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Title:           The phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia
Subject:         Nature Communications, doi:10.1038/s41467-020-15123-0
Keywords:        
Author:          Matthias I. Gröschel
Creator:         Springer
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     Item: 
      Title: The phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia
      Destination: title_link
      Children: 
       Item: 
        Title: Results
        Destination: A1
        Children: 
         Item: 
          Title: Strain collection and gene-by-gene analysis
          Destination: B1
         Item: 
          Title: S. maltophilia complex comprises 23 monophyletic lineages
          Destination: B2
         Item: 
          Title: Delineation of the S. maltophilia complex within its genus
          Destination: B3
         Item: 
          Title: Lineages are globally distributed and differ in human association
          Destination: B4
         Item: 
          Title: Resistome and virulence characteristics of S. maltophilia
          Destination: B5
         Item: 
          Title: Possible local spread derived from genetic diversity analysis
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       Item: 
        Title: Discussion
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       Item: 
        Title: Methods
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        Children: 
         Item: 
          Title: Bacterial strains and DNA isolation
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         Item: 
          Title: Whole-genome data collection and sequencing
          Destination: B8
         Item: 
          Title: Generation of full genomes by PacBio sequencing
          Destination: B9
         Item: 
          Title: Construction of a whole-genome MLST scheme
          Destination: B10
         Item: 
          Title: Whole-genome MLST scheme validation
          Destination: B11
         Item: 
          Title: Phylogenetic analysis
          Destination: B12
         Item: 
          Title: Resistome and virulence analysis
          Destination: B13
         Item: 
          Title: Statistical analysis and data management
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         Item: 
          Title: Reporting summary
          Destination: B15
       Item: 
        Title: Data availability
        Destination: M1
       Item: 
        Title: Code availability
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       Item: 
        Title: References
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       Item: 
        Title: Acknowledgements
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       Item: 
        Title: Author contributions
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       Item: 
        Title: Competing interests
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       Item: 
        Title: Additional information
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                  <author:name>Conor J. Meehan</author:name>
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                  <author:orcid>http://orcid.org/0000-0002-6234-4082</author:orcid>
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                  <author:orcid>http://orcid.org/0000-0001-9235-6730</author:orcid>
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                  <author:name>Tjip S. Werf</author:name>
                  <author:orcid>http://orcid.org/0000-0002-4824-1642</author:orcid>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <author:name>Wolfgang R. Streit</author:name>
                  <author:orcid>http://orcid.org/0000-0001-7617-7396</author:orcid>
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                  <author:orcid>http://orcid.org/0000-0001-7372-4729</author:orcid>
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                  <author:name>John W. A. Rossen</author:name>
                  <author:orcid>http://orcid.org/0000-0002-7167-8623</author:orcid>
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                  <author:name>Maha R. Farhat</author:name>
                  <author:orcid>http://orcid.org/0000-0002-3871-5760</author:orcid>
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               <rdf:li rdf:parseType="Resource">
                  <author:name>Ulrich E. Schaible</author:name>
                  <author:orcid>http://orcid.org/0000-0002-6638-7282</author:orcid>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <author:name>Ulrich Nübel</author:name>
                  <author:orcid>http://orcid.org/0000-0003-3131-1656</author:orcid>
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               <rdf:li rdf:parseType="Resource">
                  <author:name>Jan Rupp</author:name>
                  <author:orcid>http://orcid.org/0000-0001-8722-1233</author:orcid>
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                  <author:name>Thomas A. Kohl</author:name>
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                  <pdfaSchema:schema>Adobe PDF Schema</pdfaSchema:schema>
                  <pdfaSchema:property>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>A name object indicating whether the document has been modified to include trapping information</pdfaProperty:description>
                           <pdfaProperty:name>Trapped</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
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                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
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                           <pdfaProperty:description>ID of PDF/X standard</pdfaProperty:description>
                           <pdfaProperty:name>GTS_PDFXVersion</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Conformance level of PDF/X standard</pdfaProperty:description>
