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Data Set with 534 Microorganisms In Species Groups

Source: R/data.R
microorganisms.groups.Rd

A data set containing species groups and microbiological complexes, which are used in the clinical breakpoints table.

Usage

microorganisms.groups

Format

A tibble with 534 observations and 4 variables:

  • mo_group
    ID of the species group / microbiological complex

  • mo
    ID of the microorganism belonging in the species group / microbiological complex

  • mo_group_name
    Name of the species group / microbiological complex, as retrieved with mo_name()

  • mo_name
    Name of the microorganism belonging in the species group / microbiological complex, as retrieved with mo_name()

Download Our Reference Data

All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.

For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.

Visit our website for direct download links, or explore the actual files in our GitHub repository.

See also

as.mo() microorganisms

Examples

microorganisms.groups
#> # A tibble: 534 × 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 524 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…