Incorporate NARMS breakpoints

[befriendabacterium]

Description

Lovely package, well done! I work in agricultural AMR and am wondering about the possibility/feasibility/compatibility of incorporating the NARMS breakpoints for foodborne and enteric pathogens into the package (https://www.cdc.gov/narms/about/antibiotics-tested.html). I am happy to have a look and try to contribute myself (already forked!) but want to ask if you have considered this before first, and get a sense of your workflow first.

Cheers
Matt

Use Case (optional)

Researchers working on agricultural AMR

[msberends]

Thanks so much for using the package, and especially for the nice suggestion!

It looks like this could quite easily be supported. Do you happen to know whether NARMS also provides more structured documents than their website tables? They are quite hard to scrape, although it could be done.

[befriendabacterium]

Hi Matthijs - glad you like the suggestion! I'm pretty sure NARMS is mainly accessed via this not-so-convenient website table format, unfortunately! This is how people cite it when they use it from what I've seen, anyway.

However, there are some resources here which contains a link to the 2021 interpretive categories for Salmonella, E. coli, Campylobacter and Enterococcus. However, Shigella and Vibrio which are in the website tables are not there, Enterococcus is there but not on the website, and the antibiotics tested also differ a bit between the two resources (I assume some of this is because the list of tested antibiotics has evolved over the years...)!

In short, the data is currently quite poorly accessible and scattered in different locations, making incorporating it into the package both hard but all the more worthwhile if it can be done sensibly! Let me know if you would like a hand with this, maybe I can take some of the load off you.

Cheers
Matt