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(v0.8.0.9007) Enterobacterales order

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dr. M.S. (Matthijs) Berends 2019-10-30 23:02:50 +01:00
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 0.8.0.9006 Version: 0.8.0.9007
Date: 2019-10-27 Date: 2019-10-30
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),

6
NEWS.md
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@ -1,5 +1,5 @@
# AMR 0.8.0.9006 # AMR 0.8.0.9007
<small>Last updated: 27-Oct-2019</small> <small>Last updated: 30-Oct-2019</small>
### New ### New
* Support for a new MDRO guideline: Magiorakos AP, Srinivasan A *et al.* "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012). **This is now the new default guideline for the `mdro()` function.** * Support for a new MDRO guideline: Magiorakos AP, Srinivasan A *et al.* "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012). **This is now the new default guideline for the `mdro()` function.**
@ -7,7 +7,7 @@
### Changes ### Changes
* When running `as.rsi()` over a data set, it will now print the guideline that will be used if it is not specified by the user * When running `as.rsi()` over a data set, it will now print the guideline that will be used if it is not specified by the user
* Fix for `eucast_rules()`: *Stenotrophomonas maltophilia* not interpreted "R" to ceftazidime anymore (following EUCAST v3.1) * Fix for `eucast_rules()`: *Stenotrophomonas maltophilia* not interpreted "R" to ceftazidime anymore (following EUCAST v3.1)
* Fix in taxonomic info for genera that are in multiple kingdoms, like *Proteus* * Adopted Adeolu *et al.* (2016), [PMID 27620848](https://www.ncbi.nlm.nih.gov/pubmed/27620848) for the `microorganisms` data set, which means that the new order Enterobacterales now consists of a part of the existing family *Enterobacteriaceae*, but that this family has been split into other families as well (like *Morganellaceae* and *Yersiniaceae*). Although published in 2016, this information is not yet in the Catalogue of Life version of 2019. All MDRO determinations with `mdro()` will now use the Enterobacterales order for all guidelines before 2016.
* Fix for interpreting MIC values with `as.rsi()` where the input is `NA` * Fix for interpreting MIC values with `as.rsi()` where the input is `NA`
* Added "imi" as allowed abbreviation for Imipenem * Added "imi" as allowed abbreviation for Imipenem
* Fix for automatically determining columns with antibiotic results in `mdro()` and `eucast_rules()` * Fix for automatically determining columns with antibiotic results in `mdro()` and `eucast_rules()`

7
R/data.R
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@ -55,7 +55,7 @@
#' #'
#' A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using \code{\link{as.mo}}. #' A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using \code{\link{as.mo}}.
#' @inheritSection catalogue_of_life Catalogue of Life #' @inheritSection catalogue_of_life Catalogue of Life
#' @format A \code{\link{data.frame}} with 69,465 observations and 16 variables: #' @format A \code{\link{data.frame}} with 69,447 observations and 16 variables:
#' \describe{ #' \describe{
#' \item{\code{mo}}{ID of microorganism as used by this package} #' \item{\code{mo}}{ID of microorganism as used by this package}
#' \item{\code{col_id}}{Catalogue of Life ID} #' \item{\code{col_id}}{Catalogue of Life ID}
@ -72,9 +72,10 @@
#' \item{11 entries of \emph{Streptococcus} (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)} #' \item{11 entries of \emph{Streptococcus} (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)}
#' \item{2 entries of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])} #' \item{2 entries of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
#' \item{3 entries of \emph{Trichomonas} (\emph{Trichomonas vaginalis}, and its family and genus)} #' \item{3 entries of \emph{Trichomonas} (\emph{Trichomonas vaginalis}, and its family and genus)}
#' \item{1 entry of \emph{Blastocystis} (\emph{Blastocystis hominis}), although it officially does not exist (Noel et al. 2005, PMID 15634993)} #' \item{1 entry of \emph{Blastocystis} (\emph{Blastocystis hominis}), although it officially does not exist (Noel \emph{et al.} 2005, PMID 15634993)}
#' \item{5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)} #' \item{5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)}
#' \item{9,460 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications} #' \item{6 families under the Enterobacterales order, according to Adeolu \emph{et al.} (2016, PMID 27620848), that are not in the Catalogue of Life}
#' \item{12,600 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications}
#' } #' }
#' @section About the records from DSMZ (see source): #' @section About the records from DSMZ (see source):
#' Names of prokaryotes are defined as being validly published by the International Code of Nomenclature of Bacteria. Validly published are all names which are included in the Approved Lists of Bacterial Names and the names subsequently published in the International Journal of Systematic Bacteriology (IJSB) and, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) as original articles or in the validation lists. #' Names of prokaryotes are defined as being validly published by the International Code of Nomenclature of Bacteria. Validly published are all names which are included in the Approved Lists of Bacterial Names and the names subsequently published in the International Journal of Systematic Bacteriology (IJSB) and, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) as original articles or in the validation lists.

