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Interpret antimicrobial susceptibility phenotype data in a standard format tibble

Source: R/import_pheno.R
interpret_ast.Rd

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

Usage

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

Arguments

ast

A tibble containing the AST measures in standard AMRgen format, as output by import_ast. It must contain assay measurements in columns 'mic' (class mic) and/or '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_agent' 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 'R' (nonwildtype) or 'S' (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_agent 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 S/R), based on the MIC or disk diffusion data.

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

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

Examples

# import without re-interpreting resistance
pheno <- import_ncbi_ast(ecoli_ast_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_agent     mic  disk guideline method platform pheno_provided
#>   <chr>        <ab>         <mic> <dsk> <chr>     <chr>  <chr>    <sir>         
#> 1 SAMN36015110 CIP        <128.00    NA CLSI      broth… NA         R           
#> 2 SAMN11638310 CIP         256.00    NA CLSI      broth… NA         R           
#> 3 SAMN05729964 CIP          64.00    NA CLSI      Etest  Etest      R           
#> 4 SAMN10620111 CIP         >=4.00    NA CLSI      broth… NA         R           
#> 5 SAMN10620168 CIP         >=4.00    NA CLSI      broth… NA         R           
#> 6 SAMN10620104 CIP         <=0.25    NA CLSI      broth… NA         S           
#> # ℹ 21 more variables: spp_pheno <mo>, `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_ast(pheno)
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `across(...)`.
#> Caused by warning:
#> ! Some MICs were converted to the nearest higher log2 level, following the
#> CLSI interpretation guideline.

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

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