Understanding the CARD output

Watch the screencast with Kristy explaining the output from the Comprehensive Antibiotic Resistance Database (CARD) after analyzing a Salmonella genome for antimicrobial resistance (AMR) genes. The CARD database provides detailed information about detected AMR genes, including:

1. Types of Hits: CARD identifies “perfect hits” (100% identity) and “strict hits” (less than perfect but meeting criteria for reporting). Users can modify these criteria.
2. Gene Details: For each detected gene, CARD provides details like the gene’s term, gene family, associated drug classes, resistance mechanism, percent identity, and matched sequence length.
3. Some specific cases are highlighted: – A perfect match gene and an antibiotic efflux pump with 86% identity, which might warrant further investigation. – A gene with less than 40% identity, which might not be a true hit. – An Escherichia coli acrA gene found in Salmonella, which could be of interest for further study.
4. Further Investigation: CARD allows for deeper exploration using the “AMI Genes” tab, showing a visual representation of detected genes and their strict level matches, and providing further information on the sequence alignment to assess the significance of any differences.

Overall, the CARD database helps users analyze and interpret AMR gene data, providing tools for in-depth investigation and validation of potential resistance genes.