Ahmed M Moustafa, PhD

faculty photo
Assistant Professor of Pediatrics (Gastroenterology, Hepatology and Nutrition) at the Children's Hospital of Philadelphia
Department: Pediatrics

Contact information
Children's Hospital of Philadelphia
Abramson Pediatric Research Center
3615 Civic Center Boulevard Room 902C
Philadelphia, PA 19104
Lab: 2155909987
BPharm (Pharmaceutical Sciences)
Alexandria University, Alexandria, Egypt, 2009.
Ph.D. (Biomedical Sciences)
Murdoch University, Perth, Australia, 2015.
Cert (Research Mentor Training: Effective Communication and Aligning Expectations.)
Permanent link
> Perelman School of Medicine   > Faculty   > Details

Description of Other Expertise

SARS-CoV-2 Genomics and Evolution

Description of Research Expertise

Dr. Moustafa is currently the Director for the CHOP Microbiome Sequencing Core and the Co-Director for the microbial ARchive and Cryo-collection (mARC) unit under the PennCHOP Microbiome program. Dr. Moustafa’s research program focuses on evolutionary microbiology, microbial genomics and infectious diseases. The overall goals of the Moustafa laboratory are to 1) build a highly curated strain library of pathogenic and commensal microbes to fuel microbial genomics research and microbiome mechanistic studies 2) pinpoint the molecular determinants of infectious diseases using big genomics data and novel bioinformatics tools 3) bring the tools of next-generation sequencing and microbial genomics to biologists and clinicians using innovative educational approaches.
Keywords: Microbial Genomics; Bioinformatics; microbiome; Population Genetics; Phylogenetics; Bacterial Pathogenesis.

Selected Publications

Mahalak KK, Liu L, Bobokalanov J, Narrowe A, Firrman J, Bittinger K, Hu W, Jones S and Moustafa AM: Supplementation with soluble or insoluble rice-bran fibers increases short-chain fatty acid producing bacteria in the gut microbiota in vitro. Front. Nutr. Sec. Nutrition and Microbes. Frontiers, 11, Apr 2024.

Esteves Matheus Assis Côrtes, Viana Alice Slotfeldt, Viçosa Gabriela Nogueira, Botelho Ana Maria Nunes, Moustafa Ahmed M., Mansoldo Felipe Raposo Passos, Ferreira Adriana Lucia Pires, Vermelho Alane Beatriz, Ferreira-Carvalho Bernadete Teixeira, Planet Paul Joseph, Figueiredo Agnes Marie Sá: RdJ detection tests to identify a unique MRSA clone of ST105-SCCmecII lineage and its variants disseminated in the metropolitan region of Rio de Janeiro. Frontiers in Microbiology. Digvijay Verma (eds.). 14, Nov 2023.

Margaret Free, Nicole Soper, James C Slaughter, Andries Feder, Colleen Bianco, Ahmed M Moustafa, Paul Planet, C Buddy Creech, Isaac Thomsen: Evolution of Invasive and Colonizing Pediatric Staphylococcus aureus Isolates Journal of the Pediatric Infectious Diseases Society. Oxford University Press on behalf of The Journal of the Pediatric Infectious Diseases Society, 12: S3-S4, Nov 2023.

Liu L, Mahalak KK, Bobokalonov JT, Narrowe AB, Firrman J, Lemons JMS, Bittinger K, Hu W, Jones SM, Moustafa AM.: Impact of Ivermectin on the Gut Microbial Ecosystem. International Journal of Molecular Sciences. International Journal of Molecular Sciences, 24(22), November 2023.

Ahmed M. Moustafa*, Erin Theiller, Arnav Lal, Andries Feder, Apurva Narechania, Paul J. Planet*: "Redcarpet: A Tool for Rapid Recombination Detection Amidst Expanding Genomic Databases" 8th Annual MidAtlantic Bioinformatics Conference October 2023.

Erin Theiller, Elizabeth Qian, Andries Feder, Alice Slotfeld Viana, Agnes Marie Sá Figueiredo, Paul J. Planet, Ahmed M. Moustafa: "Empowering Global Disease Surveillance: The CURED Tool for Rapid Identification of Unique Clonal Biomarkers" 8th Annual MidAtlantic Bioinformatics Conference October 2023.

Nicholas J. Pitcher, Andries Feder, Nicholas Bolden, Christian F. Zirbes, Anthony J. Pamatmat, Linda Boyken, Jared J. Hill, Alyssa R. Bartels, Andrew L. Thurman, Valerie C. Reeb, Harry S. Porterfield, Ahmed M. Moustafa, Paul J. Planet, Anthony J. Fischer: Parallel Evolution of Linezolid Resistant Staphylococcus aureus in Patients with Cystic Fibrosis. Microbiol. Spectr. Matthew Culyba (eds.). ASM, Page: e0208423, September 2023 Notes: 10.1128/spectrum.02084-23.

Martínez JRW, Planet PJ, Spencer-Sandino M, Rivas L, Díaz L, Moustafa AM, Quesille-Villalobos A, Riquelme-Neira R, Alcalde-Rico M, Hanson B, Carvajal LP, Rincón S, Reyes J, Lam M, Calderon J, Araos R, García P, Arias CA, Munita JM.: Dynamics of the MRSA Population in A Chilean Hospital: A Phylogenomic Analysis (2000-2016). Microbiol. Spectr. ASM, Page: e05351-22, June 2023 Notes: 10.1128/spectrum.05351-22.

She Q, Feder A, Galis B, Jones S, Gibbs K, Hayes E, Smathers S, Thompson K, Harris R, Zackular JP, Moustafa AM, Srinivasan L, Planet PJ.: Phylogenomic analysis of colonizing and invasive Staphylococcus aureus in a neonatal intensive care unit reveals high levels of transmission of invasive strain. CHOP Research Symposium (May 2023), Philadelphia, PA, USA. CHOP RI May 2023 Notes: Best Poster Prize.

Theiller E, Galis B, Higgins S, Jones S, She Q, Planet PJ, Zackular JP, Moustafa AM.: MicrobialARC: Genomics Driven Initiative to Improve Personalized Patient Care and Pathogen Surveillance. CHOP Research Symposium (May 2023), Philadelphia, PA, USA. CHOP RI May 2023.

back to top
Last updated: 04/18/2024
The Trustees of the University of Pennsylvania