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< h1 > Property of a microorganism< / h1 >
< div class = "hidden name" > < code > mo_property.Rd< / code > < / div >
< / div >
< div class = "ref-description" >
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< p > Use these functions to return a specific property of a microorganism from the < code > < a href = 'microorganisms.html' > microorganisms< / a > < / code > data set. All input values will be evaluated internally with < code > < a href = 'as.mo.html' > as.mo< / a > < / code > .< / p >
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< / div >
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< pre class = "usage" > < span class = 'fu' > mo_fullname< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'get_locale.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_shortname< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'get_locale.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_subspecies< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'get_locale.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_species< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'get_locale.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_genus< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'get_locale.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_family< / span > (< span class = 'no' > x< / span > , < span class = 'no' > ...< / span > )
< span class = 'fu' > mo_order< / span > (< span class = 'no' > x< / span > , < span class = 'no' > ...< / span > )
< span class = 'fu' > mo_class< / span > (< span class = 'no' > x< / span > , < span class = 'no' > ...< / span > )
< span class = 'fu' > mo_phylum< / span > (< span class = 'no' > x< / span > , < span class = 'no' > ...< / span > )
< span class = 'fu' > mo_subkingdom< / span > (< span class = 'no' > x< / span > , < span class = 'no' > ...< / span > )
< span class = 'fu' > mo_kingdom< / span > (< span class = 'no' > x< / span > , < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_type< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'get_locale.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_gramstain< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'get_locale.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_TSN< / span > (< span class = 'no' > x< / span > , < span class = 'no' > ...< / span > )
< span class = 'fu' > mo_ref< / span > (< span class = 'no' > x< / span > , < span class = 'no' > ...< / span > )
< span class = 'fu' > mo_authors< / span > (< span class = 'no' > x< / span > , < span class = 'no' > ...< / span > )
< span class = 'fu' > mo_year< / span > (< span class = 'no' > x< / span > , < span class = 'no' > ...< / span > )
< span class = 'fu' > mo_taxonomy< / span > (< span class = 'no' > x< / span > , < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_property< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > property< / span > < span class = 'kw' > =< / span > < span class = 'st' > "fullname"< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'get_locale.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )< / pre >
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< h2 class = "hasAnchor" id = "arguments" > < a class = "anchor" href = "#arguments" > < / a > Arguments< / h2 >
< table class = "ref-arguments" >
< colgroup > < col class = "name" / > < col class = "desc" / > < / colgroup >
< tr >
< th > x< / th >
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< td > < p > any (vector of) text that can be coerced to a valid microorganism code with < code > < a href = 'as.mo.html' > as.mo< / a > < / code > < / p > < / td >
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< / tr >
< tr >
< th > language< / th >
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< td > < p > language of the returned text, defaults to system language (see < code > < a href = 'get_locale.html' > get_locale< / a > < / code > ) and can also be set with < code > < a href = 'https://www.rdocumentation.org/packages/base/topics/options' > getOption< / a > ("AMR_locale")< / code > . Use < code > language = NULL< / code > or < code > language = ""< / code > to prevent translation.< / p > < / td >
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< / tr >
< tr >
< th > ...< / th >
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< td > < p > other parameters passed on to < code > < a href = 'as.mo.html' > as.mo< / a > < / code > < / p > < / td >
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< / tr >
< tr >
< th > property< / th >
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< td > < p > one of the column names of one of the < code > < a href = 'microorganisms.html' > microorganisms< / a > < / code > data set or < code > "shortname"< / code > < / p > < / td >
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< / tr >
< / table >
< h2 class = "hasAnchor" id = "value" > < a class = "anchor" href = "#value" > < / a > Value< / h2 >
< ul >
< li > < p > An < code > integer< / code > in case of < code > mo_TSN< / code > and < code > mo_year< / code > < / p > < / li >
< li > < p > A < code > list< / code > in case of < code > mo_taxonomy< / code > < / p > < / li >
< li > < p > A < code > character< / code > in all other cases< / p > < / li >
< / ul >
< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
< p > All functions will return the most recently known taxonomic property according to ITIS, except for < code > mo_ref< / code > , < code > mo_authors< / code > and < code > mo_year< / code > . This leads to the following results:< / p > < ul >
< li > < p > < code > mo_fullname("Chlamydia psittaci")< / code > will return < code > "Chlamydophila psittaci"< / code > (with a warning about the renaming)< / p > < / li >
< li > < p > < code > mo_ref("Chlamydia psittaci")< / code > will return < code > "Page, 1968"< / code > (with a warning about the renaming)< / p > < / li >
< li > < p > < code > mo_ref("Chlamydophila psittaci")< / code > will return < code > "Everett et al., 1999"< / code > (without a warning)< / p > < / li >
< / ul >
< h2 class = "hasAnchor" id = "supported-languages" > < a class = "anchor" href = "#supported-languages" > < / a > Supported languages< / h2 >
