Centre for Health Informatics, Australian Institute of Health Innovation, University of New South Wales, Australia.
Database (Oxford). 2011 Dec 2;2011:bar054. doi: 10.1093/database/bar054. Print 2011.
Antibiotic resistance in bacteria is often due to acquisition of resistance genes associated with different mobile genetic elements. In Gram-negative bacteria, many resistance genes are found as part of small mobile genetic elements called gene cassettes, generally found integrated into larger elements called integrons. Integrons carrying antibiotic resistance gene cassettes are often associated with mobile elements and here are designated 'mobile resistance integrons' (MRIs). More than one cassette can be inserted in the same integron to create arrays that contribute to the spread of multi-resistance. In many sequences in databases such as GenBank, only the genes within cassettes, rather than whole cassettes, are annotated and the same gene/cassette may be given different names in different entries, hampering analysis. We have developed the Repository of Antibiotic resistance Cassettes (RAC) website to provide an archive of gene cassettes that includes alternative gene names from multiple nomenclature systems and allows the community to contribute new cassettes. RAC also offers an additional function that allows users to submit sequences containing cassettes or arrays for annotation using the automatic annotation system Attacca. Attacca recognizes features (gene cassettes, integron regions) and identifies cassette arrays as patterns of features and can also distinguish minor cassette variants that may encode different resistance phenotypes (aacA4 cassettes and bla cassettes-encoding β-lactamases). Gaps in annotations are manually reviewed and those found to correspond to novel cassettes are assigned unique names. While there are other websites dedicated to integrons or antibiotic resistance genes, none includes a complete list of antibiotic resistance gene cassettes in MRI or offers consistent annotation and appropriate naming of all of these cassettes in submitted sequences. RAC thus provides a unique resource for researchers, which should reduce confusion and improve the quality of annotations of gene cassettes in integrons associated with antibiotic resistance. DATABASE URL: http://www2.chi.unsw.edu.au/rac.
细菌的抗生素耐药性通常是由于获得与不同移动遗传元件相关的耐药基因所致。在革兰氏阴性菌中，许多耐药基因作为称为基因盒的小型移动遗传元件的一部分被发现，这些基因盒通常整合到称为整合子的较大元件中。携带抗生素耐药基因盒的整合子通常与移动元件相关，因此被称为“移动耐药整合子”（MRIs）。在同一个整合子中可以插入多个盒，从而形成有助于多耐药传播的阵列。在 GenBank 等数据库中的许多序列中，只有盒内的基因而不是整个盒被注释，并且同一个基因/盒在不同的条目中有不同的名称，这阻碍了分析。我们开发了抗生素耐药基因盒库（RAC）网站，以提供一个基因盒档案，其中包括来自多个命名系统的替代基因名称，并允许社区贡献新的盒。RAC 还提供了一个额外的功能，允许用户提交包含盒或阵列的序列，使用自动注释系统 Attacca 进行注释。Attacca 识别特征（基因盒、整合子区域），并将盒阵列识别为特征模式，还可以区分可能编码不同耐药表型的微小盒变体（aacA4 盒和编码β-内酰胺酶的 bla 盒）。注释中的空白由人工进行审查，发现与新盒对应的空白被赋予唯一的名称。虽然有其他专门针对整合子或抗生素耐药基因的网站，但没有一个网站包含 MRI 中所有抗生素耐药基因盒的完整列表，也没有在提交的序列中提供所有这些盒的一致注释和适当命名。因此，RAC 为研究人员提供了一个独特的资源，这应该减少混乱并提高与抗生素耐药性相关的整合子中基因盒注释的质量。数据库 URL：http://www2.chi.unsw.edu.au/rac.
