mirror of https://github.com/msberends/AMR.git
386 lines
19 KiB
R
386 lines
19 KiB
R
# ==================================================================== #
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# TITLE: #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in The Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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# This script runs in 20-30 minutes and renews all guidelines of CLSI and EUCAST!
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# Run it with source("data-raw/reproduction_of_clinical_breakpoints.R")
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library(dplyr)
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library(readr)
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library(tidyr)
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devtools::load_all()
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# Install the WHONET software on Windows (http://www.whonet.org/software.html),
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# and copy the folder C:\WHONET\Resources to the data-raw/WHONET/ folder
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# (for ASIARS-Net update, also copy C:\WHONET\Codes to the data-raw/WHONET/ folder)
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# BE SURE TO RUN data-raw/reproduction_of_microorganisms.groups.R FIRST TO GET THE GROUPS!
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# READ DATA ----
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whonet_organisms <- read_tsv("data-raw/WHONET/Resources/Organisms.txt", na = c("", "NA", "-"), show_col_types = FALSE) %>%
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# remove old taxonomic names
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filter(TAXONOMIC_STATUS == "C") %>%
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mutate(ORGANISM_CODE = toupper(WHONET_ORG_CODE))
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whonet_breakpoints <- read_tsv("data-raw/WHONET/Resources/Breakpoints.txt", na = c("", "NA", "-"),
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show_col_types = FALSE, guess_max = Inf) %>%
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filter(GUIDELINES %in% c("CLSI", "EUCAST"))
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whonet_antibiotics <- read_tsv("data-raw/WHONET/Resources/Antibiotics.txt", na = c("", "NA", "-"), show_col_types = FALSE) %>%
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arrange(WHONET_ABX_CODE) %>%
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distinct(WHONET_ABX_CODE, .keep_all = TRUE)
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# MICROORGANISMS WHONET CODES ----
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whonet_organisms <- whonet_organisms %>%
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select(ORGANISM_CODE, ORGANISM, SPECIES_GROUP, GBIF_TAXON_ID) %>%
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mutate(
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# this one was called Issatchenkia orientalis, but it should be:
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ORGANISM = if_else(ORGANISM_CODE == "ckr", "Candida krusei", ORGANISM)
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) %>%
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# try to match on GBIF identifier
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left_join(microorganisms %>% distinct(mo, gbif, status) %>% filter(!is.na(gbif)), by = c("GBIF_TAXON_ID" = "gbif")) %>%
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# remove duplicates
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arrange(ORGANISM_CODE, GBIF_TAXON_ID, status) %>%
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distinct(ORGANISM_CODE, .keep_all = TRUE) %>%
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# add Enterobacterales, which is a subkingdom code in their data
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bind_rows(data.frame(ORGANISM_CODE = "ebc", ORGANISM = "Enterobacterales", mo = as.mo("Enterobacterales"))) %>%
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arrange(ORGANISM)
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## Add new WHO codes to microorganisms.codes ----
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matched <- whonet_organisms %>% filter(!is.na(mo))
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unmatched <- whonet_organisms %>% filter(is.na(mo))
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# generate the mo codes and add their names
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message("Getting MO codes for WHONET input...")
