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Scholarly Works (5 results)

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UC San Diego Electronic Theses and Dissertations (2024)

Bacteriophages are viruses of bacteria that are among the leading alternative antimicrobials for treatment of the multidrug resistant (MDR) and opportunistic pathogen Pseudomonas aeruginosa. Although phage therapy is now generally considered safe, access to the treatment remains limited and its efficacy remains unproven. The goal of this dissertation is to develop innovative phage processes and intravenous treatment regimens to combat MDR P. aeruginosa. In the third chapter, I evaluate how to select phages to combat P. aeruginosa and study the interactions between different phage strains during combination treatment. In two-phage cocktail treatment, I found that mixing phages with inequal activities diminishes initial treatment potency. Sequential treatment with the same phages improved potency but generated unique patterns of resistance. This study provides new insight on how to formulate and administer phage combinations based on the infectivity of each phage to its bacterial host. In the fourth chapter, I develop and optimize the standardized production of phages by introducing cross-flow filtration to improve the removal of endotoxin from phage preparations. The simultaneous washing and concentration of phage particles was found to improve endotoxin removal across multiple Gram-negative species. Leveraging the kinetics of each phage, the accumulation of phage-resistant bioburden could then be reduced in an improved purification process. In the fifth chapter, I validate the targeting and replication of clinical phages during the treatment of patients infected by multidrug resistant P. aeruginosa. Phages suitable for therapy were determined by screening across a multi-infection isolate library. The efficacy of clinical phage treatments were then validated using a combination of microbiological and metagenomic markers of failure or success. In conclusion, this thesis provides insights into current barriers for phage therapy. Identifying and characterizing individual phage properties will have important implications on how to treat and reduce the mortality of MDR P. aeruginosa infections.

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UC San Diego Previously Published Works (2013)
Deoxyribonucleic acid (DNA) of the human immunodeficiency virus (HIV) provides the most sensitive measurement of residual infection in patients on effective combination antiretroviral therapy (cART). Droplet digital PCR (ddPCR) has recently been shown to provide highly accurate quantification of DNA copy number, but its application to quantification of HIV DNA, or other equally rare targets, has not been reported. This paper demonstrates and analyzes the application of ddPCR to measure the frequency of total HIV DNA (pol copies per million cells), and episomal 2-LTR (long terminal repeat) circles in cells isolated from infected patients. Analysis of over 300 clinical samples, including over 150 clinical samples assayed in triplicate by ddPCR and by real-time PCR (qPCR), demonstrates a significant increase in precision, with an average 5-fold decrease in the coefficient of variation of pol copy numbers and a >20-fold accuracy improvement for 2-LTR circles. Additional benefits of the ddPCR assay over qPCR include absolute quantification without reliance on an external standard and relative insensitivity to mismatches in primer and probe sequences. These features make digital PCR an attractive alternative for measurement of HIV DNA in clinical specimens. The improved sensitivity and precision of measurement of these rare events should facilitate measurements to characterize the latent HIV reservoir and interventions to eradicate it.
    Cover page: Highly Precise Measurement of HIV DNA by Droplet Digital PCR
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    • Peer Reviewed
    UCLA Previously Published Works (2023)
    BACKGROUND/OBJECTIVES: There is currently no widely accepted approach to identify patients at increased risk for sporadic pancreatic cancer (PC). We aimed to compare the performance of two machine-learning models with a regression-based model in predicting pancreatic ductal adenocarcinoma (PDAC), the most common form of PC. METHODS: This retrospective cohort study consisted of patients 50-84 years of age enrolled in either Kaiser Permanente Southern California (KPSC, model training, internal validation) or the Veterans Affairs (VA, external testing) between 2008 and 2017. The performance of random survival forests (RSF) and eXtreme gradient boosting (XGB) models were compared to that of COX proportional hazards regression (COX). Heterogeneity of the three models were assessed. RESULTS: The KPSC and the VA cohorts consisted of 1.8 and 2.7 million patients with 1792 and 4582 incident PDAC cases within 18 months, respectively. Predictors selected into all three models included age, abdominal pain, weight change, and glycated hemoglobin (A1c). Additionally, RSF selected change in alanine transaminase (ALT), whereas the XGB and COX selected the rate of change in ALT. The COX model appeared to have lower AUC (KPSC: 0.737, 95% CI 0.710-0.764; VA: 0.706, 0.699-0.714), compared to those of RSF (KPSC: 0.767, 0.744-0.791; VA: 0.731, 0.724-0.739) and XGB (KPSC: 0.779, 0.755-0.802; VA: 0.742, 0.735-0.750). Among patients with top 5% predicted risk from all three models (N = 29,663), 117 developed PDAC, of which RSF, XGB and COX captured 84 (9 unique), 87 (4 unique), 87 (19 unique) cases, respectively. CONCLUSIONS: The three models complement each other, but each has unique contributions.
      Cover page: Machine learning versus regression for prediction of sporadic pancreatic cancer.
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      • Peer Reviewed
      UCLA Previously Published Works (2024)

