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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="">1.8.1.9030</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</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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<div class="section level2">
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<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
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<p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 500 observations and 53 variables:</p><ul><li><p><code>Identification number</code><br> ID of the sample</p></li>
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<p>A [tibble<a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a> with 500 observations and 53 variables:</p><ul><li><p><code>Identification number</code><br> ID of the sample</p></li>
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<li><p><code>Specimen number</code><br> ID of the specimen</p></li>
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<li><p><code>Organism</code><br> Name of the microorganism. Before analysis, you should transform this to a valid microbial class, using <code><a href="as.mo.html">as.mo()</a></code>.</p></li>
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<li><p><code>Country</code><br> Country of origin</p></li>
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<li><p><code>AMP_ND10:CIP_EE</code><br> 28 different antibiotics. You can lookup the abbreviations in the <a href="antibiotics.html">antibiotics</a> data set, or use e.g. <code><a href="ab_property.html">ab_name("AMP")</a></code> to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using <code><a href="as.rsi.html">as.rsi()</a></code>.</p></li>
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</ul></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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<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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<p>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. 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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</div>
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><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">WHONET</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Identification number Specimen number Organism Country</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 fe41d7bafa 1748 SPN Belgium</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 91f175ec37 1767 eco The Netherlands</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 cc4015056e 1343 eco The Netherlands</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 e864b692f5 1894 MAP Denmark</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 3d051fe345 1739 PVU Belgium</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 c80762a08d 1846 103 The Netherlands</span>
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<span class="r-out co"><span class="r-pr">#></span> Laboratory Last name First name Sex Age</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 National Laboratory of Belgium Abel B. F 68</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 National Laboratory of The Netherlands Delacroix F. M 89</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 National Laboratory of The Netherlands Steensen F. M 85</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 National Laboratory of Denmark Beyersdorf L. M 62</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 National Laboratory of Belgium Hummel W. M 86</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 National Laboratory of The Netherlands Eikenboom J. F 53</span>
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<span class="r-out co"><span class="r-pr">#></span> Age category Date of admission Specimen date Specimen type</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 55-74 2005-01-12 2005-01-30 Urine</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 75+ 2006-07-30 2006-08-16 Urine</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 75+ 2014-03-05 2014-03-14 Urine</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 55-74 2014-10-22 2014-11-01 Urine</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 75+ 2016-10-28 2016-11-17 Urine</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 25-54 2017-12-21 2018-01-02 Urine</span>
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<span class="r-out co"><span class="r-pr">#></span> Specimen type (Numeric) Reason Isolate number Organism type Serotype</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 2 Unknown 1748 Bacteria </span>
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<span class="r-out co"><span class="r-pr">#></span> 2 2 Unknown 1767 Bacteria </span>
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<span class="r-out co"><span class="r-pr">#></span> 3 2 Unknown 1343 Bacteria </span>
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<span class="r-out co"><span class="r-pr">#></span> 4 2 Unknown 1894 Bacteria </span>
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<span class="r-out co"><span class="r-pr">#></span> 5 2 Unknown 1739 Bacteria </span>
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<span class="r-out co"><span class="r-pr">#></span> 6 2 Unknown 1846 Bacteria </span>
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<span class="r-out co"><span class="r-pr">#></span> Beta-lactamase ESBL Carbapenemase MRSA screening test</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 FALSE FALSE FALSE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 FALSE FALSE FALSE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 FALSE FALSE FALSE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 FALSE FALSE FALSE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 FALSE FALSE FALSE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 FALSE FALSE FALSE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> Inducible clindamycin resistance Comment Date of data entry AMP_ND10 AMC_ED20</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 FALSE 2005-01-30 S S</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 FALSE 2006-08-16 <NA> S</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 FALSE 2014-03-14 S S</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 FALSE 2014-11-01 R <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 5 FALSE 2016-11-17 R R</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 FALSE 2018-01-02 S S</span>
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<span class="r-out co"><span class="r-pr">#></span> TZP_ED30 FEP_ED30 CTX_ED5 FOX_ED30 CAZ_ED10 CRO_ED30 CIP_ED5 AMK_ED30</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 S <NA> <NA> <NA> R <NA> <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 2 <NA> <NA> <NA> <NA> R <NA> <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 3 S <NA> <NA> <NA> <NA> <NA> <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 4 <NA> <NA> <NA> <NA> R <NA> <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 5 S <NA> S R S S S <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 6 S <NA> S S S S S <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> GEN_ED10 TOB_ED10 SXT_ED1.2 IPM_ND10 PEN_ND1 AMP_ND2 AMC_ND2 CHL_ND30 VAN_ED5</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 R R S <NA> S S S <NA> S</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 S <NA> R <NA> R <NA> S <NA> S</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 <NA> <NA> <NA> <NA> S S S <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 4 R R <NA> <NA> R R <NA> <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 5 S S R I R R R <NA> R</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 S S S S R S S <NA> R</span>
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<span class="r-out co"><span class="r-pr">#></span> OXA_ED1 ERY_ED15 CLI_ED2 TCY_ED30 RIF_ED5 PEN_EE AMP_EE CRO_EE CIP_EE</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 <NA> S <NA> S <NA> S S <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 2 <NA> S S S <NA> R <NA> <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 3 <NA> <NA> S <NA> <NA> S S <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 4 <NA> <NA> S <NA> <NA> R R <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 5 <NA> R <NA> R R R R S S</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 <NA> R <NA> <NA> R R S S S</span>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">WHONET</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 500 × 53</span></span>
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<span class="r-out co"><span class="r-pr">#></span> Identif…¹ Speci…² Organ…³ Country Labor…⁴ Last …⁵ First…⁶ Sex Age Age c…⁷</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> fe41d7ba… <span style="text-decoration: underline;">1</span>748 SPN Belgium Nation… Abel B. F 68 55-74 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 91f175ec… <span style="text-decoration: underline;">1</span>767 eco The Ne… Nation… Delacr… F. M 89 75+ </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> cc401505… <span style="text-decoration: underline;">1</span>343 eco The Ne… Nation… Steens… F. M 85 75+ </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> e864b692… <span style="text-decoration: underline;">1</span>894 MAP Denmark Nation… Beyers… L. M 62 55-74 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 3d051fe3… <span style="text-decoration: underline;">1</span>739 PVU Belgium Nation… Hummel W. M 86 75+ </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> c80762a0… <span style="text-decoration: underline;">1</span>846 103 The Ne… Nation… Eikenb… J. F 53 25-54 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 8022d372… <span style="text-decoration: underline;">1</span>628 103 Denmark Nation… Leclerc S. F 77 75+ </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> f3dc5f55… <span style="text-decoration: underline;">1</span>493 eco The Ne… Nation… Delacr… W. M 53 25-54 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 15add38f… <span style="text-decoration: underline;">1</span>847 eco France Nation… Van La… S. F 63 55-74 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> fd41248d… <span style="text-decoration: underline;">1</span>458 eco Germany Nation… Moulin O. F 75 75+ </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 490 more rows, 43 more variables: `Date of admission` <date>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># `Specimen date` <date>, `Specimen type` <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># `Specimen type (Numeric)` <dbl>, Reason <chr>, `Isolate number` <int>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># `Organism type` <chr>, Serotype <chr>, `Beta-lactamase` <lgl>, ESBL <lgl>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Carbapenemase <lgl>, `MRSA screening test` <lgl>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># `Inducible clindamycin resistance` <lgl>, Comment <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># `Date of data entry` <date>, AMP_ND10 <rsi>, AMC_ED20 <rsi>, …</span></span>
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</code></pre></div>
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</div>
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</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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