Direct Metatranscriptome RNA-seq and Multiplex RT-PCR Amplicon Sequencing on Nanopore MinION – Promising Strategies for Multiplex Identification of Viable Pathogens in Food

Viable pathogenic bacteria are major biohazards that pose a significant threat to food safety. Despite the recent developments in detection platforms, multiplex identification of viable pathogens in food remains a major challenge. A novel strategy is developed through direct metatranscriptome RNA-seq and multiplex RT-PCR amplicon sequencing on Nanopore MinION to achieve real-time multiplex identification of viable pathogens in food. Specifically, this study reports an optimized universal Nanopore sample extraction and library preparation protocol applicable to both Gram-positive and Gram-negative pathogenic bacteria, demonstrated using a cocktail culture of E. coli O157:H7, Salmonella enteritidis, and Listeria monocytogenes, which were selected based on their impact on economic loss or prevalence in recent outbreaks. Further evaluation and validation confirmed the accuracy of direct metatranscriptome RNA-seq and multiplex RT-PCR amplicon sequencing using Sanger sequencing and selective media. The study also included a comparison of different bioinformatic pipelines for metatranscriptomic and amplicon genomic analysis. MEGAN without rRNA mapping showed the highest accuracy of multiplex identification using the metatranscriptomic data. EPI2ME also demonstrated high accuracy using multiplex RT-PCR amplicon sequencing. In addition, a systemic comparison was drawn between Nanopore sequencing of the direct metatranscriptome RNA-seq and RT-PCR amplicons. Both methods are comparable ...
Source: Frontiers in Microbiology - Category: Microbiology Source Type: research

Related Links:

