CARD (ARO:3004134) suspiciously prevalent in H pylori. Second opinion?

[SJohnsonMayo]

Hi all,

This is referring to the entry for Helicobacter pylori 23S rRNA with mutation conferring resistance to clarithromycin (ARO:3004134) https://card.mcmaster.ca/ontology/41261

I noticed that when I uploaded 10 strains (only 3 of which tested positive for clarithromycin resistance), every strain had 2 mutations called: C1707T and A2144G. I uploaded a couple other random strains from NCBI, they also had the same mutations. Additionally, on the prevalence table on the linked page, it says that the 23s rRNA mutations are 100% prevalent in H. pylori, so I suspect these two mutations will always be called.

[arpcard]

Would you be able to send us the strains you uploaded or, if not, confirm for us that each strain has a T at position 1707 and a G at position 2144? I first need to see if this is an issue with RGI reporting (if the sites don't actually have those nucleotides) or an issue with curation (if these mutations should not be considered resistance-associated). Thanks!

[SJohnsonMayo]

Sure, is there an email address that would be best to send them to?