Group-Specific Gene Expression Profiles from Diverse Phylogroups Reveals Common and coli Escherichia mRNA Profiling of Uropathogenic In Vivo 2014

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 UTIassociated 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. Received 17 March 2014 Accepted 10 June 2014 Published 5 August 2014 Citation Bielecki P, Muthukumarasamy U, Eckweiler D, Bielecka A, Pohl S, Schanz A, Niemeyer U, Oumeraci T, von Neuhoff N, Ghigo J-M, Häussler S. 2014. In vivo mRNA profiling of uropathogenic Escherichia coli from diverse phylogroups reveals common and group-specific gene expression profiles. mBio 5(4):e01075-14. doi:10.1128/mBio.01075-14. Editor Scott Hultgren, Washington University School of Medicine Copyright © 2014 Bielecki et al. This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited. Address correspondence to Susanne Häussler, susanne.haeussler@twincore.de. To successfully thrive in the host environment during the course of an infection, pathogens have to rapidly adapt to the specific conditions encountered. Thereby, a key to understanding microbial pathogenesis lies in knowledge of which genes are expressed to initiate and maintain the infection and of the global impact of the host environment on the transcriptional profile of the pathogen (1). Urinary tract infections (UTI) are one of the most common bacterial infections worldwide, and most of them (over 80%) are caused by uropathogenic Escherichia coli (UPEC) (2). It is widely accepted that UPEC strains originate from the distal gut microbiota where they mostly behave as commensals (3), although UPEC strains are armed with extra virulence genes (4). Those virulence genes are often present on strain-specific pathogenicity islands (PAIs), which are clusters of virulencerelated genes (5–7). PAIs are diverse in content and genome location and, as more sequence information of more examples of the islands accumulates, greater insights into their role in disease can be expected (8, 9). UTI is recognized as presence of the bacteria in urine (bacteriuria). During the course of infection, bacterial cells are attaching to human epithelial cells, utilizing chaperone usher (CU) fimbriae that contain adhesins on their tips (10). The prototypical CU type I fimbriae adhesion can lead to intracellular invasion of bladder epithelial cells (11). UPEC strains are known to enter the cytoplasm and form biofilm-like structures called intracellular bacterial communities (IBC) (12). After maturation of IBC, the UPEC cells can disperse into urine, or as part of the host response the infected epithelial cells may be exfoliated and released into urine. RESEARCH ARTICLE July/August 2014 Volume 5 Issue 4 e01075-14 ® mbio.asm. org 1 m b.asm . rg on N ovem er 5, 2014 P ubished by m b.asm . rg D ow nladed fom Exfoliated cells are replaced with transition epithelial cells, which may be as well invaded by UPEC, where it forms quiescent intracellular reservoirs (QIR) characterized by their persistence and antibiotic resistance (13). In vitro studies and various animal models have been valuable for exploring UPEC pathogenesis (14, 15) and have led to significant advances in understanding key pathogenicity mechanisms (16–22). Knowledge of UPEC gene expression during naturally occurring UTI will further add to the full understanding of microbial pathogenesis of this widespread bacterial pathogen. Indeed, investigation of complex transcriptional adaptation processes of UPECs to the human host is expected to uncover key regulatory components and to provide unique insight into bacterial pathogenicity (23). Furthermore, the identification of E. coli virulence genes associated with UTIs is potentially valuable in differentiating UPEC from nonuropathogenic E. coli and might lead to the introduction of virulence typing strategies into clinical microbiol-