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Update clinical breakpoints and fix some as.mo() bugs (#117)
* Updates clinical breakpoints EUCAST/CLSI 2023, fixes #102, fixes #112, fixes #113, fixes #114, fixes #115 * docs * implement ecoffs * unit tests
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Dr. Matthijs Berends
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@@ -73,6 +73,7 @@ whonet_organisms.bak <- whonet_organisms
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# generate the mo codes and add their names
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whonet_organisms <- whonet_organisms.bak %>%
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mutate(mo = as.mo(gsub("(sero[a-z]*| complex| nontypable| non[-][a-zA-Z]+|var[.]| not .*|sp[.],.*|, .*variant.*|, .*toxin.*|, microaer.*| beta-haem[.])", "", ORGANISM),
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minimum_matching_score = 0.6,
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keep_synonyms = TRUE,
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language = "en"),
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mo = case_when(ORGANISM %like% "Anaerobic" & ORGANISM %like% "negative" ~ as.mo("B_ANAER-NEG"),
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@@ -86,17 +87,21 @@ whonet_organisms <- whonet_organisms.bak %>%
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new_mo_codes <- whonet_organisms %>%
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mutate(
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first_part = sapply(ORGANISM, function(x) strsplit(gsub("[^a-zA-Z _-]+", "", x), " ")[[1]][1], USE.NAMES = FALSE),
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keep = mo_name %like_case% first_part | ORGANISM %like% "Gram " | ORGANISM == "Other" | ORGANISM %like% "anaerobic")
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keep = mo_name %like_case% first_part | ORGANISM %like% "Gram " | ORGANISM == "Other" | ORGANISM %like% "anaerobic") %>%
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filter(keep == TRUE) %>%
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transmute(code = toupper(ORGANISM_CODE),
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mo = mo)
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# update microorganisms.codes with the latest WHONET codes
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microorganisms.codes <- microorganisms.codes %>%
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microorganisms.codes2 <- microorganisms.codes %>%
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# remove all old WHONET codes, whether we (in the end) keep them or not
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filter(!toupper(code) %in% toupper(whonet_organisms$ORGANISM_CODE)) %>%
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filter(!toupper(code) %in% toupper(new_mo_codes$code)) %>%
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# and add the new ones
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bind_rows(new_mo_codes %>%
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filter(keep == TRUE) %>%
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transmute(code = toupper(ORGANISM_CODE),
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mo = mo)) %>%
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bind_rows(new_mo_codes) %>%
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arrange(code)
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# new codes:
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microorganisms.codes2$code[which(!microorganisms.codes2$code %in% microorganisms.codes$code)]
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mo_name(microorganisms.codes2$mo[which(!microorganisms.codes2$code %in% microorganisms.codes$code)], keep_synonyms = TRUE)
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microorganisms.codes <- microorganisms.codes2
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# Run this part to update ASIARS-Net:
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# start
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@@ -140,11 +145,11 @@ whonet_antibiotics <- read_tsv("data-raw/WHONET/Resources/Antibiotics.txt", na =
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breakpoints <- whonet_breakpoints %>%
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mutate(code = toupper(ORGANISM_CODE)) %>%
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left_join(bind_rows(microorganisms.codes,
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left_join(bind_rows(microorganisms.codes %>% filter(!code %in% c("ALL", "GEN")),
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# GEN (Generic) and ALL (All) are PK/PD codes
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data.frame(code = c("ALL", "GEN"),
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mo = rep(as.mo("UNKNOWN"), 2))))
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# these ones lack a MO name, they cannot be used:
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# these ones lack an MO name, they cannot be used:
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unknown <- breakpoints %>%
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filter(is.na(mo)) %>%
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pull(code) %>%
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@@ -159,9 +164,13 @@ breakpoints %>%
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filter(!WHONET_ABX_CODE %in% whonet_antibiotics$WHONET_ABX_CODE) %>%
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count(YEAR, GUIDELINES, WHONET_ABX_CODE) %>%
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arrange(desc(YEAR))
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breakpoints %>%
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filter(!WHONET_ABX_CODE %in% whonet_antibiotics$WHONET_ABX_CODE) %>%
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pull(WHONET_ABX_CODE) %>%
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unique()
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# we cannot use them
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breakpoints <- breakpoints %>%
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filter(WHONET_ABX_CODE %in% whonet_antibiotics$WHONET_ABX_CODE)
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# breakpoints <- breakpoints %>%
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# filter(WHONET_ABX_CODE %in% whonet_antibiotics$WHONET_ABX_CODE)
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# now check with our own antibiotics
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breakpoints %>%
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filter(!toupper(WHONET_ABX_CODE) %in% antibiotics$ab) %>%
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@@ -171,19 +180,19 @@ breakpoints %>%
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breakpoints_new <- breakpoints %>%
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# only last available 10 years
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filter(YEAR > max(YEAR) - 10) %>%
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# filter(YEAR > max(YEAR) - 10) %>%
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transmute(
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guideline = paste(GUIDELINES, YEAR),
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method = TEST_METHOD,
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site = gsub(".*(UTI|urinary|urine).*", "UTI", SITE_OF_INFECTION, ignore.case = TRUE),
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site = SITE_OF_INFECTION,
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mo,
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rank_index = case_when(
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is.na(mo_rank(mo)) ~ 6, # for UNKNOWN, B_GRAMN, B_ANAER, B_ANAER-NEG, etc.
