Publications by authors named "Laurent Guillier"

50 Publications

Occurrence and risk assessment of sesame as an allergen in selected Middle Eastern foods available in Montreal, Canada.

Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2021 Apr 5;38(4):550-562. Epub 2021 Mar 5.

Food Risk Analysis and Regulatory Excellence Platform (PARERA), Department of Food Science and Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec, Canada.

Sesame allergy is a public health problem in many countries around the world. The purpose of this study is to determine the occurrence of sesame allergen in unlabelled or labelled free-sesame Middle Eastern foods with or without Precautionary Allergen Labelling (PAL) 'may contain' and estimate the risk incurred by the Canadian population allergic to sesame with a focus on products purchased in Middle Eastern grocery stores and bakeries in Montreal, Canada. A total of 571 samples were analysed to determine the level of sesame protein. Of the 571 samples analysed, 19% (109/571) contained sesame (results >LOQ) with concentrations of sesame proteins varying between 0.5 and 1,875 mg kg and 35% (199/571) contained traces (a value between LOD and LOQ). Unpackaged products were found to present the highest proportion of sesame containing samples (36%). For packaged products, 16% (27/173) of samples with PAL and 3% (5/173) without PAL were found to contain sesame. A probabilistic approach was used to estimate the risk incurred by the Canadian consumers allergic to sesame. Our evaluation estimated that 33 to 308 allergic reactions may occur out of 10 000 individuals ingesting one type of bakery product contaminated at a level of 0.6-74 mg kg sesame proteins. The incidence and level of sesame cross-contact reported in this study demonstrate that sesame allergic consumers could react if they ignore the precautionary allergen statements on product labels. Attention to sesame as a potential cross-contact agent and as a priority allergen calls for better management, given the growing interest in this ingredient to be included in food formulations. Enhanced risk management efforts must be coupled with targeted risk communication covering both producers and consumers as to the need to adopt and an approach for the application of precautionary allergen labelling based on risk.
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http://dx.doi.org/10.1080/19440049.2021.1881622DOI Listing
April 2021

A microscopy-based approach for determining growth probability and lag time of individual bacterial cells.

Food Res Int 2021 02 24;140:110052. Epub 2020 Dec 24.

French Agency for Food, Environmental and Occupational Health & Safety (Anses), Laboratory for Food Safety, Université Paris-Est, Maisons-Alfort F-94701, France. Electronic address:

The development of relevant predictive models for single-cell lag time and growth probability near growth limits is of critical importance for predicting pathogen behavior in foods. The classical methods for data acquisition in this field are based on turbidity measurements of culture media in microplate wells inoculated with approximately one bacterial cell per well. Yet, these methods are labour intensive and would benefit from higher throughput. In this study, we developed a quantitative experimental method using automated microscopy to determine the single-cell growth probability and lag time. The developed method consists of the use of direct cell observation with phase-contrast microscopy equipped with a 100× objective and a high-resolution device camera. The method is not a time-lapse method but is based on the observation of high numbers of colonies for a given time. Automation of image acquisition and image analysis was used to reach a high throughput. The single-cell growth probabilities and lag times of four strains of Listeria monocytogenes were determined at 4 °C. The microscopic method was shown to be a promising method for the determination of individual lag times and growth probability at the single-cell level.
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http://dx.doi.org/10.1016/j.foodres.2020.110052DOI Listing
February 2021

Contribution of Foods and Poor Food-Handling Practices to the Burden of Foodborne Infectious Diseases in France.

Foods 2020 Nov 11;9(11). Epub 2020 Nov 11.

National Veterinary School of Alfort, 94700 Maisons-Alfort, France.

The foodborne disease burden (FBDB) related to 26 major biological hazards in France was attributed to foods and poor food-handling practices at the final food preparation step, in order to develop effective intervention strategies, especially food safety campaigns. spp. and non-typhoidal accounted for more than 60% of the FBDB. Approximately 30% of the FBDB were attributed to 11 other hazards including bacteria, viruses and parasites. Meats were estimated as the main contributing food category causing (50-69%) (CI90) of the FBDB with (33-44%), (9-21%), (4-20%) (CI90) of the FBDB for poultry, pork and beef, respectively. Dairy products, eggs, raw produce and complex foods caused each approximately (5-20%) (CI90) of the FBDB. When foods are contaminated before the final preparation step, we estimated that inadequate cooking, cross-contamination and inadequate storage contribute for (19-49%), (7-34%) and (9-23%) (CI90) of the FBDB, respectively; (15-33%) (CI90) of the FBDB were attributed to the initial contamination of ready-to-eat foods-without any contribution from final food handlers. The thorough implementation of good hygienic practices (GHPs) at the final food preparation step could potentially reduce the FBDB by (67-85%) (CI90) (mainly with the prevention of cross-contamination and adequate cooking and storage).
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http://dx.doi.org/10.3390/foods9111644DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7697675PMC
November 2020

Natural outbreaks and bioterrorism: How to deal with the two sides of the same coin?

J Glob Health 2020 Dec;10(2):020317

Bacteriology Unit, French Armed Forces Biomedical Research Institute (IRBA), Bretigny sur Orge, France.

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http://dx.doi.org/10.7189/jogh.10.020317DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7535343PMC
December 2020

Rapid assessment and prediction of the efficiency of two preservatives against S. aureus in cosmetic products using High Content Screening-Confocal Laser Scanning Microscopy.

PLoS One 2020 27;15(7):e0236059. Epub 2020 Jul 27.

Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France.

Most cosmetic products are susceptible to microbiological spoilage due to contaminations that could happen during fabrication or by consumer's repetitive manipulation. The composition of cosmetic products must guarantee efficient bacterial inactivation all along with the product shelf life, which is usually assessed by challenge-tests. A challenge-test consists in inoculating specific bacteria, i.e. Staphylococcus aureus, in the formula and then investigating the bacterial log reduction over time. The main limitation of this method is relative to the time-consuming protocol, where 30 days are needed to obtain results. In this study, we have proposed a rapid alternative method coupling High Content Screening-Confocal Laser Scanning Microscopy (HCS-CLSM), image analysis and modeling. It consists in acquiring real-time S. aureus inactivation kinetics on short-time periods (typically 4h) and in predicting the efficiency of preservatives on longer scale periods (up to 7 days). The action of two preservatives, chlorphenesin and benzyl alcohol, was evaluated against S. aureus at several concentrations in a cosmetic matrix. From these datasets, we compared two secondary models to determine the logarithm reduction time (Dc) for each preservative concentration. Afterwards, we used two primary inactivation models to predict log reductions for up to 7 days and we compared them to observed log reductions. The IQ model better fits datasets and the Q value gives information about the matrix level of interference.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0236059PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7384607PMC
September 2020

Modeling the Inactivation of Viruses from the Family in Response to Temperature and Relative Humidity in Suspensions or on Surfaces.