In the United States, the consumption of fresh fruits and vegetables has increased during recent years as consumers seek to make healthier lifestyle choices. However, the number of outbreaks associated with fresh produce that involve cases in more than one state (multistate) has increased concomitantly. As the distance along the farm-to-fork continuum has lengthened over time, there are also more opportunities for fresh produce contamination with bacterial pathogens before it reaches the consumer. This review provides an overview of the three bacterial pathogens (i.e., pathogenic Escherichia coli, Listeria monocytogenes, a...
Source: Frontiers in Microbiology - Category: Microbiology Source Type: research
koh Disease outbreaks caused by the ingestion of contaminated vegetables and fruits pose a significant problem to human health. The sources of contamination of these food products at the preharvest level of agricultural production, most importantly, agricultural soil and irrigation water, serve as potential reservoirs of some clinically significant foodborne pathogenic bacteria. These clinically important bacteria include: Klebsiella spp., Salmonella spp., Citrobacter spp., Shigella spp., Enterobacter spp., Listeria monocytogenes and pathogenic E. coli (and E. coli O157:H7) all of which have the potential to cause dise...
Source: International Journal of Environmental Research and Public Health - Category: Environmental Health Authors: Tags: Review Source Type: research
(BfR Federal Institute for Risk Assessment) To make food even safer for humans, experts from scientific institutions, food regulatory authorities and the business community will discuss current developments and strategies at the 'Zoonoses and Food Safety' Symposium at the German Federal Institute for Risk Assessment (BfR) on 4 and 5 November 2019, in Berlin-Marienfelde. Because some micro-organisms in food can cause health problems. Campylobacter in raw milk, salmonella in eggs or listeria in ready-to-eat foods often lead to outbreaks affecting numerous patients.
Source: EurekAlert! - Infectious and Emerging Diseases - Category: Infectious Diseases Source Type: news
Foodborne diseases (FBDs) are infections of the gastrointestinal tract caused by foodborne pathogens (FBPs) such as bacteria (Salmonella, Listeria monocytogenes and Shiga toxin-producing E. coli (STEC)) and several viruses, but also parasites and some fungi. Artificial intelligence (AI) and its sub-discipline machine learning (ML) are re-emerging and gaining an ever increasing popularity in the scientific community and industry, and could lead to actionable knowledge in diverse ranges of sectors including epidemiological investigations of FBD outbreaks and antimicrobial resistance (AMR). As genotyping using whole-genome se...
Source: Frontiers in Microbiology - Category: Microbiology Source Type: research
This study aimed at investigating the influence of two key parameters (concentration of curcumin and illumination time) on the effects of curcumin-based photodynamic sterilization on the preservation of fresh-cut Hami melons. The results indicated that illumination with 50 μmol/L curcumin for 60 min using a blue LED lamp reduced the total aerobic microorganism count by ~1.8 log CFU/g in fresh-cut Hami melons. Besides this, the effects of photodynamic sterilization on the soluble solids content, color, water content, firmness, and sensory indices of the fresh-cut Hami melons were also evaluated. Compared to the contr...
Source: Molecules - Category: Chemistry Authors: Tags: Article Source Type: research
Publication date: Available online 25 June 2019Source: Food ControlAuthor(s): Zijin Zhou, Sophie Zuber, Matteo Campagnoli, Thierry Putallaz, Frank Devlieghere, Mieke UyttendaeleAbstractThe microbial safety of black peppercorns (Piper nigrum L.) has raised concerns due to increasing numbers of reported foodborne outbreaks and food safety alerts. To avoid quality degradation caused by excessive thermal processing, mild steaming treatments (
Source: Food Control - Category: Food Science Source Type: research
Abstract Fresh vegetables are important components of an everyday balanced diet making ready to-eat-salads (RTE) a commodity widely consumed. However, in the past few years these products have been linked with outbreaks of salmonellosis and listeriosis; thus the continuous investigation of their safety is an essential requirement. A total of 216 samples of ready-to-eat salads from the Cypriot market were analysed to determine the microbiological quality and safety, along with physicochemical attributes of the salads and identify possible correlations between them. The samples were randomly collected from four reta...
Source: Food Microbiology - Category: Food Science Authors: Tags: Food Microbiol Source Type: research
In conclusion, the results improve our understanding on the characteristics of lncRNAs and mRNAs on regulating host immune response against C. perfringens type C infection, which will provide a reference for future research into exploring C. perfringens-related diseases in human. Introduction Clostridium perfringens (C. perfringens) is a Gram-positive anaerobic rod and ranks as the second most common bacteria that causes fulminant, fatal infectious and immune diseases (Scharff, 2012; Grass et al., 2013). These diseases are characterized by fever, pain, gas production, local edema, and severe tissue destruction, the...
Source: Frontiers in cellular and infection microbiology - Category: Microbiology Source Type: research
Conclusion Starter cultures are an important tool that contributes to ensure the safety of fermented meat products. Indeed, the microorganisms that constitute starter cultures may inhibit or reduce the growth of spoilage and/or pathogenic populations through mechanisms, such as production of certain metabolites or competitive exclusion. Thus, the use of starter cultures may reduce the need for chemical additives, such as nitrites and nitrates. Furthermore, the lower residual levels of nitrates and nitrites detected in fermented meat products inoculated with starter cultures are due to the ability of starters to metabolize...
Source: Frontiers in Microbiology - Category: Microbiology Source Type: research
Yulia Kroupitski1, Rachel Gollop1, Eduard Belausov2, Riky Pinto1 and Shlomo Sela (Saldinger)1* 1Microbial Food-Safety Research Unit, Department of Food Science, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel 2Confocal Microscopy Unit, Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel Human pathogens on plants (HPOP) have evolved complex interactions with their plant host. Stomatal internalization is one such mode of interaction, where bacteria are attracted to stomata and penetrate into the substomatal cavity by a process med...
Source: Frontiers in Microbiology - Category: Microbiology Source Type: research
More News: Databases & Libraries | Gastroenteritis | Listeria | Microbiology | Nanotechnology | Outbreaks | Salmonella | Study