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unmatched <- unmatched %>%
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mutate(mo = as.mo(gsub("(sero[a-z]*| nontypable| non[-][a-zA-Z]+|var[.]| not .*|sp[.],.*|, .*variant.*|, .*toxin.*|, microaer.*| beta-haem[.])", "", ORGANISM),
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minimum_matching_score = 0.55,
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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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ORGANISM %like% "Anaerobic" & ORGANISM %like% "positive" ~ as.mo("B_ANAER-POS"),
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ORGANISM %like% "Anaerobic" ~ as.mo("B_ANAER"),
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TRUE ~ mo),
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mo_name = mo_name(mo,
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keep_synonyms = TRUE,
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language = "en"))
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# check if coercion at least resembles the first part (genus)
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unmatched <- unmatched %>%
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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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arrange(keep)
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unmatched %>%
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View()
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unmatched <- unmatched %>%
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filter(keep == TRUE)
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organisms <- matched %>% transmute(code = toupper(ORGANISM_CODE), group = SPECIES_GROUP, mo) %>%
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bind_rows(unmatched %>% transmute(code = toupper(ORGANISM_CODE), group = SPECIES_GROUP, mo)) %>%
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mutate(name = mo_name(mo, keep_synonyms = TRUE)) %>%
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arrange(code)
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# some subspecies exist, while their upper species do not, add them as the species level:
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subspp <- organisms %>%
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filter(mo_species(mo, keep_synonyms = TRUE) == mo_subspecies(mo, keep_synonyms = TRUE) &
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mo_species(mo, keep_synonyms = TRUE) != "" &
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mo_genus(mo, keep_synonyms = TRUE) != "Salmonella") %>%
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mutate(mo = as.mo(paste(mo_genus(mo, keep_synonyms = TRUE),
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mo_species(mo, keep_synonyms = TRUE)),
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keep_synonyms = TRUE),
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name = mo_name(mo, keep_synonyms = TRUE))
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organisms <- organisms %>%
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filter(!code %in% subspp$code) %>%
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bind_rows(subspp) %>%
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arrange(code)
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# add the groups
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organisms <- organisms %>%
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bind_rows(tibble(code = organisms %>% filter(!is.na(group)) %>% pull(group) %>% unique(),
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group = NA,
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mo = organisms %>% filter(!is.na(group)) %>% pull(group) %>% unique() %>% as.mo(keep_synonyms = TRUE),
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name = mo_name(mo, keep_synonyms = TRUE))) %>%
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arrange(code, group) %>%
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select(-group) %>%
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distinct()
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# 2023-07-08 SGM is also Strep gamma in WHONET, must only be Slowly-growing Mycobacterium
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organisms <- organisms %>%
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filter(!(code == "SGM" & name %like% "Streptococcus"))
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# this must be empty:
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organisms$code[organisms$code %>% duplicated()]
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saveRDS(organisms, "data-raw/organisms.rds", version = 2)
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#---
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# AT THIS POINT, `organisms` is clean and all entries have an mo code
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#---
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# update microorganisms.codes with the latest WHONET codes
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microorganisms.codes2 <- microorganisms.codes %>%
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# remove all old WHONET codes, whether we (in the end) keep them or not
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filter(!toupper(code) %in% toupper(organisms$code)) %>%
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# and add the new ones
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bind_rows(organisms %>% select(code, mo)) %>%
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arrange(code) %>%
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distinct(code, .keep_all = TRUE)
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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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# asiarsnet <- read_tsv("data-raw/WHONET/Codes/ASIARS_Net_Organisms_ForwardLookup.txt")
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# asiarsnet <- asiarsnet %>%
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# mutate(WHONET_Code = toupper(WHONET_Code)) %>%
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# left_join(whonet_organisms %>% mutate(WHONET_Code = toupper(ORGANISM_CODE))) %>%
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# mutate(
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# mo1 = as.mo(ORGANISM_CODE),
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# mo2 = as.mo(ORGANISM)
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# ) %>%
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# mutate(mo = if_else(mo2 == "UNKNOWN" | is.na(mo2), mo1, mo2)) %>%
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# filter(!is.na(mo))
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# insert1 <- asiarsnet %>% transmute(code = WHONET_Code, mo)
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# insert2 <- asiarsnet %>% transmute(code = as.character(ASIARS_Net_Code), mo)
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# # these will be updated
