Center for Scientific Excellence for Food Research and Analysis



Field of Interest

cSEFRA focuses on the establishment of rapid and accurate testing services for the analysis of food, water, and agricultural products. Food products are evaluated for their chemical and microbial quality in accordance with ISO standards. We aim to provide effective means of control of foodborne pathogens by using mixtures of bacterial viruses (phage cocktails) and their products to create a biological treatment for various bacterial pathogens. In addition, we aim to become one of the strongest, most reliable centers in testing the quality and safety of food, water, and agriculture products in Egypt, the Middle East, and North Africa.


The specific area/ research questions the center is interested in

cSEFRA is interested in four main research areas:

1. Provide microbiological and chemical testing services that complies with ISO standards

2. Provide professional training in the food safety areas.

3. Introduce an organic phage therapy technology and phage based products against pathogenic bacteria.

4. Develop in house methodologies that can accelerate the identification of pathogenic bacteria


The major lab techniques or research facilities that are unique to the center's research area

Phage isolation, amplification and typing techniques: for the production of phage for page therapy application (biocontrol) to control bacterial contamination of food to improve food safety.

Molecular techniques: for the production of phage based products to control bacterial contamination.

VITEK MS analyzer: by applying the internal and Original Equipment Manufactural (OEM) Methods, automated VITEK MS analyzer will be used for phenotyping characterization for fast and accurate detection of different pathogenic microorganisms.

Freeze Dryer: For long term preservation of different reference strains at optimum and suitable cryoprotectant agents in accordance to ISO standards.

Fermenter: For Large scale production of phage and for phage products productions.

High-performance liquid chromatographic (HPLC): for the determination of aflatoxin, heavy metals, and trace elements according to ISO standards.


The Center PI

Prof. Dr. Ayman El-Shibiny

Professor of Biomedical Sciences

Director of the center of Scientific Excellence for Food Research and Analysis (cSEFRA)

Director General for Research

Director of Center for Microbiology and Phage Therapy (CMP)

Vice Director of Accreditation

Acting Director of center for genomics


Brief about the PI 

Dr. Ayman El-Shibiny is currently working as a professor of biomedical sciences, director general for research and vice director of accreditation unit at the University of Science and Technology at Zewail City. El-Shibiny got his Doctor of Philosophy degree in Microbiology from The University of Nottingham, UK in 2006. Prior to joining Zewail City, El-Shibiny worked as a postdoctoral fellow at a number of universities including University of Nottingham (UK), Cardiff University (UK), and The Evergreen State College (USA). As a microbiologist, El-Shibiny’s research interests cover a broad range of topics related to Food Safety and Human Health. He established the first Phage Therapy lab in Egypt at Zewail City. His main research area is Phage Therapy and his current research interests include the therapeutic use of bacteriophages as a possible alternative to treat and control antibiotic-resistant pathogens in food, veterinary, and human.

Contact e-mail of the Director 



A list of the researchers in the center and their affiliation to the lab (technicians, lab managers, postdocs, Ph.D. students, masters students, research assistants, interns, or junior researchers)

1. Mr. Mohamed Gad, Lab Manager

2. Abdallah AbdelSattar, research assistant and MSc student

3. Mennatallah Mamdouh, MSc student 

4. Nada Adel, research assistant, and MSc student

5. Fatma Abdelrahman, research assistant, and MSc student

6. Anan Safwat, research assistant and MSc student

7. Rana Ramadan, research assistant, and MSc student

8. Samar Hamed, MSc student 

9. Nedaa Mohamed, MSc student

10. Nouran Elsayed, research assistant, and MSc student

11. Mohamed Shokry, research assistant and MSc student


Abdallah S. Abdelsattar, Warda M. Farouk, Shrouk Mohamed Gouda, Anan Safwat, Toka A. Hakim, Ayman El-Shibiny (2021). Utilization of Ocimum basilicum extracts for zinc oxide nanoparticles synthesis and their antibacterial activity after a novel combination with phage. Materials Letters.


