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< h1 > How to determine multi-drug resistance (MDR)< / h1 >
< h4 class = "author" > Matthijs S. Berends< / h4 >
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< h4 class = "date" > 30 September 2019< / h4 >
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< div class = "hidden name" > < code > MDR.Rmd< / code > < / div >
< / div >
< p > With the function < code > < a href = "../reference/mdro.html" > mdro()< / a > < / code > , you can determine multi-drug resistant organisms (MDRO). It currently support these guidelines:< / p >
< ul >
< li > “Intrinsic Resistance and Exceptional Phenotypes Tables”, by EUCAST (European Committee on Antimicrobial Susceptibility Testing)< / li >
< li > “Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis”, by WHO (World Health Organization)< / li >
< li > “WIP-Richtlijn Bijzonder Resistente Micro-organismen (BRMO)”, by RIVM (Rijksinstituut voor de Volksgezondheid, the Netherlands National Institute for Public Health and the Environment)< / li >
< / ul >
< p > As an example, I will make a data set to determine multi-drug resistant TB:< / p >
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< div class = "sourceCode" id = "cb1" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb1-1" data-line-number = "1" > < span class = "co" > # a helper function to get a random vector with values S, I and R< / span > < / a >
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< a class = "sourceLine" id = "cb1-2" data-line-number = "2" > < span class = "co" > # with the probabilities 50% - 10% - 40%< / span > < / a >
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< a class = "sourceLine" id = "cb1-3" data-line-number = "3" > sample_rsi < -< span class = "st" > < / span > < span class = "cf" > function< / span > () {< / a >
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< a class = "sourceLine" id = "cb1-4" data-line-number = "4" > < span class = "kw" > < a href = "https://rdrr.io/r/base/sample.html" > sample< / a > < / span > (< span class = "kw" > < a href = "https://rdrr.io/r/base/c.html" > c< / a > < / span > (< span class = "st" > "S"< / span > , < span class = "st" > "I"< / span > , < span class = "st" > "R"< / span > ),< / a >
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< a class = "sourceLine" id = "cb1-5" data-line-number = "5" > < span class = "dt" > size =< / span > < span class = "dv" > 5000< / span > ,< / a >
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< a class = "sourceLine" id = "cb1-6" data-line-number = "6" > < span class = "dt" > prob =< / span > < span class = "kw" > < a href = "https://rdrr.io/r/base/c.html" > c< / a > < / span > (< span class = "fl" > 0.5< / span > , < span class = "fl" > 0.1< / span > , < span class = "fl" > 0.4< / span > ),< / a >
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< a class = "sourceLine" id = "cb1-7" data-line-number = "7" > < span class = "dt" > replace =< / span > < span class = "ot" > TRUE< / span > )< / a >
< a class = "sourceLine" id = "cb1-8" data-line-number = "8" > }< / a >
< a class = "sourceLine" id = "cb1-9" data-line-number = "9" > < / a >
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< a class = "sourceLine" id = "cb1-10" data-line-number = "10" > my_TB_data < -< span class = "st" > < / span > < span class = "kw" > < a href = "https://rdrr.io/r/base/data.frame.html" > data.frame< / a > < / span > (< span class = "dt" > rifampicin =< / span > < span class = "kw" > sample_rsi< / span > (),< / a >
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< a class = "sourceLine" id = "cb1-11" data-line-number = "11" > < span class = "dt" > isoniazid =< / span > < span class = "kw" > sample_rsi< / span > (),< / a >
< a class = "sourceLine" id = "cb1-12" data-line-number = "12" > < span class = "dt" > gatifloxacin =< / span > < span class = "kw" > sample_rsi< / span > (),< / a >
< a class = "sourceLine" id = "cb1-13" data-line-number = "13" > < span class = "dt" > ethambutol =< / span > < span class = "kw" > sample_rsi< / span > (),< / a >
< a class = "sourceLine" id = "cb1-14" data-line-number = "14" > < span class = "dt" > pyrazinamide =< / span > < span class = "kw" > sample_rsi< / span > (),< / a >
< a class = "sourceLine" id = "cb1-15" data-line-number = "15" > < span class = "dt" > moxifloxacin =< / span > < span class = "kw" > sample_rsi< / span > (),< / a >
< a class = "sourceLine" id = "cb1-16" data-line-number = "16" > < span class = "dt" > kanamycin =< / span > < span class = "kw" > sample_rsi< / span > ())< / a > < / code > < / pre > < / div >
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< p > Because all column names are automatically verified for valid drug names or codes, this would have worked exactly the same:< / p >