Appl Environ Microbiol 2020 09 1;86(18). Epub 2020 Sep 1.

Risk Assessment Department, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France.

Temperature and relative humidity are major factors determining virus inactivation in the environment. This article reviews inactivation data regarding coronaviruses on surfaces and in liquids from published studies and develops secondary models to predict coronaviruses inactivation as a function of temperature and relative humidity. A total of 102 values (i.e., the time to obtain a log reduction of virus infectivity), including values for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), were collected from 26 published studies. The values obtained from the different coronaviruses and studies were found to be generally consistent. Five different models were fitted to the global data set of values. The most appropriate model considered temperature and relative humidity. A spreadsheet predicting the inactivation of coronaviruses and the associated uncertainty is presented and can be used to predict virus inactivation for untested temperatures, time points, or any coronavirus strains belonging to and genera. The prediction of the persistence of SARS-CoV-2 on fomites is essential in investigating the importance of contact transmission. This study collects available information on inactivation kinetics of coronaviruses in both solid and liquid fomites and creates a mathematical model for the impact of temperature and relative humidity on virus persistence. The predictions of the model can support more robust decision-making and could be useful in various public health contexts. A calculator for the natural clearance of SARS-CoV-2 depending on temperature and relative humidity could be a valuable operational tool for public authorities.
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http://dx.doi.org/10.1128/AEM.01244-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7480392PMC
September 2020

Source Attribution Study of Sporadic Derby Cases in France.

Front Microbiol 2020 14;11:889. Epub 2020 May 14.

Laboratoire de Sécurité des Aliments, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Université PARIS-EST, Maisons-Alfort, France.

subsp. serovar Derby is one of the most frequent causes of gastroenteritis in humans. In Europe, this pathogen is one of the top five most commonly reported serovars in human cases. In France, Derby has been among the ten most frequently isolated serovars in humans since the year 2000. The main animal hosts of this serovar are pigs and poultry, and white meat is the main source of human contamination. We have previously shown that this serovar is polyphyletic and that three distinct genetic lineages of Derby cohabit in France. Two of them are associated with pork and one with poultry. In this study, we conducted a source attribution study based on single nucleotide polymorphism analysis of a large collection of 440 Derby human and non-human isolates collected in 2014-2015, to determine the contribution of each lineage to human contamination. In France, the two lineages associated with pork strains, and corresponding to the multilocus sequence typing (MLST) profiles ST39-ST40 and ST682 were responsible for 94% of human contaminations. Interestingly, the ST40 profile is responsible for the majority of human cases (71%). An analysis of epidemiologic data and the structure of the pork sector in France allowed us to explain the spread and the sporadic pattern of human cases that occurred in the studied period.
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http://dx.doi.org/10.3389/fmicb.2020.00889DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7240076PMC
May 2020

AB_SA: Accessory genes-Based Source Attribution - tracing the source of Typhimurium environmental strains.

Microb Genom 2020 07;6(7)

Laboratory for Food Safety, ANSES, University of Paris-EST, Maisons-Alfort, France.

The partitioning of pathogenic strains isolated in environmental or human cases to their sources is challenging. The pathogens usually colonize multiple animal hosts, including livestock, which contaminate the food-production chain and the environment (e.g. soil and water), posing an additional public-health burden and major challenges in the identification of the source. Genomic data opens up new opportunities for the development of statistical models aiming to indicate the likely source of pathogen contamination. Here, we propose a computationally fast and efficient multinomial logistic regression source-attribution classifier to predict the animal source of bacterial isolates based on 'source-enriched' loci extracted from the accessory-genome profiles of a pangenomic dataset. Depending on the accuracy of the model's self-attribution step, the modeller selects the number of candidate accessory genes that best fit the model for calculating the likelihood of (source) category membership. The Accessory genes-Based Source Attribution (AB_SA) method was applied to a dataset of strains of Typhimurium and its monophasic variant (. 1,4,[5],12:i:-). The model was trained on 69 strains with known animal-source categories (i.e. poultry, ruminant and pig). The AB_SA method helped to identify 8 genes as predictors among the 2802 accessory genes. The self-attribution accuracy was 80 %. The AB_SA model was then able to classify 25 of the 29 . Typhimurium and . 1,4,[5],12:i:- isolates collected from the environment (considered to be of unknown source) into a specific category (i.e. animal source), with more than 85 % of probability. The AB_SA method herein described provides a user-friendly and valuable tool for performing source-attribution studies in only a few steps. AB_SA is written in R and freely available at https://github.com/lguillier/AB_SA.
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http://dx.doi.org/10.1099/mgen.0.000366DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7478624PMC
July 2020

Four European Salmonella Typhimurium datasets collected to develop WGS-based source attribution methods.

Sci Data 2020 03 3;7(1):75. Epub 2020 Mar 3.

Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.

Zoonotic Salmonella causes millions of human salmonellosis infections worldwide each year. Information about the source of the bacteria guides risk managers on control and preventive strategies. Source attribution is the effort to quantify the number of sporadic human cases of a specific illness to specific sources and animal reservoirs. Source attribution methods for Salmonella have so far been based on traditional wet-lab typing methods. With the change to whole genome sequencing there is a need to develop new methods for source attribution based on sequencing data. Four European datasets collected in Denmark (DK), Germany (DE), the United Kingdom (UK) and France (FR) are presented in this descriptor. The datasets contain sequenced samples of Salmonella Typhimurium and its monophasic variants isolated from human, food, animal and the environment. The objective of the datasets was either to attribute the human salmonellosis cases to animal reservoirs or to investigate contamination of the environment by attributing the environmental isolates to different animal reservoirs.
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http://dx.doi.org/10.1038/s41597-020-0417-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7054362PMC
March 2020

Dynamics of mobile genetic elements of Listeria monocytogenes persisting in ready-to-eat seafood processing plants in France.

