Ahmed M. Moustafa, BPharm, PhD
About Ahmed M. Moustafa, BPharm, PhD
Titles
Sequencing Core Director, Microbiome Center
Assistant Professor of Pediatrics (Gastroenterology, Hepatology and Nutrition), Perelman School of Medicine at the University of Pennsylvania
Assistant Professor of Pediatrics in Microbiology, Perelman School of Medicine at the University of Pennsylvania
Awards and Honors
2019, Best Poster Prize. Symposium on Advances in Genomics, Epidemiology, and Statistics (SAGES), University of Pennsylvania
2018, Award from the National Human Genome Research Institute to defray the cost of programming course at CSHL
2014, Travel award, Murdoch University to International Pasteurellaceae Conference, Prato, Italy
2011-2015, PhD scholarship, Murdoch University
2009, Grade High Distinction, Alexandria University
2008, Travel and Training Award in a Hungarian community pharmacy, International Pharmaceutical Student's Federation
Leadership and Memberships
Memberships in Professional Organizations
International
2015-present, European Society of Clinical Microbiology and Infectious Diseases
National
2020-present, Pediatric Infectious Diseases Society
2020-present, National Center for Biotechnology Information (NCBI), NIH
2015-present, American Society for Microbiology
Editorial and Academic Positions
Editorial Positions
Ad-Hoc Reviewer
Frontiers Veterinary Science
Veterinary Microbiology
Cladistics
mSphere
}Gene
PLOS ONE
The Veterinary Journal
Antimicrobial Resistance and Infection Control
Letters in Applied Microbiology
Education & training
Undergraduate Degree
BPharm - Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
Graduate Degree
PhD in Biomedical Sciences - School of Veterinary and Life Sciences, Murdoch University, Perth, Australia
Fellowship
Post-doctoral Fellow, Infectious Diseases - Paul Planet Lab, Children’s Hospital of Philadelphia, Philadelphia, PA
Publications
Publications
2023
Bianco C, Moustafa AM, O'Brien, Martin M, Read TD, Kreiswirth B, Planet PJ. : Pre-epidemic evolution of USA300 clade and molecular key for classification. Frontiers in Cellular and Infection Microbiology 13, Jan 2023.
Firrman J, Liu L, Mahalak K, Hu W, Bittinger K, Moustafa A, Jones SM, Narrowe A, Tomasula P.: An in vitro analysis of how lactose modifies the gut microbiota structure and function of adults in a donor-independent manner. Front Nutr 9: 1040744, Jan 2023.
Mahalak KK, Firrman J, Narrowe AB, Hu W, Jones SM, Bittinger K, Moustafa AM, Liu L.: Fructooligosaccharides (FOS) differentially modifies the in vitro gut microbiota in an age-dependent manner. Front Nutr 9: 1058910, Jan 2023.
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.
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.
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.
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.
Smith AB, Specker JT, Hewlett KK, Scoggins TR, Knight M, Lustig AM, Li Y, Evans KM, Guo Y, She Q, Christopher MW, Garrett TJ, Moustafa AM, Van Tyne D, Prentice BM, Zackular JP: Liberation of host heme by Clostridioides difficile-mediated damage enhances Enterococcus faecalis fitness during infection. American Society for Microbiology. Kimberly A Kline (eds.). 2023.
2022
Viana AS, Botelho AM, Feder A, Moustafa AM, Silva DNS, Martini CL, Ferreira ALP, Silva-Carvalho¹ MC, Carvalho BT, Planet PJ, Figueiredo AMS. High frequency of triclosan low-dose resistance among CC5 MRSA and risk of misclassification of the SCCmec into types. J. Antimicrob. Chemother.. 2022, dkac322. https://doi.org/10.1093/jac/dkac322.
Marques AD, Sherrill-Mix S, Everett J, Reddy S, Hokama P, Roche AM, Hwang Y, Glascock A, Whiteside SA, Graham-Wooten J, Khatib LA, Fitzgerald AS, Moustafa AM, Bianco C, Rajagopal S, Helton J, Deming R, Denu L, Azad A, Kitt E, Coffin SE, Newbern C, Mell JC, Planet PJ, Badjatia N, Richards B, Wang Z, Cannuscio CC, Strelau K, Jaskowiak-Barr A, Cressman L, Loughrey S, Ganguly A, Feldman MD, Collman RG, Rodino KG, Kelly BJ, Bushman FD. SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021. mBio. 2022, 13(1). doi: 10.1128/mbio.03788-21.
2021
Saenkham P, Hyre AN, Hanson BS, Donati GL, Adams LG, Ryan C, Londoño A, Moustafa AM, Planet PJ, Subashchandrabose S. Copper resistance promotes fitness of Methicillin-Resistant S. aureus during urinary tract infection. mBio. 2021, 12(5). doi: 10.1128/mBio.02038-21.
Moustafa AM, Planet PJ. Emerging SARS-CoV-2 diversity revealed by rapid whole genome sequence typing. Genome Biol. Evol. 2021, 13(9): evab197.
Viana AS*, Botelho AM*, Moustafa AM*, Boge CLK, Ferreira ALP, Silva-Carvalho MC, Guimarães MA, Costa BSS, de Mattos MC, Maciel SP, Echevarria-Lima J, Narechania A, O’Brien K, Ryan C, Gerber JS, Ferreira-Carvalho BT, Figueiredo AMS, Planet PJ. Multidrug-resistant MRSA associated with bacteremia and monocyte evasion, Rio de Janeiro, Brazil. Emerg Infect Dis. 2021, 27(11): 21-0097. (*=1st coauthorship)
Moustafa AM, Planet PJ. Jumping a moving train: SARS-CoV-2 evolution in real time. J Pediatr Infect Dis. 2021, piab051.