34
R/mdro.R
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@ -424,6 +424,9 @@ mdro <- function(x,
} }
} }
trans_tbl2 <- function(txt, rows, lst) { trans_tbl2 <- function(txt, rows, lst) {
if (info == TRUE) {
message(blue(txt, "..."), appendLF = FALSE)
}
# function specific for the CMI paper of 2012 (Magiorakos et al.) # function specific for the CMI paper of 2012 (Magiorakos et al.)
lst_vector <- unlist(lst)[!is.na(unlist(lst))] lst_vector <- unlist(lst)[!is.na(unlist(lst))]
x$total_groups <- NA_integer_ x$total_groups <- NA_integer_
@ -447,12 +450,15 @@ mdro <- function(x,
# MDR (=2): >=3 groups affected # MDR (=2): >=3 groups affected
x[which(x$row_number %in% rows & x$affected_groups >= 3), "MDRO"] <<- 2 x[which(x$row_number %in% rows & x$affected_groups >= 3), "MDRO"] <<- 2
# XDR (=3): all but <=2 groups affected # XDR (=3): all but <=2 groups affected
x[which(x$row_number %in% rows & x$total_groups - x$affected_groups <= 2), "MDRO"] <<- 3 x[which(x$row_number %in% rows & (x$total_groups - x$affected_groups) <= 2), "MDRO"] <<- 3
# PDR (=4): all agents are R # PDR (=4): all agents are R
x[filter_at(x[rows, ], x[filter_at(x[rows, ],
vars(lst_vector), vars(lst_vector),
all_vars(. %in% c("R", "I")))$row_number, all_vars(. %in% c("R", "I")))$row_number,
"MDRO"] <<- 4 "MDRO"] <<- 4
if (info == TRUE) {
message(blue(" OK"))
}
} }
x <- x %>% x <- x %>%
@ -461,7 +467,7 @@ mdro <- function(x,
left_join_microorganisms(by = col_mo) %>% left_join_microorganisms(by = col_mo) %>%
# add unconfirmed to where genus is available # add unconfirmed to where genus is available
mutate(MDRO = ifelse(!is.na(genus), 1, NA_integer_), mutate(MDRO = ifelse(!is.na(genus), 1, NA_integer_),
row_number = seq_len(nrow(x))) %>% row_number = seq_len(nrow(.))) %>%
# transform to data.frame so subsetting is possible with x[y, z] (might not be the case with tibble/data.table/...) # transform to data.frame so subsetting is possible with x[y, z] (might not be the case with tibble/data.table/...)
as.data.frame(stringsAsFactors = FALSE) as.data.frame(stringsAsFactors = FALSE)
@ -572,7 +578,7 @@ mdro <- function(x,
FOS, FOS,
QDA, QDA,
c(TCY, DOX, MNO))) c(TCY, DOX, MNO)))
trans_tbl2(paste("Table 2 -", italic("Enterococcus"), "spp"), trans_tbl2(paste("Table 2 -", italic("Enterococcus"), "spp."),
which(x$genus == "Enterococcus"), which(x$genus == "Enterococcus"),
list(GEH, list(GEH,
STH, STH,
@ -585,8 +591,10 @@ mdro <- function(x,
AMP, AMP,
QDA, QDA,
c(DOX, MNO))) c(DOX, MNO)))
trans_tbl2(paste("Table 3 -", italic("Enterobacteriaceae")), trans_tbl2(paste0("Table 3 - ", italic("Enterobacteriaceae"),
which(x$family == "Enterobacteriaceae"), " (before the taxonomic reclassification by Adeolu ", italic("et al."), ", 2016)"),
# this new order was previously 'Enterobacteriales' and contained only the family 'Enterobacteriaceae':
which(x$order == "Enterobacterales"),
list(c(GEN, TOB, AMK, NET), list(c(GEN, TOB, AMK, NET),
CPT, CPT,
c(TCC, TZP), c(TCC, TZP),
@ -615,7 +623,7 @@ mdro <- function(x,
ATM, ATM,
FOS, FOS,
