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arpcard / rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
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Resistance genes not identified by RGI #238

Closed btroppo closed 11 months ago

btroppo commented 11 months ago

Hello, what is the main reason for not all resistance genes being present in CARD? For example, a protein sequence was identified by RGI as a loose hit (30-40% identity) to Bcr-1 from Pseudomonas spp., however if that same sequence is searched in another database, i.e. NCBI nr or Uniprot, the protein is identified with 100% aa identity to a Bcr family drug resistance efflux transporter from E. albertii. Although these two proteins confer resistance to bicyclomycin, they are only share 35% aa identity

springwang24 commented 11 months ago

Hello,

Thank you for your question. For a gene to be included in the CARD, it must have been published in a peer reviewed article with evidence of an elevated MIC. The discrepancy between the CARD and other databases, like NCBI, is because many sequences in NCBI have homology to AMR gene sequences but this does not guarantee they are ARGs or that any variants that have been published are AMR determinants.

If you have found a bicyclomycin resistant protein with a publication containing the supporting evidence that we do not have in the CARD, then this is a missed curation. Please feel free to link the reference for us to take a look!

I hope this helps.

-- Spring Wang Junior CARD Curator

raphenya commented 11 months ago

Thank you @springwang24! @btroppo please re-open the issue if you have more questions or information. Cheers.