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本文引用的文献

1
Genome Wide Search for Biomarkers to Diagnose Yersinia Infections.全基因组搜索诊断耶尔森氏菌感染的生物标志物。
Indian J Microbiol. 2015 Dec;55(4):366-74. doi: 10.1007/s12088-015-0552-6. Epub 2015 Sep 9.
2
Rapid and Sensitive Detection of Vibrio alginolyticus by Loop-Mediated Isothermal Amplification Combined with a Lateral Flow Dipstick Targeted to the rpoX Gene.环介导等温扩增结合针对rpoX基因的侧向流动试纸条快速灵敏检测溶藻弧菌
J Aquat Anim Health. 2015 Sep;27(3):156-63. doi: 10.1080/08997659.2015.1037468.
3
Intra-Genomic Heterogeneity in 16S rRNA Genes in Strictly Anaerobic Clinical Isolates from Periodontal Abscesses.牙周脓肿严格厌氧临床分离株中16S rRNA基因的基因组内异质性
PLoS One. 2015 Jun 23;10(6):e0130265. doi: 10.1371/journal.pone.0130265. eCollection 2015.
4
Genome Wide Analysis for Searching Novel Markers to Rapidly Identify Clostridium Strains.全基因组分析以寻找新型标记物来快速鉴定梭菌菌株。
Indian J Microbiol. 2015 Sep;55(3):250-7. doi: 10.1007/s12088-015-0535-7. Epub 2015 May 14.
5
Insights into the Origin of Clostridium botulinum Strains: Evolution of Distinct Restriction Endonuclease Sites in rrs (16S rRNA gene).肉毒梭菌菌株起源的研究进展：rrs（16S rRNA 基因）中独特限制性内切酶位点的进化。
Indian J Microbiol. 2015 Jun;55(2):140-50. doi: 10.1007/s12088-015-0514-z. Epub 2015 Jan 18.
6
Development of Genomic Tools for the Identification of Certain Pseudomonas up to Species Level.用于鉴定某些假单胞菌至种水平的基因组工具的开发。
Indian J Microbiol. 2013 Sep;53(3):253-63. doi: 10.1007/s12088-013-0412-1. Epub 2013 Apr 23.
7
Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology.基质辅助激光解吸电离飞行时间质谱：临床微生物学常规实践的根本性转变。
Clin Microbiol Rev. 2013 Jul;26(3):547-603. doi: 10.1128/CMR.00072-12.
8
A pentaplex PCR assay for detection and characterization of Vibrio vulnificus and Vibrio parahaemolyticus isolates.一种用于检测和鉴定创伤弧菌和副溶血性弧菌分离株的五重 PCR 检测方法。
Lett Appl Microbiol. 2013 Sep;57(3):233-40. doi: 10.1111/lam.12101. Epub 2013 Jun 13.
9
Development of duplex-PCR for identification of Aeromonas species.建立用于鉴定气单胞菌属的双重 PCR 方法。
Rev Soc Bras Med Trop. 2013 May-Jun;46(3):355-7. doi: 10.1590/0037-8682-1344-2013.
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Molecular epidemiology of Vibrio cholerae causing outbreaks & sporadic cholera in northern India.印度北部引起暴发和散发霍乱的霍乱弧菌的分子流行病学研究。
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用于快速鉴定弧菌属物种的全基因组分析

Genome Wide Analysis for Rapid Identification of Vibrio Species.

作者信息

Kalia Vipin Chandra, Kumar Prasun, Kumar Ravi, Mishra Anjali, Koul Shikha

机构信息

Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007 India ; Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India.

Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007 India.

出版信息

Indian J Microbiol. 2015 Dec;55(4):375-83. doi: 10.1007/s12088-015-0553-5. Epub 2015 Sep 7.

DOI:10.1007/s12088-015-0553-5
PMID:26543262
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4627950/
Abstract

The highly conserved 16S rRNA (rrs) gene is generally used for bacterial identification. In organisms possessing multiple copies of rrs, high intra-genomic heterogeneity does not allow easy distinction among different species. In order to identify Vibrio species, a wide range of genes have been employed. There is an urgent requirement of a consensus gene, which can be used as biomarker for rapid identification. Eight sequenced genomes of Vibrio species were screened for selecting genes which were common among all the genomes. Out of 108 common genes, 24 genes of sizes varying from 0.11 to 3.94 kb were subjected to in silico digestion with 10 type II restriction endonucleases (RE). A few unique genes-dapF, fadA, hisD, ilvH, lpxC, recF, recR, rph and ruvB in combination with certain REs provided unique digestion patterns, which can be used as biomarkers. This protocol can be exploited for rapid diagnosis of Vibrio species.

摘要

高度保守的16S rRNA（rrs）基因通常用于细菌鉴定。在拥有多个rrs拷贝的生物体中，高基因组内异质性使得不同物种之间难以区分。为了鉴定弧菌属物种，人们采用了多种基因。迫切需要一种共识基因，可作为快速鉴定的生物标志物。对8个已测序的弧菌属物种基因组进行筛选，以选择在所有基因组中都常见的基因。在108个常见基因中，选择了24个大小从0.11到3.94 kb不等的基因，用10种II型限制性内切酶（RE）进行电子消化。一些独特的基因——dapF、fadA、hisD、ilvH、lpxC、recF、recR、rph和ruvB与某些RE结合，提供了独特的消化模式，可作为生物标志物。该方案可用于弧菌属物种的快速诊断。