SDSU / UCSD · Joint Doctoral Program
Translational microbiology · Phage therapy · genomics & microbiome
I investigate how phages (viruses that infect bacteria) can help address antibiotic-resistant infections, how bacteria and microbial communities change during treatment. My research covers therapeutic phage isolation and characterization, bacterial genetics, metagenomics and microbial ecology.
Doctoral researcher in Cell and Molecular Biology, currently exploring postdoctoral opportunities.
Selected study · Co-first author · 2023
Our 2023 case report assessed the progress of phage therapy for a MDR Achromobacter infection in an 11-year-old patient with cystic fibrosis. I isolated, characterized, and prepared the phages as well as tracking the progress of the treatment course using metagenomics on longitudinal blood and sputum samples.
Rather than targeting the 16S marker gene, we used WGS shotgun sequencing to obtain all DNA across in the sample, including bacterial, fungal, and viral DNA. This makes it possible to investigate the target pathogen and therapeutic phages within a broader microbial context, in addition to microbiome shifts.
the case reportA clinical case report describing one treatment course; the same patient received two more rounds of phages, manuscript for the subsequent rounds is in prep.
Research
Phages infect bacteria, making them ideal candidates for treating MDR infections. But finding a good phage is only the beginning: its bacterial host can and will develop resistance and the CF lung boasts a complex microbial community. My project in the Segall Lab focuses on understanding these dynamics, with a focus on Achromobacter infections in cystic fibrosis.
I have contributed to approximately eight phage-therapy cases under investigational new drug (IND) or emergency IND authorizations. My work includes isolating, characterizing, and testing phages and phage–antibiotic synergy and antagonism, preparing phage cocktails and quantifying endotoxin contamination in magistral preps, evaluating phage stability and losses to storage, syringes, tubing, and vials.
I combine isolate genomics, phage-susceptibility assays, SNP analyses and genetic complementations to investigate bacterial factors involved in phage infection. My dissertation aims to connect resistance mutations with changes in antibiotic susceptibility and bacterial fitness.
I analyze shotgun metagenomes from sputum and blood collected before, during, and after therapy. My ecological research asks how community composition changes and whether groups of bacteria with similar metabolic roles respond together. My dissertation aims to model those patterns.
Methods
Publications
Tarasenko A, Papudeshi B, Nguyen V, et al. bioRxiv.
What Achromobacter genetic factors are important for phage infectivity?
Papudeshi B, Roach MJ, Mallawaarachchi V, et al. Bioinformatics Advances 5(1):vbaf004.
An automated workflow for screening phage genomes for therapeutic suitability for phage therapy.
Bradley JS*, Hajama H*, Akong K, et al. Pediatric Infectious Disease Journal 42(9):754–759. *Equal contribution.
WGS shotgun metagenomic analysis of sputum and blood during a clinical phage-therapy treatment course.
Cobián Güemes AG, Le T, Rojas MI, et al. Viruses 15(8):1665.
Isolating and characterizing phages for therapeutic applications against Achromobacter.
Teaching
I have taught advanced cell and molecular biology laboratories at SDSU, supported experimental troubleshooting, and provided small-group tutoring. I have presented my phage-therapy research at Viruses of Microbes, the Cystic Fibrosis Workshop, UC Irvine, and other research meetings.
Talks, teaching, and awards in my CVAbout
I am a doctoral researcher in the SDSU–UC San Diego Joint Doctoral Program in Cell and Molecular Biology, working with Anca M. Segall. I earned my B.S. in Biology at SDSU in 2020, following degrees in biology and chemistry at Santa Barbara City College. For my postdoctoral work, I am interested in linking mechanisms of phage infection with bacterial evolution and microbial-community responses.
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