• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利：CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法，用中文像聊天一样搜索，搜遍4000万医学文献。AI智能推荐，让科研检索更轻松。

立即免费搜索

文件翻译

保留排版，准确专业，支持PDF/Word/PPT等文件格式，支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述，25分钟生成高质量综述，智能提取关键信息，辅助科研写作。

立即免费体验

CSESA：一个基于 CRISPR 新整合的间隔区对预测沙门氏菌血清型的 R 包。

CSESA: an R package to predict Salmonella enterica serotype based on newly incorporated spacer pairs of CRISPR.

机构信息

Academy of Military Medical Sciences, Beijing, China.

Center for Disease Control and Prevention of PLA, Beijing, China.

出版信息

BMC Bioinformatics. 2019 Apr 27;20(1):215. doi: 10.1186/s12859-019-2806-5.

DOI:10.1186/s12859-019-2806-5
PMID:31029079
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6486994/
Abstract

BACKGROUND

Salmonella enterica is a major cause of bacterial food-borne disease worldwide. Immunological serotyping is the most commonly used typing method to characterize S. enterica isolates, but is time-consuming and requires expensive reagents. Here, we developed an R package CSESA (CRISPR-based Salmonella enterica Serotype Analyzer) to predict the serotype based on the CRISPR loci of S. enterica.

RESULTS

CSESA has implemented the CRISPR typing method CLSPT and extended its coverage on diverse S. enterica serotypes. This package takes CRISPR sequences or the genome sequences as input and provides users with the predicted serotypes. CSESA has shown excellent performance with currently available sequences of S. enterica.

CONCLUSIONS

CSESA is a convenient and useful tool for the prediction of S. enterica serotypes. The application of CSESA package can improve the efficiency of serotyping for S. enterica and reduce the burden of manpower resources. CSESA is freely available from CRAN at https://cran.r-project.org/web/packages/CSESA/ .

摘要

背景

肠沙门氏菌是全球范围内导致细菌性食源性疾病的主要原因。免疫血清学分型是用于表征肠沙门氏菌分离株的最常用分型方法，但耗时且需要昂贵的试剂。在这里，我们开发了一个基于 CRISPR 的肠沙门氏菌血清型分析器（CSESA）的 R 包，用于基于肠沙门氏菌的 CRISPR 基因座预测血清型。

结果

CSESA 实现了 CRISPR 分型方法 CLSPT，并扩展了其对不同肠沙门氏菌血清型的覆盖范围。该软件包以 CRISPR 序列或基因组序列为输入，并为用户提供预测的血清型。CSESA 对目前可用的肠沙门氏菌序列表现出优异的性能。

结论

CSESA 是预测肠沙门氏菌血清型的便捷、有用的工具。CSESA 软件包的应用可以提高肠沙门氏菌血清分型的效率，减少人力资源的负担。CSESA 可在 https://cran.r-project.org/web/packages/CSESA/ 从 CRAN 免费获得。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b4ba/6486994/644185266802/12859_2019_2806_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b4ba/6486994/7f05fa624a14/12859_2019_2806_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b4ba/6486994/60ee1e3783b9/12859_2019_2806_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b4ba/6486994/644185266802/12859_2019_2806_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b4ba/6486994/7f05fa624a14/12859_2019_2806_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b4ba/6486994/60ee1e3783b9/12859_2019_2806_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b4ba/6486994/644185266802/12859_2019_2806_Fig3_HTML.jpg

