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@@ -10,7 +10,7 @@
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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="">1.8.2.9064</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9065</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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@@ -153,8 +153,10 @@
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</dl></div>
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<div class="section level2">
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<h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
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<p>This algorithm was described in: Berends MS <em>et al.</em> (2022). <strong>AMR: An R Package for Working with Antimicrobial Resistance Data</strong>. <em>Journal of Statistical Software</em>, 104(3), 1-31; <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">doi:10.18637/jss.v104.i03</a>
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<p>This algorithm was originally described in: Berends MS <em>et al.</em> (2022). <strong>AMR: An R Package for Working with Antimicrobial Resistance Data</strong>. <em>Journal of Statistical Software</em>, 104(3), 1-31; <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">doi:10.18637/jss.v104.i03</a>
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.</p>
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<p>Later, the work of Bartlett A <em>et al.</em> about bacterial pathogens infecting humans (2022, <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a>
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) was incorporated.</p>
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</div>
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<div class="section level2">
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<h2 id="matching-score-for-microorganisms">Matching Score for Microorganisms<a class="anchor" aria-label="anchor" href="#matching-score-for-microorganisms"></a></h2>
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@@ -168,12 +170,14 @@
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<li><p><i>lev</i> is the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance" class="external-link">Levenshtein distance function</a> (counting any insertion as 1, and any deletion or substitution as 2) that is needed to change <i>x</i> into <i>n</i>;</p></li>
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<li><p><i>p<sub>n</sub></i> is the human pathogenic prevalence group of <i>n</i>, as described below;</p></li>
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<li><p><i>k<sub>n</sub></i> is the taxonomic kingdom of <i>n</i>, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.</p></li>
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</ul><p>The grouping into human pathogenic prevalence (\(p\)) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence:</p>
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<p><strong>Group 1</strong> (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is <em>Enterococcus</em>, <em>Staphylococcus</em> or <em>Streptococcus</em>. This group consequently contains all common Gram-negative bacteria, such as <em>Pseudomonas</em> and <em>Legionella</em> and all species within the order Enterobacterales.</p>
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<p><strong>Group 2</strong> consists of all microorganisms where the taxonomic phylum is Pseudomonadota (previously named Proteobacteria), Bacillota (previously named Firmicutes), Actinomycetota (previously named Actinobacteria) or Sarcomastigophora, or where the taxonomic genus is <em>Absidia</em>, <em>Acanthamoeba</em>, <em>Acholeplasma</em>, <em>Acremonium</em>, <em>Actinotignum</em>, <em>Aedes</em>, <em>Alistipes</em>, <em>Alloprevotella</em>, <em>Alternaria</em>, <em>Amoeba</em>, <em>Anaerosalibacter</em>, <em>Ancylostoma</em>, <em>Angiostrongylus</em>, <em>Anisakis</em>, <em>Anopheles</em>, <em>Apophysomyces</em>, <em>Arachnia</em>, <em>Aspergillus</em>, <em>Aureobasidium</em>, <em>Bacteroides</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Bergeyella</em>, <em>Blastocystis</em>, <em>Blastomyces</em>, <em>Borrelia</em>, <em>Brachyspira</em>, <em>Branhamella</em>, <em>Butyricimonas</em>, <em>Candida</em>, <em>Capillaria</em>, <em>Capnocytophaga</em>, <em>Catabacter</em>, <em>Cetobacterium</em>, <em>Chaetomium</em>, <em>Chlamydia</em>, <em>Chlamydophila</em>, <em>Christensenella</em>, <em>Chryseobacterium</em>, <em>Chrysonilia</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Contracaecum</em>, <em>Cordylobia</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Deinococcus</em>, <em>Demodex</em>, <em>Dermatobia</em>, <em>Dientamoeba</em>, <em>Diphyllobothrium</em>, <em>Dirofilaria</em>, <em>Dysgonomonas</em>, <em>Echinostoma</em>, <em>Elizabethkingia</em>, <em>Empedobacter</em>, <em>Entamoeba</em>, <em>Enterobius</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Fasciola</em>, <em>Flavobacterium</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Fusobacterium</em>, <em>Giardia</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Hendersonula</em>, <em>Heterophyes</em>, <em>Histomonas</em>, <em>Histoplasma</em>, <em>Hymenolepis</em>, <em>Hypomyces</em>, <em>Hysterothylacium</em>, <em>Leishmania</em>, <em>Lelliottia</em>, <em>Leptosphaeria</em>, <em>Leptotrichia</em>, <em>Lucilia</em>, <em>Lumbricus</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Metagonimus</em>, <em>Meyerozyma</em>, <em>Microsporidium</em>, <em>Microsporum</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Mycoplasma</em>, <em>Myroides</em>, <em>Necator</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Odoribacter</em>, <em>Oesophagostomum</em>, <em>Oidiodendron</em>, <em>Opisthorchis</em>, <em>Ornithobacterium</em>, <em>Parabacteroides</em>, <em>Pediculus</em>, <em>Pedobacter</em>, <em>Phlebotomus</em>, <em>Phocaeicola</em>, <em>Phocanema</em>, <em>Phoma</em>, <em>Pichia</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Pneumocystis</em>, <em>Porphyromonas</em>, <em>Prevotella</em>, <em>Pseudallescheria</em>, <em>Pseudoterranova</em>, <em>Pulex</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Riemerella</em>, <em>Saccharomyces</em>, <em>Sarcoptes</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Sphingobacterium</em>, <em>Spirometra</em>, <em>Spiroplasma</em>, <em>Sporobolomyces</em>, <em>Stachybotrys</em>, <em>Streptobacillus</em>, <em>Strongyloides</em>, <em>Syngamus</em>, <em>Taenia</em>, <em>Tannerella</em>, <em>Tenacibaculum</em>, <em>Terrimonas</em>, <em>Toxocara</em>, <em>Treponema</em>, <em>Trichinella</em>, <em>Trichobilharzia</em>, <em>Trichoderma</em>, <em>Trichomonas</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Trichostrongylus</em>, <em>Trichuris</em>, <em>Tritirachium</em>, <em>Trombicula</em>, <em>Trypanosoma</em>, <em>Tunga</em>, <em>Ureaplasma</em>, <em>Victivallis</em>, <em>Wautersiella</em>, <em>Weeksella</em> or <em>Wuchereria</em>.</p>