      Background

      Cardiometabolic disease (CMD) disproportionately affects African American/Black (AA) and Latino communities. CMD disparities are exacerbated by their underrepresentation in clinical trials for CMD treatments including nutritional interventions. The study aimed to (1) form a precision nutrition community consultant panel (PNCCP) representative of Latino and AA communities in Los Angeles to identify barriers and facilitators to recruitment and retention of diverse communities into nutrition clinical trials and (2) develop culturally informed strategies to improve trial diversity.

      Methods

      A deliberative community engagement approach was used to form a PNCCP for the Nutrition for Precision Health (NPH) trial, part of the of the All of Us research initiative. The PNCCP included individuals that provide services for Latino and AA communities who met during 11 virtual sessions over 1 year. Discussion topics included enhancing recruitment and cultural acceptance of the NPH trial. We summarized CCP recommendations by theme using an inductive qualitative approach.

      Results

      The PNCCP included 17 adults (35% AA, 47% Latino). Four thematic recommendations emerged: reducing structural barriers to recruitment, the need for recruitment materials to be culturally tailored and participant-centered, community-engaged trial recruitment, and making nutrition trial procedures inclusive and acceptable. We outlined the study response to feedback, including the constraints that limited implementation of suggestions.

      Conclusion

      This study centers community voices regarding the recruitment and retention of AA and Latino communities into a nutrition clinical trial. It highlights the importance of community engagement early on in protocol development and maintaining flexibility to enhance inclusion of diverse communities in nutrition clinical trials.
        Cover page: Community-Engaged Approaches for Improving the Inclusion of Diverse Communities in a Nutrition Clinical Trial
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        • Peer Reviewed
        UC San Diego Previously Published Works (2024)
        Left ventricular assist devices (LVAD) are increasingly used for management of heart failure; infection remains a frequent complication. Phage therapy has been successful in a variety of antibiotic refractory infections and is of interest in treating LVAD infections. We performed a retrospective review of four patients that underwent five separate courses of intravenous (IV) phage therapy with concomitant antibiotic for treatment of endovascular Pseudomonas aeruginosa LVAD infection. We assessed phage susceptibility, bacterial strain sequencing, serum neutralization, biofilm activity, and shelf-life of phage preparations. Five treatments of one to four wild-type virulent phage(s) were administered for 14-51 days after informed consent and regulatory approval. There was no successful outcome. Breakthrough bacteremia occurred in four of five treatments. Two patients died from the underlying infection. We noted a variable decline in phage susceptibility following three of five treatments, four of four tested developed serum neutralization, and prophage presence was confirmed in isolates of two tested patients. Two phage preparations showed an initial titer drop. Phage biofilm activity was confirmed in two. Phage susceptibility alone was not predictive of clinical efficacy in P. aeruginosa endovascular LVAD infection. IV phage was associated with serum neutralization in most cases though lack of clinical effect may be multifactorial including presence of multiple bacterial isolates with varying phage susceptibility, presence of prophages, decline in phage titers, and possible lack of biofilm activity. Breakthrough bacteremia occurred frequently (while the organism remained susceptible to administered phage) and is an important safety consideration.
          Cover page: Pseudomonas aeruginosa ventricular assist device infections: findings from ineffective phage therapies in five cases.Creative Commons 'BY' version 4.0 license
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