This function imports an antibiotic susceptibility testing (AST) dataset, processes the data, and optionally interprets the results based on MIC or disk diffusion data. It assumes that the input file is a tab-delimited text file (e.g., TSV) or CSV (which may be commpressed) and parses relevant columns (antibiotic names, species names, MIC or disk data) into suitable classes using the AMR package. It optionally can use the AMR package to interpret susceptibility phenotype (SIR) based on EUCAST or CLSI guidelines (human breakpoints and/or ECOFF). If expected columns are not found warnings will be given, and interpretation may not be possible.
Usage
import_ncbi_ast(
input,
sample_col = "#BioSample",
source = NULL,
species = NULL,
ab = NULL,
interpret_eucast = FALSE,
interpret_clsi = FALSE,
interpret_ecoff = FALSE
)Arguments
- input
A string representing a dataframe, or a path to an input file, containing the AST data in NCBI antibiogram format. These files can be downloaded from NCBI AST browser, e.g. https://www.ncbi.nlm.nih.gov/pathogens/ast#Pseudomonas%20aeruginosa
- sample_col
A string indicating the name of the column with sample identifiers. If
NULL, assume this is '#BioSample'.- source
(optional) A single value to record as the source of these data points, e.g. "NCBI_browser". By default, the field 'BioProject' will be used to indicate the source for each row in the input file, but if this is missing or you want to override it with a single value for all samples, you may provide a source name via this parameter.
- species
(optional) Name of the species to use for phenotype interpretation. By default, the field 'Scientific name' will be assumed to specify the species for each row in the input file, 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 field 'Antibiotic' will be assumed to specify the antibiotic for each row in the input file, 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.
- 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 ECOFF human breakpoints. These will be reported in a new columnpheno_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 columnpheno_clsi, of class 'sir'.- 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 columnecoff, of class 'sir' and coded as 'R' (nonwildtype) or 'S' (wildtype).
Value
A data frame with the processed AST data, including additional columns:
id: The biological sample identifier (renamed from#BioSampleor specified column).spp_pheno: The species phenotype, formatted using theas.mofunction.drug_agent: The antibiotic used in the test, formatted using theas.abfunction.mic: The minimum inhibitory concentration (MIC) value, formatted using theas.micfunction.disk: The disk diffusion measurement (in mm), formatted using theas.diskfunction.method: The AST platform recorded in the input file as the source of the measurement.guideline: The AST standard recorded in the input file as being used for the AST assay.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.pheno_provided: The original phenotype interpretation provided in the input file.source: The source of each data point (renamed fromBioProjectin the input file, or replaced with a single value passed in as the 'source' parameter).
Examples
# small example E. coli AST data from NCBI
ecoli_ast_raw
#> # A tibble: 10 × 21
#> `#BioSample` `Organism group` `Scientific name` `Isolation type` Location
#> <chr> <chr> <chr> <chr> <chr>
#> 1 SAMN36015110 E.coli and Shigella Escherichia coli clinical India: A…
#> 2 SAMN11638310 E.coli and Shigella Escherichia coli clinical India
#> 3 SAMN05729964 E.coli and Shigella Escherichia coli clinical Brazil: …
#> 4 SAMN10620111 E.coli and Shigella Escherichia coli clinical USA: Roc…
#> 5 SAMN10620168 E.coli and Shigella Escherichia coli clinical USA: Roc…
#> 6 SAMN10620104 E.coli and Shigella Escherichia coli clinical USA: Roc…
#> 7 SAMN10620102 E.coli and Shigella Escherichia coli clinical USA: Roc…
#> 8 SAMN10620129 E.coli and Shigella Escherichia coli clinical USA: Roc…
#> 9 SAMN10620121 E.coli and Shigella Escherichia coli clinical USA: Roc…
#> 10 SAMN10620086 E.coli and Shigella Escherichia coli clinical USA: Roc…
#> # ℹ 16 more variables: `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>,
#> # pheno_clsi_disk <sir>, ecoff_mic <sir>, ecoff_disk <sir>
# import without re-interpreting resistance
pheno <- import_ncbi_ast(ecoli_ast_raw)
#> Warning: Expected column 'BioProject' not found in input
head(pheno)
#> # A tibble: 6 × 28
#> id drug_agent mic disk guideline method pheno_provided spp_pheno
#> <chr> <ab> <mic> <dsk> <chr> <chr> <sir> <mo>
#> 1 SAMN360… CIP <128.00 NA CLSI NA R B_ESCHR_COLI
#> 2 SAMN116… CIP 256.00 NA CLSI NA R B_ESCHR_COLI
#> 3 SAMN057… CIP 64.00 NA CLSI Etest R B_ESCHR_COLI
#> 4 SAMN106… CIP >=4.00 NA CLSI NA R B_ESCHR_COLI
#> 5 SAMN106… CIP >=4.00 NA CLSI NA R B_ESCHR_COLI
#> 6 SAMN106… CIP <=0.25 NA CLSI NA S 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>, …
# import and re-interpret resistance (S/I/R) and WT/NWT (vs ECOFF) using AMR package
pheno <- import_ncbi_ast(ecoli_ast_raw, interpret_eucast = TRUE, interpret_ecoff = TRUE)
#> Warning: Expected column 'BioProject' not found in input
head(pheno)
#> # A tibble: 6 × 32
#> id drug_agent mic disk pheno_eucast ecoff guideline method
#> <chr> <ab> <mic> <dsk> <sir> <sir> <chr> <chr>
#> 1 SAMN36015110 CIP <128.00 NA NI NI CLSI NA
#> 2 SAMN11638310 CIP 256.00 NA R R CLSI NA
#> 3 SAMN05729964 CIP 64.00 NA R R CLSI Etest
#> 4 SAMN10620111 CIP >=4.00 NA R R CLSI NA
#> 5 SAMN10620168 CIP >=4.00 NA R R CLSI NA
#> 6 SAMN10620104 CIP <=0.25 NA S NI CLSI NA
#> # ℹ 24 more variables: pheno_provided <sir>, 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>, …