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<p><strong>Group 3</strong> consists of all other microorganisms.</p>
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<p>All characters in \(x\) and \(n\) are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.</p>
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<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.688\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.079\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
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</ul><p>The grouping into human pathogenic prevalence (\(p\)) is based on recent work from Bartlett <em>et al.</em> (2022, <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a>
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) who extensively studied medical-scientific literature to categorise all bacterial species into these groups:</p><ul><li><p><strong>Established</strong>, if a taxonomic species has infected at least three persons in three or more references. These records have <code>prevalence = 1.0</code> in the <a href="microorganisms.html">microorganisms</a> data set.</p></li>
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<li><p><strong>Putative</strong>, if a taxonomic species has fewer than three known cases. These records have <code>prevalence = 2.0</code> in the <a href="microorganisms.html">microorganisms</a> data set.</p></li>
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</ul><p>Furthermore,</p><ul><li><p>Any <em>other</em> bacterial genus, species or subspecies of which the genus is present in the two aforementioned groups, has <code>prevalence = 2.5</code> in the <a href="microorganisms.html">microorganisms</a> data set.</p></li>
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<li><p>Any <em>non-bacterial</em> genus, species or subspecies of which the genus is present in the following list, also has <code>prevalence = 2.5</code> in the <a href="microorganisms.html">microorganisms</a> data set: <em>Absidia</em>, <em>Acanthamoeba</em>, <em>Acremonium</em>, <em>Aedes</em>, <em>Alternaria</em>, <em>Amoeba</em>, <em>Ancylostoma</em>, <em>Angiostrongylus</em>, <em>Anisakis</em>, <em>Anopheles</em>, <em>Apophysomyces</em>, <em>Aspergillus</em>, <em>Aureobasidium</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Blastocystis</em>, <em>Blastomyces</em>, <em>Candida</em>, <em>Capillaria</em>, <em>Chaetomium</em>, <em>Chrysonilia</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Contracaecum</em>, <em>Cordylobia</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Demodex</em>, <em>Dermatobia</em>, <em>Dientamoeba</em>, <em>Diphyllobothrium</em>, <em>Dirofilaria</em>, <em>Echinostoma</em>, <em>Entamoeba</em>, <em>Enterobius</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Fasciola</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Giardia</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Hendersonula</em>, <em>Heterophyes</em>, <em>Histomonas</em>, <em>Histoplasma</em>, <em>Hymenolepis</em>, <em>Hypomyces</em>, <em>Hysterothylacium</em>, <em>Leishmania</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Metagonimus</em>, <em>Meyerozyma</em>, <em>Microsporidium</em>, <em>Microsporum</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Necator</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oesophagostomum</em>, <em>Oidiodendron</em>, <em>Opisthorchis</em>, <em>Pediculus</em>, <em>Phlebotomus</em>, <em>Phoma</em>, <em>Pichia</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Pneumocystis</em>, <em>Pseudallescheria</em>, <em>Pseudoterranova</em>, <em>Pulex</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Saccharomyces</em>, <em>Sarcoptes</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Spirometra</em>, <em>Sporobolomyces</em>, <em>Stachybotrys</em>, <em>Strongyloides</em>, <em>Syngamus</em>, <em>Taenia</em>, <em>Toxocara</em>, <em>Trichinella</em>, <em>Trichobilharzia</em>, <em>Trichoderma</em>, <em>Trichomonas</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Trichostrongylus</em>, <em>Trichuris</em>, <em>Tritirachium</em>, <em>Trombicula</em>, <em>Trypanosoma</em>, <em>Tunga</em> or <em>Wuchereria</em>.</p></li>
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<li><p>All other records have <code>prevalence = 3.0</code> in the <a href="microorganisms.html">microorganisms</a> data set.</p></li>
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</ul><p>When calculating the matching score, all characters in \(x\) and \(n\) are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.</p>
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<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.688\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.095\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
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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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@@ -193,31 +197,31 @@
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<span class="r-out co"><span class="r-pr">#></span> [1] B_ESCHR_COLI</span>
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<span class="r-in"><span><span class="fu"><a href="as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Matching scores are based on the resemblance between the input and the full</span>
