{"id":{"repo_id":"buffalo","oai_identifier":"oai:ubir.buffalo.edu:10477/86432"},"canonical_url":"https://search.dev.ndltd.org/etd/buffalo/oai:ubir.buffalo.edu:10477/86432","repository":{"repo_id":"buffalo","name":"Buffalo","base_url":"https://ubir.buffalo.edu/oai/request"},"display":{"title":"Genomic Microevolution of Nontypeable Haemophilus influenzae During Persistent Chronic Obstructive Pulmonary Disease Infection: A Focus on IgA Protease","abstract":"Ph.D.","abstract_html":"Ph.D.","abstract_has_math":false,"creators":["Gallo, Mary; 0000-0003-1659-6833"],"institution":"State University of New York at Buffalo","degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":["Murphy, Timothy","Microbiology and Immunology"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2025,"date_issued":"2025-02-21T17:22:22Z","date_published":"2025-02-21T17:22:22Z","updated_at":"2026-07-27T19:05:32Z","subjects":["microbiology"],"languages":["eng"],"rights":["Users of works found in University at Buffalo Institutional Repository (UBIR) are responsible for identifying and contacting the copyright owner for permission to reuse. University at Buffalo Libraries do not manage rights for copyright-protected works and cannot assist with permissions.","Copyright retained by author."],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/10477/86432","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Murphy, Timothy","Microbiology and Immunology"]},{"key":"dc:creator","label":"Author","values":["Gallo, Mary; 0000-0003-1659-6833"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2025-02-21T17:22:22Z","2020"]},{"key":"dc:publisher","label":"Institution","values":["State University of New York at Buffalo"]},{"key":"dc:type","label":"Dc Type","values":["Text","Dissertation"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["microbiology"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Users of works found in University at Buffalo Institutional Repository (UBIR) are responsible for identifying and contacting the copyright owner for permission to reuse. University at Buffalo Libraries do not manage rights for copyright-protected works and cannot assist with permissions.","Copyright retained by author."]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/10477/86432"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Ph.D.","Nontypeable Haemophilus influenzae (NTHi) is an exclusively human pathobiont that contributes substantially to the progression of chronic obstructive pulmonary disease (COPD). COPD is the third leading cause of death in the US and worldwide, and is responsible for over $30 billion in healthcare costs annually. NTHi is the primary bacterial cause of acute exacerbations of COPD, but also persistently infects the lower airways, contributing to chronic inflammation and disease progression. NTHi is adapted to survive in the hostile environment of COPD airways. We hypothesize that NTHi undergoes in-host genetic microevolution to facilitate persistent infection. Whole genome sequencing of the first isolate upon acquisition and the final isolate before clearance of persistently infecting strains of NTHi revealed multiple changes in the genome. We observed a large genomic inversion, single nucleotide polymorphisms, and slipped strand mispairing of simple sequence repeats in genes associated with virulence as a major mechanism of survival. We more rigorously investigated one virulence factor that is important for intracellular survival, IgA protease. Selected strains of NTHi that expressed IgA protease variants A1, A2, and B1 upon initial acquisition by the patient stopped expression during persistence in the airways. The changes in expression were conferred by indels within the open reading frame of the iga genes, ranging in size from 1 to 49 basepairs in length and often found within a mononuclear repeat, suggesting slipped strand mispairing. By contrast, IgA protease B2 is dynamically regulated throughout persistence in the human respiratory tract, modulated by a 7-basepair repeat, TCAAAAT, immediately downstream of the start codon. Changes in the number of repeats determine whether the gene is in or out of frame, thus determining IgA protease B2 expression. Because IgA protease is an important virulence factor for NTHi, this enzyme is a potential therapeutic target for pathogen-specific eradication while preserving normal host flora, a major advance over currently available antibiotics. We tested a novel small molecule inhibitor, MP851, for its efficacy in inhibiting all 4 variants of IgA protease in an in vitro assay and using a quantitative ELISA system. MP851 inhibits all four variants of IgA protease at levels that are not toxic to human respiratory epithelial cell lines. We conclude that NTHi undergoes microevolutionary changes in its genome during persistent infection within the human host. The changes reveal potential virulence factors employed by the bacterium for continued persistence in the respiratory tract in COPD. Targeting these specific factors holds promise for specific eradication of a persistent pathogen while preserving normal flora, thus reducing adverse effects and the potential for antimicrobial resistance. This approach has the potential to transform the treatment of bacterial infection in COPD, which has relied on broad spectrum antibiotics for the past 70 years.","**To request an accessible version of the file(s) associated with this item, contact library@buffalo.edu. Please include the item's persistent URL [http://hdl.handle.net/. . .] in your request.