Hamdy Abdelhamid, Omar E. Morsy, Ayman El-Shibiny, Reda Abdelbaset (2021). Detection of foodborne pathogens using novel vertical capacitive sensors. Alexandria Engineering Journal,


Mohamed S. Fayez, Toka A. Hakim, Mona M. Agwa, Mohamed Abdelmoteleb, Rania G. Aly, Nada N. Montaser, Abdallah S. Abdelsattar, Nouran Rezk and Ayman El-Shibiny (2021). Topically Applied Bacteriophage to Control Multi-Drug Resistant Klebsiella pneumoniae Infected Wound in a Rat Model. Antibiotics 2021, 10, 1048.


Abdallah S. Abdelsattar, Anan Safwat, Rana Nofal, Amera E. Taha, Salsabil Makky, Ayman El-Shibiny (2021). Isolation and Characterization of Bacteriophages ZCSE6 against Salmonella spp.: Phage Application in Milk. Biologics 1, 164–176. biologics1020010.


Loay Bedda, Fayrouz Mahmoud, Radwa Klkhateib, Alyaa Dawoud, Hassan Gamal, Abdallah S. Abdelsattar, Ayman El-Shibiny (2021). SARS-CoV-2: Evaluation and Evolution. Coronaviruses. Volume 2, Issue 8, DOI: 10.2174/2666796702666210712104119.


Shaimaa F. Mouftah, Jose´ F. Cobo-Dı´az, AvelinoA´ lvarez-Ordo´ ñez, Menattallah Elserafy, Nehal A. Saif1, Asmaa Sadat, Ayman El-Shibiny, Mohamed Elhadidy (2021). High-throughput sequencing reveals genetic determinants associated with antibiotic resistance in Campylobacter spp. from farm-to-fork. PLoS ONE, 2021, 16(6 June).


Abdallah S. Abdelsattar, Rana Nofal, Salsabil Makky, Anan Safwat, Amera Taha and Ayman El-Shibiny (2021). The Synergistic Effect of Biosynthesized Silver Nanoparticles and Phage ZCSE2 as a Novel Approach to Combat Multidrug-Resistant Salmonella enterica. Antibiotics 2021, 10, 678.


Abdallah S. Abdelsattar, Alyaa Dawoud, Salsabil Makky, Rana Nofal, Ramy K. Aziz  and Ayman El-Shibiny (2021). Bacteriophages: From Isolation to Application. Current Pharmaceutical Biotechnology, 2021, 22, 1-24. DOI: 10.2174/1389201022666210426092002.


Alsaadi, A., Beamud, B., Easwaran, M., Abdelrahman, F., Ayman El-Shibiny, Alghoribi, M.F., Domingo-Calap, P (2021). Learning From Mistakes: The Role of Phages in Pandemics. Frontiers in Microbiology, 2021, 12, 653107.


Mohamed El-Telbany, Gamal El-Didamony, Ahmed Askora, Eman Ariny, Dalia Abdallah, Ian F. Connerton, and Ayman El-Shibiny (2021). Bacteriophages to Control Multi-Drug Resistant Enterococcus faecalis Infection of Dental Root Canals. Microorganisms 2021, 9, 517. 10.3390/microorganisms9030517.


Fatma Abdelrahman, Maheswaran Easwaran , Oluwasegun I. Daramola, Samar Ragab, Stephanie Lynch, Tolulope J. Oduselu, Fazal Mehmood Khan, Akomolafe Ayobami, Fazal Adnan, Eduard Torrents, Swapnil Sanmukh, and Ayman El-Shibiny (2021) Phage-Encoded Endolysins. Antibiotics 2021, 10, 124. antibiotics10020124.


Hadeel Hosney, Eslam G. Al Sakkari, Ahmad Mustafa, Ibrahim Ashour, Ibrahim Mustafa, Ayman El Shibiny (2019). A cleaner enzymatic approach for producing non phthalate plasticiser to replace toxic based phthalates. Clean Technologies and Environmental Policy.


Kamel S. Sultan, Tamer A. Ali, Nada A. Fahmy, Ayman El-Shibiny (2019). Using millimeter-waves for rapid detection of pathogenic bacteria in food based on bacteriophage. Engineering Reports. 2019;e12026.


Abdallah S. Abdelsattar, Fatma Abdelrahman, Alyaa Dawoud, Ian F. Connerton and Ayman El-Shibiny (2019). Encapsulation of E. coli phage ZCEC5 in chitosan-alginate beads as a delivery system in phage therapy. AMB Express. 17;9(1):87. doi: 10.1186/s13568-019-0810-9.


