mirror of https://github.com/msberends/AMR.git
348 lines
16 KiB
R
348 lines
16 KiB
R
# ==================================================================== #
|
||
# TITLE #
|
||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||
# #
|
||
# SOURCE #
|
||
# https://github.com/msberends/AMR #
|
||
# #
|
||
# CITE AS #
|
||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||
# https://doi.org/10.18637/jss.v104.i03 #
|
||
# #
|
||
# Developed at the University of Groningen and the University Medical #
|
||
# Center Groningen in The Netherlands, in collaboration with many #
|
||
# colleagues from around the world, see our website. #
|
||
# #
|
||
# This R package is free software; you can freely use and distribute #
|
||
# it for both personal and commercial purposes under the terms of the #
|
||
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
||
# the Free Software Foundation. #
|
||
# We created this package for both routine data analysis and academic #
|
||
# research and it was publicly released in the hope that it will be #
|
||
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
||
# #
|
||
# Visit our website for the full manual and a complete tutorial about #
|
||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||
# ==================================================================== #
|
||
|
||
# This script runs in under a minute and renews all guidelines of CLSI and EUCAST!
|
||
# Run it with source("data-raw/reproduction_of_clinical_breakpoints.R")
|
||
|
||
library(dplyr)
|
||
library(readr)
|
||
library(tidyr)
|
||
devtools::load_all()
|
||
|
||
# Install the WHONET 2022 software on Windows (http://www.whonet.org/software.html),
|
||
# and copy the folder C:\WHONET\Resources to the data-raw/WHONET/ folder
|
||
# (for ASIARS-Net update, also copy C:\WHONET\Codes to the data-raw/WHONET/ folder)
|
||
|
||
|
||
# MICROORGANISMS WHONET CODES ----
|
||
|
||
whonet_organisms <- read_tsv("data-raw/WHONET/Resources/Organisms.txt", na = c("", "NA", "-"), show_col_types = FALSE) %>%
|
||
# remove old taxonomic names
|
||
filter(TAXONOMIC_STATUS == "C") %>%
|
||
transmute(ORGANISM_CODE = tolower(WHONET_ORG_CODE), ORGANISM) %>%
|
||
mutate(
|
||
# what's wrong here? all these are only in the table on subspecies level (where species == subspecies), not on species level
|
||
ORGANISM = if_else(ORGANISM_CODE == "sau", "Staphylococcus aureus", ORGANISM),
|
||
ORGANISM = if_else(ORGANISM_CODE == "pam", "Pasteurella multocida", ORGANISM),
|
||
ORGANISM = if_else(ORGANISM_CODE == "kpn", "Klebsiella pneumoniae", ORGANISM),
|
||
ORGANISM = if_else(ORGANISM_CODE == "caj", "Campylobacter jejuni", ORGANISM),
|
||
ORGANISM = if_else(ORGANISM_CODE == "mmo", "Morganella morganii", ORGANISM),
|
||
ORGANISM = if_else(ORGANISM_CODE == "sap", "Staphylococcus saprophyticus", ORGANISM),
|
||
ORGANISM = if_else(ORGANISM_CODE == "fne", "Fusobacterium necrophorum", ORGANISM),
|
||
