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.

Links
Search PubMed for articles
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.
Executive Leadership for the Microbiome Centers Consortium
Google Scholar Account
Github account where I maintain the bioinformatics tools I develop

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

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 SAA, 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 AK, 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: a meta-analysis of genome-predicted serotype prevalence to inform potential vaccine coverage. PLoS Medicine 23(1): e1004879, January 2026.

Kelliher JM, Mirzayi C, Bordenstein SR, Oliver A, Kellogg CA, Hatcher EL, Berg M, Baldrian P, Aljumaah M, Miller CML, Mungall C, Novak V, Palucki A, Smith E, Tabassum N, Bonito G, Brister JR, Chain PSG, Chen M, Degregori S, Dundore-Arias JP, Emerson JB, Fernandes VMC, Flores R, Gonzalez A, Hansen ZA, Jackson SA, Moustafa AM, Northen TR, Pariente N, Pett-Ridge J, Record S, Reji L, Reysenbach A-L, Rich VI, Richardson L, Roux S, Schriml LM, Shabman RS, Sierra MA, Sullivan MB, Sundaramurthy P, Thibault KM, Thompson LR, Tighe S, Vereen E, Eloe-Fadrosh EA. : STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies. 2025. Nature Microbiology 10: 3059-3068, December 2025.

Strysko J, Thela T, Feder A, Thubuka J, Machiya T, Mkubwa J, Mochankana K, Tiroyakgosi C, Kgomanyane K, Ntereke TD, Zankere T, Lechiile K, Gatonye T, Tembo CV, Vurayai M, Mannathoko N, Mokomane M, Moustafa AM, Goldfarb DM, Richard-Greenblatt M, McGann C, Coffin SE, Nakstad B, Cancedda C, Lautenbach E, Bogoshi D, Smith AM, Planet PJ.: Carbapenem-resistant Acinetobacter baumannii at a hospital in Botswana: detecting a protracted outbreak using whole genome sequencing. Microbiol Spectr. 14(1): e01768-25, November 2025.

McGann C, Strysko J, Bayani O, Moorad B, Ntlhako N, Nwako N, Hu W, Tanes C, Moustafa AM, Jones SM, Nakstad B, Gezmu AM, Arscott-Mills T, Goldfarb DM, Steenhoff AP, Richard-Greenblatt M, Machiya T, Thela T, Mokomane M, Paganotti GM, Vurayai M, Zalot M, Boustany M, Planet PJ, Coffin S, Bittinger K: Effect of maternal HIV status on the early neonatal microbiome. Journal of the Pediatric Infectious Diseases Society 14(10): piaf076, October 2025 Notes: https://doi.org/10.1093/jpids/piaf076.

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): 102, August 2025 Notes: https://doi.org/10.3390/sci7030102.

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 Conference, Barcelona, Spain, Podium 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. GRS Staphylococcal Diseases Conference, Barcelona, Spain, Poster August 2025.

Lemons JMS, Firrman J, Mahalak KK, Liu L, Narrowe AB, Higgins S, Moustafa AM, Baudot A, Deyaert S, Van den Abbeele P: The Effect of Sodium Benzoate on the Gut Microbiome Across Age Groups. Foods 14(17): 2949, August 2025 Notes: https://doi.org/10.3390/foods14172949.

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 1(6): e00008-25, July 2025 Notes: https://doi.org/10.1128/asmcr.00008-25.

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 Notes: https://doi.org/10.1371/journal.pone.0326353.