Abstract
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.
Highlights
Antibiotic resistance in bacteria is often due to the acquisition of mobile resistance genes by horizontal gene transfer [1] mediated by the actions of two different types of mobile elements
In Gram-negative bacteria, in particular, a wide range of antibiotic resistance genes are found as part of small mobile elements of the second type, called gene cassettes [2]
Class 1 integrons are the most commonly identified in clinical isolates, several other intI/attI combinations are with associated mobile elements and resistance cassettes. intI2/attI2 of Class 2 integrons are usually found as part of the transposon Tn7 [7] in which conserved regions different from the 50-CS and 30-conserved segment (30-CS) flank the cassette array (Figure 1D). intI3/attI3 of Class 3 integrons are thought to be associated with a transposon [8] and a few examples of Class 4 integrons have been identified to be inserted in integrative conjugative elements [9], whereas the sequence of the only available example of a Class 5 integron, found on a plasmid (GenBank accession AJ277063), ends within the cassette array
Summary
Antibiotic resistance in bacteria is often due to the acquisition of mobile resistance genes by horizontal ( called lateral) gene transfer [1] mediated by the actions of two different types of mobile elements. IntI3/attI3 of Class 3 integrons are thought to be associated with a transposon [8] and a few examples of Class 4 integrons have been identified to be inserted in integrative conjugative elements [9], whereas the sequence of the only available example of a Class 5 integron, found on a plasmid (GenBank accession AJ277063), ends within the cassette array These five types of integron associated with mobile elements and carrying a few cassettes mainly encoding antibiotic resistance genes are designated ‘mobile-resistance integrons’ (MRIs) to distinguish them from chromosomal integrons (CIs; referred to as ‘superintegrons’). If the user provides explicit written permission or when the cassette is published elsewhere (in GenBank or a journal), it will be added to the public cassette database with a reference to the appropriate GenBank entry or paper
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