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(v3.0.1.9042) add EUCAST breakpoint table v16 to interpretive_rules()

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dr. M.S. (Matthijs) Berends
2026-04-02 11:42:19 +02:00
parent 3a736bc484
commit 26613d774b
33 changed files with 1765 additions and 1584 deletions
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67
data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R
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@@ -386,18 +386,39 @@ breakpoints_new <- breakpoints_new |> filter(!wrong)
# There's a problem with C. diff in EUCAST where breakpoint_R is missing - they are listed as normal human breakpoints but are ECOFF
# 2025-04-20/ fixed now
# determine rank again now that some changes were made on taxonomic level (genus -> species)
breakpoints_new <- breakpoints_new |>
mutate(rank_index = case_when(
mo_rank(mo, keep_synonyms = TRUE) %like% "(infra|sub)" ~ 1,
mo_rank(mo, keep_synonyms = TRUE) == "species" ~ 2,
mo_rank(mo, keep_synonyms = TRUE) == "species group" ~ 2.5,
mo_rank(mo, keep_synonyms = TRUE) == "genus" ~ 3,
mo_rank(mo, keep_synonyms = TRUE) == "family" ~ 4,
mo_rank(mo, keep_synonyms = TRUE) == "order" ~ 5,
mo != "UNKNOWN" ~ 6, # for B_ANAER, etc.
TRUE ~ 7
))
# WHONET sets for EUCAST 2026 TMP breakpoints for all Klebsiella, but this is now only for non-aerogenes species
kleb_spp <- microorganisms |> filter(rank == "species", genus == "Klebsiella", !species %in% c("", "aerogenes")) |> pull(mo)
kleb_tmp_mic <- breakpoints_new |>
filter(guideline == "EUCAST 2026", method == "MIC", ab == "TMP", mo == as.mo("Klebsiella")) |>
uncount(length(kleb_spp)) |>
mutate(mo = kleb_spp)
kleb_tmp_disk <- breakpoints_new |>
filter(guideline == "EUCAST 2026", method == "DISK", ab == "TMP", mo == as.mo("Klebsiella")) |>
uncount(length(kleb_spp)) |>
mutate(mo = kleb_spp)
breakpoints_new <- breakpoints_new |>
filter(!(guideline == "EUCAST 2026" & method == "MIC" & ab == "TMP" & mo == as.mo("Klebsiella"))) |>
bind_rows(kleb_tmp_mic,
kleb_tmp_disk)
# WHONET contains wrong EUCAST breakpoints for enterococci/SXT: disk should be 23/23, not 21/50, and MIC should be 1/1, not 0.032/1
# applies to all previous years, since v11 (2011)
breakpoints_new |> filter(guideline %like% "EUCAST", ab == "SXT", mo == as.mo("Enterococcus"), type == "human")
breakpoints_new$breakpoint_S[breakpoints_new$guideline %like% "EUCAST" & breakpoints_new$ab == "SXT" & breakpoints_new$mo == as.mo("Enterococcus") & breakpoints_new$type == "human" & breakpoints_new$method == "DISK"] <- 23
breakpoints_new$breakpoint_R[breakpoints_new$guideline %like% "EUCAST" & breakpoints_new$ab == "SXT" & breakpoints_new$mo == as.mo("Enterococcus") & breakpoints_new$type == "human" & breakpoints_new$method == "DISK"] <- 23
breakpoints_new$breakpoint_S[breakpoints_new$guideline %like% "EUCAST" & breakpoints_new$ab == "SXT" & breakpoints_new$mo == as.mo("Enterococcus") & breakpoints_new$type == "human" & breakpoints_new$method == "MIC"] <- 1
breakpoints_new$breakpoint_R[breakpoints_new$guideline %like% "EUCAST" & breakpoints_new$ab == "SXT" & breakpoints_new$mo == as.mo("Enterococcus") & breakpoints_new$type == "human" & breakpoints_new$method == "MIC"] <- 1
