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
Abramson Pediatric Research Center
3615 Civic Center Boulevard Room 902C
Philadelphia, PA 19104
Lab: 2155909987
Email:
moustafaam@chop.edu
moustafaam@chop.edu
Publications
Links
Search PubMed for articles
Google Scholar Account
Co-Director for the Center for Microbial Medicine, a Center of Emphasis established at CHOP in August 2024.
Executive Leadership for the Microbiome Centers Consortium
The Sequencing Core provides expertise in next-generation sequencing of microbiome samples and single microbial isolates.
Github account where I maintain the bioinformatics tools I develop
Search PubMed for articles
Google Scholar Account
Co-Director for the Center for Microbial Medicine, a Center of Emphasis established at CHOP in August 2024.
Executive Leadership for the Microbiome Centers Consortium
The Sequencing Core provides expertise in next-generation sequencing of microbiome samples and single microbial isolates.
Github account where I maintain the bioinformatics tools I develop
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.
Permanent linkBPharm (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.
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
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.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, 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.
Martínez JRW, Alcalde-Rico M, Jara-Videla E, Reyes J, Carvajal LP, Rincon S, Ríos R, Diaz L, Quesille-Villalobos A, Riquelme-Neira R, Rivas L, Moustafa AM, Hanson B, Undurraga EA, Olivares-Pacheco J, García P, Araos R, Planet PJ, Arias CA, Munita JM.: Geographic divergence of methicillin-resistant Staphylococcus aureus ST5-SCCmecI in the aftermath of a major earthquake and tsunami: impact of a plasmid harboring heavy metal resistance genes. mBio March 2025.
She Q, Srinivasan L, Theiller E, Galis BE, Napper T, Feder A, Arvanitis A, Jones SM, Hayes E, Puopolo KM, Baldassano RN, David MZ, Coffin SE, Gibbs KA, Smith K, Harris RM, Zackular JP, Moustafa AM, Planet PJ.: Transmission of Staphylococcus aureus in the neonatal intensive care unit predicts invasive infection medRxiv (under review at Nat. Comm.) February 2025.
Liu S, Rodriguez J, Munteanu V, Ronkowski C, Sharma N, Alser M, Andreace F, Blekhman R, Błaszczyk D, Chikhi R, Crandall K, Della Libera K, Francis D, Frolova A, Gancz A, Huntley N, Jaiswal P, Kosciolek T, Łabaj P, Łabaj W, Luan T, Mason C, Moustafa AM, Muralidharan H, Mutlu O, Ghiasi N, Rahnavard A, Sun F, Tian S, Tierney B, Van Syoc E, Vicedomini R, Zackular J, Zelikovsky A, Zielińska K, Ganda E, Davenport E (R), Pop M, Koslicki D, Mangul S.: Analysis of metagenomic data. Nature Reviews Methods Primers 5, Jan 2025.
Mulcrone PL, Narrowe A, Jones S, Hu W, Bittinger K, Moustafa AM, Firrman, J. : Monitoring the impact of chlorinated drinking water on the developing gut microbiota of adolescent mice using genetic profiling. International Journal of Environmental Studies Page: 1-18, Jan 2025.