Hamza Hajama

I am a candidate in the Cell and Molecular biology Joint Doctoral Program at SDSUxUCSD.
In my research, I use a combination of (meta-)genomic, microbial genetic, & molecular biology tools to investigate how phages (bacteriophages: viruses that infect bacteria) can help address the globally growing concern of antimicrobial resistance.
My dissertation explores this question by performing and tracking the impact/progress of phage therapy in the context of multi-drug-resistant Achromobacter infections in Cystic Fibrosis patients.
I am particularly interested in how phages affect the target pathogen population (genomics), and indirectly impact the microbiome and microbial ecology (metagenomics) in-vivo.

Research

A central theme I am interested in is what makes a phage successful in-vivo and how to define the success of phage therapy. To investigate this, a few questions are asked:
1. what changes during phage therapy, and why?
2. what factors impact the success of phage therapy in-vivo?
3. what happens to the ecology/microbiome beyond the target pathogen?
To answer these questions, and others, we have isolated, purified, and administered phage-therapy under FDA authorization (IND) to multiple patients, and are using bioinformatic, genetic, and molecular biology approaches to track and assess the changes in pathogen evolution, microbiome composition, and patient prognosis before, during, and after phage therapy.

Publications

• Canto-Encalada G, Hajama H, Saldivar A, Adekunle A, Willkeen G, Segall AM, Zuniga C. “A Flux-to-AI Discovery Framework Reveals Carbon-Regulated Intermittent Non-Canonical Nitrification in Achromobacter xylosoxidans.” BMC Microbiology. October 2026. DOI
• Tarasenko A, Papudeshi B, Nyugen V, Grigson SR, Bouras G, Mallawaarachchi V, Hutton ALK, Green R, Ramsay J, Hajama H, et al. “Host species background, defence systems, and phage tail gene architecture shape phage infectivity in cystic fibrosis-associated Achromobacter.” bioRxiv. July 2026. DOI
• Papudeshi B, Roach MJ, Mallawaarachchi V, Bouras G, Grigson SR, Giles SK, Harker CM, Hutton ALK, Tarasenko A, Inglis LK, Vega AA, Souza C, Boling L, Hajama H, et al. “Sphae: an automated toolkit for predicting phage therapy candidates from sequencing data.” Bioinformatic Advances. 2025 Jan 17;5(1):vbaf004. DOI
• Bradley JS*, Hajama H*, Akong K, Jordan M, Stout D, Rowe RS, Conrad DJ, Hingtgen S, Segall AM. “Bacteriophage Therapy of Multidrug-resistant Achromobacter in an 11-Year-old Boy with Cystic Fibrosis Assessed by Metagenome Analysis.” Pediatric Infectious Disease Journal. 2023; 42(9):p 754-759. DOI
• Cobián Güemes AG, Le T, Rojas MI, Jacobson NE, Villela H, McNair K, Hung S-H, Han L, Boling L, Octavio JC, Hajama H, et al. “Compounding Achromobacter Phages for Therapeutic Applications.” Viruses. 2023; 15(8):1665. DOI

* = co-first/equal contributions
For an up-to-date list, check out Google Scholar.

