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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="">2.1.1.9224</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9227</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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@@ -60,8 +60,9 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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<div class="section level2">
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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">eucast_rules</span><span class="op">(</span><span class="va">x</span>, col_mo <span class="op">=</span> <span class="cn">NULL</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>
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<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>
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<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>, version_breakpoints <span class="op">=</span> <span class="fl">14</span>, version_expertrules <span class="op">=</span> <span class="fl">3.3</span>,</span>
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<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>
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<span> <span class="st">"expected_phenotypes"</span><span class="op">)</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, version_breakpoints <span class="op">=</span> <span class="fl">14</span>,</span>
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<span> version_expected_phenotypes <span class="op">=</span> <span class="fl">1.2</span>, version_expertrules <span class="op">=</span> <span class="fl">3.3</span>,</span>
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<span> ampc_cephalosporin_resistance <span class="op">=</span> <span class="cn">NA</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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<span> custom_rules <span class="op">=</span> <span class="cn">NULL</span>, overwrite <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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@@ -98,7 +99,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
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<dt id="arg-rules">rules<a class="anchor" aria-label="anchor" href="#arg-rules"></a></dt>
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<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 using the package option <code><a href="AMR-options.html">AMR_eucastrules</a></code>: <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>
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<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>"expected_phenotypes"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"custom"</code>, <code>"all"</code>, and defaults to <code>c("breakpoints", "expected_phenotypes")</code>. The default value can be set to another value using the package option <code><a href="AMR-options.html">AMR_eucastrules</a></code>: <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>
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<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
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@@ -109,6 +110,10 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
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<dd><p>the version number to use for the EUCAST Clinical Breakpoints guideline. Can be "14.0", "13.1", "12.0", "11.0", or "10.0".</p></dd>
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<dt id="arg-version-expected-phenotypes">version_expected_phenotypes<a class="anchor" aria-label="anchor" href="#arg-version-expected-phenotypes"></a></dt>
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<dd><p>the version number to use for the EUCAST Expected Phenotypes. Can be "1.2".</p></dd>
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<dt id="arg-version-expertrules">version_expertrules<a class="anchor" aria-label="anchor" href="#arg-version-expertrules"></a></dt>
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<dd><p>the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be "3.3", "3.2", or "3.1".</p></dd>
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@@ -176,7 +181,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
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<p>To define antimicrobials 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>
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<p>The following antimicrobials 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://atcddd.fhi.no/atc/structure_and_principles/" class="external-link">ATC code</a>)', sorted alphabetically:</p>
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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>), 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&showdescription=no" class="external-link">J01DB07</a>), cefazedone (<code>CZD</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DB06&showdescriptLine truncated
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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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@@ -216,7 +221,7 @@ 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></span>
|
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<span class="r-in"><span><span class="co"># apply EUCAST rules: some results wil be changed</span></span></span>
|
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<span class="r-in"><span><span class="va">b</span> <span class="op"><-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span><span class="op">)</span></span></span>
|
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<span class="r-in"><span><span class="va">b</span> <span class="op"><-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">eucast_rules()</span>: not all columns with antimicrobial results are of</span>
|
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<span class="r-wrn co"><span class="r-pr">#></span> class 'sir'. Transform them on beforehand, with e.g.:</span>
|
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<span class="r-wrn co"><span class="r-pr">#></span> - a %>% as.sir(CXM:AMX)</span>
|
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@@ -225,43 +230,43 @@ 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 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 S</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 Escherichia coli R - - - - S S</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 Klebsiella pneumoniae R R - - - S S</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 Pseudomonas aeruginosa R R - - R S S</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> 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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 Pseudomonas aeruginosa R R - - R R R</span>
|
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<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"><-</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-in"><span><span class="va">c</span> <span class="op"><-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</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">#></span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">eucast_rules()</span>: not all columns with antimicrobial results are of</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> class 'sir'. Transform them on beforehand, with e.g.:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> - a %>% as.sir(CXM:AMX)</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> - a %>% mutate_if(is_sir_eligible, as.sir)</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> - a %>% mutate(across(where(is_sir_eligible), as.sir))</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">#></span> row col mo_fullname old new rule rule_group</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1 AMX Staphylococcus aureus - S Breakpoints</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1 CXM Staphylococcus aureus - S Breakpoints</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1 CAZ Staphylococcus aureus - R Expert Rules</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1 COL Staphylococcus aureus - R Expert Rules</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 2 CAZ Enterococcus faecalis - R Expert Rules</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 2 COL Enterococcus faecalis - R Expert Rules</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> rule_name</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Staphylococcus</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 Staphylococcus</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 Table 4: Intrinsic resistance in gram-positive bacteria</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 Table 4: Intrinsic resistance in gram-positive bacteria</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 Table 4: Intrinsic resistance in gram-positive bacteria</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 Table 4: Intrinsic resistance in gram-positive bacteria</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> rule_source</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 'EUCAST Clinical Breakpoint Tables' v14.0, 2024</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 'EUCAST Clinical Breakpoint Tables' v14.0, 2024</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></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">#></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">#></span> 6 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3, 2021</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> row col mo_fullname old new rule rule_group</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1 AMX Staphylococcus aureus - S Breakpoints</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1 CXM Staphylococcus aureus - S Breakpoints</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1 CAZ Staphylococcus aureus - R Expected phenotypes</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 2 CAZ Enterococcus faecalis - R Expected phenotypes</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 2 CXM Enterococcus faecalis - R Expected phenotypes</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 2 FOX Enterococcus faecalis S R Expected phenotypes</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> rule_name</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Staphylococcus</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 Staphylococcus</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 Table 4: Expected resistant phenotype in gram-positive bacteria</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 Table 4: Expected resistant phenotype in gram-positive bacteria</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 Table 4: Expected resistant phenotype in gram-positive bacteria</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 Table 4: Expected resistant phenotype in gram-positive bacteria</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> rule_source</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 'EUCAST Clinical Breakpoint Tables' v14.0, 2024</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 'EUCAST Clinical Breakpoint Tables' v14.0, 2024</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 'EUCAST Expected Resistant Phenotypes' v1.2, 2023</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 'EUCAST Expected Resistant Phenotypes' v1.2, 2023</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 'EUCAST Expected Resistant Phenotypes' v1.2, 2023</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 'EUCAST Expected Resistant Phenotypes' v1.2, 2023</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>
|
||||
|
||||
Reference in new issue
Block a user