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<img src="../logo.svg" class="logo" alt=""><h1>Apply EUCAST Rules</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/eucast_rules.R" class="external-link"><code>R/eucast_rules.R</code></a></small>
<div class="d-none name"><code>eucast_rules.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <a href="https://www.eucast.org" class="external-link">https://www.eucast.org</a>), see <em>Source</em>. Use <code>eucast_dosage()</code> to get a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with advised dosages of a certain bug-drug combination, which is based on the <a href="dosage.html">dosage</a> data set.</p>
<p>To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see <em>Details</em>.</p>
</div>
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">eucast_rules</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> col_mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> rules <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_eucastrules"</span>, default <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"breakpoints"</span>, <span class="st">"expert"</span><span class="op">)</span><span class="op">)</span>,</span>
<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> version_breakpoints <span class="op">=</span> <span class="fl">11</span>,</span>
<span> version_expertrules <span class="op">=</span> <span class="fl">3.3</span>,</span>
<span> ampc_cephalosporin_resistance <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> custom_rules <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">eucast_dosage</span><span class="op">(</span><span class="va">ab</span>, administration <span class="op">=</span> <span class="st">"iv"</span>, version_breakpoints <span class="op">=</span> <span class="fl">11</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
<ul><li><p>EUCAST Expert Rules. Version 2.0, 2012.<br>
Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility testing.</strong> <em>Clin Microbiol Infect.</em> 2013;19(2):141-60; <a href="https://doi.org/10.1111/j.1469-0691.2011.03703.x" class="external-link">doi:10.1111/j.1469-0691.2011.03703.x</a></p></li>
<li><p>EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. <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></li>
<li><p>EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. <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></li>
<li><p>EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.3, 2021. <a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf" class="external-link">(link)</a></p></li>
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. <a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx" class="external-link">(link)</a></p></li>
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020. <a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx" class="external-link">(link)</a></p></li>
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 11.0, 2021. <a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_11.0_Breakpoint_Tables.xlsx" class="external-link">(link)</a></p></li>
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 12.0, 2022. <a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_12.0_Breakpoint_Tables.xlsx" class="external-link">(link)</a></p></li>
</ul></div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>x</dt>
<dd><p>a data set with antibiotic columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></dd>
<dt>col_mo</dt>
<dd><p>column name of the IDs of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dt>info</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether progress should be printed to the console, defaults to only print while in interactive sessions</p></dd>
<dt>rules</dt>
<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector that specifies which rules should be applied. Must be one or more of <code>"breakpoints"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"custom"</code>, <code>"all"</code>, and defaults to <code>c("breakpoints", "expert")</code>. The default value can be set to another value, e.g. using <code>options(AMR_eucastrules = "all")</code>. If using <code>"custom"</code>, be sure to fill in argument <code>custom_rules</code> too. Custom rules can be created with <code><a href="custom_eucast_rules.html">custom_eucast_rules()</a></code>.</p></dd>
<dt>verbose</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.</p></dd>
<dt>version_breakpoints</dt>
<dd><p>the version number to use for the EUCAST Clinical Breakpoints guideline. Can be either "11.0" or "10.0".</p></dd>
<dt>version_expertrules</dt>
<dd><p>the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.3", "3.2" or "3.1".</p></dd>
<dt>ampc_cephalosporin_resistance</dt>
<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants, defaults to <code>NA</code>. Currently only works when <code>version_expertrules</code> is <code>3.2</code> and higher; these version of '<em>EUCAST Expert Rules on Enterobacterales</em>' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three agents. A value of <code>NA</code> (the default) for this argument will remove results for these three agents, while e.g. a value of <code>"R"</code> will make the results for these agents resistant. Use <code>NULL</code> or <code>FALSE</code> to not alter results for these three agents of AmpC de-repressed cephalosporin-resistant mutants. Using <code>TRUE</code> is equal to using <code>"R"</code>. <br> For <em>EUCAST Expert Rules</em> v3.2, this rule applies to: <em>Citrobacter braakii</em>, <em>Citrobacter freundii</em>, <em>Citrobacter gillenii</em>, <em>Citrobacter murliniae</em>, <em>Citrobacter rodenticum</em>, <em>Citrobacter sedlakii</em>, <em>Citrobacter werkmanii</em>, <em>Citrobacter youngae</em>, <em>Enterobacter</em>, <em>Hafnia alvei</em>, <em>Klebsiella aerogenes</em>, <em>Morganella morganii</em>, <em>Providencia</em> and <em>Serratia</em>.</p></dd>
<dt>only_rsi_columns</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antibiotic columns must be detected that were transformed to class <code>&lt;rsi&gt;</code> (see <code><a href="as.rsi.html">as.rsi()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></dd>
