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DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 2.1.1.9070
Date: 2024-07-19
Version: 2.1.1.9071
Date: 2024-09-19
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by

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NEWS.md
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@ -1,4 +1,4 @@
# AMR 2.1.1.9070
# AMR 2.1.1.9071
*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)*

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man/as.mo.Rd
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@ -74,7 +74,7 @@ A \link{character} \link{vector} with additional class \code{\link{mo}}
Use this function to get a valid microorganism code (\code{\link{mo}}) based on arbitrary user input. Determination is done using intelligent rules and the complete taxonomic tree of the kingdoms Animalia, Archaea, Bacteria, Chromista, and Protozoa, and most microbial species from the kingdom Fungi (see \emph{Source}). The input can be almost anything: a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (such as \code{"S. aureus"}), an abbreviation known in the field (such as \code{"MRSA"}), or just a genus. See \emph{Examples}.
}
\details{
A microorganism (MO) code from this package (class: \code{\link{mo}}) is human readable and typically looks like these examples:
A microorganism (MO) code from this package (class: \code{\link{mo}}) is human-readable and typically looks like these examples:
\if{html}{\out{<div class="sourceCode">}}\preformatted{ Code Full name
--------------- --------------------------------------
@ -86,8 +86,9 @@ A microorganism (MO) code from this package (class: \code{\link{mo}}) is human r
| | | \\---> subspecies, a 3-5 letter acronym
| | \\----> species, a 3-6 letter acronym
| \\----> genus, a 4-8 letter acronym
\\----> taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
F (Fungi), PL (Plantae), P (Protozoa)
\\----> kingdom: A (Archaea), AN (Animalia), B (Bacteria),
C (Chromista), F (Fungi), PL (Plantae),
P (Protozoa)
}\if{html}{\out{</div>}}
Values that cannot be coerced will be considered 'unknown' and will return the MO code \code{UNKNOWN} with a warning.
@ -97,9 +98,9 @@ Use the \code{\link[=mo_property]{mo_*}} functions to get properties based on th
The \code{\link[=as.mo]{as.mo()}} function uses a novel and scientifically validated (\doi{10.18637/jss.v104.i03}) matching score algorithm (see \emph{Matching Score for Microorganisms} below) to match input against the \link[=microorganisms]{available microbial taxonomy} in this package. This implicates that e.g. \code{"E. coli"} (a microorganism highly prevalent in humans) will return the microbial ID of \emph{Escherichia coli} and not \emph{Entamoeba coli} (a microorganism less prevalent in humans), although the latter would alphabetically come first.
\subsection{Coping with Uncertain Results}{
Results of non-exact taxonomic input are based on their \link[=mo_matching_score]{matching score}. The lowest allowed score can be set with the \code{minimum_matching_score} argument. At default this will be determined based on the character length of the input, and the \link[=microorganisms]{taxonomic kingdom} and \link[=mo_matching_score]{human pathogenicity} of the taxonomic outcome. If values are matched with uncertainty, a message will be shown to suggest the user to evaluate the results with \code{\link[=mo_uncertainties]{mo_uncertainties()}}, which returns a \link{data.frame} with all specifications.
Results of non-exact taxonomic input are based on their \link[=mo_matching_score]{matching score}. The lowest allowed score can be set with the \code{minimum_matching_score} argument. At default this will be determined based on the character length of the input, the \link[=microorganisms]{taxonomic kingdom}, and the \link[=mo_matching_score]{human pathogenicity} of the taxonomic outcome. If values are matched with uncertainty, a message will be shown to suggest the user to inspect the results with \code{\link[=mo_uncertainties]{mo_uncertainties()}}, which returns a \link{data.frame} with all specifications.
To increase the quality of matching, the \code{cleaning_regex} argument can be used to clean the input (i.e., \code{x}). This must be a \link[base:regex]{regular expression} that matches parts of the input that should be removed before the input is matched against the \link[=microorganisms]{available microbial taxonomy}. It will be matched Perl-compatible and case-insensitive. The default value of \code{cleaning_regex} is the outcome of the helper function \code{\link[=mo_cleaning_regex]{mo_cleaning_regex()}}.
