P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 18:01:50 +02:00
Code Releases Activity

(v0.8.0.9007) Enterobacterales order

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-10-30 23:02:50 +01:00
parent 7ff2ad8188
commit 09c4b04cd0
22 changed files with 156 additions and 55 deletions
Download Patch File Download Diff File Expand all files Collapse all files

16
data-raw/eucast_rules.tsv
View File

@ -5,13 +5,13 @@
# and all separate EARS-Net letter codes like 'AMC'. They can be separated by comma: 'AMC, fluoroquinolones'.
# The 'if_mo_property' column can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain".
# The like.is.one_of column must be 'like' or 'is' or 'one_of' ('like' will read the 'this_value' column as regular expression)
# The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group can be found in: LiPuma J, Curr Opin Pulm Med. 2005 Nov;11(6):528-33. (PMID 16217180).
# The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group can be found in: LiPuma J (2005, PMID 16217180).
# >>>>> IF YOU WANT TO IMPORT THIS FILE INTO YOUR OWN SOFTWARE, HAVE THE FIRST 10 LINES SKIPPED <<<<<
# -------------------------------------------------------------------------------------------------------------------------------
if_mo_property like.is.one_of this_value and_these_antibiotics have_these_values then_change_these_antibiotics to_value reference.rule reference.rule_group
order is Enterobacteriales AMP S AMX S Enterobacteriales (Order) Breakpoints
order is Enterobacteriales AMP I AMX I Enterobacteriales (Order) Breakpoints
order is Enterobacteriales AMP R AMX R Enterobacteriales (Order) Breakpoints
order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints
order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints
order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints
genus is Staphylococcus PEN, FOX S AMP, AMX, PIP, TIC S Staphylococcus Breakpoints
genus is Staphylococcus PEN, FOX R, S OXA, FLC S Staphylococcus Breakpoints
genus is Staphylococcus FOX R all_betalactams R Staphylococcus Breakpoints
@ -109,7 +109,7 @@ genus_species is Kingella kingae ERY S AZM, CLR S Kingella kingae Breakpoints
genus_species is Kingella kingae ERY I AZM, CLR I Kingella kingae Breakpoints
genus_species is Kingella kingae ERY R AZM, CLR R Kingella kingae Breakpoints
genus_species is Kingella kingae TCY S DOX S Kingella kingae Breakpoints
family is Enterobacteriaceae PEN, glycopeptides, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
order is Enterobacterales PEN, glycopeptides, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
genus_species is Enterobacter cloacae aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
@ -177,11 +177,11 @@ genus is .* ERY I AZM, CLR I Table 11: Interpretive rules for macrolides, lincos
genus is .* ERY R AZM, CLR R Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules
genus is Staphylococcus TOB R KAN, AMK R Table 12: Interpretive rules for aminoglycosides Expert Rules
genus is Staphylococcus GEN R aminoglycosides R Table 12: Interpretive rules for aminoglycosides Expert Rules
family is Enterobacteriaceae GEN, TOB I, S GEN R Table 12: Interpretive rules for aminoglycosides Expert Rules
family is Enterobacteriaceae GEN, TOB R, I TOB R Table 12: Interpretive rules for aminoglycosides Expert Rules
order is Enterobacterales GEN, TOB I, S GEN R Table 12: Interpretive rules for aminoglycosides Expert Rules
order is Enterobacterales GEN, TOB R, I TOB R Table 12: Interpretive rules for aminoglycosides Expert Rules
genus is Staphylococcus MFX R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules
genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules
family is Enterobacteriaceae CIP R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules
order is Enterobacterales CIP R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules
genus_species is Neisseria gonorrhoeae CIP R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules
genus is .* AMC R AMP, AMX R Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R Other rules
genus is .* TZP R PIP R Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R Other rules

Can't render this file because it contains an unexpected character in line 6 and column 96.

91
data-raw/reproduction_of_microorganisms.R
View File

@ -663,6 +663,97 @@ MOs <- MOs %>%
species_id = ""),
)
# Incorporate new microbial order for Gammaproteobacteria - Adeolu et al. (2016), PMID 27620848
MOs[which(MOs$family == "Enterobacteriaceae"), "family"] <- ""
MOs[which(MOs$genus %in% c("Escherichia",
"Atlantibacter",
"Biostraticola",
"Buttiauxella",
"Cedecea",
"Citrobacter",
"Cronobacter",
"Enterobacillus",
"Enterobacter",
"Franconibacter",
"Gibbsiella",
"Izhakiella",
"Klebsiella",
"Kluyvera",
"Kosakonia",
"Leclercia",
"Lelliottia",
"Mangrovibacter",
"Pluralibacter",
"Pseudocitrobacter",
"Raoultella",
"Rosenbergiella",
"Saccharobacter",
"Salmonella",
"Shigella",
"Shimwellia",
"Siccibacter",
"Trabulsiella",
"Yokenella")), "family"] <- "Enterobacteriaceae"
MOs[which(MOs$genus %in% c("Erwinia",
"Buchnera",
"Pantoea",
"Phaseolibacter",
"Tatumella",
"Wigglesworthia")), "family"] <- "Erwiniaceae"
MOs[which(MOs$genus %in% c("Pectobacterium",
"Brenneria",
"Dickeya",
"Lonsdalea",
"Sodalis")), "family"] <- "Pectobacteriaceae"
MOs[which(MOs$genus %in% c("Yersinia",
"Chania",
"Ewingella",
"Rahnella",
"Rouxiella",
"Samsonia",
"Serratia")), "family"] <- "Yersiniaceae"
MOs[which(MOs$genus %in% c("Hafnia",
"Edwardsiella",
"Obesumbacterium")), "family"] <- "Hafniaceae"
MOs[which(MOs$genus %in% c("Morganella",
"Arsenophonus",
"Cosenzaea",
"Moellerella",
"Photorhabdus",
"Proteus",
"Providencia",
"Xenorhabdus")), "family"] <- "Morganellaceae"
MOs[which(MOs$genus %in% c("Budvicia",
"Leminorella",
"Pragia")), "family"] <- "Budviciaceae"
MOs[which(MOs$family %in% c("Enterobacteriaceae",
"Erwiniaceae",
"Pectobacteriaceae",
"Yersiniaceae",
"Hafniaceae",
"Morganellaceae",
"Budviciaceae")), "order"] <- "Enterobacterales"
new_families <- MOs %>%
filter(order == "Enterobacterales") %>%
pull(family) %>%
unique()
class(MOs$mo) <- "character"
MOs <- rbind(MOs %>% filter(!(rank == "family" & fullname %in% new_families)),
AMR::microorganisms %>%
filter(family == "Enterobacteriaceae" & rank == "family") %>%
rbind(., ., ., ., ., ., .) %>%
mutate(fullname = new_families,
source = "manually added",
ref = "Adeolu et al., 2016",
family = fullname, mo = paste0("B_[FAM]_",
toupper(abbreviate(new_families,
minlength = 8,
use.classes = TRUE,
method = "both.sides",
strict = FALSE)))))
MOs[which(MOs$order == "Enterobacteriales"), "order"] <- "Enterobacterales"
MOs[which(MOs$fullname == "Enterobacteriales"), "fullname"] <- "Enterobacterales"
MOs <- MOs %>%
group_by(kingdom) %>%
distinct(fullname, .keep_all = TRUE) %>%