                           <pdfaProperty:name>GTS_PDFXConformance</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Company creating the PDF</pdfaProperty:description>
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                        <rdf:li rdf:parseType="Resource">
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                           <pdfaProperty:description>Date when document was last modified</pdfaProperty:description>
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                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>Mirrors crossmark:CrosMarkDomains</pdfaProperty:description>
                           <pdfaProperty:name>CrossMarkDomains</pdfaProperty:name>
                           <pdfaProperty:valueType>Seq Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Mirrors crossmark:DOI</pdfaProperty:description>
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                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
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                  <pdfaSchema:prefix>xmpMM</pdfaSchema:prefix>
                  <pdfaSchema:schema>XMP Media Management Schema</pdfaSchema:schema>
                  <pdfaSchema:property>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>UUID based identifier for specific incarnation of a document</pdfaProperty:description>
                           <pdfaProperty:name>InstanceID</pdfaProperty:name>
                           <pdfaProperty:valueType>URI</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>The common identifier for all versions and renditions of a document.</pdfaProperty:description>
                           <pdfaProperty:name>OriginalDocumentID</pdfaProperty:name>
                           <pdfaProperty:valueType>URI</pdfaProperty:valueType>
                        </rdf:li>
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               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <pdfaSchema:namespaceURI>http://www.aiim.org/pdfa/ns/id/</pdfaSchema:namespaceURI>
                  <pdfaSchema:prefix>pdfaid</pdfaSchema:prefix>
                  <pdfaSchema:schema>PDF/A ID Schema</pdfaSchema:schema>
                  <pdfaSchema:property>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Part of PDF/A standard</pdfaProperty:description>
                           <pdfaProperty:name>part</pdfaProperty:name>
                           <pdfaProperty:valueType>Integer</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Amendment of PDF/A standard</pdfaProperty:description>
                           <pdfaProperty:name>amd</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Conformance level of PDF/A standard</pdfaProperty:description>
                           <pdfaProperty:name>conformance</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                     </rdf:Seq>
                  </pdfaSchema:property>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
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                  <pdfaSchema:prefix>crossmark</pdfaSchema:prefix>
                  <pdfaSchema:schema>crossmark</pdfaSchema:schema>
                  <pdfaSchema:property>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>CrossMarkDomains</pdfaProperty:description>
                           <pdfaProperty:name>CrossMarkDomains</pdfaProperty:name>
                           <pdfaProperty:valueType>Seq Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>CrossmarkDomainExclusive</pdfaProperty:description>
                           <pdfaProperty:name>CrossmarkDomainExclusive</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Usual same as prism:doi</pdfaProperty:description>
                           <pdfaProperty:name>DOI</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>The date when a publication was published.</pdfaProperty:description>
                           <pdfaProperty:name>MajorVersionDate</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                     </rdf:Seq>
                  </pdfaSchema:property>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
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                  <pdfaSchema:property>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>The aggregation type specifies the unit of aggregation for a content collection. 
Comment 
PRISM recommends that the PRISM Aggregation Type Controlled Vocabulary be used to provide values for this element. 
Note: PRISM recommends against the use of the #other value currently allowed in this controlled vocabulary. In lieu of using #other please reach out to the PRISM group at info@prismstandard.org to request addition of your term to the Aggregation Type Controlled Vocabulary. 

</pdfaProperty:description>
                           <pdfaProperty:name>aggregationType</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>Copyright </pdfaProperty:description>
                           <pdfaProperty:name>copyright</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>The Digital Object Identifier for the article.
The DOI may also be used as the dc:identifier. If used as a dc:identifier, the URI form should be captured, and the bare identifier should also be captured using prism:doi. If an alternate unique identifier is used as the required dc:identifier, then the DOI should be specified as a bare identifier within prism:doi only. 
If the URL associated with a DOI is to be specified, then prism:url may be used in conjunction with prism:doi in order to provide the service endpoint (i.e. the URL). 
</pdfaProperty:description>
                           <pdfaProperty:name>doi</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>ISSN for an electronic version of the issue in which the resource occurs. 
Permits publishers to include a second ISSN, identifying an electronic version of the issue in which the resource occurs (therefore e(lectronic)Issn. If used, prism:eIssn MUST contain the ISSN of the electronic version. See prism:issn. 
