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Rosa Rodrigues de Souza C, Bergis H, Ng P, Guillier L, Félix B, Leclercq A, Gnanou Besse N. Corrigendum to "Assessment of the relationship between the MLST genetic diversity of Listeria monocytogenes and growth under selective and non-selective conditions" [Food Microbiol. 114 (2023) 104303]. Food Microbiol 2024; 119:104444. [PMID: 38225044 DOI: 10.1016/j.fm.2023.104444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Affiliation(s)
- Carolina Rosa Rodrigues de Souza
- Agence Nationale de Securite Sanitaire, French Agency for Food, Environmental and Occupational Health Safety, Laboratory for Food Safety (Anses, 14 Rue Pierre et Marie Curie, 94702, Maisons Alfort Cedex, France; School of Veterinary Medicine and Animal Science (FMVZ-UNESP), Botucatu, Brazil
| | - Hélène Bergis
- Agence Nationale de Securite Sanitaire, French Agency for Food, Environmental and Occupational Health Safety, Laboratory for Food Safety (Anses, 14 Rue Pierre et Marie Curie, 94702, Maisons Alfort Cedex, France
| | - Patricia Ng
- Agence Nationale de Securite Sanitaire, French Agency for Food, Environmental and Occupational Health Safety, Laboratory for Food Safety (Anses, 14 Rue Pierre et Marie Curie, 94702, Maisons Alfort Cedex, France
| | - Laurent Guillier
- Agence Nationale de Securite Sanitaire, Risk Assessment Department, France
| | - Benjamin Félix
- Agence Nationale de Securite Sanitaire, French Agency for Food, Environmental and Occupational Health Safety, Laboratory for Food Safety (Anses, 14 Rue Pierre et Marie Curie, 94702, Maisons Alfort Cedex, France
| | | | - Nathalie Gnanou Besse
- Agence Nationale de Securite Sanitaire, French Agency for Food, Environmental and Occupational Health Safety, Laboratory for Food Safety (Anses, 14 Rue Pierre et Marie Curie, 94702, Maisons Alfort Cedex, France.
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Gonzales-Barron U, Cadavez V, De Oliveira Mota J, Guillier L, Sanaa M. A Critical Review of Risk Assessment Models for Listeria monocytogenes in Produce. Foods 2024; 13:1111. [PMID: 38611415 PMCID: PMC11011655 DOI: 10.3390/foods13071111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/23/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
A review of quantitative risk assessment (QRA) models of Listeria monocytogenes in produce was carried out, with the objective of appraising and contrasting the effectiveness of the control strategies placed along the food chains. Despite nine of the thirteen QRA models recovered being focused on fresh or RTE leafy greens, none of them represented important factors or sources of contamination in the primary production, such as the type of cultivation, water, fertilisers or irrigation method/practices. Cross-contamination at processing and during consumer's handling was modelled using transfer rates, which were shown to moderately drive the final risk of listeriosis, therefore highlighting the importance of accurately representing the transfer coefficient parameters. Many QRA models coincided in the fact that temperature fluctuations at retail or temperature abuse at home were key factors contributing to increasing the risk of listeriosis. In addition to a primary module that could help assess current on-farm practices and potential control measures, future QRA models for minimally processed produce should also contain a refined sanitisation module able to estimate the effectiveness of various sanitisers as a function of type, concentration and exposure time. Finally, L. monocytogenes growth in the products down the supply chain should be estimated by using realistic time-temperature trajectories, and validated microbial kinetic parameters, both of them currently available in the literature.
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Affiliation(s)
- Ursula Gonzales-Barron
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal;
- Laboratório para a Sustentabilidade e Tecnologia em Regiões de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Vasco Cadavez
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal;
- Laboratório para a Sustentabilidade e Tecnologia em Regiões de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | | | - Laurent Guillier
- Risk Assessment Department, French Agency for Food, Environmental and Occupational Health & Safety (Anses), 14 rue Pierre et Marie Curie Maisons-Alfort, 94700 Maisons-Alfort, France;
| | - Moez Sanaa
- Nutrition and Food Safety Department, World Health Organization, 1202 Geneva, Switzerland
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Pouillot R, Kiermeier A, Guillier L, Cadavez V, Sanaa M. Updated Parameters for Listeria monocytogenes Dose-Response Model Considering Pathogen Virulence and Age and Sex of Consumer. Foods 2024; 13:751. [PMID: 38472864 PMCID: PMC10931010 DOI: 10.3390/foods13050751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 02/16/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Better knowledge regarding the Listeria monocytogenes dose-response (DR) model is needed to refine the assessment of the risk of foodborne listeriosis. In 2018, the European Food Safety Agency (EFSA) derived a lognormal Poisson DR model for 14 different age-sex sub-groups, marginally to strain virulence. In the present study, new sets of parameters are developed by integrating the EFSA model for these sub-groups together with three classes of strain virulence characteristics ("less virulent", "virulent", and "more virulent"). Considering classes of virulence leads to estimated relative risks (RRs) of listeriosis following the ingestion of 1000 bacteria of "less virulent" vs. "more virulent" strains ranging from 21.6 to 24.1, depending on the sub-group. These relatively low RRs when compared with RRs linked to comorbidities described in the literature suggest that the influence of comorbidity on the occurrence of invasive listeriosis for a given exposure is much more important than the influence of the virulence of the strains. The updated model parameters allow better prediction of the risk of invasive listeriosis across a population of interest, provided the necessary data on population demographics and the proportional contribution of strain virulence classes in food products of interest are available. An R package is made available to facilitate the use of these dose-response models.
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Affiliation(s)
- Régis Pouillot
- Independent Researcher, 18 rue Mohamed Al Ghazi, Rabat 10170, Morocco
| | - Andreas Kiermeier
- Statistical Process Improvement Consulting and Training Pty Ltd., Gumeracha 5233, Australia;
| | - Laurent Guillier
- Risk Assessment Department, French Agency for Food, Environmental and Occupational Health & Safety (Anses), 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort, France
| | - Vasco Cadavez
- Centro de Investigação de Montanha (CIMO), Campus de Santa Apolónia, Instituto Politécnico de Bragança, 5300-253 Bragança, Portugal;
- Laboratório para a Sustentabilidade e Tecnologia em Regiões de Montanha, Campus de Santa Apolónia, Instituto Politécnico de Bragança, 5300-253 Bragança, Portugal
| | - Moez Sanaa
- Nutrition and Food Safety Department, World Health Organization, 1211 Geneva, Switzerland
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Gonzales-Barron U, Cadavez V, De Oliveira Mota J, Guillier L, Sanaa M. A Critical Review of Risk Assessment Models for Listeria monocytogenes in Seafood. Foods 2024; 13:716. [PMID: 38472829 PMCID: PMC10930801 DOI: 10.3390/foods13050716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/22/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024] Open
Abstract
Invasive listeriosis, due to its severe nature in susceptible populations, has been the focus of many quantitative risk assessment (QRA) models aiming to provide a valuable guide in future risk management efforts. A review of the published QRA models of Listeria monocytogenes in seafood was performed, with the objective of appraising the effectiveness of the control strategies at different points along the food chain. It is worth noting, however, that the outcomes of a QRA model are context-specific, and influenced by the country and target population, the assumptions that are employed, and the model architecture itself. Studies containing QRA models were retrieved through a literature search using properly connected keywords on Scopus and PubMed®. All 13 QRA models that were recovered were of short scope, covering, at most, the period from the end of processing to consumption; the majority (85%) focused on smoked or gravad fish. Since the modelled pathways commenced with the packaged product, none of the QRA models addressed cross-contamination events. Many models agreed that keeping the product's temperature at 4.0-4.5 °C leads to greater reductions in the final risk of listeriosis than reducing the shelf life by one week and that the effectiveness of both measures can be surpassed by reducing the initial occurrence of L. monocytogenes in the product (at the end of processing). It is, therefore, necessary that future QRA models for RTE seafood contain a processing module that can provide insight into intervention strategies that can retard L. monocytogenes' growth, such as the use of bacteriocins, ad hoc starter cultures and/or organic acids, and other strategies seeking to reduce cross-contamination at the facilities, such as stringent controls for sanitation procedures. Since risk estimates were shown to be moderately driven by growth kinetic parameters, namely, the exponential growth rate, the minimum temperature for growth, and the maximum population density, further work is needed to reduce uncertainties.
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Affiliation(s)
- Ursula Gonzales-Barron
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal;
- Laboratório para a Sustentabilidade e Tecnologia em Regiões de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Vasco Cadavez
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal;
- Laboratório para a Sustentabilidade e Tecnologia em Regiões de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Juliana De Oliveira Mota
- Department of Nutrition and Food Safety, World Health Organization (WHO), CH-1211 Geneva, Switzerland
| | - Laurent Guillier
- Risk Assessment Department, French Agency for Food, Environmental and Occupational Health & Safety (Anses), 14 Rue Pierre et Marie Curie, 94701 Maisons-Alfort, France;
| | - Moez Sanaa
- Department of Nutrition and Food Safety, World Health Organization (WHO), CH-1211 Geneva, Switzerland
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Gonzales-Barron U, Cadavez V, De Oliveira Mota J, Guillier L, Sanaa M. A Critical Review of Risk Assessment Models for Listeria monocytogenes in Meat and Meat Products. Foods 2024; 13:359. [PMID: 38338495 PMCID: PMC10855662 DOI: 10.3390/foods13030359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
A review of the published quantitative risk assessment (QRA) models of L. monocytogenes in meat and meat products was performed, with the objective of appraising the intervention strategies deemed suitable for implementation along the food chain as well as their relative effectiveness. A systematic review retrieved 23 QRA models; most of them (87%) focused on ready-to-eat meat products and the majority (78%) also covered short supply chains (end processing/retail to consumption, or consumption only). The processing-to-table scope was the choice of models for processed meats such as chorizo, bulk-cooked meat, fermented sausage and dry-cured pork, in which the effects of processing were simulated. Sensitivity analysis demonstrated the importance of obtaining accurate estimates for lag time, growth rate and maximum microbial density, in particular when affected by growth inhibitors and lactic acid bacteria. In the case of deli meats, QRA models showed that delicatessen meats sliced at retail were associated with a higher risk of listeriosis than manufacture pre-packed deli meats. Many models converged on the fact that (1) controlling cold storage temperature led to greater reductions in the final risk than decreasing the time to consumption and, furthermore, that (2) lower numbers and less prevalence of L. monocytogenes at the end of processing were far more effective than keeping low temperatures and/or short times during retail and/or home storage. Therefore, future listeriosis QRA models for meat products should encompass a processing module in order to assess the intervention strategies that lead to lower numbers and prevalence, such as the use of bio-preservation and novel technologies. Future models should be built upon accurate microbial kinetic parameters, and should realistically represent cross-contamination events along the food chain.
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Affiliation(s)
- Ursula Gonzales-Barron
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal;
- Laboratório para a Sustentabilidade e Tecnologia em Regiões de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Vasco Cadavez
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal;
- Laboratório para a Sustentabilidade e Tecnologia em Regiões de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Juliana De Oliveira Mota
- Department of Nutrition and Food Safety, World Health Organization (WHO), CH-1211 Geneva, Switzerland;
| | - Laurent Guillier
- Risk Assessment Department, French Agency for Food, Environmental and Occupational Health & Safety (Anses), 14 Rue Pierre et Marie Curie, 94701 Maisons-Alfort, France;
| | - Moez Sanaa
- Department of Nutrition and Food Safety, World Health Organization (WHO), CH-1211 Geneva, Switzerland;
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Chikhi L, Mancier M, Brugère H, Lombard B, Faouzi L, Guillier L, Gnanou Besse N. Comparison of Listeria monocytogenes alternative detection methods for food microbiology official controls in Europe. Int J Food Microbiol 2024; 408:110448. [PMID: 37890286 DOI: 10.1016/j.ijfoodmicro.2023.110448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/12/2023] [Accepted: 10/14/2023] [Indexed: 10/29/2023]
Abstract
Listeriosis remains one of the most severe foodborne diseases regarding mortality rate. L. monocytogenes can grow under stressful conditions and contaminate various food categories. Regulation (EC) No 2073/2005 modified on microbiological criteria for foodstuffs includes either qualitative or quantitative food safety criteria on L. monocytogenes and mentions EN ISO 11290-1 Standard as the reference detection method. The use of alternative certified methods is allowed at European level for own checks and by certain European countries in the frame of official controls. Here we report the comparison of alternative certified methods for the detection of L. monocytogenes, according to the criteria expressed by the National Reference Laboratories (NRLs) for L. monocytogenes network in Europe, through an enquiry conducted in 2022 by the European Union Reference Laboratory (EURL) for L. monocytogenes. Emerging detection methods make it possible to diversify the panel of available detection methods. Each method has advantages and limitations and the choice of a method depends on the needs, organization and objectives of the laboratory. Our study focused on a comparison by category in order to provide an overview of the differences between the methods as complete and simple as possible, mainly by examining the certification files of the alternative methods, which constitute a reliable and publicly accessible source of information about performances of the methods.
