Issue with AMR gene identification using tools like CARD (RGI), abricate, Patric, ariba, amrfinderplus.

Question

[sharmatina189059]

Dear All,

I retrieved the lpxD gene sequence from the CARD database and then used the RGI tool or BLAST tool (available under the analyze option in the CARD GUI). However, the same gene sequence shows no hits in either the protein or nucleotide sequences. Can anyone explain why this might be?

I’m asking because I suspected that some AMR genes were present in my genome, but when I performed Prokka annotation, I found these AMR genes which appeared to be absent in the CARD analysis.