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160 results for “Listeria monocytogenes”
The self-cleaning properties of biomimetic surfaces to repel Escherichia coli and Listeria monocytogenes attachment, adhesion, and retention
<p>Surface hydrophobicity and roughness were determined for unmodified wax surfaces (control), biomimetic wax surfaces, and Gladioli leaves. The self-cleaning properties of the biomimetic and control surfaces were compared by measuring their propensity to repel <em>Escherichia coli</em> and <em>Listeria monocytogenes</em> attachment, adhesion, and retention in mono- and co-culture conditions.</p>
Datasets of Listeria monocytogenes phenotypes colected in the EJP OH LISTADAPT project
<p>LISTADAPT datasets</p> <p>This repository gathered the phenotypic datasets in the LISTADAPT project (https://onehealthejp.eu/projects/jrp7-listadapt/)<br> It includes the Listeria monocytogenes phenotypic data associated to:<br> - biofilm formation<br> - MIC of antimicrobials<br> - Growth and survival in soil microsom<br> - Growth and survival in stressed conditions (culture medium)</p> <p>200 strains: 100 isolated in main RTE foods and 100 isolated from environment/farm/animals are studied.</p> <p>A versionning of the files is proposed, permitting to determine the more recent files in the repository. </p> <p> </p>
The OHEJP BeONE Project – Listeria monocytogenes genome assembly dataset
<p><strong>Dataset</strong></p> <p>This dataset comprises the genome assemblies of 1,426 <em>Listeria monocytogenes</em> samples collected by the BeONE Consortium on behalf of the One Health European Joint Programme “BeONE: Building Integrative Tools for One Health Surveillance” (<a href="https://onehealthejp.eu/jrp-beone/">https://onehealthejp.eu/jrp-beone/</a>). Additionally, a complementary dataset is also made available (<a href="https://zenodo.org/record/7116878">https://zenodo.org/record/7116878</a>), comprising genome assemblies of 1,874 <em>L. monocytogenes</em> samples selected among the Whole-Genome Sequencing (WGS) data publicly available in the European Nucleotide Archive (ENA) or in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA).</p> <p>File “<strong>BeONE_Lm_metadata.xlsx</strong>” contains the genome assembly statistics for each isolate, including European Nucleotide Archive accession numbers and <em>in-silico</em> Multi Locus Sequence Type, and information regarding year of sampling, country and source.</p> <p>The archive “<strong>BeONE_Lm_assemblies.zip</strong>” contains all the genome assemblies (.fasta format) of each isolate presented in the metadata file.</p> <p> </p> <p><strong>Dataset selection and curation</strong></p> <p>This anonymized dataset of <em>L. monocytogenes </em>genome assemblies was generated using Next Generation Sequencing data collected within the BeONE Consortium available at the European Nucleotide Archive under BioProject Accession Number <a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB57166">PRJEB57166</a>. Read quality control, trimming and assembly were performed with Aquamis v1.3.9 (<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8145556/">Deneke et al. 2021</a>) using default parameters. Assembly quality control (QC), including contamination assessment, as well as MLST ST determination were performed with the same pipeline. All genome assemblies passing the QC were included in the final dataset. Among the others, we noticed that a considerable proportion of assemblies was flagged as “QC fail” exclusively due to the “NumContamSNVs” parameter, suggesting that this setting might have been too strict. After manual inspection of a random subset, assemblies for which the percentage of reads corresponding to the correct species was >98% were recovered and integrated in the final dataset (those samples are labeled in the Metadata file). In total, 1,426 isolates passed the dataset curation step and were included in the final dataset.</p> <p> </p> <p><strong>Funding</strong></p> <p>This work was supported by funding from the European Union’s Horizon 2020 Research and Innovation programme under grant agreement No 773830: One Health European Joint Programme.</p> <p> </p> <p><strong>Acknowledgements</strong></p> <p>We thank the National Distributed Computing Infrastructure of Portugal (INCD) for providing the necessary resources to run the genome assemblies. INCD was funded by FCT and FEDER under the project 22153-01/SAICT/2016.</p> <p> </p>