BMC Genomics 2020 Feb 6;21(1):130. Epub 2020 Feb 6.

ANSES, Laboratory for Food Safety, Boulogne-sur-Mer, France.

Background: Listeria monocytogenes Clonal Complexes (CCs) have been epidemiologically associated with foods, especially ready-to-eat (RTE) products for which the most likely source of contamination depends on the occurrence of persisting clones in food-processing environments (FPEs). As the ability of L. monocytogenes to adapt to environmental stressors met in the food chain challenges the efforts to its eradication from FPEs, the threat of persistent strains to the food industry and public health authorities continues to rise. In this study, 94 food and FPEs L. monocytogenes isolates, representing persistent subtypes contaminating three French seafood facilities over 2-6 years, were whole-genome sequenced to characterize their genetic diversity and determine the biomarkers associated with long-term survival in FPEs.

Results: Food and FPEs isolates belonged to five CCs, comprising long-term intra- and inter-plant persisting clones. Mobile genetic elements (MGEs) such as plasmids, prophages and transposons were highly conserved within CCs, some of which harboured genes for resistance to chemical compounds and biocides used in the processing plants. Some of these genes were found in a 90.8 kbp plasmid, predicted to be" mobilizable", identical in isolates from CC204 and CC155, and highly similar to an 81.6 kbp plasmid from isolates belonging to CC7. These similarities suggest horizontal transfer between isolates, accompanied by deletion and homologous recombination in isolates from CC7. Prophage profiles characterized persistent clonal strains and several prophage-loci were plant-associated. Notably, a persistent clone from CC101 harboured a novel 31.5 kbp genomic island that we named Listeria genomic island 3 (LGI3), composed by plant-associated loci and chromosomally integrating cadmium-resistance determinants cadA1C.

Conclusions: Genome-wide analysis indicated that inter- and intra-plant persisting clones harbour conserved MGEs, likely acquired in FPEs and maintained by selective pressures. The presence of closely related plasmids in L. monocytogenes CCs supports the hypothesis of horizontal gene transfer conferring enhanced survival to FPE-associated stressors, especially in hard-to-clean harbourage sites. Investigating the MGEs evolutionary and transmission dynamics provides additional resolution to trace-back potentially persistent clones. The biomarkers herein discovered provide new tools for better designing effective strategies for the removal or reduction of resident L. monocytogenes in FPEs to prevent contamination of RTE seafood.
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http://dx.doi.org/10.1186/s12864-020-6544-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7006209PMC
February 2020

Biofilm Formation of Strains Under Food Processing Environments and Pan-Genome-Wide Association Study.

Front Microbiol 2019 21;10:2698. Epub 2019 Nov 21.

Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France.

Concerns about food contamination by are on the rise with increasing consumption of ready-to-eat foods. Biofilm production of is presumed to be one of the ways that confer its increased resistance and persistence in the food chain. In this study, a collection of isolates from foods and food processing environments (FPEs) representing persistent, prevalent, and rarely detected genotypes was evaluated for biofilm forming capacities including adhesion and sessile biomass production under diverse environmental conditions. The quantity of sessile biomass varied according to growth conditions, lineage, serotype as well as genotype but association of clonal complex (CC) 26 genotype with biofilm production was evidenced under cold temperature. In general, relative biofilm productivity of each strain varied inconsistently across growth conditions. Under our experimental conditions, there were no clear associations between biofilm formation efficiency and persistent or prevalent genotypes. Distinct extrinsic factors affected specific steps of biofilm formation. Sudden nutrient deprivation enhanced cellular adhesion while a prolonged nutrient deficiency impeded biofilm maturation. Salt addition increased biofilm production, moreover, nutrient limitation supplemented by salt significantly stimulated biofilm formation. Pan-genome-wide association study (Pan-GWAS) assessed genetic composition with regard to biofilm phenotypes for the first time. The number of reported genes differed depending on the growth conditions and the number of common genes was low. However, a broad overview of the ontology contents revealed similar patterns regardless of the conditions. Functional analysis showed that functions related to transformation/competence and surface proteins including Internalins were highly enriched.
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http://dx.doi.org/10.3389/fmicb.2019.02698DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6882377PMC
November 2019

Critical Orientation in the Jungle of Currently Available Methods and Types of Data for Source Attribution of Foodborne Diseases.

Front Microbiol 2019 12;10:2578. Epub 2019 Nov 12.

Department of Biostatistics, Biomathematics, Pharmacoepidemiology and Infectious Diseases (B2PHI), Institut National de la Santé et de la Recherche Médicale (INSERM), UVSQ, Institut Pasteur, Université Paris-Saclay, Paris, France.

With increased interest in source attribution of foodborne pathogens, there is a need to sort and assess the applicability of currently available methods. Herewith we reviewed the most frequently applied methods for source attribution of foodborne diseases, discussing their main strengths and weaknesses to be considered when choosing the most appropriate methods based on the type, quality, and quantity of data available, the research questions to be addressed, and the (epidemiological and microbiological) characteristics of the pathogens in question. A variety of source attribution approaches have been applied in recent years. These methods can be defined as top-down, bottom-up, or combined. Top-down approaches assign the human cases back to their sources of infection based on epidemiological (e.g., outbreak data analysis, case-control/cohort studies, etc.), microbiological (i.e., microbial subtyping), or combined (e.g., the so-called 'source-assigned case-control study' design) methods. Methods based on microbial subtyping are further differentiable according to the modeling framework adopted as frequency-matching (e.g., the Dutch and Danish models) or population genetics (e.g., Asymmetric Island Models and STRUCTURE) models, relying on the modeling of either phenotyping or genotyping data of pathogen strains from human cases and putative sources. Conversely, bottom-up approaches like comparative exposure assessment start from the level of contamination (prevalence and concentration) of a given pathogen in each source, and then go upwards in the transmission chain incorporating factors related to human exposure to these sources and dose-response relationships. Other approaches are intervention studies, including 'natural experiments,' and expert elicitations. A number of methodological challenges concerning all these approaches are discussed. In absence of an universally agreed upon 'gold' standard, i.e., a single method that satisfies all situations and needs for all pathogens, combining different approaches or applying them in a comparative fashion seems to be a promising way forward.
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http://dx.doi.org/10.3389/fmicb.2019.02578DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6861836PMC
November 2019

A Simple and Robust Statistical Method to Define Genetic Relatedness of Samples Related to Outbreaks at the Genomic Scale - Application to Retrospective Foodborne Outbreak Investigations.