To increase the quality of matching, the \code{cleaning_regex} argument is used to clean the input. This must be a \link[base:regex]{regular expression} that matches parts of the input that should be removed before the input is matched against the \link[=microorganisms]{available microbial taxonomy}. It will be matched Perl-compatible and case-insensitive. The default value of \code{cleaning_regex} is the outcome of the helper function \code{\link[=mo_cleaning_regex]{mo_cleaning_regex()}}.
There are three helper functions that can be run after using the \code{\link[=as.mo]{as.mo()}} function:
\itemize{
@ -127,7 +128,14 @@ With \code{Becker = TRUE}, the following staphylococci will be converted to thei
\item Coagulase-positive: \emph{S. agnetis}, \emph{S. argenteus}, \emph{S. coagulans}, \emph{S. cornubiensis}, \emph{S. delphini}, \emph{S. hyicus}, \emph{S. hyicus chromogenes}, \emph{S. hyicus hyicus}, \emph{S. intermedius}, \emph{S. lutrae}, \emph{S. pseudintermedius}, \emph{S. roterodami}, \emph{S. schleiferi coagulans}, \emph{S. schweitzeri}, \emph{S. simiae}, and \emph{S. singaporensis}
}
For newly named staphylococcal species, such as \emph{S. brunensis} (2024) and \emph{S. shinii} (2023), we look up the scientific reference to make sure the species are considered for the correct coagulase group.
This is based on:
\itemize{
\item Becker K \emph{et al.} (2014). \strong{Coagulase-Negative Staphylococci.} \emph{Clin Microbiol Rev.} 27(4): 870-926; \doi{10.1128/CMR.00109-13}
\item Becker K \emph{et al.} (2019). \strong{Implications of identifying the recently defined members of the \emph{S. aureus} complex, \emph{S. argenteus} and \emph{S. schweitzeri}: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).} \emph{Clin Microbiol Infect}; \doi{10.1016/j.cmi.2019.02.028}
\item Becker K \emph{et al.} (2020). \strong{Emergence of coagulase-negative staphylococci.} \emph{Expert Rev Anti Infect Ther.} 18(4):349-366; \doi{10.1080/14787210.2020.1730813}
}
For newly named staphylococcal species, such as \emph{S. brunensis} (2024) and \emph{S. shinii} (2023), we looked up the scientific reference to make sure the species are considered for the correct coagulase group.
}
\subsection{Lancefield Groups in Streptococci}{
@ -143,17 +151,17 @@ With \code{Lancefield = TRUE}, the following streptococci will be converted to t
\item Streptococcus Group K: \emph{S. salivarius}, \emph{S. salivarius salivarius}, and \emph{S. salivarius thermophilus}
\item Streptococcus Group L: \emph{S. dysgalactiae}, \emph{S. dysgalactiae dysgalactiae}, and \emph{S. dysgalactiae equisimilis}
}
This is based on:
\itemize{
\item Lancefield RC (1933). \strong{A serological differentiation of human and other groups of hemolytic streptococci.} \emph{J Exp Med.} 57(4): 571-95; \doi{10.1084/jem.57.4.571}
}
}
}
\section{Source}{
\enumerate{
\itemize{
\item Berends MS \emph{et al.} (2022). \strong{AMR: An R Package for Working with Antimicrobial Resistance Data}. \emph{Journal of Statistical Software}, 104(3), 1-31; \doi{10.18637/jss.v104.i03}
\item Becker K \emph{et al.} (2014). \strong{Coagulase-Negative Staphylococci.} \emph{Clin Microbiol Rev.} 27(4): 870-926; \doi{10.1128/CMR.00109-13}
\item Becker K \emph{et al.} (2019). \strong{Implications of identifying the recently defined members of the \emph{S. aureus} complex, \emph{S. argenteus} and \emph{S. schweitzeri}: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).} \emph{Clin Microbiol Infect}; \doi{10.1016/j.cmi.2019.02.028}
\item Becker K \emph{et al.} (2020). \strong{Emergence of coagulase-negative staphylococci.} \emph{Expert Rev Anti Infect Ther.} 18(4):349-366; \doi{10.1080/14787210.2020.1730813}
\item Lancefield RC (1933). \strong{A serological differentiation of human and other groups of hemolytic streptococci.} \emph{J Exp Med.} 57(4): 571-95; \doi{10.1084/jem.57.4.571}
\item Berends MS \emph{et al.} (2022). \strong{Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019/} \emph{Micro.rganisms} 10(9), 1801; \doi{10.3390/microorganisms10091801}
\item Parte, AC \emph{et al.} (2020). \strong{List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.} International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \doi{10.1099/ijsem.0.004332}. Accessed from \url{https://lpsn.dsmz.de} on June 24th, 2024.