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Affiliation(s)
- Lucas Chikhi
- Agence Nationale de Sécurité Sanitaire, French agency for food, environmental and occupational health safety, Laboratory for food safety (ANSES), 14 rue Pierre et Marie Curie, 94702 Maisons Alfort cedex, France; Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse, Toulouse, France
| | - Mélanie Mancier
- Agence Nationale de Sécurité Sanitaire, French agency for food, environmental and occupational health safety, Laboratory for food safety (ANSES), 14 rue Pierre et Marie Curie, 94702 Maisons Alfort cedex, France; Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse, Toulouse, France
| | - Hubert Brugère
- Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse, Toulouse, France; IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France.
| | - Bertrand Lombard
- ANSES, Research and Reference Division, Strategy and Programmes Directorate, 14 rue Pierre et Marie Curie, 94702 Maisons-Alfort cedex, France.
| | - Lyazrhi Faouzi
- Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse, Toulouse, France.
| | | | - Nathalie Gnanou Besse
- Agence Nationale de Sécurité Sanitaire, French agency for food, environmental and occupational health safety, Laboratory for food safety (ANSES), 14 rue Pierre et Marie Curie, 94702 Maisons Alfort cedex, France.
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Gonzales-Barron U, Cadavez V, Guillier L, Sanaa M. A Critical Review of Risk Assessment Models for Listeria monocytogenes in Dairy Products. Foods 2023; 12:4436. [PMID: 38137240 PMCID: PMC10742501 DOI: 10.3390/foods12244436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/06/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
A review of the published quantitative risk assessment (QRA) models of L. monocytogenes in dairy products was undertaken in order to identify and appraise the relative effectiveness of control measures and intervention strategies implemented at primary production, processing, retail, and consumer practices. A systematic literature search retrieved 18 QRA models, most of them (9) investigated raw and pasteurized milk cheeses, with the majority covering long supply chains (4 farm-to-table and 3 processing-to-table scopes). On-farm contamination sources, either from shedding animals or from the broad environment, have been demonstrated by different QRA models to impact the risk of listeriosis, in particular for raw milk cheeses. Through scenarios and sensitivity analysis, QRA models demonstrated the importance of the modeled growth rate and lag phase duration and showed that the risk contribution of consumers' practices is greater than in retail conditions. Storage temperature was proven to be more determinant of the final risk than storage time. Despite the pathogen's known ability to reside in damp spots or niches, re-contamination and/or cross-contamination were modeled in only two QRA studies. Future QRA models in dairy products should entail the full farm-to-table scope, should represent cross-contamination and the use of novel technologies, and should estimate L. monocytogenes growth more accurately by means of better-informed kinetic parameters and realistic time-temperature trajectories.
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Affiliation(s)
- Ursula Gonzales-Barron
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal;
- Laboratório Para a Sustentabilidade e Tecnologia em Regiões de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Vasco Cadavez
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal;
- Laboratório Para a Sustentabilidade e Tecnologia em Regiões de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Laurent Guillier
- Risk Assessment Department, French Agency for Food, Environmental and Occupational Health & Safety (Anses), 14 Rue Pierre et Marie Curie Maisons-Alfort, 94701 Maisons-Alfort, France
| | - Moez Sanaa
- Nutrition and Food Safety Department, World Health Organization (WHO), CH-1211 Geneva, Switzerland
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Luong NDM, Guillier L, Federighi M, Guillois Y, Kooh P, Maillard AL, Pivette M, Boué G, Martin-Latil S, Chaix E, Duret S. An agent-based model to simulate SARS-CoV-2 contamination of surfaces and meat cuts in processing plants. Int J Food Microbiol 2023; 404:110321. [PMID: 37499271 DOI: 10.1016/j.ijfoodmicro.2023.110321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/24/2023] [Accepted: 07/10/2023] [Indexed: 07/29/2023]
Abstract
At the beginning of the COVID-19 pandemic, several contamination clusters were reported in food-processing plants in France and several countries worldwide. Therefore, a need arose to better understand viral transmission in such occupational environments from multiple perspectives: the protection of workers in hotspots of viral circulation; the prevention of supply disruption due to the closure of plants; and the prevention of cluster expansion due to exports of food products contaminated by the virus to other locations. This paper outlines a simulation-based approach (using agent-based models) to study the effects of measures taken to prevent the contamination of workers, surfaces, and food products. The model includes user-defined parameters to integrate characteristics relating to SARS-CoV-2 (variant of concern to be considered, symptom onset…), food-processing plants (dimensions, ventilation…), and other sociodemographic transmission factors based on laboratory experiments as well as industrial and epidemiological investigations. Simulations were performed for a typical meat-processing plant in different scenarios for illustration purposes. The results suggested that increasing the mask-wearing ratio led to great reductions in the probability of observing clusters of more than 25 infections. In the case of clusters, masks being worn by all workers limited the presence of contamination (defined as levels of at least 5 log10 viral RNA copies) on meat cuts at less than 0.05 % and maintained the production capacity of the plant at optimal levels. Increasing the average distance between two workers from less than 1 m to more than 2 m decreased the cluster-occurrence probability by up to 15 % as well as contamination of food products during cluster situations. The developed approach can open up several perspectives in terms of potential communication-support tools for the agri-food sector and further reuses or adaptations for other hazards and occupational environments.
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Affiliation(s)
| | | | - Michel Federighi
- UMR INRAE 1014 SECALIM, Oniris, Nantes, Cedex 03, France; ENVA, 94701 Maisons-Alfort, France; Laboratory for Food Safety, ANSES, University of Paris-EST, Maisons-Alfort, France.
| | - Yvonnick Guillois
- Santé Publique France, Direction des régions, Bretagne, Saint-Maurice, France.
| | - Pauline Kooh
- Risk Assessment Department, ANSES, Maisons-Alfort, France.
| | - Anne-Laure Maillard
- Santé Publique France, Direction des régions, Bretagne, Saint-Maurice, France.
| | - Mathilde Pivette
- Santé Publique France, Direction des régions, Bretagne, Saint-Maurice, France.
| | - Géraldine Boué
- UMR INRAE 1014 SECALIM, Oniris, Nantes, Cedex 03, France.
| | - Sandra Martin-Latil
- Laboratory for Food Safety, ANSES, University of Paris-EST, Maisons-Alfort, France.
| | - Estelle Chaix
- Risk Assessment Department, ANSES, Maisons-Alfort, France.
| | - Steven Duret
- Université Paris-Saclay, INRAE, FRISE, Antony, France.
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Rosa Rodrigues de Souza C, Bergis H, Ng P, Guillier L, Félix B, Leclercq A, Gnanou Besse N. Assessment of the relationship between the MLST genetic diversity of Listeria monocytogenes and growth under selective and non-selective conditions. Food Microbiol 2023; 114:104303. [PMID: 37290879 DOI: 10.1016/j.fm.2023.104303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/13/2023] [Accepted: 05/02/2023] [Indexed: 06/10/2023]
Abstract
Listeria monocytogenes can grow under stressful conditions and contaminate various food categories. Progresss in DNA sequencing-based identification methods, such as multi-locus sequence typing (MLST) now allow for more accurate characterization of pathogens. L. monocytogenes MLST genetic diversity is reflected by the different prevalence of the "clonal complexes" (CCs) in foods or infections. Better understanding of the growth potentials of L. monocytogenes is essential for quantitative risk assessment and efficient detection across CCs genetic diversity. Using optical density measurements taken with an automated spectrophotometer, we compared the maximal growth rate and lag phase of 39 strains from 13 different CCs and various food origins, in 3 broths mimicking stresful food conditions (8 °C, aw 0.95 and pH5) and in ISO Standard enrichment broths (Half Fraser and Fraser). This is important as growth could influence risk through pathogen multiplication in food. Besides, enrichment problems could lead to a lack of detection of some CCs. Despite small differences highlighting natural intraspecific variability, our results show that growth performances of L. monocytogenes strains under the conditions tested in selective and non-selective broth do not appear to be strongly correlated to CCs and cannot explain higher CC "virulence" or prevalence.
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Affiliation(s)
- Carolina Rosa Rodrigues de Souza
- Agence Nationale de Sécurité Sanitaire, French Agency for Food, Environmental and Occupational Health Safety. Laboratory for Food Safety (Anses, 14 rue Pierre et Marie Curie, 94702 Maisons Alfort cedex, France; School of Veterinary Medicine and Animal Science (FMVZ-UNESP), Botucatu, Brazil.
| | - Hélène Bergis
- Agence Nationale de Sécurité Sanitaire, French Agency for Food, Environmental and Occupational Health Safety. Laboratory for Food Safety (Anses, 14 rue Pierre et Marie Curie, 94702 Maisons Alfort cedex, France.
| | - Patricia Ng
- Agence Nationale de Sécurité Sanitaire, French Agency for Food, Environmental and Occupational Health Safety. Laboratory for Food Safety (Anses, 14 rue Pierre et Marie Curie, 94702 Maisons Alfort cedex, France.
| | - Laurent Guillier
- Agence Nationale de Sécurité Sanitaire, Risk Assessment Department, France.
| | - Benjamin Félix
- Agence Nationale de Sécurité Sanitaire, French Agency for Food, Environmental and Occupational Health Safety. Laboratory for Food Safety (Anses, 14 rue Pierre et Marie Curie, 94702 Maisons Alfort cedex, France.
| | | | - Nathalie Gnanou Besse
- Agence Nationale de Sécurité Sanitaire, French Agency for Food, Environmental and Occupational Health Safety. Laboratory for Food Safety (Anses, 14 rue Pierre et Marie Curie, 94702 Maisons Alfort cedex, France.
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Redondo HG, Guillier L, Bemrah N, Jakobsen LS, Thomsen ST, Pires SM. Harmonized approach to estimate the burden of disease of dietary exposure to four chemical contaminants - A French study. Sci Total Environ 2023:164804. [PMID: 37302596 DOI: 10.1016/j.scitotenv.2023.164804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 06/08/2023] [Accepted: 06/08/2023] [Indexed: 06/13/2023]
Abstract
Exposure to chemical contaminants found in foods has been associated with various adverse health effects. Burden of disease studies are increasingly used to estimate the public health impact of such exposures. The aims of this study were to estimate the burden of disease due to dietary exposure to four chemicals in France in 2019 (lead (Pb), cadmium (Cd), methylmercury (MeHg), and inorganic arsenic (i-As)), and to develop harmonized methods that can be applied for other chemicals and countries. We used national food consumption data from the third French national food consumption survey, chemical food monitoring data from the Second French Total Diet Study (TDS), dose-response data and disability weights from scientific literature, and disease incidence and demographics from national statistics. We adopted a risk assessment approach to estimate disease burden, incidence, mortality, and Disability-Adjusted Life Years (DALYs) attributable to dietary exposure to the chemicals. In all models, we harmonized food classification and exposure assessment. We propagated uncertainty through the calculations using Monte Carlo simulation. We estimated that, among these chemicals, i-As and Pb were responsible for the highest disease burden. i-As was estimated to cause 820 DALYs, or approximately 1.25 DALYs per 100,000 inhabitants. The estimated burden of Pb was 1834 to 5936 DALYs, or 2.7 (lower bound) to 8.96 (upper bound) DALYs/100,000. The burden of MeHg (192 DALYs), and Cd (0 DALY) was substantially lower. The foods contributing most to disease burden was drinks (30 %), "other foods" (mostly composite dishes) (19 %), and fish and seafood (7 %). Interpretation of estimates needs to consider all underlying uncertainties, linked with data and knowledge gaps. The harmonized models are the first to make use of data from TDS, which are available in several other countries. Thus, they can be applied to estimate the burden and to rank food-associated chemicals at national level.
