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Salamandane A, Leech J, Almeida R, Silva C, Crispie F, Cotter PD, Malfeito-Ferreira M, Brito L. Metagenomic analysis of the bacterial microbiome, resistome and virulome distinguishes Portuguese Serra da Estrela PDO cheeses from similar non-PDO cheeses: An exploratory approach. Food Res Int 2024; 189:114556. [PMID: 38876593 DOI: 10.1016/j.foodres.2024.114556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/16/2024] [Accepted: 05/26/2024] [Indexed: 06/16/2024]
Abstract
This study aimed to evaluate the microbiome, resistome and virulome of two types of Portuguese cheese using high throughput sequencing (HTS). Culture-dependent chromogenic methods were also used for certain groups/microorganisms. Eight samples of raw ewe's milk cheese were obtained from four producers: two producers with cheeses with a PDO (Protected Designation of Origin) label and the other two producers with cheeses without a PDO label. Agar-based culture methods were used to quantify total mesophiles, Enterobacteriaceae, Escherichia coli, Staphylococcus, Enterococcus and lactic acid bacteria. The presence of Listeria monocytogenes and Salmonella was also investigated. The selected isolates were identified by 16S rRNA gene sequencing and evaluated to determine antibiotic resistance and the presence of virulence genes. The eight cheese samples analyzed broadly complied with EC regulations in terms of the microbiological safety criteria. The HTS results demonstrated that Leuconostoc mesenteroides, Lactococcus lactis, Lactobacillus plantarum, Lacticaseibacillus rhamnosus, Enterococcus durans and Lactobacillus coryniformis were the most prevalent bacterial species in cheeses. The composition of the bacterial community varied, not only between PDO and non-PDO cheeses, but also between producers, particularly between the two non-PDO cheeses. Alpha-diversity analyses showed that PDO cheeses had greater bacterial diversity than non-PDO cheeses, demonstrating that the diversity of spontaneously fermented foods is significantly higher in cheeses produced without the addition of food preservatives and dairy ferments. Despite complying with microbiological regulations, both PDO and non-PDO cheeses harbored potential virulence genes as well as antibiotic resistance genes. However, PDO cheeses exhibited fewer of these virulence and antibiotic resistance genes compared to non-PDO cheeses. Therefore, the combination of conventional microbiological methods and the metagenomic approach could contribute to improving the attribution of the PDO label to this type of cheese.
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Affiliation(s)
- Acácio Salamandane
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal; Faculdade de Ciências de Saúde, Universidade Lúrio, Campus Universitário de Marrere, Nampula 4250, Mozambique
| | - John Leech
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
| | - Rita Almeida
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Carolina Silva
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Fiona Crispie
- Teagasc Food Research Centre, Fermoy, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Fermoy, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland; VistaMilk, Ireland
| | - Manuel Malfeito-Ferreira
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Luísa Brito
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal.
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Aizpurua O, Dunn RR, Hansen LH, Gilbert MTP, Alberdi A. Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data. Crit Rev Biotechnol 2023:1-19. [PMID: 37731336 DOI: 10.1080/07388551.2023.2254933] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/27/2023] [Indexed: 09/22/2023]
Abstract
Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.
