title: In vivo mRNA profiling of uropathogenic Escherichia coli from diverse phylogroups reveals common and group-specific gene expression profiles.
abstract: mRNA profiling of pathogens during the course of human infections gives detailed information on the expression levels of relevant genes that drive pathogenicity and adaptation and at the same time allows for the delineation of phylogenetic relatedness of pathogens that cause specific diseases. In this study, we used mRNA sequencing to acquire information on the expression of Escherichia coli pathogenicity genes during urinary tract infections (UTI) in humans and to assign the UTI-associated E. coli isolates to different phylogenetic groups. Whereas the in vivo gene expression profiles of the majority of genes were conserved among 21 E. coli strains in the urine of elderly patients suffering from an acute UTI, the specific gene expression profiles of the flexible genomes was diverse and reflected phylogenetic relationships. Furthermore, genes transcribed in vivo relative to laboratory media included well-described virulence factors, small regulatory RNAs, as well as genes not previously linked to bacterial virulence. Knowledge on relevant transcriptional responses that drive pathogenicity and adaptation of isolates to the human host might lead to the introduction of a virulence typing strategy into clinical microbiology, potentially facilitating management and prevention of the disease. Importance: Urinary tract infections (UTI) are very common; at least half of all women experience UTI, most of which are caused by pathogenic Escherichia coli strains. In this study, we applied massive parallel cDNA sequencing (RNA-seq) to provide unbiased, deep, and accurate insight into the nature and the dimension of the uropathogenic E. coli gene expression profile during an acute UTI within the human host. This work was undertaken to identify key players in physiological adaptation processes and, hence, potential targets for new infection prevention and therapy interventions specifically aimed at sabotaging bacterial adaptation to the human host.
authors.affiliation: Institute for Molecular Bacteriology, Twincore, Centre for Clinical and Experimental Infection Research, A Joint Venture of the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany.
authors.forename: Piotr
authors.initials: P
authors.lastname: Bielecki
authors.forename: Uthayakumar
authors.initials: U
authors.lastname: Muthukumarasamy
authors.forename: Denitsa
authors.initials: D
authors.lastname: Eckweiler
authors.forename: Agata
authors.initials: A
authors.lastname: Bielecka
authors.forename: Sarah
authors.initials: S
authors.lastname: Pohl
authors.affiliation: Private Practice, Salzgitter, Germany.
authors.forename: Ansgar
authors.initials: A
authors.lastname: Schanz
authors.affiliation: Private Practice, Wolfenbuettel, Germany.
authors.forename: Ute
authors.initials: U
authors.lastname: Niemeyer
authors.affiliation: Institute of Cell and Molecular Pathology, Hannover Medical School (MHH), Hannover, Germany.
authors.forename: Tonio
authors.initials: T
authors.lastname: Oumeraci
authors.affiliation: Institute of Cell and Molecular Pathology, Hannover Medical School (MHH), Hannover, Germany.
authors.forename: Nils
authors.initials: N
authors.lastname: von Neuhoff
authors.affiliation: Institute Pasteur, Unité de Génétique des Biofilms, Paris, France.
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Ghigo
authors.affiliation: susanne.haeussler@twincore.de.
authors.forename: Susanne
authors.initials: S
authors.lastname: Häussler
mesh_terms: D000368:Aged; D029968:Escherichia coli Proteins / Q000235:genetics; D005260:Female; D006801:Humans; D008297:Male; D008875:Middle Aged; D010802:Phylogeny; D012333:RNA, Messenger / Q000235:genetics*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D014552:Urinary Tract Infections / Q000382:microbiology; D056689:Uropathogenic Escherichia coli / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity; D014774:Virulence / Q000235:genetics; D037521:Virulence Factors / Q000235:genetics
chemical_list: D029968:Escherichia coli Proteins; D012333:RNA, Messenger; D037521:Virulence Factors
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