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Interpret antimicrobial susceptibility phenotype data in a standard format tibble

Source: R/import_pheno.R
interpret_pheno.Rd

This function applies human EUCAST or CLSI breakpoints, and/or ECOFF, to interpret antimicrobial susceptibility testing (AST) data.

Usage

interpret_pheno(
  ast,
  interpret_ecoff = TRUE,
  interpret_eucast = TRUE,
  interpret_clsi = TRUE,
  species = NULL,
  ab = NULL
)

Arguments

ast

A tibble containing the phenotype measures in standard AMRgen format, as output by import_pheno(). It must contain assay measurements in columns mic (class mic) and/or disk (class disk). Interpretation requires an organism (column spp_pheno of class mo, or a single value passed via the species parameter) and an antibiotic (column drug of class ab, or a single value passed via the ab parameter).

interpret_ecoff

A logical value (default is FALSE). If TRUE, the function will interpret the wildtype vs nonwildtype status for each row based on the MIC or disk diffusion values, against epidemiological cut-off (ECOFF) values. These will be reported in a new column ecoff, of class sir and coded as NWT (nonwildtype) or WT (wildtype).

interpret_eucast

A logical value (default is FALSE). If TRUE, the function will interpret the susceptibility phenotype (SIR) for each row based on the MIC or disk diffusion values, against EUCAST human breakpoints. These will be reported in a new column pheno_eucast, of class sir.

interpret_clsi

A logical value (default is FALSE). If TRUE, the function will interpret the susceptibility phenotype (SIR) for each row based on the MIC or disk diffusion values, against CLSI human breakpoints. These will be reported in a new column pheno_clsi, of class sir.

species

(optional) Name of the species to use for phenotype interpretation. By default, the spp_pheno field in the input file will be assumed to specify the species for each sample, but if this is missing or you want to override it in the interpretation step, you may provide a single species name via this parameter.

ab

(optional) Name of the antibiotic to use for phenotype interpretation. By default, the drug field in the input file will be assumed to specify the antibiotic for each sample, but if this is missing or you want to override it in the interpretation step, you may provide a single antibiotic name via this parameter.

Value

A copy of the input table, with additional columns:

  • pheno_eucast: The phenotype newly interpreted against EUCAST human breakpoint standards (as S/I/R), based on the MIC or disk diffusion data.

  • pheno_clsi: The phenotype newly interpreted against CLSI human breakpoint standards (as S/I/R), based on the MIC or disk diffusion data.

  • ecoff: The phenotype newly interpreted against the ECOFF (as WT/NWT), based on the MIC or disk diffusion data.

  • spp_pheno: The species phenotype, formatted using the AMR::as.mo() function (either taken from field spp_pheno in the input table, or the single value specified by species parameter).

  • drug: The antibiotic used in the test, formatted using the AMR::as.ab() function (either taken from field drug in the input table, or the single value specified by ab parameter).

Examples

# import without re-interpreting resistance
pheno <- import_ncbi_pheno(ecoli_pheno_raw)
#> Warning: Expected AST method column 'Laboratory typing method' not found in input
#> Warning: Expected column 'BioProject' not found in input
head(pheno)
#> # A tibble: 6 × 29
#>   id    drug    mic  disk guideline method  platform pheno_provided spp_pheno   
#>   <chr> <ab>  <mic> <dsk> <chr>     <chr>   <chr>    <sir>          <mo>        
#> 1 SAMN… CIP  256.00    NA CLSI      broth … NA         R            B_ESCHR_COLI
#> 2 SAMN… CIP   64.00    NA CLSI      Etest   Etest      R            B_ESCHR_COLI
#> 3 SAMN… CIP  >=4.00    NA CLSI      broth … NA         R            B_ESCHR_COLI
#> 4 SAMN… CIP  >=4.00    NA CLSI      broth … NA         R            B_ESCHR_COLI
#> 5 SAMN… CIP  <=0.25    NA CLSI      broth … NA         S            B_ESCHR_COLI
#> 6 SAMN… CIP  >=4.00    NA CLSI      broth … NA         R            B_ESCHR_COLI
#> # ℹ 20 more variables: `Organism group` <chr>, `Scientific name` <chr>,
#> #   `Isolation type` <chr>, Location <chr>, `Isolation source` <chr>,
#> #   Isolate <chr>, Antibiotic <chr>, `Resistance phenotype` <chr>,
#> #   `Measurement sign` <chr>, `MIC (mg/L)` <dbl>, `Disk diffusion (mm)` <lgl>,
#> #   `Laboratory typing platform` <chr>, Vendor <chr>,
#> #   `Laboratory typing method version or reagent` <chr>,
#> #   `Testing standard` <chr>, `Create date` <dttm>, pheno_clsi_mic <sir>, …

# interpret phenotypes
pheno <- interpret_pheno(pheno)

if (FALSE) { # \dontrun{
pheno <- read_csv("AST.csv") %>%
  # convert antibiotic field to 'drug' of class 'ab'
  mutate(drug = as.ab(antibiotic)) %>%
  mutate(mic = paste0(sign, MIC)) %>%
  mutate(mic = as.mic(mic)) # create a single 'mic' column of class 'mic'

pheno <- interpret_pheno(pheno, species = "Escherichia coli")
} # }