Front Microbiol 2019 24;10:2413. Epub 2019 Oct 24.

ANSES, Laboratory for Food Safety, Université PARIS-EST, Maisons-Alfort, France.

The investigation of foodborne outbreaks (FBOs) from genomic data typically relies on inspecting the relatedness of samples through a phylogenomic tree computed on either SNPs, genes, kmers, or alleles (i.e., cgMLST and wgMLST). The phylogenomic reconstruction is often time-consuming, computation-intensive and depends on hidden assumptions, pipelines implementation and their parameterization. In the context of FBO investigations, robust links between isolates are required in a timely manner to trigger appropriate management actions. Here, we propose a non-parametric statistical method to assert the relatedness of samples (i.e., outbreak cases) or whether to reject them (i.e., non-outbreak cases). With typical computation running within minutes on a desktop computer, we benchmarked the ability of three non-parametric statistical tests (i.e., Wilcoxon rank-sum, Kolmogorov-Smirnov and Kruskal-Wallis) on six different genomic features (i.e., SNPs, SNPs excluding recombination events, genes, kmers, cgMLST alleles, and wgMLST alleles) to discriminate outbreak cases (i.e., positive control: C+) from non-outbreak cases (i.e., negative control: C-). We leveraged four well-characterized and retrospectively investigated FBOs of Typhimurium and its monophasic variant . 1,4,[5],12:i:- from France, setting positive and negative controls in all the assays. We show that the approaches relying on pairwise SNP differences distinguished all four considered outbreaks in contrast to the other tested genomic features (i.e., genes, kmers, cgMLST alleles, and wgMLST alleles). The freely available non-parametric method written in R has been designed to be independent of both the phylogenomic reconstruction and the detection methods of genomic features (i.e., SNPs, genes, kmers, or alleles), making it widely and easily usable to anybody working on genomic data from suspected samples.
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http://dx.doi.org/10.3389/fmicb.2019.02413DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821717PMC
October 2019

Exploring Listeria monocytogenes Transcriptomes in Correlation with Divergence of Lineages and Virulence as Measured in Galleria mellonella.

Appl Environ Microbiol 2019 11 16;85(21). Epub 2019 Oct 16.

Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, Dijon, France

As for many opportunistic pathogens, the virulence potential of is highly heterogeneous between isolates and correlated, to some extent, with phylogeny and gene repertoires. In sharp contrast with copious data on intraspecies genome diversity, little is known about transcriptome diversity despite the role of complex genetic regulation in pathogenicity. The current study implemented RNA sequencing to characterize the transcriptome profiles of 33 isolates under optimal growth conditions. Transcript levels of conserved single-copy genes were comprehensively explored from several perspectives, including phylogeny, -predicted virulence category based on epidemiological multilocus sequence typing (MLST) data, and virulence phenotype assessed in Comparing baseline transcriptomes between isolates was intrinsically more complex than standard genome comparison because of the inherent plasticity of gene expression in response to environmental conditions. We show that the relevance of correlation analyses and their statistical power can be enhanced by using principal-component analysis to remove the first level of irrelevant, highly coordinated changes linked to growth phase. Our results highlight the major contribution of transcription factors with key roles in virulence to the diversity of transcriptomes. Divergence in the basal transcript levels of a substantial fraction of the transcriptome was observed between lineages I and II, echoing previously reported epidemiological differences. Correlation analysis with virulence identified numerous sugar metabolism-related genes, suggesting that specific pathways might play roles in the onset of infection in is a multifaceted bacterium able to proliferate in a wide range of environments from soil to mammalian host cells. The accumulated genomic data underscore the contribution of intraspecies variations in gene repertoire to differential adaptation strategies between strains, including infection and stress resistance. It seems very likely that the fine-tuning of the transcriptional regulatory network is also a key component of the phenotypic diversity, albeit more difficult to investigate than genome content. Some studies reported incongruity in the basal transcriptome between isolates, suggesting a putative relationship with phenotypes, but small isolate numbers hampered proper correlation analyses with respect to their characteristics. The present study is the embodiment of the promising approach that consists of analyzing correlations between transcriptomes and various isolate characteristics. Statistically significant correlations were found with phylogenetic groups, epidemiological evidence of virulence potential, and virulence in larvae used as an model.
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http://dx.doi.org/10.1128/AEM.01370-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6803300PMC
November 2019

Evaluation of methods for elution of HEV particles in naturally contaminated sausage, figatellu and pig liver.

Food Microbiol 2019 Dec 30;84:103235. Epub 2019 May 30.

Université Paris-Est, Anses, Laboratory for Food Safety, F-94700, Maisons-Alfort, France. Electronic address:

Foodborne transmission of HEV is a growing public health concern in industrialised countries, where the disease is mainly autochthonous, caused by zoonotic HEV of either genotype 3 or 4. Foodstuffs containing pig's liver were suspected on several occasions to be the cause of autochthonous cases of HEV infection, while the transmission was associated with animal contact and the ingestion of raw or uncooked meat, especially liver. In assessing the risk related to the presence of HEV in food, detection methods were previously developed but HEV detection rates seem to vary with the type of samples and methods. As foodstuff containing pig liver can be contaminated with HEV internally, an efficient virus extraction procedure is required. The aim of this study was to evaluate six methods for their efficiency in releasing HEV viral particles from figatelli, pig liver sausages and liver samples previously tested positive for the presence of HEV. The ratio weight to volume of elution buffer (1:5) and the FastPrep®-24 homogeniser showed to significantly improve the quantity of HEV genomes released per gram of figatelli and pig liver sausages. To our knowledge, this study is the first to evaluate several methods for elution of HEV particles from naturally contaminated pig liver products, and may be extended for quantifying other viral genomes from food of animal origin.
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http://dx.doi.org/10.1016/j.fm.2019.05.019DOI Listing
December 2019

LiSEQ - whole-genome sequencing of a cross-sectional survey of Listeria monocytogenes in ready-to-eat foods and human clinical cases in Europe.