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Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - M T P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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Tast Lahti E, Karamehmedovic N, Riedel H, Blom L, Boel J, Delibato E, Denis M, van Essen-Zandbergen A, Garcia-Fernandez A, Hendriksen R, Heydecke A, van Hoek AHAM, Huby T, Kwit R, Lucarelli C, Lundin K, Michelacci V, Owczarek S, Ring I, Sejer Kjeldgaard J, Sjögren I, Skóra M, Torpdahl M, Ugarte-Ruiz M, Veldman K, Ventola E, Zajac M, Jernberg C. One Health surveillance-A cross-sectoral detection, characterization, and notification of foodborne pathogens. Front Public Health 2023; 11:1129083. [PMID: 36969662 PMCID: PMC10034719 DOI: 10.3389/fpubh.2023.1129083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/16/2023] [Indexed: 03/29/2023] Open
Abstract
Introduction Several Proficiency Test (PT) or External Quality Assessment (EQA) schemes are currently available for assessing the ability of laboratories to detect and characterize enteropathogenic bacteria, but they are usually targeting one sector, covering either public health, food safety or animal health. In addition to sector-specific PTs/EQAs for detection, cross-sectoral panels would be useful for assessment of the capacity to detect and characterize foodborne pathogens in a One Health (OH) perspective and further improving food safety and interpretation of cross-sectoral surveillance data. The aims of the study were to assess the cross-sectoral capability of European public health, animal health and food safety laboratories to detect, characterize and notify findings of the foodborne pathogens Campylobacter spp., Salmonella spp. and Yersinia enterocolitica, and to develop recommendations for future cross-sectoral PTs and EQAs within OH. The PT/EQA scheme developed within this study consisted of a test panel of five samples, designed to represent a theoretical outbreak scenario. Methods A total of 15 laboratories from animal health, public health and food safety sectors were enrolled in eight countries: Denmark, France, Italy, the Netherlands, Poland, Spain, Sweden, and the United Kingdom. The laboratories analyzed the samples according to the methods used in the laboratory and reported the target organisms at species level, and if applicable, serovar for Salmonella and bioserotype for Yersinia. Results All 15 laboratories analyzed the samples for Salmonella, 13 for Campylobacter and 11 for Yersinia. Analytical errors were predominately false negative results. One sample (S. Stockholm and Y. enterocolitica O:3/BT4) with lower concentrations of target organisms was especially challenging, resulting in six out of seven false negative results. These findings were associated with laboratories using smaller sample sizes and not using enrichment methods. Detection of Salmonella was most commonly mandatory to notify within the three sectors in the eight countries participating in the pilot whereas findings of Campylobacter and Y. enterocolitica were notifiable from human samples, but less commonly from animal and food samples. Discussion The results of the pilot PT/EQA conducted in this study confirmed the possibility to apply a cross-sectoral approach for assessment of the joint OH capacity to detect and characterize foodborne pathogens.
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Affiliation(s)
- Elina Tast Lahti
- Department of Epidemiology and Disease Control, National Veterinary Institute (SVA), Uppsala, Sweden
- *Correspondence: Elina Tast Lahti
| | | | - Hilde Riedel
- Department of Biology, Swedish Food Agency, Uppsala, Sweden
| | - Linnea Blom
- Department of Biology, Swedish Food Agency, Uppsala, Sweden
| | - Jeppe Boel
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut (SSI), Copenhagen, Denmark
| | - Elisabetta Delibato
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Martine Denis
- Research Unit of Hygiene and Quality of Poultry and Pork Products, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Ploufragan, France
| | - Alieda van Essen-Zandbergen
- Department of Bacteriology, Host-Pathogen Interaction, and Diagnostics Development, Wageningen Bioveterinary Research (WBVR) Part of Wageningen University and Research (WUR), Lelystad, Netherlands
| | | | - Rene Hendriksen
- Technical University of Denmark, The National Food Institute (DTU Food), Copenhagen, Denmark
| | - Anna Heydecke
- Center for Research and Development, Uppsala University/Region Gävleborg, Gävle, Sweden
| | - Angela H. A. M. van Hoek
- Centre for Infectious Disease Control (Department Zoonoses and Environmental Microbiology), Dutch National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Tom Huby
- Animal and Plant Health Agency (APHA), Weybridge, United Kingdom
| | - Renata Kwit
- Department of Microbiology, National Veterinary Research Institute (PIWet), Pulawy, Poland
| | - Claudia Lucarelli
- Department of Infectious Diseases, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Karl Lundin
