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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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). This function returns a <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with the levels <em>Pathogenic</em>, <em>Potentially pathogenic</em>, <em>Non-pathogenic</em>, and <em>Unknown</em>.</p>
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<p>Determination of the Gram stain (<code>mo_gramstain()</code>) will be based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, <a href="https://pubmed.ncbi.nlm.nih.gov/11837318/" class="external-link">PMID 11837318</a>), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were later renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, <a href="https://pubmed.ncbi.nlm.nih.gov/34694987/" class="external-link">PMID 34694987</a>). Bacteria in these phyla are considered Gram-positive in this <code>AMR</code> package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>. Functions <code>mo_is_gram_negative()</code> and <code>mo_is_gram_positive()</code> always return <code>TRUE</code> or <code>FALSE</code> (or <code>NA</code> when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
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<p>Determination of yeasts (<code>mo_is_yeast()</code>) will be based on the taxonomic kingdom and class. <em>Budding yeasts</em> are yeasts that reproduce asexually through a process called budding, where a new cell develops from a small protrusion on the parent cell. Taxonomically, these are members of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes) or Pichiomycetes. <em>True yeasts</em> quite specifically refers to yeasts in the underlying order Saccharomycetales (such as <em>Saccharomyces cerevisiae</em>). Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes or Pichiomycetes, the function will return <code>TRUE</code>. It returns <code>FALSE</code> otherwise (or <code>NA</code> when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>).</p>
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<p>Determination of intrinsic resistance (<code>mo_is_intrinsic_resistant()</code>) will be based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, which is based on <a href="https://www.eucast.org/expert_rules_and_expected_phenotypes" class="external-link">'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3</a> (2021). The <code>mo_is_intrinsic_resistant()</code> function can be vectorised over both argument <code>x</code> (input for microorganisms) and <code>ab</code> (input for antimicrobials).</p>
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<p>Determination of intrinsic resistance (<code>mo_is_intrinsic_resistant()</code>) will be based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, which is based on <a href="https://www.eucast.org/expert_rules_and_expected_phenotypes" class="external-link">'EUCAST Expected Resistant Phenotypes' v1.2</a> (2023). The <code>mo_is_intrinsic_resistant()</code> function can be vectorised over both argument <code>x</code> (input for microorganisms) and <code>ab</code> (input for antimicrobials).</p>
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<p>Determination of bacterial oxygen tolerance (<code>mo_oxygen_tolerance()</code>) will be based on BacDive, see <em>Source</em>. The function <code>mo_is_anaerobic()</code> only returns <code>TRUE</code> if the oxygen tolerance is <code>"anaerobe"</code>, indicting an obligate anaerobic species or genus. It always returns <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
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<p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species. <a href="https://www.mycobank.org" class="external-link">This MycoBank URL</a> will be used for fungi wherever available , <a href="https://www.mycobank.org" class="external-link">this LPSN URL</a> for bacteria wherever available, and <a href="https://www.gbif.org" class="external-link">this GBIF link</a> otherwise.</p>
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<p>SNOMED codes (<code>mo_snomed()</code>) was last updated on July 16th, 2024. See <em>Source</em> and the <a href="microorganisms.html">microorganisms</a> data set for more info.</p>
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<span class="r-in"><span><span class="op">}</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">mo_is_intrinsic_resistant()</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">mo_genus()</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 20 × 2</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 16 × 2</span></span>
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<span class="r-out co"><span class="r-pr">#></span> `mo_genus()` n</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>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Escherichia 467</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Serratia 25</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Enterobacter 23</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Citrobacter 11</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Haemophilus 8</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Acinetobacter 6</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Morganella 6</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> Pantoea 4</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> Salmonella 3</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">13</span> Neisseria 2</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">14</span> Stenotrophomonas 2</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">15</span> Campylobacter 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">16</span> Enterococcus 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">17</span> Hafnia 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">18</span> Lactobacillus 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">19</span> Leuconostoc 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">20</span> Pseudescherichia 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Acinetobacter 6</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Morganella 6</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Pantoea 4</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> Salmonella 3</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> Stenotrophomonas 2</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">13</span> Enterococcus 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">14</span> Hafnia 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">15</span> Leuconostoc 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">16</span> Pseudescherichia 1</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># get a list with the complete taxonomy (from kingdom to subspecies)</span></span></span>
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<span class="r-in"><span><span class="fu">mo_taxonomy</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
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