Microb Genom 2019 02 18;5(2). Epub 2019 Feb 18.

2​National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections at University of Liverpool, Liverpool, UK.

We present the LiSEQ (Listeria SEQuencing) project, funded by the European Food Safety Agency (EFSA) to compare Listeria monocytogenes isolates collected in the European Union from ready-to-eat foods, compartments along the food chain (e.g. food-producing animals, food-processing environments) and humans. In this article, we report the molecular characterization of a selection of this data set employing whole-genome sequencing analysis. We present an overview of the strain diversity observed in different sampled sources, and characterize the isolates based on their virulence and resistance profile. We integrate into our analysis the global L. monocytogenes genome collection described by Moura and colleagues in 2016 to assess the representativeness of the LiSEQ collection in the context of known L. monocytogenes strain diversity.
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http://dx.doi.org/10.1099/mgen.0.000257DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6421348PMC
February 2019

Inhibitory activity of phenolic acids against Listeria monocytogenes: Deciphering the mechanisms of action using three different models.

Food Microbiol 2019 Jun 24;80:18-24. Epub 2018 Dec 24.

Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France. Electronic address:

Phenolic compounds are well known for their antimicrobial activity. They may provide an interesting solution to ensure food safety by preventing the growth of foodborne pathogens while addressing the wishes of consumers for the use of natural preservatives in food and favoring the reuse of agro-industry byproducts. However, their mechanism of action is still not very well understood. Here, we aimed to decipher the complex mechanism of action of eight phenolic acids by decomposing their effects, such as the general effect of the decrease of extracellular pH (γ(pH)) and specific inhibitory effects of the undissociated (γ(A)) and dissociated (γ(A)) forms. We thus developed three different models and applied them to a dataset of Listeria monocytogenes growth rates experimentally obtained in the presence of various concentrations of phenolic acids at several pHs. The model that best fits the dataset was selected for each phenolic acid to explore the potential mechanisms. The results show that the antimicrobial activity is mainly due to the effect of the undissociated forms, except for chlorogenic and gallic acids, for which the antimicrobial activity is mainly due to a decrease in extracellular pH. In addition, the dissociated forms of p-coumaric and ferulic acids show significant inhibitory activity.
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http://dx.doi.org/10.1016/j.fm.2018.12.010DOI Listing
June 2019

Insights from genome-wide approaches to identify variants associated to phenotypes at pan-genome scale: Application to L. monocytogenes' ability to grow in cold conditions.

Int J Food Microbiol 2019 Feb 29;291:181-188. Epub 2018 Nov 29.

French Agency for Food, Environmental and Occupational Health & Safety (Anses), Laboratory for Food Safety, Université Paris-Est, Maisons-Alfort F-94701, France. Electronic address:

Intraspecific variability of the behavior of most foodborne pathogens is well described and taken into account in Quantitative Microbial Risk Assessment (QMRA), but factors (strain origin, serotype, …) explaining these differences are scarce or contradictory between studies. Nowadays, Whole Genome Sequencing (WGS) offers new opportunities to explain intraspecific variability of food pathogens, based on various recently published bioinformatics tools. The objective of this study is to get a better insight into different existing bioinformatics approaches to associate bacterial phenotype(s) and genotype(s). Therefore, a dataset of 51 L. monocytogenes strains, isolated from multiple sources (i.e. different food matrices and environments) and belonging to 17 clonal complexes (CC), were selected to represent large population diversity. Furthermore, the phenotypic variability of growth at low temperature was determined (i.e. qualitative phenotype), and the whole genomes of selected strains were sequenced. The almost exhaustive gene content, as well as the core genome SNPs based phylogenetic reconstruction, were derived from the whole sequenced genomes. A Bayesian inference method was applied to identify the branches on which the phenotype distribution evolves within sub-lineages. Two different Genome Wide Association Studies (i.e. gene- and SNP-based GWAS) were independently performed in order to link genetic mutations to the phenotype of interest. The genomic analyses presented in this study were successfully applied on the selected dataset. The Bayesian phylogenetic approach emphasized an association with "slow" growth ability at 2 °C of the lineage I, as well as CC9 of the lineage II. Moreover, both gene- and SNP-GWAS approaches displayed significant statistical associations with the tested phenotype. A list of 114 significantly associated genes, including genes already known to be involved in the cold adaption mechanism of L. monocytogenes and genes associated to mobile genetic elements (MGE), resulted from the gene-GWAS. On the other hand, a group of 184 highly associated SNPs were highlighted by SNP-GWAS, including SNPs detected in genes which were already likely involved in cold adaption; hypothetical proteins; and intergenic regions where for example promotors and regulators can be located. The successful application of combined bioinformatics approaches associating WGS-genotypes and specific phenotypes, could contribute to improve prediction of microbial behaviors in food. The implementation of this information in hazard identification and exposure assessment processes will open new possibilities to feed QMRA-models.
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http://dx.doi.org/10.1016/j.ijfoodmicro.2018.11.028DOI Listing
February 2019

Development of a Real-Time Cell Analysis (RTCA) Method as a Fast and Accurate Method for Detecting Infectious Particles of the Adapted Strain of Hepatitis A Virus.

Front Cell Infect Microbiol 2018 25;8:335. Epub 2018 Sep 25.

Laboratory for Food Safety, Université Paris Est, ANSES, Maisons-Alfort, France.