Miller JJ, Shah IT, Hatten J, Barekatain Y, Mueller EA, Moustafa AM, Edwards RL, Dowd CS, Planet PJ, Muller FL, Jez JM, Odom John AR. Structure-guided microbial targeting of antistaphylococcal prodrugs. eLife. 2021, 10:e66657.
Moustafa AM, Bianco C, Denu L, Ahmed A, Coffin SE, Neide B, Everett J, Reddy S, Rabut E, Deseignora J, Feldman MD, Rodino KG, Bushman F, Harris RM, Chang Mell J, Planet PJ. Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. Open Forum Infect Dis. 2021, 8(7):ofab300.
Perelman SS, James DBA, Boguslawski KM, Nelson CW, Ilmain JK, Zwack EE, Prescott RA, Mohamed A, Tam K, Chan R, Narechania A, Pawline MB, Vozhilla N, Moustafa AM, Kim SY, Dittmann M, Ekiert DC, Bhabha G, Shopsin B, Planet PJ, Koralov SB, Torres VJ. Genetic variation of staphylococcal LukAB toxin determines receptor tropism. Nat Microbiol. 2021, (6):731-745.
Moustafa AM, Velusamy SK, Denu L, Narechania A, Fine DH, Planet PJ. Adaptation by Ancient Horizontal Acquisition of Butyrate Metabolism Genes in Aggregatibacter actinomycetemcomitans. mBio. 2021, 12(2). doi: 10.1128/mBio.03581-20.
2020
Moustafa AM, Lal A and Planet PJ. Comparative genomics in infectious disease. Curr Opin Microbiol 2020, 53:61-70.
Moustafa AM and Planet PJ. WhatsGNU: a tool for identifying proteomic novelty. Genome Biol 2020, 21:58.
2019
Riquelme S*, Lozano C*, Moustafa AM*, Liimatta K, Tomlinson KL, Britto C, Khanal S, Gill SK, Narechania A, Azcona-Gutiérrez JM, DiMango E, Saénz Y, Planet PJ, Prince A. CFTR-PTEN–dependent mitochondrial metabolic dysfunction promotes Pseudomonas aeruginosa airway infection. Sci Transl Med 2019, 11(499):eaav4634. (*=1st coauthorship)
Acker KP, Wong Fok Lung T, West E, Craft J, Narechania A, Smith H, O'Brien K, Moustafa AM, Lauren C, Planet PJ, Prince A. Strains of Staphylococcus aureus that colonize and infect skin harbor mutations in metabolic genes. iScience 2019, 19:281-290.
Botelho AM, Cerqueira e Costa MO, Moustafa AM, Beltrame CO, Ferreira FA, Côrtes MF, Costa BSS, Silva DNS, Bandeira PT, Lima NCB, Souza RC, de Almeida LGP, Vasconcelos ATR, Narechania A, Ryan C, O'Brien K, Kolokotronis SO, Planet PJ, Nicolás MF, Figueiredo AMS. Local diversification of methicillin-resistant Staphylococcus aureus ST239 in South America after its rapid worldwide dissemination. Front Microbiol 2019, 10:82.
2018
Zapotoczna M, Pelicioli-Riboldi G, Moustafa AM, Dickson E, Narechania A, Morrissey JA, Planet PJ, Holden MTG, Waldron KJ, Geoghegan JA. Mobile genetic element-encoded hypertolerance to copper protects Staphylococcus aureus from killing by host phagocytes. mBio 2018, 9(5):e00550-18.
2017
Moustafa AM and Bennett MD. Development of loop-mediated isothermal amplification–based diagnostic assays for detection of Pasteurella multocida and hemorrhagic septicemia–associated P multocida serotype B:2. AJVR 2017, 78(2):134-43.
2015
Moustafa AM, Ali SN, Bennett MD, Hyndman TH, Robertson ID, Edwards J. A case-control study of haemorrhagic septicaemia in buffaloes and cattle in Karachi, Pakistan, in 2012. Transbound Emerg Dis 2015. doi: 10.1111/tbed.12393.
Moustafa AM, Seemann T, Gladman S, Adler B, Harper M, Boyce JD, Bennett MD. Comparative genomic analysis of Asian haemorrhagic septicaemia-associated strains of Pasteurella multocida identifies more than 90 haemorrhagic septicaemia-specific genes. PLoS ONE 2015, 10(7):e0130296.
Moustafa AM, Bennett MD, Edwards J, Azim K, Mesaik MA, Choudhary MI, Pathanasophon P, Worarach A, Ali Q, Abubakar M, Anjum R. Molecular typing of haemorrhagic septicaemia-associated Pasteurella multocida isolates from Pakistan and Thailand using multilocus sequence typing and pulsed-field gel electrophoresis. Res Vet Sci 2013, 95:986-90.
Abstracts (includes Posters and Scientific Presentations)
2023
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.
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.
Lectures by Invitation
2023
Moustafa AM. Microbial Genomics Big-Data Mining and its applications in understanding infectious diseases. PS Drexel M&I means Drexel Microbiology and Immunology Department Seminar (January 2023), Philadelphia, PA, USA.
2022
Moustafa AM. "American Society of Microbiology Meeting with Senator Cory Booker (D-NJ)". Meeting Lead, Washington DC, USA. Jan 2022.
Moustafa AM. "Alignment-free Recombination Detection Using Genomic Database Distributions of Exact Protein Matches". ASM Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatic Pipeline, Baltimore, MD, USA. Oct 2022.