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Year : 2012  |  Volume : 30  |  Issue : 2  |  Page : 141-149

Pathogenomics of uropathogenic Escherichia coli

Department of Microbiology, CSM Medical University, Lucknow - 226 003, Uttar Pradesh, India

Date of Submission19-Oct-2011
Date of Acceptance08-Jan-2012
Date of Web Publication28-May-2012

Correspondence Address:
J Agarwal
Department of Microbiology, CSM Medical University, Lucknow - 226 003, Uttar Pradesh
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Source of Support: None, Conflict of Interest: None

DOI: 10.4103/0255-0857.96657

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 ~ Abstract 

Subset of faecal E. coli that can enter, colonize urinary tract and cause infection are known as uropathogenic E. coli (UPEC). UPEC strains act as opportunistic intracellular pathogens taking advantage of host susceptibility using a diverse array of virulence factors. Presence of specific virulence associated genes on genomic/pathogenicity islands and involvement of horizontal gene transfer appears to account for evolution and diversity of UPEC. Recent success in large-scale genome sequencing and comparative genomics has helped in unravelling UPEC pathogenomics. Here we review recent findings regarding virulence characteristics of UPEC and mechanisms involved in pathogenesis of urinary tract infection.

Keywords: Pathogenesis of urinary tract infection, urinary tract infections, urovirulence factors, uropathogenic E. coli

How to cite this article:
Agarwal J, Srivastava S, Singh M. Pathogenomics of uropathogenic Escherichia coli. Indian J Med Microbiol 2012;30:141-9

How to cite this URL:
Agarwal J, Srivastava S, Singh M. Pathogenomics of uropathogenic Escherichia coli. Indian J Med Microbiol [serial online] 2012 [cited 2021 Jan 19];30:141-9. Available from:

 ~ Introduction Top

Urinary tract infections (UTIs) are common bacterial infections associated with considerable morbidity and health care cost. With varied clinical spectrum of severity ranging from asymptomatic bacteriuria to cystitis and pyelonephritis to septic shock with multi organ system failure, they remain one of the most common but largely misunderstood and challenging infectious diseases seen in clinical practice. UTIs are especially problematic for women; 50-80% of women will suffer at least one episode of UTI in their lifetime and 20-50% of these women will have recurrent episodes.  Escherichia More Details coli remains the predominant uropathogen (70 to 90%) isolated from acute community-acquired uncomplicated infections in anatomically normal, unobstructed urinary tracts and is also responsible for 85% of asymptomatic bacteriuria (ABU) and for more than 60% of recurrent cystitis. [1]

Some strains of E. coli deviate from their commensal status as intestinal flora of mammals and take on a more pathogenic course with the capability to cause disease both within and outside the gut. These pathogenic strains are broadly categorized as either diarrheogenic E. coli or extra-intestinal pathogenic E. coli (ExPEC). ExPEC have retained the ability to survive in gut without consequence, but have the capacity to disseminate and colonize other host sites including blood, central nervous system and urinary tract, resulting in disease. Subsets of faecal E. coli with specific virulence factors that can colonize periurethral area, enter urinary tract and cause disease are known as uropathogenic E. coli (UPEC). This diversity among various E. coli pathotypes is due to the presence of specific virulence-associated genes usually carried by a variety of pathogenicity islands (PAIs), bacteriophages, plasmids and/or transposons. [2]

Given the flexibility in gene content and the possibility of transfer of genes among different eco or pathotypes in intestinal tract, it is vital to understand the genetic basis of their differences, and the evolution of virulence, commensalism and colonization capabilities.

 ~ Origin and Diversity of E. coli pathotypes Top

Data from comparative genomics supports pivotal role played by horizontal gene transfer (HGT) leading to the presence of distinct and variable 'genomic islands' (GIs) within the conserved 'chromosomal backbone' in several bacterial lineages of E. coli. This newly acquired DNA if beneficial may be stably integrated into the genome through the process of natural selection thus leading to bacterial evolution. This additional DNA frequently lies within known insertion 'hotspots' i.e. tRNA and tmRNA. Foreign DNA segments include chromosomally captured plasmids, bacteriophage genomes, archetypal GIs and various mosaic and degenerate elements. [2],[3]

Though ExPEC are predominant in ~20% of healthy people as they can stably colonize the host intestine; in contrast to diarrheogenic E. coli; mere gut colonization by ExPEC is not sufficient, as they have to reach an extra intestinal site in the host to cause disease. Since colonizing sites outside the gut are unlikely to provide any transmissibility advantage; so-called 'extra intestinal virulence factors' probably evolved to enhance survival in the gut and/or transmission between hosts and are therefore shared with some commensal strains and account for their diversity. [2] Thus, E. coli genome consists of a core genome and a flexible gene pool conferring pathotype or ecotype specific fitness traits. The ability of strains to 'accumulate' such fitness traits directs their virulence potential.

Comprehensive analysis of the contribution of five PAIs to urovirulence of UPEC strain 536 indicates that each island increases the strain's adaptability and fitness in the urinary tract. [4] In vivo transcriptome analysis on UPEC has shown up regulation of important virulence factors indicating role of bladder environment in inducing virulence. [5] A complex balance between the host status and the expression of virulence factors in the bacteria marks the boundary between commensalism and infection.

What makes uropathogenic E.coli

The UPEC strains belong to a restricted set of clones expressing specific lipopolysaccharide (LPS; O), capsular (K) and flagellar (H) antigens (O:K:H serotype). [2] In the late 1970s, it was recognized for the first time that E. coli strains causing UTIs typically agglutinate human erythrocytes despite the presence of mannose, mediated primarily by fimbriae. [6] Subsequently, studies have revealed that UPEC express several surface structures and secrete protein molecules some of them cytotoxic, peculiar to them.

