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
The Sequencing Core provides expertise in next-generation sequencing of microbiome samples and single microbial isolates.
Executive Leadership for the Microbiome Centers Consortium
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.
Google Scholar Account

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

Strysko J, Hu W, Mochankana K, John-Thubuka J, Zankere T, Gopolang B, Theiller E, Jones SM, Tembo CV, Ntereke TD, Gatonye T, Lechiile K, Keatholetswe T, Bianco C, Coffin SE, McGann C, Bittinger K, Lautenbach E, Mannathoko N, Mokomane M, Mosepele M, Richard-Greenblatt M, Nakstad B, Goldfarb DM, Planet P*, Moustafa AM*.: Integrated epidemiologic investigation and genomic confirmation of a Klebsiella pneumoniae neonatal sepsis outbreak in Botswana. PLOS Global Public Health 6(6): e0006468, June 2026 Notes: https://doi.org/10.1371/journal.pgph.0006468.

Duan J, Marques AD, Hogenauer M, Hwang Y, Zhang Y, Timperman A, Higgins S, Wilson NG, Fitts EA, Lim HK, Bittinger K, Moustafa AM, Collman RG, Bushman FD.: Optimizing methods for virome analysis based on studies of a synthetic viral community. mSystems 11: e00188-26, June 2026 Notes: https://doi.org/10.1128/msystems.00188-26.

Odih EE, Abdulahi J, Amulele A, Bates M, Heinz E, Hu W, Jain K, Magobo R, Olwagen CP, Tembo J, Sonda T, Strysko J, Tigoi CC, Bittinger K, Cornick J, Foster-Nyarko E, Gumbi W, Jones SM, Musyani CL, McGann CM, Moustafa AM, Musicha P, Mwansa JCL, Ndumba ML, Stanton TD, Omuoyo DO, Pearse O, Phillips LT, Planet PJ, Rodrigues CMC, Secka F, Sands K, Theiller E, Zuza AM, Basu S, Chan GJ, Iregbu KC, Mazarati JB, Alemayehu SS, Walsh TR, Zahra R, Dramowski A, Fwoloshi S, Appiah-Korang L, Madrid L, Obeng-Nkrumah N, Ojok D, Wadugu BD, Whitelaw AC, Bhargava A, Jindal A, Agarwal RK, Aiken AM, Berkley JA, Coffin SE, Feasey NA, Govender NP, Hamer DH, Madhi SA, Sankar MJ, Wyres KL, Holt KE.: Contribution of nosocomial transmission to Klebsiella pneumoniae neonatal sepsis in Africa and South Asia: an observational study of infection clusters inferred from pathogen genomics and temporal data. PLoS Medicine 23(5): e1005077, May 2026 Notes: https://doi.org/10.1371/journal.pmed.1005077.

Theiller E, Rajagopol S, Higgins S, Torres DI, Napper T, Galis BE, Dash A, Qian E, Hamlette L, She Q, Tanes C, L'Etoile N, Feder A, Slotfeldt Viana A, Assis Côrtes Esteves MC, Abt MC, Coffin SE, Hayes E, Potter RF, Zackular JP, Srinivasan L, Sá Figueiredo AM*, Planet PJ*, Moustafa AM*.: Empowering global disease surveillance with CURED: a tool for rapid identification of unique genomic biomarkers. mSystems 11: e01063-25, March 2026 Notes: https://doi.org/10.1128/msystems.01063-25.

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, Potter RF, Smith K, Harris RM, Zackular JP*, Moustafa AM*, Planet PJ*.: Rapid dissemination of Staphylococcus aureus in the neonatal intensive care unit is associated with invasive infection. Nature Communications 17(2550): https://doi.org/10.1038/s41467-026-69074-z, February 2026 Notes: https://doi.org/10.1038/s41467-026-69074-z.

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 Notes: https://doi.org/10.1371/journal.pmed.1004879.

Mmolai S, Gatonye T, Gopolang B, Tembo CV, Keatholetswe T, Coffin SE, Richard-Greenblatt M, Annavajhala MK, Hoar C, Bédard E, Moustafa A, Planet P, Strysko J.: Stewarding the hospital sink drain: a narrative review of practical approaches for controlling gram negative pathogens in low- and middle-income countries. Antimicrob Resist Infect Control. 15(1): 25, January 2026 Notes: https://doi.org/10.1186/s13756-026-01701-2.

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.