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Affiliation(s)
- Hernán G Redondo
- National Food Institute, Technical University of Denmark, Lyngby, Denmark.
| | - Laurent Guillier
- ANSES, Risk Assessment Department, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Nawel Bemrah
- ANSES, Risk Assessment Department, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | | | | | - Sara M Pires
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
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11
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Munir MT, Mtimet N, Guillier L, Meurens F, Fravalo P, Federighi M, Kooh P. Physical Treatments to Control Clostridium botulinum Hazards in Food. Foods 2023; 12:foods12081580. [PMID: 37107375 PMCID: PMC10137509 DOI: 10.3390/foods12081580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 03/30/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Clostridium botulinum produces Botulinum neurotoxins (BoNTs), causing a rare but potentially deadly type of food poisoning called foodborne botulism. This review aims to provide information on the bacterium, spores, toxins, and botulisms, and describe the use of physical treatments (e.g., heating, pressure, irradiation, and other emerging technologies) to control this biological hazard in food. As the spores of this bacterium can resist various harsh environmental conditions, such as high temperatures, the thermal inactivation of 12-log of C. botulinum type A spores remains the standard for the commercial sterilization of food products. However, recent advancements in non-thermal physical treatments present an alternative to thermal sterilization with some limitations. Low- (<2 kGy) and medium (3-5 kGy)-dose ionizing irradiations are effective for a log reduction of vegetative cells and spores, respectively; however, very high doses (>10 kGy) are required to inactivate BoNTs. High-pressure processing (HPP), even at 1.5 GPa, does not inactivate the spores and requires heat combination to achieve its goal. Other emerging technologies have also shown some promise against vegetative cells and spores; however, their application to C. botulinum is very limited. Various factors related to bacteria (e.g., vegetative stage, growth conditions, injury status, type of bacteria, etc.) food matrix (e.g., compositions, state, pH, temperature, aw, etc.), and the method (e.g., power, energy, frequency, distance from the source to target, etc.) influence the efficacy of these treatments against C. botulinum. Moreover, the mode of action of different physical technologies is different, which provides an opportunity to combine different physical treatment methods in order to achieve additive and/or synergistic effects. This review is intended to guide the decision-makers, researchers, and educators in using physical treatments to control C. botulinum hazards.
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Affiliation(s)
- Muhammad Tanveer Munir
- EnvA, Unit of Hygiene, Quality and Food Safety, 94700 Maisons-Alfort, France
- Anses, Laboratory of Food Safety, 94700 Maisons-Alfort, France
| | - Narjes Mtimet
- EnvA, Unit of Hygiene, Quality and Food Safety, 94700 Maisons-Alfort, France
- Anses, Laboratory of Food Safety, 94700 Maisons-Alfort, France
| | | | - François Meurens
- INRAE, Oniris, BIOEPAR, 44307 Nantes, France
- Swine and Poultry Infectious Diseases Research Center, Faculty of Veterinary Medicine, University of Montreal, St-Hyacinthe, QC J2S 2M2, Canada
| | - Phillipe Fravalo
- Chaire Agroalimentaire du Cnam, Conservatoire des Arts et Métiers, EPN7, 22440 Ploufragan, France
| | - Michel Federighi
- EnvA, Unit of Hygiene, Quality and Food Safety, 94700 Maisons-Alfort, France
- Anses, Laboratory of Food Safety, 94700 Maisons-Alfort, France
| | - Pauline Kooh
- Anses, Unit UERALIM, 94700 Maisons-Alfort, France
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12
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Meurens F, Carlin F, Federighi M, Filippitzi ME, Fournier M, Fravalo P, Ganière JP, Grisot L, Guillier L, Hilaire D, Kooh P, Le Bouquin-Leneveu S, Le Maréchal C, Mazuet C, Morvan H, Petit K, Vaillancourt JP, Woudstra C. Clostridium botulinum type C, D, C/D, and D/C: An update. Front Microbiol 2023; 13:1099184. [PMID: 36687640 PMCID: PMC9849819 DOI: 10.3389/fmicb.2022.1099184] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/06/2022] [Indexed: 01/07/2023] Open
Abstract
Clostridium botulinum is the main causative agent of botulism, a neurological disease encountered in humans as well as animals. Nine types of botulinum neurotoxins (BoNTs) have been described so far. Amongst these "toxinotypes," the A, the B and E are the most frequently encountered in humans while the C, D, C/D and D/C are mostly affecting domestic and wild birds as well as cattle. In France for instance, many cases and outbreaks are reported in these animal species every year. However, underestimation is very likely at least for avifauna species where the detection of dead animals can be challenging. Knowledge about BoNTs C, D, C/D, and D/C and the diseases they cause in animals and humans is still scarce and unclear. Specifically, the potential role of animal botulism outbreaks in cattle and poultry as a source of human illness needs to be further assessed. In this narrative review, we present the current knowledge about toxinotypes C, D, C/D, and D/C in cattle and poultry with, amongst various other aspects, their epidemiological cycles. We also discuss the zoonotic potential of these toxinotypes and some possible ways of risk mitigation. An adapted and effective management of botulism outbreaks in livestock also requires a better understanding of these less common and known toxinotypes.
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Affiliation(s)
- François Meurens
- INRAE, Oniris, BIOEPAR, Nantes, France,Department of Veterinary Microbiology and Immunology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada,*Correspondence: François Meurens,
| | | | | | - Maria-Eleni Filippitzi
- Laboratory of Animal Health Economics, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Matthieu Fournier
- Univ Rouen Normandie, Univ Caen Normandie, CNRS, M2C, UMR 6143, Rouen, France
| | - Philippe Fravalo
- Chaire Agroalimentaire du Cnam, Conservatoire des Arts et Métiers, EPN7, Ploufragan, France
| | | | | | | | | | - Pauline Kooh
- Risk Assessment Department, ANSES, Maisons-Alfort, France
| | - Sophie Le Bouquin-Leneveu
- Hygiene and Quality of Poultry and Pig Products Unit, ANSES, French Agency for Food, Environmental and Occupational Health Safety, Ploufragan, France
| | - Caroline Le Maréchal
- Hygiene and Quality of Poultry and Pig Products Unit, ANSES, French Agency for Food, Environmental and Occupational Health Safety, Ploufragan, France
| | - Christelle Mazuet
- Institut Pasteur, Université Paris Cité, CNR Bactéries anaérobies et Botulisme, Paris, France
| | | | - Karine Petit
- Risk Assessment Department, ANSES, Maisons-Alfort, France
| | - Jean-Pierre Vaillancourt
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Cédric Woudstra
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
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13
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Chaix E, Boni M, Guillier L, Bertagnoli S, Mailles A, Collignon C, Kooh P, Ferraris O, Martin-Latil S, Manuguerra JC, Haddad N. Risk of Monkeypox virus (MPXV) transmission through the handling and consumption of food. Microb Risk Anal 2022; 22:100237. [PMID: 36320929 PMCID: PMC9595349 DOI: 10.1016/j.mran.2022.100237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/22/2022] [Accepted: 10/22/2022] [Indexed: 06/07/2023]
Abstract
Monkeypox (MPX) is a zoonotic infectious disease caused by Monkeypox virus (MPXV), an enveloped DNA virus belonging to the Poxviridae family and the Orthopoxvirus genus. Since early May 2022, a growing number of human cases of Monkeypox have been reported in non-endemic countries, with no history of contact with animals imported from endemic and enzootic areas, or travel to an area where the virus usually circulated before May 2022. This qualitative risk assessment aimed to investigate the probability that MPXV transmission occurs through food during its handling and consumption. The risk assessment used "top-down" (based on epidemiological data) and "bottom-up" (following the agent through the food chain to assess the risk of foodborne transmission to human) approaches, which were combined. The "top-down" approach first concluded that bushmeat was the only food suspected as a source of contamination in recorded cases of MPXV, by contact or ingestion. The "bottom-up" approach then evaluated the chain of events required for a human to become ill after handling or consuming food. This approach involves several conditions: (i) the food must be contaminated with MPXV (naturally, by an infected handler or after contact with a contaminated surface); (ii) the food must contain viable virus when it reaches the handler or consumer; (iii) the person must be exposed to the virus and; (iv) the person must be infected after exposure. Throughout the risk assessment, some data gaps were identified and highlighted. The conclusions of the top-down and bottom-up approaches are consistent and suggest that the risk of transmission of MPXV through food is hypothetical and that such an occurrence was never reported. In case of contamination, cooking (e.g., 12 min at 70°C) could be considered effective in inactivating Poxviridae in foods. Recommendations for risk management are proposed. To our knowledge, this is the first risk assessment performed on foodborne transmission of MPXV.
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Affiliation(s)
- Estelle Chaix
- Risk Assessment Department, ANSES, National Agency for Food Environmental and Occupational Health and Safety, Île-de-France, Maisons-Alfort, France
| | - Mickaël Boni
- Institut de recherche biomédicale des armées, Brétigny-sur-Orge, France
| | - Laurent Guillier
- Risk Assessment Department, ANSES, National Agency for Food Environmental and Occupational Health and Safety, Île-de-France, Maisons-Alfort, France
| | - Stéphane Bertagnoli
- École nationale vétérinaire de Toulouse, Université de Toulouse, ENVT, INRAE, IHAP, Toulouse F-31076, France
| | - Alexandra Mailles
- Santé publique France, French national public health agency, Saint-Maurice, France
| | - Catherine Collignon
- Risk Assessment Department, ANSES, National Agency for Food Environmental and Occupational Health and Safety, Île-de-France, Maisons-Alfort, France
| | - Pauline Kooh
- Risk Assessment Department, ANSES, National Agency for Food Environmental and Occupational Health and Safety, Île-de-France, Maisons-Alfort, France
| | - Olivier Ferraris
- Institut de recherche biomédicale des armées, Brétigny-sur-Orge, France
| | - Sandra Martin-Latil
- Laboratory for Food Safety, ANSES, University of Paris-EST, Maisons-Alfort, France
| | - Jean-Claude Manuguerra
- Environment and Infectious Risks Unit, Laboratory for Urgent Response to Biological Threats (CIBU), Institut Pasteur, Université Paris Cité, France
| | - Nadia Haddad
- Laboratoire de Santé Animale, ANSES, INRAE, Ecole nationale vétérinaire d'Alfort, UMR BIPAR, Maisons-Alfort F-94700, France
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14
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Le Bouquin S, Lucas C, Souillard R, Le Maréchal C, Petit K, Kooh P, Jourdan-Da Silva N, Meurens F, Guillier L, Mazuet C. Human and animal botulism surveillance in France from 2008 to 2019. Front Public Health 2022; 10:1003917. [PMID: 36504929 PMCID: PMC9730534 DOI: 10.3389/fpubh.2022.1003917] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/08/2022] [Indexed: 11/27/2022] Open
Abstract
Botulism is a human and animal neurological disease caused by the action of bacterial neurotoxins (botulinum toxins) produced by bacteria from the genus Clostridium. This disease induces flaccid paralysis that can result in respiratory paralysis and heart failure. Due to its serious potential impact on public health, botulism is a closely monitored notifiable disease in France through a case-based passive surveillance system. In humans, this disease is rare, with an average of 10 outbreaks reported each year, mainly due to the consumption of contaminated foods. Type B and to a lesser extend type A are responsible for the majority of cases of foodborne botulism. Each year, an average of 30 outbreaks are recorded on poultry farms, about 20 cases in wild birds and about 10 outbreaks in cattle, involving a large number of animals. Mosaic forms C/D and D/C in birds and cattle, respectively, are the predominant types in animals in France. Types C and D have also been observed to a lesser extent in animals. With the exception of botulinum toxin E, which was exceptionally detected throughout the period in wild birds, the types of botulism found in animal outbreaks are different from those identified in human outbreaks over the last ten years in France and no human botulism outbreaks investigated have been linked to animal botulism. In line with the One Health concept, we present the first integrative approach to the routine surveillance of botulism in humans and animals in France.
