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@@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9227</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9228</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -119,7 +119,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
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<dt id="arg-ampc-cephalosporin-resistance">ampc_cephalosporin_resistance<a class="anchor" aria-label="anchor" href="#arg-ampc-cephalosporin-resistance"></a></dt>
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<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 - the default is <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 drugs. A value of <code>NA</code> (the default) for this argument will remove results for these three drugs, while e.g. a value of <code>"R"</code> will make the results for these drugs resistant. Use <code>NULL</code> or <code>FALSE</code> to not alter results for these three drugs 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>
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<dd><p>(only applies when <code>rules</code> contains <code>"expert"</code> or <code>"all"</code>) 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 - the default is <code>NA</code>. Currently only works when <code>version_expertrules</code> is <code>3.2</code> and higher; these versions 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 drugs. A value of <code>NA</code> (the default) for this argument will remove results for these three drugs, while e.g. a value of <code>"R"</code> will make the results for these drugs resistant. Use <code>NULL</code> or <code>FALSE</code> to not alter results for these three drugs 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>
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<dt id="arg-only-sir-columns">only_sir_columns<a class="anchor" aria-label="anchor" href="#arg-only-sir-columns"></a></dt>
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@@ -184,10 +184,12 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
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<p>Amikacin (<code>AMK</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01GB06&showdescription=no" class="external-link">J01GB06</a>), amoxicillin (<code>AMX</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA04&showdescription=no" class="external-link">J01CA04</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CR02&showdescription=no" class="external-link">J01CR02</a>), ampicillin (<code>AMP</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA01&showdescription=no" class="external-link">J01CA01</a>), ampicillin/sulbactam (<code>SAM</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CR01&showdescription=no" class="external-link">J01CR01</a>), apramycin (<code>APR</code>, <a href="https://atcddd.fhi.no/atcvet/atcvet_index/?code=QA07AA92&showdescription=no" class="external-link">QA07AA92</a>), arbekacin (<code>ARB</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01GB12&showdescription=no" class="external-link">J01GB12</a>), aspoxicillin (<code>APX</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA19&showdescription=no" class="external-link">J01CA19</a>), azidocillin (<code>AZD</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CE04&showdescription=no" class="external-link">J01CE04</a>), azithromycin (<code>AZM</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01FA10&showdescription=no" class="external-link">J01FA10</a>), azlocillin (<code>AZL</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA09&showdescription=no" class="external-link">J01CA09</a>), aztreonam (<code>ATM</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DF01&showdescription=no" class="external-link">J01DF01</a>), bacampicillin (<code>BAM</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA06&showdescription=no" class="external-link">J01CA06</a>), bekanamycin (<code>BEK</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01GB13&showdescription=no" class="external-link">J01GB13</a>), benzathine benzylpenicillin (<code>BNB</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CE08&showdescription=no" class="external-link">J01CE08</a>), benzathine phenoxymethylpenicillin (<code>BNP</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CE10&showdescription=no" class="external-link">J01CE10</a>), benzylpenicillin (<code>PEN</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CE01&showdescription=no" class="external-link">J01CE01</a>), besifloxacin (<code>BES</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=S01AE08&showdescription=no" class="external-link">S01AE08</a>), biapenem (<code>BIA</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DH05&showdescription=no" class="external-link">J01DH05</a>), bleomycin (<code>BLM</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=L01DC01&showdescription=no" class="external-link">L01DC01</a>), brodimoprim (<code>BDP</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01EA02&showdescription=no" class="external-link">J01EA02</a>), carbenicillin (<code>CRB</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA03&showdescription=no" class="external-link">J01CA03</a>), carindacillin (<code>CRN</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA05&showdescription=no" class="external-link">J01CA05</a>), carumonam (<code>CAR</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DF02&showdescription=no" class="external-link">J01DF02</a>), cefacetrile (<code>CAC</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DB10&showdescription=no" class="external-link">J01DB10</a>), cefaclor (<code>CEC</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DC04&showdescription=no" class="external-link">J01DC04</a>), cefadroxil (<code>CFR</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DB05&showdescription=no" class="external-link">J01DB05</a>), cefalexin (<code>LEX</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DB01&showdescription=no" class="external-link">J01DB01</a>), cefaloridine (<code>RID</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DB02&showdescription=no" class="external-link">J01DB02</a>), cefalotin (<code>CEP</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DB03&showdescription=no" class="external-link">J01DB03</a>), cefamandole (<code>MAN</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DC03&showdescription=no" class="external-link">J01DC03</a>), cefapirin (<code>HAP</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DB08&showdescription=no" class="external-link">J01DB08</a>), cefatrizine (<code>CTZ</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DB07&showdescripLine truncated
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</div>
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<div class="section level2">
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<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
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<h2 id="download-our-reference-data">Download Our Reference Data<a class="anchor" aria-label="anchor" href="#download-our-reference-data"></a></h2>
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<p>All data sets in this <code>AMR</code> package (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, 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>
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<p>All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.</p>
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<p>For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.</p>
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<p>Visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for direct download links</a>, or explore the actual files in <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
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</div>
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<div class="section level2">
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@@ -230,8 +232,8 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
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<span class="r-in"><span></span></span>
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<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>
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<span class="r-out co"><span class="r-pr">#></span> mo VAN AMX COL CAZ CXM PEN FOX</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 Staphylococcus aureus - S - R S S S</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 Enterococcus faecalis - - - R R S R</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 Staphylococcus aureus - S R R S S S</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 Enterococcus faecalis - - R R R S R</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 Escherichia coli R - - - - R S</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 Klebsiella pneumoniae R R - - - R S</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 Pseudomonas aeruginosa R R - - R R R</span>
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@@ -250,9 +252,9 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
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<span class="r-out co"><span class="r-pr">#></span> 1 1 AMX Staphylococcus aureus - S Breakpoints</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 1 CXM Staphylococcus aureus - S Breakpoints</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 1 CAZ Staphylococcus aureus - R Expected phenotypes</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 2 CAZ Enterococcus faecalis - R Expected phenotypes</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 2 CXM Enterococcus faecalis - R Expected phenotypes</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 2 FOX Enterococcus faecalis S R Expected phenotypes</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 1 COL Staphylococcus aureus - R Expected phenotypes</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 2 CAZ Enterococcus faecalis - R Expected phenotypes</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 2 COL Enterococcus faecalis - R Expected phenotypes</span>
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<span class="r-out co"><span class="r-pr">#></span> rule_name</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 Staphylococcus</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 Staphylococcus</span>
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