scholarly journals A Practical Method to Implement Strain-Level Metagenomics-Based Foodborne Outbreak Investigation and Source Tracking in Routine

2020 ◽  
Vol 8 (8) ◽  
pp. 1191
Author(s):  
Florence E. Buytaers ◽  
Assia Saltykova ◽  
Sarah Denayer ◽  
Bavo Verhaegen ◽  
Kevin Vanneste ◽  
...  
Keyword(s):  
Food Product ◽  
Practical Method ◽  
Outbreak Investigation ◽  
Source Tracking ◽  
Foodborne Outbreak ◽  
Accurate Identification ◽  
Shotgun Metagenomics ◽  
Chain Reactions ◽  
Food Isolate ◽  
Food Matrices

The management of a foodborne outbreak depends on the rapid and accurate identification of the responsible food source. Conventional methods based on isolation of the pathogen from the food matrix and target-specific real-time polymerase chain reactions (qPCRs) are used in routine. In recent years, the use of whole genome sequencing (WGS) of bacterial isolates has proven its value to collect relevant information for strain characterization as well as tracing the origin of the contamination by linking the food isolate with the patient’s isolate with high resolution. However, the isolation of a bacterial pathogen from food matrices is often time-consuming and not always successful. Therefore, we aimed to improve outbreak investigation by developing a method that can be implemented in reference laboratories to characterize the pathogen in the food vehicle without its prior isolation and link it back to human cases. We tested and validated a shotgun metagenomics approach by spiking food pathogens in specific food matrices using the Shiga toxin-producing Escherichia coli (STEC) as a case study. Different DNA extraction kits and enrichment procedures were investigated to obtain the most practical workflow. We demonstrated the feasibility of shotgun metagenomics to obtain the same information as in ISO/TS 13136:2012 and WGS of the isolate in parallel by inferring the genome of the contaminant and characterizing it in a shorter timeframe. This was achieved in food samples containing different E. coli strains, including a combination of different STEC strains. For the first time, we also managed to link individual strains from a food product to isolates from human cases, demonstrating the power of shotgun metagenomics for rapid outbreak investigation and source tracking.

scholarly journals Application of a strain-level shotgun metagenomics approach on food samples: resolution of the source of a Salmonella food-borne outbreak

2021 ◽  
Vol 7 (4) ◽  
Author(s):  
Florence E. Buytaers ◽  
Assia Saltykova ◽  
Wesley Mattheus ◽  
Bavo Verhaegen ◽  
Nancy H. C. Roosens ◽  
...  
Keyword(s):  
Food Samples ◽  
Strain Level ◽  
Outbreak Investigation ◽  
Reference Laboratory ◽  
Shotgun Metagenomics ◽  
Content Type ◽  
National Reference ◽  
Link Type ◽  
Food Borne ◽  
Food Isolate

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.

scholarly journals Whole Genome Sequencing Provides an Added Value to the Investigation of Staphylococcal Food Poisoning Outbreaks

2021 ◽  
Vol 12 ◽  
Author(s):  
Stéphanie Nouws ◽  
Bert Bogaerts ◽  
Bavo Verhaegen ◽  
Sarah Denayer ◽  
Lasse Laeremans ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Protein A ◽  
Food Poisoning ◽  
Gene Profiling ◽  
Added Value ◽  
Outbreak Investigation ◽  
Whole Genome ◽  
Foodborne Outbreak ◽  
Chain Reactions

Through staphylococcal enterotoxin (SE) production, Staphylococcus aureus is a common cause of food poisoning. Detection of staphylococcal food poisoning (SFP) is mostly performed using immunoassays, which, however, only detect five of 27 SEs described to date. Polymerase chain reactions are, therefore, frequently used in complement to identify a bigger arsenal of SE at the gene level (se) but are labor-intensive. Complete se profiling of isolates from different sources, i.e., food and human cases, is, however, important to provide an indication of their potential link within foodborne outbreak investigation. In addition to complete se gene profiling, relatedness between isolates is determined with more certainty using pulsed-field gel electrophoresis, Staphylococcus protein A gene typing and other methods, but these are shown to lack resolution. We evaluated how whole genome sequencing (WGS) can offer a solution to these shortcomings. By WGS analysis of a selection of S. aureus isolates, including some belonging to a confirmed foodborne outbreak, its added value as the ultimate multiplexing method was demonstrated. In contrast to PCR-based se gene detection for which primers are sometimes shown to be non-specific, WGS enabled complete se gene profiling with high performance, provided that a database containing reference sequences for all se genes was constructed and employed. The custom compiled database and applied parameters were made publicly available in an online user-friendly interface. As an all-in-one approach with high resolution, WGS additionally allowed inferring correct isolate relationships. The different DNA extraction kits that were tested affected neither se gene profiling nor relatedness determination, which is interesting for data sharing during SFP outbreak investigation. Although confirming the production of enterotoxins remains important for SFP investigation, we delivered a proof-of-concept that WGS is a valid alternative and/or complementary tool for outbreak investigation.