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< div class = "sourceCode" id = "cb2" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb2-1" data-line-number = "1" > my_TB_data < -< span class = "st" > < / span > < span class = "kw" > < a href = "https://rdrr.io/r/base/data.frame.html" > data.frame< / a > < / span > (< span class = "dt" > RIF =< / span > < span class = "kw" > sample_rsi< / span > (),< / a >
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< a class = "sourceLine" id = "cb2-2" data-line-number = "2" > < span class = "dt" > INH =< / span > < span class = "kw" > sample_rsi< / span > (),< / a >
< a class = "sourceLine" id = "cb2-3" data-line-number = "3" > < span class = "dt" > GAT =< / span > < span class = "kw" > sample_rsi< / span > (),< / a >
< a class = "sourceLine" id = "cb2-4" data-line-number = "4" > < span class = "dt" > ETH =< / span > < span class = "kw" > sample_rsi< / span > (),< / a >
< a class = "sourceLine" id = "cb2-5" data-line-number = "5" > < span class = "dt" > PZA =< / span > < span class = "kw" > sample_rsi< / span > (),< / a >
< a class = "sourceLine" id = "cb2-6" data-line-number = "6" > < span class = "dt" > MFX =< / span > < span class = "kw" > sample_rsi< / span > (),< / a >
< a class = "sourceLine" id = "cb2-7" data-line-number = "7" > < span class = "dt" > KAN =< / span > < span class = "kw" > sample_rsi< / span > ())< / a > < / code > < / pre > < / div >
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< p > The data set looks like this now:< / p >
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< div class = "sourceCode" id = "cb3" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb3-1" data-line-number = "1" > < span class = "kw" > < a href = "https://rdrr.io/r/utils/head.html" > head< / a > < / span > (my_TB_data)< / a >
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< a class = "sourceLine" id = "cb3-2" data-line-number = "2" > < span class = "co" > # rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin< / span > < / a >
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< a class = "sourceLine" id = "cb3-3" data-line-number = "3" > < span class = "co" > # 1 R S R R S R< / span > < / a >
< a class = "sourceLine" id = "cb3-4" data-line-number = "4" > < span class = "co" > # 2 I R S R R R< / span > < / a >
< a class = "sourceLine" id = "cb3-5" data-line-number = "5" > < span class = "co" > # 3 R R R S R R< / span > < / a >
< a class = "sourceLine" id = "cb3-6" data-line-number = "6" > < span class = "co" > # 4 R S I I R S< / span > < / a >
< a class = "sourceLine" id = "cb3-7" data-line-number = "7" > < span class = "co" > # 5 S S I I R S< / span > < / a >
< a class = "sourceLine" id = "cb3-8" data-line-number = "8" > < span class = "co" > # 6 S S S R S S< / span > < / a >
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< a class = "sourceLine" id = "cb3-9" data-line-number = "9" > < span class = "co" > # kanamycin< / span > < / a >
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< a class = "sourceLine" id = "cb3-10" data-line-number = "10" > < span class = "co" > # 1 R< / span > < / a >
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< a class = "sourceLine" id = "cb3-11" data-line-number = "11" > < span class = "co" > # 2 S< / span > < / a >
< a class = "sourceLine" id = "cb3-12" data-line-number = "12" > < span class = "co" > # 3 S< / span > < / a >
< a class = "sourceLine" id = "cb3-13" data-line-number = "13" > < span class = "co" > # 4 R< / span > < / a >
< a class = "sourceLine" id = "cb3-14" data-line-number = "14" > < span class = "co" > # 5 R< / span > < / a >
< a class = "sourceLine" id = "cb3-15" data-line-number = "15" > < span class = "co" > # 6 S< / span > < / a > < / code > < / pre > < / div >
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< p > We can now add the interpretation of MDR-TB to our data set:< / p >
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< div class = "sourceCode" id = "cb4" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb4-1" data-line-number = "1" > my_TB_data< span class = "op" > $< / span > mdr < -< span class = "st" > < / span > < span class = "kw" > < a href = "../reference/mdro.html" > mdr_tb< / a > < / span > (my_TB_data)< / a >
< a class = "sourceLine" id = "cb4-2" data-line-number = "2" > < span class = "co" > # < / span > < span class = "al" > NOTE< / span > < span class = "co" > : No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.< / span > < / a >
< a class = "sourceLine" id = "cb4-3" data-line-number = "3" > < span class = "co" > # Determining multidrug-resistant organisms (MDRO), according to:< / span > < / a >
< a class = "sourceLine" id = "cb4-4" data-line-number = "4" > < span class = "co" > # Guideline: Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis< / span > < / a >
