In tuv292/abx_idx: Modeling the Susceptibility of a Bacterial Community to Antibiotics

Antibiotic susceptibility

library(tidyverse)
library(usethis)

Allowed values

allowed_taxonomic_rank_values <- c(
  "Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species")

allowed_susceptibility_values <- c("susceptible", "resistant")

Vancomycin

Manually curated Lactobacillus database from abx susceptibility paper. Don't take phenotype info from this paper. The info in table 1 indicates the conditions under which the strain was grown for the experiment, not all conditions under which it can be grown. There is more good info on other abx to take from this paper.

susceptibility_lactobacillus <- read_csv( "Lactobacillus_data.csv") %>%
  mutate(antibiotic = "vancomycin") %>%
  select(taxon = name, rank, antibiotic, value = vancomycin, doi) %>%
  mutate(taxon = str_replace_all(taxon, "\\s+", " ")) %>%
  # Policy of this package is not to work with subspecies, but instead to
  # convert subspecies name to an equivalent species name, and pretend the
  # subspecies is just a different species.
  mutate(taxon = str_remove(taxon, " \\w+ subsp\\.")) %>%
  mutate(value = if_else(value, "susceptible", "resistant"))

susceptibility_lactobacillus %>%
  count(antibiotic, value)

Other info

susceptibility_misc <- read_csv("susceptibility_misc.csv")

susceptibility_misc %>%
  count(antibiotic, value)

Final checks

taxon_susceptibility <- bind_rows(
  susceptibility_misc, susceptibility_lactobacillus)
taxon_susceptibility %>%
  count(antibiotic, value)

Check for unexpected taxonomic rank values

taxon_susceptibility %>%
  filter(!(rank %in% allowed_taxonomic_rank_values))

Check for unexpected susceptibility values

taxon_susceptibility %>%
  filter(!(value %in% allowed_susceptibility_values))

Export

taxon_susceptibility <- as.data.frame(taxon_susceptibility)
usethis::use_data(taxon_susceptibility, overwrite = T)

Review paper on drug class: https://doi.org/10.1016/j.bcp.2017.01.003

Tet protection genes on mobile elements: http://faculty.washington.edu/marilynr/ https://doi.org/10.1016/j.femsle.2005.02.034

The Clinical and Laboratory Standards Institute (CLSI) guidelines assesses abx resistance.

tuv292/abx_idx documentation built on Jan. 12, 2023, 12:48 a.m.