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(v3.0.1.9084) Fix breakpoint infer rules

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dr. M.S. (Matthijs) Berends
2026-07-09 17:14:59 +02:00
parent ea996c8361
commit 9237bfbc19
24 changed files with 545 additions and 318 deletions
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66
data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R
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@@ -503,6 +503,72 @@ dim(breakpoints_new)
dim(clinical_breakpoints)
# Correct anaerobic bacteria in EUCAST ----
eucast_anaerobe_corrections <- tibble::tribble(
~guideline, ~type, ~host, ~method, ~site, ~mo, ~rank_index, ~ab, ~ref_tbl, ~disk_dose, ~breakpoint_S, ~breakpoint_R, ~uti, ~is_SDD,
# Prevotella spp.
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Prevotella"), 3, as.ab("AMP"), "Prevotella", NA, 0.5, 0.5, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Prevotella"), 3, as.ab("AMP"), "Prevotella", "2 mcg", 25, 25, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Prevotella"), 3, as.ab("SAM"), "Prevotella", "10/10 mcg", 33, 33, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Prevotella"), 3, as.ab("AMX"), "Prevotella", NA, 0.25, 0.25, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Prevotella"), 3, as.ab("AMC"), "Prevotella", "2/1 mcg", 24, 24, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Prevotella"), 3, as.ab("ETP"), "Prevotella", NA, 0.5, 0.5, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Prevotella"), 3, as.ab("ETP"), "Prevotella", "10 mcg", 29, 29, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Prevotella"), 3, as.ab("IPM"), "Prevotella", NA, 0.125, 0.125, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Prevotella"), 3, as.ab("IPM"), "Prevotella", "10 mcg", 35, 35, FALSE, FALSE,
# Fusobacterium necrophorum
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Fusobacterium necrophorum"), 2, as.ab("AMP"), "F. necrophorum", NA, 0.5, 0.5, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Fusobacterium necrophorum"), 2, as.ab("AMP"), "F. necrophorum", "2 mcg", 27, 27, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Fusobacterium necrophorum"), 2, as.ab("SAM"), "F. necrophorum", NA, 0.5, 0.5, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Fusobacterium necrophorum"), 2, as.ab("SAM"), "F. necrophorum", "10/10 mcg", 33, 33, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Fusobacterium necrophorum"), 2, as.ab("AMX"), "F. necrophorum", NA, 0.5, 0.5, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Fusobacterium necrophorum"), 2, as.ab("AMC"), "F. necrophorum", NA, 0.5, 0.5, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Fusobacterium necrophorum"), 2, as.ab("AMC"), "F. necrophorum", "2/1 mcg", 23, 23, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Fusobacterium necrophorum"), 2, as.ab("ETP"), "F. necrophorum", NA, 0.06, 0.06, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Fusobacterium necrophorum"), 2, as.ab("ETP"), "F. necrophorum", "10 mcg", 35, 35, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Fusobacterium necrophorum"), 2, as.ab("IPM"), "F. necrophorum", NA, 0.125, 0.125, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Fusobacterium necrophorum"), 2, as.ab("IPM"), "F. necrophorum", "10 mcg", 36, 36, FALSE, FALSE,
# Clostridium perfringens
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Clostridium perfringens"), 2, as.ab("AMP"), "C. perfringens", NA, 0.25, 0.25, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Clostridium perfringens"), 2, as.ab("AMP"), "C. perfringens", "2 mcg", 23, 23, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Clostridium perfringens"), 2, as.ab("SAM"), "C. perfringens", NA, 0.25, 0.25, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Clostridium perfringens"), 2, as.ab("SAM"), "C. perfringens", "10/10 mcg", 27, 27, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Clostridium perfringens"), 2, as.ab("AMX"), "C. perfringens", NA, 0.25, 0.25, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Clostridium perfringens"), 2, as.ab("AMC"), "C. perfringens", NA, 0.25, 0.25, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Clostridium perfringens"), 2, as.ab("AMC"), "C. perfringens", "2/1 mcg", 23, 23, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Clostridium perfringens"), 2, as.ab("ETP"), "C. perfringens", NA, 0.5, 0.5, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Clostridium perfringens"), 2, as.ab("ETP"), "C. perfringens", "10 mcg", 24, 24, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Clostridium perfringens"), 2, as.ab("IPM"), "C. perfringens", NA, 0.5, 0.5, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Clostridium perfringens"), 2, as.ab("IPM"), "C. perfringens", "10 mcg", 25, 25, FALSE, FALSE,
# Cutibacterium acnes
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Cutibacterium acnes"), 2, as.ab("AMP"), "C. acnes", NA, 0.25, 0.25, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Cutibacterium acnes"), 2, as.ab("AMP"), "C. acnes", "2 mcg", 23, 23, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Cutibacterium acnes"), 2, as.ab("SAM"), "C. acnes", "10/10 mcg", 33, 33, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Cutibacterium acnes"), 2, as.ab("AMX"), "C. acnes", NA, 0.25, 0.25, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Cutibacterium acnes"), 2, as.ab("AMC"), "C. acnes", "2/1 mcg", 24, 24, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Cutibacterium acnes"), 2, as.ab("CTX"), "C. acnes", "5 mcg", 26, 26, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Cutibacterium acnes"), 2, as.ab("CRO"), "C. acnes", NA, 0.06, 0.06, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Cutibacterium acnes"), 2, as.ab("CRO"), "C. acnes", "30 mcg", 33, 33, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Cutibacterium acnes"), 2, as.ab("ETP"), "C. acnes", NA, 0.25, 0.25, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Cutibacterium acnes"), 2, as.ab("ETP"), "C. acnes", "10 mcg", 28, 28, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Cutibacterium acnes"), 2, as.ab("IPM"), "C. acnes", NA, 0.03, 0.03, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Cutibacterium acnes"), 2, as.ab("IPM"), "C. acnes", "10 mcg", 39, 39, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Cutibacterium acnes"), 2, as.ab("LNZ"), "C. acnes", NA, 2, 2, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Cutibacterium acnes"), 2, as.ab("LNZ"), "C. acnes", "10 mcg", 34, 34, FALSE, FALSE
)
breakpoints_new <- clinical_breakpoints |>
bind_rows(eucast_anaerobe_corrections) |>
bind_rows(eucast_anaerobe_corrections |> mutate(guideline = "EUCAST 2026")) |>
bind_rows(eucast_anaerobe_corrections |> mutate(guideline = "EUCAST 2023")) |>
bind_rows(eucast_anaerobe_corrections |> mutate(guideline = "EUCAST 2024"))
# SAVE TO PACKAGE ----
# determine rank again now that some changes were made on taxonomic level (genus -> species)