Flaherty Visiting Professor’s research on Salmonella

February 4, 2019

James M Flaherty Visiting Professorship 2017/18 Visit Report

Name:                              Professor Lawrence D Goodridge

Home University:      McGill University

University visited:     University College Dublin

Purpose of Visit:

The goal of this visit was to further strengthen the research, teaching and outreach activities between the Food Safety and Quality Program (FSQP) at McGill University, and the Center for Food Safety (CFS) at University College Dublin. Research activities included development of a collaborative approach to studying the virulence and pathogenesis of Salmonella spp., which was based on whole genome comparative analysis of Salmonella isolates from Canada and Ireland, to identify known and previously unknown virulence and AMR genes, which was combined with phenotypic virulence data to produce a map of features explaining the pathogenicity of Salmonella. This approach, which we call Syst-Omics, represents an emerging approach to the study of foodborne pathogens. Dr. Goodridge also contributed to the teaching program at UCD, by contributing two lectures to students in the Food Safety Program. Both lectures focused on aspects of food safety including genomics of Shiga toxin producing Escherichia coli, and methods to characterize and control Salmonella in foods. Outreach activities included forming a new collaboration with the Food Safety Authority of Ireland to develop faster approaches to detect foodborne outbreaks, furthering a collaboration with the Department of Agriculture, Food and the Marine, and the development of a proposal for a World Health Organization collaborating Center in Precision Food Safety that includes the Food Safety and Quality Program at McGill University and the Center for Food Safety at University College Dublin (UCD).

Frank Hayes (Kerry Group), Professor Goodridge (Flaherty Visiting Professor), Professor Deeks (President UCD), Pamela Byrne (Food Safety Authority of Ireland), Professor Sheá Fanning (Picture Colm Mahady / Fennells – Copyright© Fennell Photography 2018)

Visit Details

Research & development conducted:
Salmonella is a leading cause of foodborne illness in Canada and Ireland. More than 2,500 serotypes of Salmonella enterica are known, and these serotypes have been defined according to the Kaufmann-White-Le Minor classification (KWL) scheme; however, misinterpretation of serotypes can result from weak or non-specific antibody agglutination reactions and loss of antigen expression. In silico (genomics) serotyping methods have become increasingly popular as the cost of whole genome sequencing (WGS) continues to decrease. During my time in Ireland, I compared in silico serotyping using online programs SISTR (developed by the Public Health Agency of Canada) and SeqSero (developed by the Centers for Disease Control and Prevention in the USA) to traditional KWL serotyping of 128 S. enterica Canadian and Irish isolates of food and agricultural origin, as part of an overall research program called Syst-Omics, which combines genomics and phenotypic approaches to study microbial pathogens.

Lectures, seminars, talks, events:

During my time at UCD, I taught several lectures in graduate classes related to Food Safety. I also presented an invited talk at an international conference that was hosted by faculty members at UCD. Additionally, I presented two talks to government agencies involved in food safety in Ireland, and finally, I presented my Flaherty lecture. Exact details for each of these talks are presented below.

  • Lectures in Graduate Food Safety Classes at University College Dublin:
    Date: February 27, 2018
    Lecture title: E. coli as a commensal and a pathogen
  • Graduate Class: PHPS 40810, Public Health & Population Sci: Food Safety:
    Date: March 27, 2018
    Lecture title: Strain to strain variability in foodborne pathogens
  • Graduate Class: BSEN40040, Biosystems Engineering: Engineering Design for Food Quality and Safety
    Invited talk at an International Conference
    Date: March 23, 2018
    Title of talk: How IoT will change food safety
    Conference: Internet of Things for Food (IoT4F) (
  • Food Safety talks hosted by Irish Food Safety Agencies:
    Date: May 8, 2018
    Title of Talk: Whole Genome Sequencing Identifies the Presence of an Emerging Group of Prophages within the Enterobacteriace
  • Government Agency: Department of Agriculture, Food & the Marine:
    Date: May 10, 2018
    Title of Talk: Syst-OMICS: The Canadian Experience. A modern approach to reducing foodborne disease
  • Government Agency: Food Safety Authority of Ireland
    Flaherty Lecture:
    Date: April 25, 2018
    Title of Talk: Microbial Phenogenomics: Precision Food Safety Solutions for the Global Food Supply
    Host: University College Dublin

