Saha Saurav B, Uttam Vishwas, Verma Vivek
Department of Computational Biology and Bioinformatics, JSBB, SHIATS Allahabad, Uttar Pradesh, India.
Clinical Vaccine R&D Center, Chonnam National University Hwasun Hospital, Jeonnam, South Korea.
J Clin Pathol. 2015 Aug;68(8):648-51. doi: 10.1136/jclinpath-2015-202927. Epub 2015 May 2.
Despite medical advancements, Escherichia coli-associated infections remain a major public health concern and although an abundant information about E. coli and its antibiotic resistance mechanisms is available, no effective tool exists that integrates gene and genomic data in context to drug resistance, thus raising a need to develop a repository that facilitates integration and assimilation of factors governing drug resistance in E. coli.
User-friendly Comprehensive Antibiotic resistance Repository of Escherichia coli (u-CARE) is a manually curated catalogue of 52 antibiotics with reported resistance, 107 genes, transcription factors and single nucleotide polymorphism (SNPs) involved in multiple drug resistance of this pathogen. Each gene page provides detailed information about its resistance mechanisms, while antibiotic page consists of summary, chemical description and structural descriptors with links to external public databases like GO, CDD, DEG, Ecocyc, KEGG, Drug Bank, PubChem and UniProt. Moreover, the database integrates this reductive information to holistic data such as strain-specific and segment-specific pathogenic islands and operons. In addition, the database offers rich user interface for the visualisation and retrieval of information using various search criteria such as sequence, keyword, image and class search.
u-CARE is aimed to cater to the needs of researchers working in the field of antimicrobial drug resistance with minimal knowledge of bioinformatics. This database is also intended as a guide book to medical practitioners to avoid use of antibiotics against which resistance has already been reported in E. coli. The database is available from: http://www.e-bioinformatics.net/ucare.
尽管医学取得了进步，但大肠杆菌相关感染仍是一个重大的公共卫生问题。虽然已有大量关于大肠杆菌及其抗生素耐药机制的信息，但尚无有效的工具能够将基因和基因组数据与耐药性相关联进行整合，因此需要开发一个有助于整合和吸收大肠杆菌耐药性相关因素的知识库。
用户友好型大肠杆菌综合抗生素耐药知识库（u-CARE）是一个经过人工整理的目录，包含52种有耐药性报道的抗生素、107个与该病原体多重耐药相关的基因、转录因子和单核苷酸多态性（SNP）。每个基因页面提供了其耐药机制的详细信息，而抗生素页面则包含总结、化学描述和结构描述符，并链接到外部公共数据库，如基因本体论（GO）、保守结构域数据库（CDD）、死亡基因数据库（DEG）、大肠杆菌代谢数据库（Ecocyc）、京都基因与基因组百科全书（KEGG）、药物银行（Drug Bank）、化学数据库（PubChem）和通用蛋白质数据库（UniProt）。此外，该数据库将这些简化信息整合到整体数据中，如菌株特异性和片段特异性致病岛及操纵子。此外，该数据库提供了丰富的用户界面，可使用各种搜索标准（如序列、关键词、图像和类别搜索）来可视化和检索信息。
u-CARE旨在满足对抗菌药物耐药性领域研究且生物信息学知识有限的研究人员的需求。该数据库也旨在作为医学从业者的指南，以避免使用大肠杆菌已出现耐药性报道的抗生素。该数据库可从以下网址获取：http://www.e-bioinformatics.net/ucare 。