- Clinical Microbiology, Uppsala University Hospital, Uppsala, Sweden
| | - Valeria Michelacci
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Slawomir Owczarek
- Department of Infectious Diseases, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Isaac Ring
- Animal and Plant Health Agency (APHA), Weybridge, United Kingdom
| | - Jette Sejer Kjeldgaard
- Technical University of Denmark, The National Food Institute (DTU Food), Copenhagen, Denmark
| | | | - Milena Skóra
- Department of Microbiology, National Veterinary Research Institute (PIWet), Pulawy, Poland
| | - Mia Torpdahl
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut (SSI), Copenhagen, Denmark
| | - María Ugarte-Ruiz
- VISAVET Health Surveillance Centre, Universidad Complutense Madrid, Madrid, Spain
| | - Kees Veldman
- Department of Bacteriology, Host-Pathogen Interaction, and Diagnostics Development, Wageningen Bioveterinary Research (WBVR) Part of Wageningen University and Research (WUR), Lelystad, Netherlands
| | - Eleonora Ventola
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Magdalena Zajac
- Department of Microbiology, National Veterinary Research Institute (PIWet), Pulawy, Poland
| | - Cecilia Jernberg
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
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Buytaers FE, Saltykova A, Mattheus W, Verhaegen B, Roosens NHC, Vanneste K, Laisnez V, Hammami N, Pochet B, Cantaert V, Marchal K, Denayer S, De Keersmaecker SC. Application of a strain-level shotgun metagenomics approach on food samples: resolution of the source of a Salmonella food-borne outbreak. Microb Genom 2021; 7:000547. [PMID: 33826490 PMCID: PMC8208685 DOI: 10.1099/mgen.0.000547] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 02/23/2021] [Indexed: 02/04/2023] Open
Abstract
Food-borne outbreak investigation currently relies on the time-consuming and challenging bacterial isolation from food, to be able to link food-derived strains to more easily obtained isolates from infected people. When no food isolate can be obtained, the source of the outbreak cannot be unambiguously determined. Shotgun metagenomics approaches applied to the food samples could circumvent this need for isolation from the suspected source, but require downstream strain-level data analysis to be able to accurately link to the human isolate. Until now, this approach has not yet been applied outside research settings to analyse real food-borne outbreak samples. In September 2019, a Salmonella outbreak occurred in a hotel school in Bruges, Belgium, affecting over 200 students and teachers. Following standard procedures, the Belgian National Reference Center for human salmonellosis and the National Reference Laboratory for Salmonella in food and feed used conventional analysis based on isolation, serotyping and MLVA (multilocus variable number tandem repeat analysis) comparison, followed by whole-genome sequencing, to confirm the source of the contamination over 2 weeks after receipt of the sample, which was freshly prepared tartar sauce in a meal cooked at the school. Our team used this outbreak as a case study to deliver a proof of concept for a short-read strain-level shotgun metagenomics approach for source tracking. We received two suspect food samples: the full meal and some freshly made tartar sauce served with this meal, requiring the use of raw eggs. After analysis, we could prove, without isolation, that Salmonella was present in both samples, and we obtained an inferred genome of a Salmonella enterica subsp. enterica serovar Enteritidis that could be linked back to the human isolates of the outbreak in a phylogenetic tree. These metagenomics-derived outbreak strains were separated from sporadic cases as well as from another outbreak circulating in Europe at the same time period. This is, to our knowledge, the first Salmonella food-borne outbreak investigation uniquely linking the food source using a metagenomics approach and this in a fast time frame.
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Affiliation(s)
- Florence E. Buytaers
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Assia Saltykova
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Wesley Mattheus
- National Reference Center for Salmonella and Shigella spp., Sciensano, Brussels, Belgium
| | - Bavo Verhaegen
- National Reference Laboratory for Salmonella and Food-Borne Infections, Food-Borne Pathogens, Sciensano, Brussels, Belgium
| | | | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | - Brigitte Pochet
- Federal Agency for the Security of the Food Chain, Brussels, Belgium
| | - Vera Cantaert
- Federal Agency for the Security of the Food Chain, Brussels, Belgium
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Information Technology, IDlab, IMEC, Ghent University, Ghent, Belgium
- Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Sarah Denayer
- National Reference Laboratory for Salmonella and Food-Borne Infections, Food-Borne Pathogens, Sciensano, Brussels, Belgium
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