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<h1 data-toc-skip>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">30 July 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/EUCAST.Rmd"><code>vignettes/EUCAST.Rmd</code></a></small>
<div class="hidden name"><code>EUCAST.Rmd</code></div>
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<div id="introduction" class="section level2">
<h2 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h2>
<p>What are EUCAST rules? The European Committee on Antimicrobial Susceptibility Testing (EUCAST) states <a href="http://www.eucast.org/expert_rules_and_intrinsic_resistance/">on their website</a>:</p>
<blockquote>
<p><em>EUCAST expert rules are a tabulated collection of expert knowledge on intrinsic resistances, exceptional resistance phenotypes and interpretive rules that may be applied to antimicrobial susceptibility testing in order to reduce errors and make appropriate recommendations for reporting particular resistances.</em></p>
</blockquote>
<p>In Europe, a lot of medical microbiological laboratories already apply these rules (<a href="https://www.eurosurveillance.org/content/10.2807/1560-7917.ES2015.20.2.21008">Brown <em>et al.</em>, 2015</a>). Our package features their latest insights on intrinsic resistance and exceptional phenotypes (version 10.0, 2020). Moreover, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function we use for this purpose can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R in isolates when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.</p>
</div>
<div id="examples" class="section level2">
<h2 class="hasAnchor">
<a href="#examples" class="anchor"></a>Examples</h2>
<p>These rules can be used to discard impossible bug-drug combinations in your data. For example, <em>Klebsiella</em> produces beta-lactamase that prevents ampicillin (or amoxicillin) from working against it. In other words, practically every strain of <em>Klebsiella</em> is resistant to ampicillin.</p>
<p>Sometimes, laboratory data can still contain such strains with ampicillin being susceptible to ampicillin. This could be because an antibiogram is available before an identification is available, and the antibiogram is then not re-interpreted based on the identification (namely, <em>Klebsiella</em>). EUCAST expert rules solve this, that can be applied using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:</p>
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="no">oops</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="kw">mo</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Klebsiella"</span>,
<span class="st">"Escherichia"</span>),
<span class="kw">ampicillin</span> <span class="kw">=</span> <span class="st">"S"</span>)
<span class="no">oops</span>
<span class="co"># mo ampicillin</span>
<span class="co"># 1 Klebsiella S</span>
<span class="co"># 2 Escherichia S</span>
<span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(<span class="no">oops</span>, <span class="kw">info</span> <span class="kw">=</span> <span class="fl">FALSE</span>)
<span class="co"># mo ampicillin</span>
<span class="co"># 1 Klebsiella R</span>
<span class="co"># 2 Escherichia S</span></pre></body></html></div>
<p>EUCAST rules can not only be used for correction, they can also be used for filling in known resistance and susceptibility based on results of other antimicrobials drugs. This process is called <em>interpretive reading</em> and is part of the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function as well:</p>
<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">data</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="kw">mo</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Staphylococcus aureus"</span>,
<span class="st">"Enterococcus faecalis"</span>,
<span class="st">"Escherichia coli"</span>,
<span class="st">"Klebsiella pneumoniae"</span>,
<span class="st">"Pseudomonas aeruginosa"</span>),
<span class="kw">VAN</span> <span class="kw">=</span> <span class="st">"-"</span>, <span class="co"># Vancomycin</span>
<span class="kw">AMX</span> <span class="kw">=</span> <span class="st">"-"</span>, <span class="co"># Amoxicillin</span>
<span class="kw">COL</span> <span class="kw">=</span> <span class="st">"-"</span>, <span class="co"># Colistin</span>
<span class="kw">CAZ</span> <span class="kw">=</span> <span class="st">"-"</span>, <span class="co"># Ceftazidime</span>
<span class="kw">CXM</span> <span class="kw">=</span> <span class="st">"-"</span>, <span class="co"># Cefuroxime</span>
<span class="kw">PEN</span> <span class="kw">=</span> <span class="st">"S"</span>, <span class="co"># Penicillin G</span>
<span class="kw">FOX</span> <span class="kw">=</span> <span class="st">"S"</span>, <span class="co"># Cefoxitin</span>
<span class="kw">stringsAsFactors</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div>
<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">data</span></pre></body></html></div>
<table class="table">
<thead><tr class="header">
<th align="left">mo</th>
<th align="center">VAN</th>
<th align="center">AMX</th>
<th align="center">COL</th>
<th align="center">CAZ</th>
<th align="center">CXM</th>
<th align="center">PEN</th>
<th align="center">FOX</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">Staphylococcus aureus</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="left">Enterococcus faecalis</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="odd">
<td align="left">Escherichia coli</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="left">Klebsiella pneumoniae</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="odd">
<td align="left">Pseudomonas aeruginosa</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
</tbody>
</table>
<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(<span class="no">data</span>)</pre></body></html></div>
<pre><code># Warning: Not all columns with antimicrobial results are of class &lt;rsi&gt;.
# Transform eligible columns to class &lt;rsi&gt; on beforehand: your_data %&gt;% mutate_if(is.rsi.eligible, as.rsi)</code></pre>
<table class="table">
<thead><tr class="header">
<th align="left">mo</th>
<th align="center">VAN</th>
<th align="center">AMX</th>
<th align="center">COL</th>
<th align="center">CAZ</th>
<th align="center">CXM</th>
<th align="center">PEN</th>
<th align="center">FOX</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">Staphylococcus aureus</td>
<td align="center">-</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="left">Enterococcus faecalis</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="left">Escherichia coli</td>
<td align="center">R</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">R</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="left">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">R</td>
<td align="center">S</td>
</tr>
<tr class="odd">
<td align="left">Pseudomonas aeruginosa</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
</tr>
</tbody>
</table>
</div>
</div>
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