Development of food safety risk assessment tools based on molecular typing and WGS of Campylobacter jejuni genome

Abstract The ‘learning‐by‐doing’ EU‐FORA fellowship programme in the development of risk assessment tools based on molecular typing and WGS of Campylobacter jejuni genome was structured into two main activities: the primary one focused on training on risk assessment methodology and the secondary one in starting and enhancing the cooperation between the hosting and home organisations, or other joint activities. The primary activities had three subsequent work packages (WPs): WP1 data organisation, WP2 cluster and association analyses, and WP3 development of risk assessment models. The secondary activities have branched into one workshop and the initiation of a cooperation programme between the hosting and home organisations. In the last quarter, the fellow had contributed to the characterisation of some pathogens in possible response to a changing climate, part of the CLEFSA project. The fellow attended various forms of training: online and on‐site courses, and also participated at several conferences and meetings for improving his knowledge and skills, contributing to performing the Campylobacter risk assessment and source attribution.

[1]  MSD manual: professional version , 2020, JAC-antimicrobial resistance.

[2]  M. Aerts,et al.  Technical specifications on harmonised monitoring of antimicrobial resistance in zoonotic and indicator bacteria from food‐producing animals and food , 2019, EFSA journal. European Food Safety Authority.

[3]  I. Jongenburger,et al.  Validation by interlaboratory trials of EN ISO 10272 - Microbiology of the food chain - Horizontal method for detection and enumeration of Campylobacter spp. - Part 1: Detection method. , 2019, International journal of food microbiology.

[4]  Dr. J. Andrews,et al.  Fault Tree Analysis , 2006, System Safety Engineering and Risk Assessment.

[5]  Keith A Jolley,et al.  Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications , 2018, Wellcome open research.

[6]  Alexandre P. Francisco,et al.  GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens , 2017, bioRxiv.

[7]  Eduardo N. Taboada,et al.  Whole-Genome Sequencing in Epidemiology of Campylobacter jejuni Infections , 2017, Journal of Clinical Microbiology.

[8]  Si Ming Man,et al.  Global Epidemiology of Campylobacter Infection , 2015, Clinical Microbiology Reviews.

[9]  B. Korczak,et al.  Source Attribution of Human Campylobacter Isolates by MLST and Fla-Typing and Association of Genotypes with Quinolone Resistance , 2013, PloS one.

[10]  P. Whyte,et al.  Molecular Epidemiology of Campylobacter Isolates from Poultry Production Units in Southern Ireland , 2011, PloS one.

[11]  Si Ming Man The clinical importance of emerging Campylobacter species , 2011, Nature Reviews Gastroenterology &Hepatology.

[12]  Alison J. Cody,et al.  Extended Sequence Typing of Campylobacter spp., United Kingdom , 2008, Emerging infectious diseases.

[13]  Griffin,et al.  Overview of methods for source attribution for human illness from food-borne microbiological hazards - Scientific Opinion of the Panel on Biological Hazards. , 2008, EFSA journal. European Food Safety Authority.

[14]  Clifton A. Ericson,et al.  Failure Mode and Effects Analysis , 2005 .

[15]  Gehua Wang,et al.  Colony Multiplex PCR Assay for Identification and Differentiation of Campylobacter jejuni, C. coli, C. lari, C. upsaliensis, and C. fetus subsp. fetus , 2002, Journal of Clinical Microbiology.

[16]  I. Nachamkin,et al.  Flagellin gene typing of Campylobacter jejuni by restriction fragment length polymorphism analysis , 1993, Journal of clinical microbiology.

[17]  Griffin,et al.  Overview of methods for source attribution for human illness from food-borne microbiological hazards , 2008 .

[18]  Kathleen,et al.  Flagellin Gene Typing of Campylobacterjejuni by Restriction , 2022 .