Presentations

• hajama H*, Segall, AM. "Phage therapy shifts lung and blood microbiomes of two CF patients: metagenomic insights.” Viruses of Microbes (VoM2026) , Prague, Czech Republic. (July 2026).
• hajama H*, Segall, AM. "TBD: Tracking Bacteria-phage Dynamics in phage therapy - Part2: beyond the target pair” SDSU Graduate Student Seminars, CA, USA. (March, 2026).
• hajama H*, Rowe R, Akong K, Stout D, Ramchandar N, Bradley JS, Segall AM. "Genomic and genetic analyses tracking the response of Achromobacter to phage therapy in CF patients” Conference on Bacteriophages, Washington, DC, USA. (August 2025).
• hajama H, Boling L, LaMadrid B, Souza C, Jacobson N, Segall AM*. "Genetic Response of Achromobacter xylosoxidans phage therapy in a CF patient” Cystic Fibrosis Workshop, Telluride, CO, USA. (June 2025).
• hajama H*, Segall, AM. "TBD: Tracking Bacteria-phage Dynamics in CF phage therapy” San Diego State University Graduate Student Seminars, CA, USA. (March, 2025).
• hajama H*, Segall, AM. "Genetic Response of Achromobacter xylosoxidans phage therapy in a CF patient" Invited Talk, UCI McGaugh Hall , Irvine, CA, United States. (December 2024).
• hajama H*, Boling, L, LaMadrid B, Rowe R, Jacobson N, Akong K, Jordan M, Stout D, Taylor B, Ramchandar N, Bradley J, Segall AM, "Genetic Response of Achromobacter xylosoxidans phage therapy in a CF patient," Lake Arrowhead Microbial Genomics Meeting, Lake Arrowhead, CA, United States. (September 2024).
• LaMadrid B*, hajama H, Fahey S, Rowe R, Segall AM. "Mutations in targeted Achromobacter xylosoxidans selected in response to phage therapy in the lungs of a cystic fibrosis patient" SDSU S3 Symposium , San Diego, CA, United States. (March 2024).
• hajama H*, Rowe SR, LaMadrid B, Bradley JS, Akong K, Segall AM. "Mutational response of Achromobacter xylosoxidans to phage therapy in a CF patient” Viruses of Microbes (VoM2024), Cairns, Australia. (July 2024).
• Canto-Encalada GG*, hajama H, Willkeen G, Segall AM, Rohwer FL, Zuniga C. "Reconstruction of a genome-scale metabolic model of the emerging human pathogen Achromobacter xylosoxidans” Conference on Microbial Ecology and Evolution (MEEhubs). (January 2024).
• hajama H*, Rowe R, Jordan M, Mielke J, Akong K, Bradley JS, Rohwer FL, Segall AM. "unTangling Bacterial Data: gauging phage therapy effectiveness of an Achromobacter infection in a CF pediatric patient” 8th Biennial Workshop on Cystic Fibrosis: Ecology, Evolution, and Eradication, Telluride, CO. (June 2023).
• hajama H*, Cobián-Güemes AG, Rojas MI, Boling L, McNair K, Rowe R, Jordan M, Mielke J, Akong K, Bradley JS, Conrad D, Edwards R, Rohwer FL, Segall AM. "Phage therapy of an Achromobacter infection in a pediatric cystic fibrosis patient.” 22nd Microbiology Student Symposium (MSG), Berkeley, CA. (April 2023).
• hajama H*, Cobián-Güemes AG, Rojas MI, Boling L, McNair K, Rowe R, Jordan M, Mielke J, Akong K, Bradley JS, Conrad D, Edwards R, Rohwer FL, Segall AM. "Phage therapy of an Achromobacter infection in a pediatric cystic fibrosis patient.” Student Research Symposium (S3), San Diego, CA. (March 2023).
• hajama H*, Segall AM. "Achromobacter Phages for Cystic Fibrosis Therapy in the Segall Lab” UCSD Joint BioSci-CMM invited talk, San Diego, CA. (October 2022).
• hajama H*, Cobián-Güemes AG, Rojas MI, Boling L, Tram Le, An M, McNair K, Rowe R, Jordan M, Mielke J, Akong K, Bradley JS, Conrad D, Edwards R, Rohwer FL, Segall AM. "Phage therapy of an Achromobacter infection in a pediatric cystic fibrosis patient” Molecular Genetics of Bacteria and Phages (MGBP) conference, Madison, WI. (August 2022).
• hajama H, Ryan Rowe An M, Willkeen G, McNair K, Papudeshi B, Conrad D, Edwards R, Rohwer FL, Segall AM*. "Phage-host relationships relevant to phage therapy for pan-resistant Achromobacter infections in cystic fibrosis patients” Viruses of Microbes (VoM22) conference, Guimaraes, Portugal. (July 2022).
• hajama H*, An M, Jacobson N, Willkeen G, McNair K, Cobián-Güemes AG, Rowe R, Rojas MI, Rohwer FL, Segall AM. "Prophages and resistance to phage therapy in Achromobacter infections of cystic fibrosis patients” Student Research Symposium (SRS22), San Diego, CA. (March 2022).
• hajama H*, Jacobson N, Segall AM. "Segall Lab Phage Therapy” Viral Information Institute Annual Meeting, Virtual, San Diego, CA. (January 2021).

* = presenting author

Appointments

Education

Professional Affiliations

• The American Society for Microbiology (ASM)
• The International Society for Viruses of Microorganisms (iSVM)
• The American Association for the Advancement of Science (AAAS)
• Southern California Branch of the American Society for Microbiology (SCASM)

Contact

Hamza Hajama
Department of Biology
San Diego State University
San Diego, CA / USA
Email