相似文献

1
CSESA: an R package to predict Salmonella enterica serotype based on newly incorporated spacer pairs of CRISPR.CSESA：一个基于 CRISPR 新整合的间隔区对预测沙门氏菌血清型的 R 包。
BMC Bioinformatics. 2019 Apr 27;20(1):215. doi: 10.1186/s12859-019-2806-5.
2
New clustered regularly interspaced short palindromic repeat locus spacer pair typing method based on the newly incorporated spacer for Salmonella enterica.基于新纳入间隔序列的肠炎沙门氏菌新型成簇规律间隔短回文重复序列位点间隔序列对分型方法
J Clin Microbiol. 2014 Aug;52(8):2955-62. doi: 10.1128/JCM.00696-14. Epub 2014 Jun 4.
3
Whole-genome sequencing analysis and CRISPR genotyping of rare antibiotic-resistant Salmonella enterica serovars isolated from food and related sources.对从食品及相关来源分离的罕见耐药性沙门氏菌血清型进行全基因组测序分析和 CRISPR 基因分型。
Food Microbiol. 2021 Feb;93:103601. doi: 10.1016/j.fm.2020.103601. Epub 2020 Aug 4.
4
Genetic analysis of Salmonella enterica serovar Gallinarum biovar Pullorum based on characterization and evolution of CRISPR sequence.基于CRISPR序列特征及进化的鸡白痢沙门氏菌遗传分析
Vet Microbiol. 2017 May;203:81-87. doi: 10.1016/j.vetmic.2017.02.010. Epub 2017 Feb 27.
5
CRISPR Typing of Salmonella Isolates from Different Resources.从不同来源分离的沙门氏菌的 CRISPR 分型。
Methods Mol Biol. 2021;2182:45-50. doi: 10.1007/978-1-0716-0791-6_6.
6
Novel virulence gene and clustered regularly interspaced short palindromic repeat (CRISPR) multilocus sequence typing scheme for subtyping of the major serovars of Salmonella enterica subsp. enterica.新型毒力基因和成簇规律间隔短回文重复序列（CRISPR）多位点序列分型方案，用于对肠沙门氏菌亚种肠沙门氏菌的主要血清型进行亚型分型。
Appl Environ Microbiol. 2011 Mar;77(6):1946-56. doi: 10.1128/AEM.02625-10. Epub 2011 Jan 28.
7
High-Resolution Identification of Multiple Salmonella Serovars in a Single Sample by Using CRISPR-SeroSeq.利用 CRISPR-SeroSeq 对单个样本中的多种沙门氏菌血清型进行高分辨率鉴定。
Appl Environ Microbiol. 2018 Oct 17;84(21). doi: 10.1128/AEM.01859-18. Print 2018 Nov 1.
8
Characterization of CRISPR array in Salmonella enterica from asymptomatic people and patients.对无症状人群和患者体内沙门氏菌中的 CRISPR 基因簇进行分析。
Int J Food Microbiol. 2021 Oct 2;355:109338. doi: 10.1016/j.ijfoodmicro.2021.109338. Epub 2021 Jul 24.
9
Incidence of Salmonella serovars isolated from commercial animal feed mills in the United States and serovar identification using CRISPR analysis.美国商业动物饲料厂分离的沙门氏菌血清型的发生率和使用 CRISPR 分析进行血清型鉴定。
J Appl Microbiol. 2021 Jun;130(6):2141-2146. doi: 10.1111/jam.14933. Epub 2020 Nov 29.
10
Conserved CRISPR arrays in Salmonella enterica serovar Infantis can serve as qPCR targets to detect Infantis in mixed serovar populations.沙门氏菌肠炎亚种中的保守 CRISPR 数组可用作 qPCR 靶标，以检测混合血清型群体中的肠炎亚种。
Lett Appl Microbiol. 2020 Aug;71(2):138-145. doi: 10.1111/lam.13296. Epub 2020 May 13.

引用本文的文献

1
Typing methods based on whole genome sequencing data.基于全基因组测序数据的分型方法。
One Health Outlook. 2020 Feb 18;2:3. doi: 10.1186/s42522-020-0010-1. eCollection 2020.

本文引用的文献

1
Characterization and evolution of Salmonella CRISPR-Cas systems.沙门氏菌CRISPR-Cas系统的特征与进化
Microbiology (Reading). 2015 Feb;161(2):374-386. doi: 10.1099/mic.0.000005.
2
New clustered regularly interspaced short palindromic repeat locus spacer pair typing method based on the newly incorporated spacer for Salmonella enterica.基于新纳入间隔序列的肠炎沙门氏菌新型成簇规律间隔短回文重复序列位点间隔序列对分型方法
J Clin Microbiol. 2014 Aug;52(8):2955-62. doi: 10.1128/JCM.00696-14. Epub 2014 Jun 4.
3
The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp. enterica.
CRISPR-Cas 系统在肠炎沙门氏菌亚种内的进化历史和诊断效用。
PeerJ. 2014 Apr 17;2:e340. doi: 10.7717/peerj.340. eCollection 2014.
4
Comparison of typing methods with a new procedure based on sequence characterization for Salmonella serovar prediction.基于序列特征的新型沙门氏菌血清型预测方法与传统分型方法的比较。
J Clin Microbiol. 2013 Jun;51(6):1786-97. doi: 10.1128/JCM.03201-12. Epub 2013 Apr 3.
5
CRISPR typing and subtyping for improved laboratory surveillance of Salmonella infections.CRISPR 分型和亚型分析可提高沙门氏菌感染的实验室监测水平。
PLoS One. 2012;7(5):e36995. doi: 10.1371/journal.pone.0036995. Epub 2012 May 18.
6
Prediction system for rapid identification of Salmonella serotypes based on pulsed-field gel electrophoresis fingerprints.基于脉冲场凝胶电泳指纹图谱的沙门氏菌血清型快速鉴定预测系统。
J Clin Microbiol. 2012 May;50(5):1524-32. doi: 10.1128/JCM.00111-12. Epub 2012 Feb 29.
7
Methodologies for Salmonella enterica subsp. enterica subtyping: gold standards and alternatives.肠沙门氏菌亚种肠亚种分型方法：金标准和替代方法。
Appl Environ Microbiol. 2011 Nov;77(22):7877-85. doi: 10.1128/AEM.05527-11. Epub 2011 Aug 19.
8
The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella.短小、缓慢且专一的 Escherichia 和 Salmonella 的 CRISPR 与抗 CRISPR。
PLoS One. 2010 Jun 15;5(6):e11126. doi: 10.1371/journal.pone.0011126.
9
The global burden of nontyphoidal Salmonella gastroenteritis.非伤寒型沙门氏菌肠炎的全球负担。
Clin Infect Dis. 2010 Mar 15;50(6):882-9. doi: 10.1086/650733.
10
BLAST+: architecture and applications.BLAST+：体系结构与应用。
BMC Bioinformatics. 2009 Dec 15;10:421. doi: 10.1186/1471-2105-10-421.