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# bind_rows(insert1, insert2) %>%
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# rename(mo_new = mo) %>%
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# left_join(microorganisms.codes) %>%
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# filter(mo != mo_new)
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# microorganisms.codes <- microorganisms.codes %>%
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# filter(!code %in% c(insert1$code, insert2$code)) %>%
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# bind_rows(insert1, insert2) %>%
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# arrange(code)
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# # end
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## Save to package ----
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class(microorganisms.codes$mo) <- c("mo", "character")
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usethis::use_data(microorganisms.codes, overwrite = TRUE, compress = "xz", version = 2)
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rm(microorganisms.codes)
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devtools::load_all()
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# BREAKPOINTS ----
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# now that we have the correct MO codes, get the breakpoints and convert them
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whonet_breakpoints %>%
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count(GUIDELINES, BREAKPOINT_TYPE) %>%
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pivot_wider(names_from = BREAKPOINT_TYPE, values_from = n) %>%
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janitor::adorn_totals(where = c("row", "col"))
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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 %>% 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 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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unique()
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breakpoints %>%
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filter(code %in% unknown) %>%
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count(GUIDELINES, YEAR, ORGANISM_CODE, BREAKPOINT_TYPE, sort = TRUE)
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# 2024-02-22: clu and kma are know (see below), fix the PBI one
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breakpoints$mo[breakpoints$ORGANISM_CODE == "PBI"] <- as.mo("Parabacteroides")
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breakpoints$ORGANISM_CODE[breakpoints$ORGANISM_CODE == "PBI"] <- "Parabacteroides"
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# 2023-07-08: these codes are currently: clu, kma. No clue (are not in MO list of WHONET), so remove them:
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breakpoints <- breakpoints %>%
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filter(!is.na(mo))
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# and these ones have unknown antibiotics according to WHONET itself:
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breakpoints %>%
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filter(!WHONET_ABX_CODE %in% whonet_antibiotics$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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# they are at the moment all old codes that have the right replacements in `antibiotics`, so we can use as.ab()
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## Build new breakpoints table ----
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breakpoints_new <- breakpoints %>%
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filter(!is.na(WHONET_ABX_CODE)) %>%
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transmute(
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guideline = paste(GUIDELINES, YEAR),
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type = ifelse(BREAKPOINT_TYPE == "ECOFF", "ECOFF", tolower(BREAKPOINT_TYPE)),
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host = ifelse(BREAKPOINT_TYPE == "ECOFF", "ECOFF", tolower(HOST)),
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method = TEST_METHOD,
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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, 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) == "species group" ~ 2.5,
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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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ref_tbl = ifelse(type == "ECOFF" & is.na(REFERENCE_TABLE), "ECOFF", REFERENCE_TABLE),
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disk_dose = POTENCY,
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breakpoint_S = ifelse(type == "ECOFF" & is.na(S) & !is.na(ECV_ECOFF), ECV_ECOFF, S),
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breakpoint_R = ifelse(type == "ECOFF" & is.na(R) & !is.na(ECV_ECOFF), ECV_ECOFF, R),
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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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gsub("μ", "u", ., fixed = TRUE) %>% # this is 'mu', \u03bc
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gsub("µ", "u", ., fixed = TRUE) %>% # this is 'micro', u00b5 (yes, they look the same)
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gsub("–", "-", ., fixed = TRUE)) %>%
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arrange(desc(guideline), mo, ab, type, method) %>%
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filter(!(is.na(breakpoint_S) & is.na(breakpoint_R)) & !is.na(mo) & !is.na(ab)) %>%
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distinct(guideline, type, host, ab, mo, method, site, breakpoint_S, .keep_all = TRUE)
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# check the strange duplicates
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breakpoints_new %>%
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mutate(id = paste(guideline, type, host, 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, type, host, ab, mo, method, site, .keep_all = TRUE)
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# fix reference table names
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breakpoints_new %>% filter(guideline %like% "EUCAST", is.na(ref_tbl)) %>% View()
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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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# regarding animal breakpoints, CLSI has adults and foals for horses, but only for amikacin - remove them
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breakpoints_new <- breakpoints_new |>
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filter(host %unlike% "foal") |>
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mutate(host = ifelse(host %like% "horse", "horse", host))
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# FIXES FOR WHONET ERRORS ----
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# WHONET has no >1024 but instead uses 1025, 513, etc, so as.mic() cannot be used to clean.
