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127 lines
4.2 KiB
Markdown
127 lines
4.2 KiB
Markdown
# Apply EUCAST rules
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## Introduction
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What are EUCAST rules? The European Committee on Antimicrobial
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Susceptibility Testing (EUCAST) states [on their
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website](https://www.eucast.org/expert_rules_and_expected_phenotypes):
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> *EUCAST expert rules (see below) are a tabulated collection of expert
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> knowledge on interpretive rules, expected resistant phenotypes and
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> expected susceptible phenotypes which should be applied to
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> antimicrobial susceptibility testing in order to reduce testing,
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> reduce errors and make appropriate recommendations for reporting
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> particular resistances.*
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In Europe, a lot of medical microbiological laboratories already apply
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these rules ([Brown *et al.*,
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2015](https://www.eurosurveillance.org/content/10.2807/1560-7917.ES2015.20.2.21008)).
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Our package features their latest insights on expected resistant
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phenotypes (v1.2, 2023).
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## Examples
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These rules can be used to discard improbable bug-drug combinations in
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your data. For example, *Klebsiella* produces beta-lactamase that
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prevents ampicillin (or amoxicillin) from working against it. In other
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words, practically every strain of *Klebsiella* is resistant to
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ampicillin.
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Sometimes, laboratory data can still contain such strains with
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*Klebsiella* being susceptible to ampicillin. This could be because an
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antibiogram is available before an identification is available, and the
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antibiogram is then not re-interpreted based on the identification. The
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[`eucast_rules()`](https://amr-for-r.org/reference/eucast_rules.md)
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function resolves this, by applying the latest ‘EUCAST Expected
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Resistant Phenotypes’ guideline:
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``` r
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oops <- tibble::tibble(
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mo = c(
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"Klebsiella pneumoniae",
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"Escherichia coli"
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),
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ampicillin = as.sir("S")
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)
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oops
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#> # A tibble: 2 × 2
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#> mo ampicillin
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#> <chr> <sir>
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#> 1 Klebsiella pneumoniae S
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#> 2 Escherichia coli S
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eucast_rules(oops, info = FALSE, overwrite = TRUE)
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#> # A tibble: 2 × 2
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#> mo ampicillin
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#> <chr> <sir>
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#> 1 Klebsiella pneumoniae R
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#> 2 Escherichia coli S
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```
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A more convenient function is
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[`mo_is_intrinsic_resistant()`](https://amr-for-r.org/reference/mo_property.md)
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that uses the same guideline, but allows to check for one or more
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specific microorganisms or antimicrobials:
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``` r
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mo_is_intrinsic_resistant(
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c("Klebsiella pneumoniae", "Escherichia coli"),
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"ampicillin"
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)
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#> [1] TRUE FALSE
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mo_is_intrinsic_resistant(
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"Klebsiella pneumoniae",
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c("ampicillin", "kanamycin")
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)
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#> [1] TRUE FALSE
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```
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EUCAST rules can not only be used for correction, they can also be used
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for filling in known resistance and susceptibility based on results of
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other antimicrobials drugs. This process is called *interpretive
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reading*, and is basically a form of imputation:
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``` r
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data <- tibble::tibble(
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mo = c(
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"Staphylococcus aureus",
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"Enterococcus faecalis",
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"Escherichia coli",
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"Klebsiella pneumoniae",
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"Pseudomonas aeruginosa"
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),
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VAN = "-", # Vancomycin
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AMX = "-", # Amoxicillin
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COL = "-", # Colistin
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CAZ = "-", # Ceftazidime
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CXM = "-", # Cefuroxime
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PEN = "S", # Benzylenicillin
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FOX = "S" # Cefoxitin
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)
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```
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``` r
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data
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```
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| mo | VAN | AMX | COL | CAZ | CXM | PEN | FOX |
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|:-----------------------|:---:|:---:|:---:|:---:|:---:|:---:|:---:|
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| Staphylococcus aureus | \- | \- | \- | \- | \- | S | S |
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| Enterococcus faecalis | \- | \- | \- | \- | \- | S | S |
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| Escherichia coli | \- | \- | \- | \- | \- | S | S |
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| Klebsiella pneumoniae | \- | \- | \- | \- | \- | S | S |
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| Pseudomonas aeruginosa | \- | \- | \- | \- | \- | S | S |
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``` r
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eucast_rules(data, overwrite = TRUE)
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```
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| mo | VAN | AMX | COL | CAZ | CXM | PEN | FOX |
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|:-----------------------|:---:|:---:|:---:|:---:|:---:|:---:|:---:|
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| Staphylococcus aureus | \- | S | R | R | S | S | S |
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| Enterococcus faecalis | \- | \- | R | R | R | S | R |
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| Escherichia coli | R | \- | \- | \- | \- | R | S |
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| Klebsiella pneumoniae | R | R | \- | \- | \- | R | S |
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| Pseudomonas aeruginosa | R | R | \- | \- | R | R | R |
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