< p > Supported languages are < code > "en"< / code > (English), < code > "de"< / code > (German), < code > "nl"< / code > (Dutch), < code > "es"< / code > (Spanish), < code > "it"< / code > (Italian), < code > "fr"< / code > (French), and < code > "pt"< / code > (Portuguese).< / p >
< h2 class = "hasAnchor" id = "itis" > < a class = "anchor" href = "#itis" > < / a > ITIS< / h2 >
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< p > < img src = 'figures/logo_itis.jpg' height = 60px style = margin-bottom:5px / > < br / >
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This package contains the < strong > complete microbial taxonomic data< / strong > (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, < a href = 'https://www.itis.gov' > https://www.itis.gov< / a > ).< / p >
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< p > All ~20,000 (sub)species from < strong > the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package< / strong > , as well as all their ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since ITIS honours the taxonomic branching order of bacterial phyla according to Cavalier-Smith (2002), which defines that all bacteria are classified into either subkingdom Negibacteria or subkingdom Posibacteria.< / p >
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< p > ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].< / p >
< h2 class = "hasAnchor" id = "source" > < a class = "anchor" href = "#source" > < / a > Source< / h2 >
< p > [1] Becker K < em > et al.< / em > < strong > Coagulase-Negative Staphylococci< / strong > . 2014. Clin Microbiol Rev. 27(4): 870– < a href = 'https://dx.doi.org/10.1128/CMR.00109-13' > https://dx.doi.org/10.1128/CMR.00109-13< / a > < / p >
< p > [2] Lancefield RC < strong > A serological differentiation of human and other groups of hemolytic streptococci< / strong > . 1933. J Exp Med. 57(4): 571– < a href = 'https://dx.doi.org/10.1084/jem.57.4.571' > https://dx.doi.org/10.1084/jem.57.4.571< / a > < / p >
< p > [3] Integrated Taxonomic Information System (ITIS). Retrieved September 2018. < a href = 'http://www.itis.gov' > http://www.itis.gov< / a > < / p >
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< h2 class = "hasAnchor" id = "read-more-on-our-website-" > < a class = "anchor" href = "#read-more-on-our-website-" > < / a > Read more on our website!< / h2 >
< p > < img src = 'figures/logo.png' height = 40px style = margin-bottom:5px / > < br / >
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On our website < a href = 'https://msberends.gitlab.io/AMR' > https://msberends.gitlab.io/AMR< / a > you can find < a href = 'https://msberends.gitlab.io/AMR/articles/AMR.html' > a comprehensive tutorial< / a > about how to conduct AMR analysis, the < a href = 'https://msberends.gitlab.io/AMR/reference' > complete documentation of all functions< / a > (which reads a lot easier than here in R) and < a href = 'https://msberends.gitlab.io/AMR/articles/WHONET.html' > an example analysis using WHONET data< / a > .< / p >
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< h2 class = "hasAnchor" id = "see-also" > < a class = "anchor" href = "#see-also" > < / a > See also< / h2 >
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< div class = 'dont-index' > < p > < code > < a href = 'microorganisms.html' > microorganisms< / a > < / code > < / p > < / div >
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< h2 class = "hasAnchor" id = "examples" > < a class = "anchor" href = "#examples" > < / a > Examples< / h2 >
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< pre class = "examples" > < span class = 'co' > # NOT RUN {< / span >
< span class = 'co' > # All properties of Escherichia coli< / span >
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< span class = 'co' > ## taxonomic properties< / span >
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< span class = 'fu' > mo_kingdom< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Bacteria"< / span >
< span class = 'fu' > mo_subkingdom< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Negibacteria"< / span >
< span class = 'fu' > mo_phylum< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Proteobacteria"< / span >
< span class = 'fu' > mo_class< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Gammaproteobacteria"< / span >
< span class = 'fu' > mo_order< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Enterobacteriales"< / span >
< span class = 'fu' > mo_family< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Enterobacteriaceae"< / span >
< span class = 'fu' > mo_genus< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Escherichia"< / span >
< span class = 'fu' > mo_species< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "coli"< / span >
< span class = 'fu' > mo_subspecies< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # NA< / span >
< span class = 'fu' > mo_TSN< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # 285 (Taxonomic Serial Number)< / span >
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< span class = 'co' > ## colloquial properties< / span >
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< span class = 'fu' > mo_fullname< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Escherichia coli"< / span >
< span class = 'fu' > mo_shortname< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "E. coli"< / span >
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< span class = 'co' > ## other properties< / span >
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< span class = 'fu' > mo_gramstain< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Gram negative"< / span >
< span class = 'fu' > mo_type< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Bacteria" (equal to kingdom)< / span >
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< span class = 'co' > ## scientific reference< / span >
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< span class = 'fu' > mo_ref< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Castellani and Chalmers, 1919"< / span >
< span class = 'fu' > mo_authors< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Castellani and Chalmers"< / span >
< span class = 'fu' > mo_year< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # 1919< / span >