Hepatitis A virus (HAV) is one of the most common agents causing acute liver disease worldwide. HAV has been increasingly reported as the cause of foodborne disease outbreaks. The standard method currently available for detection of the genome of HAV in vulnerable foodstuffs is by RT-qPCR (ISO 15216). Despite its usefulness in the investigation of foodborne viruses, the use of RT-qPCR in food virology has been shown to overestimate the quantity of infectious virus or to highly underestimate the effect of the treatment on virus inactivation. The gold standard methods currently used for evaluating the efficacy of inactivation treatments on the adapted strain of HAV (HM175/18f) are either the plaque assay or the end-point dilution assay (TCID). However, both assays are labor-intensive and time-consuming. The aim of this study was to evaluate the use of the xCELLigence real-time cell analysis (RTCA) system for detecting the infectivity of the adapted strain of HAV. Kinetics of cell impedance showed that HAV induced a decrease in cell index (CI) correlated with the onset of HAV-induced cell death. In addition, the time to which the HAV-induced CI drop occurred was dependent on the viral concentration. An inverse linear relation could be established over a range of 5 log between the concentration of HAV and the time to reach 50% of CI decrease (TCI), showing that the RTCA assay could be used as a titration method for HAV. In addition, the RTCA-based assay could be performed in less than 6 days instead of 12 to 14 days with the gold standard methods. Therefore, the RTCA-based titration method is a powerful and suitable tool for high-throughput screening of anti-viral treatments. Its usefulness in HAV inactivation studies will improve the assessment of viral risk in food virology, as controlling transmission of viruses through their removal from foodstuffs is also an important challenge in reducing the burden of viral foodborne illnesses.
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http://dx.doi.org/10.3389/fcimb.2018.00335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6167467PMC
September 2019

Combining Quantitative Risk Assessment of Human Health, Food Waste, and Energy Consumption: The Next Step in the Development of the Food Cold Chain?

Risk Anal 2019 04 27;39(4):906-925. Epub 2018 Sep 27.

Laboratory for Food Safety, Université Paris-Est, Maisons-Alfort, France.

The preservation of perishable food via refrigeration in the supply chain is essential to extend shelf life and provide consumers with safe food. However, electricity consumed in refrigeration processes has an economical and an environmental impact. This study focuses on the cold chain of cooked ham, including transport, cold room in supermarket, display cabinet, transport by consumer, and domestic refrigerator, and aims to predict the risk for human health associated with Listeria monocytogenes, the amount of food wasted due to the growth of spoilage bacteria, and the electrical consumption to maintain product temperature through the cold chain. A set of eight intervention actions were tested to evaluate their impact on the three criteria. Results show that the modification of the thermostat of the domestic refrigerator has a high impact on food safety and food waste and a limited impact on the electrical consumption. Inversely, the modification of the airflow rate in the display cabinet has a high impact on electrical consumption and a limited impact on food safety and food waste. A cost-benefit analysis approach and two multicriteria decision analysis methods were used to rank the intervention actions. These three methodologies show that setting the thermostat of the domestic refrigerator to 4 °C presents the best compromise between the three criteria. The impact of decisionmaker preferences (criteria weight) and limitations of these three approaches are discussed. The approaches proposed by this study may be useful in decision making to evaluate global impact of intervention actions in issues involving conflicting outputs.
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http://dx.doi.org/10.1111/risa.13199DOI Listing
April 2019

Source Attribution of Foodborne Diseases: Potentialities, Hurdles, and Future Expectations.

Front Microbiol 2018 3;9:1983. Epub 2018 Sep 3.

Biostatistics, Biomathematics, Pharmacoepidemiology and Infectious Diseases (B2PHI), Inserm, UVSQ, Institut Pasteur, Université Paris-Saclay, Paris, France.

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http://dx.doi.org/10.3389/fmicb.2018.01983DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129602PMC
September 2018

Validation of standard method EN ISO 11290 - Part 2 for the enumeration of Listeria monocytogenes in food.

Int J Food Microbiol 2019 Jan 1;288:22-31. Epub 2018 May 1.

Université Paris Est, ANSES, Laboratory for Food Safety, F-94701 Maisons-Alfort, France. Electronic address:

The reference method for the detection and enumeration of L. monocytogenes in food (Standards EN ISO 11290-1&2) have been validated by inter-laboratory studies in the frame of the Mandate M381 from European Commission to CEN. In this paper, the inter-laboratory studies led in 2013 on 5 matrices (cold-smoked salmon, milk powdered infant food formula, vegetables, environment, and cheese) to validate Standard EN ISO 11290-2 are reported. According to the results obtained, the method of the revised Standard EN ISO 11290-2 can be considered as a good method for the enumeration of L. monocytogenes in foods and food processing environment, in particular for the matrices included in the study. Values of repeatability and reproducibility standard deviations can be considered satisfactory for this type of method with a confirmation stage, since most of them were below 0.3 log, also at low levels, close to the regulatory limit of 100 CFU/g.
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http://dx.doi.org/10.1016/j.ijfoodmicro.2018.03.023DOI Listing
January 2019

Population Genetic Structure of Strains Isolated From the Pig and Pork Production Chain in France.

Front Microbiol 2018 6;9:684. Epub 2018 Apr 6.

Maisons-Alfort Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Maisons-Alfort, France.

is an ubiquitous pathogenic bacterium, transmissible to humans through the consumption of contaminated food. The pork production sector has been hit hard by a series of -related food poisoning outbreaks in France. An overview of the diversity of strains circulating at all levels of the pork production chain, from pig farming (PF) to finished food products (FFP), is needed to identify the contamination routes and improve food safety. Until now, no typing data has been available on strains isolated across the entire pig and pork production chain. Here, we analyzed the population genetic structure of 687 strains isolated over the last 20 years in virtually all the French from three compartments of this production sector: PF, the food processing environment (FPE), and FFP. The genetic structure was described based on Multilocus sequence typing (MLST) clonal complexes (CCs). The CCs were obtained by mapping the PFGE profiles of the strains. The distribution of CCs was compared firstly between the three compartments and then with CCs obtained from 1106 strains isolated from other food production sectors in France. The predominant CCs of pig and pork strains were not equally distributed among the three compartments: the CC37, CC59, and CC77 strains, rarely found in FPE and FFP, were prevalent in PF. The two most prevalent CCs in the FPE and FFP compartments, CC9 and CC121, were rarely or never detected in PF. No CC was exclusively associated with the pork sector. Three CCs (CC5, CC6, and CC2) were considered ubiquitous, because they were observed in comparable proportions in all food production sectors. The two most prevalent CCs in all sectors were CC9 and CC121, but their distribution was disparate. CC9 was associated with meat products and food products combining several food categories, whereas CC121 was not associated with any given sector. Based on these results, CC121 is likely able to colonize a larger diversity of food products than CC9. Both CCs being associated with the food production suggests, that certain processing steps, such as slaughtering or stabilization treatments, favor their settlement and the recontamination of the food produced.
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http://dx.doi.org/10.3389/fmicb.2018.00684DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5897532PMC
April 2018

Sequence Types 121 and 14 Repeatedly Isolated Within One Year of Sampling in a Rabbit Meat Processing Plant: Persistence and Ecophysiology.