c(COL, PLB))) c(COL, PLB)))
trans_tbl2(paste("Table 5 -", italic("Acinetobacter"), "spp"), trans_tbl2(paste("Table 5 -", italic("Acinetobacter"), "spp."),
which(x$genus == "Acinetobacter"), which(x$genus == "Acinetobacter"),
list(c(GEN, TOB, AMK, NET), list(c(GEN, TOB, AMK, NET),
c(IPM, MEM, DOR), c(IPM, MEM, DOR),
@ -632,7 +640,7 @@ mdro <- function(x,
# EUCAST ------------------------------------------------------------------ # EUCAST ------------------------------------------------------------------
# Table 5 # Table 5
trans_tbl(3, trans_tbl(3,
which(x$family == "Enterobacteriaceae" which(x$order == "Enterobacterales"
| x$fullname %like% "^Pseudomonas aeruginosa" | x$fullname %like% "^Pseudomonas aeruginosa"
| x$genus == "Acinetobacter"), | x$genus == "Acinetobacter"),
COL, COL,
@ -706,7 +714,7 @@ mdro <- function(x,
if (is.na(CIP)) CIP <- "missing" if (is.na(CIP)) CIP <- "missing"
# Table 1 # Table 1
x[which((x$family == "Enterobacteriaceae" | x[which((x$order == "Enterobacterales" | # following in fact the old Enterobacteriaceae classification
x$fullname %like% "^Acinetobacter baumannii") & x$fullname %like% "^Acinetobacter baumannii") &
x[, PIP] == "R" & x[, PIP] == "R" &
x[, CTX_or_CAZ] == "R" & x[, CTX_or_CAZ] == "R" &
@ -714,7 +722,7 @@ mdro <- function(x,
x[, CIP] == "R"), x[, CIP] == "R"),
"MDRO"] <- 2 # 2 = 3MRGN "MDRO"] <- 2 # 2 = 3MRGN
x[which((x$family == "Enterobacteriaceae" | x[which((x$order == "Enterobacterales" | # following in fact the old Enterobacteriaceae classification
x$fullname %like% "^Acinetobacter baumannii") & x$fullname %like% "^Acinetobacter baumannii") &
x[, PIP] == "R" & x[, PIP] == "R" &
x[, CTX_or_CAZ] == "R" & x[, CTX_or_CAZ] == "R" &
@ -722,7 +730,7 @@ mdro <- function(x,
x[, CIP] == "R"), x[, CIP] == "R"),
"MDRO"] <- 3 # 3 = 4MRGN, overwrites 3MRGN if applicable "MDRO"] <- 3 # 3 = 4MRGN, overwrites 3MRGN if applicable
x[which((x$family == "Enterobacteriaceae" | x[which((x$order == "Enterobacterales" | # following in fact the old Enterobacteriaceae classification
x$fullname %like% "^Acinetobacter baumannii") & x$fullname %like% "^Acinetobacter baumannii") &
x[, IPM] == "R" | x[, MEM] == "R"), x[, IPM] == "R" | x[, MEM] == "R"),
"MDRO"] <- 3 # 3 = 4MRGN, always when imipenem or meropenem is R "MDRO"] <- 3 # 3 = 4MRGN, always when imipenem or meropenem is R
@ -757,17 +765,17 @@ mdro <- function(x,
# Table 1 # Table 1
trans_tbl(3, trans_tbl(3,
which(x$family == "Enterobacteriaceae"), which(x$order == "Enterobacterales"), # following in fact the old Enterobacteriaceae classification
c(aminoglycosides, fluoroquinolones), c(aminoglycosides, fluoroquinolones),
"all") "all")
trans_tbl(2, trans_tbl(2,
which(x$family == "Enterobacteriaceae"), which(x$order == "Enterobacterales"), # following in fact the old Enterobacteriaceae classification
carbapenems, carbapenems,
"any") "any")
trans_tbl(2, trans_tbl(2,
which(x$family == "Enterobacteriaceae"), which(x$order == "Enterobacterales"), # following in fact the old Enterobacteriaceae classification
ESBLs, ESBLs,
"all") "all")

