Faculty

Ahmed M Moustafa, PhD

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

Department: Pediatrics

Graduate Group Affiliations

Contact information

Children's Hospital of Philadelphia
Abramson Pediatric Research Center
3615 Civic Center Boulevard Room 902C
Philadelphia, PA 19104

Lab: 2155909987

Email:
moustafaam@chop.edu

Publications

Search PubMed for articles

Education:
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.)
PSOM ITMAT, 2022.
Cert (Leadership Essentials for Early-Career PIs )
Children's Hospital of Philadelphia, 2023.
Cert (Penn Faculty Pathways Program)
Penn, 2025.

Links
Search PubMed for articles
Executive Leadership for the Microbiome Centers Consortium
Google Scholar Account
Github account where I maintain the bioinformatics tools I develop
Co-Director for the Center for Microbial Medicine, a Center of Emphasis established at CHOP in August 2024.
The Sequencing Core provides expertise in next-generation sequencing of microbiome samples and single microbial isolates.

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 a Co-Director for the Center for Microbial Medcine at CHOP and the Director for the CHOP Microbiome Sequencing Core 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

Liu L, Lemons JMS, Firrman J, Mahalak KK, Chetty VJ, Narrowe AB, Higgins S, Moustafa AM, Baudot A, Deyaert S, Van den Abbeele P: Hydrogen Sulfide Has a Minor Impact on Human Gut Microbiota Across Age Groups. Sci 7(3): https://doi.org/10.3390/sci7030102, August 2025.

Theiller E, Galis BE, Jones S, Napper T, She Q, Srinivasan L, Zackular JP, Planet PJ, Moustafa AM: Unraveling the Epidemiological Dynamics of Staphylococcus epidermidis in Pediatric Bacteremia, GRS Staphylococcal Diseases, August 2025, Barcelona, Spain. GRS Staphylococcal Diseases August 2025.

Moustafa AM*, Theiller E, Lal A, Yamali S, Feder A, Narechania A, Planet PJ: Redcarpet: A Tool for Rapid Recombination Detection in Staphylococcus aureus and Other Species Amidst Expanding Genomic Databases, GRC Staphylococcal Diseases (August 2025), Barcelona, Spain. GRC Staphylococcal Diseases August 2025.

L’Etoile NL, Sundararaman SA, Theiller E, Miller JJ, Moustafa AM, Steenhoff AP, Odom John AR: Pocapavir for neonatal enteroviral sepsis: limitations of rapid viral sequencing on treatment decisions. ASM Case Reports. ASM, July 2025.

Free M, Soper N, Slaughter JC, Feder A, Bianco C, Moustafa AM, Planet P, Creech CB, Thomsen I: Evolution of strain diversity and virulence factor repertoire in pediatric Staphylococcus aureus isolates. PLoS One 20(7): e0326353, July 2025.

Stanton TD, Keegan SP, Abdulahi JA, Amulele AV, Bates M, Heinz E, Hooda Y, Hu W, Jain K, Kanwar S, Magobo R, Olwagen CP, Tembo JM, Sonda T, Strysko J, Tigoi CC, Amin SA, Bittinger K, Cornick J, Foster-Nyarko E, Gumbi W, Hotwani A, Iqbal N, Jones SM, Kabir F, Khan W, Musyani CL, McGann CM, Mittal V, Moustafa AM, Musicha P, Mwansa JCL, Ndumba ML, Odih EE, Omuoyo DO, Pearse O, Phillips LT, Planet PJ, Rasool AA, Rodrigues CMC, Sands K, Tanmoy AM, Theiller E, Zuza AM, Basu S, Chan GJ, Iregbu KC, Mazarati JB, Alemayehu SS, Walsh TR, Zahra R, Dramowski A, Fwoloshi S, Labi A-K, Madrid L, Obeng-Nkrumah N, Ojok D, Wadugu BD, Whitelaw AC, Bethou A, Bhargava A, Jindal A, Nanavati RN, Prasad PS, Sastry A, Farooqi JQ, Ghanchi N, Jehan F, Khan E, Agarwal RK, Aiken AM, Berkley JA, Coffin SE, Feasey NA, Govender NP, Hamer DH, Madhi SA, Nisar MI, Saha SK, Saha S, Sankar MJ, Wyres KL, Holt KE.: Distribution of capsule and O types in Klebsiella pneumoniae causing neonatal sepsis in Africa and South Asia: meta-analysis of genome-predicted serotype prevalence and potential vaccine coverage. medRxiv (Under review at PloS Medicine) June 2025.

Rotsaert C, Minnebo Y, Duysburgh C, Liu LS, Mahalak KK, Firman J, Mattei LM, Moustafa AM, Bittinger K, Hu W, Marzorati M, Michiels J, Van de Wiele T: Digestive parameters and gut microbiota load and composition along the in vivo piglet gastrointestinal tract. Journal of Animal Science. Oxford Academic, Page: skaf107, May 2025.

Lemons JMS, Narrowe AB, Firrman J, Mahalak KK, Liu L, Higgins S, Moustafa AM, Baudot A, Deyaert S, Van den Abbeele P.: The food additive butylated hydroxyanisole minimally affects the human gut microbiome ex vivo. Food Chemistry 473, May 2025.

Kelliher JM, Aljumaah M, Bordenstein SR, Brister JR, Chain PSG, Dundore-Arias JP, Emerson JB, Fernandes VMC, Flores R, Gonzalez A, Hansen ZA, Hatcher EL, Jackson SA, Kellogg CA, Madupu R, Miller CML, Mirzayi C, Moustafa AM, Mungall C, Oliver A, Pariente N, Pett-Ridge J, Record S, Reji L, Reysenbach A-L, Rich VI, Richardson L, Schriml LM, Shabman RS, Sierra MA, Sullivan MB, Sundaramurthy P, Thibault KM, Thompson LR, Tighe S, Vereen E, Eloe-Fadrosh EA.: Microbiome data management in action workshop: Atlanta, GA, USA, June 12–13, 2024 BMC Environmental Microbiome. Springer Nature, 20(40), April 2025.

Hecht AL, Mahmud N, Chaudhry S, Cao JY, Branigan GP, Lee J, Theiller E, Roggiani M, Friedman ES, Herman L, Galis BE, Jones SM, Planet PJ, Zackular JP, Kaplan DE, Serper M, Reddy KR, Moustafa AM, Goulian M, Wu GD.: Carbohydrate consumption drives adaptive mutations in Escherichia coli associated with increased risk for systemic infection. bioRxiv March 2025.