Infectious Diseases

Basic and Translational Research Laboratories

Dr. Apetrei’s Laboratory uses nonhuman primate models to address issues of simian immunodeficiency virus diversity and pathogenesis in natural hosts and upon cross-species transmission. Our overriding philosophy is that every aspect of HIV research can and should be modeled in appropriate animal models in order to understand the basic mechanisms that underlie disease processes and implement therapeutic approaches to control the deleterious consequences of HIV infection. Dr. Apetrei pioneered SIV pathogenesis in the wild and was actively involved during the last decades in modeling different aspects of HIV pathogenesis in nonhuman primate hosts. The current focus of his research is to assess the role of the gut dysfunction in the pathogenesis of HIV infection and to elaborate strategies to counter it in nonhuman primate models through multiple approaches. The lab is also involved in testing multiple approaches for cure research: virus reactivation with romidepsin, improvement of virus control and reactivation through regulatory T cells and the role of autovaccination in boosting an effective immune response that might lead to a functional cure of HIV. Dr. Apetrei is also involved in collaborative studies testing strategies to control chronic immune activation and prevent comorbidities in HIV-infected patients.

Center for Antibody Therapeutics (CAT) Lab

The major goals of the CAT are to discover monoclonal antibody (mAb)-based candidate therapeutics for prevention and treatment of diseases, as well as for diagnostics and research, by using phage and yeast display, hybridoma technology, single B cell isolation. Underpinning the efforts to achieve these goals will be in-depth understanding of disease mechanisms and the identification and validation of appropriate molecular targets for therapeutic intervention. To achieve maximum therapeutic efficacy and safety, the monoclonal antibodies (mAbs) will be engineered, as required, into various formats including antibody domains, fragments, full-size immunoglobulins, antibody drug conjugates (ADC), antibody-armed chimeric antigen receptor T-cells (CAR-T) and NK cells (CAR-NK), bispecific T-cell engagers (BiTEs), bispecific natural killer cell engagers (BiKEs), and fusion proteins. These proteins will be designed, produced and preclinically characterized in the CAT, in collaboration with industry partners through incoming or outgoing contracts. Given the experience and expertise of the CAT leadership, initial priority will be given to targets related to HIV and cancer.

Dr. Culyba’s laboratory fuses molecular and biochemical methodologies with experimental microbial evolution to study mutational phenomena and bacterial adaptation. Mutation and gene transfer events are the source of heritable variation for evolution. These genome diversifying processes can range from being relatively site-specific in the genome to being nearly random. Furthermore, beyond the mutations themselves, the DNA damage and DNA repair events associated with mutagenesis can also be deleterious to the host and are subject to multiple levels of active regulation by cells. Understanding how microorganisms respond to their environments and control the rate and specificity of mutagenesis is the focus of the laboratory. Ongoing studies are aimed at elucidating the (i) molecular mechanisms which regulate mutational phenomena in bacteria during transitions to new environments, (ii) molecular specificity determinants of enzymes involved in mutational phenomena, and (iii) new methods for tracking and detecting mutations in populations of cells. Research projects in the lab are designed to inform a variety of pressing scientific challenges, including combating the crisis of antimicrobial resistance, improving the specificity and safety of cutting-edge gene editing technologies, and building a comprehensive model of molecular evolution.

The mission of Dr. Doi’s laboratory is to identify and investigate antimicrobial resistance of clinical concern among gram-negative bacterial pathogens. The areas of research include: (i) genetic and molecular basis of emerging antimicrobial resistance mechanisms; (ii) rapid diagnosis of resistance using phenotypic, genetic and lipidomic approaches, and (iii) inhibitor-based drug discovery. Current efforts are focused on colistin resistance in Acinetobacter baumannii, a problematic healthcare-associated pathogen, and fosfomycin resistance in Escherichia coli, the predominant cause of urinary tract infection in both healthcare and community settings

Dr. Harrison’s research focuses on the epidemiology and genomic epidemiology of important vaccine-preventable and drug-resistant bacterial pathogens that are transmitted in the community and causes of hospital-associated infections (HAI’s). Pathogens studied include Streptococcus pneumoniae, group B Streptococcus, Neisseria meningitidis, Escherichia coli O157:H7, Salmonellaenterica, Clostridium difficile, Klebsiella pneumoniae, and Pseudomonasaeruginosa. He is the PI of the Microbial Genomic Epidemiology Laboratory (MiGEL), which conducts research on and provides training in genomic epidemiology and provides outbreak detection support to the Director of Infection Control at the University of Pittsburgh Medical Center (UPMC).  MiGEL uses molecular epidemiologic tools, such as pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), multilocus variable number tandem repeat analysis (MLVA) and whole genome sequencing (WGS) to study emergence and transmission of these bacteria. More recently, Dr. Harrison has been studying the use of WGS and data mining of the electronic medical record (EMR) and machine learning tools for enhanced outbreak detection in the hospital. He is also studying the utility of the peri-rectal microbiome to predict risk of HAI’s.

