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Mostafa Ghanem , BVSc, MVSc, PhD

Assistant Professor

Assistant Professor of Molecular Epidemiology

Department of Veterinary Medicine, University of Maryland, College Park

Virginia-Maryland College of Veterinary Medicine, Maryland Campus

8075 Greenmead Drive, College Park, MD 20742 8075 Greenmead Drive, Room 1413 College Park, MD 20742-3711
301 314-1191 301-314-6855 (Fax)

Protecting Our Region's Poultry Industry with Advanced Technology

Overview

Mostafa Ghanem is a veterinarian and molecular epidemiologist who uses genomics to prevent, track, and control infectious diseases of poultry and the foodborne pathogens they carry. His laboratory builds standardized sequence-typing schemes and genomic surveillance tools, designs next-generation Salmonella and Clostridium perfringens vaccines, develops metagenomic diagnostics, and creates practical biosecurity tools for avian influenza. Working at the human–animal–environment interface, he partners with diagnostic laboratories, state and federal agencies, industry, and growers across Maryland and the Delmarva Peninsula to turn genomic insight into field-ready solutions.

Areas of expertise

  • Molecular epidemiology and genomic surveillance
  • Whole-genome sequencing, MLST and cgMLST strain typing
  • Avian Mycoplasma (M. gallisepticum, M. synoviae, M. iowae)
  • Infectious coryza (Avibacterium paragallinarum) and Ornithobacterium rhinotracheale
  • Salmonella preharvest control and poultry vaccines
  • Reverse vaccinology and immunoinformatics
  • Clostridium perfringens and necrotic enteritis
  • Shotgun metagenomics and microbiome science
  • Antimicrobial resistance (genotype–phenotype)
  • Highly pathogenic avian influenza (HPAI) biosecurity and preparedness
  • One Health and food safety
  • Poultry health extension

Biography

Dr. Ghanem joined the University of Maryland in 2019 with more than 15 years of experience in poultry medicine. He holds BVSc and MVSc degrees from Alexandria University, Egypt, where he graduated first in his class and later served as a teaching assistant and practicing poultry veterinarian, and a PhD in Veterinary Preventive Medicine (molecular epidemiology) from The Ohio State University. At Ohio State he developed the first standardized MLST and core-genome MLST schemes for the major avian Mycoplasma species, work recognized with the AAAP Reed Rumsey Award and the P.P. Levine Award for the best paper in Avian Diseases, and served as Associate Director of the Infectious Diseases Molecular Epidemiology Laboratory and Research Coordinator for the Global One Health initiative.

At UMD, he directs the Molecular Epidemiology Laboratory, holds a joint research, extension, and teaching appointment, and serves as the Maryland campus liaison to the Virginia–Maryland College of Veterinary Medicine’s Center for Public Veterinary Medicine (CPVM). He is a co-founder of the UMD Center of Excellence in Microbiome Sciences, a faculty associate of the Joint Institute for Food Safety and Applied Nutrition (JIFSAN), Co-Chair of the American Association of Avian Pathologists (AAAP) Epidemiology Committee, and Chair of the USDA multistate research project NC1180 on endemic, emerging, and re-emerging poultry diseases.

Research: UMD Molecular Epidemiology Laboratory (UMDMEL)

Our mission is to translate biological insights into applied knowledge. Because DNA is a shared language across all pathogens, the same genomic toolkit- strain typing, comparative genomics, reverse vaccinology, and metagenomics- lets us move quickly from one disease problem to the next as the needs of the poultry industry and public health evolve. The program is organized around five connected themes.

1. Molecular typing and genomic surveillance

We develop and maintain standardized, internationally interoperable typing schemes for avian bacterial pathogens. Dr. Ghanem curates the global PubMLST reference databases for Mycoplasma gallisepticum, M. synoviae, M. iowae, and Avibacterium paragallinarum, which hold more than 1,300 isolates contributed from 39 countries. In 2026, the lab published the first genome-guided MLST scheme for A. paragallinarum (Journal of Clinical Microbiology), with a cgMLST scheme in development, and documented genotype–phenotype discordance in antimicrobial resistance of U.S. Ornithobacterium rhinotracheale isolates.

2. Salmonella preharvest control and next-generation vaccines

With Dr. Sharon Tennant (University of Maryland School of Medicine), we are adapting live-attenuated, non-transmissible (LANT) vaccine technology, designed to protect without persisting in the environment or spreading to people, for control of major Salmonella serogroups in chickens. In parallel, we use structural prediction and immunoinformatics to design broad-spectrum multiepitope subunit vaccines, including a candidate against multidrug-resistant Salmonella Infantis (Frontiers in Immunology, 2026).

