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<main id="main" class="col-md-9"><div class="page-header">
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<img src="../logo.svg" class="logo" alt=""><h1>How to determine multi-drug resistance (MDR)</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/MDR.Rmd" class="external-link"><code>vignettes/MDR.Rmd</code></a></small>
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<div class="d-none 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 which
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micro-organisms are multi-drug resistant organisms (MDRO).</p>
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<div class="section level3">
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<h3 id="type-of-input">Type of input<a class="anchor" aria-label="anchor" href="#type-of-input"></a>
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</h3>
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<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function takes a data set as input, such as a
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regular <code>data.frame</code>. It tries to automatically determine the
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right columns for info about your isolates, such as the name of the
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species and all columns with results of antimicrobial agents. See the
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||
help page for more info about how to set the right settings for your
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data with the command <code><a href="../reference/mdro.html">?mdro</a></code>.</p>
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<p>For WHONET data (and most other data), all settings are automatically
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set correctly.</p>
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</div>
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<div class="section level3">
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<h3 id="guidelines">Guidelines<a class="anchor" aria-label="anchor" href="#guidelines"></a>
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</h3>
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<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function support multiple guidelines. You can
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select a guideline with the <code>guideline</code> parameter. Currently
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supported guidelines are (case-insensitive):</p>
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<ul>
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<li>
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<p><code>guideline = "CMI2012"</code> (default)</p>
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<p>Magiorakos AP, Srinivasan A <em>et al.</em> “Multidrug-resistant,
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extensively drug-resistant and pandrug-resistant bacteria: an
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international expert proposal for interim standard definitions for
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acquired resistance.” Clinical Microbiology and Infection (2012) (<a href="https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext" class="external-link">link</a>)</p>
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||
</li>
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<li>
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<p><code>guideline = "EUCAST3.2"</code> (or simply
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<code>guideline = "EUCAST"</code>)</p>
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<p>The European international guideline - EUCAST Expert Rules Version
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3.2 “Intrinsic Resistance and Unusual Phenotypes” (<a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf" class="external-link">link</a>)</p>
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</li>
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<li>
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<p><code>guideline = "EUCAST3.1"</code></p>
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<p>The European international guideline - EUCAST Expert Rules Version
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3.1 “Intrinsic Resistance and Exceptional Phenotypes Tables” (<a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf" class="external-link">link</a>)</p>
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</li>
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<li>
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<p><code>guideline = "TB"</code></p>
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<p>The international guideline for multi-drug resistant tuberculosis -
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World Health Organization “Companion handbook to the WHO guidelines for
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the programmatic management of drug-resistant tuberculosis” (<a href="https://www.who.int/tb/publications/pmdt_companionhandbook/en/" class="external-link">link</a>)</p>
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||
</li>
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<li>
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<p><code>guideline = "MRGN"</code></p>
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<p>The German national guideline - Mueller <em>et al.</em> (2015)
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Antimicrobial Resistance and Infection Control 4:7. DOI:
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10.1186/s13756-015-0047-6</p>
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||
</li>
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<li>
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<p><code>guideline = "BRMO"</code></p>
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<p>The Dutch national guideline - Rijksinstituut voor Volksgezondheid en
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Milieu “WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen)
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(ZKH)” (<a href="https://www.rivm.nl/wip-richtlijn-brmo-bijzonder-resistente-micro-organismen-zkh" class="external-link">link</a>)</p>
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||
</li>
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||
</ul>
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||
<p>Please suggest your own (country-specific) guidelines by letting us
|
||
know: <a href="https://github.com/msberends/AMR/issues/new" class="external-link uri">https://github.com/msberends/AMR/issues/new</a>.</p>
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<div class="section level4">
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<h4 id="custom-guidelines">Custom Guidelines<a class="anchor" aria-label="anchor" href="#custom-guidelines"></a>
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</h4>
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<p>You can also use your own custom guideline. Custom guidelines can be