Immunoregulatory mechanisms can influence many aspects of the body’s immune responses to different antigens, and can control inflammatory responses thereby preventing pathology caused by persistent immune activation and inflammation. The Macatangay laboratory focuses on various immunoregulatory pathways in different inflammatory states, especially in HIV infection.  Specifically, the lab aims to define the role of different immunoregulatory mechanisms in: (i) the inflammatory state associated with chronic HIV infection; (ii) HIV persistence; (iii) various HIV immunotherapeutic strategies, such as in therapeutic vaccination. By using specimens obtained from the various studies at the Pittsburgh Treatment and Evaluation Unit (PTEU), the AIDS Clinical Trials Group (ACTG), and the Multicenter AIDS Cohort Study (MACS), the Macatangay lab assess the immunophenotype and frequencies of regulatory immune cell subsets, and analyzes specific suppressive functions and components of regulatory pathways in order to further understand the influence of specific immunoregulatory mechanisms in HIV pathogenesis and persistence. In doing so, they aim to improve existing or develop new immunotherapeutic strategies for the control of chronic HIV-associated inflammation and/or for the functional cure of HIV.

The goals of the Mellors Laboratory are to discover the most effective ways to prevent, treat and cure HIV-1 infection through the discovery, preclinical and clinical evaluation of new preventive and therapeutic strategies. Two large research efforts are under way.  The first includes a multidisciplinary team of laboratory scientists and clinical researchers that is investigating the mechanisms and anatomical reservoirs of HIV that persist in infected individuals despite clinically effective antiretroviral therapy (ART) and that constitute the major barrier to curing HIV infection. A broad range of technologically-advanced approaches are being applied to characterize HIV reservoirs including single cell and single molecule quantification and sequencing as well as traditional methods of virus culture and characterization. Such approaches have elucidated the sources of persistent viremia on ART, the decay of HIV-infected cells and persistent viremia during long-term ART, and the emergence of infected cell clones carrying intact proviruses. The impact of innovative therapies on HIV reservoirs is being studied in Phase I/II trials of histone deacetylase inhibitors, monoclonal antibodies to immune checkpoint ligands, monoclonal antibodies to HIV envelope glycoproteins, and TLR agonists. The second research effort is focused on understanding the emergence of variants of HIV that are resistant to antiretrovirals that are being used to prevent and treat HIV infection. The frequency and type of drug-resistant HIV variants are being characterized in international clinical trials of first-, second-, and third-line ART. Similarly, the transmission and emergence of drug-resistant HIV from the use of antiretrovirals for HIV prevention is being studied and the laboratory has been selected by the United States Agency for International Development (USAID) to be the global Center for Evaluation of Microbicide Sensitivity (GEMS Project).

Drs. Clancy and Nguyen conduct collaborative laboratory, translational and clinical research on issues relevant to the treatment, diagnosis and prevention of infections in immunosuppressed and other vulnerable patient populations.  Research teams are engaged in four inter-related areas of investigation: a) Medical mycology; b) Extensively-drug resistant (XDR) Gram negative bacterial infections and antimicrobial stewardship; c) Transplant infectious diseases; and d) Legionella control and environmental management.  Medical mycology research includes projects on mechanisms and clinical impact of antifungal drug resistance, molecular pathogenesis of invasive Candida infections, fungal diagnostics, and clinical studies and trials on fungal diseases, treatments and diagnostics.  XDR bacterial and antimicrobial stewardship research includes projects on evolution, and tolerance/resistance and pathogenic mechanisms of carbapenem-resistant Enterobacteriaceae (CRE) and other Gram negative bacteria, development of novel antibiotic treatment strategies based on bacterial genetics and pharmacokinetic-pharmacodynamic (PK-PD) principles, the clinical and economic impact of XDR infections and antimicrobial stewardship interventions, and clinical trials of new antimicrobials and diagnostic tests. Transplant Infectious Diseases research includes projects on the role of the microbiome in infections and outcomes among transplant recipients, the impact of rectal CRE carriage on transplant patients’ outcome, and clinical studies and trials on a wide range of opportunistic fungal, bacterial and viral infections. Legionella and environmental management research includes projects on the genomic epidemiology of disease-causing and water system Legionella at the VA Pittsburgh Healthcare System, and environmental remediation and control of potential pathogens.  The Clancy and Nguyen labs employ a range of cutting edge technologies in their research, including molecular biology techniques, animal models of fungal and bacterial infections, genomics, transcriptomics and microbiome profiling, and PK-PD modeling.  Projects are structured on a bedside-to-bench-to-bedside design, and involve clinical and laboratory investigators.