<dt>custom_rules</dt>
<dd><p>custom rules to apply, created with <code><a href="custom_eucast_rules.html">custom_eucast_rules()</a></code></p></dd>
<dt>...</dt>
<dd><p>column name of an antibiotic, see section <em>Antibiotics</em> below</p></dd>
<dt>ab</dt>
<dd><p>any (vector of) text that can be coerced to a valid antibiotic code with <code><a href="as.ab.html">as.ab()</a></code></p></dd>
<dt>administration</dt>
<dd><p>route of administration, either "im", "iv" or "oral"</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>The input of <code>x</code>, possibly with edited values of antibiotics. Or, if <code>verbose = TRUE</code>, a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with all original and new values of the affected bug-drug combinations.</p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p><strong>Note:</strong> This function does not translate MIC values to RSI values. Use <code><a href="as.rsi.html">as.rsi()</a></code> for that. <br><strong>Note:</strong> When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. <br></p>
<p>The file containing all EUCAST rules is located here: <a href="https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv</a>. <strong>Note:</strong> Old taxonomic names are replaced with the current taxonomy where applicable. For example, <em>Ochrobactrum anthropi</em> was renamed to <em>Brucella anthropi</em> in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The <code>AMR</code> package contains the full microbial taxonomy updated until 12 September, 2022, see <a href="microorganisms.html">microorganisms</a>.</p><div class="section">
<h3 id="custom-rules">Custom Rules<a class="anchor" aria-label="anchor" href="#custom-rules"></a></h3>
<p>Custom rules can be created using <code><a href="custom_eucast_rules.html">custom_eucast_rules()</a></code>, e.g.:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/custom_eucast_rules.html">custom_eucast_rules</a></span><span class="op">(</span><span class="va">AMC</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"R"</span>,</span>
<span> <span class="va">AMC</span> <span class="op">==</span> <span class="st">"I"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"I"</span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">example_isolates</span>, rules <span class="op">=</span> <span class="st">"custom"</span>, custom_rules <span class="op">=</span> <span class="va">x</span><span class="op">)</span></span></code></pre><p></p></div>
</div>
<div class="section">
<h3 id="-other-rules">'Other' Rules<a class="anchor" aria-label="anchor" href="#-other-rules"></a></h3>
<p>Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules, and the reliability of your data (analysis). These rules are:</p><ol><li><p>A drug <strong>with</strong> enzyme inhibitor will be set to S if the same drug <strong>without</strong> enzyme inhibitor is S</p></li>
<li><p>A drug <strong>without</strong> enzyme inhibitor will be set to R if the same drug <strong>with</strong> enzyme inhibitor is R</p></li>
</ol><p>Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set.</p>
<p>Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include <code>"other"</code> to the <code>rules</code> argument, or use <code>eucast_rules(..., rules = "all")</code>. You can also set the option <code>AMR_eucastrules</code>, i.e. run <code>options(AMR_eucastrules = "all")</code>.</p>
</div>
</div>
<div class="section level2">
<h2 id="antibiotics">Antibiotics<a class="anchor" aria-label="anchor" href="#antibiotics"></a></h2>
<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href="guess_ab_col.html">guess_ab_col()</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
<p>The following antibiotics are eligible for the functions <code>eucast_rules()</code> and <code><a href="mdro.html">mdro()</a></code>. These are shown below in the format 'name (<code>antimicrobial ID</code>, <a href="https://www.whocc.no/atc/structure_and_principles/" class="external-link">ATC code</a>)', sorted alphabetically:</p>
<p>Amikacin (<code>AMK</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01GB06&amp;showdescription=no" class="external-link">S01AE08</a>), amoxicillin (<code>AMX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA04&amp;showdescription=no" class="external-link">J01MA02</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CR02&amp;showdescription=no" class="external-link">J01MA23</a>), ampicillin (<code>AMP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA01&amp;showdescription=no" class="external-link">J01MA04</a>), ampicillin/sulbactam (<code>SAM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CR01&amp;showdescription=no" class="external-link">J01MA08</a>), arbekacin (<code>ARB</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01GB12&amp;showdescription=no" class="external-link">J01MA19</a>), aspoxicillin (<code>APX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA19&amp;showdescription=no" class="external-link">J01MA16</a>), azidocillin (<code>AZD</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE04&amp;showdescription=no" class="external-link">J01MA15</a>), azithromycin (<code>AZM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01FA10&amp;showdescription=no" class="external-link">J01MA11</a>), azlocillin (<code>AZL</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA09&amp;showdescription=no" class="external-link">J01MA12</a>), aztreonam (<code>ATM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DF01&amp;showdescription=no" class="external-link">J01MA24</a>), bacampicillin (<code>BAM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA06&amp;showdescription=no" class="external-link">J01MA07</a>), bekanamycin (<code>BEK</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01GB13&amp;showdescription=no" class="external-link">J01MA14</a>), benzathine benzylpenicillin (<code>BNB</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE08&amp;showdescription=no" class="external-link">D10AF05</a>), benzathine