Front Microbiol 2018 29;9:596. Epub 2018 Mar 29.

Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Bologna, Italy.

is a foodborne pathogen adapted to survive and persist in multiple environments. Following two previous studies on prevalence and virulence of ST121 and ST14 repeatedly collected in a the same rabbit-meat processing plant, the research questions of the present study were to: (1) assess persistence of isolates from the rabbit-plant; (2) select genes associated to physiological adaptation to the food-processing environment; (3) compare presence/absence/truncation of these genes in newly sequenced and publicly available ST121 and ST14 genomes. A total of 273 draft genomes including ST121 and ST14 newly sequenced and publicly available draft genomes were analyzed. Whole-genome Single Nucleotide Polymorfism (wgSNP) analysis was performed separately on the assemblies of ST121 and ST14 draft genomes. SNPs alignments were used to infer phylogeny. A dataset of ecophysiology genes was built based on a comprehensive literature review. The 94 selected genes were screened on the assemblies of all ST121 and ST14 draft genomes. Significant gene enrichments were evaluated by statistical analyses. A persistent ST14 clone, including 23 out of 27 newly sequenced genomes, was circulating in the rabbit-meat plant along with two not persistent clones. A significant enrichment was observed in ST121 genomes concerning stress survival islet 2 (SSI-2) (alkaline and oxidative stress), gene (resistance to benzalkonium chloride), gene cassette (resistance to 70 mg/l of cadmium chloride) and a truncated version of gene (biofilm formation). Conversely, ST14 draft genomes were enriched with a full-length version of gene along with the Genomic Island 2 (LGI 2) including the operon (arsenic resistance) and the gene cassette (resistance to 35 mg/l of cadmium chloride). Phenotypic tests confirmed ST121 as a weak biofilm producer in comparison to ST14. In conclusion, ST121 carried the gene and was phenotypically resistant to quaternary ammonium compounds. This property might contribute to the high prevalence of ST121 in food processing plants. ST14 showed greater ability to form biofilms, which might contribute to the occasional colonization and persistence on harborage sites where sanitizing procedures are difficult to display.
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http://dx.doi.org/10.3389/fmicb.2018.00596DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5890179PMC
March 2018

Validation of standard method EN ISO 11290 - Part 1 - Detection of Listeria monocytogenes in food.

Int J Food Microbiol 2019 Jan 26;288:13-21. Epub 2018 Mar 26.

ACTALIA CECALAIT, F-39800 Poligny, France.

The reference method for the detection and enumeration of L. monocytogenes in food (Standards EN ISO 11290-1&2) has been validated by inter-laboratory studies in the frame of the Mandate M381 from European Commission to CEN. In this paper, the collaborative studies led in 2013 on 5 matrices (cold-smoked salmon, milk powdered infant food formula, vegetables, environment, and cheese) to validate the recently revised Standard EN ISO 11290-Part 1 are reported. According to the results obtained, the revised Standard EN ISO 11290-1 can be considered as a good method for the detection of L. monocytogenes in foods and food processing environments, in particular for the matrices included in the study. According to the matrices, the sensitivity rate varied from 91.1% to 100%, and the specificity rate varied from 97.6% to 100%. Positive samples were most often detected after 24 h half-Fraser enrichment.
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http://dx.doi.org/10.1016/j.ijfoodmicro.2018.03.024DOI Listing
January 2019

An Assessment of Different Genomic Approaches for Inferring Phylogeny of .

Front Microbiol 2017 29;8:2351. Epub 2017 Nov 29.

European Union Reference Laboratory for Antimicrobial Resistance, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food Borne Pathogens and Genomics, Technical University of Denmark, Kongens Lyngby, Denmark.

Whole genome sequencing (WGS) has proven to be a powerful subtyping tool for foodborne pathogenic bacteria like . The interests of genome-scale analysis for national surveillance, outbreak detection or source tracking has been largely documented. The genomic data however can be exploited with many different bioinformatics methods like single nucleotide polymorphism (SNP), core-genome multi locus sequence typing (cgMLST), whole-genome multi locus sequence typing (wgMLST) or multi locus predicted protein sequence typing (MLPPST) on either core-genome (cgMLPPST) or pan-genome (wgMLPPST). Currently, there are little comparisons studies of these different analytical approaches. Our objective was to assess and compare different genomic methods that can be implemented in order to cluster isolates of . The clustering methods were evaluated on a collection of 207 genomes of food origin representative of the genetic diversity of the Anses collection. The trees were then compared using robust statistical analyses. The backward comparability between conventional typing methods and genomic methods revealed a near-perfect concordance. The importance of selecting a proper reference when calling SNPs was highlighted, although distances between strains remained identical. The analysis also revealed that the topology of the phylogenetic trees between wgMLST and cgMLST were remarkably similar. The comparison between SNP and cgMLST or SNP and wgMLST approaches showed that the topologies of phylogenic trees were statistically similar with an almost equivalent clustering. Our study revealed high concordance between wgMLST, cgMLST, and SNP approaches which are all suitable for typing of . The comparable clustering is an important observation considering that the two approaches have been variously implemented among reference laboratories.
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http://dx.doi.org/10.3389/fmicb.2017.02351DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5712588PMC
November 2017

First gene-ontology enrichment analysis based on bacterial coregenome variants: insights into adaptations of Salmonella serovars to mammalian- and avian-hosts.

BMC Microbiol 2017 Nov 28;17(1):222. Epub 2017 Nov 28.

Université PARIS-EST, Anses, Laboratory for food safety, Maisons-Alfort, France.

Background: Many of the bacterial genomic studies exploring evolution processes of the host adaptation focus on the accessory genome describing how the gains and losses of genes can explain the colonization of new habitats. Consequently, we developed a new approach focusing on the coregenome in order to describe the host adaptation of Salmonella serovars.

Methods: In the present work, we propose bioinformatic tools allowing (i) robust phylogenetic inference based on SNPs and recombination events, (ii) identification of fixed SNPs and InDels distinguishing homoplastic and non-homoplastic coregenome variants, and (iii) gene-ontology enrichment analyses to describe metabolic processes involved in adaptation of Salmonella enterica subsp. enterica to mammalian- (S. Dublin), multi- (S. Enteritidis), and avian- (S. Pullorum and S. Gallinarum) hosts.

