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referenced object 'lBB64' cannot be found Offset: 2253043 MIMEtype: application/pdf PDFMetadata: Objects: 592 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: ViewerPreferences: HideToolbar: false HideMenubar: false HideWindowUI: false FitWindow: false CenterWindow: false DisplayDocTitle: true NonFullScreenPageMode: UseNone Direction: L2R ViewArea: CropBox ViewClip: CropBox PrintArea: CropBox PageClip: CropBox PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: RESULTS Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@ed9d034 Children: Item: Title: General genomic features of selected isolates. Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@6121c9d6 Item: Title: Serotyping using in-house in silico PCRs. Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@87f383f Item: Title: Phylogenetic reconstruction and in silico determination of virulence and antimicrobial resistance profiles. Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4eb7f003 Item: Title: Pangenome analysis. Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@eafc191 Item: Title: DISCUSSION Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@612fc6eb Item: Title: MATERIALS AND METHODS Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1060b431 Children: Item: Title: Selection of clinical samples, sequencing, assembly, and annotation. Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@612679d6 Item: Title: External data. Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@11758f2a Item: Title: In silico serotyping. Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@e720b71 Item: Title: Variant calling and phylogenetic analyses. Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1b26f7b2 Item: Title: Virulence factors analysis. Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@491cc5c9 Item: Title: Resistance profile, plasmid, and prophage identification. Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@74ad1f1f Item: Title: Isolation, identification, and antimicrobial susceptibility testing. Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@6a1aab78 Item: Title: Pangenome construction. Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@462d5aee Item: Title: Data availability. Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@69b0fd6f Item: Title: SUPPLEMENTAL MATERIAL Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@757942a1 Item: Title: ACKNOWLEDGMENTS Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4a87761d Item: Title: REFERENCES Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@66d1af89 Info: Title: Revealing Genomic Insights of the Unexplored Porcine Pathogen Actinobacillus pleuropneumoniae Using Whole Genome Sequencing Author: Judith Guitart-Matas;Narjol Gonzalez-Escalona;Meghan Maguire;Anna Vilaró;Jaime Martinez-Urtaza;Lorenzo Fraile;Lourdes Migura-Garcia Subject: Research Article Keywords: Actinobacillus; whole genome sequencing; swine Creator: PTC Arbortext Advanced Print Publisher 11.1.4012/W Producer: Adobe LiveCycle PDF Generator; modified using iText® 5.5.13.2 ©2000-2020 iText Group NV (AGPL-version) CreationDate: Thu Aug 18 12:32:28 CEST 2022 ModDate: Fri Aug 19 20:58:56 CEST 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LastChar: 122 FontDescriptor: FontName: LPNADA+AdvOT65f8a23b.I Flags: Nonsymbolic FontBBox: -112, -250, 894, 873 FontFile3: true Encoding: WinAnsiEncoding Font: BaseFont: LPNADB+AdvOT46dcae81 FontSubset: true FirstChar: 37 LastChar: 250 FontDescriptor: FontName: LPNADB+AdvOT46dcae81 Flags: Nonsymbolic FontBBox: -46, -250, 838, 879 FontFile3: true Encoding: WinAnsiEncoding XMP: Revealing Genomic Insights of the Unexplored Porcine Pathogen Actinobacillus pleuropneumoniae Using Whole Genome Sequencing 10.1128/spectrum.01185-22 Judith Guitart-Matas Narjol Gonzalez-Escalona Meghan Maguire Anna Vilaró Jaime Martinez-Urtaza Lorenzo Fraile Lourdes Migura-Garcia Research Article Research Article Actinobacillus whole genome sequencing swine American Society for Microbiology Guitart-Matas et al. Copyright © 2022 Guitart-Matas et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. 20220720 2022 ABSTRACT Actinobacillus pleuropneumoniae (APP) is the causative agent of pleuropneumonia in pigs, one of the most relevant bacterial respiratory diseases in the swine industry. To date, 19 serotypes have been described based on capsular polysaccharide typing with significant virulence dissimilarities. In this study, 16 APP isolates from Spanish origin were selected to perform antimicrobial susceptibility tests and comparative genomic analysis using whole genome sequencing (WGS). To obtain a more comprehensive worldwide molecular epidemiologic analyses, all APP whole genome assemblies available at the National Center for Biotechnology Information (NCBI) at the time of the study were also included. An in-house in silico PCR approach enabled the correct serotyping of unserotyped or incorrectly serotyped isolates and allowed for the discrimination between serotypes 9 and 11. A pangenome analysis identified the presence or absence of gene clusters to be serotype specific, as well as virulence profile analyses targeting the apx operons. Antimicrobial resistance genes were correlated to the presence of specific plasmids. Altogether, this study provides new insights into the genetic variability within APP serotypes, correlates phenotypic tests with bioinformatic analyses and manifests the benefits of populated databases for a better assessment of diversity and variability of relatively unknown pathogens. Overall, genomic comparative analysis enhances the understanding of transmission and epidemiological patterns of this species and suggests vertical transmission of the pathogen, including the resistance genes, within the Spanish integrated systems. IMPORTANCE Pleuropneumonia is one of the most relevant respiratory infections in the swine industry. Despite Actinobacillus pleuropneumoniae (APP) being one of the most important pathogens in the pig production, this is the first comparative study including all available whole genome sequencing data from NCBI. Moreover, this study also includes 16 APP isolates of Spanish origin with known epidemiological relationships through vertical integrated systems. Genomic comparisons provided a deeper understanding of molecular and epidemiological knowledge between different APP serotypes. Furthermore, determination of resistance and toxin profiles allowed correlation with the presence of mobile genetic elements and specific serotype, respectively. 20220404 20220623 2165-0497 Pages: Page: Label: 1 Annotations: Annotation: Subtype: Link Rect: 147, 565, 245, 574 Annotation: Subtype: Link Rect: 50, 554, 139, 563 Annotation: Subtype: Link Rect: 435, 124, 530, 131 Annotation: Subtype: Link Rect: 400, 115, 456, 122 Annotation: Subtype: Link Rect: 444, 24, 526, 31 Annotation: Subtype: Link Rect: 508, 683, 544, 719 Page: Label: 2 Annotations: Annotation: Subtype: Link Rect: 361, 690, 366, 699 Destination: 243 Annotation: Subtype: Link Rect: 361, 677, 366, 687 Destination: 243 Annotation: Subtype: Link Rect: 313, 616, 318, 625 Destination: 243 Annotation: Subtype: Link Rect: 315, 556, 320, 565 Destination: 243 Annotation: Subtype: Link Rect: 325, 556, 329, 565 Destination: 243 Annotation: Subtype: Link Rect: 288, 519, 293, 528 Destination: null Annotation: Subtype: Link Rect: 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