# Also wrong EUCAST breakpoints for enterococci/TMP: disk should be 21/21, not 21/50, and MIC should be 1/1, not 0.032/1
breakpoints_new |> filter(guideline %like% "EUCAST", ab == "TMP", mo == as.mo("Enterococcus"), type == "human")
breakpoints_new$breakpoint_S[breakpoints_new$guideline %like% "EUCAST" & breakpoints_new$ab == "TMP" & breakpoints_new$mo == as.mo("Enterococcus") & breakpoints_new$type == "human" & breakpoints_new$method == "DISK"] <- 21
breakpoints_new$breakpoint_R[breakpoints_new$guideline %like% "EUCAST" & breakpoints_new$ab == "TMP" & breakpoints_new$mo == as.mo("Enterococcus") & breakpoints_new$type == "human" & breakpoints_new$method == "DISK"] <- 21
breakpoints_new$breakpoint_S[breakpoints_new$guideline %like% "EUCAST" & breakpoints_new$ab == "TMP" & breakpoints_new$mo == as.mo("Enterococcus") & breakpoints_new$type == "human" & breakpoints_new$method == "MIC"] <- 1
breakpoints_new$breakpoint_R[breakpoints_new$guideline %like% "EUCAST" & breakpoints_new$ab == "TMP" & breakpoints_new$mo == as.mo("Enterococcus") & breakpoints_new$type == "human" & breakpoints_new$method == "MIC"] <- 1
# WHONET still contains PK/PD rules for EUCAST >= 2024, but this was ended from v14 (2024) on
breakpoints_new <- breakpoints_new |>
filter(!(guideline %like% "EUCAST (2024|2025|2026)" & ref_tbl == "PK/PD"))
# WHONET adds one log2 level to the R breakpoint for their software, e.g. in AMC in Enterobacterales:
# EUCAST 2023 guideline: S <= 8 and R > 8
@@ -418,6 +439,7 @@ breakpoints_new <- breakpoints_new |>
breakpoint_R
))
# check the strange duplicates
breakpoints_new |>
mutate(id = paste(guideline, type, host, method, site, mo, ab, uti)) %>%
@@ -430,9 +452,8 @@ breakpoints_new <- breakpoints_new |>
distinct(guideline, type, host, method, site, mo, ab, uti, .keep_all = TRUE)
# CHECKS AND SAVE TO PACKAGE ----
# CHECKS ----
# check again
breakpoints_new |> filter(guideline == "EUCAST 2026", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
# compare with current version
clinical_breakpoints |> filter(guideline == "EUCAST 2025", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
@@ -444,6 +465,24 @@ breakpoints_new |> filter(mo == "B_STRPT_PNMN", ab == "AMP", guideline == "EUCAS
dim(breakpoints_new)
dim(clinical_breakpoints)
# SAVE TO PACKAGE ----
# determine rank again now that some changes were made on taxonomic level (genus -> species)
breakpoints_new <- breakpoints_new |>
mutate(rank_index = case_when(
mo_rank(mo, keep_synonyms = TRUE) %like% "(infra|sub)" ~ 1,
mo_rank(mo, keep_synonyms = TRUE) == "species" ~ 2,
mo_rank(mo, keep_synonyms = TRUE) == "species group" ~ 2.5,
mo_rank(mo, keep_synonyms = TRUE) == "genus" ~ 3,
mo_rank(mo, keep_synonyms = TRUE) == "family" ~ 4,
mo_rank(mo, keep_synonyms = TRUE) == "order" ~ 5,
mo != "UNKNOWN" ~ 6, # for B_ANAER, etc.
TRUE ~ 7
)) |>
# and arrange
arrange(desc(guideline), mo, ab, type, host, method)
clinical_breakpoints <- breakpoints_new
clinical_breakpoints <- clinical_breakpoints |> dataset_UTF8_to_ASCII()
usethis::use_data(clinical_breakpoints, overwrite = TRUE, compress = "xz", version = 2)