**"]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Genomic Microevolution of Nontypeable Haemophilus influenzae During Persistent Chronic Obstructive Pulmonary Disease Infection: A Focus on IgA Protease"]}]}],"canonical_facts":{"dc:contributor":["Murphy, Timothy","Microbiology and Immunology"],"dc:creator":["Gallo, Mary; 0000-0003-1659-6833"],"dc:date":["2025-02-21T17:22:22Z","2020"],"dc:description":["Ph.D.","Nontypeable Haemophilus influenzae (NTHi) is an exclusively human pathobiont that contributes substantially to the progression of chronic obstructive pulmonary disease (COPD). COPD is the third leading cause of death in the US and worldwide, and is responsible for over $30 billion in healthcare costs annually. NTHi is the primary bacterial cause of acute exacerbations of COPD, but also persistently infects the lower airways, contributing to chronic inflammation and disease progression. NTHi is adapted to survive in the hostile environment of COPD airways. We hypothesize that NTHi undergoes in-host genetic microevolution to facilitate persistent infection. Whole genome sequencing of the first isolate upon acquisition and the final isolate before clearance of persistently infecting strains of NTHi revealed multiple changes in the genome. We observed a large genomic inversion, single nucleotide polymorphisms, and slipped strand mispairing of simple sequence repeats in genes associated with virulence as a major mechanism of survival. We more rigorously investigated one virulence factor that is important for intracellular survival, IgA protease. Selected strains of NTHi that expressed IgA protease variants A1, A2, and B1 upon initial acquisition by the patient stopped expression during persistence in the airways. The changes in expression were conferred by indels within the open reading frame of the iga genes, ranging in size from 1 to 49 basepairs in length and often found within a mononuclear repeat, suggesting slipped strand mispairing. By contrast, IgA protease B2 is dynamically regulated throughout persistence in the human respiratory tract, modulated by a 7-basepair repeat, TCAAAAT, immediately downstream of the start codon. Changes in the number of repeats determine whether the gene is in or out of frame, thus determining IgA protease B2 expression. Because IgA protease is an important virulence factor for NTHi, this enzyme is a potential therapeutic target for pathogen-specific eradication while preserving normal host flora, a major advance over currently available antibiotics. We tested a novel small molecule inhibitor, MP851, for its efficacy in inhibiting all 4 variants of IgA protease in an in vitro assay and using a quantitative ELISA system. MP851 inhibits all four variants of IgA protease at levels that are not toxic to human respiratory epithelial cell lines. We conclude that NTHi undergoes microevolutionary changes in its genome during persistent infection within the human host. The changes reveal potential virulence factors employed by the bacterium for continued persistence in the respiratory tract in COPD. Targeting these specific factors holds promise for specific eradication of a persistent pathogen while preserving normal flora, thus reducing adverse effects and the potential for antimicrobial resistance. This approach has the potential to transform the treatment of bacterial infection in COPD, which has relied on broad spectrum antibiotics for the past 70 years.","**To request an accessible version of the file(s) associated with this item, contact library@buffalo.edu. Please include the item's persistent URL [http://hdl.handle.net/. . .] in your request.**"],"dc:format":["application/pdf"],"dc:identifier":["http://hdl.handle.net/10477/86432"],"dc:language":["eng"],"dc:publisher":["State University of New York at Buffalo"],"dc:rights":["Users of works found in University at Buffalo Institutional Repository (UBIR) are responsible for identifying and contacting the copyright owner for permission to reuse. University at Buffalo Libraries do not manage rights for copyright-protected works and cannot assist with permissions.","Copyright retained by author."],"dc:subject":["microbiology"],"dc:title":["Genomic Microevolution of Nontypeable Haemophilus influenzae During Persistent Chronic Obstructive Pulmonary Disease Infection: A Focus on IgA Protease"],"dc:type":["Text","Dissertation"]},"updated_at":"2026-07-27T19:05:32Z"}