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Gene cassettes and cassette arrays in mobile resistance integrons
Authors:Sally R Partridge  Guy Tsafnat  Enrico Coiera  & Jonathan R Iredell
Institution:Centre for Infectious Diseases and Microbiology, University of Sydney, Westmead Hospital, Sydney, NSW, Australia;and;Centre for Health Informatics, University of New South Wales, Sydney, NSW, Australia
Abstract:Gene cassettes are small mobile elements, consisting of little more than a single gene and recombination site, which are captured by larger elements called integrons. Several cassettes may be inserted into the same integron forming a tandem array. The discovery of integrons in the chromosome of many species has led to the identification of thousands of gene cassettes, mostly of unknown function, while integrons associated with transposons and plasmids carry mainly antibiotic resistance genes and constitute an important means of spreading resistance. An updated compilation of gene cassettes found in sequences of such 'mobile resistance integrons' in GenBank was facilitated by a specially developed automated annotation system. At least 130 different (<98% identical) cassettes that carry known or predicted antibiotic resistance genes were identified, along with many cassettes of unknown function. We list exemplar GenBank accession numbers for each and address some nomenclature issues. Various modifications to cassettes, some of which may be useful in tracking cassette epidemiology, are also described. Despite potential biases in the GenBank dataset, preliminary analysis of cassette distribution suggests interesting differences between cassettes and may provide useful information to direct more systematic studies.
Keywords:gene cassette  integron  antibiotic resistance  nomenclature  bioinformatics  computer-aided discovery
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