Incorrect reporting of R e.g CIP and Enterobacterales?

[antunderwood]

The EUCAST breakpoint table for CIP and Enterobacterales shows This is replicated in you rsi_translation data However this code yields R

> as.rsi(x = as.mic(0.5),
        mo = as.mo("E. coli"),
        ab = "CIP",
        guideline = "EUCAST")
=> Interpreting MIC values of `CIP` (ciprofloxacin) using guideline EUCAST 2020 ... OK.
Class <rsi>
[1] R

I would have expected this to be I

[antunderwood]

I also see similar for Meropenem

> as.rsi(x = as.mic("8"),
+        mo = as.mo("E. coli"),
+        ab = "Meropenem",
+        guideline = "EUCAST",
+        conserve_capped_values = T)
=> Interpreting MIC values of `Meropenem` (MEM, meropenem) using guideline EUCAST 2020 ... OK.
Class <rsi>
[1] R

[msberends]

Right! This is because the "<= S" and ">R". We now interpret it using <= S" and ">=R". So the MIC of 0.5 in this example:

as.rsi(x = as.mic(0.5),
       mo = as.mo("E. coli"),
       ab = "CIP",
       guideline = "EUCAST")

matches the value in rsi_translation$breakpoint_R.

Nice catch! Needs an immediate fix!

[antunderwood]

As far as I can tell for EUCAST, all MIC breakpoints are reported as S <= X and R > Y

[msberends]

Solved in https://github.com/msberends/AMR/commit/4e40e42011b5e16b2f0c7f4ffd206a4e8efa9b1d

[antunderwood]

Thanks for fixing this. Will you be making a new release tag with this fix?

[antunderwood]

Thanks for fixing this. Will you be making a new release tag with this fix?

[msberends]

Yes! We are in the final phase of sending a new version of this package and its manuscripts to our reviewers, so I expect it to release another CRAN version in approximately two weeks.

[antunderwood]

Great news about the the manuscript. If they ask for reviewers, I'd be happy to be considered