ORGANISM = if_else(ORGANISM_CODE == "fnu", "Fusobacterium nucleatum", ORGANISM),
|
||
ORGANISM = if_else(ORGANISM_CODE == "sdy", "Streptococcus dysgalactiae", ORGANISM),
|
||
ORGANISM = if_else(ORGANISM_CODE == "axy", "Achromobacter xylosoxidans", ORGANISM),
|
||
# and this one was called Issatchenkia orientalis, but it should be:
|
||
ORGANISM = if_else(ORGANISM_CODE == "ckr", "Candida krusei", ORGANISM)
|
||
)
|
||
|
||
# add some general codes
|
||
whonet_organisms <- whonet_organisms %>%
|
||
bind_rows(data.frame(
|
||
ORGANISM_CODE = c("ebc", "cof"),
|
||
ORGANISM = c("Enterobacterales", "Campylobacter")
|
||
))
|
||
|
||
whonet_organisms.bak <- whonet_organisms
|
||
# generate the mo codes and add their names
|
||
whonet_organisms <- whonet_organisms.bak %>%
|
||
mutate(mo = as.mo(gsub("(sero[a-z]*| complex| nontypable| non[-][a-zA-Z]+|var[.]| not .*|sp[.],.*|, .*variant.*|, .*toxin.*|, microaer.*| beta-haem[.])", "", ORGANISM),
|
||
minimum_matching_score = 0.6,
|
||
keep_synonyms = TRUE,
|
||
language = "en"),
|
||
mo = case_when(ORGANISM %like% "Anaerobic" & ORGANISM %like% "negative" ~ as.mo("B_ANAER-NEG"),
|
||
ORGANISM %like% "Anaerobic" & ORGANISM %like% "positive" ~ as.mo("B_ANAER-POS"),
|
||
ORGANISM %like% "Anaerobic" ~ as.mo("B_ANAER"),
|
||
TRUE ~ mo),
|
||
mo_name = mo_name(mo,
|
||
keep_synonyms = TRUE,
|
||
language = "en"))
|
||
# check if coercion at least resembles the first part (genus)
|
||
new_mo_codes <- whonet_organisms %>%
|
||
mutate(
|
||
first_part = sapply(ORGANISM, function(x) strsplit(gsub("[^a-zA-Z _-]+", "", x), " ")[[1]][1], USE.NAMES = FALSE),
|
||
keep = mo_name %like_case% first_part | ORGANISM %like% "Gram " | ORGANISM == "Other" | ORGANISM %like% "anaerobic") %>%
|
||
filter(keep == TRUE) %>%
|
||
transmute(code = toupper(ORGANISM_CODE),
|
||
mo = mo)
|
||
# update microorganisms.codes with the latest WHONET codes
|
||
microorganisms.codes2 <- microorganisms.codes %>%
|
||
# remove all old WHONET codes, whether we (in the end) keep them or not
|
||
filter(!toupper(code) %in% toupper(new_mo_codes$code)) %>%
|
||
# and add the new ones
|
||
bind_rows(new_mo_codes) %>%
|
||
arrange(code)
|
||
# new codes:
|
||
microorganisms.codes2$code[which(!microorganisms.codes2$code %in% microorganisms.codes$code)]
|
||
mo_name(microorganisms.codes2$mo[which(!microorganisms.codes2$code %in% microorganisms.codes$code)], keep_synonyms = TRUE)
|
||
microorganisms.codes <- microorganisms.codes2
|
||
|
||
# Run this part to update ASIARS-Net:
|
||
# start
|
||
asiarsnet <- read_tsv("data-raw/WHONET/Codes/ASIARS_Net_Organisms_ForwardLookup.txt")
|
||
asiarsnet <- asiarsnet %>%
|
||
mutate(WHONET_Code = toupper(WHONET_Code)) %>%
|
||
left_join(whonet_organisms %>% mutate(WHONET_Code = toupper(ORGANISM_CODE))) %>%
|
||
mutate(
|
||
mo1 = as.mo(ORGANISM_CODE),
|
||
mo2 = as.mo(ORGANISM)
|
||
) %>%
|
||
mutate(mo = if_else(mo2 == "UNKNOWN" | is.na(mo2), mo1, mo2)) %>%
|
||
filter(!is.na(mo))
|
||