2
R/mo_property.R
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@ -57,7 +57,7 @@
#' mo_kingdom("E. coli") # "Bacteria" #' mo_kingdom("E. coli") # "Bacteria"
#' mo_phylum("E. coli") # "Proteobacteria" #' mo_phylum("E. coli") # "Proteobacteria"
#' mo_class("E. coli") # "Gammaproteobacteria" #' mo_class("E. coli") # "Gammaproteobacteria"
#' mo_order("E. coli") # "Enterobacteriales" #' mo_order("E. coli") # "Enterobacterales" ()
#' mo_family("E. coli") # "Enterobacteriaceae" #' mo_family("E. coli") # "Enterobacteriaceae"
#' mo_genus("E. coli") # "Escherichia" #' mo_genus("E. coli") # "Escherichia"
#' mo_species("E. coli") # "coli" #' mo_species("E. coli") # "coli"

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R/sysdata.rda
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16
data-raw/eucast_rules.tsv
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@ -5,13 +5,13 @@
# and all separate EARS-Net letter codes like 'AMC'. They can be separated by comma: 'AMC, fluoroquinolones'. # 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 '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 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 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 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 Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints
order is Enterobacteriales AMP I AMX I Enterobacteriales (Order) Breakpoints order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints
order is Enterobacteriales AMP R AMX R Enterobacteriales (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 S AMP, AMX, PIP, TIC S Staphylococcus Breakpoints
genus is Staphylococcus PEN, FOX R, S OXA, FLC 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 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 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 ERY R AZM, CLR R Kingella kingae Breakpoints
genus_species is Kingella kingae TCY S DOX S 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 (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 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 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 .* 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 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 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 order is Enterobacterales 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 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 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 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_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 .* 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 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
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@ -663,6 +663,97 @@ MOs <- MOs %>%
species_id = ""), 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 %>% MOs <- MOs %>%
group_by(kingdom) %>% group_by(kingdom) %>%
distinct(fullname, .keep_all = TRUE) %>% distinct(fullname, .keep_all = TRUE) %>%

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docs/404.html
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@ -84,7 +84,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9006</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9007</span>
</span> </span>
</div> </div>

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@ -84,7 +84,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9006</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9007</span>
</span> </span>
</div> </div>

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@ -84,7 +84,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9006</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9007</span>
</span> </span>
</div> </div>

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@ -84,7 +84,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9006</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9007</span>
</span> </span>
</div> </div>

2
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@ -45,7 +45,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9006</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9007</span>
</span> </span>
</div> </div>