< a class = "sourceLine" id = "cb4-5" data-line-number = "5" > < span class = "co" > # Version: WHO/HTM/TB/2014.11< / span > < / a >
< a class = "sourceLine" id = "cb4-6" data-line-number = "6" > < span class = "co" > # Author: WHO (World Health Organization)< / span > < / a >
< a class = "sourceLine" id = "cb4-7" data-line-number = "7" > < span class = "co" > # Source: https://www.who.int/tb/publications/pmdt_companionhandbook/en/< / span > < / a >
< a class = "sourceLine" id = "cb4-8" data-line-number = "8" > < span class = "co" > # < / span > < span class = "al" > NOTE< / span > < span class = "co" > : Reliability might be improved if these antimicrobial results would be available too: CAP (capreomycin), RIB (rifabutin), RFP (rifapentine)< / span > < / a > < / code > < / pre > < / div >
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< p > We also created a package dedicated to data cleaning and checking, called the < code > clean< / code > package. It gets automatically installed with the < code > AMR< / code > package, so we only have to load it:< / p >
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< div class = "sourceCode" id = "cb5" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb5-1" data-line-number = "1" > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" > library< / a > < / span > (clean)< / a > < / code > < / pre > < / div >
< p > It contains the < code > < a href = "https://rdrr.io/pkg/clean/man/freq.html" > freq()< / a > < / code > function, to create a frequency table:< / p >
< div class = "sourceCode" id = "cb6" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb6-1" data-line-number = "1" > < span class = "kw" > < a href = "https://rdrr.io/pkg/clean/man/freq.html" > freq< / a > < / span > (my_TB_data< span class = "op" > $< / span > mdr)< / a > < / code > < / pre > < / div >
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< p > < strong > Frequency table< / strong > < / p >
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< p > Class: factor > ordered (numeric)< br >
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Length: 5,000 (of which NA: 0 = 0%)< br >
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Levels: 5: Negative < Mono-resistant < Poly-resistant < Multi-drug-resistant < …< br >
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Unique: 5< / p >
< table class = "table" >
< thead > < tr class = "header" >
< th align = "left" > < / th >
< th align = "left" > Item< / th >
< th align = "right" > Count< / th >
< th align = "right" > Percent< / th >
< th align = "right" > Cum. Count< / th >
< th align = "right" > Cum. Percent< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "left" > 1< / td >
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< td align = "left" > Mono-resistant< / td >
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< td align = "right" > 3250< / td >
< td align = "right" > 65.00%< / td >
< td align = "right" > 3250< / td >
< td align = "right" > 65.00%< / td >
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< / tr >
< tr class = "even" >
< td align = "left" > 2< / td >
< td align = "left" > Negative< / td >
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< td align = "right" > 634< / td >
< td align = "right" > 12.68%< / td >
< td align = "right" > 3884< / td >
< td align = "right" > 77.68%< / td >
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< / tr >
< tr class = "odd" >
< td align = "left" > 3< / td >
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< td align = "left" > Multi-drug-resistant< / td >
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< td align = "right" > 623< / td >
< td align = "right" > 12.46%< / td >
< td align = "right" > 4507< / td >
< td align = "right" > 90.14%< / td >
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< / tr >
< tr class = "even" >
< td align = "left" > 4< / td >
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< td align = "left" > Poly-resistant< / td >
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< td align = "right" > 282< / td >
< td align = "right" > 5.64%< / td >
< td align = "right" > 4789< / td >
< td align = "right" > 95.78%< / td >
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< / tr >
< tr class = "odd" >
< td align = "left" > 5< / td >
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< td align = "left" > Extensive drug-resistant< / td >
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< td align = "right" > 211< / td >
< td align = "right" > 4.22%< / td >
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< td align = "right" > 5000< / td >
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< td align = "right" > 100.00%< / td >
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