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Affiliation(s)
- Sophie Le Bouquin
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), National Reference Laboratory for Avian Botulism, Ploufragan-Plouzané-Niort Laboratory, Ploufragan, France,*Correspondence: Sophie Le Bouquin
| | - Camille Lucas
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), National Reference Laboratory for Avian Botulism, Ploufragan-Plouzané-Niort Laboratory, Ploufragan, France
| | - Rozenn Souillard
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), National Reference Laboratory for Avian Botulism, Ploufragan-Plouzané-Niort Laboratory, Ploufragan, France
| | - Caroline Le Maréchal
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), National Reference Laboratory for Avian Botulism, Ploufragan-Plouzané-Niort Laboratory, Ploufragan, France
| | - Karine Petit
- ANSES, Risk Assessment Department, Maisons-Alfort, France
| | - Pauline Kooh
- ANSES, Risk Assessment Department, Maisons-Alfort, France
| | - Nathalie Jourdan-Da Silva
- Sante Publique France (French Public Health Agency), Direction des Maladies Infectieuses, Saint Maurice, France
| | - François Meurens
- French National Research Institute for Agriculture, Food and Environment (INRAE), Oniris, Unit of Biology, Epidemiology and Risk Analysis in Animal Health (BIOEPAR), Nantes, France,Department of Veterinary Microbiology and Immunology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Christelle Mazuet
- Institut Pasteur, National Reference Center for Anaerobic Bacteria and Botulism, Université Paris Cité, Paris, France
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Luong NDM, Guillier L, Martin-Latil S, Batejat C, Leclercq I, Druesne C, Sanaa M, Chaix E. Database of SARS-CoV-2 and coronaviruses kinetics relevant for assessing persistence in food processing plants. Sci Data 2022; 9:654. [PMID: 36289246 PMCID: PMC9606249 DOI: 10.1038/s41597-022-01763-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/10/2022] [Indexed: 12/12/2022] Open
Abstract
SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2), a virus causing severe acute respiratory disease in humans, emerged in late 2019. This respiratory virus can spread via aerosols, fomites, contaminated hands or surfaces as for other coronaviruses. Studying their persistence under different environmental conditions represents a key step for better understanding the virus transmission. This work aimed to present a reproducible procedure for collecting data of stability and inactivation kinetics from the scientific literature. The aim was to identify data useful for characterizing the persistence of viruses in the food production plants. As a result, a large dataset related to persistence on matrices or in liquid media under different environmental conditions is presented. This procedure, combining bibliographic survey, data digitalization techniques and predictive microbiological modelling, identified 65 research articles providing 455 coronaviruses kinetics. A ranking step as well as a technical validation with a Gage Repeatability & Reproducibility process were performed to check the quality of the kinetics. All data were deposited in public repositories for future uses by other researchers. Measurement(s) | Decimal reduction time | Technology Type(s) | Modelling of kinetics | Factor Type(s) | Temperature • Relative humidity • Genus • Strain | Sample Characteristic - Organism | Coronaviridae |
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Affiliation(s)
- Ngoc-Du Martin Luong
- grid.15540.350000 0001 0584 7022Risk Assessment Department, ANSES, Maisons-Alfort, France
| | - Laurent Guillier
- grid.15540.350000 0001 0584 7022Risk Assessment Department, ANSES, Maisons-Alfort, France
| | - Sandra Martin-Latil
- grid.466400.0Laboratory for Food Safety, ANSES, University of Paris-EST, Maisons-Alfort, France
| | - Christophe Batejat
- grid.428999.70000 0001 2353 6535Institut Pasteur, Université Paris Cité, Environment and Infectious Risks Unit, Laboratory for Urgent Response to Biological Threats (CIBU), Paris, France
| | - India Leclercq
- grid.428999.70000 0001 2353 6535Institut Pasteur, Université Paris Cité, Environment and Infectious Risks Unit, Laboratory for Urgent Response to Biological Threats (CIBU), Paris, France
| | - Christine Druesne
- grid.15540.350000 0001 0584 7022Research fundings & scientific watch department, ANSES, Maisons-Alfort, France
| | - Moez Sanaa
- grid.15540.350000 0001 0584 7022Risk Assessment Department, ANSES, Maisons-Alfort, France
| | - Estelle Chaix
- grid.15540.350000 0001 0584 7022Risk Assessment Department, ANSES, Maisons-Alfort, France
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Palma F, Radomski N, Guérin A, Sévellec Y, Félix B, Bridier A, Soumet C, Roussel S, Guillier L. Genomic elements located in the accessory repertoire drive the adaptation to biocides in Listeria monocytogenes strains from different ecological niches. Food Microbiol 2022; 106:103757. [PMID: 35690455 DOI: 10.1016/j.fm.2021.103757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/04/2021] [Accepted: 01/29/2021] [Indexed: 11/25/2022]
Abstract
In response to the massive use of biocides for controlling Listeria monocytogenes (hereafter Lm) contaminations along the food chain, strains showing biocide tolerance emerged. Here, accessory genomic elements were associated with biocide tolerance through pangenome-wide associations performed on 197 Lm strains from different lineages, ecological, geographical and temporal origins. Mobile elements, including prophage-related loci, the Tn6188_qacH transposon and pLMST6_emrC plasmid, were widespread across lineage I and II food strains and associated with tolerance to benzalkonium-chloride (BC), a quaternary ammonium compound (QAC) widely used in food processing. The pLMST6_emrC was also associated with tolerance to another QAC, the didecyldimethylammonium-chloride, displaying a pleiotropic effect. While no associations were detected for chemically reactive biocides (alcohols and chlorines), genes encoding for cell-surface proteins were associated with BC or polymeric biguanide tolerance. The latter was restricted to lineage I strains from animal and the environment. In conclusion, different genetic markers, with polygenic nature or not, appear to have driven the Lm adaptation to biocide, especially in food strains but also from animal and the environment. These markers could aid to monitor and predict the spread of biocide tolerant Lm genotypes across different ecological niches, finally reducing the risk of such strains in food industrial settings.
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Affiliation(s)
- Federica Palma
- Maisons-Alfort Laboratory of food safety, University Paris-Est, ANSES, Maisons-Alfort, France.
| | - Nicolas Radomski
- Maisons-Alfort Laboratory of food safety, University Paris-Est, ANSES, Maisons-Alfort, France
| | - Alizée Guérin
- Fougères Laboratory, Antibiotics, Biocides, Residues and Resistance Unit, ANSES, Fougères, France
| | - Yann Sévellec
- Maisons-Alfort Laboratory of food safety, University Paris-Est, ANSES, Maisons-Alfort, France
| | - Benjamin Félix
- Maisons-Alfort Laboratory of food safety, University Paris-Est, ANSES, Maisons-Alfort, France
| | - Arnaud Bridier
- Fougères Laboratory, Antibiotics, Biocides, Residues and Resistance Unit, ANSES, Fougères, France
| | - Christophe Soumet
- Fougères Laboratory, Antibiotics, Biocides, Residues and Resistance Unit, ANSES, Fougères, France
| | - Sophie Roussel
- Maisons-Alfort Laboratory of food safety, University Paris-Est, ANSES, Maisons-Alfort, France
| | - Laurent Guillier
- Maisons-Alfort Laboratory of food safety, University Paris-Est, ANSES, Maisons-Alfort, France; Maisons-Alfort Risk Assessment Department, University Paris-Est, ANSES, Maisons-Alfort, France
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17
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Guillier L, Palma F, Fritsch L. Taking account of genomics in quantitative microbial risk assessment: what methods? what issues? Curr Opin Food Sci 2022. [DOI: 10.1016/j.cofs.2022.100922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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Martin CS, Jubelin G, Darsonval M, Leroy S, Leneveu-Jenvrin C, Hmidene G, Omhover L, Stahl V, Guillier L, Briandet R, Desvaux M, Dubois-Brissonnet F. Genetic, physiological, and cellular heterogeneities of bacterial pathogens in food matrices: Consequences for food safety. Compr Rev Food Sci Food Saf 2022; 21:4294-4326. [PMID: 36018457 DOI: 10.1111/1541-4337.13020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 01/28/2023]
Abstract
In complex food systems, bacteria live in heterogeneous microstructures, and the population displays phenotypic heterogeneities at the single-cell level. This review provides an overview of spatiotemporal drivers of phenotypic heterogeneity of bacterial pathogens in food matrices at three levels. The first level is the genotypic heterogeneity due to the possibility for various strains of a given species to contaminate food, each of them having specific genetic features. Then, physiological heterogeneities are induced within the same strain, due to specific microenvironments and heterogeneous adaptative responses to the food microstructure. The third level of phenotypic heterogeneity is related to cellular heterogeneity of the same strain in a specific microenvironment. Finally, we consider how these phenotypic heterogeneities at the single-cell level could be implemented in mathematical models to predict bacterial behavior and help ensure microbiological food safety.
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Affiliation(s)
- Cédric Saint Martin
- MICALIS Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France.,Université Clermont Auvergne, INRAE, UMR454 MEDIS, Clermont-Ferrand, France
| | - Grégory Jubelin
- Université Clermont Auvergne, INRAE, UMR454 MEDIS, Clermont-Ferrand, France
| | - Maud Darsonval
- MICALIS Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
| | - Sabine Leroy
- Université Clermont Auvergne, INRAE, UMR454 MEDIS, Clermont-Ferrand, France
| | - Charlène Leneveu-Jenvrin
- MICALIS Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France.,Association pour le Développement de l'Industrie de la Viande (ADIV), Clermont-Ferrand, France
| | - Ghaya Hmidene
- Risk Assessment Department, ANSES, Maisons-Alfort, France
| | - Lysiane Omhover
- Aerial, Technical Institute of Agro-Industry, Illkirch, France
| | - Valérie Stahl
- Aerial, Technical Institute of Agro-Industry, Illkirch, France
| | | | - Romain Briandet
- MICALIS Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
| | - Mickaël Desvaux
- Université Clermont Auvergne, INRAE, UMR454 MEDIS, Clermont-Ferrand, France
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De Sousa Violante M, Podeur G, Michel V, Guillier L, Radomski N, Lailler R, Le Hello S, Weill FX, Mistou MY, Mallet L. A retrospective and regional approach assessing the genomic diversity of Salmonella Dublin. NAR Genom Bioinform 2022; 4:lqac047. [PMID: 35821882 PMCID: PMC9270687 DOI: 10.1093/nargab/lqac047] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 05/30/2022] [Accepted: 06/13/2022] [Indexed: 12/02/2022] Open
Abstract
From a historically rare serotype, Salmonella enterica subsp. enterica Dublin slowly became one of the most prevalent Salmonella in cattle and raw milk cheese in some regions of France. We present a retrospective genomic analysis of 480 S. Dublin isolates to address the context, evolutionary dynamics, local diversity and the genesis processes of regional S. Dublin outbreaks events between 2015 and 2017. Samples were clustered and assessed for correlation against metadata including isolation date, isolation matrices, geographical origin and epidemiological hypotheses. Significant findings can be drawn from this work. We found that the geographical distance was a major factor explaining genetic groups in the early stages of the cheese production processes (animals, farms) while down-the-line transformation steps were more likely to host genomic diversity. This supports the hypothesis of a generalised local persistence of strains from animal to finished products, with occasional migration. We also observed that the bacterial surveillance is representative of diversity, while targeted investigations without genomics evidence often included unrelated isolates. Combining both approaches in phylogeography methods allows a better representation of the dynamics, of outbreaks.
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Affiliation(s)
- Madeleine De Sousa Violante
- Actalia, 419 route des champs laitiers , CS 50030, 74801 La Roche sur Foron, France
- INRAE, MaIAGE, Université Paris-Saclay , F-78352 Jouy-en-Josas, France
| | - Gaëtan Podeur
- Actalia, 419 route des champs laitiers , CS 50030, 74801 La Roche sur Foron, France
| | - Valérie Michel
- Actalia, 419 route des champs laitiers , CS 50030, 74801 La Roche sur Foron, France
| | - Laurent Guillier
- ANSES, 14 Rue Pierre et Marie Curie , 94700 Maisons-Alfort, France
| | - Nicolas Radomski
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise ‘Giuseppe Caporale’ (IZSAM) , via Campo Boario, 64100 Teramo, TE, Italy
| | - Renaud Lailler
- ANSES, 14 Rue Pierre et Marie Curie , 94700 Maisons-Alfort, France
| | - Simon Le Hello
- UNICAEN, Groupe de Recherche sur l’Adaptation Microbienne, GRAM 2.0, EA2656, University of Caen Normandy , Caen, France
| | - François-Xavier Weill
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella , Paris, France
| | | | - Ludovic Mallet
- Institut Claudius Regaud , 1 avenue Irène Joliot-Curie, 31059 Toulouse Cedex 9, France
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20
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Sévellec Y, Ascencio E, Douarre PE, Félix B, Gal L, Garmyn D, Guillier L, Piveteau P, Roussel S. Listeria monocytogenes: Investigation of Fitness in Soil Does Not Support the Relevance of Ecotypes. Front Microbiol 2022; 13:917588. [PMID: 35770178 PMCID: PMC9234652 DOI: 10.3389/fmicb.2022.917588] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
Listeria monocytogenes (Lm) is a ubiquitous bacterium that causes the serious foodborne illness listeriosis. Although soil is a primary reservoir and a central habitat for Lm, little information is available on the genetic features underlying the fitness of Lm strains in this complex habitat. The aim of this study was to identify (i) correlations between the strains fitness in soil, their origin and their phylogenetic position (ii) identify genetic markers allowing Lm to survive in the soil. To this end, we assembled a balanced panel of 216 Lm strains isolated from three major ecological compartments (outdoor environment, animal hosts, and food) and from 33 clonal complexes occurring worldwide. The ability of the 216 strains to survive in soil was tested phenotypically. Hierarchical clustering identified three phenotypic groups according to the survival rate (SR): phenotype 1 “poor survivors” (SR < 2%), phenotype 2 “moderate survivors” (2% < SR < 5%) and phenotype 3 “good survivors” (SR > 5%). Survival in soil depended neither on strains’ origin nor on their phylogenetic position. Genome-wide-association studies demonstrated that a greater number of genes specifically associated with a good survival in soil was found in lineage II strains (57 genes) than in lineage I strains (28 genes). Soil fitness was mainly associated with variations in genes (i) coding membrane proteins, transcription regulators, and stress resistance genes in both lineages (ii) coding proteins related to motility and (iii) of the category “phage-related genes.” The cumulative effect of these small genomic variations resulted in significant increase of soil fitness.