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@ -84,7 +84,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9006</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9007</span>
</span> </span>
</div> </div>
@ -231,11 +231,11 @@
</div> </div>
<div id="amr-0-8-0-9006" class="section level1"> <div id="amr-0-8-0-9007" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0-8-0-9006" class="anchor"></a>AMR 0.8.0.9006<small> Unreleased </small> <a href="#amr-0-8-0-9007" class="anchor"></a>AMR 0.8.0.9007<small> Unreleased </small>
</h1> </h1>
<p><small>Last updated: 27-Oct-2019</small></p> <p><small>Last updated: 30-Oct-2019</small></p>
<div id="new" class="section level3"> <div id="new" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#new" class="anchor"></a>New</h3> <a href="#new" class="anchor"></a>New</h3>
@ -250,8 +250,7 @@
<ul> <ul>
<li>When running <code><a href="../reference/as.rsi.html">as.rsi()</a></code> over a data set, it will now print the guideline that will be used if it is not specified by the user</li> <li>When running <code><a href="../reference/as.rsi.html">as.rsi()</a></code> over a data set, it will now print the guideline that will be used if it is not specified by the user</li>
<li>Fix for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>: <em>Stenotrophomonas maltophilia</em> not interpreted “R” to ceftazidime anymore (following EUCAST v3.1)</li> <li>Fix for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>: <em>Stenotrophomonas maltophilia</em> not interpreted “R” to ceftazidime anymore (following EUCAST v3.1)</li>
<li>Fix in taxonomic info for genera that are in multiple kingdoms, like <em>Proteus</em> <li>Adopted Adeolu <em>et al.</em> (2016), <a href="https://www.ncbi.nlm.nih.gov/pubmed/27620848">PMID 27620848</a> for the <code>microorganisms</code> data set, which means that the new order Enterobacterales now consists of a part of the existing family <em>Enterobacteriaceae</em>, but that this family has been split into other families as well (like <em>Morganellaceae</em> and <em>Yersiniaceae</em>). Although published in 2016, this information is not yet in the Catalogue of Life version of 2019. All MDRO determinations with <code><a href="../reference/mdro.html">mdro()</a></code> will now use the Enterobacterales order for all guidelines before 2016.</li>
</li>
<li>Fix for interpreting MIC values with <code><a href="../reference/as.rsi.html">as.rsi()</a></code> where the input is <code>NA</code> <li>Fix for interpreting MIC values with <code><a href="../reference/as.rsi.html">as.rsi()</a></code> where the input is <code>NA</code>
</li> </li>
<li>Added “imi” as allowed abbreviation for Imipenem</li> <li>Added “imi” as allowed abbreviation for Imipenem</li>
@ -1321,7 +1320,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav"> <div id="tocnav">
<h2>Contents</h2> <h2>Contents</h2>
<ul class="nav nav-pills nav-stacked"> <ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-8-0-9006">0.8.0.9006</a></li> <li><a href="#amr-0-8-0-9007">0.8.0.9007</a></li>
<li><a href="#amr-0-8-0">0.8.0</a></li> <li><a href="#amr-0-8-0">0.8.0</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li> <li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li> <li><a href="#amr-0-7-0">0.7.0</a></li>

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@ -84,7 +84,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9006</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9007</span>
</span> </span>
</div> </div>

