Center for
Global Health

Scholar

Languages: English, Arabic (native)

BIO STATEMENT

Dr. Ahmed Moustafa is an Assistant Professor of Pediatrics at the Perelman School of Medicine, University of Pennsylvania, and the Children's Hospital of Philadelphia. He is Director of the CHOP Microbiome Sequencing Core under the PennCHOP Microbiome Program, Co-Director of the Center for Microbial Medicine, and co-director of microbialARC, a pediatric pathogen biorepository that links cryopreserved isolates to whole-genome assemblies, phenotypic resistance data, and clinical metadata. He also co-leads the Biospecimen Analysis Core of the NIH-funded Penn-CHOP Virome Characterization Center.

Dr. Moustafa came to global health through his own path into science. He trained as a pharmacist in Egypt, earned his PhD at Murdoch University in Australia with field work in Pakistan, and taught himself programming during his postdoctoral training at CHOP, making him both a wet and dry lab scientist. That route convinced him of something specific: genomics can now answer the questions that matter most in hospital-acquired infections, such as who transmits to whom, which strain causes disease, and when an outbreak actually began, along with cryptic transmissions. But nearly all the tooling assumes infrastructure that most neonatal units in the world do not have.

His research program centers on evolutionary microbiology, microbial genomics, and infectious diseases, and the Moustafa laboratory pursues three overarching goals: building a highly curated strain library of pathogenic and commensal microbes to fuel microbial genomics research and microbiome mechanistic studies; pinpointing the molecular determinants of infectious diseases using large-scale genomics data and novel bioinformatics tools; and bringing the tools of next-generation sequencing and microbial genomics to biologists and clinicians through innovative educational approaches.

In practice, this plays out as two lines of work that feed each other. First, Dr. Moustafa applies genomic epidemiology to hospital-acquired infections and antimicrobial resistance, and served as senior author on a whole-genome-guided investigation of Klebsiella pneumoniae transmission in a Botswana neonatal unit. Second, he builds open-source tools that cut the cost of doing this work, including CURED, which converts genomic data into inexpensive PCR-based assays so teams can keep tracking lineages where sequencing every isolate is impossible.

Dr. Moustafa also founded and leads the Microbial Genomics Journey Workshop, a hands-on microbial bioinformatics training program with recent sessions in Ghana, Botswana, and Egypt.

Recent Global Health Projects

1. Genomic surveillance of neonatal sepsis and antimicrobial resistance in Botswana and Ghana. I led the genomic component of a 12-month surveillance study in a 36-bed neonatal unit at Princess Marina Hospital, working with the Botswana-UPenn Partnership. We combined twice-monthly colonization screening, environmental sampling, and whole-genome sequencing of bloodstream isolates to reconstruct Klebsiella pneumoniae transmission pathways and target infection prevention. I published this as senior author in PLOS Global Public Health in 2026.

2. Microbial Genomics Journey Workshop (MGJW). I founded and lead MGJW, a hands-on bioinformatics training program built for researchers who are interested in starting in microbial genomics. I have run recent sessions in Ghana, Botswana, and Egypt. In Accra in April 2026, we trained roughly 26 participants, and 23 of them advanced at least one tier in our bioinformatics experience framework. To solve the problem of what happens after a workshop ends, we built and deployed MGJW-Chat, a retrieval-augmented chatbot trained on the course materials that participants keep using afterward, at a cloud cost of about $25 per session. https://github.com/moustafa-lab-org/Microbial-Genomics-Journey-Workshop-Ghana26

Select Publications

Strysko J, Hu W, Mochankana K, et al., Planet PJ, Moustafa AM. Integrated epidemiologic investigation and genomic confirmation of a Klebsiella pneumoniae neonatal sepsis outbreak in Botswana. PLOS Global Public Health. 2026;6(6):e0006468. https://doi.org/10.1371/journal.pgph.0006468

Mmolai S, et al., Moustafa AM, Planet PJ, Strysko J. Stewarding the hospital sink drain: a narrative review of practical approaches for controlling gram-negative pathogens in low- and middle-income countries. Antimicrobial Resistance & Infection Control. 2026;15(1). https://doi.org/10.1186/s13756-026-01701-2

Theiller E, Rajagopol S, Higgins S, et al., Planet PJ, Moustafa AM. Empowering global disease surveillance with CURED: a tool for rapid identification of unique genomic biomarkers. mSystems. 2026;11(4):e01063-25. https://doi.org/10.1128/msystems.01063-25

She Q, Srinivasan L, Theiller E, et al., Moustafa AM, Planet PJ. Rapid dissemination of Staphylococcus aureus in the neonatal intensive care unit is associated with invasive infection. Nature Communications. 2026;17:2550. https://doi.org/10.1038/s41467-026-69074-z

Last Updated: 09 September 2026