3. Clostridium perfringens and necrotic enteritis

We study C. perfringens gene regulation and vaccine targets to support antibiotic-free control of necrotic enteritis. Outputs include validated reference genes for RT-qPCR in C. perfringens (Scientific Reports, 2022) and a multiepitope vaccine design against the collagen adhesin protein developed with USDA-ARS (Microorganisms, 2025).

4. Metagenomics, microbiome science, and diagnostic innovation

We benchmark shotgun metagenomic workflows for culture-independent, pathogen-agnostic detection of foodborne pathogens (Journal of Food Protection, 2025) and apply microbiome profiling to disease mechanisms, including how infectious coryza reshapes the chicken upper-respiratory microbiome (Frontiers in Veterinary Science, 2026).

5. Precision biosecurity and HPAI risk mitigation

In response to the 2022 H5N1 epizootic, Dr. Ghanem developed BEAT-HPAI (Biosecurity Enhancement and Assessment Tool), a free web-based self-assessment built on the 14 National Poultry Improvement Plan biosecurity principles that produces color-coded, farm-specific risk reports. The lab is now working with UMD computer scientists and ecologists toward an AI-enabled, data-integrated next generation of the tool.

Collaborate with us

UMDMEL welcomes partnerships with diagnostic laboratories, state and federal animal-health agencies, poultry companies and allied industry, and academic groups. We offer:

  • Molecular typing and genome sequencing: MLST, cgMLST, and whole-genome sequencing with comparative analysis for avian bacterial pathogens (Mycoplasma, A. paragallinarum, O. rhinotracheale, Pasteurella multocida, Salmonella and others), including outbreak investigation and vaccine-strain matching. Fee-based services are available to external clients.
  • Reference-database curation: assignment of new alleles and sequence types in the PubMLST databases, including confidential handling of pre-publication submissions.
  • Consultation: poultry-health diagnosis, molecular-epidemiology study design, antimicrobial-resistance genomics, metagenomics, and HPAI biosecurity.
  • Joint research and grants: vaccine development, genomic surveillance, One Health and food-safety projects, and data-science/AI applications in animal health.

The laboratory supports Maryland’s animal-health infrastructure through a memorandum of understanding with the Maryland Department of Agriculture. To discuss a project, email mghanem@umd.edu with a brief description of the pathogen, sample type, and question.

Molecular typing resources

Extension and outreach

  • Poultry Health and Applied Research (PHAR) forum, founded in 2021; a recurring regional meeting connecting the Maryland, Delaware, and Virginia Departments of Agriculture, diagnostic laboratories, USDA, the Delmarva Chicken Association, company veterinarians, and UMD Extension for real-time disease intelligence.
  • BEAT-HPAI and the HPAI Short Course, a biosecurity self-assessment tool and a six-module online course on control areas, permitted movement, biosecurity audits, and cleaning and disinfection, developed with the UMD Extension Poultry Team.
  • Commercial Poultry News and “Research to Reality”, recurring articles since 2020 and a 2026 series translating current poultry science into practical farm guidance for Delmarva producers.
  • AAAP Epidemiology Webinar Series, national continuing education for poultry veterinarians on surveillance, outbreak investigation, biosecurity, and modeling.
  • Regional leadership, Delmarva Chicken Association National Meeting program committee (since 2021; founder of its Applied Poultry Research Student Poster Session), DCA Health Committee, and UMD Extension Poultry Team.
  • Public engagement, founder of the Department of Veterinary Medicine’s Maryland Day “Veterinary Medicine and One Health” exhibit.

Public veterinary medicine and career development

As the Maryland campus liaison to the Virginia–Maryland College of Veterinary Medicine’s Center for Public Veterinary Medicine, Dr. Ghanem builds pathways into government, regulatory, public-health, and industry careers. He co-developed and moderates the national Beyond Private Practice webinar series, developed standardized DVM clerkships with USDA-APHIS (Veterinary Services and Animal Care), research, and laboratory animal medicine partners, coordinated the Washington, D.C. component of the Summer Veterinary Student Research Program, chairs the Dr. Mitchell A. Essey Veterinary Public Practice Scholarship Committee, and co-founded and advises the UMD One Health Club.