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Affiliation(s)
- Yann Sévellec
- Maisons-Alfort Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Maisons-Alfort, France
| | - Eliette Ascencio
- Agroecologie, AgroSup Dijon, INRAE, Bourgogne Franche-Comté University, Dijon, France
| | - Pierre-Emmanuel Douarre
- Maisons-Alfort Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Maisons-Alfort, France
| | - Benjamin Félix
- Maisons-Alfort Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Maisons-Alfort, France
| | - Laurent Gal
- Agroecologie, AgroSup Dijon, INRAE, Bourgogne Franche-Comté University, Dijon, France
| | - Dominique Garmyn
- Agroecologie, AgroSup Dijon, INRAE, Bourgogne Franche-Comté University, Dijon, France
| | - Laurent Guillier
- Risk Assessment Department, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), University of Paris-Est, Maisons-Alfort, France
| | | | - Sophie Roussel
- Maisons-Alfort Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Maisons-Alfort, France
- *Correspondence: Sophie Roussel,
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21
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Cherchame E, Guillier L, Lailler R, Vignaud ML, Jourdan-Da Silva N, Le Hello S, Weill FX, Cadel-Six S. Salmonella enterica subsp. enterica Welikade: guideline for phylogenetic analysis of serovars rarely involved in foodborne outbreaks. BMC Genomics 2022; 23:217. [PMID: 35303794 PMCID: PMC8933937 DOI: 10.1186/s12864-022-08439-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 02/23/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Salmonella spp. is a major foodborne pathogen with a wide variety of serovars associated with human cases and food sources. Nevertheless, in Europe a panel of ten serovars is responsible for up to 80% of confirmed human cases. Clustering studies by single nucleotide polymorphism (SNP) core-genome phylogenetic analysis of outbreaks due to these major serovars are simplified by the availability of many complete genomes in the free access databases. This is not the case for outbreaks due to less common serovars, such as Welikade, for which no reference genomes are available. In this study, we propose a method to solve this problem. We propose to perform a core genome MLST (cgMLST) analysis based on hierarchical clustering using the free-access EnteroBase to select the most suitable genome to use as a reference for SNP phylogenetic analysis. In this study, we applied this protocol to a retrospective analysis of a Salmonella enterica serovar Welikade (S. Welikade) foodborne outbreak that occurred in France in 2016. Finally, we compared the cgMLST and SNP analyses. SNP phylogenetic reconstruction was carried out considering the effect of recombination events identified by the ClonalFrameML tool. The accessory genome was also explored by phage content and virulome analyses. RESULTS Our findings revealed high clustering concordance using cgMLST and SNP analyses. Nevertheless, SNP analysis allowed for better assessment of the genetic distance among strains. The results revealed epidemic clones of S. Welikade circulating within the poultry and dairy sectors in France, responsible for sporadic and non-sporadic human cases between 2012 and 2019. CONCLUSIONS This study increases knowledge on this poorly described serovar and enriches public genome databases with 42 genomes from human and non-human S. Welikade strains, including the isolate collected in 1956 in Sri Lanka, which gave the name to this serovar. This is the first genomic analysis of an outbreak due to S. Welikade described to date.
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Affiliation(s)
- Emeline Cherchame
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), 94700, Maisons-Alfort, France. .,Present address: Data Analysis Core, Paris Brain Institute, ICM, Paris, France.
| | - Laurent Guillier
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), 94700, Maisons-Alfort, France
| | - Renaud Lailler
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), 94700, Maisons-Alfort, France
| | - Marie-Leone Vignaud
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), 94700, Maisons-Alfort, France
| | | | - Simon Le Hello
- Centre National de Référence Des Escherichia Coli, Institut Pasteur, Unité Des Bactéries Pathogènes Entériques, Shigella et Salmonella, 75015, Paris, France.,Present address: Groupe de Recherche Sur L'Adaptation Microbienne (GRAM 2.0), Normandie Univ, UNICAEN, Caen, France
| | - François-Xavier Weill
- Centre National de Référence Des Escherichia Coli, Institut Pasteur, Unité Des Bactéries Pathogènes Entériques, Shigella et Salmonella, 75015, Paris, France
| | - Sabrina Cadel-Six
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), 94700, Maisons-Alfort, France
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22
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Clinquart A, Ellies-Oury MP, Hocquette JF, Guillier L, Santé-Lhoutellier V, Prache S. Review: On-farm and processing factors affecting bovine carcass and meat quality. Animal 2022; 16 Suppl 1:100426. [PMID: 35031228 DOI: 10.1016/j.animal.2021.100426] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 11/10/2021] [Accepted: 11/18/2021] [Indexed: 11/30/2022] Open
Abstract
This paper reviews the current state of knowledge on beef carcass and meat quality, with particular emphasis on on-farm and processing factors associated with its high and inconsistent variability. The diversity of livestock systems comes from the diversity of breeds (dairy or beef), ages and gender (bulls, steers, heifers, cull cows) used to produce either mainly beef or beef and milk. In addition, there are factors linked to farming practices (including diet, especially grazing) which significantly influence the sensory, nutritional, technological and extrinsic (such as image) quality attributes of meat. These can become factors of positive differentiation when controlled by the application and certification of technical specifications. Finally, preslaughter (such as stress), slaughter (such as the chilling and hanging method of carcasses) and postslaughter (such as ageing, packaging and cooking) conditions have a strong influence on the microbiological, sensory, technological and image quality attributes of beef. In this review, potential synergisms or antagonisms between the different quality attributes are highlighted. For example, finishing cattle on grass, compared to indoor fattening on a high concentrate diet, has the advantage of producing leaner meat with a higher proportion of omega-3 fatty acids while exhibiting superior oxidative stability, but with the consequence of a darker meat colour and lower productivity, as well as higher seasonality and land surface requirements. Moreover, the control of on-farm factors is often guided by productivity (growth rate, feed conversion ratio) and carcass quality attributes (weight, conformation and fatness). Genetic selection has often been oriented in this direction, without taking other quality attributes into account. Finally, the interactions between all these factors (and especially between on-farm and slaughter or processing factors) are not considered in the quality grading schemes in European countries. This means that positive efforts at farm level may be mitigated or even eliminated by poor slaughtering or processing conditions. All these considerations explain why between-animal variability in quality can be high, even when animals come from the same farming system. The ability to predict the sensory and nutritional properties of meat according to production factors has become a major objective of the supply chain.
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Affiliation(s)
- A Clinquart
- FARAH, Faculté de Médecine vétérinaire, Université de Liège, 4000 Liège, Belgium.
| | - M P Ellies-Oury
- Bordeaux Science Agro, 33175 Gradignan, France; Université d'Auvergne, INRAE, Vetagro Sup, UMR Herbivores, 63122 Saint Genès-Champanelle, France
| | - J F Hocquette
- Université d'Auvergne, INRAE, Vetagro Sup, UMR Herbivores, 63122 Saint Genès-Champanelle, France
| | - L Guillier
- Agence nationale de sécurité de l'alimentation, de l'environnement et du travail (ANSES), Direction de l'évaluation des risques, F-94700 Maisons-Alfort, France
| | | | - S Prache
- Université d'Auvergne, INRAE, Vetagro Sup, UMR Herbivores, 63122 Saint Genès-Champanelle, France
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23
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Pasquali F, Remondini D, Snary EL, Hald T, Guillier L. Editorial: Integrating Whole Genome Sequencing Into Source Attribution and Risk Assessment of Foodborne Bacterial Pathogens. Front Microbiol 2021; 12:795098. [PMID: 34899675 PMCID: PMC8661528 DOI: 10.3389/fmicb.2021.795098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/01/2021] [Indexed: 11/20/2022] Open
Affiliation(s)
- Frederique Pasquali
- Department of Agricultural and Food Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Daniel Remondini
- Department of Physics and Astronomy, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Emma Louise Snary
- Department of Epidemiological Sciences, Animal and Plant Health Agency (APHA), Addlestone, United Kingdom
| | - Tine Hald
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Laurent Guillier
- Department of Risk Assessment, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES), Maisons-Alfort, France
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24
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Baéza E, Guillier L, Petracci M. Review: Production factors affecting poultry carcass and meat quality attributes. Animal 2021; 16 Suppl 1:100331. [PMID: 34419417 DOI: 10.1016/j.animal.2021.100331] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 12/16/2022] Open
Abstract
Poultry meat mainly comes from standard production system using high growth rate strains reared under indoor intensive conditions. However, it is possible to find also different alternative systems using outdoor extensive rearing conditions and slow-growing lines. These different production systems can affect carcass and meat quality. In this review, quality has been broken down into six properties: commercial, organoleptic, nutritional, technological, sanitary and image, the latter covering the ethical, cultural and environmental dimensions associated with the way the meat is produced, as well as its origin and being particularly valued in many quality labels. The quality of meat is built and can deteriorate along the continuum from the conception of the animal to the fork. Our review details the different factors implicated in the determinism of poultry meat properties and pinpoints critical periods, such as the preslaughter and slaughter periods, and key factors, such as the feeding regimen, via its direct effect on the fatty acid profile, the antioxidant and volatile compound contents, and indirect effects mediated via the growth rate of the bird. Our review also highlights potential antagonisms between different dimensions of quality. The genetic selection for breast meat yield, for example, has been effective in producing carcasses with higher meat yield, but resulting since a decade in the increased occurrence of quality defects and myopathies (white striping, wooden breast, spaghetti meat and deep pectoral disease). Outdoor access has positive effects on the image and nutritional properties (through its effect on the fatty acid profile of meat lipids), but it increases the exposition risk to environmental contaminants and pathologies (parasites, virus, bacteria); it also increases the variability in meat quality linked to the variability of animal performance and slaughter age. The orientation towards more agro-ecological low-input farming systems may present benefits for the image and nutritional properties, but also risks for the commercial (low carcass weight and low breast yield, irregularity in supply), organoleptic (stronger flavour, less tender and darker colour of the meat) and in terms of variability of the different properties that constitute quality. Efforts should be made in the future to better take into account the various dimensions of quality, in consumer information, payment to farmers and genetic selection.
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Affiliation(s)
- E Baéza
- INRAE, Université de Tours, UMR BOA, F-37380 Nouzilly, France.
| | - L Guillier
- Agence nationale de sécurité de l'alimentation, de l'environnement et du travail (ANSES), Direction de l'évaluation des risques, F-94700 Maisons-Alfort, France
| | - M Petracci
- Department of Agricultural and Food Sciences, University of Bologna, 47522 Cesena, Italy
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25
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Prache S, Schreurs N, Guillier L. Review: Factors affecting sheep carcass and meat quality attributes. Animal 2021; 16 Suppl 1:100330. [PMID: 34400114 DOI: 10.1016/j.animal.2021.100330] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 12/17/2022] Open
Abstract
Sheep meat comes from a wide variety of farming systems utilising outdoor extensive to indoor intensive with animals of various ages at slaughter. In Europe, slaughter may occur from 4 weeks of age in suckling light lambs to adult ages. More than any other animal species used for meat production, there are strong country-specific preferences for sheep meat quality linked to production system characteristics such as dairy or grassland-based systems. This article critically reviews the current state of knowledge on factors affecting sheep carcass and meat quality. Quality has been broken down into six core attributes: commercial, organoleptic, nutritional, technological, safety and image, the latter covering aspects of ethics, culture and environment associated with the way the meat is produced and its origin, which are particularly valued in the many quality labels in Europe. The quality of meat is built but can also deteriorate along the continuum from the conception of the animal to the consumer. Our review pinpoints critical periods, such as the gestation and the preslaughter and slaughter periods, and key factors, such as the animal diet, via its direct effect on the fatty acid profile, the antioxidant and volatile content, and indirect effects mediated via the age of the animal. It also pinpoints methodological difficulties in predicting organoleptic attributes, particularly odour and flavour. Potential antagonisms between different dimensions of quality are highlighted. For example, pasture-feeding has positive effects on the image and nutritional attributes (through its effect on the fatty acid profile of meat lipids), but it increases the risk of off-odours and off-flavours for sensitive consumersand the variability in meat quality linked to variability of animal age at slaughter. The orientation towards more agro-ecological, low-input farming systems may therefore present benefits for the image and nutritional properties of the meat, but also risks for the commercial (insufficient carcass fatness, feed deficiencies at key periods of the production cycle, irregularity in supply), organoleptic (stronger flavour and darker colour of the meat) and variability of sheep carcass and meat quality. Furthermore, the genetic selection for lean meat yield has been effective in producing carcasses that yield more meat, but at a penalty to the intramuscular fat content and eating quality of the meat, and making it more difficult to finish lambs on grass. Various tools to assess and predict quality are in development to better consider the various dimensions of quality in consumer information, payment to farmers and genetic selection.