Omar A. Taha, Phillippa L. Connerton, Ian F. Connerton and Ayman El-Shibiny (2018). Bacteriophage ZCKP1: A Potential Treatment for Klebsiella pneumoniae Isolated From Diabetic Foot Patients. Front. Microbiol. doi: 10.3389/fmicb.2018.02127.


Hadeel Hosney, Bassant Nadiem, Ibrahim Ashour, Ibrahim Mustafa, Ayman El-Shibiny (2018). Epoxidized vegetable oil and bio-based materials as PVC plasticizer. J. APPL. POLYM. SCI., DOI: 10.1002/APP.46270.


Ayman El-Shibiny and Salma El-Sahhar (2017) Bacteriophages: the possible solution to treat infections caused by pathogenic bacteria. Can J Microbiol. Nov; 63(11):865-879. doi: 10.1139/cjm-2017-0030.


Ayman El-Shibiny, Salma El-Sahhar, Mohamed Adel (2017) Phage applications for improving food safety and infection control in Egypt. Journal of Applied Microbiology. Journal of Applied Microbiology.123(2):556-567. DOI: 10.1111/jam.13500.


For the rest of the publications:

For the rest of publications


Principle Investigator (PI) of Phase iii: Applications & Products Development, Academy for Scientific Research and Technology (ASRT-Egypt) Fund. The development of new therapeutic products and delivery system for phage therapy applications in veterinary.

Principle Investigator (PI) of Center of Scientific Excellence for Food Research and Analysis (STDF-Egypt) Fund.

Principle Investigator (PI) of ZC internal grant (IRF) grant. Innovative phage delivery systems to control bacterial infections in food, farm animals, and human topical infections.

Principle Investigator (PI) of India-Egypt project, Academy for Scientific Research and Technology (ASRT-Egypt) Fund. Molecular dissection of the Pseudomonas aeruginosa phage endolysin: a step toward the next generation therapeutics.

Principle Investigator (PI) of IMHOTEP project, Academy for Scientific Research and Technology (ASRT-Egypt) Fund. Biocontrol of pathogenic E.coli carried by chicken using bacteriophages.

Principle Investigator (PI) of “MM-wave biosensing-based detection of Food-borne and Pathogenic Bacteria in Food industry using Bacteriophage” project funded by STDF, Egypt

Principle Investigator (PI) of “From research labs to marketing practice: Bacteriophage as antimicrobial for the treatment of antibiotic resistant bacteria” project, STDF_IG.

Senior collaborator of BBSRC research project titled “Bacteriophage targeting antibiotic resistant bacteria”.


  • Microbial identification using state-of-the-art automated systems
  • Antibiotic susceptibility testing (AST) using the most accurate techniques.
  • Multimode Plate Reader
  • UV/Visible Spectrophotometer
  • Freeze dryer
  • Ultracentrifuge
  • PCR Reaction
  • PCR Machine Only
  • PCR Cleanup
  • Purification PCR From Gel Agarose
  • Real Time PCR Machine Only
  • RNA Extraction
  • Shaking Incubator For Cultures
  • Ordinary Light Microscopy
  • Lyophilization/ sample
  • Insilco PCR And Primer Design
  • Insilco Primer Design For Real Time PCR
  • Incubate Tissue Culture Growth
  • Thermocycler 1000 cycle
  • Thermocycler 500 cycle
  • DNA Extraction/ sample
  • DNA Isolation Basic/ sample
  • DNA Gel Electrophoresis/ sample
  • MBC/MIC -Disc diffusion/ sample
  • MBC/MIC -Well diffusion/ sample
  • Available biochemical tests
  • Biofilm inhibition MTT assay
  • Biofilm inhibition crystal violet
  • Biofilm clearance crystal violet
  • Cytotoxicity assay
  • GenBank Submission
  • Biostatistical Analysis
  • Bench Fees For Molecular Services
  • Building Phylogenetic Tree By Clustalw
  • Advanced Bioinformatics Application to Detect The Gene Family By Designing
  • Degenerate Primer
  • Air quality/ wall swap/ sample
  • Water microbial analysis according to ISO standards/ sample
  • Food microbial analysis according to ISO standards (most pathogenic bacteria and total bacterial count/ sample
  • -80℃ storage service