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set with the <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function. This is of
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great importance if you have custom rules to determine MDROs in your
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hospital, e.g., rules that are dependent on ward, state of contact
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isolation or other variables in your data.</p>
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<p>If you are familiar with <code><a href="https://dplyr.tidyverse.org/reference/case_when.html" class="external-link">case_when()</a></code> of the
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<code>dplyr</code> package, you will recognise the input method to set
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your own rules. Rules must be set using what R considers to be the
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‘formula notation’:</p>
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<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="va">custom</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mdro.html">custom_mdro_guideline</a></span><span class="op">(</span></span>
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<span> <span class="va">CIP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&</span> <span class="va">age</span> <span class="op">></span> <span class="fl">60</span> <span class="op">~</span> <span class="st">"Elderly Type A"</span>,</span>
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<span> <span class="va">ERY</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&</span> <span class="va">age</span> <span class="op">></span> <span class="fl">60</span> <span class="op">~</span> <span class="st">"Elderly Type B"</span></span>
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<span><span class="op">)</span></span></code></pre></div>
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<p>If a row/an isolate matches the first rule, the value after the first
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<code>~</code> (in this case <em>‘Elderly Type A’</em>) will be set as
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MDRO value. Otherwise, the second rule will be tried and so on. The
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||
maximum number of rules is unlimited.</p>
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<p>You can print the rules set in the console for an overview. Colours
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will help reading it if your console supports colours.</p>
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<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="va">custom</span></span>
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<span><span class="co"># A set of custom MDRO rules:</span></span>
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<span><span class="co"># 1. If CIP is "R" and age is higher than 60 then: Elderly Type A</span></span>
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<span><span class="co"># 2. If ERY is "R" and age is higher than 60 then: Elderly Type B</span></span>
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<span><span class="co"># 3. Otherwise: Negative</span></span>
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<span><span class="co"># </span></span>
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<span><span class="co"># Unmatched rows will return NA.</span></span>
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<span><span class="co"># Results will be of class 'factor', with ordered levels: Negative < Elderly Type A < Elderly Type B</span></span></code></pre></div>
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<p>The outcome of the function can be used for the
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<code>guideline</code> argument in the <code><a href="../reference/mdro.html">mdro()</a></code> function:</p>
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<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="va">x</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">example_isolates</span>, guideline <span class="op">=</span> <span class="va">custom</span><span class="op">)</span></span>
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<span><span class="fu"><a href="https://rdrr.io/r/base/table.html" class="external-link">table</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span>
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<span><span class="co"># x</span></span>
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<span><span class="co"># Negative Elderly Type A Elderly Type B </span></span>
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<span><span class="co"># 1070 198 732</span></span></code></pre></div>
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<p>The rules set (the <code>custom</code> object in this case) could be
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exported to a shared file location using <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS()</a></code> if you
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collaborate with multiple users. The custom rules set could then be
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imported using <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS()</a></code>.</p>
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</div>
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</div>
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<div class="section level3">
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<h3 id="examples">Examples<a class="anchor" aria-label="anchor" href="#examples"></a>
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</h3>
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<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function always returns an ordered
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<code>factor</code> for predefined guidelines. For example, the output
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of the default guideline by Magiorakos <em>et al.</em> returns a
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<code>factor</code> with levels ‘Negative’, ‘MDR’, ‘XDR’ or ‘PDR’ in
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that order.</p>
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<p>The next example uses the <code>example_isolates</code> data set.
|
||
This is a data set included with this package and contains full
|
||
antibiograms of 2,000 microbial isolates. It reflects reality and can be
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||
used to practise AMR data analysis. If we test the MDR/XDR/PDR guideline
|
||
on this data set, we get:</p>
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||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
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||
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span> <span class="co"># to support pipes: %>%</span></span>
|
||
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/cleaner/" class="external-link">cleaner</a></span><span class="op">)</span> <span class="co"># to create frequency tables</span></span></code></pre></div>
|
||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||