insert1 <- asiarsnet %>% transmute(code = WHONET_Code, mo)
|
||
insert2 <- asiarsnet %>% transmute(code = as.character(ASIARS_Net_Code), mo)
|
||
# these will be updated
|
||
bind_rows(insert1, insert2) %>%
|
||
rename(mo_new = mo) %>%
|
||
left_join(microorganisms.codes) %>%
|
||
filter(mo != mo_new)
|
||
microorganisms.codes <- microorganisms.codes %>%
|
||
filter(!code %in% c(insert1$code, insert2$code)) %>%
|
||
bind_rows(insert1, insert2) %>%
|
||
arrange(code)
|
||
# end
|
||
|
||
# save to package
|
||
usethis::use_data(microorganisms.codes, overwrite = TRUE, compress = "xz", version = 2)
|
||
rm(microorganisms.codes)
|
||
devtools::load_all()
|
||
|
||
|
||
# BREAKPOINTS ----
|
||
|
||
# now that we have the right MO codes, get the breakpoints and convert them
|
||
whonet_breakpoints <- read_tsv("data-raw/WHONET/Resources/Breakpoints.txt", na = c("", "NA", "-"), show_col_types = FALSE) %>%
|
||
filter(BREAKPOINT_TYPE == "Human", GUIDELINES %in% c("CLSI", "EUCAST"))
|
||
whonet_antibiotics <- read_tsv("data-raw/WHONET/Resources/Antibiotics.txt", na = c("", "NA", "-"), show_col_types = FALSE) %>%
|
||
arrange(WHONET_ABX_CODE) %>%
|
||
distinct(WHONET_ABX_CODE, .keep_all = TRUE)
|
||
|
||
breakpoints <- whonet_breakpoints %>%
|
||
mutate(code = toupper(ORGANISM_CODE)) %>%
|
||
left_join(bind_rows(microorganisms.codes %>% filter(!code %in% c("ALL", "GEN")),
|
||
# GEN (Generic) and ALL (All) are PK/PD codes
|
||
data.frame(code = c("ALL", "GEN"),
|
||
mo = rep(as.mo("UNKNOWN"), 2))))
|
||
# these ones lack an MO name, they cannot be used:
|
||
unknown <- breakpoints %>%
|
||
filter(is.na(mo)) %>%
|
||
pull(code) %>%
|
||
unique()
|
||
breakpoints %>%
|
||
filter(code %in% unknown)
|
||
breakpoints <- breakpoints %>%
|
||
filter(!is.na(mo))
|
||
|
||
# and these ones have unknown antibiotics according to WHONET itself:
|
||
breakpoints %>%
|
||
filter(!WHONET_ABX_CODE %in% whonet_antibiotics$WHONET_ABX_CODE) %>%
|
||
count(YEAR, GUIDELINES, WHONET_ABX_CODE) %>%
|
||
arrange(desc(YEAR))
|
||
breakpoints %>%
|
||
filter(!WHONET_ABX_CODE %in% whonet_antibiotics$WHONET_ABX_CODE) %>%
|
||
pull(WHONET_ABX_CODE) %>%
|
||
unique()
|
||
# we cannot use them
|
||
# breakpoints <- breakpoints %>%
|
||
# filter(WHONET_ABX_CODE %in% whonet_antibiotics$WHONET_ABX_CODE)
|
||
# now check with our own antibiotics
|
||
breakpoints %>%
|
||
filter(!toupper(WHONET_ABX_CODE) %in% antibiotics$ab) %>%
|
||
pull(WHONET_ABX_CODE) %>%
|
||
unique()
|
||
# they are at the moment all old codes that have right replacements in `antibiotics`, so we can use as.ab()
|
||
|
||
breakpoints_new <- breakpoints %>%
|
||
# only last available 10 years
|
||
# filter(YEAR > max(YEAR) - 10) %>%
|
||
transmute(
|
||
guideline = paste(GUIDELINES, YEAR),
|
||
method = TEST_METHOD,
|
||
site = SITE_OF_INFECTION,
|
||
mo,
|
||
rank_index = case_when(
|
||
is.na(mo_rank(mo, keep_synonyms = TRUE)) ~ 6, # for UNKNOWN, B_GRAMN, B_ANAER, B_ANAER-NEG, etc.