Teaching

  • VMSC/CBSC 670 — Molecular Epidemiology of Infectious Diseases (graduate)
  • VMSC 698 — One Health Seminar (graduate)
  • Guest lectures: ANSC 262 Commercial Poultry Management; VMSC 660 Emerging and Re-emerging Infectious Diseases; MIEH 607/407 One Health: Food Safety and Security (UMD–Cairo University Global Classrooms); Molecular Epidemiology of Infectious Diseases, The Ohio State University

Lab members and trainees

Current

  • Dhiraj Chundru, PhD candidate, Comparative Biomedical Sciences, Salmonella vaccines (Ann G. Wylie Dissertation Fellow, 2026)
  • Madhusudan Timilsina, PhD student, Comparative Biomedical Sciences, metagenomics and infectious coryza

Alumni

  • Alyssa Harris, MS (2023), A. paragallinarum MLST
  • Michele  Williams, PhD, postdoctoral associate — Clostridium perfringens
  • Undergraduate researchers from UMD and the SOARE program (including Tuskegee University, Middlebury College, and California State University San Marcos), and Bolashak visiting scholars from Kazakhstan

Trainee honors include the David Bruce Snyder Award for Avian Molecular Epidemiology (2022, 2024, 2025, 2026), the Ann G. Wylie Dissertation Fellowship, Hatziolos scholarships, Center of Excellence in Microbiome Sciences fellowships, and a Northeast SARE graduate student grant.

Selected publications

Full list: Google Scholar Here. Corresponding/senior-author papers from the lab are marked *.

  1. Timilsina M, Chundru D, Ghanem M*. (2026). Impact of Avibacterium paragallinarum infection on the upper respiratory tract microbiome of chickens. Frontiers in Veterinary Science (in press).
  2. Ghanem M*, Harris A, Timilsina M, Chundru D, Williams M, Hashish A, El-Gazzar M. (2026). A standardized, genome-guided MLST scheme for Avibacterium paragallinarum. Journal of Clinical Microbiology, e0126725. doi.org/10.1128/jcm.01267-25
  3. Chundru D, Ghanem M*. (2026). In silico design of a multiepitope subunit vaccine targeting Salmonella enterica serovar Infantis. Frontiers in Immunology, 17. doi.org/10.3389/fimmu.2026.1717278
  4. Chundru D, Jessup A, Liakos E, Ghanem M*. (2026). Genotypic–phenotypic discordance of antimicrobial resistance in U.S. Ornithobacterium rhinotracheale field isolates. Journal of Applied Poultry Research, 100731. doi.org/10.1016/j.japr.2026.100731
  5. Che S, Goeringer P, Ghanem M, Rhodes J, Perdue M, Moyle J. (2026). Assessing evolving challenges and educational needs in poultry management. Journal of Applied Poultry Research, 35(2), 100697. doi.org/10.1016/j.japr.2026.100697
  6. Timilsina M, Chundru D, Pradhan AK, Blaustein RA, Ghanem M*. (2025). Benchmarking metagenomic pipelines for the detection of foodborne pathogens in simulated microbial communities. Journal of Food Protection, 88(9), 100583. doi.org/10.1016/j.jfp.2025.100583
  7. Chundru D, Bhattrai S, Timilsina M, Lillehoj H, Sun Z, Ghanem M*, Li C. (2025). In silico design, optimization, and evaluation of a multi-epitope vaccine targeting the Clostridium perfringens collagen adhesin protein. Microorganisms, 13(5). doi.org/10.3390/microorganisms13051147
  8. El-Gazzar M, Gallardo R, … Ghanem M. (2025). Avibacterium paragallinarum, the causative agent of infectious coryza: a comprehensive review. Avian Diseases, 68(S1), 362–379. doi.org/10.1637/aviandiseases-D-24-00105
  9. Bansal G, Ghanem M*, Sears KT, Galen JE, Tennant SM. (2024). Genetic engineering of Salmonella spp. for novel vaccine strategies and therapeutics. EcoSal Plus, 12(1). doi.org/10.1128/ecosalplus.esp-0004-2023
  10. Williams ML, Ghanem M*. (2022). Evaluation of candidate reference genes stability for gene expression analysis by RT-qPCR in Clostridium perfringens. Scientific Reports, 12, 19434. doi.org/10.1038/s41598-022-23804-7
  11. Ghanem M, El-Gazzar M. (2019). Development of a multilocus sequence typing assay for Mycoplasma gallisepticum. Avian Diseases, 63(4), 693–702.
  12. Ghanem M, Wang L, Zhang Y, Edwards S, Lu A, Ley D, El-Gazzar M. (2018). Core genome multilocus sequence typing: a standardized approach for molecular typing of Mycoplasma gallisepticum. Journal of Clinical Microbiology, 56(1). doi.org/10.1128/JCM.01145-17

