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RIPS（快速直观病原体监测）：一种用于监测食源性病原体基因组序列数据的工具。

RIPS (rapid intuitive pathogen surveillance): a tool for surveillance of genome sequence data from foodborne bacterial pathogens.

作者信息

Muruvanda Tim, Rand Hugh, Pettengill James, Pightling Arthur

机构信息

Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States.

出版信息

Front Bioinform. 2024 Aug 9;4:1415078. doi: 10.3389/fbinf.2024.1415078. eCollection 2024.

DOI:10.3389/fbinf.2024.1415078
PMID:39184336
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11341538/
Abstract

Monitoring data submitted to the National Center for Biotechnology Information's Pathogen Detection whole-genome sequence database, which includes the foodborne bacterial pathogens monocytogenes, , and , has proven effective for detecting emerging outbreaks. As part of the submission process, new sequence data are typed using a whole-genome multi-locus sequence typing scheme and clustered with sequences already in the database. Publicly available text files contain the results of these analyses. However, contextualizing and interpreting this information is complex. We present the Rapid Intuitive Pathogen Surveillance (RIPS) tool, which shows the results of the NCBI Rapid Reports, along with appropriate metadata, in a graphical, interactive dashboard. RIPS makes the information in the Rapid Reports useful for real-time surveillance of genome sequence databases.

摘要

提交给美国国家生物技术信息中心病原体检测全基因组序列数据库的监测数据已被证明对检测新出现的疫情有效，该数据库包括食源性病原体单核细胞增生李斯特菌、[此处原文缺失两种病原体名称]。作为提交过程的一部分，新的序列数据使用全基因组多位点序列分型方案进行分型，并与数据库中已有的序列聚类。公开可用的文本文件包含这些分析的结果。然而，将这些信息置于背景中并进行解释是复杂的。我们展示了快速直观病原体监测（RIPS）工具，它在一个图形化的交互式仪表板中展示了NCBI快速报告的结果以及适当的元数据。RIPS使快速报告中的信息对基因组序列数据库的实时监测有用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/608c/11341538/5e2909a842a3/fbinf-04-1415078-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/608c/11341538/97ff7639c99f/fbinf-04-1415078-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/608c/11341538/fb31abd70d3a/fbinf-04-1415078-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/608c/11341538/6ebde7039591/fbinf-04-1415078-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/608c/11341538/5e2909a842a3/fbinf-04-1415078-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/608c/11341538/97ff7639c99f/fbinf-04-1415078-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/608c/11341538/fb31abd70d3a/fbinf-04-1415078-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/608c/11341538/6ebde7039591/fbinf-04-1415078-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/608c/11341538/5e2909a842a3/fbinf-04-1415078-g004.jpg

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本文引用的文献

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Front Microbiol. 2023 Sep 21;14:1254777. doi: 10.3389/fmicb.2023.1254777. eCollection 2023.
2
An Overview of Foodborne Sample-Initiated Retrospective Outbreak Investigations and Interagency Collaboration in the United States.美国食源性样本启动回溯性暴发调查概述及机构间合作
J Food Prot. 2023 Jun;86(6):100089. doi: 10.1016/j.jfp.2023.100089. Epub 2023 Apr 5.
3
An Outbreak Investigation of Salmonella Typhimurium Illnesses in the United States Linked to Packaged Leafy Greens Produced at a Controlled Environment Agriculture Indoor Hydroponic Operation - 2021.
美国与受控环境农业室内水培作业生产的包装叶菜有关的鼠伤寒沙门氏菌病暴发调查-2021 年。
J Food Prot. 2023 May;86(5):100079. doi: 10.1016/j.jfp.2023.100079. Epub 2023 Mar 31.
4
Database resources of the National Center for Biotechnology Information in 2023.2023 年国立生物技术信息中心的数据库资源。
Nucleic Acids Res. 2023 Jan 6;51(D1):D29-D38. doi: 10.1093/nar/gkac1032.
5
Use of Whole Genome Sequencing by the Federal Interagency Collaboration for Genomics for Food and Feed Safety in the United States.美国联邦跨部门基因组学协作组织将全基因组测序用于食品和饲料安全领域
J Food Prot. 2022 May 1;85(5):755-772. doi: 10.4315/JFP-21-437.
6
Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens.优化开放数据以支持“同一健康”理念：确保细菌病原体基因组数据互操作性的最佳实践
One Health Outlook. 2020;2(1):20. doi: 10.1186/s42522-020-00026-3. Epub 2020 Oct 19.
7
Interpretation of Whole-Genome Sequencing for Enteric Disease Surveillance and Outbreak Investigation.肠病监测和暴发调查的全基因组测序解读。
Foodborne Pathog Dis. 2019 Jul;16(7):504-512. doi: 10.1089/fpd.2019.2650. Epub 2019 Jun 27.
8
Utilizing the Public GenomeTrakr Database for Foodborne Pathogen Traceback.利用公共基因组追踪数据库进行食源性病原体溯源。
Methods Mol Biol. 2019;1918:201-212. doi: 10.1007/978-1-4939-9000-9_17.
9
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10
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Front Microbiol. 2017 May 9;8:808. doi: 10.3389/fmicb.2017.00808. eCollection 2017.