Adding CLSI data for intrinsic resistances

[ConnorChato]

Description

Hi all,

Since the intrinsic_resistant table that comes with the package right now only contains EUCAST data and my team uses CLSI, I recently put together a separate table that takes into account the intrinsic resistance values from the most recent CLSI guide. This is formatted to play well with the AMR package, using the standard mo and ab object values for drug/bug names - it's formatted like so...

mo	ab	type	standard
AMR::mo objects	AMR::ab objects	human/animal (factor)	"CLSI"

Not sure what the current intrinsic_resistant table would do for that "type" column, but the standard could just set standard = "EUCAST" for filtering/differentiation.

Anyways, If CLSI data sharing policy would allow and you can imagine an eventual use for this stuff, I'd be happy to share it with your team and save you the manual slogging through excel files / standardizing org names etc.

Excited for that v3.0.0 release 🥳
-Connor

Impacted Field

• Medical (human) microbiology
• Veterinary microbiology
• Environmental microbiology

[msberends]

That’s great!!

How can we find out if those data are allowed to share and distribute? For the clinical breakpoints I asked Barb Jones (CEO of CLSI in 2023) personally and she allowed us - to serve the public cause. So there’s endorsement for that, but I find it a bit edgy to extend that to other CLSI guidelines as well…

[ConnorChato]

For sure, I'll definitely wait until we have some kind of official blessing. My colleague and I are doing some asking around to see if we can get confirmation from some CLSI reps that it's okay. If you have any contacts you may be able to ask on your end, that would also be helpful.