Research support

Current and recent support for the laboratory’s work comes from USDA National Institute of Food and Agriculture (AFRI Data Science for Food and Agricultural Systems; Smith-Lever Special Needs; Northeast SARE), the U.S. Poultry & Egg Association, the Maryland Agricultural Experiment Station, the UMD Grand Challenges program (Center of Excellence in Microbiome Sciences), JIFSAN, and the Virginia–Maryland College of Veterinary Medicine. Active projects include:

  • Control of major infectious diseases of poultry in backyard and integrated farms and improvement of product safety (USDA-NIFA; Co-PD)
  • Towards the biogeography of foodborne pathogen genomic diversity (USDA-NIFA DSFAS; Co-PD)
  • Mitigating infectious coryza in commercial layers through a live Avibacterium paragallinarum vaccine (Northeast SARE; Lead PD)
  • Live-attenuated vaccine candidates for control of Salmonella in chickens (U.S. Poultry & Egg Association; Maryland Agricultural Experiment Station; PI)

Honors and awards

  • Most Improved Committee Award, American Association of Avian Pathologists, AAAP Epidemiology Committee, Co-Chair (2026)
  • Certificate of Appreciation, American Association of Avian Pathologists (2026)
  • Cornerstone Award, College of Agriculture and Natural Resources, UMD, HPAI outbreak response, poultry extension team (2023)
  • P.P. Levine Award for Best Paper Published in Avian Diseases (2018)
  • Reed Rumsey Award, American Association of Avian Pathologists (2017)

Professional leadership and service

  • Chair, USDA-NIFA Multistate Research Project NC1180, Control of Endemic, Emerging, and Re-emerging Poultry Infectious Diseases in the United States (2026–present)
  • Co-Chair, AAAP Epidemiology Committee (member since 2017); lead proposer of the AAAP Epidemiology Manual
  • AAAP Liaison to the Council for Agricultural Science and Technology (CAST); member, CAST Animals Work Group
  • Review Editor, Frontiers in Microbiology; reviewer for Avian Diseases, Journal of Clinical Microbiology, Scientific Reports, and other journals
  • Grant panelist, National Science Centre, Poland
  • Memberships: AAAP, World Veterinary Poultry Association, American Society for Microbiology, Poultry Science Association, U.S. Animal Health Association, Maryland Veterinary Medical Association

In the news

  • Ag Innovation Northeast , “Maryland researchers lead the charge against bird flu threats” (2026)
  • University of Maryland Today, “Solutions to bird flu hatched” (2025); “Avian flu’s recent spread ‘changes the rules of the game’” (2024)
  • The Daily Times / DelmarvaNow, “What is avian influenza? Everything you need to know about bird flu” (2025)
  • CAST Hour podcast, Episode 1 — HPAI discussion (2024)
  • WBAL-TV 11 Baltimore, interview on the atypical canine respiratory illness (2024)

Join the lab

Prospective graduate students, veterinary students, postdoctoral researchers, and undergraduates (including pre-veterinary students) interested in molecular epidemiology, bacterial genomics, vaccine design, microbiome science, or One Health are encouraged to email mghanem@umd.edu with a CV and a short statement of interests. Graduate training is available through the Comparative Biomedical Sciences (CBSC) PhD and MS programs Here.

Education

  • PhD, Veterinary Preventive Medicine (Molecular Epidemiology), The Ohio State University
  • MVSc, Alexandria University, Egypt
  • BVSc, Alexandria University, Egypt

Professional experience

  • 2019–present: Assistant Professor of Molecular Epidemiology, Department of Veterinary Medicine, University of Maryland / Virginia–Maryland College of Veterinary Medicine
  • 2018–2019: Associate Director, Infectious Diseases Molecular Epidemiology Laboratory; Research Coordinator, Global One Health initiative, The Ohio State University
  • 2017–2018: Postdoctoral Researcher, Department of Veterinary Preventive Medicine, The Ohio State University
  • 2007–2012: Teaching Assistant, Faculty of Veterinary Medicine, Alexandria University; poultry veterinarian, commercial poultry diagnostic laboratory.

Links: Google Scholar Here| ORCID Here | Lab YouTube: youtube.com/@GhanemLab | BEAT-HPAI: go.umd.edu/HPAI