VALIDITY OF FOOD CONSUMPTION HISTORIES IN A FOODBORNE OUTBREAK INVESTIGATION

1986 ◽  
Vol 124 (5) ◽  
pp. 859-863 ◽  
Author(s):  
MICHAEL D. DECKER ◽  
ANITA L. BOOTH ◽  
MARY JANE DEWEY ◽  
R. STEVE FRICKER ◽  
ROBERT H. HUTCHESON ◽  
...  
Keyword(s):  
Food Consumption ◽  
Outbreak Investigation ◽  
Foodborne Outbreak

Bioaccessibility of Anthocyanins on in vitro Digestion Mmodels: Factors Implicated and Role in Functional Foods Development

2021 ◽  
Vol 28 ◽  
Author(s):  
Gabriel Prado ◽  
Isidora Pierattini ◽  
Guiselle Villarroel ◽  
Fernanda Fuentes ◽  
Alejandra Silva ◽  
...  
Keyword(s):  
Functional Foods ◽  
Raw Materials ◽  
Food Product ◽  
In Vitro Digestion ◽  
Raw Material ◽  
Simulated Digestion ◽  
Prevalence Of Obesity ◽  
Food Matrices

Background: Worldwide, the prevalence of obesity and related non-communicable chronic diseases is high and continues to grow. In that sense, anthocyanins (ANC) have shown beneficial health effects in preventing obesity and metabolic risk factors. Moreover, the demand for functional foods incorporating these compounds has risen significantly in the past years. Thus, there is a need for validations of the functional properties of these formulations; nevertheless, in vivo assays are complex and require a lot of resources. One approach for estimating bioactive compounds' functionality and health benefits is to evaluate their bioaccessibility on a specific food matrix, determined by various factors. This article aims to review different factors influencing the bioaccessibility of ANC evaluated on in vitro digestion models as a functionality parameter, elucidating the effect of chemical composition, raw materials, food matrices, and vehicles for the delivery of ANC. Methods: Study searches were performed using PubMed, Web of Science, Scopus, and Science Direct databases. Results: Different factors influenced bioaccessibility and stability of ANC studied by in vitro digestion which are: i) the raw material used for ANC obtention; ii) food processing; iii) other food components; iv) the extraction method and solvents used; v) the structure of ANC; vi) delivery system (e.g., microencapsulation); vii) pH of the medium; viii) the digestion stage. Conclusion: Simulated digestion systems allow to determine free or encapsulated ANC bioaccessibility in different food matrices, which offers advantages in determining the potential functionality of a food product.

scholarly journals Analytical and Sample Preparation Techniques for the Determination of Food Colorants in Food Matrices

Foods ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 58 ◽  
Author(s):  
Konstantina Ntrallou ◽  
Helen Gika ◽  
Emmanouil Tsochatzis
Keyword(s):  
Sample Preparation ◽  
Food Industry ◽  
Analytical Techniques ◽  
Food Product ◽  
Food Matrix ◽  
Nutritional Properties ◽  
Food Colorants ◽  
Food Matrices ◽  
Preparation Techniques

Color additives are widely used by the food industry to enhance the appearance, as well as the nutritional properties of a food product. However, some of these substances may pose a potential risk to human health, especially if they are consumed excessively and are regulated, giving great importance to their determination. Several matrix-dependent methods have been developed and applied to determine food colorants, by employing different analytical techniques along with appropriate sample preparation protocols. Major techniques applied for their determination are chromatography with spectophotometricdetectors and spectrophotometry, while sample preparation procedures greatly depend on the food matrix. In this review these methods are presented, covering the advancements of existing methodologies applied over the last decade.

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