phenoxymethylpenicillin (<code>BNP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE10&amp;showdescription=no" class="external-link">J01MA06</a>), benzylpenicillin (<code>PEN</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE01&amp;showdescription=no" class="external-link">J01MA01</a>), besifloxacin (<code>BES</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=S01AE08&amp;showdescription=no" class="external-link">J01MA18</a>), biapenem (<code>BIA</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DH05&amp;showdescription=no" class="external-link">J01MA03</a>), carbenicillin (<code>CRB</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA03&amp;showdescription=no" class="external-link">J01MA17</a>), carindacillin (<code>CRN</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA05&amp;showdescription=no" class="external-link">J01MA10</a>), cefacetrile (<code>CAC</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB10&amp;showdescription=no" class="external-link">J01MA21</a>), cefaclor (<code>CEC</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DC04&amp;showdescription=no" class="external-link">J01MA09</a>), cefadroxil (<code>CFR</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB05&amp;showdescription=no" class="external-link">J01MA05</a>), cefaloridine (<code>RID</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB02&amp;showdescription=no" class="external-link">P01AA05</a>), cefamandole (<code>MAN</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DC03&amp;showdescription=no" class="external-link">J01MA22</a>), cefatrizine (<code>CTZ</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB07&amp;showdescription=no" class="external-link">J01MA13</a>), cefazedone (<code>CZD</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB06&amp;showdescription=no" class="external-link">J01CA01</a>), cefazolin (<code>CZO</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB04&amp;showdescription=no" class="external-link">J01CA04</a>), cefcapene (<code>CCP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD17&amp;showdescription=no" class="external-link">J01CA12</a>), cefdinir (<code>CDR</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD15&amp;showdescription=no" class="external-link">J01CR05</a>), cefditoren (<code>DIT</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD16&amp;showdescription=no" class="external-link">J01CA13</a>), cefepime (<code>FEP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DE01&amp;showdescription=no" class="external-link">J01AA02</a>), cefetamet (<code>CAT</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD10&amp;showdescription=no" class="external-link">J01FA10</a>), cefixime (<code>CFM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD08&amp;showdescription=no" class="external-link">J01FA09</a>), cefmenoxime (<code>CMX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD05&amp;showdescription=no" class="external-link">J01CR02</a>), cefmetazole (<code>CMZ</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DC09&amp;showdescription=no" class="external-link">J01AA08</a>), cefodizime (<code>DIZ</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD09&amp;showdescription=no" class="external-link">J01FA06</a>), cefonicid (<code>CID</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DC06&amp;showdescription=no" class="external-link">J01CF04</a>), cefoperazone (<code>CFP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD12&amp;showdescription=no" class="external-link">J01CF05</a>), cefoperazone/sulbactam (<code>CSL</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD62&amp;showdescription=no" class="external-link">J01CR01</a>), ceforanide (<code>CND</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DC11&amp;showdescription=no" class="external-link">J01CA19</a>), cefotaxime (<code>CTX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD01&amp;showdescription=no" class="external-link">J01CE04</a>), cefotetan (<code>CTT</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DC05&amp;showdescription=no" class="external-link">J01CA09</a>), cefotiam (<code>CTF</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DC07&amp;showdescription=no" class="external-link">J01DF01</a>), cefoxitin (<code>FOX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DC01&amp;showdescription=no" class="external-link">J01CA06</a>), cefozopran (<code>ZOP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DE03&amp;showdescription=no" class="external-link">J01CE08</a>), cefpiramide (<code>CPM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD11&amp;showdescription=no" class="external-link">J01CE10</a>), cefpirome (<code>CPO</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DE02&amp;showdescription=no" class="external-link">J01CE01</a>), cefpodoxime (<code>CPD</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD13&amp;showdescription=no" class="external-link">J01CA03</a>), cefprozil (<code>CPR</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DC10&amp;showdescription=no" class="external-link">J01CA05</a>), cefroxadine (<code>CRD</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB11&amp;showdescription=no" class="external-link">J01CE07</a>), cefsulodin (<code>CFS</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD03&amp;showdescription=no" class="external-link">J01CF02</a>), ceftaroline (<code>CPT</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DI02&amp;showdescription=no" class="external-link">J01CF01</a>), ceftazidime (<code>CAZ</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD02&amp;showdescription=no" class="external-link">J01CA07</a>), ceftazidime/clavulanic acid (<code>CCV</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD52&amp;showdescription=no" class="external-link">J01CA18</a>), cefteram (<code>CEM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD18&amp;showdescription=no" class="external-link">J01CA11</a>), ceftezole (<code>CTL</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB12&amp;showdescription=no" class="external-link">J01CA14</a>), ceftibuten (<code>CTB</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD14&amp;showdescription=no" class="external-link">J01CF03</a>), ceftizoxime (<code>CZX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD07&amp;showdescription=no" class="external-link">J01CA10</a>), ceftobiprole medocaril (<code>CFM1</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DI01&amp;showdescription=no" class="external-link">J01CF06</a>), ceftolozane/enzyme inhibitor (<code>CEI</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DI54&amp;showdescription=no" class="external-link">J01CE06</a>), ceftriaxone (<code>CRO</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD04&amp;showdescription=no" class="external-link">J01CE05</a>), cefuroxime (<code>CXM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DC02&amp;showdescription=no" class="external-link">J01CE02</a>), cephalexin (<code>LEX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB01&amp;showdescription=no" class="external-link">J01CA02</a>), cephalothin (<code>CEP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB03&amp;showdescription=no" class="external-link">J01CA08</a>), cephapirin (<code>HAP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB08&amp;showdescription=no" class="external-link">J01CE09</a>), cephradine (<code>CED</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB09&amp;showdescription=no" class="external-link">J01CE03</a>), chloramphenicol (<code>CHL</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01BA01&amp;showdescription=no" class="external-link">J01CG01</a>), ciprofloxacin (<code>CIP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01MA02&amp;showdescription=no" class="external-link">J01CA16</a>), clarithromycin (<code>CLR</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01FA09&amp;showdescription=no" class="external-link">J01CR04</a>), clindamycin (<code>CLI</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01FF01&amp;showdescription=no" class="external-link">J01CA15</a>), clometocillin (<code>CLM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE07&amp;showdescription=no" class="external-link">J01CG02</a>), cloxacillin (<code>CLO</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CF02&amp;showdescription=no" class="external-link">J01CA17</a>), colistin (<code>COL</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01XB01&amp;showdescription=no" class="external-link">J01CR03</a>), cycloserine (<code>CYC</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J04AB01&amp;showdescription=no" class="external-link">J01DB10</a>), dalbavancin (<code>DAL</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01XA04&amp;showdescription=no" class="external-link">J01DC04</a>), daptomycin (<code>DAP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01XX09&amp;showdescription=no" class="external-link">J01DB05</a>), delafloxacin (<code>DFX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01MA23&amp;showdescription=no" class="external-link">J01DB02</a>), dibekacin (<code>DKB</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01GB09&amp;showdescription=no" class="external-link">J01DC03</a>), dicloxacillin (<code>DIC</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CF01&amp;showdescription=no" class="external-link">J01DB07</a>), dirithromycin (<code>DIR</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01FA13&amp;showdescription=no" class="external-link">J01DB06</a>), doripenem (<code>DOR</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DH04&amp;showdescription=no" class="external-link">J01DB04</a>), doxycycline (<code>DOX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01AA02&amp;showdescription=no" class="external-link">J01DD17</a>), enoxacin (<code>ENX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01MA04&amp;showdescription=no" class="external-link">J01DD15</a>), epicillin (<code>EPC</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA07&amp;showdescription=no" class="external-link">J01DD16</a>), ertapenem (<code>ETP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DH03&amp;showdescription=no" class="external-link">J01DE01</a>), erythromycin (<code>ERY</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01FA01&amp;showdescription=no" class="external-link">J01DD10</a>), fleroxacin (<code>FLE</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01MA08&amp;showdescription=no" class="external-link">J01DD08</a>), flucloxacillin (<code>FLC</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CF05&amp;showdescription=no" class="external-link">J01DD05</a>), flurithromycin (<code>FLR1</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01FA14&amp;showdescription=no" class="external-link">J01DC09</a>), fosfomycin (<code>FOS</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01XX01&amp;showdescription=no" class="external-link">J01DD09</a>), framycetin (<code>FRM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=D09AA01&amp;showdescription=no" class="external-link">J01DC06</a>), fusidic acid (<code>FUS</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01XC01&amp;showdescription=no" class="external-link">J01DD12</a>), garenoxacin (<code>GRN</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01MA19&amp;showdescription=no" class="external-link">J01DD62</a>), gatifloxacin (<code>GAT</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01MA16&amp;showdescription=no" class="external-link">J01DC11</a>), gemifloxacin (<code>GEM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01MA15&amp;showdescription=no" class="external-link">J01DD01</a>), gentamicin (<code>GEN</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01GB03&amp;showdescription=no" class="external-link">J01DC05</a>), grepafloxacin (<code>GRX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01MA11&amp;showdescription=no" class="external-link">J01DC07</a>), hetacillin (<code>HET</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA18&amp;showdescription=no" class="external-link">J01DC01</a>), imipenem (<code>IPM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DH51&amp;showdescription=no" class="external-link">J01DE03</a>), isepamicin (<code>ISE</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01GB11&amp;showdescription=no" class="external-link">J01DD11</a>), josamycin (<code>JOS</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01FA07&amp;showdescription=no" class="external-link">J01DE02</a>), kanamycin (<code>KAN</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01GB04&amp;showdescription=no" class="external-link">J01DD13</a>), latamoxef (<code>LTM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD06&amp;showdescription=no" class="external-link">J01DC10</a>), levofloxacin (<code>LVX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01MA12&amp;showdescription=no" class="external-link">J01DB11</a>), levonadifloxacin (<code>LND</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01MA24&amp;showdescription=no" class="external-link">J01DD03</a>), lincomycin (<code>LIN</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01FF02&amp;showdescription=no" class="external-link">J01DI02</a>), linezolid (<code>LNZ</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01XX08&amp;showdescription=no" class="external-link">J01DD02</a>), lomefloxacin (<code>LOM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01MA07&amp;showdescription=no" class="external-link">J01DD52</a>), loracarbef (<code>LOR</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DC08&amp;showdescription=no" class="external-link">J01DD18</a>), mecillinam (<code>MEC</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA11&amp;showdescription=no" class="external-link">J01DB12</a>), meropenem (<code>MEM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DH02&amp;showdescription=no" class="external-link">J01DD14</a>), meropenem/vaborbactam (<code>MEV</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DH52&amp;showdescription=no" class="external-link">J01DD07</a>), metampicillin (<code>MTM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA14&amp;showdescription=no" class="external-link">J01DI01</a>), methicillin (<code>MET</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CF03&amp;showdescription=no" class="external-link">J01DI54</a>), mezlocillin (<code>MEZ</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA10&amp;showdescription=no" class="external-link">J01DD04</a>), micronomicin (<code>MCR</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=S01AA22&amp;showdescription=no" class="external-link">J01DC02</a>), midecamycin (<code>MID</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01FA03&amp;showdescription=no" class="external-link">J01DB01</a>), minocycline (<code>MNO</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01AA08&amp;showdescription=no" class="external-link">J01DB03</a>), miocamycin (<code>MCM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01FA11&amp;showdescription=no" class="external-link">J01DB08</a>), moxifloxacin (<code>MFX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01MA14&amp;showdescription=no" class="external-link">J01DB09</a>), nadifloxacin (<code>NAD</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=D10AF05&amp;showdescription=no" class="external-link">J01DD06</a>), nafcillin (<code>NAF</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CF06&amp;showdescription=no" class="external-link">J01DC08</a>), nalidixic acid (<code>NAL</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01MB02&amp;showdescription=no" class="external-link">J01DH05</a>), neomycin (<code>NEO</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01GB05&amp;showdescription=no" class="external-link">J01DH04</a>), netilmicin (<code>NET</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01GB07&amp;showdescription=no" class="external-link">J01DH03</a>), nitrofurantoin (<code>NIT</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01XE01&amp;showdescription=no" class="external-link">J01DH51</a>), norfloxacin (<code>NOR</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01MA06&amp;showdescription=no" class="external-link">J01DH02</a>), ofloxacin (<code>OFX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01MA01&amp;showdescription=no" class="external-link">J01DH52</a>), oleandomycin (<code>OLE</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01FA05&amp;showdescription=no" class="external-link">J01XA02</a>), oritavancin (<code>ORI</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01XA05&amp;showdescription=no" class="external-link">J01XA01</a>), oxacillin (<code>OXA</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CF04&amp;showdescription=no" class="external-link">J01XC01</a>), pazufloxacin (<code>PAZ</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01MA18&amp;showdescription=no" class="external-link">J01FA13</a>), pefloxacin (<code>PEF</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01MA03&amp;showdescription=no" class="external-link">J01FA01</a>), penamecillin (<code>PNM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE06&amp;showdescription=no" class="external-link">J01FA14</a>), phenethicillin (<code>PHE</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE05&amp;showdescription=no" class="external-link">J01FA07</a>), phenoxymethylpenicillin (<code>PHN</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE02&amp;showdescription=no" class="external-link">J01FA03</a>), piperacillin (<code>PIP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA12&amp;showdescription=no" class="external-link">J01FA11</a>), piperacillin/tazobactam (<code>TZP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CR05&amp;showdescription=no" class="external-link">J01FA05</a>), pivampicillin (<code>PVM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA02&amp;showdescription=no" class="external-link">J01FA12</a>), pivmecillinam (<code>PME</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA08&amp;showdescription=no" class="external-link">J01FA16</a>), plazomicin (<code>PLZ</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01GB14&amp;showdescription=no" class="external-link">J01FA02</a>), polymyxin B (<code>PLB</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01XB02&amp;showdescription=no" class="external-link">J01FA15</a>), pristinamycin (<code>PRI</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01FG01&amp;showdescription=no" class="external-link">J01FA08</a>), procaine benzylpenicillin (<code>PRB</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE09&amp;showdescription=no" class="external-link">J01FF02</a>), propicillin (<code>PRP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE03&amp;showdescription=no" class="external-link">J01FG01</a>), prulifloxacin (<code>PRU</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01MA17&amp;showdescription=no" class="external-link">J01FG02</a>), quinupristin/dalfopristin (<code>QDA</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01FG02&amp;showdescription=no" class="external-link">J04AB02</a>), ribostamycin (<code>RST</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01GB10&amp;showdescription=no" class="external-link">J01XX09</a>), rifampicin (<code>RIF</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J04AB02&amp;showdescription=no" class="external-link">J01XX08</a>), rokitamycin (<code>ROK</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01FA12&amp;showdescription=no" class="external-link">J01AA07</a>), roxithromycin (<code>RXT</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01FA06&amp;showdescription=no" class="external-link">J01XB01</a>), rufloxacin (<code>RFL</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01MA10&amp;showdescription=no" class="external-link">J01XB02</a>), sisomicin (<code>SIS</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01GB08&amp;showdescription=no" class="external-link">J01XE01</a>), sitafloxacin (<code>SIT</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01MA21&amp;showdescription=no" class="external-link">J01AA12</a>), solithromycin (<code>SOL</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01FA16&amp;showdescription=no" class="external-link">J01EA01</a>), sparfloxacin (<code>SPX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01MA09&amp;showdescription=no" class="external-link">J01XX01</a>), spiramycin (<code>SPI</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01FA02&amp;showdescription=no" class="external-link">J01BA01</a>), streptoduocin (<code>STR</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01GA02&amp;showdescription=no" class="external-link">J01GB06</a>), streptomycin (<code>STR1</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01GA01&amp;showdescription=no" class="external-link">J01GB12</a>), sulbactam (<code>SUL</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CG01&amp;showdescription=no" class="external-link">J01GB13</a>), sulbenicillin (<code>SBC</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA16&amp;showdescription=no" class="external-link">J01GB09</a>), sulfadiazine (<code>SDI</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01EC02&amp;showdescription=no" class="external-link">D09AA01</a>), sulfadiazine/trimethoprim (<code>SLT1</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01EE02&amp;showdescription=no" class="external-link">J01GB03</a>), sulfadimethoxine (<code>SUD</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01ED01&amp;showdescription=no" class="external-link">J01GB11</a>), sulfadimidine (<code>SDM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01EB03&amp;showdescription=no" class="external-link">J01GB04</a>), sulfadimidine/trimethoprim (<code>SLT2</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01EE05&amp;showdescription=no" class="external-link">S01AA22</a>), sulfafurazole (<code>SLF</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01EB05&amp;showdescription=no" class="external-link">J01GB05</a>), sulfaisodimidine (<code>SLF1</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01EB01&amp;showdescription=no" class="external-link">J01GB07</a>), sulfalene (<code>SLF2</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01ED02&amp;showdescription=no" class="external-link">J01GB14</a>), sulfamazone (<code>SZO</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01ED09&amp;showdescription=no" class="external-link">J01GB10</a>), sulfamerazine (<code>SLF3</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01ED07&amp;showdescription=no" class="external-link">J01GB08</a>), sulfamerazine/trimethoprim (<code>SLT3</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01EE07&amp;showdescription=no" class="external-link">J01GA02</a>), sulfamethizole (<code>SLF4</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01EB02&amp;showdescription=no" class="external-link">J01GA01</a>), sulfamethoxazole (<code>SMX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01EC01&amp;showdescription=no" class="external-link">J01GB01</a>), sulfamethoxypyridazine (<code>SLF5</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01ED05&amp;showdescription=no" class="external-link">J01EE01</a>), sulfametomidine (<code>SLF6</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01ED03&amp;showdescription=no" class="external-link">J01MB02</a>), sulfametoxydiazine (<code>SLF7</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01ED04&amp;showdescription=no" class="external-link">J01FF01</a>), sulfametrole/trimethoprim (<code>SLT4</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01EE03&amp;showdescription=no" class="external-link">J01XA04</a>), sulfamoxole (<code>SLF8</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01EC03&amp;showdescription=no" class="external-link">J01XA05</a>), sulfamoxole/trimethoprim (<code>SLT5</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01EE04&amp;showdescription=no" class="external-link">J01XA03</a>), sulfanilamide (<code>SLF9</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01EB06&amp;showdescription=no" class="external-link">J04AB01</a>), sulfaperin (<code>SLF10</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01ED06&amp;showdescription=no" class="external-link">J01XX11</a>), sulfaphenazole (<code>SLF11</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01ED08&amp;showdescription=no" class="external-link">J01EC02</a>), sulfapyridine (<code>SLF12</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01EB04&amp;showdescription=no" class="external-link">J01ED01</a>), sulfathiazole (<code>SUT</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01EB07&amp;showdescription=no" class="external-link">J01EB03</a>), sulfathiourea (<code>SLF13</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01EB08&amp;showdescription=no" class="external-link">J01EB05</a>), sultamicillin (<code>SLT6</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CR04&amp;showdescription=no" class="external-link">J01EB01</a>), talampicillin (<code>TAL</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA15&amp;showdescription=no" class="external-link">J01ED02</a>), tazobactam (<code>TAZ</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CG02&amp;showdescription=no" class="external-link">J01ED09</a>), tedizolid (<code>TZD</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01XX11&amp;showdescription=no" class="external-link">J01ED07</a>), teicoplanin (<code>TEC</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01XA02&amp;showdescription=no" class="external-link">J01EB02</a>), telavancin (<code>TLV</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01XA03&amp;showdescription=no" class="external-link">J01EC01</a>), telithromycin (<code>TLT</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01FA15&amp;showdescription=no" class="external-link">J01ED05</a>), temafloxacin (<code>TMX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01MA05&amp;showdescription=no" class="external-link">J01ED03</a>), temocillin (<code>TEM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA17&amp;showdescription=no" class="external-link">J01ED04</a>), tetracycline (<code>TCY</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01AA07&amp;showdescription=no" class="external-link">J01EC03</a>), ticarcillin (<code>TIC</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA13&amp;showdescription=no" class="external-link">J01EB06</a>), ticarcillin/clavulanic acid (<code>TCC</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CR03&amp;showdescription=no" class="external-link">J01ED06</a>), tigecycline (<code>TGC</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01AA12&amp;showdescription=no" class="external-link">J01ED08</a>), tilbroquinol (<code>TBQ</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=P01AA05&amp;showdescription=no" class="external-link">J01EB04</a>), tobramycin (<code>TOB</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01GB01&amp;showdescription=no" class="external-link">J01EB07</a>), tosufloxacin (<code>TFX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01MA22&amp;showdescription=no" class="external-link">J01EB08</a>), trimethoprim (<code>TMP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01EA01&amp;showdescription=no" class="external-link">J01EE02</a>), trimethoprim/sulfamethoxazole (<code>SXT</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01EE01&amp;showdescription=no" class="external-link">J01EE05</a>), troleandomycin (<code>TRL</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01FA08&amp;showdescription=no" class="external-link">J01EE07</a>), trovafloxacin (<code>TVA</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01MA13&amp;showdescription=no" class="external-link">J01EE03</a>), vancomycin (<code>VAN</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01XA01&amp;showdescription=no" class="external-link">J01EE04</a>)</p>
</div>
<div class="section level2">
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
</div>
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="va">a</span> <span class="op">&lt;-</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>
<span class="r-in"><span> mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> <span class="st">"Staphylococcus aureus"</span>,</span></span>
<span class="r-in"><span> <span class="st">"Enterococcus faecalis"</span>,</span></span>
<span class="r-in"><span> <span class="st">"Escherichia coli"</span>,</span></span>
<span class="r-in"><span> <span class="st">"Klebsiella pneumoniae"</span>,</span></span>
<span class="r-in"><span> <span class="st">"Pseudomonas aeruginosa"</span></span></span>
<span class="r-in"><span> <span class="op">)</span>,</span></span>
<span class="r-in"><span> VAN <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Vancomycin</span></span></span>
<span class="r-in"><span> AMX <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Amoxicillin</span></span></span>
<span class="r-in"><span> COL <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Colistin</span></span></span>
<span class="r-in"><span> CAZ <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Ceftazidime</span></span></span>
<span class="r-in"><span> CXM <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Cefuroxime</span></span></span>
<span class="r-in"><span> PEN <span class="op">=</span> <span class="st">"S"</span>, <span class="co"># Benzylpenicillin</span></span></span>
<span class="r-in"><span> FOX <span class="op">=</span> <span class="st">"S"</span>, <span class="co"># Cefoxitin</span></span></span>
<span class="r-in"><span> stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><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">a</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo VAN AMX COL CAZ CXM PEN FOX</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Staphylococcus aureus - - - - - S S</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 Enterococcus faecalis - - - - - S S</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 Escherichia coli - - - - - S S</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 Klebsiella pneumoniae - - - - - S S</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 Pseudomonas aeruginosa - - - - - S S</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># apply EUCAST rules: some results wil be changed</span></span></span>
