as.sir(): capped MIC prefix handling incorrect when S breakpoint equals lowest valid MIC (e.g. CIP in Staphylococcus)

[msberends]

Bug report

Reported by an AMR package user.

Summary

When the EUCAST S breakpoint is set to the lowest clinically meaningful MIC (e.g. CIP in Staphylococcus aureus: S ≤ 0.001, R > 2), capped MIC values with a < or <= prefix are interpreted incorrectly depending on capped_mic_handling:

• "standard" (default): <=0.5, <=0.25 → NI instead of I
• "lenient": <=0.5, <0.5, <=0.25, <0.25 → S even though these values are not below the S breakpoint (0.001)
• "none": returns I for all of the above, which is arguably correct

Reproducible example

my_mic <- as.mic(c(">4", ">=4", ">2", ">=2", 2, 1, 0.5, 0.25, 0.125,
                   0.012, 0.06, 0.03, 0.02, 0.01, 0.001,
                   "<=0.5", "<0.5", "<=0.25", "<0.25"))

tibble(
  mic                    = my_mic,
  interpretation         = as.sir(my_mic, mo = "Staphylococcus aureus", ab = "CIP"),
  no_handling            = as.sir(my_mic, mo = "Staphylococcus aureus", ab = "CIP", capped_mic_handling = "none"),
  lenient_interpretation = as.sir(my_mic, mo = "Staphylococcus aureus", ab = "CIP", capped_mic_handling = "lenient"),
  standard_interpretation= as.sir(my_mic, mo = "Staphylococcus aureus", ab = "CIP", capped_mic_handling = "standard")
)

Observed output

mic	interpretation	no_handling	lenient	standard
>=2.000	NI	I	R	NI
<=0.500	NI	I	S	NI
<0.500	S	I	S	S
<=0.250	NI	I	S	NI
<0.250	S	I	S	S

Expected behaviour

For capped_mic_handling = "lenient": < and <= prefixed MICs that are above the S breakpoint should return I, not S. The current implementation of "lenient" unconditionally maps all </<= values to S, ignoring whether the capped value actually falls below the S breakpoint.

Suggested fix: In "lenient" mode, only return S when the numeric part of the capped MIC is strictly below the S breakpoint. If the numeric part is ≥ S breakpoint (but ≤ R breakpoint), return I instead.

This would make <0.5, <=0.5, <0.25, <=0.25 all return I for CIP/S. aureus (EUCAST), which is clinically correct — a MIC reported as <=0.5 is definitely not susceptible when S requires MIC ≤ 0.001.

Context

• Drug/organism: Ciprofloxacin (CIP) in Staphylococcus aureus, EUCAST 2026
• Breakpoints: S ≤ 0.001 mg/L, R > 2 mg/L
• AMR version: (please confirm)
• R version: (please confirm)