75f887f6b9f9db9e4caf6f7002fa275c pmc_10457828.pdf dde84303ed3b8c213d8b5e0546867f9b7a02b9ef pmc_10457828.pdf 6a2d167f1235d76b0981bf4249b804ab919cd430cf677a1e968f1590103ae1c8 pmc_10457828.pdf Title: Comparative Genomic Analyses of Virulence and Antimicrobial Resistance in Citrobacter werkmanii, an Emerging Opportunistic Pathogen Subject: Citrobacter werkmanii is an emerging and opportunistic human pathogen found in developing countries and is a causative agent of wound, urinary tract, and blood infections. The present study conducted comparative genomic analyses of a C. werkmanii strain collection from diverse geographical locations and sources to identify the relevant virulence and antimicrobial resistance genes. Pangenome analyses divided the examined C. werkmanii strains into five distinct clades; the subsequent classification identified genes with functional roles in carbohydrate and general metabolism for the core genome and genes with a role in secretion, adherence, and the mobilome for the shell and cloud genomes. A maximum-likelihood phylogenetic tree with a heatmap, showing the virulence and antimicrobial genes’ presence or absence, demonstrated the presence of genes with functional roles in secretion systems, adherence, enterobactin, and siderophore among the strains belonging to the different clades. C. werkmanii strains in clade V, predominantly from clinical sources, harbored genes implicated in type II and type Vb secretion systems as well as multidrug resistance to aminoglycoside, beta-lactamase, fluoroquinolone, phenicol, trimethoprim, macrolides, sulfonamide, and tetracycline. In summary, these comparative genomic analyses have demonstrated highly pathogenic and multidrug-resistant genetic profiles in C. werkmanii strains, indicating a virulence potential for this commensal and opportunistic human pathogen. Keywords: Citrobacter; nosocomial infections; virulence; antimicrobial resistance; comparative genomics; emerging pathogens; pangenomics; whole-genome sequencing Author: José R. Aguirre-Sánchez, Beatriz Quiñones, José A. Ortiz-Muñoz, Rogelio Prieto-Alvarado, Inés F. Vega-López, Jaime Martínez-Urtaza, Bertram G. Lee and Cristóbal Chaidez Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Wed Aug 23 11:03:44 2023 CEST ModDate: Fri Aug 25 05:32:06 2023 CEST Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 17 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 6366628 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- QWPABL+VnURWPalladioL Type 1 Custom yes yes no 10 0 IYMQHR+URWPalladioL-Bold Type 1 Custom yes yes no 15 0 SSDTRV+URWPalladioL-Roma Type 1 Custom yes yes no 20 0 DBQAZG+URWPalladioL-Ital Type 1 Custom yes yes no 24 0 PZVHYC+URWPalladioL-BoldItal Type 1 Custom yes yes no 28 0 JYPLJJ+VnURWPalladioL-Bold Type 1 Custom yes yes no 32 0 SIXRFS+TimesNewRomanPS-BoldItalicMT Type 1C WinAnsi yes yes no 50 0 VIWIOF+CMSY10 Type 1 Builtin yes yes no 72 0 CAMXTK+EURM10 Type 1 Builtin yes yes no 79 0 HPMELP+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 100 0 HPMEMB+PalatinoLinotype TrueType WinAnsi yes yes no 103 0 HPMEMD+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 106 0 BOLMEN+SFRM0900 Type 1 Custom yes yes no 162 0 HPMELP+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 174 0 HPMEMB+PalatinoLinotype TrueType WinAnsi yes yes no 177 0 HPMEMD+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 180 0 HPMELP+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 227 0 HPMEMB+PalatinoLinotype TrueType WinAnsi yes yes no 230 0 HPMEMD+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 233 0 HPMELP+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 264 0 HPMEMB+PalatinoLinotype TrueType WinAnsi yes yes no 267 0 HPMEMD+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 270 0 Jhove (Rel. 1.28.0, 2023-05-18) Date: 2024-01-18 02:28:26 CET RepresentationInformation: pmc_10457828.pdf ReportingModule: PDF-hul, Rel. 1.12.4 (2023-03-16) LastModified: 2023-09-16 02:16:59 CEST Size: 6366628 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 568 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Destination: section.1 Item: Title: Materials and Methods Destination: section.2 Children: Item: Title: Bacterial Strain Isolation and Growth Conditions Destination: subsection.2.1 Item: Title: Genome Sequencing and Annotation Destination: subsection.2.2 Item: Title: Phylogenetic, Comparative Genomics, and Pangenome Analyses Destination: subsection.2.3 Item: Title: Statistical Analyses Destination: subsection.2.4 Item: Title: Results Destination: section.3 Children: Item: Title: Characterization of Citrobacter Strains from River Water Destination: subsection.3.1 Item: Title: Pangenome Analyses of C. werkmanii Strains from Diverse Sources and Locations Destination: subsection.3.2 Item: Title: Virulence and Antimicrobial Resistance Gene Identification Destination: subsection.3.3 Item: Title: Discussion Destination: section.4 Item: Title: References Destination: section.A. Info: Title: Comparative Genomic Analyses of Virulence and Antimicrobial Resistance in Citrobacter werkmanii, an Emerging Opportunistic Pathogen Author: José R. Aguirre-Sánchez, Beatriz Quiñones, José A. Ortiz-Muñoz, Rogelio Prieto-Alvarado, Inés F. Vega-López, Jaime Martínez-Urtaza, Bertram G. Lee and Cristóbal Chaidez Subject: Citrobacter werkmanii is an emerging and opportunistic human pathogen found in developing countries and is a causative agent of wound, urinary tract, and blood infections. The present study conducted comparative genomic analyses of a C. werkmanii strain collection from diverse geographical locations and sources to identify the relevant virulence and antimicrobial resistance genes. Pangenome analyses divided the examined C. werkmanii strains into five distinct clades; the subsequent classification identified genes with functional roles in carbohydrate and general metabolism for the core genome and genes with a role in secretion, adherence, and the mobilome for the shell and cloud genomes. A maximum-likelihood phylogenetic tree with a heatmap, showing the virulence and antimicrobial genes’ presence or absence, demonstrated the presence of genes with functional roles in secretion systems, adherence, enterobactin, and siderophore among the strains belonging to the different clades. C. werkmanii strains in clade V, predominantly from clinical sources, harbored genes implicated in type II and type Vb secretion systems as well as multidrug resistance to aminoglycoside, beta-lactamase, fluoroquinolone, phenicol, trimethoprim, macrolides, sulfonamide, and tetracycline. In summary, these comparative genomic analyses have demonstrated highly pathogenic and multidrug-resistant genetic profiles in C. werkmanii strains, indicating a virulence potential for this commensal and opportunistic human pathogen. 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