mirror of https://github.com/msberends/AMR.git
181 lines
14 KiB
R
181 lines
14 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/mdro.R
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\name{mdro}
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\alias{mdro}
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\alias{brmo}
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\alias{mrgn}
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\alias{mdr_tb}
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\alias{mdr_cmi2012}
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\alias{eucast_exceptional_phenotypes}
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\title{Determine multidrug-resistant organisms (MDRO)}
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\source{
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Please see Details for the list of publications used for this function.
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}
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\usage{
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mdro(x, guideline = NULL, col_mo = NULL, info = TRUE,
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verbose = FALSE, pct_required_classes = 0.5, ...)
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brmo(x, guideline = "BRMO", ...)
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mrgn(x, guideline = "MRGN", ...)
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mdr_tb(x, guideline = "TB", ...)
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mdr_cmi2012(x, guideline = "CMI2012", ...)
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eucast_exceptional_phenotypes(x, guideline = "EUCAST", ...)
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}
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\arguments{
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\item{x}{data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}}
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\item{guideline}{a specific guideline to follow. When left empty, the publication by Magiorakos \emph{et al.} (2012, Clinical Microbiology and Infection) will be followed, see Details.}
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\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link{as.mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
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\item{info}{print progress}
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\item{verbose}{a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.}
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\item{pct_required_classes}{minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for \emph{S. aureus}. Setting this \code{pct_required_classes} argument to \code{0.5} (default) means that for every \emph{S. aureus} isolate at least 8 different classes must be available. Any lower number of available classes will return \code{NA} for that isolate.}
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\item{...}{column name of an antibiotic, see section Antibiotics}
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}
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\value{
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\itemize{
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\item{CMI 2012 paper - function \code{mdr_cmi2012()} or \code{mdro()}:\cr Ordered factor with levels \code{Negative < Multi-drug-resistant (MDR) < Extensively drug-resistant (XDR) < Pandrug-resistant (PDR)}}
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\item{TB guideline - function \code{mdr_tb()} or \code{mdro(..., guideline = "TB")}:\cr Ordered factor with levels \code{Negative < Mono-resistant < Poly-resistant < Multi-drug-resistant < Extensively drug-resistant}}
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\item{German guideline - function \code{mrgn()} or \code{mdro(..., guideline = "MRGN")}:\cr Ordered factor with levels \code{Negative < 3MRGN < 4MRGN}}
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\item{Everything else:\cr Ordered factor with levels \code{Negative < Positive, unconfirmed < Positive}. The value \code{"Positive, unconfirmed"} means that, according to the guideline, it is not entirely sure if the isolate is multi-drug resistant and this should be confirmed with additional (e.g. molecular) tests}
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}
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}
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\description{
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Determine which isolates are multidrug-resistant organisms (MDRO) according to (country-specific) guidelines.
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}
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\details{
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For the \code{pct_required_classes} argument, values above 1 will be divided by 100. This is to support both fractions (\code{0.75} or \code{3/4}) and percentages (\code{75}).
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Currently supported guidelines are (case-insensitive):
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\itemize{
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\item{\code{guideline = "CMI2012"}: Magiorakos AP, Srinivasan A \emph{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) (\href{https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext}{link})}
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\item{\code{guideline = "EUCAST"}: The European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\href{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{link})}
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\item{\code{guideline = "TB"}: The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (\href{https://www.who.int/tb/publications/pmdt_companionhandbook/en/}{link})}
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\item{\code{guideline = "MRGN"}: The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6}
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\item{\code{guideline = "BRMO"}: The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]" (\href{https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH}{link})}
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}
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Please suggest your own (country-specific) guidelines by letting us know: \url{https://gitlab.com/msberends/AMR/issues/new}.
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\strong{Note:} Every test that involves the Enterobacteriaceae family, will internally be performed using its newly named order Enterobacterales, since the Enterobacteriaceae family has been taxonomically reclassified by Adeolu \emph{et al.} in 2016. Before that, Enterobacteriaceae was the only family under the Enterobacteriales (with an i) order. All species under the old Enterobacteriaceae family are still under the new Enterobacterales (without an i) order, but divided into multiple families. The way tests are performed now by this \code{mdro()} function makes sure that results from before 2016 and after 2016 are identical.
