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Predict antimicrobial resistance
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Determine multi-drug resistance (MDR)
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<h1>How to determine multi-drug resistance (MDR)</h1>
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<h4 class="author">Matthijs S. Berends</h4>
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<h4 class="date">23 May 2019</h4>
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<div class="hidden name"><code>MDR.Rmd</code></div>
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<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>
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<ul>
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<li>“Intrinsic Resistance and Exceptional Phenotypes Tables”, by EUCAST (European Committee on Antimicrobial Susceptibility Testing)</li>
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<li>“Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis”, by WHO (World Health Organization)</li>
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<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>
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</ul>
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<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" title="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" title="2"><span class="co"># with the probabilities 50%-10%-40%</span></a>
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<a class="sourceLine" id="cb1-3" title="3">sample_rsi <-<span class="st"> </span><span class="cf">function</span>() {</a>
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<a class="sourceLine" id="cb1-4" title="4"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/sample">sample</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">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" title="5"> <span class="dt">size =</span> <span class="dv">5000</span>,</a>
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<a class="sourceLine" id="cb1-6" title="6"> <span class="dt">prob =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">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" title="7"> <span class="dt">replace =</span> <span class="ot">TRUE</span>)</a>
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<a class="sourceLine" id="cb1-8" title="8">}</a>
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<a class="sourceLine" id="cb1-9" title="9"></a>
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<a class="sourceLine" id="cb1-10" title="10">my_TB_data <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">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" title="11"> <span class="dt">isoniazid =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb1-12" title="12"> <span class="dt">gatifloxacin =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb1-13" title="13"> <span class="dt">ethambutol =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb1-14" title="14"> <span class="dt">pyrazinamide =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb1-15" title="15"> <span class="dt">moxifloxacin =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb1-16" title="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" title="1">my_TB_data <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">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" title="2"> <span class="dt">INH =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb2-3" title="3"> <span class="dt">GAT =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb2-4" title="4"> <span class="dt">ETH =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb2-5" title="5"> <span class="dt">PZA =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb2-6" title="6"> <span class="dt">MFX =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb2-7" title="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" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></span>(my_TB_data)</a>
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<a class="sourceLine" id="cb3-2" title="2"><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></a>
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<a class="sourceLine" id="cb3-3" title="3"><span class="co"># 1 R R R R R S</span></a>
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<a class="sourceLine" id="cb3-4" title="4"><span class="co"># 2 S R R S R S</span></a>
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<a class="sourceLine" id="cb3-5" title="5"><span class="co"># 3 R S S I S S</span></a>
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<a class="sourceLine" id="cb3-6" title="6"><span class="co"># 4 R S S R S S</span></a>
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<a class="sourceLine" id="cb3-7" title="7"><span class="co"># 5 R R S I I R</span></a>
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<a class="sourceLine" id="cb3-8" title="8"><span class="co"># 6 R S S S S S</span></a>
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<a class="sourceLine" id="cb3-9" title="9"><span class="co"># kanamycin</span></a>