|
||
mo_rank(mo, keep_synonyms = TRUE) %like% "(infra|sub)" ~ 1,
|
||
mo_rank(mo, keep_synonyms = TRUE) == "species" ~ 2,
|
||
mo_rank(mo, keep_synonyms = TRUE) == "genus" ~ 3,
|
||
mo_rank(mo, keep_synonyms = TRUE) == "family" ~ 4,
|
||
mo_rank(mo, keep_synonyms = TRUE) == "order" ~ 5,
|
||
TRUE ~ 6
|
||
),
|
||
ab = as.ab(WHONET_ABX_CODE),
|
||
ref_tbl = REFERENCE_TABLE,
|
||
disk_dose = POTENCY,
|
||
breakpoint_S = S,
|
||
breakpoint_R = R,
|
||
uti = ifelse(is.na(site), FALSE, gsub(".*(UTI|urinary|urine).*", "UTI", site) == "UTI")
|
||
) %>%
|
||
# Greek symbols and EM dash symbols are not allowed by CRAN, so replace them with ASCII:
|
||
mutate(disk_dose = disk_dose %>%
|
||
gsub("μ", "u", ., fixed = TRUE) %>% # this is 'mu', \u03bc
|
||
gsub("µ", "u", ., fixed = TRUE) %>% # this is 'micro', u00b5 (yes, they look the same)
|
||
gsub("–", "-", ., fixed = TRUE)) %>%
|
||
arrange(desc(guideline), ab, mo, method) %>%
|
||
filter(!(is.na(breakpoint_S) & is.na(breakpoint_R)) & !is.na(mo) & !is.na(ab)) %>%
|
||
distinct(guideline, ab, mo, method, site, breakpoint_S, .keep_all = TRUE)
|
||
|
||
# check the strange duplicates
|
||
breakpoints_new %>%
|
||
mutate(id = paste(guideline, ab, mo, method, site)) %>%
|
||
filter(id %in% .$id[which(duplicated(id))])
|
||
# remove duplicates
|
||
breakpoints_new <- breakpoints_new %>%
|
||
distinct(guideline, ab, mo, method, site, .keep_all = TRUE)
|
||
|
||
# fix reference table names
|
||
breakpoints_new %>% filter(guideline %like% "EUCAST", is.na(ref_tbl))
|
||
breakpoints_new <- breakpoints_new %>%
|
||
mutate(ref_tbl = case_when(is.na(ref_tbl) & guideline %like% "EUCAST 202" ~ lead(ref_tbl),
|
||
is.na(ref_tbl) ~ "Unknown",
|
||
TRUE ~ ref_tbl))
|
||
|
||
# clean disk zones
|
||
breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_S"] <- as.double(as.disk(breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_S", drop = TRUE]))
|
||
breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_R"] <- as.double(as.disk(breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_R", drop = TRUE]))
|
||
|
||
# WHONET has no >1024 but instead uses 1025, 513, etc, so as.mic() cannot be used to clean.
|
||
# instead, clean based on MIC factor levels
|
||
m <- unique(as.double(as.mic(levels(as.mic(1)))))
|
||
breakpoints_new[which(breakpoints_new$method == "MIC" &
|
||
is.na(breakpoints_new$breakpoint_S)), "breakpoint_S"] <- min(m)
|
||
breakpoints_new[which(breakpoints_new$method == "MIC" &
|
||
is.na(breakpoints_new$breakpoint_R)), "breakpoint_R"] <- max(m)
|
||
# raise these one higher valid MIC factor level:
|
||
breakpoints_new[which(breakpoints_new$breakpoint_R == 129), "breakpoint_R"] <- m[which(m == 128) + 1]
|
||
breakpoints_new[which(breakpoints_new$breakpoint_R == 257), "breakpoint_R"] <- m[which(m == 256) + 1]
|
||
breakpoints_new[which(breakpoints_new$breakpoint_R == 513), "breakpoint_R"] <- m[which(m == 512) + 1]
|
||
breakpoints_new[which(breakpoints_new$breakpoint_R == 1025), "breakpoint_R"] <- m[which(m == 1024) + 1]
|
||
|
||
# WHONET adds one log2 level to the R breakpoint for their software, e.g. in AMC in Enterobacterales:
|
||
# EUCAST 2022 guideline: S <= 8 and R > 8
|
||
# WHONET file: S <= 8 and R >= 16
|
||
breakpoints_new %>% filter(guideline == "EUCAST 2023", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
|
||
# this will make an MIC of 12 I, which should be R, so:
|
||
breakpoints_new <- breakpoints_new %>%
|
||
mutate(breakpoint_R = ifelse(guideline %like% "EUCAST" & method == "MIC" & log2(breakpoint_R) - log2(breakpoint_S) != 0,
