A data set containing species groups and microbiological complexes, which are used in the clinical breakpoints table.
Format
A tibble with 521 observations and 4 variables:
mo_group
ID of the species group / microbiological complexmo
ID of the microorganism belonging in the species group / microbiological complexmo_group_name
Name of the species group / microbiological complex, as retrieved withmo_name()
mo_name
Name of the microorganism belonging in the species group / microbiological complex, as retrieved withmo_name()
Details
Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. Please visit our website for the download links. The actual files are of course available on our GitHub repository.
Examples
microorganisms.groups
#> # A tibble: 521 × 4
#> mo_group mo mo_group_name mo_name
#> <mo> <mo> <chr> <chr>
#> 1 B_ACNTB_BMNN-C B_ACNTB_BMNN Acinetobacter baumannii complex Acinetobacter ba…
#> 2 B_ACNTB_BMNN-C B_ACNTB_CLCC Acinetobacter baumannii complex Acinetobacter ca…
#> 3 B_ACNTB_BMNN-C B_ACNTB_LCTC Acinetobacter baumannii complex Acinetobacter di…
#> 4 B_ACNTB_BMNN-C B_ACNTB_NSCM Acinetobacter baumannii complex Acinetobacter no…
#> 5 B_ACNTB_BMNN-C B_ACNTB_PITT Acinetobacter baumannii complex Acinetobacter pi…
#> 6 B_ACNTB_BMNN-C B_ACNTB_SFRT Acinetobacter baumannii complex Acinetobacter se…
#> 7 B_BCTRD_FRGL-C B_BCTRD_FRGL Bacteroides fragilis complex Bacteroides frag…
#> 8 B_BCTRD_FRGL-C B_BCTRD_OVTS Bacteroides fragilis complex Bacteroides ovat…
#> 9 B_BCTRD_FRGL-C B_BCTRD_THTT Bacteroides fragilis complex Bacteroides thet…
#> 10 B_BCTRD_FRGL-C B_PHCCL_VLGT Bacteroides fragilis complex Bacteroides vulg…
#> # ℹ 511 more rows
# these are all species in the Bacteroides fragilis group, as per WHONET:
microorganisms.groups[microorganisms.groups$mo_group == "B_BCTRD_FRGL-C", ]
#> # A tibble: 5 × 4
#> mo_group mo mo_group_name mo_name
#> <mo> <mo> <chr> <chr>
#> 1 B_BCTRD_FRGL-C B_BCTRD_FRGL Bacteroides fragilis complex Bacteroides fragilis
#> 2 B_BCTRD_FRGL-C B_BCTRD_OVTS Bacteroides fragilis complex Bacteroides ovatus
#> 3 B_BCTRD_FRGL-C B_BCTRD_THTT Bacteroides fragilis complex Bacteroides thetaiot…
#> 4 B_BCTRD_FRGL-C B_PHCCL_VLGT Bacteroides fragilis complex Bacteroides vulgatus
#> 5 B_BCTRD_FRGL-C B_PRBCT_DSTS Bacteroides fragilis complex Parabacteroides dist…