Corrigendum to “Exploiting the explosion of information associated with whole genome sequencing to tackle Shiga toxin-producing Escherichia coli (STEC) in global food production systems” [Int. J. Food Microbiol. 187 (2014) 57–72]

International Journal of Food Microbiology (Impact Factor: 3.08). 07/2014; 187C:57-72. DOI: 10.1016/j.ijfoodmicro.2014.07.002
Source: PubMed


The rates of foodborne disease caused by gastrointestinal pathogens continue to be a concern in both the developed and developing worlds. The growing world population, the increasing complexity of agri-food networks and the wide range of foods now associated with STEC are potential drivers for increased risk of human disease. It is vital that new developments in technology, such as whole genome sequencing (WGS), are effectively utilized to help address the issues associated with these pathogenic microorganisms. This position paper, arising from an OECD funded workshop, provides a brief overview of next generation sequencing technologies and software. It then uses the agent-host-environment paradigm as a basis to investigate the potential benefits and pitfalls of WGS in the examination of (1) the evolution and virulence of STEC, (2) epidemiology from bedside diagnostics to investigations of outbreaks and sporadic cases and (3) food protection from routine analysis of foodstuffs to global food networks. A number of key recommendations are made that include: validation and standardization of acquisition, processing and storage of sequence data including the development of an open access "WGSNET"; building up of sequence databases from both prospective and retrospective isolates; development of a suite of open-access software specific for STEC accessible to non-bioinformaticians that promotes understanding of both the computational and biological aspects of the problems at hand; prioritization of research funding to both produce and integrate genotypic and phenotypic information suitable for risk assessment; training to develop a supply of individuals working in bioinformatics/software development; training for clinicians, epidemiologists, the food industry and other stakeholders to ensure uptake of the technology and finally review of progress of implementation of WGS. Currently the benefits of WGS are being slowly teased out by academic, government, and industry or private sector researchers around the world. The next phase will require a coordinated international approach to ensure that it's potential to contribute to the challenge of STEC disease can be realized in a cost effective and timely manner.

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Available from: Eelco Franz, Feb 04, 2015
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    • "However, these association studies might be confounded by food and host effects. Within serogroup O157 considerable attention has been given to the non-random distribution of genotypes among bovine and human clinical isolates, showing considerable genome divergence (Franz et al., 2014). However, observed non-random distribution of clades and lineages among bovine and human clinical isolates might be the result of a differentiation in virulence, transmission capacity and survival, or some combination (Franz et al., 2012). "
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    ABSTRACT: The potential for using whole genome sequencing (WGS) data in microbiological risk assessment (MRA) has been discussed on several occasions since the beginning of this century. Still, the proposed heuristic approaches have never been applied in a practical framework. This is due to the non-trivial problem of mapping microbial information consisting of thousands of loci onto a probabilistic scale for risks. The paradigm change for MRA involves translation of multidimensional microbial genotypic information to much reduced (integrated) phenotypic information and onwards to a single measure of human risk (i.e. probability of illness).
    International Journal of Food Microbiology 04/2015; 22. DOI:10.1016/j.ijfoodmicro.2015.04.009 · 3.08 Impact Factor
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    ABSTRACT: Foodborne diseases are an important cause of human illness worldwide. Humans acquire these infections from a variety of sources and routes of transmission. Many efforts have been made in the last decades to prevent and control foodborne diseases, particularly foodborne zoonoses. However, information on the impact of these interventions is limited. To identify and prioritize successful food safety interventions, it is important to attribute the burden of human illness to the specific sources. Defining scientific concepts and harmonizing terminology for "source attribution" is essential for understanding and improving attribution methodologies and for sharing knowledge within the scientific community. We propose harmonized nomenclature, and describe the various approaches for human illness source attribution and their usefulness to address specific public health questions.
    Foodborne Pathogens and Disease 06/2009; 6(4):417-24. DOI:10.1089/fpd.2008.0208 · 1.91 Impact Factor
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    ABSTRACT: The complexity regarding Shiga toxin-producing Escherichia coli (STEC) in food safety enforcement as well as clinical care primarily relates to the current inability of an accurate risk assessment of individual strains due to the large variety in serotype and genetic content associated with (severe) disease. In order to classify the clinical and/or epidemic potential of a STEC isolate at an early stage it is crucial to identify virulence characteristics of putative pathogens from genomic information, which is referred to as 'predictive hazard identification'. This study aimed at identifying associations between virulence factors, phylogenetic groups, isolation sources and seropathotypes. Most non-O157 STEC in the Netherlands belong to phylogroup B1 and are characterized by the presence of ehxA, iha and stx2, but absence of eae. The large variability in the number of virulence factors present among serogroups and seropathotypes demonstrated that this was merely indicative for the virulence potential. While all the virulence gene associations have been worked out, it appeared that there is no specific pattern that would unambiguously enable hazard identification for an STEC strain. However, the strong correlations between virulence factors indicate that these arrays are not a random collection but are rather specific sets. Especially the presence of eae was strongly correlated to the presence of many of the other virulence genes, including all non-LEE encoded effectors. Different stx-subtypes were associated with different virulence profiles. The factors ehxA and ureC were significantly associated with HUS-associated strains (HAS) and not correlated to the presence of eae. This indicates their candidacy as important pathogenicity markers next to eae and stx2a.
    PLoS ONE 03/2015; 10(3):e0120353. DOI:10.1371/journal.pone.0120353 · 3.23 Impact Factor
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