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Nouws S, Verhaegen B, Denayer S, Crombé F, Piérard D, Bogaerts B, Vanneste K, Marchal K, Roosens NHC, De Keersmaecker SCJ. Transforming Shiga toxin-producing Escherichia coli surveillance through whole genome sequencing in food safety practices. Front Microbiol 2023; 14:1204630. [PMID: 37520372 PMCID: PMC10381951 DOI: 10.3389/fmicb.2023.1204630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/22/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction Shiga toxin-producing Escherichia coli (STEC) is a gastrointestinal pathogen causing foodborne outbreaks. Whole Genome Sequencing (WGS) in STEC surveillance holds promise in outbreak prevention and confinement, in broadening STEC epidemiology and in contributing to risk assessment and source attribution. However, despite international recommendations, WGS is often restricted to assist outbreak investigation and is not yet fully implemented in food safety surveillance across all European countries, in contrast to for example in the United States. Methods In this study, WGS was retrospectively applied to isolates collected within the context of Belgian food safety surveillance and combined with data from clinical isolates to evaluate its benefits. A cross-sector WGS-based collection of 754 strains from 1998 to 2020 was analyzed. Results We confirmed that WGS in food safety surveillance allows accurate detection of genomic relationships between human cases and strains isolated from food samples, including those dispersed over time and geographical locations. Identifying these links can reveal new insights into outbreaks and direct epidemiological investigations to facilitate outbreak management. Complete WGS-based isolate characterization enabled expanding epidemiological insights related to circulating serotypes, virulence genes and antimicrobial resistance across different reservoirs. Moreover, associations between virulence genes and severe disease were determined by incorporating human metadata into the data analysis. Gaps in the surveillance system were identified and suggestions for optimization related to sample centralization, harmonizing isolation methods, and expanding sampling strategies were formulated. Discussion This study contributes to developing a representative WGS-based collection of circulating STEC strains and by illustrating its benefits, it aims to incite policymakers to support WGS uptake in food safety surveillance.
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Affiliation(s)
- Stéphanie Nouws
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
- IDlab, Department of Information Technology, Ghent University—IMEC, Ghent, Belgium
| | - Bavo Verhaegen
- National Reference Laboratory for Shiga Toxin-Producing Escherichia coli (NRL STEC) and for Foodborne Outbreaks (NRL FBO), Foodborne Pathogens, Sciensano, Brussels, Belgium
| | - Sarah Denayer
- National Reference Laboratory for Shiga Toxin-Producing Escherichia coli (NRL STEC) and for Foodborne Outbreaks (NRL FBO), Foodborne Pathogens, Sciensano, Brussels, Belgium
| | - Florence Crombé
- National Reference Centre for Shiga Toxin-Producing Escherichia coli (NRC STEC), Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Denis Piérard
- National Reference Centre for Shiga Toxin-Producing Escherichia coli (NRC STEC), Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Bert Bogaerts
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kathleen Marchal
- IDlab, Department of Information Technology, Ghent University—IMEC, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
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Rocha R, Couto N, Pinto RP, Vaz-Velho M, Fernandes P, Santos J. Microbiological Characterization of Protected Designation of Origin Serra da Estrela Cheese. Foods 2023; 12:foods12102008. [PMID: 37238829 DOI: 10.3390/foods12102008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/29/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Serra da Estrela is the oldest and most recognizable traditional protected designation of origin (PDO) cheese from Portugal. It has been extensively studied over the years, but the latest microbial characterization is 20 years old. Hence, this work aimed to perform an updated characterization of Serra da Estrela PDO cheeses and raw materials. Our analysis showed that lactic acid bacteria content on Serra da Estrela cheeses exceeded 8.8 log CFUsg-1, in all analyzed samples, with lactococci, lactobacilli and Leuconostoc spp. predominating over enterococci strains. Moreover, lactococci and lactobacilli abundance increased across the production season, while enterococci dropped considerably in late manufactures. Lastly, Leuconostoc spp. content remained unchanged in all analyzed periods. A correspondence analysis showed that L. paracasei, L. lactis, E. durans, E. faecium and L. mesenteroides are transversal in Serra da Estrela cheese manufacturing and were closely associated with milk, curd and cheese matrices. Additionally, L. casei, L. plantarum and L. curvatus were specifically associated with cheese matrices, possibly active during ripening and contributing for the development of these cheeses' organoleptic characteristics.