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}
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\section{Antibiotics}{
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To define antibiotics column names, leave as it is to determine it automatically with \code{\link{guess_ab_col}} or input a text (case-insensitive), or use \code{NULL} to skip a column (e.g. \code{TIC = NULL} to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
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The following antibiotics are used for the functions \code{\link{eucast_rules}} and \code{\link{mdro}}. These are shown below in the format '\strong{antimicrobial ID}: name (\href{https://www.whocc.no/atc/structure_and_principles/}{ATC code})', sorted by name:
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\strong{AMK}: amikacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB06}{J01GB06}),
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\strong{AMX}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}),
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\strong{AMC}: amoxicillin/clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR02}{J01CR02}),
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\strong{AMP}: ampicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA01}{J01CA01}),
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\strong{SAM}: ampicillin/sulbactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR01}{J01CR01}),
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\strong{AZM}: azithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA10}{J01FA10}),
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\strong{AZL}: azlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA09}{J01CA09}),
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\strong{ATM}: aztreonam (\href{https://www.whocc.no/atc_ddd_index/?code=J01DF01}{J01DF01}),
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\strong{CAP}: capreomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB30}{J04AB30}),
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\strong{RID}: cefaloridine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB02}{J01DB02}),
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\strong{CZO}: cefazolin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB04}{J01DB04}),
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\strong{FEP}: cefepime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DE01}{J01DE01}),
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\strong{CTX}: cefotaxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD01}{J01DD01}),
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\strong{CTT}: cefotetan (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC05}{J01DC05}),
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\strong{FOX}: cefoxitin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC01}{J01DC01}),
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\strong{CPT}: ceftaroline (\href{https://www.whocc.no/atc_ddd_index/?code=J01DI02}{J01DI02}),
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\strong{CAZ}: ceftazidime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD02}{J01DD02}),
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\strong{CRO}: ceftriaxone (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD04}{J01DD04}),
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\strong{CXM}: cefuroxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC02}{J01DC02}),
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\strong{CED}: cephradine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB09}{J01DB09}),
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\strong{CHL}: chloramphenicol (\href{https://www.whocc.no/atc_ddd_index/?code=J01BA01}{J01BA01}),
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\strong{CIP}: ciprofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA02}{J01MA02}),
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\strong{CLR}: clarithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA09}{J01FA09}),
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\strong{CLI}: clindamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF01}{J01FF01}),
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\strong{COL}: colistin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB01}{J01XB01}),
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\strong{DAP}: daptomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX09}{J01XX09}),
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\strong{DOR}: doripenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH04}{J01DH04}),
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\strong{DOX}: doxycycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA02}{J01AA02}),
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\strong{ETP}: ertapenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH03}{J01DH03}),
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\strong{ERY}: erythromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA01}{J01FA01}),
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\strong{ETH}: ethambutol (\href{https://www.whocc.no/atc_ddd_index/?code=J04AK02}{J04AK02}),
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\strong{FLC}: flucloxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF05}{J01CF05}),
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\strong{FOS}: fosfomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX01}{J01XX01}),
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\strong{FUS}: fusidic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XC01}{J01XC01}),
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\strong{GAT}: gatifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA16}{J01MA16}),
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\strong{GEN}: gentamicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB03}{J01GB03}),
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\strong{GEH}: gentamicin-high (no ATC code),
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\strong{IPM}: imipenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH51}{J01DH51}),
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\strong{INH}: isoniazid (\href{https://www.whocc.no/atc_ddd_index/?code=J04AC01}{J04AC01}),
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\strong{KAN}: kanamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB04}{J01GB04}),
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\strong{LVX}: levofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA12}{J01MA12}),
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\strong{LIN}: lincomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF02}{J01FF02}),
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\strong{LNZ}: linezolid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX08}{J01XX08}),
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\strong{MEM}: meropenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH02}{J01DH02}),
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\strong{MTR}: metronidazole (\href{https://www.whocc.no/atc_ddd_index/?code=J01XD01}{J01XD01}),
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\strong{MEZ}: mezlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA10}{J01CA10}),
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\strong{MNO}: minocycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA08}{J01AA08}),
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\strong{MFX}: moxifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA14}{J01MA14}),
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\strong{NAL}: nalidixic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01MB02}{J01MB02}),
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\strong{NEO}: neomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB05}{J01GB05}),
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\strong{NET}: netilmicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB07}{J01GB07}),
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\strong{NIT}: nitrofurantoin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XE01}{J01XE01}),
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\strong{NOR}: norfloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA06}{J01MA06}),
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\strong{NOV}: novobiocin (\href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}),
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\strong{OFX}: ofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01MA01}),
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\strong{OXA}: oxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF04}{J01CF04}),
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\strong{PEN}: penicillin G (\href{https://www.whocc.no/atc_ddd_index/?code=J01CE01}{J01CE01}),
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\strong{PIP}: piperacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA12}{J01CA12}),
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\strong{TZP}: piperacillin/tazobactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR05}{J01CR05}),
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\strong{PLB}: polymyxin B (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB02}{J01XB02}),
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\strong{PRI}: pristinamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG01}{J01FG01}),
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\strong{PZA}: pyrazinamide (\href{https://www.whocc.no/atc_ddd_index/?code=J04AK01}{J04AK01}),
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\strong{QDA}: quinupristin/dalfopristin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG02}{J01FG02}),
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\strong{RIB}: rifabutin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB04}{J04AB04}),
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\strong{RIF}: rifampicin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
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\strong{RFP}: rifapentine (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB05}{J04AB05}),
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\strong{RXT}: roxithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}),
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\strong{SIS}: sisomicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB08}{J01GB08}),
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\strong{STH}: streptomycin-high (no ATC code),
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\strong{TEC}: teicoplanin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA02}{J01XA02}),
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\strong{TLV}: telavancin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA03}{J01XA03}),
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\strong{TCY}: tetracycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA07}{J01AA07}),
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\strong{TIC}: ticarcillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA13}{J01CA13}),
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\strong{TCC}: ticarcillin/clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR03}{J01CR03}),
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\strong{TGC}: tigecycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA12}{J01AA12}),
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\strong{TOB}: tobramycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB01}{J01GB01}),
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\strong{TMP}: trimethoprim (\href{https://www.whocc.no/atc_ddd_index/?code=J01EA01}{J01EA01}),
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\strong{SXT}: trimethoprim/sulfamethoxazole (\href{https://www.whocc.no/atc_ddd_index/?code=J01EE01}{J01EE01}),
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\strong{VAN}: vancomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA01}{J01XA01}).
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}
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\section{Read more on our website!}{
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On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
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}
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\examples{
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library(dplyr)
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example_isolates \%>\%
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mdro() \%>\%
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freq()
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\donttest{
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example_isolates \%>\%
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mutate(EUCAST = eucast_exceptional_phenotypes(.),
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BRMO = brmo(.),
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MRGN = mrgn(.))
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example_isolates \%>\%
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rename(PIP = TZP) \%>\% # no piperacillin, so take piperacillin/tazobactam
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mrgn() \%>\% # check German guideline
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freq() # check frequencies
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}
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}
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