Dr. Parikh’s translational research laboratory uses novel technical approaches to solve public health problems in the research areas of HIV prevention and drug resistance.  Dr. Parikh leads the USAID/PEPFAR-funded Global Evaluation of Microbicide Sensitivity (GEMS) Project whose goals are to characterize resistance risk from pre-exposure prophylaxis (PrEP) trials and demonstration projects, identify the most effective and efficient HIV testing and resistance monitoring strategies, generate evidence-based policy recommendations for HIV diagnostic testing frequency and ARV resistance monitoring, and monitor seroconverters from PrEP roll-out programs for ARV resistance in selected clinics in South Africa, Zimbabwe, and Kenya.  The GEMS project brings together a diverse team of laboratory scientists, mathematical modelers, policy experts, health economists, in-country stakeholders, demonstration project teams and others towards the common public health goal of minimizing resistance risk during PrEP roll-out.  Her laboratory also serves as the Virology Core for the Microbicides Trial Network (MTN), with the aim of confirming virologic endpoints for all MTN studies, assessing population and low-frequency resistance in seroconverters from HIV prevention trials, developing new assays and addressing research questions relevant to the field of HIV prevention, and providing virology support to MTN protocols, international clinical research sites, and community working groups.  In addition to these major projects, Dr. Parikh’s lab is investigating the detection of Y chromosome DNA in genital tract specimens using quantitative real-time PCR as a biomarker for unprotected sex and evaluating new HIV diagnostic algorithms using antigen-based rapid tests for identifying seroconverters.

Ryan is pursuing a career as a pharmacist-scientist to design individualized approaches to antimicrobial therapy that prevent and treat infections due to drug-resistant pathogens. To meet this goal, he has pursued NIH career development awards and assembled a team of mentors and advisors with the experience and passion to guide in establishing a research career. He has received advanced training in molecular biology and pharmacokinetic-pharmacodynamic (PK-PD) techniques that build upon training in pharmacology and Infectious Diseases. The new tools, skills, and techniques gained through his training have positioned him to realize the long-term goal of becoming an independently-funded investigator.

Dr. Sluis-Cremer’s laboratory implements a multi-disciplinary approach that includes biophysics, biochemistry, virology and analysis of clinical samples to gain insight into: (i) the mechanisms of action of antiretroviral drugs; (ii) antiviral and antimicrobial drug resistance; and (iii) understanding how HIV-1 persists in infected individuals despite potent antiretroviral therapy. To elucidate how antiviral drugs inhibit virus replication, the lab uses state-of-the-art biophysical methods, including transient kinetic and single-molecule fluorescence approaches, to define how small molecules affect retroviral enzyme function, the intramolecular protein conformational dynamics, and the intermolecular enzyme-substrate interactions. The knowledge gained from this work is critical for the development of new inhibitors, and for understanding how mutations in the viral enzyme confer drug resistance. For HIV-1, the resistance research is focused on the identification of drug resistance mutations that are selected in infected-individuals failing therapy, defining the mechanisms by which these mutations decrease drug susceptibility using biochemical and virology approaches, and to predict how acquired or transmitted drug resistance mutations impact future treatment options. The Sluis-Cremer laboratory has also recently expanded their resistance portfolio to characterize bacterial resistance to the antibiotic fosfomycin, and to explore novel therapeutic approaches to reverse fosfomycin resistance. In regard to HIV-1 persistence, they are focused on characterizing the latent pool of HIV-1 infection that resides in resting CD4+ T cells, in particular the naïve and central memory subsets, using novel primary cell models of HIV-1 latency and by studying purified subsets of the resting CD4+ T cell population from HIV-infected individuals on suppressive antiretroviral therapy.

The Van Tyne Lab studies how bacteria evolve during human infection to resist antibiotics and the host immune system, using comparative genomics and functional approaches. We sequence bacterial strains from human infections and use functional genomics to identify and characterize novel resistance mechanisms. These include the ability of bacteria to resist the host immune system, or to persist in the face of antibiotic pressure. We also work with other research groups to develop new  antibiotics that can treat drug-resistant bacterial infections. We help characterize new types of antimicrobial molecules, and understand how novel compounds kill bacteria. We are also developing bacteriophages as novel therapeutics.