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mo_rank(mo) %like% "(infra|sub)" ~ 1,
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mo_rank(mo) == "species" ~ 2,
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mo_rank(mo) == "genus" ~ 3,
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mo_rank(mo) == "family" ~ 4,
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mo_rank(mo) == "order" ~ 5,
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is.na(mo_rank(mo, keep_synonyms = TRUE)) ~ 6, # for UNKNOWN, B_GRAMN, B_ANAER, B_ANAER-NEG, etc.
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mo_rank(mo, keep_synonyms = TRUE) %like% "(infra|sub)" ~ 1,
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mo_rank(mo, keep_synonyms = TRUE) == "species" ~ 2,
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mo_rank(mo, keep_synonyms = TRUE) == "genus" ~ 3,
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mo_rank(mo, keep_synonyms = TRUE) == "family" ~ 4,
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mo_rank(mo, keep_synonyms = TRUE) == "order" ~ 5,
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TRUE ~ 6
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),
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ab = as.ab(WHONET_ABX_CODE),
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@@ -191,7 +200,7 @@ breakpoints_new <- breakpoints %>%
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disk_dose = POTENCY,
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breakpoint_S = S,
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breakpoint_R = R,
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uti = ifelse(is.na(site), FALSE, site == "UTI")
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uti = ifelse(is.na(site), FALSE, gsub(".*(UTI|urinary|urine).*", "UTI", site) == "UTI")
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) %>%
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# Greek symbols and EM dash symbols are not allowed by CRAN, so replace them with ASCII:
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mutate(disk_dose = disk_dose %>%
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@@ -206,8 +215,18 @@ breakpoints_new <- breakpoints %>%
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breakpoints_new %>%
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mutate(id = paste(guideline, ab, mo, method, site)) %>%
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filter(id %in% .$id[which(duplicated(id))])
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# remove duplicates
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breakpoints_new <- breakpoints_new %>%
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distinct(guideline, ab, mo, method, site, .keep_all = TRUE)
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# clean disk zones and MICs
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# fix reference table names
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breakpoints_new %>% filter(guideline %like% "EUCAST", is.na(ref_tbl))
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breakpoints_new <- breakpoints_new %>%
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mutate(ref_tbl = case_when(is.na(ref_tbl) & guideline %like% "EUCAST 202" ~ lead(ref_tbl),
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is.na(ref_tbl) ~ "Unknown",
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TRUE ~ ref_tbl))
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# clean disk zones
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breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_S"] <- as.double(as.disk(breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_S", drop = TRUE]))
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breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_R"] <- as.double(as.disk(breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_R", drop = TRUE]))
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@@ -227,7 +246,7 @@ breakpoints_new[which(breakpoints_new$breakpoint_R == 1025), "breakpoint_R"] <-
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# WHONET adds one log2 level to the R breakpoint for their software, e.g. in AMC in Enterobacterales:
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# EUCAST 2022 guideline: S <= 8 and R > 8
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# WHONET file: S <= 8 and R >= 16
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breakpoints_new %>% filter(guideline == "EUCAST 2022", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
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breakpoints_new %>% filter(guideline == "EUCAST 2023", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
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# this will make an MIC of 12 I, which should be R, so:
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breakpoints_new <- breakpoints_new %>%
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mutate(breakpoint_R = ifelse(guideline %like% "EUCAST" & method == "MIC" & log2(breakpoint_R) - log2(breakpoint_S) != 0,
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@@ -235,6 +254,7 @@ breakpoints_new <- breakpoints_new %>%
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breakpoint_R
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))
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# fix disks as well
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breakpoints_new %>% filter(guideline == "EUCAST 2023", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "DISK")
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breakpoints_new <- breakpoints_new %>%
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mutate(breakpoint_R = ifelse(guideline %like% "EUCAST" & method == "DISK" & breakpoint_S - breakpoint_R != 0,
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breakpoint_R + 1,
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@@ -244,7 +264,7 @@ breakpoints_new <- breakpoints_new %>%
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breakpoints_new[which(is.na(breakpoints_new$breakpoint_R)), "breakpoint_R"] <- breakpoints_new[which(is.na(breakpoints_new$breakpoint_R)), "breakpoint_S"]
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# check again
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breakpoints_new %>% filter(guideline == "EUCAST 2022", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
