Host-specific induction of Escherichia coli fitness genes during human urinary tract infection

Abstract

Uropathogenic Escherichia coli (UPEC) is the predominant etiological agent of uncomplicated urinary tract infection (UTI), manifested by inflammation of the urinary bladder, in humans and is a major global public health concern. Molecular pathogenesis of UPEC has been primarily examined using murine models of UTI. Translational research to develop novel therapeutics against this major pathogen, which is becoming increasingly antibiotic resistant, requires a thorough understanding of mechanisms involved in pathogenesis during human UTIs. Total RNA-sequencing (RNAseq) and comparative transcriptional analysis of UTI samples to the UPEC isolates cultured in human urine and laboratory medium were used to identify novel fitness genes that were specifically expressed during human infection. Evidence for UPEC genes involved in ion transport, including copper efflux, nickel and potassium import systems, as key fitness factors in uropathogenesis were generated using an experimental model of UTI. Translational application of this study was investigated by targeting Cus, a bacterial copper efflux system. Copper supplementation in drinking water reduces E. coli colonization in the urinary bladder of mice. Additionally, our results suggest that anaerobic processes in UPEC are involved in promoting fitness during UTI in humans. In summary, RNA-seq was used to establish the transcriptional signature in UPEC during naturally occurring, community acquired UTI in women and multiple novel fitness genes used by UPEC during human infection were identified. The repertoire of UPEC genes involved in UTI presented here will facilitate further translational studies to develop innovative strategies against UTI caused by UPEC.is a global public health concern, especially for women (1). In the United States alone, 7-11 million cases of UTI are reported annually resulting in expenditures of $3.5 billion (2, 3). UPEC is the predominant cause (75-95% of cases) of UTIs in otherwise healthy individuals (1). UTIs caused by UPEC are one of the most common indications for antibiotic prescription and rapid increase in antibiotic resistance in UPEC (4) requires development of next-generation therapeutic agents (5). A targeted approach that selectively diminishes in vivo fitness of pathogens has been proposed as a promising alternative to treatment with conventional antibiotics (6). The molecular mechanisms of UPEC pathogenesis have been extensively investigated, primarily using murine models (7-9). Identification of nextgeneration therapeutics against UPEC, however, requires a thorough knowledge of the fitness and virulence mechanisms involved in the pathogenesis of community-acquired UTIs in humans.Transcriptional profiling, a powerful functional genomic tool, can be used to elucidate host-pathogen interaction during infection (10, 11). UPEC represents a heterogeneous group of bacterial strains (12, 13) and DNA microarrays, based on the sequence of a pyelonephritis strain CFT073, were used in a previous study to determine UPEC genes highly expressed ...

Blocking Yersiniabactin Import Attenuates Extraintestinal Pathogenic Escherichia coli in Cystitis and Pyelonephritis and Represents a Novel Target To Prevent Urinary Tract Infection

“…Differences in gene expression exhibited by each E. coli strain in two samples (normal urine sample and UTI urine sample compared to LB) were determined by calculating the log 2 -fold change (FC) of the RPKM values. A comprehensive report of this clinical study is presented by Subashchandrabose and colleagues (25). A heat map of differential gene expression was produced in R version 2.15.1 (R Development Core Team) (26) with the package "pheatmap" (27), and histograms of transcript abundance were generated with Artemis (Wellcome Trust Sanger Institute) (28).…”

Uropathogenic enterobacteria use the yersiniabactin metallophore system to acquire nickel

“…While uropathogenic E. coli may encounter nickel toxicity in some environmental niches, nickel scarcity appears to be typical of host environments during urinary pathogenesis (9). Thus, if Ybt acted solely as an extracellular nickel ion sink, it would risk starving the cells for nutritionally important nickel ions.…”

“…We tested this hypothesis by assessing the relationship between Ni-Ybt import and the activity of [NiFe]-hydrogenase isozymes, which have been implicated in UPEC virulence (9). We utilized benzyl viologen to monitor the redox activity of [NiFe]-hydrogenase isozymes (30) in UTI89 grown with different nickel sources.…”

“…Deletion of the [NiFe]-hydrogenase-containing formate hydrogenlyase complex, which is involved in mixed-acid fermentation of glucose (24), resulted in decreased UPEC fitness in a murine UTI model (9). Nickel-dependent urease catalyzes the hydrolysis of urea to ammonia and carbon dioxide and is common in Klebsiella and Proteus, where it is recognized as a classic urovirulence factor (25).…”

Survival in amoeba—a major selection pressure on the presence of bacterial copper and zinc resistance determinants? Identification of a “copper pathogenicity island”

“…Such structures allow accumulation of Zn 2+ in the intracellular organelles followed by its utilization in biological processes specific for a given cell type. In particular, macrophages employ Zn 2+ and Cu + to attack Fe-S clusters essential for bacterial survival (Braymer and Giedroc 2014;Dupont et al 2011;Festa and Thiele 2012;Kashyap et al 2014;Macomber and Imlay 2009;Neyrolles et al 2015;Subashchandrabose et al 2014;Xu and Imlay 2012). We hypothesize that such a mechanism, where bacterial killing occurs through accumulation of Zn 2+ and Cu + in the phagosome/vacuole, originated in protozoa long before multicellular life arose and that it later evolved in eukaryotic phagocytes.…”