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Affiliation(s)
- S Prache
- Université d'Auvergne, INRA, Vetagro Sup, UMR Herbivores, 63122 St-Genès-Champanelle, France.
| | - N Schreurs
- Animal Science, School of Agriculture and Environment, PN433, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - L Guillier
- Université Paris Est, Anses, Risk Assessment Department, 94701 Maisons-Alfort, France
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26
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Koch L, Lopes AA, Maiguy A, Guillier S, Guillier L, Tournier JN, Biot F. Natural outbreaks and bioterrorism: How to deal with the two sides of the same coin? J Glob Health 2021; 10:020317. [PMID: 33110519 PMCID: PMC7535343 DOI: 10.7189/jogh.10.020317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Lionel Koch
- Bacteriology Unit, French Armed Forces Biomedical Research Institute (IRBA), Bretigny sur Orge, France
| | - Anne-Aurelie Lopes
- Pediatric Emergency Department, AP-HP, Robert Debre Hospital, Paris, Sorbonne University, France
| | | | - Sophie Guillier
- Bacteriology Unit, French Armed Forces Biomedical Research Institute (IRBA), Bretigny sur Orge, France
| | - Laurent Guillier
- Risk Assessment Department, University of Paris-Est, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Maisons-Alfort, France
| | - Jean-Nicolas Tournier
- Department of Microbiology and Infectious Diseases, French Armed Forces Biomedical Research Institute (IRBA), Bretigny sur Orge, France
| | - Fabrice Biot
- Bacteriology Unit, French Armed Forces Biomedical Research Institute (IRBA), Bretigny sur Orge, France
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27
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Nia Y, Lombard B, Gentil S, Neveux L, Mutel I, Guillier F, Messio S, Pairaud S, Herbin S, Guillier L, Auvray F, Hennekinne JA. Development and validation of the Standard method EN ISO 19020 - microbiology of the food chain - Horizontal method for the immunoenzymatic detection of staphylococcal enterotoxins in foodstuffs. Int J Food Microbiol 2021; 354:109319. [PMID: 34247023 DOI: 10.1016/j.ijfoodmicro.2021.109319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/10/2021] [Accepted: 06/22/2021] [Indexed: 01/01/2023]
Abstract
In the frame of the CEN Mandate M/381 from the European Commission to CEN (European Committee for Standardization), a method for the detection of staphylococcal enterotoxins in foodstuffs has been developed, validated and standardized. An extraction procedure based on dialysis concentration followed by an immuno-enzymatic detection has been defined. In addition, performance criteria (minimum values of sensitivity, specificity and level of detection) to be achieved by the commercially available immuno-enzymatic kits that could be used to detect staphylococcal enterotoxins in food matrices, were developed. A 2-stage validation study was conducted: The first stage aimed at selecting the commercial kits to be included in the second stage, which consisted in an interlaboratory study, using eight matrices covering five food categories (ready-to-eat food, meat products, milk products, dessert and fish). Results showed that two detection kits included in the study met the pre-defined performance criteria. The implementation of dialysis concentration step increased significantly the sensitivity of the method. The method developed allowed to achieve the Benchmark Dose lower limit (BMD10) estimated at 6.1 ng. In 2019, finally, the European Commission recognized this standard as the European Union reference method for the detection of staphylococcal enterotoxins in food.
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Affiliation(s)
- Y Nia
- Université Paris Est, ANSES, Laboratory for Food Safety, Maisons-Alfort location, F-94701 Maisons-Alfort, France.
| | - B Lombard
- Université Paris Est, ANSES, Laboratory for Food Safety, Maisons-Alfort location, F-94701 Maisons-Alfort, France
| | - S Gentil
- Université Paris Est, ANSES, Laboratory for Food Safety, Maisons-Alfort location, F-94701 Maisons-Alfort, France
| | - L Neveux
- Université Paris Est, ANSES, Laboratory for Food Safety, Maisons-Alfort location, F-94701 Maisons-Alfort, France
| | - I Mutel
- Université Paris Est, ANSES, Laboratory for Food Safety, Maisons-Alfort location, F-94701 Maisons-Alfort, France
| | - F Guillier
- Université Paris Est, ANSES, Laboratory for Food Safety, Maisons-Alfort location, F-94701 Maisons-Alfort, France
| | - S Messio
- Université Paris Est, ANSES, Laboratory for Food Safety, Maisons-Alfort location, F-94701 Maisons-Alfort, France
| | - S Pairaud
- Université Paris Est, ANSES, Laboratory for Food Safety, Maisons-Alfort location, F-94701 Maisons-Alfort, France
| | - S Herbin
- Université Paris Est, ANSES, Laboratory for Food Safety, Maisons-Alfort location, F-94701 Maisons-Alfort, France
| | - L Guillier
- Université Paris Est, ANSES, Laboratory for Food Safety, Maisons-Alfort location, F-94701 Maisons-Alfort, France
| | - F Auvray
- Université Paris Est, ANSES, Laboratory for Food Safety, Maisons-Alfort location, F-94701 Maisons-Alfort, France
| | - J A Hennekinne
- Université Paris Est, ANSES, Laboratory for Food Safety, Maisons-Alfort location, F-94701 Maisons-Alfort, France
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28
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Touma J, La Vieille S, Guillier L, Barrere V, Manny E, Théolier J, Dominguez S, Godefroy SB. 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; 38:550-562. [DOI: 10.1080/19440049.2021.1881622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Joseph Touma
- Food Risk Analysis and Regulatory Excellence Platform (PARERA), Department of Food Science and Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec, Canada
- Department of Heavy Metals and Colorants, Lebanese Agricultural Research Institute, Beirut, Lebanon
| | - Sébastien La Vieille
- Food Risk Analysis and Regulatory Excellence Platform (PARERA), Department of Food Science and Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec, Canada
- Food Directorate, Health Canada, Ottawa, Ontario, Canada
| | - Laurent Guillier
- Risk Assessment Department, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Maisons-Alfort, France
| | - Virginie Barrere
- Food Risk Analysis and Regulatory Excellence Platform (PARERA), Department of Food Science and Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec, Canada
| | - Emilie Manny
- Food Risk Analysis and Regulatory Excellence Platform (PARERA), Department of Food Science and Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec, Canada
| | - Jérémie Théolier
- Food Risk Analysis and Regulatory Excellence Platform (PARERA), Department of Food Science and Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec, Canada
| | - Silvia Dominguez
- Food Risk Analysis and Regulatory Excellence Platform (PARERA), Department of Food Science and Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec, Canada
| | - Samuel Benrejeb Godefroy
- Food Risk Analysis and Regulatory Excellence Platform (PARERA), Department of Food Science and Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec, Canada
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Fritsch L, Baleswaran A, Bergis H, Lintz A, Hamon E, Stahl V, Augustin JC, Guillier L. A microscopy-based approach for determining growth probability and lag time of individual bacterial cells. Food Res Int 2021; 140:110052. [PMID: 33648277 DOI: 10.1016/j.foodres.2020.110052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 12/13/2020] [Accepted: 12/16/2020] [Indexed: 12/01/2022]
Abstract
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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Affiliation(s)
- Lena Fritsch
- French Agency for Food, Environmental and Occupational Health & Safety (Anses), Laboratory for Food Safety, Université Paris-Est, Maisons-Alfort F-94701, France
| | - Abirami Baleswaran
- French Agency for Food, Environmental and Occupational Health & Safety (Anses), Laboratory for Food Safety, Université Paris-Est, Maisons-Alfort F-94701, France
| | - Hélène Bergis
- French Agency for Food, Environmental and Occupational Health & Safety (Anses), Laboratory for Food Safety, Université Paris-Est, Maisons-Alfort F-94701, France
| | - Adrienne Lintz
- Aérial, Technical Institute of Food Industry, Parc d'innovation, 250 rue Laurent Fries, 67400 Illkirch, France
| | - Erwann Hamon
- Aérial, Technical Institute of Food Industry, Parc d'innovation, 250 rue Laurent Fries, 67400 Illkirch, France
| | - Valérie Stahl
- Aérial, Technical Institute of Food Industry, Parc d'innovation, 250 rue Laurent Fries, 67400 Illkirch, France
| | - Jean-Christophe Augustin
- French Agency for Food, Environmental and Occupational Health & Safety (Anses), Laboratory for Food Safety, Université Paris-Est, Maisons-Alfort F-94701, France; Ecole Nationale Vétérinaire d'Alfort, 94700 Maisons-Alfort, France
| | - Laurent Guillier
- French Agency for Food, Environmental and Occupational Health & Safety (Anses), Laboratory for Food Safety, Université Paris-Est, Maisons-Alfort F-94701, France.
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Guillier L, Martin-Latil S, Chaix E, Thébault A, Pavio N, Le Poder S, Batéjat C, Biot F, Koch L, Schaffner DW, Sanaa M. Modeling the Inactivation of Viruses from the Coronaviridae Family in Response to Temperature and Relative Humidity in Suspensions or on Surfaces. Appl Environ Microbiol 2020. [PMID: 32680860 DOI: 10.1128/2020.05.26.20114025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
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 D values (i.e., the time to obtain a log10 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 D 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 Alphacoronavirus and Betacoronavirus genera.IMPORTANCE 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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Affiliation(s)
- Laurent Guillier
- Risk Assessment Department, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Sandra Martin-Latil
- Laboratory for Food Safety, French Agency for Food, Environmental, and Occupational Health and Safety, University of Paris-EST, Maisons-Alfort, France
| | - Estelle Chaix
- Risk Assessment Department, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Anne Thébault
- Risk Assessment Department, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Nicole Pavio
- UMR Virologie 1161, ENVA, INRAE, Anses, Maisons-Alfort, France
| | | | - Christophe Batéjat
- Environment and Infectious Risks Unit, Laboratory for Urgent Response to Biological Threats (CIBU), Institut Pasteur, Paris, France
| | - Fabrice Biot
- Bacteriology Unit, French Armed Forces Biomedical Research Institute (IRBA), Brétigny-sur-Orge, France
| | - Lionel Koch
- Bacteriology Unit, French Armed Forces Biomedical Research Institute (IRBA), Brétigny-sur-Orge, France
| | - Donald W Schaffner
- Department of Food Science, Rutgers University, New Brunswick, New Jersey, USA
| | - Moez Sanaa
- Risk Assessment Department, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
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31
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Guillier L, Martin-Latil S, Chaix E, Thébault A, Pavio N, Le Poder S, Batéjat C, Biot F, Koch L, Schaffner DW, Sanaa M. Modeling the Inactivation of Viruses from the Coronaviridae Family in Response to Temperature and Relative Humidity in Suspensions or on Surfaces. Appl Environ Microbiol 2020; 86:e01244-20. [PMID: 32680860 PMCID: PMC7480392 DOI: 10.1128/aem.01244-20] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 07/15/2020] [Indexed: 02/08/2023] Open
Abstract
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 D values (i.e., the time to obtain a log10 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 D 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 Alphacoronavirus and Betacoronavirus genera.IMPORTANCE 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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Affiliation(s)
- Laurent Guillier
- Risk Assessment Department, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Sandra Martin-Latil
- Laboratory for Food Safety, French Agency for Food, Environmental, and Occupational Health and Safety, University of Paris-EST, Maisons-Alfort, France
| | - Estelle Chaix
- Risk Assessment Department, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Anne Thébault
- Risk Assessment Department, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Nicole Pavio
- UMR Virologie 1161, ENVA, INRAE, Anses, Maisons-Alfort, France
| | | | - Christophe Batéjat
- Environment and Infectious Risks Unit, Laboratory for Urgent Response to Biological Threats (CIBU), Institut Pasteur, Paris, France
| | - Fabrice Biot
- Bacteriology Unit, French Armed Forces Biomedical Research Institute (IRBA), Brétigny-sur-Orge, France
| | - Lionel Koch
- Bacteriology Unit, French Armed Forces Biomedical Research Institute (IRBA), Brétigny-sur-Orge, France
| | - Donald W Schaffner
- Department of Food Science, Rutgers University, New Brunswick, New Jersey, USA
| | - Moez Sanaa
- Risk Assessment Department, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
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Almoughrabie S, Ngari C, Guillier L, Briandet R, Poulet V, Dubois-Brissonnet F. 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; 15:e0236059. [PMID: 32716948 PMCID: PMC7384607 DOI: 10.1371/journal.pone.0236059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 06/26/2020] [Indexed: 11/18/2022] Open
Abstract
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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Affiliation(s)
- Samia Almoughrabie
- Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
| | | | - Laurent Guillier
- Direction de l’évaluation des risques, ANSES, Agence nationale de sécurité de l’alimentation, de l’environnement et du travail, Maisons-Alfort, France
| | - Romain Briandet
- Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
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Guillier L, Gourmelon M, Lozach S, Cadel-Six S, Vignaud ML, Munck N, Hald T, Palma F. AB_SA: Accessory genes-Based Source Attribution - tracing the source of Salmonella enterica Typhimurium environmental strains. Microb Genom 2020; 6:mgen000366. [PMID: 32320376 PMCID: PMC7478624 DOI: 10.1099/mgen.0.000366] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/20/2020] [Indexed: 12/31/2022] Open
Abstract
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 Salmonella enterica Typhimurium and its monophasic variant (S. enterica 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 S. enterica Typhimurium and S. enterica 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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Affiliation(s)
- Laurent Guillier
- Laboratory for Food Safety, ANSES, University of Paris-EST, Maisons-Alfort, France
- Risk Assessment Department, ANSES, University of Paris-EST, Maisons-Alfort, France
| | - Michèle Gourmelon
- RBE–SGMM, Health, Environment and Microbiology Laboratory, IFREMER, Plouzané, France
| | - Solen Lozach
- RBE–SGMM, Health, Environment and Microbiology Laboratory, IFREMER, Plouzané, France
| | - Sabrina Cadel-Six
- Laboratory for Food Safety, ANSES, University of Paris-EST, Maisons-Alfort, France
| | - Marie-Léone Vignaud
- Laboratory for Food Safety, ANSES, University of Paris-EST, Maisons-Alfort, France
| | - Nanna Munck
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Tine Hald
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Federica Palma
- Laboratory for Food Safety, ANSES, University of Paris-EST, Maisons-Alfort, France
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Sévellec Y, Granier SA, Le Hello S, Weill FX, Guillier L, Mistou MY, Cadel-Six S. Source Attribution Study of Sporadic Salmonella Derby Cases in France. Front Microbiol 2020; 11:889. [PMID: 32477304 PMCID: PMC7240076 DOI: 10.3389/fmicb.2020.00889] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/16/2020] [Indexed: 12/20/2022] Open
Abstract
Salmonella enterica subsp. enterica 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, S. 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 S. 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 S. 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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Affiliation(s)
- Yann Sévellec
- 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
| | - Sophie A. Granier
- 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
- Laboratoire de Fougères, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Fougères, France
| | - Simon Le Hello
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Institut Pasteur, Paris, France
| | - François-Xavier Weill
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Institut Pasteur, Paris, France
| | - Laurent Guillier
- 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
| | - Michel-Yves Mistou
- 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
| | - Sabrina Cadel-Six
- 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
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Munck N, Leekitcharoenphon P, Litrup E, Kaas R, Meinen A, Guillier L, Tang Y, Malorny B, Palma F, Borowiak M, Gourmelon M, Simon S, Banerji S, Petrovska L, Dallman TJ, Hald T. Four European Salmonella Typhimurium datasets collected to develop WGS-based source attribution methods. Sci Data 2020; 7:75. [PMID: 32127544 PMCID: PMC7054362 DOI: 10.1038/s41597-020-0417-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/03/2020] [Indexed: 11/22/2022] Open
Abstract
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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Affiliation(s)
- Nanna Munck
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.
| | - Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Eva Litrup
- Foodborne Infections, Department of Bacteria, Parasites and Fungi, Statens Serum Institute, Copenhagen, Denmark
| | - Rolf Kaas
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Anika Meinen
- Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Laurent Guillier
- Université Paris Est, ANSES, Laboratory for Food Safety, F-94701, Maisons-Alfort, France
| | - Yue Tang
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey, UK
| | - Burkhard Malorny
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Federica Palma
- Université Paris Est, ANSES, Laboratory for Food Safety, F-94701, Maisons-Alfort, France
| | - Maria Borowiak
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Michèle Gourmelon
- Ifremer, Environment and Microbiology Laboratory, RBE, SGMM, Plouzané, France
| | - Sandra Simon
- National Reference Center for Salmonella and other bacterial enteric pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Sangeeta Banerji
- National Reference Center for Salmonella and other bacterial enteric pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Liljana Petrovska
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey, UK
| | | | - Tine Hald
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
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Palma F, Brauge T, Radomski N, Mallet L, Felten A, Mistou MY, Brisabois A, Guillier L, Midelet-Bourdin G. Dynamics of mobile genetic elements of Listeria monocytogenes persisting in ready-to-eat seafood processing plants in France. BMC Genomics 2020; 21:130. [PMID: 32028892 PMCID: PMC7006209 DOI: 10.1186/s12864-020-6544-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 01/30/2020] [Indexed: 12/20/2022] Open
Abstract
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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Affiliation(s)
- Federica Palma
- ANSES, Laboratory for Food Safety, University Paris-Est, Maisons-Alfort, France
| | - Thomas Brauge
- ANSES, Laboratory for Food Safety, Boulogne-sur-Mer, France
| | - Nicolas Radomski
- ANSES, Laboratory for Food Safety, University Paris-Est, Maisons-Alfort, France
| | - Ludovic Mallet
- ANSES, Laboratory for Food Safety, University Paris-Est, Maisons-Alfort, France
| | - Arnaud Felten
- ANSES, Laboratory for Food Safety, University Paris-Est, Maisons-Alfort, France
| | - Michel-Yves Mistou
- ANSES, Laboratory for Food Safety, University Paris-Est, Maisons-Alfort, France
- INRAE, MaIAGE, University Paris-Saclay, Jouy-en-Josas, France
| | - Anne Brisabois
- ANSES, Laboratory for Food Safety, University Paris-Est, Maisons-Alfort, France
- ANSES, Laboratory for Food Safety, Boulogne-sur-Mer, France
| | - Laurent Guillier
- ANSES, Laboratory for Food Safety, University Paris-Est, Maisons-Alfort, France
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Lee BH, Cole S, Badel-Berchoux S, Guillier L, Felix B, Krezdorn N, Hébraud M, Bernardi T, Sultan I, Piveteau P. Biofilm Formation of Listeria monocytogenes Strains Under Food Processing Environments and Pan-Genome-Wide Association Study. Front Microbiol 2019; 10:2698. [PMID: 31824466 PMCID: PMC6882377 DOI: 10.3389/fmicb.2019.02698] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 11/06/2019] [Indexed: 01/24/2023] Open
Abstract
Concerns about food contamination by Listeria monocytogenes are on the rise with increasing consumption of ready-to-eat foods. Biofilm production of L. monocytogenes 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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Affiliation(s)
- Bo-Hyung Lee
- École Doctorale des Sciences de la Vie, Santé, Agronomie, Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
- BioFilm Control SAS, Biopôle Clermont Limagne, Saint-Beauzire, France
- GenXPro GmbH, Frankfurt am Main, Germany
| | - Sophie Cole
- BioFilm Control SAS, Biopôle Clermont Limagne, Saint-Beauzire, France
| | | | - Laurent Guillier
- 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
| | - Benjamin Felix
- 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
| | | | - Michel Hébraud
- UMR MEDiS, Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne, Clermont-Ferrand, France
| | - Thierry Bernardi
- BioFilm Control SAS, Biopôle Clermont Limagne, Saint-Beauzire, France
| | - Ibrahim Sultan
- MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - Pascal Piveteau
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
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Mughini-Gras L, Kooh P, Fravalo P, Augustin JC, Guillier L, David J, Thébault A, Carlin F, Leclercq A, Jourdan-Da-Silva N, Pavio N, Villena I, Sanaa M, Watier L. Critical Orientation in the Jungle of Currently Available Methods and Types of Data for Source Attribution of Foodborne Diseases. Front Microbiol 2019; 10:2578. [PMID: 31798549 PMCID: PMC6861836 DOI: 10.3389/fmicb.2019.02578] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/24/2019] [Indexed: 12/29/2022] Open
Abstract
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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Affiliation(s)
- Lapo Mughini-Gras
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands.,Faculty of Veterinary Medicine, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
| | - Pauline Kooh
- Department of Risk Assessment, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Philippe Fravalo
- Research Chair in Meat-Safety, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | | | - Laurent Guillier
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Julie David
- Ploufragan-Plouzané Laboratory, French Agency for Food, Environmental and Occupational Health and Safety, Ploufragan, France
| | - Anne Thébault
- Department of Risk Assessment, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Frederic Carlin
- UMR 408 SQPOV "Sécurité et Qualité des Produits d'Origine Végétale" INRA, Avignon Université, Avignon, France
| | - Alexandre Leclercq
- Institut Pasteur, Biology of Infection Unit, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France
| | | | - Nicole Pavio
- Laboratory for Animal Health, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Isabelle Villena
- Laboratory of Parasitology-Mycology, EA ESCAPE, University of Reims Champagne-Ardenne, Reims, France
| | - Moez Sanaa
- Department of Risk Assessment, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Laurence Watier
- 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
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Radomski N, Cadel-Six S, Cherchame E, Felten A, Barbet P, Palma F, Mallet L, Le Hello S, Weill FX, Guillier L, Mistou MY. A Simple and Robust Statistical Method to Define Genetic Relatedness of Samples Related to Outbreaks at the Genomic Scale - Application to Retrospective Salmonella Foodborne Outbreak Investigations. Front Microbiol 2019; 10:2413. [PMID: 31708892 PMCID: PMC6821717 DOI: 10.3389/fmicb.2019.02413] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/07/2019] [Indexed: 12/21/2022] Open
Abstract
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 Salmonella Typhimurium and its monophasic variant S. 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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Affiliation(s)
- Nicolas Radomski
- ANSES, Laboratory for Food Safety, Université PARIS-EST, Maisons-Alfort, France
| | - Sabrina Cadel-Six
- ANSES, Laboratory for Food Safety, Université PARIS-EST, Maisons-Alfort, France
| | - Emeline Cherchame
- ANSES, Laboratory for Food Safety, Université PARIS-EST, Maisons-Alfort, France
| | - Arnaud Felten
- ANSES, Laboratory for Food Safety, Université PARIS-EST, Maisons-Alfort, France
| | - Pauline Barbet
- ANSES, Laboratory for Food Safety, Université PARIS-EST, Maisons-Alfort, France
| | - Federica Palma
- ANSES, Laboratory for Food Safety, Université PARIS-EST, Maisons-Alfort, France
| | - Ludovic Mallet
- ANSES, Laboratory for Food Safety, Université PARIS-EST, Maisons-Alfort, France
| | - Simon Le Hello
- Unité des Bactéries Pathogènes Entériques, Institut Pasteur, Centre National de Référence des Salmonella, Paris, France
| | - François-Xavier Weill
- Unité des Bactéries Pathogènes Entériques, Institut Pasteur, Centre National de Référence des Salmonella, Paris, France
| | - Laurent Guillier
- ANSES, Laboratory for Food Safety, Université PARIS-EST, Maisons-Alfort, France
| | - Michel-Yves Mistou
- ANSES, Laboratory for Food Safety, Université PARIS-EST, Maisons-Alfort, France
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Pernin A, Guillier L, Dubois-Brissonnet F. Inhibitory activity of phenolic acids against Listeria monocytogenes: Deciphering the mechanisms of action using three different models. Food Microbiol 2019; 80:18-24. [DOI: 10.1016/j.fm.2018.12.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/25/2018] [Accepted: 12/17/2018] [Indexed: 01/22/2023]
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41
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Duret S, Hoang HM, Derens-Bertheau E, Delahaye A, Laguerre O, Guillier L. 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; 39:906-925. [PMID: 30261117 DOI: 10.1111/risa.13199] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 08/21/2018] [Accepted: 08/24/2018] [Indexed: 06/08/2023]
Abstract
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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Affiliation(s)
- Steven Duret
- Irstea, Refrigeration Processes Engineering Research Unit, Antony cedex, France
| | - Hong-Minh Hoang
- Irstea, Refrigeration Processes Engineering Research Unit, Antony cedex, France
| | | | - Anthony Delahaye
- Irstea, Refrigeration Processes Engineering Research Unit, Antony cedex, France
| | - Onrawee Laguerre
- Irstea, Refrigeration Processes Engineering Research Unit, Antony cedex, France
| | - Laurent Guillier
- Laboratory for Food Safety, Université Paris-Est, Maisons-Alfort, France
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Painset A, Björkman JT, Kiil K, Guillier L, Mariet JF, Félix B, Amar C, Rotariu O, Roussel S, Perez-Reche F, Brisse S, Moura A, Lecuit M, Forbes K, Strachan N, Grant K, Møller-Nielsen E, Dallman TJ. 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; 5:e000257. [PMID: 30775964 PMCID: PMC6421348 DOI: 10.1099/mgen.0.000257] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 01/29/2019] [Indexed: 12/20/2022] Open
Abstract
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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Affiliation(s)
- Anaïs Painset
- Public Health England Gastrointestinal Bacteria Reference Unit, 61 Colindale Avenue, London, NW9 5EQ, UK
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections at University of Liverpool, Liverpool, UK
| | - Jonas T. Björkman
- Statens Serum Institut, 5 Artillerivej, DK-2300, Copenhagen S, Denmark
| | - Kristoffer Kiil
- Statens Serum Institut, 5 Artillerivej, DK-2300, Copenhagen S, Denmark
| | - Laurent Guillier
- 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
| | - Jean-François Mariet
- 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
| | - Benjamin Félix
- 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
| | - Corinne Amar
- Public Health England Gastrointestinal Bacteria Reference Unit, 61 Colindale Avenue, London, NW9 5EQ, UK
| | - Ovidiu Rotariu
- School of Biological Sciences, The University of Aberdeen, Cruickshank Building. St Machar Drive, Aberdeen, Scotland, AB24 3UU, UK
| | - Sophie Roussel
- 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
| | - Francisco Perez-Reche
- Institute of Complex Systems and Mathematical Biology, SUPA, School of Natural and Computing Sciences, University of Aberdeen, Aberdeen, Scotland, UK
| | | | | | | | - Ken Forbes
- School of Medicine and Dentistry, The University of Aberdeen, Foresterhill, Aberdeen, Scotland, AB25 2ZD, UK
| | - Norval Strachan
- School of Biological Sciences, The University of Aberdeen, Cruickshank Building. St Machar Drive, Aberdeen, Scotland, AB24 3UU, UK
| | - Kathie Grant
- Public Health England Gastrointestinal Bacteria Reference Unit, 61 Colindale Avenue, London, NW9 5EQ, UK
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections at University of Liverpool, Liverpool, UK
| | | | - Timothy J. Dallman