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< span class = 'co' > # Abbreviations known in the field< / span >
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< span class = 'fu' > mo_genus< / span > (< span class = 'st' > "MRSA"< / span > ) < span class = 'co' > # "Staphylococcus"< / span >
< span class = 'fu' > mo_species< / span > (< span class = 'st' > "MRSA"< / span > ) < span class = 'co' > # "aureus"< / span >
< span class = 'fu' > mo_shortname< / span > (< span class = 'st' > "MRSA"< / span > ) < span class = 'co' > # "S. aureus"< / span >
< span class = 'fu' > mo_gramstain< / span > (< span class = 'st' > "MRSA"< / span > ) < span class = 'co' > # "Gram positive"< / span >
< span class = 'fu' > mo_genus< / span > (< span class = 'st' > "VISA"< / span > ) < span class = 'co' > # "Staphylococcus"< / span >
< span class = 'fu' > mo_species< / span > (< span class = 'st' > "VISA"< / span > ) < span class = 'co' > # "aureus"< / span >
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< span class = 'co' > # Known subspecies< / span >
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< span class = 'fu' > mo_genus< / span > (< span class = 'st' > "doylei"< / span > ) < span class = 'co' > # "Campylobacter"< / span >
< span class = 'fu' > mo_species< / span > (< span class = 'st' > "doylei"< / span > ) < span class = 'co' > # "jejuni"< / span >
< span class = 'fu' > mo_fullname< / span > (< span class = 'st' > "doylei"< / span > ) < span class = 'co' > # "Campylobacter jejuni doylei"< / span >
< span class = 'fu' > mo_fullname< / span > (< span class = 'st' > "K. pneu rh"< / span > ) < span class = 'co' > # "Klebsiella pneumoniae rhinoscleromatis"< / span >
< span class = 'fu' > mo_shortname< / span > (< span class = 'st' > "K. pneu rh"< / span > ) < span class = 'co' > # "K. pneumoniae"< / span >
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< span class = 'co' > # Becker classification, see ?as.mo< / span >
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< span class = 'fu' > mo_fullname< / span > (< span class = 'st' > "S. epi"< / span > ) < span class = 'co' > # "Staphylococcus epidermidis"< / span >
< span class = 'fu' > mo_fullname< / span > (< span class = 'st' > "S. epi"< / span > , < span class = 'kw' > Becker< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ) < span class = 'co' > # "Coagulase Negative Staphylococcus (CoNS)"< / span >
< span class = 'fu' > mo_shortname< / span > (< span class = 'st' > "S. epi"< / span > ) < span class = 'co' > # "S. epidermidis"< / span >
< span class = 'fu' > mo_shortname< / span > (< span class = 'st' > "S. epi"< / span > , < span class = 'kw' > Becker< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ) < span class = 'co' > # "CoNS"< / span >
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< span class = 'co' > # Lancefield classification, see ?as.mo< / span >
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< span class = 'fu' > mo_fullname< / span > (< span class = 'st' > "S. pyo"< / span > ) < span class = 'co' > # "Streptococcus pyogenes"< / span >
< span class = 'fu' > mo_fullname< / span > (< span class = 'st' > "S. pyo"< / span > , < span class = 'kw' > Lancefield< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ) < span class = 'co' > # "Streptococcus group A"< / span >
< span class = 'fu' > mo_shortname< / span > (< span class = 'st' > "S. pyo"< / span > ) < span class = 'co' > # "S. pyogenes"< / span >
< span class = 'fu' > mo_shortname< / span > (< span class = 'st' > "S. pyo"< / span > , < span class = 'kw' > Lancefield< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ) < span class = 'co' > # "GAS" ('Group A streptococci')< / span >
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< span class = 'co' > # Language support for German, Dutch, Spanish, Portuguese, Italian and French< / span >
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< span class = 'fu' > mo_gramstain< / span > (< span class = 'st' > "E. coli"< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'st' > "de"< / span > ) < span class = 'co' > # "Gramnegativ"< / span >
< span class = 'fu' > mo_gramstain< / span > (< span class = 'st' > "E. coli"< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'st' > "nl"< / span > ) < span class = 'co' > # "Gram-negatief"< / span >
< span class = 'fu' > mo_gramstain< / span > (< span class = 'st' > "E. coli"< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'st' > "es"< / span > ) < span class = 'co' > # "Gram negativo"< / span >
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< span class = 'co' > # mo_type is equal to mo_kingdom, but mo_kingdom will remain official< / span >
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< span class = 'fu' > mo_kingdom< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Bacteria" on a German system< / span >
< span class = 'fu' > mo_type< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Bakterien" on a German system< / span >
< span class = 'fu' > mo_type< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Bacteria" on an English system< / span >
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< span class = 'fu' > mo_fullname< / span > (< span class = 'st' > "S. pyogenes"< / span > ,
< span class = 'kw' > Lancefield< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ,
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< span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'st' > "de"< / span > ) < span class = 'co' > # "Streptococcus Gruppe A"< / span >
< span class = 'fu' > mo_fullname< / span > (< span class = 'st' > "S. pyogenes"< / span > ,
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< span class = 'kw' > Lancefield< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ,
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< span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'st' > "nl"< / span > ) < span class = 'co' > # "Streptococcus groep A"< / span >
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< span class = 'co' > # Get a list with the complete taxonomy (subkingdom to subspecies)< / span >
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< span class = 'fu' > mo_taxonomy< / span > (< span class = 'st' > "E. coli"< / span > )
< span class = 'co' > # }< / span > < / pre >
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