9
docs/reference/microorganisms.html
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@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9007</span>
</span> </span>
</div> </div>
@ -242,7 +242,7 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 69,465 observations and 16 variables:</p><dl class='dl-horizontal'> <p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 69,447 observations and 16 variables:</p><dl class='dl-horizontal'>
<dt><code>mo</code></dt><dd><p>ID of microorganism as used by this package</p></dd> <dt><code>mo</code></dt><dd><p>ID of microorganism as used by this package</p></dd>
<dt><code>col_id</code></dt><dd><p>Catalogue of Life ID</p></dd> <dt><code>col_id</code></dt><dd><p>Catalogue of Life ID</p></dd>
<dt><code>fullname</code></dt><dd><p>Full name, like <code>"Escherichia coli"</code></p></dd> <dt><code>fullname</code></dt><dd><p>Full name, like <code>"Escherichia coli"</code></p></dd>
@ -264,9 +264,10 @@
<li><p>11 entries of <em>Streptococcus</em> (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)</p></li> <li><p>11 entries of <em>Streptococcus</em> (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)</p></li>
<li><p>2 entries of <em>Staphylococcus</em> (coagulase-negative [CoNS] and coagulase-positive [CoPS])</p></li> <li><p>2 entries of <em>Staphylococcus</em> (coagulase-negative [CoNS] and coagulase-positive [CoPS])</p></li>
<li><p>3 entries of <em>Trichomonas</em> (<em>Trichomonas vaginalis</em>, and its family and genus)</p></li> <li><p>3 entries of <em>Trichomonas</em> (<em>Trichomonas vaginalis</em>, and its family and genus)</p></li>
<li><p>1 entry of <em>Blastocystis</em> (<em>Blastocystis hominis</em>), although it officially does not exist (Noel et al. 2005, PMID 15634993)</p></li> <li><p>1 entry of <em>Blastocystis</em> (<em>Blastocystis hominis</em>), although it officially does not exist (Noel <em>et al.</em> 2005, PMID 15634993)</p></li>
<li><p>5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)</p></li> <li><p>5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)</p></li>
<li><p>9,460 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications</p></li> <li><p>6 families under the Enterobacterales order, according to Adeolu <em>et al.</em> (2016, PMID 27620848), that are not in the Catalogue of Life</p></li>
<li><p>12,600 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications</p></li>
</ul> </ul>
<h2 class="hasAnchor" id="about-the-records-from-dsmz-see-source-"><a class="anchor" href="#about-the-records-from-dsmz-see-source-"></a>About the records from DSMZ (see source)</h2> <h2 class="hasAnchor" id="about-the-records-from-dsmz-see-source-"><a class="anchor" href="#about-the-records-from-dsmz-see-source-"></a>About the records from DSMZ (see source)</h2>

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@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9007</span>
</span> </span>
</div> </div>
@ -356,7 +356,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class='fu'>mo_kingdom</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria"</span> <span class='fu'>mo_kingdom</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria"</span>
<span class='fu'>mo_phylum</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Proteobacteria"</span> <span class='fu'>mo_phylum</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Proteobacteria"</span>
<span class='fu'>mo_class</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Gammaproteobacteria"</span> <span class='fu'>mo_class</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Gammaproteobacteria"</span>
<span class='fu'>mo_order</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Enterobacteriales"</span> <span class='fu'>mo_order</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Enterobacterales" ()</span>
<span class='fu'>mo_family</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Enterobacteriaceae"</span> <span class='fu'>mo_family</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Enterobacteriaceae"</span>
<span class='fu'>mo_genus</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia"</span> <span class='fu'>mo_genus</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia"</span>
<span class='fu'>mo_species</span>(<span class='st'>"E. coli"</span>) <span class='co'># "coli"</span> <span class='fu'>mo_species</span>(<span class='st'>"E. coli"</span>) <span class='co'># "coli"</span>