Insights into the genetic diversity of Listeria monocytogenes from bivalves
<p>Fasta files to 30 genomes described in a publication</p>
User Guide – Dashboard on Listeria monocytogenes
<p>The EFSA dashboard on <em>Listeria</em> <em>monocytogenes</em> is a graphical user interface for searching and querying the large amount of data collected each year by EFSA from EU Member States and other reporting countries based on Zoonoses Directive 2003/99/EC. The <em>Listeria</em> <em>monocytogenes</em> dashboard shows summary statistics for the monitoring results of the pathogen with regard to major ready-to-eat food categories, <em>Listeria</em> <em>monocytogenes</em>-positive official samples in the context of food safety criteria in accordance with Regulation (EC) No 2073/2005 and official samples exceeding the food safety criteria limit of 100 CFU/g for specified food matrices. Other monitoring statistics for <em>Listeria monocytogenes</em> in ready-to-eat foods are also displayed. The <em>Listeria</em> <em>monocytogenes</em> data and related statistics can be displayed interactively using charts, graphs and maps in the online EFSA dashboard. The main statistics can also be viewed and downloaded in tabular format. Detailed information on the use and features of the <em>Listeria monocytogenes</em> dashboard can be found in the present user guide that can also be downloaded from the online tool.</p>
Salmonella, Shiga toxin-producing Escherichia coli O157:H7 and Listeria monocytogenes numbers during dry-aging of beef loins
<p>This dataset contains bacterial count data and loin characteristics from an experimental study assessing the survival/growth of <em>Salmonella</em>, <em>Escherichia coli</em> O157:H7 and <em>Listeria monocytogenes</em> during dry-aging of beef loins, after artificial inoculation. </p> <p>Four different csv files are provided with tabular data. A detailed description of the data is provided in the readme file.</p> <p> </p>
Sequencing data of RNA editing, RNA modifications, and transcriptional units in Listeria monocytogenes
<p>Sequencing data for "RNA editing, RNA modifications, and transcriptional units in <em>Listeria monocytogenes</em>" manuscript, which is submitted to BMC genomics.</p>
Akkermansia muciniphila reduces diet-induced susceptibility to Listeria monocytogenes infection
<p>A high fat (HF) diet decreases levels of <em>Akkermansia muciniphila</em> in the gut and reduces resistance to the foodborne pathogen <em>Listeria monocytogenes</em>. We demonstrate that short-term gavage with <em>A. muciniphila</em> increases resistance to oral and systemic <em>L. monocytogenes</em> infection in mice fed a HF diet. <em>A. muciniphila</em> normalized diet-induced inflammation in the gut and liver prior to infection and reduced inflammatory cell infiltration in the ileum to levels similar to mice fed a low fat diet. <em>A. muciniphila</em> administration had minimal impact upon the microbiota and microbial metabolites and did not affect individual taxa or impact the Bacteroidetes to Firmicutes ratio. In summary, <em>A. muciniphila</em> increased resistance to <em>L. monocytogenes</em> infection in mice fed a HF diet, through normalising immune/physiological effects that more closely resembled mice fed a LF diet. The findings suggest an interaction between <em>A. muciniphila</em> and the host to reverse the effects of a westernized diet in this model.</p>
Prevalence of Listeria monocytogenes and other Listeria species in fish, fish products and fish processing environment: A systematic review and meta-analysis
<p>Dane wykorzytsane w publikajci "Prevalence of <em>Listeria monocytogenes</em> and other <em>Listeria</em> species in fish, fish products and fish processing environment: A systematic review and meta-analysis" . Dane obejmują wyniki surowe z baz artykułów, dane wykorzystane do wykonania metaanalizy oraz wyniki surowe uzyskane po przeprowadzaniu metaanalizy</p>
Webinar: Casos de Microbiología Predictiva enfocada en Listeria monocytogenes y alimentos listos para consumo
<p>Webinar "Cases of Predictive Microbiology applied to Listeria monocytogenes in RTE foods" recorded for the Hispanic Community by invitation of the University of Vermont - Extension (In Spanish).</p>
Genome assemblies and respective cgMLST profiles of a diverse dataset comprising 1,874 Listeria monocytogenes isolates