- Public Health England Gastrointestinal Bacteria Reference Unit, 61 Colindale Avenue, London, NW9 5EQ, UK
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections at University of Liverpool, Liverpool, UK
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Rollier P, Lombard B, Guillier L, François D, Romero K, Pierru S, Bouhier L, Gnanou Besse N. Validation of standard method EN ISO 11290 - Part 2 for the enumeration of Listeria monocytogenes in food. Int J Food Microbiol 2019; 288:22-31. [DOI: 10.1016/j.ijfoodmicro.2018.03.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 10/31/2017] [Accepted: 03/23/2018] [Indexed: 11/30/2022]
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Gnanou Besse N, Lombard B, Guillier L, François D, Romero K, Pierru S, Bouhier L, Rollier P. Validation of standard method EN ISO 11290 - Part 1 - Detection of Listeria monocytogenes in food. Int J Food Microbiol 2019; 288:13-21. [DOI: 10.1016/j.ijfoodmicro.2018.03.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 01/18/2018] [Accepted: 03/23/2018] [Indexed: 10/17/2022]
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Fritsch L, Felten A, Palma F, Mariet JF, Radomski N, Mistou MY, Augustin JC, Guillier L. 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 2018; 291:181-188. [PMID: 30530095 DOI: 10.1016/j.ijfoodmicro.2018.11.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 10/09/2018] [Accepted: 11/28/2018] [Indexed: 10/27/2022]
Abstract
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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Affiliation(s)
- Lena Fritsch
- French Agency for Food, Environmental and Occupational Health & Safety (Anses), Laboratory for Food Safety, Université Paris-Est, Maisons-Alfort F-94701, France
| | - Arnaud Felten
- French Agency for Food, Environmental and Occupational Health & Safety (Anses), Laboratory for Food Safety, Université Paris-Est, Maisons-Alfort F-94701, France
| | - Federica Palma
- French Agency for Food, Environmental and Occupational Health & Safety (Anses), Laboratory for Food Safety, Université Paris-Est, Maisons-Alfort F-94701, France
| | - Jean-François Mariet
- French Agency for Food, Environmental and Occupational Health & Safety (Anses), Laboratory for Food Safety, Université Paris-Est, Maisons-Alfort F-94701, France
| | - Nicolas Radomski
- French Agency for Food, Environmental and Occupational Health & Safety (Anses), Laboratory for Food Safety, Université Paris-Est, Maisons-Alfort F-94701, France
| | - Michel-Yves Mistou
- French Agency for Food, Environmental and Occupational Health & Safety (Anses), Laboratory for Food Safety, Université Paris-Est, Maisons-Alfort F-94701, France
| | - Jean-Christophe Augustin
- French Agency for Food, Environmental and Occupational Health & Safety (Anses), Laboratory for Food Safety, Université Paris-Est, Maisons-Alfort F-94701, France; Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort F-94704, France
| | - Laurent Guillier
- French Agency for Food, Environmental and Occupational Health & Safety (Anses), Laboratory for Food Safety, Université Paris-Est, Maisons-Alfort F-94701, France.
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Lebourgeois S, Fraisse A, Hennechart-Collette C, Guillier L, Perelle S, Martin-Latil S. 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; 8:335. [PMID: 30319992 PMCID: PMC6167467 DOI: 10.3389/fcimb.2018.00335] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 08/30/2018] [Indexed: 11/26/2022] Open
Abstract
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 (TCID50). 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 log10 between the concentration of HAV and the time to reach 50% of CI decrease (TCI50), 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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Affiliation(s)
- Samuel Lebourgeois
- Laboratory for Food Safety, Université Paris Est, ANSES, Maisons-Alfort, France
| | - Audrey Fraisse
- Laboratory for Food Safety, Université Paris Est, ANSES, Maisons-Alfort, France
| | | | - Laurent Guillier
- Laboratory for Food Safety, Université Paris Est, ANSES, Maisons-Alfort, France
| | - Sylvie Perelle
- Laboratory for Food Safety, Université Paris Est, ANSES, Maisons-Alfort, France
| | - Sandra Martin-Latil
- Laboratory for Food Safety, Université Paris Est, ANSES, Maisons-Alfort, France
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47
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Mughini-Gras L, Kooh P, Augustin JC, David J, Fravalo P, Guillier L, Jourdan-Da-Silva N, Thébault A, Sanaa M, Watier L. Source Attribution of Foodborne Diseases: Potentialities, Hurdles, and Future Expectations. Front Microbiol 2018; 9:1983. [PMID: 30233509 PMCID: PMC6129602 DOI: 10.3389/fmicb.2018.01983] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 08/06/2018] [Indexed: 11/21/2022] Open
Affiliation(s)
- Lapo Mughini-Gras
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands.,Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Pauline Kooh
- Risk Assessment Department, French Agency for Food, Environmental and Occupational Health & Safety (Anses), Maisons-Alfort, France
| | | | - Julie David
- Ploufragan-Plouzané Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (Anses), Ploufragan, France
| | - Philippe Fravalo
- NSERC Industrial Research Chair in Meat-Safety (CRSV), Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - Laurent Guillier
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (Anses), Maisons-Alfort, France
| | | | - Anne Thébault
- Risk Assessment Department, French Agency for Food, Environmental and Occupational Health & Safety (Anses), Maisons-Alfort, France
| | - Moez Sanaa
- Risk Assessment Department, French Agency for Food, Environmental and Occupational Health & Safety (Anses), Maisons-Alfort, France
| | - Laurence Watier
- Biostatistics, Biomathematics, Pharmacoepidemiology and Infectious Diseases (B2PHI), Inserm, UVSQ, Institut Pasteur, Université Paris-Saclay, Paris, France
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Bennour Hennekinne R, Guillier L, Fazeuilh L, Ells T, Forsythe S, Jackson E, Meheut T, Gnanou Besse N. Survival of Cronobacter in powdered infant formula and their variation in biofilm formation. Lett Appl Microbiol 2018; 66:496-505. [PMID: 29575083 DOI: 10.1111/lam.12879] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 03/01/2018] [Accepted: 03/06/2018] [Indexed: 12/24/2022]
Abstract
Cronobacter is a ubiquitous Gram-negative pathogen bacterium capable of surviving in low water activity environments, in particular powdered infant formula (PIF). Seven Cronobacter strains representing four different species (C. sakazakii, n = 4; C. malonaticus, n = 1; C. muytjensii, n = 1; C. turicensis, n = 1) were subjected to dry stress and stored in PIF at room temperature. The resulting survivor curves showed that Cronobacter sp. can survive for extended periods of at least 3 months with a significant, but moderate, variability regarding the level of resistance between species; however, no correlation was evident regarding the origin of strains. These results are evaluated with regard to other key characteristics, including genomic profiles and biofilm formation capacities of the strains. SIGNIFICANCE AND IMPACT OF THE STUDY Cronobacter can survive extended periods of at least 3 months in PIF, with moderately significant interspecific variability in desiccation resistance. Results are evaluated with regard to genomic profiles and biofilm formation capacities of the strains, and contribute to an improved understanding of the environmental persistence of Cronobacter in contaminated PIF, and subsequent risk to infant exposure.
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Affiliation(s)
| | - L Guillier
- Laboratory for Food Safety, Université Paris-Est, Anses, Maisons-Alfort, France
| | - L Fazeuilh
- Laboratory for Food Safety, Université Paris-Est, Anses, Maisons-Alfort, France
| | - T Ells
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, Kentville, NS, Canada
| | - S Forsythe
- foodmicrobe.com, Adams Hill, Keyworth, Nottingham, UK
| | - E Jackson
- Department of Biology, University of Nevada, Reno, NV, USA
| | - T Meheut
- Laboratory for Food Safety, Université Paris-Est, Anses, Maisons-Alfort, France
| | - N Gnanou Besse
- Laboratory for Food Safety, Université Paris-Est, Anses, Maisons-Alfort, France
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49
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Félix B, Feurer C, Maillet A, Guillier L, Boscher E, Kerouanton A, Denis M, Roussel S. Population Genetic Structure of Listeria monocytogenes Strains Isolated From the Pig and Pork Production Chain in France. Front Microbiol 2018; 9:684. [PMID: 29681897 PMCID: PMC5897532 DOI: 10.3389/fmicb.2018.00684] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 03/22/2018] [Indexed: 12/17/2022] Open
Abstract
Listeria monocytogenes 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 L. monocytogenes-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 L. monocytogenes strains isolated over the last 20 years in virtually all the French départements 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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Affiliation(s)
- Benjamin Félix
- 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
| | - Carole Feurer
- The French Institute for Pig and Pork Industry, IFIP, Le Rheu, France
| | - Aurelien Maillet
- 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
| | - Laurent Guillier
- 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
| | - Evelyne Boscher
- Hygiene and Quality of Poultry and Pig Products Unit, Bretagne Loire University, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Ploufragan, France
| | - Annaëlle Kerouanton
- Hygiene and Quality of Poultry and Pig Products Unit, Bretagne Loire University, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Ploufragan, France
| | - Martine Denis
- Hygiene and Quality of Poultry and Pig Products Unit, Bretagne Loire University, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Ploufragan, France
| | - Sophie Roussel
- 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
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50
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Pasquali F, Palma F, Guillier L, Lucchi A, De Cesare A, Manfreda G. Listeria monocytogenes Sequence Types 121 and 14 Repeatedly Isolated Within One Year of Sampling in a Rabbit Meat Processing Plant: Persistence and Ecophysiology. Front Microbiol 2018; 9:596. [PMID: 29662481 PMCID: PMC5890179 DOI: 10.3389/fmicb.2018.00596] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Accepted: 03/15/2018] [Indexed: 01/15/2023] Open
Abstract
Listeria monocytogenes is a foodborne pathogen adapted to survive and persist in multiple environments. Following two previous studies on prevalence and virulence of L. monocytogenes 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 L. monocytogenes 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 L. monocytogenes 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), qacH gene (resistance to benzalkonium chloride), cadA1C gene cassette (resistance to 70 mg/l of cadmium chloride) and a truncated version of actA gene (biofilm formation). Conversely, ST14 draft genomes were enriched with a full-length version of actA gene along with the Listeria Genomic Island 2 (LGI 2) including the ars operon (arsenic resistance) and the cadA4C 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 qacH 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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Affiliation(s)
- Frédérique Pasquali
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Bologna, Italy
| | - Federica Palma
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Bologna, Italy
| | - Laurent Guillier
- Laboratoire de Sécurité des Aliments, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Maisons-Alfort, France
| | - Alex Lucchi
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Bologna, Italy
| | - Alessandra De Cesare
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Bologna, Italy
| | - Gerardo Manfreda
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Bologna, Italy
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