HYBRID EVENT: You can participate in person at Rome, Italy or Virtually from your home or work.
September 16-18, 2024 | Rome, Italy
FAT 2022

David Gally

David Gally, Speaker at Food Science Congress 2022
University of Edinburgh, United Kingdom
Title : Source attribution of foodborne bacterial pathogens using machine learning approaches


Foodborne pathogens continue to be a major threat to human health and threaten the viability of particular foods and major outbreaks have profound economic and social consequences.  At Food Standards Scotland (FSS), we work with academic, commercial and public health partners to keep food safe and this includes instigating and supporting genomic studies on bacterial isolates associated with human infections from food or drink such as Salmonella, E. coli and Listeria.  A key target is accurate source attribution i.e. prediction of animal and/or geographical origins of such pathogens based on their whole genome sequence and there have been a number of groups applying machine-learning (ML) methods to improve what we can predict about both the source and infection threat of an isolate based on its genome sequence.  As with all ML approaches, there is the need to have as much high-quality input training data as possible on which to build the models. 

At FSS we have had a historical focus on source attribution for Campylobacter and Shiga toxigenic E. coli and are currently involved in projects focused on Salmonella Typhimurium and Escherichia coli isolated from human, cattle, pigs and poultry with three main aims:

(1) to predict the likely animal source of any human or food isolate;

(2) to predict the infection threat to humans of an isolate from an animal or food source;

(3) to identify the genetic elements more likely to be associated with particular hosts.

The presentation will introduce the main research in this area and our main findings about the accuracy of the methods and how it can be applied to enhance food safety and public health.


Mr David Gally is the Chief Scientific Advisor for Food Standards Scotland and hold a personal chair in Microbial Genetics (since 2006) at the Roslin Institute, University of Edinburgh where he lead an Institute Strategic Programme on the ‘Control of Infectious Diseases in Livestock’. His training is as a Microbiologist with a degree and PhD from Newcastle University, followed by research positions in Michigan & North Carolina. After a Medical Research Council Fellowship (1994-98), He obtained a Lectureship in Bacteriology at Edinburgh Vet School and then a Veterinary Fellowship to study the biology of enterohaemorrhagic E. coli (EHEC) O157 in cattle working in partnership with scientists in the UK and around the world. His main current research interests are around predictive genomics, phage therapy and bacterial gene regulation.