</pdfaProperty:description>
                           <pdfaProperty:name>issn</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>Title of the magazine, or other publication, in which a resource was/will be published. 
Typically this will be used to provide the name of the magazine an article appeared in as metadata for the article, along with information such as the article title, the publisher, volume, number, and cover date. 

Note: Publication name can be used to differentiate between a print magazine and the online version if the names are different such as “magazine” and “magazine.com.” 
</pdfaProperty:description>
                           <pdfaProperty:name>publicationName</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>This element provides the url for an article or unit of content. 
The attribute platform is optionally allowed for situations in which multiple URLs must be specified. PRISM recommends that a subset of the PCV platform values, namely “mobile” and “web”, be used in conjunction with this element. 
NOTE: PRISM recommends against the use of the #other value allowed in the PRISM Platform controlled vocabulary. In lieu of using #other please reach out to the PRISM group at prism-wg@yahoogroups.com to request addition of your term to the Platform Controlled Vocabulary. 
</pdfaProperty:description>
                           <pdfaProperty:name>url</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
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                  </pdfaSchema:property>
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                  <pdfaSchema:prefix>sn</pdfaSchema:prefix>
                  <pdfaSchema:schema>Springer Nature ORCID Schema</pdfaSchema:schema>
                  <pdfaSchema:property>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>Author information: contains the name of each author and his/her ORCID (ORCiD: Open Researcher and Contributor ID). An ORCID is a persistent identifier (a non-proprietary alphanumeric code) to uniquely identify scientific and other academic authors.</pdfaProperty:description>
                           <pdfaProperty:name>authorInfo</pdfaProperty:name>
                           <pdfaProperty:valueType>Bag AuthorInformation</pdfaProperty:valueType>
                        </rdf:li>
                     </rdf:Seq>
                  </pdfaSchema:property>
                  <pdfaSchema:valueType>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaType:description>Specifies the types of author information: name and ORCID of an author.</pdfaType:description>
                           <pdfaType:namespaceURI>http://springernature.com/ns/xmpExtensions/2.0/authorInfo/</pdfaType:namespaceURI>
                           <pdfaType:prefix>author</pdfaType:prefix>
                           <pdfaType:type>AuthorInformation</pdfaType:type>
                           <pdfaType:field>
                              <rdf:Seq>
                                 <rdf:li rdf:parseType="Resource">
                                    <pdfaField:description>Gives the name of an author.</pdfaField:description>
                                    <pdfaField:name>name</pdfaField:name>
                                    <pdfaField:valueType>Text</pdfaField:valueType>
                                 </rdf:li>
                                 <rdf:li rdf:parseType="Resource">
                                    <pdfaField:description>Gives the ORCID of an author.</pdfaField:description>
                                    <pdfaField:name>orcid</pdfaField:name>
                                    <pdfaField:valueType>URI</pdfaField:valueType>
                                 </rdf:li>
                              </rdf:Seq>
                           </pdfaType:field>
                        </rdf:li>
                     </rdf:Seq>
                  </pdfaSchema:valueType>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <pdfaSchema:namespaceURI>http://www.niso.org/schemas/jav/1.0/</pdfaSchema:namespaceURI>
                  <pdfaSchema:prefix>jav</pdfaSchema:prefix>
                  <pdfaSchema:schema>NISO</pdfaSchema:schema>
                  <pdfaSchema:property>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>Values for Journal Article Version are one of the following:
AO = Author’s Original
SMUR = Submitted Manuscript Under Review
AM = Accepted Manuscript
P = Proof
VoR = Version of Record
CVoR = Corrected Version of Record
EVoR = Enhanced Version of Record</pdfaProperty:description>
                           <pdfaProperty:name>journal_article_version</pdfaProperty:name>
                           <pdfaProperty:valueType>Closed Choice of Text</pdfaProperty:valueType>
                        </rdf:li>
                     </rdf:Seq>
                  </pdfaSchema:property>
               </rdf:li>
            </rdf:Bag>
         </pdfaExtension:schemas>
      </rdf:Description>
   </rdf:RDF>
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