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# instead, clean based on MIC factor levels
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m <- unique(as.double(as.mic(levels(as.mic(1)))))
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breakpoints_new[which(breakpoints_new$method == "MIC" &
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is.na(breakpoints_new$breakpoint_S)), "breakpoint_S"] <- min(m)
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breakpoints_new[which(breakpoints_new$method == "MIC" &
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is.na(breakpoints_new$breakpoint_R)), "breakpoint_R"] <- max(m)
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# raise these one higher valid MIC factor level:
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breakpoints_new[which(breakpoints_new$breakpoint_R == 129), "breakpoint_R"] <- 128
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breakpoints_new[which(breakpoints_new$breakpoint_R == 257), "breakpoint_R"] <- 256
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breakpoints_new[which(breakpoints_new$breakpoint_R == 513), "breakpoint_R"] <- 512
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breakpoints_new[which(breakpoints_new$breakpoint_R == 1025), "breakpoint_R"] <- 1024
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# fix streptococci in WHONET table of EUCAST: Strep A, B, C and G must only include these groups and not all streptococci:
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breakpoints_new$mo[breakpoints_new$mo == "B_STRPT" & breakpoints_new$ref_tbl %like% "^strep.* a.* b.*c.*g"] <- as.mo("B_STRPT_ABCG")
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# Haemophilus same error (must only be H. influenzae)
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breakpoints_new$mo[breakpoints_new$mo == "B_HMPHL" & breakpoints_new$ref_tbl %like% "^h.* influenzae"] <- as.mo("B_HMPHL_INFL")
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# EUCAST says that for H. parainfluenzae the H. influenza rules can be used, so add them
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breakpoints_new <- breakpoints_new %>%
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bind_rows(
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breakpoints_new %>%
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filter(guideline %like% "EUCAST", mo == "B_HMPHL_INFL") %>%
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mutate(mo = as.mo("B_HMPHL_PRNF"))
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) %>%
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arrange(desc(guideline), mo, ab, type, host, method)
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# Achromobacter denitrificans is in WHONET included in their A. xylosoxidans table, must be removed
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breakpoints_new <- breakpoints_new %>% filter(mo != as.mo("Achromobacter denitrificans"))
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# WHONET contains gentamicin breakpoints for viridans streptocci, which are intrinsic R - they meant genta-high, which is ALSO in their table, so we just remove gentamicin in viridans streptococci
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breakpoints_new <- breakpoints_new %>% filter(!(mo == as.mo("Streptococcus viridans") & ab == "GEN"))
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# Nitrofurantoin in Staph (EUCAST) only applies to S. saprophyticus, while WHONET has the DISK correct but the MIC on genus level
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breakpoints_new$mo[breakpoints_new$mo == "B_STPHY" & breakpoints_new$ab == "NIT" & breakpoints_new$guideline %like% "EUCAST"] <- as.mo("B_STPHY_SPRP")
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# WHONET sets the 2023 breakpoints for SAM to MIC of 16/32 for Enterobacterales, should be MIC 8/32 like AMC (see issue #123 on github.com/msberends/AMR)
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# UPDATE 2024-02-22: fixed now
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# breakpoints_new$breakpoint_S[breakpoints_new$mo == "B_[ORD]_ENTRBCTR" & breakpoints_new$ab == "SAM" & breakpoints_new$guideline %like% "CLSI 2023" & breakpoints_new$method == "MIC"] <- 8
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# determine rank again now that some changes were made on taxonomic level (genus -> species)
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breakpoints_new <- breakpoints_new %>%
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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) == "species group" ~ 2.5,
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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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# 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 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 according to EUCAST, 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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pmax(breakpoint_S, breakpoint_R / 2),
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breakpoint_R
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||
))
|
||
# fix disks as well
|
||
breakpoints_new %>% filter(guideline == "EUCAST 2023", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "DISK")
|
||
breakpoints_new <- breakpoints_new %>%
|
||
mutate(breakpoint_R = ifelse(guideline %like% "EUCAST" & method == "DISK" & breakpoint_S - breakpoint_R != 0,
|
||
breakpoint_R + 1,
|
||
breakpoint_R
|
||
))
|
||
# fill missing R breakpoint where there is an S breakpoint
|
||
breakpoints_new[which(is.na(breakpoints_new$breakpoint_R)), "breakpoint_R"] <- breakpoints_new[which(is.na(breakpoints_new$breakpoint_R)), "breakpoint_S"]
|
||
|
||
|
||
# CHECKS AND SAVE TO PACKAGE ----
|
||
|
||
# check again
|
||
breakpoints_new %>% filter(guideline == "EUCAST 2023", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
|
||
# compare with current version
|
||
clinical_breakpoints %>% filter(guideline == "EUCAST 2022", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
|
||
|
||
# must have "human" and "ECOFF"
|
||
breakpoints_new %>% filter(mo == "B_STRPT_PNMN", ab == "AMP", guideline == "EUCAST 2020", method == "MIC")
|
||
|
||
# check dimensions
|
||
dim(breakpoints_new)
|
||
dim(clinical_breakpoints)
|
||
|
||
clinical_breakpoints <- breakpoints_new
|
||
clinical_breakpoints <- clinical_breakpoints %>% dataset_UTF8_to_ASCII()
|
||
usethis::use_data(clinical_breakpoints, overwrite = TRUE, compress = "xz", version = 2)
|
||
rm(clinical_breakpoints)
|
||
devtools::load_all(".")
|