|
||
pmax(breakpoint_S, breakpoint_R / 2),
|
||
breakpoint_R
|
||
))
|
||
# 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
|
||
))
|
||
# fix 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"]
|
||
|
||
# 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")
|
||
|
||
# check dimensions
|
||
dim(breakpoints_new)
|
||
dim(clinical_breakpoints)
|
||
|
||
# ECOFFs ----
|
||
|
||
# ECOFF = Epidemiological Cut-Off
|
||
whonet_ecoff <- read_tsv("data-raw/WHONET/Resources/Breakpoints.txt", na = c("", "NA", "-"), show_col_types = FALSE) %>%
|
||
filter(BREAKPOINT_TYPE == "ECOFF", GUIDELINES %in% c("CLSI", "EUCAST"))
|
||
|
||
ecoff <- whonet_ecoff %>%
|
||
filter(!ORGANISM_CODE %in% c("clu", "BFX", "PFX", "kma", "cdh")) %>%
|
||
transmute(guideline = paste(GUIDELINES, YEAR),
|
||
mo = as.mo(ORGANISM_CODE, keep_synonyms = TRUE),
|
||
ab = as.ab(WHONET_ABX_CODE),
|
||
method = TEST_METHOD,
|
||
ecoff = as.double(ECV_ECOFF)) %>%
|
||
filter(!is.na(ecoff)) %>%
|
||
distinct()
|
||
|
||
# join to breakpoints
|
||
breakpoints_new <- breakpoints_new %>%
|
||
bind_rows(breakpoints_new %>%
|
||
right_join(ecoff, by = c("guideline", "mo", "ab", "method"))) %>%
|
||
mutate(ref_tbl = ifelse(is.na(ref_tbl), "ECOFF", ref_tbl)) %>%
|
||
distinct(guideline, ab, mo, method, site, .keep_all = TRUE) %>%
|
||
arrange(desc(guideline), ab, mo, method) %>%
|
||
mutate(rank_index = case_when(
|
||
is.na(mo_rank(mo, keep_synonyms = TRUE)) ~ 6, # for UNKNOWN, B_GRAMN, B_ANAER, B_ANAER-NEG, etc.
|
||
mo_rank(mo, keep_synonyms = TRUE) %like% "(infra|sub)" ~ 1,
|
||
mo_rank(mo, keep_synonyms = TRUE) == "species" ~ 2,
|
||
mo_rank(mo, keep_synonyms = TRUE) == "genus" ~ 3,
|
||
mo_rank(mo, keep_synonyms = TRUE) == "family" ~ 4,
|
||
mo_rank(mo, keep_synonyms = TRUE) == "order" ~ 5,
|
||
TRUE ~ 6
|
||
)) %>%
|
||
mutate(uti = ifelse(is.na(uti), FALSE, uti)) %>%
|
||
relocate(ecoff, .after = breakpoint_R)
|
||
|
||
breakpoints_new.bak <- mutate(uti = ifelse(is.na(uti), FALSE, uti), .after = ecoff)
|
||
|
||
# EXTEND CoNS/CoPS/GAS/GBS ----
|
||
|
||
# extend all coagulase-postive/-negative staphylococci
|
||
CoNS <- breakpoints_new %>% filter(mo == as.mo("CoNS"))
|
||
for (m in MO_CONS[mo_subspecies(MO_CONS, keep_synonyms = TRUE) == ""]) {
|
||
breakpoints_new <- breakpoints_new %>%
|
||
bind_rows(CoNS %>%
|
||
mutate(mo = m))
|
||
}
|
||
CoPS <- breakpoints_new %>% filter(mo == as.mo("CoPS"))
|
||
for (m in MO_COPS[mo_subspecies(MO_COPS, keep_synonyms = TRUE) == ""]) {
|
||
breakpoints_new <- breakpoints_new %>%
|
||
bind_rows(CoPS %>%
|
||
mutate(mo = m))
|
||
}
|
||
# do the same for group A and B streptococci
|
||
breakpoints_new <- breakpoints_new %>%
|
||
bind_rows(breakpoints_new %>%
|
||
filter(mo == as.mo("Streptococcus Group A")) %>%
|
||
mutate(mo = as.mo("Streptococcus pyogenes"))) %>%
|
||
bind_rows(breakpoints_new %>%
|
||
filter(mo == as.mo("Streptococcus Group B")) %>%
|
||
mutate(mo = as.mo("Streptococcus agalactiae")))
|
||
# remove duplicates again for CoNS/CoPS/GBS and arrange
|
||
breakpoints_new <- breakpoints_new %>%
|
||
mutate(mo = as.mo(mo, keep_synonyms = TRUE)) %>%
|
||
distinct(guideline, ab, mo, method, site, .keep_all = TRUE) %>%
|
||
arrange(desc(guideline), ab, mo, method)
|
||
|
||
|
||
# Save to package ----
|
||
|
||
clinical_breakpoints <- breakpoints_new
|
||
usethis::use_data(clinical_breakpoints, overwrite = TRUE, compress = "xz", version = 2)
|
||
rm(clinical_breakpoints)
|
||
devtools::load_all(".")
|