d68a67bb57b72514b7e1ae9d5dbf9c2c 269888.pdf fc78ae1b519b706db45656d6cc345776a9d19e89 269888.pdf e09b5318d6921c32460bc0d3083134ec910896b5ea02de147b152133317ce101 269888.pdf Title: Taxonomic Identification of Different Species of the Genus Aeromonas by Whole-Genome Sequencing and Use of Their Species-Specific -Lactamases as Phylogenetic Markers Subject: Some Aeromonas species, potentially pathogenic for humans, are known to express up to three different classes of chromosomal -lactamases, which may become hyperproduced and cause treatment failure. The aim of this study was to assess the utility of these species-specific -lactamase genes as phylogenetic markers using whole-genome sequencing data. Core-genome alignments were generated for 36 Aeromonas genomes from seven different species and scanned for antimicrobial resistance genes. Core-genome alignment confirmed the MALDI-TOF identification of most of the isolates and re-identified an A. hydrophila isolate as A. dhakensis. Three (B, C and D) of the four Ambler classes of -lactamase genes were found in A. sobria, A. allosacharophila, A. hydrophila and A. dhakensis (blaCphA, blaAmpC and blaOXA). A. veronii only showed class-B- and class-D-like matches (blaCphA and blaOXA), whereas those for A. media, A. rivipollensis and A. caviae were class C and D (blaCMY, blaMOX and blaOXA427). The phylogenetic tree derived from concatenated sequences of -lactamase genes successfully clustered each species. Some isolates also had resistance to sulfonamides, quinolones and aminoglycosides. Whole-genome sequencing proved to be a useful method to identify Aeromonas at the species level, which led to the unexpected identification of A. dhakensis and A.rivipollensis and revealed the resistome of each isolate. Keywords: MOX; FOX; cephamicinases; beta-lactamases; Aeromonas dhakensis; Aeromonas rivipollensis; core-genome Author: Xavier Bertran, Marc Rubio, Laura Gómez, Teresa Llovet, Carme Muñoz, Ferran Navarro and Elisenda Miro Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Fri Apr 9 08:42:46 2021 CEST ModDate: Tue Apr 13 12:23:11 2021 CEST Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 13 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 938371 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- SOZKOC+VnURWPalladioL-Bold Type 1 Custom yes yes no 10 0 HHFREY+EURM7 Type 1 Builtin yes yes no 15 0 LMNBDN+VnURWPalladioL Type 1 Custom yes yes no 19 0 CAMXTK+EURM10 Type 1 Builtin yes yes no 23 0 QKYVNY+URWPalladioL-Ital Type 1 Custom yes yes no 27 0 GFKZKZ+URWPalladioL-Bold Type 1 Custom yes yes no 32 0 AAFICW+URWPalladioL-Roma Type 1 Custom yes yes no 36 0 ZYYJXI+EURB10 Type 1 Builtin yes yes no 40 0 YYFPCJ+TimesNewRomanPS-BoldItalicMT Type 1C WinAnsi yes yes no 49 0 MCBCCI+SourceSansRoman-Regular Type 1C Custom yes yes no 71 0 MCBCCM+SourceSansRoman.613wght Type 1C Custom yes yes no 75 0 MCBCCO+SourceSansRoman-Bold Type 1C Custom yes yes no 79 0 HHHPNP+TimesNewRoman CID TrueType Identity-H yes yes yes 104 0 HHHPOB+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 110 0 HHHPOD+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 113 0 HHHPPF+PalatinoLinotype TrueType WinAnsi yes yes no 116 0 CRJHCU+PazoMath-Italic Type 1 Builtin yes yes no 123 0 HHHPNP+TimesNewRoman CID TrueType Identity-H yes yes yes 134 0 HHHPOB+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 140 0 HHHPOD+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 143 0 HHHPPE+PalatinoLinotype CID TrueType Identity-H yes yes yes 146 0 HHHPPF+PalatinoLinotype TrueType WinAnsi yes yes no 152 0 VIWIOF+CMSY10 Type 1 Builtin yes yes no 162 0 Jhove (Rel. 1.22.1, 2019-04-17) Date: 2023-01-11 02:31:05 CET RepresentationInformation: 269888.pdf ReportingModule: PDF-hul, Rel. 1.12.1 (2019-04-17) LastModified: 2023-01-10 12:07:02 CET Size: 938371 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 398 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4923ab24 Item: Title: Results Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@44c8afef Children: Item: Title: Identification by MALDI-TOF Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7b69c6ba Item: Title: WGS