Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Buytaers FE

PROVIDER: S-EPMC7463776 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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

Buytaers Florence E FE Saltykova Assia A Denayer Sarah S Verhaegen Bavo B Vanneste Kevin K Roosens Nancy H C NHC Piérard Denis D Marchal Kathleen K De Keersmaecker Sigrid C J SCJ

Microorganisms 20200805 8

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 li ...[more]

PMID: 32764329

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Project description:This Opinion considers the application of whole genome sequencing (WGS) and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne pathogens. WGS offers the highest level of bacterial strain discrimination for food-borne outbreak investigation and source-attribution as well as potential for more precise hazard identification, thereby facilitating more targeted risk assessment and risk management. WGS improves linking of sporadic cases associated with different food products and geographical regions to a point source outbreak and can facilitate epidemiological investigations, allowing also the use of previously sequenced genomes. Source attribution may be favoured by improved identification of transmission pathways, through the integration of spatial-temporal factors and the detection of multidirectional transmission and pathogen-host interactions. Metagenomics has potential, especially in relation to the detection and characterisation of non-culturable, difficult-to-culture or slow-growing microorganisms, for tracking of hazard-related genetic determinants and the dynamic evaluation of the composition and functionality of complex microbial communities. A SWOT analysis is provided on the use of WGS and metagenomics for Salmonella and Shigatoxin-producing Escherichia coli (STEC) serotyping and the identification of antimicrobial resistance determinants in bacteria. Close agreement between phenotypic and WGS-based genotyping data has been observed. WGS provides additional information on the nature and localisation of antimicrobial resistance determinants and on their dissemination potential by horizontal gene transfer, as well as on genes relating to virulence and biological fitness. Interoperable data will play a major role in the future use of WGS and metagenomic data. Capacity building based on harmonised, quality controlled operational systems within European laboratories and worldwide is essential for the investigation of cross-border outbreaks and for the development of international standardised risk assessments of food-borne microorganisms.

Project description:UNLABELLED:Human norovirus (NoV) is the most frequent cause of epidemic nonbacterial acute gastroenteritis worldwide. We investigated the impact of nonthermal or cold atmospheric pressure plasma (CAPP) on the inactivation of a clinical human outbreak NoV, GII.4. Three different dilutions of a NoV-positive stool sample were prepared and subsequently treated with CAPP for various lengths of time, up to 15 min. NoV viral loads were quantified by quantitative real-time reverse transcription PCR (RT-qPCR). Increased CAPP treatment time led to increased NoV reduction; samples treated for the longest time had the lowest viral load. From the initial starting quantity of 2.36 × 10(4) genomic equivalents/ml, sample exposure to CAPP reduced this value by 1.23 log10 and 1.69 log10 genomic equivalents/ml after 10 and 15 min, respectively (P < 0.01). CAPP treatment of surfaces carrying a lower viral load reduced NoV by at least 1 log10 after CAPP exposure for 2 min (P < 0.05) and 1 min (P < 0.05), respectively. Our results suggest that NoV can be inactivated by CAPP treatment. The lack of cell culture assays prevents our ability to estimate infectivity. It is possible that some detectable, intact virus particles were rendered noninfectious. We conclude that CAPP treatment of surfaces may be a useful strategy to reduce the risk of NoV transmission in crowded environments. IMPORTANCE:Human gastroenteritis is most frequently caused by noroviruses, which are spread person to person and via surfaces, often in facilities with crowds of people. Disinfection of surfaces that come into contact with infected humans is critical for the prevention of cross-contamination and further transmission of the virus. However, effective disinfection cannot be done easily in mass catering environments or health care facilities. We evaluated the efficacy of cold atmospheric pressure plasma, an innovative airborne disinfection method, on surfaces inoculated with norovirus. We used a clinically relevant strain of norovirus from an outbreak in Germany. Cold plasma was able to inactivate the virus on the tested surfaces, suggesting that this method could be used for continuous disinfection of contaminated surfaces. The use of a clinical strain of norovirus strengthens the reliability of our results as it is a strain relevant to outbreaks in humans.

Project description: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.

Project description:BACKGROUND:On June 18, 2017, the public health service was alerted about 43 students in the training institute in Rabat who were admitted to the emergency room for acute gastroenteritis following the uptake of a meal a day before. OBJECTIVE:This study aimed to investigate the foodborne disease outbreak by confirming the outbreak, identifying the source of contamination, and recommending control measures. METHODS:We conducted a case-control study. Cases and controls were selected in a ratio of 1:1. We defined a case as any member of the training institute who attended the Ramadan buffet in the institute's restaurant and who had presented, in the weekend of June 16 to 20, 2017, symptoms of diarrhea or vomiting with at least one of the following signs: abdominal pain, fever, headache, nausea, and dizziness. A control was defined as anyone who attended the Ramadan buffet in the institute's restaurant but had not presented any symptoms from June 16 to 20, 2017. We conducted a bivariate and multivariable analysis. Stools of ill students were collected, and a food specimen was collected for bacterial testing. RESULTS:A total of 50 cases and 50 controls were selected. Among the cases, males were predominant (43/50, 86%); the median age was 21 years. A total of 47 cases sought medical care. There were no hospitalizations and no deaths. The episode was short with an estimated average incubation period of 9 hours. The epidemic curve oriented toward a common source of contamination. Among food items, briwates were strongly associated with the illness with an odd ratio of 14.23 (95% CI 5.04-40.04; P<.001). Laboratory testing of briwates showed presence of Escherichia coli O157 and Staphylococcus aureus. CONCLUSIONS:This foodborne disease outbreak was likely caused by briwates that was contaminated with S aureus and E coli. We recommended strengthening hygiene measures. Food handling techniques should be taught as part of continuous professional development for food handlers.

Dataset Information

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

Publications

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

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