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<span class="r-out co"><span class="r-pr">#></span> taxonomic name, and the pathogenicity in humans. See ?mo_matching_score.</span>
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<span class="r-out co"><span class="r-pr">#></span> taxonomic name, and the pathogenicity in humans according to Bartlett et</span>
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<span class="r-out co"><span class="r-pr">#></span> al. (2022). See ?mo_matching_score.</span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> --------------------------------------------------------------------------------</span>
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<span class="r-out co"><span class="r-pr">#></span> "K. pneumoniae" -> Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786)</span>
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<span class="r-out co"><span class="r-pr">#></span> Based on input "K pneumoniae"</span>
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<span class="r-out co"><span class="r-pr">#></span> Also matched: Klebsiella pneumoniae ozaenae (0.707), Klebsiella</span>
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<span class="r-out co"><span class="r-pr">#></span> pneumoniae pneumoniae (0.688), Klebsiella pneumoniae rhinoscleromatis</span>
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<span class="r-out co"><span class="r-pr">#></span> (0.658), Kosakonia pseudosacchari (0.542), Kalamiella piersonii</span>
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<span class="r-out co"><span class="r-pr">#></span> (0.525), Kangiella profundi (0.500), Klebsiella pasteurii (0.500),</span>
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<span class="r-out co"><span class="r-pr">#></span> Klebsiella planticola (0.500), Kushneria pakistanensis (0.500),</span>
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<span class="r-out co"><span class="r-pr">#></span> Kushneria phosphatilytica (0.500), Kushneria phyllosphaerae (0.500),</span>
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<span class="r-out co"><span class="r-pr">#></span> Kroppenstedtia pulmonis (0.304), Kibdelosporangium phytohabitans</span>
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<span class="r-out co"><span class="r-pr">#></span> (0.282), Kitasatospora putterlickiae (0.269), Kibdelosporangium</span>
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<span class="r-out co"><span class="r-pr">#></span> philippinense (0.266), Kitasatospora psammotica (0.260), Kangsaoukella</span>
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<span class="r-out co"><span class="r-pr">#></span> pontilimi (0.250), Keratinibaculum paraultunense (0.250),</span>
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<span class="r-out co"><span class="r-pr">#></span> Kibdelosporangium persicum (0.250), Kingella potus (0.250), Kitasatoa</span>
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<span class="r-out co"><span class="r-pr">#></span> purpurea (0.250), Kitasatospora paracochleata (0.250), Kitasatospora</span>
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<span class="r-out co"><span class="r-pr">#></span> paracochleatus (0.250), Kitasatospora paranensis (0.250) and</span>
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<span class="r-out co"><span class="r-pr">#></span> Kitasatospora phosalacinea (0.250) [showing first 25]</span>
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<span class="r-out co"><span class="r-pr">#></span> (0.658), Klebsiella pasteurii (0.500), Klebsiella planticola (0.500),</span>
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<span class="r-out co"><span class="r-pr">#></span> Kingella potus (0.250), Kosakonia pseudosacchari (0.217),</span>
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<span class="r-out co"><span class="r-pr">#></span> Kroppenstedtia pulmonis (0.203), Kaistella palustris (0.200), Kocuria</span>
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<span class="r-out co"><span class="r-pr">#></span> palustris (0.200), Kocuria pelophila (0.200), Kocuria polaris (0.200),</span>
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<span class="r-out co"><span class="r-pr">#></span> Kibdelosporangium phytohabitans (0.188), Kitasatospora putterlickiae</span>
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<span class="r-out co"><span class="r-pr">#></span> (0.179), Kibdelosporangium philippinense (0.177), Kalamiella piersonii</span>
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<span class="r-out co"><span class="r-pr">#></span> (0.175), Kitasatospora psammotica (0.174), Kallotenue papyrolyticum</span>
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<span class="r-out co"><span class="r-pr">#></span> (0.167), Kangiella profundi (0.167), Kangsaoukella pontilimi (0.167),</span>
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<span class="r-out co"><span class="r-pr">#></span> Katagnymene pelagic (0.167), Keratinibaculum paraultunense (0.167),</span>
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<span class="r-out co"><span class="r-pr">#></span> Kibdelosporangium persicum (0.167), Kitasatoa purpurea (0.167) and</span>
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<span class="r-out co"><span class="r-pr">#></span> Kitasatospora paracochleata (0.167) [showing first 25]</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="fu">mo_matching_score</span><span class="op">(</span></span></span>
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<span class="r-in"><span> x <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
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<span class="r-in"><span> n <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">"Escherichia coli"</span>, <span class="st">"Entamoeba coli"</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.68750000 0.07936508</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.6875000 0.0952381</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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