ampC detection for Yersinia

[csavin75]

Hello,

I’ve noticed that the antimicrobial‑resistance gene ampC is only reported for Yersinia when the --plus option is used. Because ampC is an intrinsic chromosomal resistance gene of Yersinia enterocolitica, I would expect it to be detected automatically — just like the blaA and vatF genes, which are reported without the --plus flag.

Could you please adjust the pipeline so that ampC is reported by default, orprovide clarification on why ampC currently requires the --plus option.

Thank you for your help!

[evolarjun]

Hi @csavin75,

I am assuming the --plus flag is the same as the --plus flag for AMRFinderPlus. Intrinsic resistance genes like many chromosomal ampCs are in the 'plus' category in the AMRFinderPlus database because in some taxa they have no effect on resistance.

I realize that behavior is not necessarily consistent with the treatment of blaA and vat(F) in Yersinia. The reason the chromosomal ampC were initially put in the 'plus' category is that early versions of AMRFinderPlus focused on a few taxa like E. coli where the vast majority of the chromosomal ampC variants do not contribute to resistance.

Is there a reason it is problematic to use the --plus flag?

Arjun

[csavin75]

Hi @evolarjun,

Thank you for the clarification.

You’re right, the “--plus” flag works the same way as it does in AMRFinderPlus.

In my view, it makes more sense to treat ampC like blaA and vat(F), since all of these are natural resistance genes in Yersinia. Users who are unaware of this option and run AMRFinderPlus only for canonical AMR genes would otherwise miss ampC, even though it is present in the genome.

Moreover, the “--plus” flag was specifically introduced to enable the discovery of additional functional categories such as virulence factors, stress‑response genes, and similar elements.

Thank you for your help.
Cyril