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Affiliation(s)
- Rui Rocha
- CISAS-Center for Research and Development in Agrifood Systems and Sustainability, Instituto Politécnico de Viana do Castelo, Rua Escola Industrial e Comercial de Nun'Álvares, 4900-347 Viana do Castelo, Portugal
| | - Nélson Couto
- Escola Superior de Tecnologia e Gestão, Instituto Politécnico de Viana do Castelo, Avenida do Atlântico no. 644, 4900-348 Viana do Castelo, Portugal
| | - Ricardo Pereira Pinto
- CISAS-Center for Research and Development in Agrifood Systems and Sustainability, Instituto Politécnico de Viana do Castelo, Rua Escola Industrial e Comercial de Nun'Álvares, 4900-347 Viana do Castelo, Portugal
| | - Manuela Vaz-Velho
- CISAS-Center for Research and Development in Agrifood Systems and Sustainability, Instituto Politécnico de Viana do Castelo, Rua Escola Industrial e Comercial de Nun'Álvares, 4900-347 Viana do Castelo, Portugal
- Escola Superior de Tecnologia e Gestão, Instituto Politécnico de Viana do Castelo, Avenida do Atlântico no. 644, 4900-348 Viana do Castelo, Portugal
| | - Paulo Fernandes
- CISAS-Center for Research and Development in Agrifood Systems and Sustainability, Instituto Politécnico de Viana do Castelo, Rua Escola Industrial e Comercial de Nun'Álvares, 4900-347 Viana do Castelo, Portugal
- Escola Superior de Tecnologia e Gestão, Instituto Politécnico de Viana do Castelo, Avenida do Atlântico no. 644, 4900-348 Viana do Castelo, Portugal
| | - Joana Santos
- CISAS-Center for Research and Development in Agrifood Systems and Sustainability, Instituto Politécnico de Viana do Castelo, Rua Escola Industrial e Comercial de Nun'Álvares, 4900-347 Viana do Castelo, Portugal
- Escola Superior de Tecnologia e Gestão, Instituto Politécnico de Viana do Castelo, Avenida do Atlântico no. 644, 4900-348 Viana do Castelo, Portugal
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Microbial risk assessment of Escherichia coli shiga-toxin producers (STEC) in raw sheep's milk cheeses in Italy. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108951] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Outbreak of STEC O157:H7 linked to a milk pasteurisation failure at a dairy farm in England, 2019. Epidemiol Infect 2022; 150:e114. [PMID: 35581924 PMCID: PMC9252982 DOI: 10.1017/s0950268822000929] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In November 2019, an outbreak of Shiga toxin-producing Escherichia coli O157:H7 was detected in South Yorkshire, England. Initial investigations established consumption of milk from a local dairy as a common exposure. A sample of pasteurised milk tested the next day failed the phosphatase test, indicating contamination of the pasteurised milk by unpasteurised (raw) milk. The dairy owner agreed to immediately cease production and initiate a recall. Inspection of the pasteuriser revealed a damaged seal on the flow divert valve. Ultimately, there were 21 confirmed cases linked to the outbreak, of which 11 (52%) were female, and 12/21 (57%) were either <15 or >65 years of age. Twelve (57%) patients were treated in hospital, and three cases developed haemolytic uraemic syndrome. Although the outbreak strain was not detected in the milk samples, it was detected in faecal samples from the cattle on the farm. Outbreaks of gastrointestinal disease caused by milk pasteurisation failures are rare in the UK. However, such outbreaks are a major public health concern as, unlike unpasteurised milk, pasteurised milk is marketed as ‘safe to drink’ and sold to a larger, and more dispersed, population. The rapid, co-ordinated multi-agency investigation initiated in response to this outbreak undoubtedly prevented further cases.
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Bisht A, Kamble MP, Choudhary P, Chaturvedi K, Kohli G, Juneja VK, Sehgal S, Taneja NK. A surveillance of food borne disease outbreaks in India: 2009–2018. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107630] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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McLauchlin J, Aird H, Elliott A, Forester E, Jørgensen F, Willis C. Microbiological quality of raw drinking milk and unpasteurised dairy products: results from England 2013-2019. Epidemiol Infect 2020; 148:e135. [PMID: 32406346 PMCID: PMC7374804 DOI: 10.1017/s0950268820001016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 03/21/2020] [Accepted: 05/11/2020] [Indexed: 11/06/2022] Open
Abstract
The aim of this study was to review microbiology results from testing >2500 raw drinking milk and dairy products made with unpasteurised milk examined in England between 2013 and 2019. Samples were collected as part of incidents of contamination, investigation of infections or as part of routine monitoring and were tested using standard methods for a range of both pathogens and hygiene indicators. Results from testing samples of raw cow's milk or cheese made from unpasteurised milk for routine monitoring purposes were overall of better microbiological quality than those collected during incident or investigations of infections. Results from routine monitoring were satisfactory for 62% of milks, 82% of cream, 100% of ice-cream, 51% of butter, 63% of kefir and 79% of cheeses, with 5% of all samples being considered potentially hazardous. Analysis of data from cheese demonstrated a significant association between increasing levels of indicator Escherichia coli with elevated levels of coagulase positive staphylococci and decreased probability of isolation of Shiga toxin-producing E. coli. These data highlight the public health risk associated with these products and provide further justification for controls applied to raw drinking milk and dairy products made with unpasteurised milk.
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Affiliation(s)
- J. McLauchlin
- Public Health England, National Infection Service, Food Water and Environmental Microbiology Services, Colindale, London, UK
| | - H. Aird
- Public Health England, National Infection Service, Food Water and Environmental Microbiology Laboratory York, National Agri-Food Innovation Campus, York, UK
| | - A. Elliott
- Public Health England, National Infection Service, Food Water and Environmental Microbiology Laboratory Porton, Porton Down, Salisbury, UK
- Public Health England, National Infection Service, Field Services, South West, Bristol, UK
| | - E. Forester
- Public Health England, National Infection Service, Food Water and Environmental Microbiology Laboratory York, National Agri-Food Innovation Campus, York, UK
- Public Health England, National Infection Service, Field Services, North West Office, Liverpool, UK
| | - F. Jørgensen
- Public Health England, National Infection Service, Food Water and Environmental Microbiology Laboratory Porton, Porton Down, Salisbury, UK
| | - C. Willis
- Public Health England, National Infection Service, Food Water and Environmental Microbiology Laboratory Porton, Porton Down, Salisbury, UK
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Jenkins C, Monteiro Pires S, Morabito S, Niskanen T, Scheutz F, da Silva Felício MT, Messens W, Bolton D. Pathogenicity assessment of Shiga toxin‐producing Escherichia coli (STEC) and the public health risk posed by contamination of food with STEC. EFSA J 2020. [DOI: 10.2903/j.efsa.2020.5967] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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