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Repository of Antibiotic resistance Cassettes

Bacteria that cause infections are becoming increasingly resistant to antibiotics. In Gram-negative bacteria much of this resistance is caused by mobile resistance genes. Our ability to monitor and predict the spread of resistance in these organisms largely depends on our ability to understand the genetic elements responsible for spread of these resistance genes. We have developed unique technologies that allow us to create an archive of relevant elements and to identify them in bacterial DNA sequences. The aim of this project is to make our knowledge repository of antibiotic resistance gene cassettes (an important mechanism for the spread of resistance) available to the wider research community and to allow researchers to annotate sequences containing gene cassettes using our system and contribute new entries to the repository as these are found.

This system is an on-line application that allows microbiologists to:

  1. browse and explore the gene cassette repository
  2. annotate cassette array sequences using our knowledge base and the Attacca annotation engine
  3. contribute new cassettes not yet in the database and obtain unique names for them

Getting Started

You can browse the cassette database (click on Browse Cassettes above) and once you have registered (click on Login, then register new user), you can annotate sequences using the Attacca engine (Tsafnat G, Coiera E, Partridge SR, Schaeffer J, Iredell JR. Context-driven discovery of gene cassettes in mobile integrons using a computational grammar. BMC Bioinformatics. 2009;10:281).

To annotate a sequence

  1. Select "Annotate new sequence" (login required)
  2. Enter a short description/name for the sequence you want to annotate (this is for your own use)
  3. Choose a sequence type from the drop down (this will affect how your sequence is processed)
  4. Choose the type of DNA molecule if known
  5. Adding species information is optional
  6. Paste in your sequence or upload a FASTA file using the Browse button (up to 5MB per file)
  7. Click "Annotate" to start the annotation process
  8. The sequence will appear in your work area under "My sequences".
  9. You can annotate more sequences without waiting for the annotation to complete.

Important note

By submitting a sequence to be annotated by this system you agree that if a new cassette is identified in your sequence:

  1. It will be assigned a unique name and you will be given this name

  2. It will be added to your own private database on our system where it can't be browsed or used for annotation by other users until it is published by you (i.e. not through this system).
  3. When published by you (i.e. in GenBank or a paper) or by your express permission the cassette will be moved to the public database. It will then appear in the relevant lists under "Browse cassettes" and will be included in the features used to annotate submitted sequences. A reference to the relevant paper will be included in the notes of this cassette.

Sequence Annotation

When a sequence is first submitted its status will be listed as "in progress". Annotation time will depend on the length of your sequence, the load on our system and whether a review is required or not. You can now close the browser and return to the "My sequences" page at a later time to check the status of your sequences.

When the annotation of the sequence is complete, it will say "annotated". Annotated sequences that you no longer require can be deleted by clicking on the "Delete" icon.

If your sequence contains known cassettes from the cassette database and no problems are detected by the system, its status will be changed to "annotated" and you will be able to see the annotation report by clicking on the "View" icon.

In some cases, the system will identify that a review is needed. The status of the sequence will change to "under review" while we review the annotation to ensure its accuracy. After this has been done it's status may change to "annotated" and/or you may receive an e-mail with further information.

If a cassette that is not in our database is identified during the review process then it will be added to your own private database and you will be contacted with its new unique name. Please refer to the important note above.

How to cite

Acknowledgements

RAC is an ANDS funded data capture project funded by ANDS DC5F grant and New South Wales Health Capacity Building and Infrastructure Grant.