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breakpoints_new %>% filter(guideline == "EUCAST 2023", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
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# compare with current version
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clinical_breakpoints %>% filter(guideline == "EUCAST 2022", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
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@@ -252,6 +272,72 @@ clinical_breakpoints %>% filter(guideline == "EUCAST 2022", ab == "AMC", mo == "
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dim(breakpoints_new)
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dim(clinical_breakpoints)
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# ECOFFs ----
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# ECOFF = Epidemiological Cut-Off
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whonet_ecoff <- read_tsv("data-raw/WHONET/Resources/Breakpoints.txt", na = c("", "NA", "-"), show_col_types = FALSE) %>%
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filter(BREAKPOINT_TYPE == "ECOFF", GUIDELINES %in% c("CLSI", "EUCAST"))
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ecoff <- whonet_ecoff %>%
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filter(!ORGANISM_CODE %in% c("clu", "BFX", "PFX", "kma", "cdh")) %>%
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transmute(guideline = paste(GUIDELINES, YEAR),
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mo = as.mo(ORGANISM_CODE, keep_synonyms = TRUE),
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ab = as.ab(WHONET_ABX_CODE),
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method = TEST_METHOD,
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ecoff = as.double(ECV_ECOFF)) %>%
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filter(!is.na(ecoff)) %>%
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distinct()
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# join to breakpoints
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breakpoints_new <- breakpoints_new %>%
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bind_rows(breakpoints_new %>%
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right_join(ecoff, by = c("guideline", "mo", "ab", "method"))) %>%
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mutate(ref_tbl = ifelse(is.na(ref_tbl), "ECOFF", ref_tbl)) %>%
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distinct(guideline, ab, mo, method, site, .keep_all = TRUE) %>%
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arrange(desc(guideline), ab, mo, method) %>%
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mutate(rank_index = case_when(
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is.na(mo_rank(mo, keep_synonyms = TRUE)) ~ 6, # for UNKNOWN, B_GRAMN, B_ANAER, B_ANAER-NEG, etc.
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mo_rank(mo, keep_synonyms = TRUE) %like% "(infra|sub)" ~ 1,
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mo_rank(mo, keep_synonyms = TRUE) == "species" ~ 2,
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mo_rank(mo, keep_synonyms = TRUE) == "genus" ~ 3,
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mo_rank(mo, keep_synonyms = TRUE) == "family" ~ 4,
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mo_rank(mo, keep_synonyms = TRUE) == "order" ~ 5,
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TRUE ~ 6
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)) %>%
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mutate(uti = ifelse(is.na(uti), FALSE, uti)) %>%
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relocate(ecoff, .after = breakpoint_R)
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breakpoints_new.bak <- mutate(uti = ifelse(is.na(uti), FALSE, uti), .after = ecoff)
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# EXTEND CoNS/CoPS/GAS/GBS ----
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# extend all coagulase-postive/-negative staphylococci
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CoNS <- breakpoints_new %>% filter(mo == as.mo("CoNS"))
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for (m in MO_CONS[mo_subspecies(MO_CONS, keep_synonyms = TRUE) == ""]) {
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breakpoints_new <- breakpoints_new %>%
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bind_rows(CoNS %>%
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mutate(mo = m))
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}
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CoPS <- breakpoints_new %>% filter(mo == as.mo("CoPS"))
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for (m in MO_COPS[mo_subspecies(MO_COPS, keep_synonyms = TRUE) == ""]) {
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breakpoints_new <- breakpoints_new %>%
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bind_rows(CoPS %>%
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mutate(mo = m))
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}
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# do the same for group A and B streptococci
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breakpoints_new <- breakpoints_new %>%
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bind_rows(breakpoints_new %>%
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filter(mo == as.mo("Streptococcus Group A")) %>%
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mutate(mo = as.mo("Streptococcus pyogenes"))) %>%
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bind_rows(breakpoints_new %>%
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filter(mo == as.mo("Streptococcus Group B")) %>%
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mutate(mo = as.mo("Streptococcus agalactiae")))
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# remove duplicates again for CoNS/CoPS/GBS and arrange
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breakpoints_new <- breakpoints_new %>%
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mutate(mo = as.mo(mo, keep_synonyms = TRUE)) %>%
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distinct(guideline, ab, mo, method, site, .keep_all = TRUE) %>%
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arrange(desc(guideline), ab, mo, method)
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# Save to package ----
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