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Antimicrobial Resistance Genes

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Finlay Maguire edited this page Sep 11, 2021 · 5 revisions

Antimicrobial Resistance Genes

What is an AMR gene in an ecological sense? This review paper is a good place to start.

In the context of the Comprehensive Antibiotic Resistance Database it is any gene that has a paper showing elevated AMR.

This is an excellent review of the ways sequencing is used to study AMR (and figure 1 is a great summary of the classes of antimicrobials and sources of resistance).

For CARD specific details including RGI: the state of the CARD videos provide a great introduction.

Types of AMR

Using the language of CARD, the 3 biggest types (although there are more):

  • homolog models: genes that confer resistance if they are present (and expressed) such as beta-lactamases which destroy certain antimicrobials (beta-lactams such as penicillin)

  • variant models: genes that confer resistance if they have specific mutations such as rRNAs and KatG.

  • efflux models: groups of genes that create can actively pump out antimicrobials from the cell (very expression level dependent).

Actively Maintained AMR databases

There are many dead/dying and unmaintained AMR databases even ones published relatively recently! Make sure the one you use has been updated in the last couple of months. The big 3 actively curated and constantly maintained databases are:

  • CARD (used by RGI tool to identify AMR genes)

  • NCBI AMR catalogue (used by NCBI AMRFinderPlus tool to identify AMR genes)

  • ResFinder (used by ResFinder tool to identify AMR genes)

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