Analysis of frozen strawberries involved in a large norovirus gastroenteritis outbreak using next generation sequencing and digital PCR

Bartsch, Christina; Höper, Dirk W.; Mäde, Dietrich; Johne, Reimar

doi:10.1016/j.fm.2018.06.019

Cited by 50 publications

(35 citation statements)

References 32 publications

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“…In addition, there are methods for detecting counterfeit honey, which can be used to analyze plant, geographical and insect sources [59,60], and to identify different animal species in meat [61,62], fish [63,64], and dairy products [65]. Other NGS applications focus on the analysis of microorganisms for pathogenic reasons, such as the detection of noroviruses [66] or Salmonella [67,68], but also due to their technological influences, for example during fermentation processes [69,70].…”

Section: Genomics-based Methodsmentioning

confidence: 99%

Food authentication in real life: How to link nontargeted approaches with routine analytics?

Creydt¹,

Fischer²

2020

Electrophoresis

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In times of increasing globalization and the resulting complexity of trade flows, securing food quality is an increasing challenge. The development of analytical methods for checking the integrity and, thus, the safety of food is one of the central questions for actors from science, politics, and industry. Targeted methods, for the detection of a few selected analytes, still play the most important role in routine analysis. In the past 5 years, nontargeted methods that do not aim at individual analytes but on analyte profiles that are as comprehensive as possible have increasingly come into focus. Instead of investigating individual chemical structures, data patterns are collected, evaluated and, depending on the problem, fed into databases that can be used for further nontargeted approaches. Alternatively, individual markers can be extracted and transferred to targeted methods. Such an approach requires (i) the availability of authentic reference material, (ii) the corresponding highresolution laboratory infrastructure, and (iii) extensive expertise in processing and storing very large amounts of data. Probably due to the requirements mentioned above, only a few methods have really established themselves in routine analysis. This review article focuses on the establishment of nontargeted methods in routine laboratories. Challenges are summarized and possible solutions are presented.

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Section: Genomics-based Methodsmentioning

confidence: 99%

Food authentication in real life: How to link nontargeted approaches with routine analytics?

Creydt¹,

Fischer²

2020

Electrophoresis

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“…Positive samples were further subjected to reverse transcription droplet digital PCR (RT-ddPCR) in order to quantify the amount of HEV RNA in the samples. The RT-ddPCR method for quantification of human norovirus RNA was used essentially as described [ 32 ]; however, it was used with HEV-specific primers and probes. Briefly, the one-step RT-ddPCR kit for probes and the QX200™ droplet digital PCR system (Bio-Rad Laboratories, Hercules, CA, USA) was used in a total reaction volume of 20 μL containing 5 μL template RNA, each 500 nM primer JHEVF (5′-GGTGGTTTCTGGGGTGAC-3′) and JHEVR (5′-AGGGGTTGGTTGGATGAA-3′) and 150 nM probe JHEVP (5′-FAM-TGATTCTCAGCCCTTCGC-BHQ1-3′) [ 33 ].…”

Section: Methodsmentioning

confidence: 99%

Interlaboratory Validation of a Detection Method for Hepatitis E Virus RNA in Pig Liver

Trojnar

Contzen

Moor³

et al. 2020

Microorganisms

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Background: In the last years, the number of notified hepatitis E cases in humans has continuously increased in Europe. Foodborne infection with the zoonotic hepatitis E virus (HEV) genotype 3 is considered the major cause of this disease. Undercooked liver and raw sausages containing the liver of pigs and wild boar are at high risk of containing HEV. However, so far, no standardized method for the detection of HEV-RNA in pig liver is available. Methods: An international collaborative study on method reproducibility involving 11 laboratories was performed for an HEV-RNA detection method, which consists of steps of sample homogenization, RNA extraction and real-time RT-PCR detection, including a process control. Naturally contaminated pork liver samples containing two different amounts of HEV and a HEV-negative pork liver sample were tested by all laboratories using the method. Results: Valid results were retrieved from 10 laboratories. A specificity of 100% and a sensitivity of 79% were calculated for the method. False negative results were only retrieved from the sample containing very low HEV amounts near the detection limit. Conclusions: The results show that the method is highly specific, sufficiently sensitive and robust for use in different laboratories. The method can, therefore, be applied to routine food control as well as in monitoring studies.

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“…With these techniques, the list of novel noroviruses has expanded especially for animals [32,33]. We and others have followed this agnostic metagenomics strategy, sequencing the whole virome of foods linked to foodborne outbreaks [34,35], samples from the production chain [36][37][38], or artificially contaminated samples to allow method validation [39][40][41]. One study also assessed a common, simple workflow for RNA or DNA metagenomics of various matrices (cultured-cell supernatants, stool, tissue and food) for the detection of any kind of pathogen (virus, bacteria and parasites) [42].…”

Section: Current Approaches In Food Virologymentioning

confidence: 99%

“…One study also assessed a common, simple workflow for RNA or DNA metagenomics of various matrices (cultured-cell supernatants, stool, tissue and food) for the detection of any kind of pathogen (virus, bacteria and parasites) [42]. In complex matrices, the abundance of reads assigned to human viruses was very low [34,36,37,[39][40][41][42], or even null for certain viruses [42], reflecting the very low levels of viral contamination in food. Yet, this strategy applied on berries linked to HAV and norovirus outbreaks allowed the sequencing of a nearly-complete HAV IB genome [35] and portions of the norovirus genome closely related to the virus identified in patients [34], respectively.…”

Section: Current Approaches In Food Virologymentioning

confidence: 99%

“…In complex matrices, the abundance of reads assigned to human viruses was very low [34,36,37,[39][40][41][42], or even null for certain viruses [42], reflecting the very low levels of viral contamination in food. Yet, this strategy applied on berries linked to HAV and norovirus outbreaks allowed the sequencing of a nearly-complete HAV IB genome [35] and portions of the norovirus genome closely related to the virus identified in patients [34], respectively. This underlines the potential of NGS to help identify the etiological agents and their possible origin in foodborne outbreaks, but also the limits posed by the detection level of the technique.…”

Section: Current Approaches In Food Virologymentioning

confidence: 99%

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Novel opportunities for NGS-based one health surveillance of foodborne viruses

et al. 2020

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Foodborne viral infections rank among the top 5 causes of disease, with noroviruses and hepatitis A causing the greatest burden globally. Contamination of foods by infected food handlers or through environmental pollution are the main sources of foodborne illness, with a lesser role for consumption of products from infected animals. Viral partial genomic sequencing has been used for more than two decades to track foodborne outbreaks and whole genome or metagenomics next-generation-sequencing (NGS) are new additions to the toolbox of food microbiology laboratories. We discuss developments in the field of targeted and metagenomic NGS, with an emphasis on application in food virology, the challenges and possible solutions towards future routine application.

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Analysis of frozen strawberries involved in a large norovirus gastroenteritis outbreak using next generation sequencing and digital PCR

Cited by 50 publications

References 32 publications

Food authentication in real life: How to link nontargeted approaches with routine analytics?

Food authentication in real life: How to link nontargeted approaches with routine analytics?

Interlaboratory Validation of a Detection Method for Hepatitis E Virus RNA in Pig Liver

Novel opportunities for NGS-based one health surveillance of foodborne viruses

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