<p><strong>Dataset</strong></p> <p>This dataset comprises the genome assemblies and respective 1,748-loci core-genome (cg) Multiple Locus Sequence Type (MLST) profiles [Pasteur schema (<a href="https://pubmed.ncbi.nlm.nih.gov/27723724/">Moura et al. 2016</a>) available in <a href="https://chewbbaca.online/species/6/schemas/1">chewie-NS</a> (<a href="https://academic.oup.com/nar/article/49/D1/D660/5929238">Mamede et al. 2022</a>)] of a final set of 1,874 <em>Listeria monocytogenes</em> samples selected among the Whole-Genome Sequencing (WGS) data publicly available in the European Nucleotide Archive (ENA) or in the <a href="https://www.ncbi.nlm.nih.gov/">National Center for Biotechnology Information</a> (NCBI) Sequence Read Archive (SRA) at the beginning of the analysis (November 2021). This set of samples was carefully selected to cover a wide genetic diversity (assessed in terms of Sequence Type [ST]). In total, 204 different STs are represented in this dataset, with ST121, ST6, ST9, ST1 and ST155 being in the top 5 and, together, corresponding to 37.9% of the dataset.</p> <p>File “Lm_metadata.xlsx” contains metadata information for each isolate, including ENA/SRA accession number, BioProject and in-silico MLST ST.</p> <p>The directory “assemblies/” contains all the genome assemblies (.fasta format) of each isolate presented in the metadata file. </p> <p>The file “profiles/Lm_profile.tsv” corresponds to a tab separated file with the 1,748-loci cgMLST profile of each isolate presented in the metadata file. These profiles were determined as explained below.</p> <p> </p> <p><strong>Dataset selection and curation</strong></p> <p>With the objective of creating a diverse dataset of <em>L. monocytogenes </em>genome assemblies, we collected information about the genetic diversity (STs) of the isolates available at <a href="https://bigsdb.pasteur.fr/listeria/">BIGSdb-Lm</a> database in the beginning of this analysis (November 2021) and in other previous works. Based on this information, we selected an initial dataset comprising 1,957 samples associated with three previous studies (<a href="https://pubmed.ncbi.nlm.nih.gov/27723724/">Moura et al. 2016</a>; <a href="https://pubmed.ncbi.nlm.nih.gov/28827366/">Maury et al. 2017</a>; <a href="https://pubmed.ncbi.nlm.nih.gov/30775964/">Painset et al. 2019</a>). Their WGS data was downloaded from ENA/SRA with <a href="https://github.com/rpetit3/fastq-dl">fastq-dl</a> v1.0.6. Read quality control, trimming and assembly were performed with the Aquamis v1.3.9 (<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8145556/">Deneke et al. 2021</a>) using default parameters. Assembly quality control (QC), including contamination assessment, as well as MLST ST determination were performed with the same pipeline. All genome assemblies passing the QC were included in the final dataset. Among the others, we noticed that a considerable proportion of assemblies was flagged as “QC fail” exclusively due to the “NumContamSNVs” parameter, suggesting that this setting might have been too strict. After manual inspection of a random subset, assemblies for which the percentage of reads corresponding to the correct species was >98% were recovered and integrated in the final dataset (those samples are labeled in the Metadata file). In total, 1,874 isolates passed the dataset curation step and were included in the final dataset. cgMLST profiles of each of these isolates were determined with chewBBACA v2.8.5 (<a href="https://pubmed.ncbi.nlm.nih.gov/29543149/">Silva et al. 2018</a>), using the 1,748-loci Pasteur schema (<a href="https://pubmed.ncbi.nlm.nih.gov/27723724/">Moura et al. 2016</a>) available in <a href="https://chewbbaca.online/species/6/schemas/1">chewie-NS</a> (<a href="https://academic.oup.com/nar/article/49/D1/D660/5929238">Mamede et al. 2022</a>) and downloaded on June 23<sup>rd</sup>, 2022.</p> <p> </p> <p><strong>Acknowledgements</strong></p> <p>We thank the National Distributed Computing Infrastructure of Portugal (INCD) for providing the necessary resources to run the genome assemblies. INCD was funded by FCT and FEDER under the project 22153-01/SAICT/2016.</p>
Data on the Blackthorn fruit peel: phenolic compounds and antimicrobial synergy with blue light against Listeria monocytogenes
