A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source(). They will all be searched when using as.mo() and consequently all the mo_* functions.
Format
A tibble with 4 971 observations and 2 variables:
code
Commonly used code of a microorganism. This is a unique identifier.mo
ID of the microorganism in the microorganisms data set
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.
Examples
microorganisms.codes
#> # A tibble: 4,971 × 2
#> code mo
#> <chr> <mo>
#> 1 1011 B_GRAMP
#> 2 1012 B_GRAMP
#> 3 1013 B_GRAMN
#> 4 1014 B_GRAMN
#> 5 1015 F_YEAST
#> 6 103 B_ESCHR_COLI
#> 7 104 B_SLMNL_ENTR_ENTR
#> 8 1100 B_STRPT
#> 9 1101 B_STRPT_VIRI
#> 10 1102 B_STRPT_HAEM
#> # ℹ 4,961 more rows
# 'ECO' or 'eco' is the WHONET code for E. coli:
microorganisms.codes[microorganisms.codes$code == "ECO", ]
#> # A tibble: 1 × 2
#> code mo
#> <chr> <mo>
#> 1 ECO B_ESCHR_COLI
# and therefore, 'eco' will be understood as E. coli in this package:
mo_info("eco")
#> $mo
#> [1] "B_ESCHR_COLI"
#>
#> $rank
#> [1] "species"
#>
#> $kingdom
#> [1] "Bacteria"
#>
#> $phylum
#> [1] "Pseudomonadota"
#>
#> $class
#> [1] "Gammaproteobacteria"
#>
#> $order
#> [1] "Enterobacterales"
#>
#> $family
#> [1] "Enterobacteriaceae"
#>
#> $genus
#> [1] "Escherichia"
#>
#> $species
#> [1] "coli"
#>
#> $subspecies
#> [1] ""
#>
#> $status
#> [1] "accepted"
#>
#> $synonyms
#> NULL
#>
#> $gramstain
#> [1] "Gram-negative"
#>
#> $oxygen_tolerance
#> [1] "facultative anaerobe"
#>
#> $url
#> [1] "https://lpsn.dsmz.de/species/escherichia-coli"
#>
#> $ref
#> [1] "Castellani et al., 1919"
#>
#> $snomed
#> [1] "1095001000112106" "715307006" "737528008" "416989002"
#> [5] "116397003" "414097009" "414098004" "414099007"
#> [9] "414100004" "116395006" "735270003" "116396007"
#> [13] "83285000" "116394005" "112283007" "710886005"
#> [17] "710887001" "710888006" "710889003" "414132004"
#> [21] "721892009" "416812001" "416740004" "417216001"
#> [25] "457541006" "710253004" "416530004" "417189006"
#> [29] "409800005" "713925008" "444771000124108" "838549008"
#>
#> $lpsn
#> [1] "776057"
#>
#> $mycobank
#> [1] NA
#>
#> $gbif
#> [1] "11286021"
#>
#> $group_members
#> character(0)
#>
# works for all AMR functions:
mo_is_intrinsic_resistant("eco", ab = "vancomycin")
#> [1] TRUE