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Import and Process Kleborate Results

Source: R/import_geno.R
import_kleborate.Rd

This function imports and processes genotyping results from Kleborate (https://github.com/klebgenomics/Kleborate), extracting antimicrobial resistance determinants and mapping them to standardised drug classes.

Usage

import_kleborate(
  input_table,
  sample_col = "strain",
  kleborate_class_table = kleborate_classes,
  hgvs = TRUE
)

Arguments

input_table

A character string specifying a dataframe or path to the Kleborate results table (TSV format).

sample_col

A character string specifying the column that identifies samples in the dataset (default strain).

kleborate_class_table

A tibble containing a reference table mapping Kleborate drug class column names (Kleborate_Class) to standardised drug classes (drug_class). Defaults to kleborate_classes, which is provided internally.

hgvs

Logical indicating whether to expect mutations in HGVS nomenclature syntax (used in Kleborate releases since v3.1.3). Default TRUE, which expects mutations formatted as e.g. "GyrA:p.S83F". Set to FALSE if your results were generated using older versions where mutations were formatted as e.g. "GyrA_83F".

Value

A data frame with the processed genotype data, with harmonised gene names, mapped drug agents, and drug classes which can be used for other functions of the ARMgen package:

  • id: The sample identifier (character).

  • marker: The name of the genotype marker as it appears in the input (e.g. GyrA:p.S83F for recent versions of Kleborate, or GyrA-83F for earlier versions not using HGVS nomenclature) (character).

  • gene: The gene identifier (character).

  • mutation: The mutation detected within the gene, converted to HGVS nomenclature syntax (e.g. Ser83Phe) (character).

  • drug_class: Name of the antibiotic group associated with the genotype marker, compatible with AMR pkg, drawn from the Kleborate column in which the marker was reported (character).

  • drug: Values are recorded as NA as Kleborate doesn't report markers assigned to individual drug level.

  • variation type: Type of variation, e.g. Gene presence detected, Protein variant detected, Nucleotide variant detected, Inactivating mutation detected. ... Other fields specific to the input file

Details

The function performs the following steps:

  • Reads the Kleborate output table.

  • Transforms Kleborate output into long form (i.e., one AMR determinant per row).

  • Maps Kleborate drug classes to standardised drug class names recognised by the AMR pkg. This processing ensures compatibility with downstream AMRgen analysis workflows.

Examples

# example Kleborate data from EUSCAPE project
kleborate_raw
#> # A tibble: 1,490 × 122
#>    strain    species species_match contig_count    N50 largest_contig total_size
#>    <chr>     <chr>   <chr>                <dbl>  <dbl>          <dbl>      <dbl>
#>  1 SAMEA349… Klebsi… strong                 141 230759         470757    5578320
#>  2 SAMEA349… Klebsi… strong                  88 370309         938079    5384685
#>  3 SAMEA349… Klebsi… strong                  90 238750         529125    5446454
#>  4 SAMEA349… Klebsi… strong                 144 207582         663698    5574298
#>  5 SAMEA349… Klebsi… strong                 142 263498         678692    5486238
#>  6 SAMEA349… Klebsi… strong                  79 285199         991412    5529803
#>  7 SAMEA349… Klebsi… strong                 280 178980         585359    5817055
#>  8 SAMEA349… Klebsi… strong                 108 209418         517450    5379124
#>  9 SAMEA349… Klebsi… strong                 134 371444         984005    5558705
#> 10 SAMEA349… Klebsi… strong                 142 197944         636773    5497421
#> # ℹ 1,480 more rows
#> # ℹ 115 more variables: GC_content <dbl>, ambiguous_bases <chr>,
#> #   QC_warnings <chr>, ST <chr>, gapA <dbl>, infB <dbl>, mdh <dbl>, pgi <dbl>,
#> #   phoE <dbl>, rpoB <dbl>, tonB <dbl>, YbST <chr>, Yersiniabactin <chr>,
#> #   ybtS <chr>, ybtX <chr>, ybtQ <chr>, ybtP <chr>, ybtA <chr>, irp2 <chr>,
#> #   irp1 <chr>, ybtU <chr>, ybtT <chr>, ybtE <chr>, fyuA <chr>,
#> #   spurious_ybt_hits <chr>, CbST <chr>, Colibactin <chr>, clbA <chr>, …

# import first few rows of this data frame and parse it to standard genotype table format
kleborate_geno <- import_kleborate(kleborate_raw %>% head(n = 10))

# parse the output of an older version of Kleborate (v3.1.3) before
# HGVS syntax was introduced for mutations
kleborate_geno <- import_kleborate(kleborate_raw_v313 %>% head(n = 10), hgvs = FALSE)