Results: The 'VARCall' workflow produced a robust phylogenetic inference confirming that the monophyletic clade S. Dublin diverged from the polyphyletic clade S. Enteritidis which includes the divergent clades S. Pullorum and S. Gallinarum (i). The scripts 'phyloFixedVar' and 'FixedVar' detected non-synonymous and non-homoplastic fixed variants supporting the phylogenetic reconstruction (ii). The scripts 'GetGOxML' and 'EveryGO' identified representative metabolic pathways related to host adaptation using the first gene-ontology enrichment analysis based on bacterial coregenome variants (iii).

Conclusions: We propose in the present manuscript a new coregenome approach coupling identification of fixed SNPs and InDels with regards to inferred phylogenetic clades, and gene-ontology enrichment analysis in order to describe the adaptation of Salmonella serovars Dublin (i.e. mammalian-hosts), Enteritidis (i.e. multi-hosts), Pullorum (i.e. avian-hosts) and Gallinarum (i.e. avian-hosts) at the coregenome scale. All these polyvalent Bioinformatic tools can be applied on other bacterial genus without additional developments.
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http://dx.doi.org/10.1186/s12866-017-1132-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5706153PMC
November 2017

Genome Target Evaluator (GTEvaluator): A workflow exploiting genome dataset to measure the sensitivity and specificity of genetic markers.

PLoS One 2017 27;12(7):e0182082. Epub 2017 Jul 27.

Université PARIS-EST, ANSES, Laboratory for Food Safety, Maisons-Alfort, France.

Most of the bacterial typing methods used to discriminate isolates in medical or food safety microbiology are based on genetic markers used as targets in PCR or hybridization experiments. These DNA typing methods are important tools for studying prevalence and epidemiology, for conducting surveillance, investigations and control of biological hazard sources. In that perspective, it is crucial to insure that the chosen genetic markers have the greatest specificity and sensitivity. The wealth of whole-genome sequences available for many bacterial species offers the opportunity to evaluate the performance of these genetic markers. In the present study, we have developed GTEvaluator, a bioinformatics workflow which ranks genetic markers depending on their sensitivity and specificity towards groups of well-defined genomes. GTEvaluator identifies the most performant genetic markers to target individuals among a population. The individuals (i.e. a group of genomes within a collection) are defined by any kind of particular phenotypic or biological properties inside a related population (i.e. collection of genomes). The performance of the genetic markers is computed by a distance value which takes into account both sensitivity and specificity. In this study we report two examples of GTEvaluator application. In the first example Bacillus phenotypic markers were evaluated for their capacity to distinguish B. cereus from B. thuringiensis. In the second experiment, GTEvaluator measured the performance of genetic markers dedicated to the molecular serotyping of Salmonella enterica. In one in silico experiment it was possible to test 64 markers onto 134 genomes corresponding to 14 different serotypes.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0182082PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5531552PMC
October 2017

Impact of environmental factors on the culturability and viability of Listeria monocytogenes under conditions encountered in food processing plants.

Int J Food Microbiol 2017 Mar 21;244:74-81. Epub 2016 Dec 21.

Université Paris-Est, Anses, Laboratory for Food Safety, 94701 Maisons-Alfort, France. Electronic address:

The ability of Listeria monocytogenes to adhere to and persist on surfaces for months or even years may be responsible for its transmission from contaminated surfaces to food products. Hence the necessity to find effective means to prevent the establishment of L. monocytogenes in food processing environments. The aim of this study was to assess, through a fractional experimental design, the environmental factors that could affect the survival of L. monocytogenes cells on surfaces to thereby prevent the persistence of this pathogen in conditions mimicking those encountered in food processing plants: culture with smoked salmon juice or meat exudate, use of two materials with different hygiene status, biofilm of L. monocytogenes in pure-culture or dual-culture with a Pseudomonas fluorescens strain, application of a drying step after cleaning and disinfection (C&D) and comparison of two strains of L. monocytogenes. Bacterial survival was assessed by culture, qPCR to quantify total cells, and propidium monoazide coupled with qPCR to quantify viable cells and highlight viable but non-culturable (VBNC) cells. Our results showed that failure to apply C&D causes cell persistence on surfaces. Moreover, the sanitation procedure leads only to a loss of culturability and appearance of VBNC populations. However, an additional daily drying step after C&D optimises the effectiveness of these procedures to reduce culturable populations. Our results reinforce the importance to use molecular tools to monitor viable pathogens in food processing plants to avoid underestimating the amounts of cells using only methods based on cell culture.
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http://dx.doi.org/10.1016/j.ijfoodmicro.2016.12.012DOI Listing
March 2017

Bacillus cereus-induced food-borne outbreaks in France, 2007 to 2014: epidemiology and genetic characterisation.

Euro Surveill 2016 Dec;21(48)

Université Paris-Est, ANSES, Laboratory for Food Safety, Maisons-Alfort Cedex, France.

The aim of this study was to identify and characterise Bacillus cereus from a unique national collection of 564 strains associated with 140 strong-evidence food-borne outbreaks (FBOs) occurring in France during 2007 to 2014. Starchy food and vegetables were the most frequent food vehicles identified; 747 of 911 human cases occurred in institutional catering contexts. Incubation period was significantly shorter for emetic strains compared with diarrhoeal strains A sub-panel of 149 strains strictly associated to 74 FBOs and selected on Coliphage M13-PCR pattern, was studied for detection of the genes encoding cereulide, diarrhoeic toxins (Nhe, Hbl, CytK1 and CytK2) and haemolysin (HlyII), as well as panC phylogenetic classification. This clustered the strains into 12 genetic signatures (GSs) highlighting the virulence potential of each strain. GS1 (nhe genes only) and GS2 (nhe, hbl and cytK2), were the most prevalent GS and may have a large impact on human health as they were present in 28% and 31% of FBOs, respectively. Our study provides a convenient molecular scheme for characterisation of B. cereus strains responsible for FBOs in order to improve the monitoring and investigation of B. cereus-induced FBOs, assess emerging clusters and diversity of strains.
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http://dx.doi.org/10.2807/1560-7917.ES.2016.21.48.30413DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5388111PMC
December 2016