7
man/microorganisms.Rd
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@ -4,7 +4,7 @@
\name{microorganisms} \name{microorganisms}
\alias{microorganisms} \alias{microorganisms}
\title{Data set with ~70,000 microorganisms} \title{Data set with ~70,000 microorganisms}
\format{A \code{\link{data.frame}} with 69,465 observations and 16 variables: \format{A \code{\link{data.frame}} with 69,447 observations and 16 variables:
\describe{ \describe{
\item{\code{mo}}{ID of microorganism as used by this package} \item{\code{mo}}{ID of microorganism as used by this package}
\item{\code{col_id}}{Catalogue of Life ID} \item{\code{col_id}}{Catalogue of Life ID}
@ -33,9 +33,10 @@ Manually added were:
\item{11 entries of \emph{Streptococcus} (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)} \item{11 entries of \emph{Streptococcus} (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)}
\item{2 entries of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])} \item{2 entries of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
\item{3 entries of \emph{Trichomonas} (\emph{Trichomonas vaginalis}, and its family and genus)} \item{3 entries of \emph{Trichomonas} (\emph{Trichomonas vaginalis}, and its family and genus)}
\item{1 entry of \emph{Blastocystis} (\emph{Blastocystis hominis}), although it officially does not exist (Noel et al. 2005, PMID 15634993)} \item{1 entry of \emph{Blastocystis} (\emph{Blastocystis hominis}), although it officially does not exist (Noel \emph{et al.} 2005, PMID 15634993)}
\item{5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)} \item{5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)}
\item{9,460 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications} \item{6 families under the Enterobacterales order, according to Adeolu \emph{et al.} (2016, PMID 27620848), that are not in the Catalogue of Life}
\item{12,600 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications}
} }
} }
\section{About the records from DSMZ (see source)}{ \section{About the records from DSMZ (see source)}{

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man/mo_property.Rd
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@ -134,7 +134,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
mo_kingdom("E. coli") # "Bacteria" mo_kingdom("E. coli") # "Bacteria"
mo_phylum("E. coli") # "Proteobacteria" mo_phylum("E. coli") # "Proteobacteria"
mo_class("E. coli") # "Gammaproteobacteria" mo_class("E. coli") # "Gammaproteobacteria"
mo_order("E. coli") # "Enterobacteriales" mo_order("E. coli") # "Enterobacterales" ()
mo_family("E. coli") # "Enterobacteriaceae" mo_family("E. coli") # "Enterobacteriaceae"
mo_genus("E. coli") # "Escherichia" mo_genus("E. coli") # "Escherichia"
mo_species("E. coli") # "coli" mo_species("E. coli") # "coli"

2
tests/testthat/test-misc.R
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@ -44,6 +44,6 @@ test_that("looking up ab columns works", {
expect_warning(generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE)) expect_warning(generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))
expect_warning(get_column_abx(example_isolates, hard_dependencies = "FUS")) expect_warning(get_column_abx(example_isolates, hard_dependencies = "FUS"))
expect_message(get_column_abx(example_isolates, soft_dependencies = "FUS")) expect_message(get_column_abx(example_isolates, soft_dependencies = "FUS"))
expect_message(get_column_abx(dplyr::rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE)) expect_warning(get_column_abx(dplyr::rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE))
expect_warning(get_column_abx(dplyr::rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE)) expect_warning(get_column_abx(dplyr::rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
}) })

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@ -28,7 +28,7 @@ test_that("mo_property works", {
expect_equal(mo_kingdom("Escherichia coli"), "Bacteria") expect_equal(mo_kingdom("Escherichia coli"), "Bacteria")
expect_equal(mo_phylum("Escherichia coli"), "Proteobacteria") expect_equal(mo_phylum("Escherichia coli"), "Proteobacteria")
expect_equal(mo_class("Escherichia coli"), "Gammaproteobacteria") expect_equal(mo_class("Escherichia coli"), "Gammaproteobacteria")
expect_equal(mo_order("Escherichia coli"), "Enterobacteriales") expect_equal(mo_order("Escherichia coli"), "Enterobacterales")
expect_equal(mo_family("Escherichia coli"), "Enterobacteriaceae") expect_equal(mo_family("Escherichia coli"), "Enterobacteriaceae")
expect_equal(mo_genus("Escherichia coli"), "Escherichia") expect_equal(mo_genus("Escherichia coli"), "Escherichia")
expect_equal(mo_species("Escherichia coli"), "coli") expect_equal(mo_species("Escherichia coli"), "coli")