\item Vincent, R \emph{et al} (2013). \strong{MycoBank gearing up for new horizons.} IMA Fungus, 4(2), 371-9; \doi{10.5598/imafungus.2013.04.02.16}. Accessed from \url{https://www.mycobank.org} on June 24th, 2024.
\item GBIF Secretariat (2023). GBIF Backbone Taxonomy. Checklist dataset \doi{10.15468/39omei}. Accessed from \url{https://www.gbif.org} on June 24th, 2024.

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man/as.sir.Rd
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@ -18,7 +18,8 @@ For interpretations of minimum inhibitory concentration (MIC) values and disk di
\itemize{
\item \strong{CLSI M39: Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data}, 2011-2024, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
\item \strong{CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing}, 2011-2024, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m100/}.
\item \strong{CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals}, 2019-2024, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/veterinary-medicine/documents/vet01//}.
\item \strong{CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals}, 2019-2024, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/veterinary-medicine/documents/vet01/}.
\item \strong{CLSI VET09: Understanding Susceptibility Test Data as a Component of Antimicrobial Stewardship in Veterinary Settings}, 2019-2024, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/veterinary-medicine/documents/vet09/}.
\item \strong{EUCAST Breakpoint tables for interpretation of MICs and zone diameters}, 2011-2024, \emph{European Committee on Antimicrobial Susceptibility Testing} (EUCAST). \url{https://www.eucast.org/clinical_breakpoints}.
\item \strong{WHONET} as a source for machine-reading the clinical breakpoints (\href{https://msberends.github.io/AMR/reference/clinical_breakpoints.html#imported-from-whonet}{read more here}), 1989-2024, \emph{WHO Collaborating Centre for Surveillance of Antimicrobial Resistance}. \url{https://whonet.org/}.
}
@ -140,7 +141,7 @@ These breakpoints are currently implemented:
\itemize{
\item For \strong{clinical microbiology}: EUCAST 2011-2024 and CLSI 2011-2024;
\item For \strong{veterinary microbiology}: EUCAST 2021-2024 and CLSI 2019-2024;
\item ECOFFs (Epidemiological cut-off values): EUCAST 2020-2024 and CLSI 2022-2024.
\item For \strong{ECOFFs} (Epidemiological Cut-off Values): EUCAST 2020-2024 and CLSI 2022-2024.
}
All breakpoints used for interpretation are available in our \link{clinical_breakpoints} data set.
@ -162,7 +163,7 @@ your_data \%>\% mutate_if(is.mic, as.sir, ab = "column_with_antibiotics", mo = "
your_data \%>\% mutate_if(is.mic, as.sir, ab = c("cipro", "ampicillin", ...), mo = c("E. coli", "K. pneumoniae", ...))
# for veterinary breakpoints, also set `host`:
your_data \%>\% mutate_if(is.mic, as.sir, host = "column_with_animal_hosts", guideline = "CLSI")
your_data \%>\% mutate_if(is.mic, as.sir, host = "column_with_animal_species", guideline = "CLSI")
}\if{html}{\out{</div>}}
\item Operators like "<=" will be stripped before interpretation. When using \code{conserve_capped_values = TRUE}, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (\code{conserve_capped_values = FALSE}) considers ">2" to be lower than ">=4" and might in this case return "S" or "I".
