RPA-CRISPR/Cas12a assay was designed to detect the LipL32, SecY and lfb1 genes of pathogenic Leptospira spp. The RPA-NALFIA targeting LipL32 observed the LOD at 105 copies/reaction. In comparison, the RPA-CRISPR/Cas12a targeting LipL32 and SecY demonstrated a limit of detection (LOD) of 100 copies/reaction, …

Modeling Gardnerella Host-Pathogen Interaction: Characterization Of Vaginolysin And The Opacity Phenotype, Erin M. Garcia

Theses and Dissertations

Bacterial vaginosis (BV) describes a dysbiotic state of the vaginal mucosa, during which the dominance by beneficial lactobacilli species is lost, the vaginal pH increases, and the flora comprising the vaginal microbiome becomes more diverse. Bacterial taxa associated with this dysbiotic state interact to form a dense polymicrobial biofilm on the surface of the vaginal epithelium. This shift in the vaginal microflora is clinically important, even when symptoms are not noted, as women with BV are at increased risk for acquisition of other sexually transmitted infections, including HIV, and are more than two times as likely to experience preterm birth. …

Metaproteomic Analysis Of Human Gut Microbiome In Digestive And Metabolic Diseases, Sheng Pan, Ru Chen

Faculty, Staff and Students Publications

Metaproteomics, as a subfield of proteomics, has quickly emerged as a pivotal tool for global characterization of a microbiome system at a functional level. It has been increasingly applied in studying human digestive and metabolic diseases, and provides information-rich data to identify the dysbiosis of human gut microbiome related to healthy or disease states to elucidate the molecular events underlying host-microbiota interplays. While significant technical challenges still exist, this emerging technology has been demonstrated to provide essential information in interrogating functional changes in the human gut microbiome, complementary to metagenomics and metatranscriptomics. This chapter overviews the overall metaproteomic work flow …

Resistance To Ectromelia Virus Infection Requires Cgas In Bone Marrow-Derived Cells Which Can Be Bypassed With Cgamp Therapy., Eric B. Wong, Brian Montoya, Maria Ferez, Colby Stotesbury, Luis J. Sigal

Department of Microbiology and Immunology Faculty Papers

Cells sensing infection produce Type I interferons (IFN-I) to stimulate Interferon Stimulated Genes (ISGs) that confer resistance to viruses. During lympho-hematogenous spread of the mouse pathogen ectromelia virus (ECTV), the adaptor STING and the transcription factor IRF7 are required for IFN-I and ISG induction and resistance to ECTV. However, it is unknown which cells sense ECTV and which pathogen recognition receptor (PRR) upstream of STING is required for IFN-I and ISG induction. We found that cyclic-GMP-AMP (cGAMP) synthase (cGAS), a DNA-sensing PRR, is required in bone marrow-derived (BMD) but not in other cells for IFN-I and ISG induction and for …

Examining Multiple Cellular Pathways At Once Using Multiplex Hextuple Luciferase Assaying, Alejandro Sarrion-Perdigones, Lyra Chang, Yezabel Gonzalez, Tatiana Gallego-Flores, Damian W Young, Koen J T Venken

Faculty, Staff and Students Publications

Sensitive simultaneous assessment of multiple signaling pathways within the same cells requires orthogonal reporters that can assay over large dynamic ranges. Luciferases are such genetically encoded candidates due to their sensitivity, versatility, and cost-effectiveness. We expand luciferase multiplexing in post-lysis endpoint luciferase assays from two to six. Light emissions are distinguished by a combination of distinct substrates and emission spectra deconvolution. All six luciferase reporter units are stitched together into one plasmid facilitating delivery of all reporter units through a process we termed solotransfection, minimizing experimental errors. We engineer a multiplex hextuple luciferase assay to probe pathway fluxes through five …

Langerhans Cells Orchestrate The Protective Antiviral Innate Immune Response In The Lymph Node., Eric B. Wong, Brian Montoya, Colby Stotesbury, Maria Ferez, Ren-Huan Xu, Luis J. Sigal

Department of Microbiology and Immunology Faculty Papers

During disseminating viral infections, a swift innate immune response (IIR) in the draining lymph node (dLN) that restricts systemic viral spread is critical for optimal resistance to disease. However, it is unclear how this IIR is orchestrated. We show that after footpad infection of mice with ectromelia virus, dendritic cells (DCs) highly expressing major histocompatibility complex class II (MHC class II^hi DCs), including CD207⁺ epidermal Langerhans cells (LCs), CD103⁺CD207⁺ double-positive dermal DCs (DP-DCs), and CD103⁻CD207⁻ double-negative dermal DCs (DN-DCs) migrate to the dLN from the skin carrying virus. MHC class II^{hi …}

Nlrp6 In Gram-Positive Pneumonia And Sepsis, Laxman Ghimire

LSU Doctoral Dissertations

Acute lower respiratory infections (pneumonia) and pneumonia-derived sepsis are among the leading causes of death in the world causing 7.8 million deaths annually. In this regard, Methicillin-resistant Staphylococcus aureus (MRSA) is endemic in the US and implicated for causing high mortality-associated necrotizing pneumonia and aggravating viral pneumonia with superinfection. Additionally, sepsis is the 7^th leading cause of death among newborns in the US and is responsible for more than 750,000 hospitalization cases every year. Although there is a plethora of research in both pneumonia and sepsis, the detailed pathophysiology still remains elusive. Understanding the host defense mechanism will help …

Reverse Zoonosis Of Pandemic A(H1n1)Pdm09 Influenza Viruses At The Swine/Human Interface, Daniel Gene Darnell

Theses and Dissertations (ETD)

The 2009 pandemic influenza A(H1N1)pdm09 virus emerged from the swine population. Despite frequent zoonotic events, swine influenza viruses had not become established in humans previously and little is known about host-barriers which prevent swine influenza viruses from efficiently infecting humans. Thus, the emergence of the H1N1pdm09 viruses in humans and the subsequent reverse zoonoses back to swine offered an extremely valuable opportunity to expand current knowledge. We used our active swine farm surveillance platform in combination with viruses from the USDA surveillance program to look for evidence of interspecies transmission of H1N1pdm09 viruses in the US. We found phylogenetic evidence …

Inactivated Rabies Virus-Based Ebola Vaccine Preserved By Vaporization Is Heat-Stable And Immunogenic Against Ebola And Protects Against Rabies Challenge., Drishya Kurup, Christine R. Fisher, Todd G. Smith, Tiago Abreu-Mota, Yong Yang, Felix R. Jackson, Nadia Gallardo-Romero, Richard Franka, Victor Bronshtein, Matthias J. Schnell

Department of Microbiology and Immunology Faculty Papers

BACKGROUND: Ebola virus (EBOV) is a highly lethal member of the Filoviridae family associated with human hemorrhagic disease. Despite being a sporadic disease, it caused a large outbreak in 2014-2016 in West Africa and another outbreak recently in the Democratic Republic of Congo. Several vaccine candidates are currently in preclinical and clinical studies but none are stable without cold chain storage.

METHODS: We used preservation by vaporization (PBV), a novel processing technology to heat-stabilize FiloRab1 (inactivated rabies-based Ebola vaccine), a candidate Ebola vaccine, and stored the vials at temperatures ranging from 4°C to 50°C for 10 days to 12 months. …