Once we have an annotated genome we can begin to search for antimicrobial resistance genes (ARGs). It is possible to search through all the annotations manually, however there are specialised databases and bioinformatic tools available to help automate the process of identifying ARGs. These tools typically work by comparing the input genome against known ARG databases; they use different algorithms to perform sequence alignment and find regions of the genome that match database entries, and then report on the gene ID, function, and resistance mechanisms of the hits.

Open access resources for identifying ARGs: 

• CARD – the Comprehensive Antibiotic Resistance Database (CARD) is an expert-curated collection of molecular sequences and mutations linked to AMR.
• AMRFinderPlus – a bioinformatic tool that identifies antimicrobial resistance genes
• ResFinder – An online tool for the identification of ARGs and prediction of phenotypes in bacterial sequencing data. 
• ABRicate – A bioinformatic tool for the mass screening of sequencing data for ARGs and virulence genes.
• Resistance Gene Identifier (RGI) –  A tool provided by CARD for the prediction of ARGs from protein or nucleotide data. 

When using these tools it is good practice to manually inspect the identified genes, especially if there are low-confidence predictions, in order to ensure there are no false positive hits. 

In the next section we will cover some of the different ways in which you can investigate these genes further using EMBL-EBI resources.