<span class="r-in"><span><span class="va">b</span> <span class="op">&lt;-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `eucast_rules()`: not all columns with antimicrobial results are of</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> class &lt;rsi&gt; . Transform them on beforehand, with e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> - a %&gt;% as.rsi(CXM:AMX)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> - a %&gt;% mutate_if(is.rsi.eligible, as.rsi)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> - a %&gt;% mutate(across(where(is.rsi.eligible), as.rsi))</span>
<span class="r-in"><span></span></span>
<span class="r-in"><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">b</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo VAN AMX COL CAZ CXM PEN FOX</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Staphylococcus aureus - S R R S S S</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 Enterococcus faecalis - - R R R S R</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 Escherichia coli R - - - - R S</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 Klebsiella pneumoniae R R - - - R S</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 Pseudomonas aeruginosa R R - - R R R</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># do not apply EUCAST rules, but rather get a data.frame</span></span></span>
<span class="r-in"><span><span class="co"># containing all details about the transformations:</span></span></span>
<span class="r-in"><span><span class="va">c</span> <span class="op">&lt;-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `eucast_rules()`: not all columns with antimicrobial results are of</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> class &lt;rsi&gt; . Transform them on beforehand, with e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> - a %&gt;% as.rsi(CXM:AMX)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> - a %&gt;% mutate_if(is.rsi.eligible, as.rsi)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> - a %&gt;% mutate(across(where(is.rsi.eligible), as.rsi))</span>
<span class="r-in"><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">c</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> row col mo_fullname old new rule rule_group</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1 AMX Staphylococcus aureus - S Breakpoints</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1 CXM Staphylococcus aureus - S Breakpoints</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1 CAZ Staphylococcus aureus - R Expert Rules</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1 COL Staphylococcus aureus - R Expert Rules</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 2 CAZ Enterococcus faecalis - R Expert Rules</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 2 COL Enterococcus faecalis - R Expert Rules</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> rule_name</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Staphylococcus</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 Staphylococcus</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 Table 4: Intrinsic resistance in gram-positive bacteria</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 Table 4: Intrinsic resistance in gram-positive bacteria</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 Table 4: Intrinsic resistance in gram-positive bacteria</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 Table 4: Intrinsic resistance in gram-positive bacteria</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> rule_source</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 'EUCAST Clinical Breakpoint Tables' v11.0, 2021</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 'EUCAST Clinical Breakpoint Tables' v11.0, 2021</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3, 2021</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3, 2021</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3, 2021</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3, 2021</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Dosage guidelines:</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">eucast_dosage</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"tobra"</span>, <span class="st">"genta"</span>, <span class="st">"cipro"</span><span class="op">)</span>, <span class="st">"iv"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Dosages for antimicrobial drugs, as meant for 'EUCAST Clinical Breakpoint</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Tables' v11.0 (2021). This note will be shown once per session.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ab name standard_dosage high_dosage </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> TOB Tobramycin 6-7 mg/kg x 1 iv <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> GEN Gentamicin 6-7 mg/kg x 1 iv <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> CIP Ciprofloxacin 0.4 g x 2 iv 0.4 g x 3 iv</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">eucast_dosage</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"tobra"</span>, <span class="st">"genta"</span>, <span class="st">"cipro"</span><span class="op">)</span>, <span class="st">"iv"</span>, version_breakpoints <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Dosages for antimicrobial drugs, as meant for 'EUCAST Clinical Breakpoint</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Tables' v10.0 (2020). This note will be shown once per session.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ab name standard_dosage high_dosage </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> TOB Tobramycin 6-7 mg/kg x 1 iv <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> GEN Gentamicin 6-7 mg/kg x 1 iv <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> CIP Ciprofloxacin 0.4 g x 2 iv 0.4 g x 3 iv</span>
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