Experimental procedures & results:

Methods: Traditional serotyping was performed using antisera-based agglutination assays according to standard KWL practices. Whole genome sequencing (WGS) was performed on 128 S. enterica isolates from Canada and Ireland on an Illumina MiSeq platform with 300-bp paired-end libraries and 30X coverage, and the raw reads were assembled using the A5 pipeline. All information regarding the S. enterica isolates including metadata and whole genome sequences are online in the Salmonella Food Systomics (SalFOS) database at In silico serotyping was performed using SISTR and SeqSero and a WGS tree based on core genome SNPs was constructed using HARVEST and edited using iTOL to compare KWL and in silico methods.

Results: SISTR identified 88% of isolates correctly (compared to the KWL serotype) and 12% incorrectly (identified the wrong serotype compared to KWL) of which 8% of incorrect results were for serotypes outside the top 100 illness causing serotypes in Canada and Ireland. SeqSero identified 68% of isolates correctly and 8% incorrectly. Furthermore, SeqSero produced 24% ambiguous (reported more than one serotype) results and could not identify the serotype of rough S. enterica isolates. The WGS core genome SNP tree demonstrated that isolates from individual serotypes clustered together, highlighting the genomes that produced incorrect and ambiguous in silico results (Figure 1).

Summary: These results indicate that SISTR is a reliable and accurate method for molecular serotyping of common foodborne serotypes of S. enterica.

Contacts made:
During my time in Dublin, I made several contacts at UCD and at two government agencies related to food safety. These contacts are as follows:

University College Dublin
Professor Seamus Fanning, Professor of Food Safety and Zoonoses (Host)
Professor Francis Butler, Professor of Biosystems Engineering
Professor Nick Holden, Professor of Biosystems and Food Engineering

Food Safety Authority of Ireland
Wayne Anderson, Director of Food Science and Standards
Pamela Byrne, Chief Executive Officer at the Food Safety Authority of Ireland

Department of Agriculture Food and the Marine
Rosemarie Slowey, Research Officer

Future Continuing Collaboration 
During my time in Ireland, I made several important connections that have led to ongoing collaborative efforts to improve the food safety systems of Canada, Ireland and the world. For example, the people that I met at the Food Safety Authority of Ireland (Dr. Wayne Anderson), along with my colleagues at UCD (Professor Seamus Fanning), formed the basis for a $10 million dollar (CAD) research proposal that was recently submitted, that aims to develop a faster approach to detect foodborne outbreaks in Canada and Ireland. The global impact of the McGill (Canada) UCD (Ireland) collaboration is exemplified by a future proposal that will be submitted to the World Health Organization (WHO) to develop a virtual collaborating centre in the area of food safety and genomics. The virtual centre will include the laboratories of Professor Goodridge (McGill) and Professor Fanning (UCD). The mission of the centre will include the develop of precision food safety approaches based on the use of genomics to improve the global food supply, and will include an emphasis on training personnel in developing countries in genomic techniques related to food safety, and foodborne outbreak investigation.

In conclusion, my time at UCD in Dublin, Ireland was a productive one. My research led to validation of a new tool that will enhance food safety in both Canada and Ireland. I also formed collaborations with professors and government officials, which will solidify ongoing collaborations between food safety researchers in Canada and Ireland, in keeping with the mission of the ICUF, which is to “to nurture the great friendship between these countries, through the support of scholarly exchange”.

Dr Lawrence D Goodridge, McGill University – Flaherty Visiting Professor 2017/18