High-Throughput Sequencing and Predictive Microbiology: Mapping the microbiome to manage risk during production

Have you ever wondered what microorganisms are found in a facility and where exactly they reside? In what combinations and proportions do they appear? How do they grow, move and survive? How does the production environment affect them and how they, the environment? Is it possible to use this information to predict and prevent spoilage or even outbreaks and reduce food safety risks? 

The SAFE project, a 3-year initiative, brought together the industry, government and academia in Ireland, and with the use of High Throughput/Next Generation Sequencing (HTS/NGS) mapped the microbiome of food manufacturing facilities across the region. The results from the project provide insight for developing models to predict the likelihood of occurrence of a pathogen or a spoiler within a production environment before it actually occurs. This enables a preventive approach to food safety, thereby reducing or eliminating the potential for holding a shipment, wasting product, or the brand damage associated with a product recall. 

This webinar is a prelude to initiate a similar collaborative project here in the U.S. between IFSH, Creme Global and food companies interested in participating in the project.

Presentation Materials

Complete Webinar Presentations Materials May be Accessed Here


Institute for Food Safety and Health (IFSH)

The Institute for Food Safety and Health (IFSH) is a world-class consortium of the Illinois Institute of Technology (IIT), the US Food and Drug Administration (FDA) and the food Industry. It builds on and expands the vital work of the National Center for Food Safety and Technology (NCFST – est. 1988), producing knowledge-based outcomes in the areas of food safety, food defense, and nutrition for stakeholders in government, industry, and academia.


IFSH High-Throughput Sequencing Initiative (IHI)

The IFSH High-Throughput Sequencing Initiative or IHI is one of the newest enterprises in IFSH to provide the latest technology for the researchers especially in the food industry. The IHI offers HTS Laboratory and analytical services to all especially our colleagues in the food companies.


Creme Global

Creme Global is a scientific modelling, data analytics and computing company that delivers predictive analytics and modeling to help whole industries make better decisions. The company’s experts in mathematical modelling, statistics, software development, food science and nutrition develop and deploy the software models for consumer intake modelling, product safety assessment, regulatory affairs and innovation projects.



Dr. Behzad Imanian

Institute for Food Safety and Health, Illinois Tech

Since March 2016, Dr. Imanian has been leading the High-Throughput Sequencing (HTS) Initiative or IHI in IFSH in the Illinois Tech. The IFSH HTS laboratory he helped to establish is equipped with advanced HTS sequencers, and it offers a variety of services that include Whole Genome Sequencing (WGS), metagenomics (16s rDNA and shotgun sequencing) for environmental monitoring, transcriptomics (RNA-seq) and other HTS applications. In addition to directing the HTS laboratory, Dr. Imanian has established the bioinformatics facility in IFSH. This facility currently houses three High Performance Computers (HPCs), and it will be expanding in the future. The IFSH bioinformatics Center is capable of providing analytical services from quality control, genome and transcriptome assembly to annotation, SNP and phylogenetic analyses and much more to all the researchers in the IFSH, IIT, the food industry as well as outside collaborators. The center also provides direct access to the IFSH HPCs for all our collaborators who desire to conduct the analytical work on their data themselves.

Prof. Seamus Fanning

University College Dublin

In 2002, Professor Fanning was appointed to the Chair of Food Safety & Zoonoses at UCD. Currently, his research themes include the application of molecular methods to Food Safety as applied for the control of zoonotic disease agents of public health importance. The activities of this group have focused on extending our understanding of the molecular mechanisms of antimicrobial and biocide resistance in zoonotic bacteria and how they relate to external environmental stresses. Professor Fanning was appointed to the National Zoonoses Committee (NZC) in 2012 and is a lead microbiologist with the China National Center for Food Safety & Risk Assessment (CFSA) in Beijing. He currently serves as an Editor of Research in Microbiology and FEMS Microbiology Letters and is a member of the Editorial Boards of Applied & Environmental Microbiology; Foodborne Pathogens & Disease; the Journal of Food Protection & Microbial Drug Resistance. 

Dr. Scott Nguyen

Creme Global & University College Dublin

Scott received a PhD in Microbiology & Immunology at the University of Oklahoma Health Sciences Center (2013) with studies on the human pathogen Streptococcus pyogenes and streptococcal bacteriophages. Subsequently, he was a postdoctoral microbiologist at the USDA U.S. Meat Animal Research Center (2015-2017, USMARC) in Clay Center, Nebraska, studying Enterobacteriaceae in cattle and humans with a primary focus on Salmonella and next-generation sequencing. He joined the UCD Centre for Food Safety (2018-present) as a molecular microbiologist/bioinformatician under Prof. Seamus Fanning with a focus on foodborne pathogens (primarily Salmonella, Yersinia, and Escherichia).

Noel Rogers

Creme Global

Noel works as a Data Scientist in Creme Global specialising in mathematical modelling and statistics. He has a background in physics and maths with an MSc in Mathematics from Maynooth University and an MSc in Data Analytics from Dublin Institute of Technology. He has extensive experience in data analytics and mathematical modelling across a number of domains including financial risk, fraud, chemical exposure and food safety.

Brendan Ring

Creme Global

Brendan is the Commercial Director in Creme Global and has worked with a wide range of companies in the food, medical and ICT space over the last two decades. Experienced in engaging with C-level management and technical teams to scope complex requirements and deliver scientific solutions. He completed an engineering degree in Dublin City University and an MBA in the University of Cambridge.


10:30 am – 10:40 am

Introduction: HTS, bioinformatics & collaborative projects in IFSH
Dr. Behzad Imanian

10:40 am – 10:50 am

The field of predictive microbiology: An overview
Prof. Seamus Fanning

10:50 am – 11:00 am

Microbiological analysis from the SAFE project
Dr. Scott Nguyen

11:00 am – 11:10 am

Developing predictive models: Our approach
Noel Rogers

11:10 am – 11:20 am 

The Service Implementation
Brendan Ring

11:20 am – 11:45 am

Questions & Answers
Please Note

You can forward your questions ahead of time to Dr. Behzad Imanian, bimanian@iit.edu. You will also be able to pose your questions through text during the webinar.


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