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Check and Retrieve Breakpoints for an Antibiotic

Source: R/breakpoints.R
checkBreakpoints.Rd

This function checks the clinical breakpoints for a specified antibiotic and species using the getBreakpoints function. It handles cases where multiple breakpoint sites exist and uses the specified site or the one with the highest susceptibility breakpoint.

Usage

checkBreakpoints(
  species,
  guide = "EUCAST 2024",
  antibiotic,
  assay = "MIC",
  bp_site = NULL
)

Arguments

species

A character string representing the species of interest (e.g., "Escherichia coli").

guide

A character string indicating the guideline for breakpoints (default, "EUCAST 2024").

antibiotic

A character string indicating the antibiotic for which to check breakpoints (e.g., "Ciprofloxacin").

assay

A character string specifying the assay type (either "MIC" or "Disk"). Default is "MIC".

bp_site

A character string specifying the breakpoint site to use (optional). If provided, the function uses this site; otherwise, if different breakpoints are specified for different sites it selects the one with the highest susceptibility breakpoint.

Value

A list containing:

  • breakpoint_S: The susceptibility breakpoint (e.g., MIC or disk size).

  • breakpoint_R: The resistance breakpoint (e.g., MIC or disk size).

  • bp_standard: The breakpoint site used, if multiple breakpoints are set in the guidelines.

Details

The function first attempts to retrieve breakpoints using the getBreakpoints function. If multiple breakpoint sites are found, it handles the situation by:

  • Using the specified site if it exists.

  • Selecting the breakpoint with the highest susceptibility value if the specified site is not found.

  • Returning a message about the selected site and breakpoint values.

Examples

checkBreakpoints(species="Escherichia coli", guide="EUCAST 2024", 
                      antibiotic="Ciprofloxacin", assay="MIC")
#>   MIC breakpoints determined using AMR package: S <= 0.25 and R > 0.5
#>   NOTE: Multiple breakpoint entries, for different sites: Non-meningitis; Meningitis. Using the one with the highest S breakpoint (Non-meningitis).
#> $breakpoint_S
#> [1] 0.25
#> 
#> $breakpoint_R
#> [1] 0.5
#> 
#> $bp_standard
#> [1] "Non-meningitis"
#>