German-Wide Interlaboratory Study Compares Consistency, Accuracy and Reproducibility of Whole-Genome Short Read Sequencing

We compared the consistency, accuracy and reproducibility of next-generation short read sequencing between ten laboratories involved in food safety (research institutes, state laboratories, universities and companies) from Germany and Austria. Participants were asked to sequence six DNA samples of three bacterial species (Campylobacter jejuni, Listeria monocytogenes and Salmonella enterica) in duplicate, according to their routine in-house sequencing protocol. Four different types of Illumina sequencing platforms (MiSeq, NextSeq, iSeq, NovaSeq) and one Ion Torrent sequencing instrument (S5) were involved in the study. Sequence quality parameters were determined for all data sets and centrally compared between laboratories. SNP and cgMLST calling were performed to assess the reproducibility of sequence data collected for individual samples. Overall, we found Illumina short read data to be more accurate (higher base calling accuracy, fewer miss-assemblies) and consistent (little variability between independent sequencing runs within a laboratory) than Ion Torrent sequence data, with little variation between the different Illumina instruments. Two laboratories with Illumina instruments submitted sequence data with lower quality, probably due to the use of a library preparation kit, which shows difficulty in sequencing low GC genome regions. Differences in data quality were more evident after assembling short reads into genome assemblies, with Ion Torrent assemblies featuring a g...
Source: Frontiers in Microbiology - Category: Microbiology Source Type: research

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Abstract Following implementation of Health Canada's Policy on Listeria monocytogenes in Ready-to-Eat Foods by Canadian food safety authorities in 2011, a four-year study (2012-2016) was carried out to gain baseline information on the occurrence of bacterial pathogens, notably the prevalence and levels of Listeria monocytogenes (L. monocytogenes) in various product types of ready-to-eat (RTE) fresh-cut fruits and fresh-cut vegetables sold at retail in Canada. A total of 10,070 pre-packaged samples, including 4691 fresh-cut fruit and 5379 fresh-cut vegetable samples were collected from retail stores across Canada a...
Source: International Journal of Food Microbiology - Category: Food Science Authors: Tags: Int J Food Microbiol Source Type: research
Authors: Balali GI, Yar DD, Afua Dela VG, Adjei-Kusi P Abstract Microbes are found all over the globe with some few exceptions, including sterilized surfaces. They include normal flora that is nonpathogenic, which contribute to the larger percentage, and pathogenic species which are few. Hence, the activities of humans cannot be completely separated from microbes. Thus, many pathogenic microbes have found their way into fresh fruits and vegetables which are a great source of a healthy diet for humans. The growing demand for fresh fruits and vegetables has necessitated larger production. The larger production of veg...
Source: International Journal of Microbiology - Category: Microbiology Tags: Int J Microbiol Source Type: research
Once a dangerous new pathogen is out, as we are seeing, it can be difficult if not impossible to prevent it going global. One as contagious as SARS-CoV-2 has the potential to infect the whole of humanity. Eighty per cent of cases may be benign, but with such a large pool of susceptible hosts, the numbers who experience severe illness and die can still be shockingly high. So the only sensible answer to the question, how do we stop this from happening again, is: by doing all we can to prevent such pathogens infecting humans in the first place. And that means taking a long, hard look at our relationship with the natural world...
Source: TIME: Health - Category: Consumer Health News Authors: Tags: Uncategorized COVID-19 Source Type: news
te; T Abstract Bacteria within biofilms are more resistant to antibiotics and chemical agents than planktonic bacteria in suspension. Treatment of biofilm-associated infections inevitably involves high dosages and prolonged courses of antimicrobial agents; therefore, there is a potential risk of the development of antimicrobial resistance (AMR). Due to the high prevalence of AMR and its association with biofilm formation, investigation of more effective anti-biofilm agents is required. From ancient times, herbs and spices have been used to preserve foods, and their antimicrobial, anti-biofilm and anti-quorum sensi...
Source: Current Pharmaceutical Design - Category: Drugs & Pharmacology Authors: Tags: Curr Pharm Des 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
Publication date: Available online 3 October 2019Source: Food HydrocolloidsAuthor(s): Hossein Haghighi, Serge Kameni Leugoue, Frank Pfeifer, Heinz Wilhelm Siesler, Fabio Licciardello, Patrizia Fava, Andrea PulvirentiAbstractThe main aim of this study was to characterize microstructural, physical, optical, mechanical, water barrier and antimicrobial properties of chitosan-polyvinyl alcohol blend films (CS-PVA) enriched with ethyl lauroyl arginate (LAE) (1–10% w/v) for food packaging applications. The film microstructure was determined by scanning electron microscopy. Active films containing 10% LAE showed cracks on th...
Source: Food Hydrocolloids - Category: Food Science Source Type: research
Publication date: August 2019Source: LWT, Volume 111Author(s): Mohammad Amin Nouri Ala, Yasser ShahbaziAbstractThe aims of the present study were to evaluate the effects of carboxymethyl cellulose (CMC) coatings containing Ziziphora clinopodioides (ZEO; 0, 0.25 and 0.5%) and Mentha spicata (MEO; 0 and 0.5%) essential oils on pathogenic bacteria (i.e. Listeria monocytogenes, Staphylococcus aureus, Escherichia coli O157:H7, Salmonella typhimurium and Campylobacter jejuni) and shelf life extension of fresh and sauced chicken breast fillets under refrigerated condition for two weeks. The order of bacterial spoilage population ...
Source: LWT Food Science and Technology - Category: Food Science 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
Conclusion This study confirms the in vitro antibacterial activity of BIOCITRO® against Gram-negative and Gram-positive bacteria. For most of the strains, the product reached the bactericidal effect at the same concentration of the bacteriostatic effect and maximum difference between MIC and MBC was two dilution steps. The less susceptible species of the study were S. enterica ssp. enterica and E. coli with MBC90 values of 256 and 128 μg/mL, respectively, while the most susceptible was C. perfringens with MBC90 of 16 μg/mL. After short exposition time to the product, the significant effect over the viability of ...
Source: Frontiers in Microbiology - Category: Microbiology Source Type: research
This study aimed to evaluate the antimicrobial and anti-QS potential of organic extracts of onion varieties and its representative phenolic compounds quercetin aglycone and quercetin 3-β-D-glucoside in the QS model bacteria Chromobacterium violaceum ATCC 12472, Pseudomonas aeruginosa PAO1, and Serratia marcescens MG1. Three phenolic extracts were obtained: red onion extract in methanol acidified with 2.5% acetic acid (RO-1), white onion extract in methanol (WO-1) and white onion extract in methanol ammonium (WO-2). Quercetin 4-O-glucoside and quercetin 3,4-O-diglucoside were identified as the predominant compounds in ...
Source: Frontiers in Microbiology - Category: Microbiology Source Type: research
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