<p>The dataset contains results obtained during a project funded by the National Science Centre, Poland [Grant number 2022/45/B/NZ9/00299 (OPUS-23)].</p>
ListeriaPredict Webinar - Application of novel predictive microbiology techniques to shelf-life studies on Listeria monocytogenes
<p>An EFSA funded ListeriaPredict Webinar - Application of novel predictive microbiology techniques to shelf-life studies on Listeria monocytogenes</p>
Data from: Extending RAD tag analysis to microbial ecology: a comparison between multi locus sequence typing (MLST) and 2b-RAD to investigate Listeria monocytogenes genetic structure
The advent of next-generation sequencing (NGS) has dramatically changed bacterial typing technologies, increasing our ability to differentiate bacterial isolates. Despite it is now possible to sequence a bacterial genome in a few days and at reasonable costs, most genetic analyses do not require whole-genome sequencing, which also remains impractical for large population samples due to the cost of individual library preparation and bioinformatics. More traditional sequencing approaches, however, such as MultiLocus Sequence Typing (mlst) are quite laborious and time-consuming, especially for large-scale analyses. In this study, a genotyping approach based on restriction site-associated (RAD) tag sequencing, 2b-RAD, was applied to characterize Listeria monocytogenes strains. To verify the feasibility of the method, an in silico analysis was performed on 30 available complete genomes. For the same set of strains, in silico mlst analysis was conducted as well. Subsequently, 2b-RAD and mlst analyses were experimentally carried out on 58 isolates collected from food samples or food-processing sites. The obtained results demonstrate that 2b-RAD predicts mlst types and often provides more detailed information on population structure than mlst. Moreover, the majority of variants differentiating identical sequence type isolates mapped against accessory fragments, thus providing additional information to characterize strains. Although mlst still represents a reliable typing method, large-scale studies on molecular epidemiology and public health, as well as bacterial phylogenetics, population genetics and biosafety could benefit of a low cost and fast turnaround time approach such as the 2b-RAD analysis proposed here.
Systematic review and meta-analysis of the occurrence of Listeria monocytogenes in fresh produce in selected developing countries
<p>This dataset contain the supplementary data for "<a><span>Sy</span></a><span><span></span></span><span>stematic review and meta-analysis of the occurrence of <em>Listeria monocytogenes</em> in fresh produce in selected developing countries"</span></p>
Supplementary data: ONT for Listeria monocytogenes outbreak detection
<p>Supplementary data for the publication "Oxford Nanopore’s 2024 sequencing technology for Listeria monocytogenes outbreak detection and source attribution: progress and clone-specific challenges"</p> <ol> <li><em>L. monocytogenes </em>assemblies generated from <ul> <li>Illumina-only data (shovill)</li> <li>ONT-only data (100x coverage, sup@v5.0 + flye + flye polisher + medaka [model r103_min_high_g360])</li> <li>ONT + Illumina data (100x ONT coverage, sup@v5.0 + flye + flye polisher + polypolish)</li> </ul> </li> <li>Raw ONT pod5 data from three<em> L. monocytogenes </em>isolates (N19-1094, N21-2956, N23-1883) with GAAG6mAC / GT4mCTTC methylations, among other methylated motifs</li> </ol>
Transcutaneous Immunization With an Attenuated Listeria Monocytogenes Vector Vaccine
ClinicalTrials.gov study NCT01311817. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Data from: Extending RAD tag analysis to microbial ecology: a comparison between multi locus sequence typing (MLST) and 2b-RAD to investigate Listeria monocytogenes genetic structure
Open the record for dataset details and reuse information.
An Efficacy and Safety Study of JNJ-64041757, a Live Attenuated Listeria Monocytogenes Immunotherapy, in Combination With Nivolumab Versus Nivolumab Monotherapy in Participants With Advanced Adenocarc
ClinicalTrials.gov study NCT03371381. IPD Sharing: Not stated. Countries: 3. Publications: 0.
Data from: Advancing risk assessment: mechanistic dose–response modelling of Listeria monocytogenes infection in human populations
Open the record for dataset details and reuse information.
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