}
@ -176,7 +177,7 @@ your_data \%>\% mutate_if(is.disk, as.sir, ab = "column_with_antibiotics", mo =
your_data \%>\% mutate_if(is.disk, as.sir, ab = c("cipro", "ampicillin", ...), mo = c("E. coli", "K. pneumoniae", ...))
# for veterinary breakpoints, also set `host`:
your_data \%>\% mutate_if(is.disk, as.sir, host = "column_with_animal_hosts", guideline = "CLSI")
your_data \%>\% mutate_if(is.disk, as.sir, host = "column_with_animal_species", guideline = "CLSI")
}\if{html}{\out{</div>}}
}
\item For \strong{interpreting a complete data set}, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running \code{as.sir(your_data)}.
@ -205,11 +206,15 @@ For veterinary guidelines, these might be the best options:
\if{html}{\out{<div class="sourceCode">}}\preformatted{ options(AMR_guideline = "CLSI")
options(AMR_breakpoint_type = "animal")
}\if{html}{\out{</div>}}
When applying veterinary breakpoints (by setting \code{host} or by setting \code{breakpoint_type = "animal"}), the \href{https://clsi.org/standards/products/veterinary-medicine/documents/vet09/}{CLSI VET09 guideline} will be applied to cope with missing animal species-specific breakpoints.
}
\subsection{After Interpretation}{
After using \code{\link[=as.sir]{as.sir()}}, you can use the \code{\link[=eucast_rules]{eucast_rules()}} defined by EUCAST to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
To determine which isolates are multi-drug resistant, be sure to run \code{\link[=mdro]{mdro()}} (which applies the MDR/PDR/XDR guideline from 2012 at default) on a data set that contains S/I/R values. Read more about \link[=mdro]{interpreting multidrug-resistant organisms here}.
}
\subsection{Machine-Readable Clinical Breakpoints}{

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man/mo_property.Rd
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@ -363,13 +363,8 @@ This function uses \code{\link[=as.mo]{as.mo()}} internally, which uses an advan
\section{Source}{
\enumerate{
\itemize{
\item Berends MS \emph{et al.} (2022). \strong{AMR: An R Package for Working with Antimicrobial Resistance Data}. \emph{Journal of Statistical Software}, 104(3), 1-31; \doi{10.18637/jss.v104.i03}
\item Becker K \emph{et al.} (2014). \strong{Coagulase-Negative Staphylococci.} \emph{Clin Microbiol Rev.} 27(4): 870-926; \doi{10.1128/CMR.00109-13}
\item Becker K \emph{et al.} (2019). \strong{Implications of identifying the recently defined members of the \emph{S. aureus} complex, \emph{S. argenteus} and \emph{S. schweitzeri}: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).} \emph{Clin Microbiol Infect}; \doi{10.1016/j.cmi.2019.02.028}
\item Becker K \emph{et al.} (2020). \strong{Emergence of coagulase-negative staphylococci.} \emph{Expert Rev Anti Infect Ther.} 18(4):349-366; \doi{10.1080/14787210.2020.1730813}
\item Lancefield RC (1933). \strong{A serological differentiation of human and other groups of hemolytic streptococci.} \emph{J Exp Med.} 57(4): 571-95; \doi{10.1084/jem.57.4.571}
\item Berends MS \emph{et al.} (2022). \strong{Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019/} \emph{Micro.rganisms} 10(9), 1801; \doi{10.3390/microorganisms10091801}
\item Parte, AC \emph{et al.} (2020). \strong{List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.} International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \doi{10.1099/ijsem.0.004332}. Accessed from \url{https://lpsn.dsmz.de} on June 24th, 2024.
\item Vincent, R \emph{et al} (2013). \strong{MycoBank gearing up for new horizons.} IMA Fungus, 4(2), 371-9; \doi{10.5598/imafungus.2013.04.02.16}. Accessed from \url{https://www.mycobank.org} on June 24th, 2024.
\item GBIF Secretariat (2023). GBIF Backbone Taxonomy. Checklist dataset \doi{10.15468/39omei}. Accessed from \url{https://www.gbif.org} on June 24th, 2024.