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      A database for risk assessment and comparative genomic analysis of foodborne Vibrio parahaemolyticus in China

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          Abstract

          Vibrio parahaemolyticus is a major foodborne pathogen worldwide. The increasing number of cases of V. parahaemolyticus infections in China indicates an urgent need to evaluate the prevalence and genetic diversity of this pathogenic bacterium. In this paper, we introduce the Foodborne Vibrio parahaemolyticus genome database (FVPGD), the first scientific database of foodborne V. parahaemolyticus distribution and genomic data in China, based on our previous investigations of V. parahaemolyticus contamination in different kinds of food samples across China from 2011 to 2016. The dataset includes records of 2,499 food samples and 643  V. parahaemolyticus strains from supermarkets and marketplaces distributed over 39 cities in China; 268 whole-genome sequences have been deposited in this database. A spatial view on the risk situations of V. parahaemolyticus contamination in different food types is provided. Additionally, the database provides a functional interface of sequence BLAST, core genome multilocus sequence typing, and phylogenetic analysis. The database will become a powerful tool for risk assessment and outbreak investigations of foodborne pathogens in China.

          Abstract

          Measurement(s) Microbial Contamination • sequence_assembly • DNA
          Technology Type(s) the most probable number method • sequence assembly process • DNA sequencing
          Sample Characteristic - Organism Vibrio parahaemolyticus
          Sample Characteristic - Location China

          Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12629891

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          Parallelization of MAFFT for large-scale multiple sequence alignments

          Abstract Summary We report an update for the MAFFT multiple sequence alignment program to enable parallel calculation of large numbers of sequences. The G-INS-1 option of MAFFT was recently reported to have higher accuracy than other methods for large data, but this method has been impractical for most large-scale analyses, due to the requirement of large computational resources. We introduce a scalable variant, G-large-INS-1, which has equivalent accuracy to G-INS-1 and is applicable to 50 000 or more sequences. Availability and implementation This feature is available in MAFFT versions 7.355 or later at https://mafft.cbrc.jp/alignment/software/mpi.html. Supplementary information Supplementary data are available at Bioinformatics online.
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            A genomic overview of the population structure of Salmonella

            For many decades, Salmonella enterica has been subdivided by serological properties into serovars or further subdivided for epidemiological tracing by a variety of diagnostic tests with higher resolution. Recently, it has been proposed that so-called eBurst groups (eBGs) based on the alleles of seven housekeeping genes (legacy multilocus sequence typing [MLST]) corresponded to natural populations and could replace serotyping. However, this approach lacks the resolution needed for epidemiological tracing and the existence of natural populations had not been independently validated by independent criteria. Here, we describe EnteroBase, a web-based platform that assembles draft genomes from Illumina short reads in the public domain or that are uploaded by users. EnteroBase implements legacy MLST as well as ribosomal gene MLST (rMLST), core genome MLST (cgMLST), and whole genome MLST (wgMLST) and currently contains over 100,000 assembled genomes from Salmonella. It also provides graphical tools for visual interrogation of these genotypes and those based on core single nucleotide polymorphisms (SNPs). eBGs based on legacy MLST are largely consistent with eBGs based on rMLST, thus demonstrating that these correspond to natural populations. rMLST also facilitated the selection of representative genotypes for SNP analyses of the entire breadth of diversity within Salmonella. In contrast, cgMLST provides the resolution needed for epidemiological investigations. These observations show that genomic genotyping, with the assistance of EnteroBase, can be applied at all levels of diversity within the Salmonella genus.
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              Why prokaryotes have pangenomes

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                Author and article information

                Contributors
                wuqp203@163.com
                Journal
                Sci Data
                Scientific Data
                Nature Publishing Group UK (London )
                2052-4463
                2 October 2020
                2 October 2020
                2020
                : 7
                : 321
                Affiliations
                [1 ]GRID grid.464309.c, ISNI 0000 0004 6431 5677, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, , Guangdong Academy of Sciences, ; Guangzhou, 510070 China
                [2 ]GRID grid.258164.c, ISNI 0000 0004 1790 3548, Department of Food Science and Technology, , Jinan University, ; Guangzhou, 510000 China
                [3 ]GRID grid.20561.30, ISNI 0000 0000 9546 5767, College of Food Science, , South China Agricultural University, ; Guangzhou, 510642 China
                Article
                671
                10.1038/s41597-020-00671-3
                7532206
                33009407
                d641d367-2966-46c2-bb50-31c28d01d449
                © The Author(s) 2020

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                The Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the metadata files associated with this article.

                History
                : 29 April 2020
                : 13 August 2020
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100003453, Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation);
                Award ID: 2019A1515010810
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100001809, National Natural Science Foundation of China (National Science Foundation of China);
                Award ID: 31730070
                Award Recipient :
                Categories
                Data Descriptor
                Custom metadata
                © The Author(s) 2020

                pathogens,infection,microbial ecology
                pathogens, infection, microbial ecology

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