<span> <span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||
<span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="op">)</span> <span class="co"># show frequency table of the result</span></span>
|
||
<span><span class="co"># Warning: in mdro(): NA introduced for isolates where the available percentage of</span></span>
|
||
<span><span class="co"># antimicrobial classes was below 50% (set with pct_required_classes)</span></span></code></pre></div>
|
||
<p>(16 isolates had no test results)</p>
|
||
<p><strong>Frequency table</strong></p>
|
||
<p>Class: factor > ordered (numeric)<br>
|
||
Length: 2,000<br>
|
||
Levels: 4: Negative < Multi-drug-resistant (MDR) < Extensively
|
||
drug-resistant …<br>
|
||
Available: 1,729 (86.45%, NA: 271 = 13.55%)<br>
|
||
Unique: 2</p>
|
||
<table style="width:100%;" class="table">
|
||
<colgroup>
|
||
<col width="4%">
|
||
<col width="38%">
|
||
<col width="9%">
|
||
<col width="12%">
|
||
<col width="16%">
|
||
<col width="19%">
|
||
</colgroup>
|
||
<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>
|
||
<td align="left">Negative</td>
|
||
<td align="right">1601</td>
|
||
<td align="right">92.6%</td>
|
||
<td align="right">1601</td>
|
||
<td align="right">92.6%</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left">2</td>
|
||
<td align="left">Multi-drug-resistant (MDR)</td>
|
||
<td align="right">128</td>
|
||
<td align="right">7.4%</td>
|
||
<td align="right">1729</td>
|
||
<td align="right">100.0%</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p>For another example, I will create a data set to determine multi-drug
|
||
resistant TB:</p>
|
||
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="co"># random_sir() is a helper function to generate</span></span>
|
||
<span><span class="co"># a random vector with values S, I and R</span></span>
|
||
<span><span class="va">my_TB_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span>
|
||
<span> rifampicin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||
<span> isoniazid <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||
<span> gatifloxacin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||
<span> ethambutol <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||
<span> pyrazinamide <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||
<span> moxifloxacin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||
<span> kanamycin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span></span>
|
||
<span><span class="op">)</span></span></code></pre></div>
|
||
<p>Because all column names are automatically verified for valid drug
|
||
names or codes, this would have worked exactly the same way:</p>
|
||
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="va">my_TB_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span>
|
||
<span> RIF <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||
<span> INH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||
<span> GAT <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||
<span> ETH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||
<span> PZA <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||
<span> MFX <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||
<span> KAN <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span></span>
|
||
<span><span class="op">)</span></span></code></pre></div>
|
||
<p>The data set now looks like this:</p>
|
||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
|
||
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
|
||
<span><span class="co"># 1 I S S I S I</span></span>
|
||
<span><span class="co"># 2 R R R R I S</span></span>
|
||
<span><span class="co"># 3 R I R R I R</span></span>
|
||
<span><span class="co"># 4 R S I S S I</span></span>
|
||
<span><span class="co"># 5 I I S S S I</span></span>
|
||
<span><span class="co"># 6 I I I R R I</span></span>
|
||
<span><span class="co"># kanamycin</span></span>
|
||
<span><span class="co"># 1 S</span></span>
|
||
<span><span class="co"># 2 S</span></span>
|
||
<span><span class="co"># 3 I</span></span>
|
||
<span><span class="co"># 4 R</span></span>
|
||
<span><span class="co"># 5 I</span></span>
|
||
<span><span class="co"># 6 S</span></span></code></pre></div>
|
||
<p>We can now add the interpretation of MDR-TB to our data set. You can
|
||
use:</p>
|
||
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></span></code></pre></div>
|
||
<p>or its shortcut <code><a href="../reference/mdro.html">mdr_tb()</a></code>:</p>
|
||
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="va">my_TB_data</span><span class="op">$</span><span class="va">mdr</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mdro.html">mdr_tb</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
|
||
<span><span class="co"># ℹ No column found as input for col_mo, assuming all rows contain</span></span>
|
||
<span><span class="co"># Mycobacterium tuberculosis.</span></span></code></pre></div>
|
||
<p>Create a frequency table of the results:</p>
|
||
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">$</span><span class="va">mdr</span><span class="op">)</span></span></code></pre></div>
|
||
<p><strong>Frequency table</strong></p>
|
||
<p>Class: factor > ordered (numeric)<br>
|
||
Length: 5,000<br>
|
||
Levels: 5: Negative < Mono-resistant < Poly-resistant <
|
||
Multi-drug-resistant <…<br>
|
||
Available: 5,000 (100%, NA: 0 = 0%)<br>
|
||
Unique: 5</p>
|
||
<table style="width:100%;" class="table">
|
||
<colgroup>
|
||
<col width="4%">
|
||
<col width="38%">
|
||
<col width="9%">
|
||
<col width="12%">
|
||
<col width="16%">
|
||
<col width="19%">
|
||
</colgroup>
|
||
<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>
|
||
<td align="left">Mono-resistant</td>
|
||
<td align="right">3238</td>
|
||
<td align="right">64.76%</td>
|
||
<td align="right">3238</td>
|
||
<td align="right">64.76%</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left">2</td>
|
||
<td align="left">Negative</td>
|
||
<td align="right">994</td>
|
||
<td align="right">19.88%</td>
|
||
<td align="right">4232</td>
|
||
<td align="right">84.64%</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="left">3</td>
|
||
<td align="left">Multi-drug-resistant</td>
|
||
<td align="right">425</td>
|
||
<td align="right">8.50%</td>
|
||
<td align="right">4657</td>
|
||
<td align="right">93.14%</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left">4</td>
|
||
<td align="left">Poly-resistant</td>
|
||
<td align="right">247</td>
|
||
<td align="right">4.94%</td>
|
||
<td align="right">4904</td>
|
||
<td align="right">98.08%</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="left">5</td>
|
||
<td align="left">Extensively drug-resistant</td>
|
||
<td align="right">96</td>
|
||
<td align="right">1.92%</td>
|
||
<td align="right">5000</td>
|
||
<td align="right">100.00%</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||
</nav></aside>
|
||
</div>
|
||
|
||
|
||
|
||
<footer><div class="pkgdown-footer-left">
|
||
<p></p>
|
||
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
|
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</div>
|
||
|
||
<div class="pkgdown-footer-right">
|
||
<p></p>
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<p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_umcg.svg" style="max-width: 150px;"></a></p>
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