Analysis: Core-Genome Alignment Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@46daef40 Item: Title: Antimicrobial Susceptibility Testing Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@12f41634 Item: Title: -Lactamases Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@13c27452 Item: Title: Characterisation of Other Mechanisms of Resistance to Antimicrobials Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@262b2c86 Item: Title: Discussion Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@371a67ec Item: Title: Materials and Methods Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@5ed828d Children: Item: Title: Identification and Antimicrobial Susceptibility Testing Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@50d0686 Item: Title: DNA Extraction and Whole-Genome Sequencing Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7a3d45bd Item: Title: Computational Analysis Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1e7c7811 Children: Item: Title: Whole-Genome Comparison Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@77ec78b9 Item: Title: Detection of Antimicrobial Resistance Genes Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1a3869f4 Item: Title: Antimicrobial Resistance Genes Phylogenetic Tree Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@a38d7a3 Item: Title: References Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@77f99a05 Info: Title: Taxonomic Identification of Different Species of the Genus Aeromonas by Whole-Genome Sequencing and Use of Their Species-Specific -Lactamases as Phylogenetic Markers Author: Xavier Bertran, Marc Rubio, Laura Gómez, Teresa Llovet, Carme Muñoz, Ferran Navarro and Elisenda Miro Subject: Some Aeromonas species, potentially pathogenic for humans, are known to express up to three different classes of chromosomal -lactamases, which may become hyperproduced and cause treatment failure. The aim of this study was to assess the utility of these species-specific -lactamase genes as phylogenetic markers using whole-genome sequencing data. Core-genome alignments were generated for 36 Aeromonas genomes from seven different species and scanned for antimicrobial resistance genes. Core-genome alignment confirmed the MALDI-TOF identification of most of the isolates and re-identified an A. hydrophila isolate as A. dhakensis. Three (B, C and D) of the four Ambler classes of -lactamase genes were found in A. sobria, A. allosacharophila, A. hydrophila and A. dhakensis (blaCphA, blaAmpC and blaOXA). A. veronii only showed class-B- and class-D-like matches (blaCphA and blaOXA), whereas those for A. media, A. rivipollensis and A. caviae were class C and D (blaCMY, blaMOX and blaOXA427). The phylogenetic tree derived from concatenated sequences of -lactamase genes successfully clustered each species. Some isolates also had resistance to sulfonamides, quinolones and aminoglycosides. Whole-genome sequencing proved to be a useful method to identify Aeromonas at the species level, which led to the unexpected identification of A. dhakensis and A.rivipollensis and revealed the resistome of each isolate. Keywords: MOX; FOX; cephamicinases; beta-lactamases; Aeromonas dhakensis; Aeromonas rivipollensis; core-genome Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Fri Apr 09 08:42:46 CEST 2021 ModDate: Tue Apr 13 12:23:11 CEST 2021 ID: 0x58417a06efc85de55a6f844d5ce961f8, 0x58417a06efc85de55a6f844d5ce961f8 Filters: FilterPipeline: FlateDecode Fonts: Type1: Font: BaseFont: GFKZKZ+URWPalladioL-Bold FontSubset: true FirstChar: 2 LastChar: 241 FontDescriptor: FontName: GFKZKZ+URWPalladioL-Bold Flags: Symbolic FontBBox: -152, -301, 1000, 935 FontFile: true EncodingDictionary: Differences: true Font: BaseFont: VIWIOF+CMSY10 FontSubset: true FirstChar: 0 LastChar: 48 FontDescriptor: FontName: VIWIOF+CMSY10 Flags: Symbolic FontBBox: -29, -960, 1116, 775 FontFile: true Font: BaseFont: LMNBDN+VnURWPalladioL FontSubset: true FirstChar: 129 LastChar: 226 FontDescriptor: FontName: LMNBDN+VnURWPalladioL Flags: Symbolic FontBBox: -166, -283, 1021, 943 FontFile: true EncodingDictionary: 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