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<a class="sourceLine" id="cb3-10" title="10"><span class="co"># 1 S</span></a>
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<a class="sourceLine" id="cb3-11" title="11"><span class="co"># 2 R</span></a>
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<a class="sourceLine" id="cb3-12" title="12"><span class="co"># 3 S</span></a>
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<a class="sourceLine" id="cb3-13" title="13"><span class="co"># 4 R</span></a>
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<a class="sourceLine" id="cb3-14" title="14"><span class="co"># 5 S</span></a>
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<a class="sourceLine" id="cb3-15" title="15"><span class="co"># 6 I</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" title="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>
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<a class="sourceLine" id="cb4-2" title="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>
|
||
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<a class="sourceLine" id="cb4-3" title="3"><span class="co"># Determining multidrug-resistant organisms (MDRO), according to:</span></a>
|
||
|
|
<a class="sourceLine" id="cb4-4" title="4"><span class="co"># Guideline: Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis</span></a>
|
||
|
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<a class="sourceLine" id="cb4-5" title="5"><span class="co"># Version: WHO/HTM/TB/2014.11</span></a>
|
||
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<a class="sourceLine" id="cb4-6" title="6"><span class="co"># Author: WHO (World Health Organization)</span></a>
|
||
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<a class="sourceLine" id="cb4-7" title="7"><span class="co"># Source: https://www.who.int/tb/publications/pmdt_companionhandbook/en/</span></a>
|
||
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<a class="sourceLine" id="cb4-8" title="8"><span class="co"># Warning: Reliability might be improved if these antimicrobial results</span></a>
|
||
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|
<a class="sourceLine" id="cb4-9" title="9"><span class="co"># would be available too: `CAP` (capreomycin), `RIB` (rifabutin), `RFP`</span></a>
|
||
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<a class="sourceLine" id="cb4-10" title="10"><span class="co"># (rifapentine)</span></a></code></pre></div>
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||
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|
<p>And review the result with a frequency table:</p>
|
||
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|
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="../reference/freq.html">freq</a></span>(my_TB_data<span class="op">$</span>mdr)</a>
|
||
|
|
<a class="sourceLine" id="cb5-2" title="2"><span class="co"># </span></a>
|
||
|
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<a class="sourceLine" id="cb5-3" title="3"><span class="co"># </span></a>
|
||
|
|
<a class="sourceLine" id="cb5-4" title="4"><span class="co"># **Frequency table of `mdr` from `my_TB_data` (5,000 x 8)** </span></a>
|
||
|
|
<a class="sourceLine" id="cb5-5" title="5"><span class="co"># </span></a>
|
||
|
|
<a class="sourceLine" id="cb5-6" title="6"><span class="co"># Class: `factor` > `ordered` (`numeric`) </span></a>
|
||
|
|
<a class="sourceLine" id="cb5-7" title="7"><span class="co"># Length: 5,000 (of which NA: 0 = 0.00%) </span></a>
|
||
|
|
<a class="sourceLine" id="cb5-8" title="8"><span class="co"># Levels: 5: `Negative` < `Mono-resistance` < `Poly-resistance` < `Multidrug res...` </span></a>
|
||
|
|
<a class="sourceLine" id="cb5-9" title="9"><span class="co"># Unique: 5</span></a>
|
||
|
|
<a class="sourceLine" id="cb5-10" title="10"><span class="co"># </span></a>
|
||
|
|
<a class="sourceLine" id="cb5-11" title="11"><span class="co"># </span></a>
|
||
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<a class="sourceLine" id="cb5-12" title="12"><span class="co"># | |Item | Count| Percent| Cum. Count| Cum. Percent|</span></a>
|
||
|
|
<a class="sourceLine" id="cb5-13" title="13"><span class="co"># |:--|:-------------------------|-----:|-------:|----------:|------------:|</span></a>
|
||
|
|
<a class="sourceLine" id="cb5-14" title="14"><span class="co"># |1 |Mono-resistance | 3,297| 65.9%| 3,297| 65.9%|</span></a>
|
||
|
|
<a class="sourceLine" id="cb5-15" title="15"><span class="co"># |2 |Negative | 627| 12.5%| 3,924| 78.5%|</span></a>
|
||
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|
<a class="sourceLine" id="cb5-16" title="16"><span class="co"># |3 |Multidrug resistance | 612| 12.2%| 4,536| 90.7%|</span></a>
|
||
|
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<a class="sourceLine" id="cb5-17" title="17"><span class="co"># |4 |Poly-resistance | 263| 5.3%| 4,799| 96.0%|</span></a>
|
||
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<a class="sourceLine" id="cb5-18" title="18"><span class="co"># |5 |Extensive drug resistance | 201| 4.0%| 5,000| 100.0%|</span></a></code></pre></div>
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