Introduction to the AMR package

Matthijs S. Berends

This R package was intended to make microbial epidemiology easier. Most functions contain extensive help pages to get started.

The AMR package basically does four important things:

1. It cleanses existing data, by transforming it to reproducible and profound classes, making the most efficient use of R. These functions all use artificial intelligence to guess results that you would expect:

   • Use as.mo to get an ID of a microorganism. The IDs are human readable for the trained eye - the ID of Klebsiella pneumoniae is “B_KLBSL_PNE” (B stands for Bacteria) and the ID of S. aureus is “B_STPHY_AUR”. The function takes almost any text as input that looks like the name or code of a microorganism like “E. coli”, “esco” and “esccol”. Even as.mo("MRSA") will return the ID of S. aureus. Moreover, it can group all coagulase negative and positive Staphylococci, and can transform Streptococci into Lancefield groups. To find bacteria based on your input, it uses Artificial Intelligence to look up values in the included ITIS data, consisting of more than 18,000 microorganisms.
   • Use as.rsi to transform values to valid antimicrobial results. It produces just S, I or R based on your input and warns about invalid values. Even values like “<=0.002; S” (combined MIC/RSI) will result in “S”.
   • Use as.mic to cleanse your MIC values. It produces a so-called factor (called ordinal in SPSS) with valid MIC values as levels. A value like “<=0.002; S” (combined MIC/RSI) will result in “<=0.002”.
   • Use as.atc to get the ATC code of an antibiotic as defined by the WHO. This package contains a database with most LIS codes, official names, DDDs and even trade names of antibiotics. For example, the values “Furabid”, “Furadantin”, “nitro” all return the ATC code of Nitrofurantoine.

2. It enhances existing data and adds new data from data sets included in this package.

   • Use EUCAST_rules to apply EUCAST expert rules to isolates.
   • Use first_isolate to identify the first isolates of every patient using guidelines from the CLSI (Clinical and Laboratory Standards Institute).
     • You can also identify first weighted isolates of every patient, an adjusted version of the CLSI guideline. This takes into account key antibiotics of every strain and compares them.
   • Use MDRO (abbreviation of Multi Drug Resistant Organisms) to check your isolates for exceptional resistance with country-specific guidelines or EUCAST rules. Currently, national guidelines for Germany and the Netherlands are supported.
   • The data set microorganisms contains the complete taxonomic tree of more than 18,000 microorganisms (bacteria, fungi/yeasts and protozoa). Furthermore, the colloquial name and Gram stain are available, which enables resistance analysis of e.g. different antibiotics per Gram stain. The package also contains functions to look up values in this data set like mo_genus, mo_family, mo_gramstain or even mo_phylum. As they use as.mo internally, they also use artificial intelligence. For example, mo_genus("MRSA") and mo_genus("S. aureus") will both return "Staphylococcus". They also come with support for German, Dutch, French, Italian, Spanish and Portuguese. These functions can be used to add new variables to your data.
   • The data set antibiotics contains the ATC code, LIS codes, official name, trivial name and DDD of both oral and parenteral administration. It also contains a total of 298 trade names. Use functions like ab_name and ab_tradenames to look up values. The ab_* functions use as.atc internally so they support AI to guess your expected result. For example, ab_name("Fluclox"), ab_name("Floxapen") and ab_name("J01CF05") will all return "Flucloxacillin". These functions can again be used to add new variables to your data.

3. It analyses the data with convenient functions that use well-known methods.

   • Calculate the resistance (and even co-resistance) of microbial isolates with the portion_R, portion_IR, portion_I, portion_SI and portion_S functions. Similarly, the number of isolates can be determined with the count_R, count_IR, count_I, count_SI and count_S functions. All these functions can be used with the dplyr package (e.g. in conjunction with summarise)
   • Plot AMR results with geom_rsi, a function made for the ggplot2 package
   • Predict antimicrobial resistance for the nextcoming years using logistic regression models with the resistance_predict function
   • Conduct descriptive statistics to enhance base R: calculate kurtosis, skewness and create frequency tables

4. It teaches the user how to use all the above actions.

   • The package contains extensive help pages with many examples.
   • It also contains an example data set called septic_patients. This data set contains:
     • 2,000 blood culture isolates from anonymised septic patients between 2001 and 2017 in the Northern Netherlands
     • Results of 40 antibiotics (each antibiotic in its own column) with a total of 38,414 antimicrobial results
     • Real and genuine data

mo_shortname("Chlamydia psittaci")
# Note: 'Chlamydia psittaci' (Page, 1968) was renamed 'Chlamydophila psittaci' (Everett et al., 1999)
# [1] "C. psittaci"

mo_class("E. coli")
# [1] "Gammaproteobacteria"

mo_family("E. coli")
# [1] "Enterobacteriaceae"

mo_ref("E. coli")
# [1] "Castellani and Chalmers, 1919"

mo_phylum("C. elegans")
# [1] "Cyanobacteria"                   # Bacteria?!
mo_fullname("C. elegans")
# [1] "Chroococcus limneticus elegans"  # Because a microorganism was found