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@ -180,15 +180,15 @@
</header><div class="row">
</header><script src="MDR_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>How to determine multi-drug resistance (MDR)</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">28 May 2020</h4>
<h4 class="date">09 July 2020</h4>
<small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/MDR.Rmd"><code>vignettes/MDR.Rmd</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/MDR.Rmd"><code>vignettes/MDR.Rmd</code></a></small>
<div class="hidden name"><code>MDR.Rmd</code></div>
</div>
@ -209,16 +209,20 @@
<ul>
<li>
<p><code>guideline = "CMI2012"</code> (default)</p>
Magiorakos AP, Srinivasan A <em>et al.</em> “Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.” Clinical Microbiology and Infection (2012) (<a href="https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext">link</a>)</li>
<p>Magiorakos AP, Srinivasan A <em>et al.</em> “Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.” Clinical Microbiology and Infection (2012) (<a href="https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext">link</a>)</p>
</li>
<li>
<p><code>guideline = "EUCAST"</code></p>
The European international guideline - EUCAST Expert Rules Version 3.1 “Intrinsic Resistance and Exceptional Phenotypes Tables” (<a href="http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf">link</a>)</li>
<p>The European international guideline - EUCAST Expert Rules Version 3.1 “Intrinsic Resistance and Exceptional Phenotypes Tables” (<a href="http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf">link</a>)</p>
</li>
<li>
<p><code>guideline = "TB"</code></p>
The international guideline for multi-drug resistant tuberculosis - World Health Organization “Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis” (<a href="https://www.who.int/tb/publications/pmdt_companionhandbook/en/">link</a>)</li>
<p>The international guideline for multi-drug resistant tuberculosis - World Health Organization “Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis” (<a href="https://www.who.int/tb/publications/pmdt_companionhandbook/en/">link</a>)</p>
</li>
<li>
<p><code>guideline = "MRGN"</code></p>
The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. (<a href="https://doi.org/10.1186/s13756-015-0047-6">link</a>)</li>
<p>The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. (<a href="https://doi.org/10.1186/s13756-015-0047-6">link</a>)</p>
</li>
<li>
<p><code>guideline = "BRMO"</code></p>
<p>The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu “WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]” (<a href="https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH">link</a>)</p>
@ -278,7 +282,7 @@ Unique: 2</p>
<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="co"># a helper function to get a random vector with values S, I and R</span>
<span class="co"># with the probabilities 50% - 10% - 40%</span>
<span class="no">sample_rsi</span> <span class="kw">&lt;-</span> <span class="kw">function</span>() {
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(<span class="fu"><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>),
<span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(<span class="fu"><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>),
<span class="kw">size</span> <span class="kw">=</span> <span class="fl">5000</span>,
<span class="kw">prob</span> <span class="kw">=</span> <span class="fu"><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>),
<span class="kw">replace</span> <span class="kw">=</span> <span class="fl">TRUE</span>)
@ -302,15 +306,15 @@ Unique: 2</p>
<p>The data set now looks like this:</p>
<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="no">my_TB_data</span>)
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
<span class="co"># 1 S R R S R R</span>
<span class="co"># 2 R S R S R S</span>
<span class="co"># 3 R R S S R S</span>
<span class="co"># 4 S S S S R S</span>
<span class="co"># 5 S R S S R S</span>
<span class="co"># 6 R S R S S S</span>
<span class="co"># 1 S R R S S I</span>
<span class="co"># 2 S R S S S S</span>
<span class="co"># 3 S S S S S S</span>
<span class="co"># 4 S R S S S R</span>
<span class="co"># 5 R S S S R R</span>
<span class="co"># 6 S R I R R S</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 R</span>
<span class="co"># 2 I</span>
<span class="co"># 1 S</span>
<span class="co"># 2 R</span>
<span class="co"># 3 R</span>
<span class="co"># 4 S</span>
<span class="co"># 5 R</span>
@ -343,40 +347,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3245</td>
<td align="right">64.90%</td>
<td align="right">3245</td>
<td align="right">64.90%</td>
<td align="right">3300</td>
<td align="right">66.00%</td>
<td align="right">3300</td>
<td align="right">66.00%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">678</td>
<td align="right">13.56%</td>
<td align="right">3923</td>
<td align="right">78.46%</td>
<td align="right">636</td>
<td align="right">12.72%</td>
<td align="right">3936</td>
<td align="right">78.72%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">607</td>
<td align="right">12.14%</td>
<td align="right">4530</td>
<td align="right">90.60%</td>
<td align="right">561</td>
<td align="right">11.22%</td>
<td align="right">4497</td>
<td align="right">89.94%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">262</td>
<td align="right">5.24%</td>
<td align="right">4792</td>
<td align="right">95.84%</td>
<td align="right">310</td>
<td align="right">6.20%</td>
<td align="right">4807</td>
<td align="right">96.14%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">208</td>
<td align="right">4.16%</td>
<td align="right">193</td>
<td align="right">3.86%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>