Individual genes or clusters of genes encoding a single complete virulence factor (VF) are not enough to let bacteria cause disease, rather complementary sets of VFs together promote bacterial survival and growth within the urinary tract in the face of a strong innate immune response from host. [7] UPEC typically express an array of fimbrial and afimbrial adhesins, secreted toxins, haemolysin, iron acquisition systems, capsular polysaccharide etc. to facilitate extra intestinal survival and enable UPEC to colonize and exert cytopathic effects in urinary tract. These have been elucidated using whole-genome screening approaches, including transcriptomic, proteomic and signature-tagged mutagenesis [Table 1]. UPEC generally lack the type III secretion system to inject VFs into target host cells; used by many diarrheogenic E. coli isolates. [6],[8],[9]
Table 1: Virulence factors of uropathogenic E. coli

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Adhesive organelles promote UPEC binding and entry into the host epithelial cells within urinary tract. [10] A UPEC strain was shown to have genes for ten putative chaperone-usher pilus systems, two putative type IV pili and at least seven putative autotransporter proteins. [11] Cross-talk among pilus operons within a bacterial cell through a process known as phase-variation, triggered by environmental cues, can result in switch in expression from one pilus type to another. [12],[13] The large repertoire of pilus systems provides UPEC multiple binding specificities and ability to colonize various sites throughout the urinary tract. Flagella propel bacteria through urine and mucus layers and are shown to be involved in UPEC ascension from the bladder to the kidneys in ascending models of UTI. [14] Biofilm production is one of the several putative virulence determinants possessed by UPEC. It is a dynamic process that can bring about wide variety of physiological events like antibiotic tolerance, expression of virulence factors and increased resistance to host defence mechanisms. [15] Studies have shown that isolates collected from urine had a greater capacity to form in vitro biofilm than those collected from faeces. [16] A newly identified autotransporter protein expressed at the cell surface of UPEC strain CFT073, named UpaH is shown to contribute to biofilm formation and bladder colonization. [17]

Iron acquisition systems pilfer host iron stores for metabolic functions and seize much needed iron away from the host. Many outer membrane proteins in UPEC are part of iron transport systems or putative iron-regulating virulence proteins. [6],[8],[9],[18] The genomic analysis of UPEC strain CFT073 revealed number of characterized outer membrane iron compound receptors, siderophore biosynthesis systems and putative TonB-dependent receptors. [11] UPEC strains produce up to four different siderophores, namely enterobactin, salmochelin, aerobactin and  Yersinia More Detailsbactin. [19]

The relationship among virulence properties of E. coli, phylogenetic background and antibiotic resistance is an intricate phenomenon. B2, the most frequent biotype among UPEC, seems to be the only biotype showing a relationship between quinolone resistance (acquisition of the gyrA mutation, the most common way to acquire resistance) and low virulence due to lack of PAIs, resulting from two different mechanisms that act simultaneously as proposed by Piatti et al. [20] They further suggest that the prevalence of group B2 among both uropathogenic and commensal E. coli isolates, independent of VF carriage is due to the superior adaptability and genomic 'plasticity' of the species. The lack of fimbrial antigens is irreversible but may be appropriate where bacteria, without particular damage and through avoidance of host defences, can achieve new niches to colonize or cause infections and spread antimicrobial resistance indicating bacterial evolution.

In an individual with structural abnormalities of the urinary tract or with a catheter, organisms of low pathogenicity can cause infection and the above-described properties of the bacteria are not essential.

Genomic analysis of uropathogenic E. coli

The genome size of naturally occurring E. coli isolates ranges from approximately 4.5 to 5.5 Mb [commensal E. coli K-12 isolate MG1655 (4.64 Mb); enterohaemorrhagic E. coli strains O157:H7 Sakai (5.50 Mb); enteroaggregative E. coli strain O42 (5.36 Mb) and UPEC isolates CFT073 (5.23 Mb), 536 (4.94 Mb), UTI89 (5.07 Mb)]. [21] The observed differences in genome size of ExPEC and a commensal E. coli strain presumably reflect the requirement of more genes for survival outside the gut. Functional genomics strategy of UPEC strain UTI89 revealed that it shares 70% of its open reading frames with the benign E. coli strain MG1655. [22]

Lloyd et al. [21] have shown that of the total 5,379 genes of UPEC strain CFT073; 2,820 (52.4%) were common to 10 E. coli strains which included pyelonephritis strains (CFT204, CFT269 and CFT325), cystitis strains isolated from the urine of women with first episodes of cystitis (F3, F11, F24 and F54); fecal/commensal E. coli isolates (EFC4 and EFC9) and the laboratory-adapted faecal/commensal E. coli isolate (K-12 MG1655). Over 173 UPEC-specific genes found by comparative genomic hybridization (CGH) were present in all UPEC strains but in none of the faecal/commensal strains. When the sequences of three additionally sequenced UPEC strains (UTI89, 536 and F11) and a commensal strain (HS) were added to the analysis, 131 genes were shown to be present in all UPEC strains but in none of the faecal/commensal strains; 106 of these 131 genes were found within 22 gene clusters of 2 or more genes indicating that the genes are not randomly distributed. Recently, an Indian group has published complete genome sequence of UPEC strain NA114 with genome size of 4.935 Mb. [23] Authors found several virulence genes, including iha, sat, fimH, kpsM, iutA and malX, corresponding to the genes of E. coli CFT073; fyuA and usp etc corresponding to UPEC strain UTI89 and other virulence factors such as pap, fim and genes for iron uptake systems such as the hemin uptake system and the yersiniabactin siderophore (ybt). PCR-based analysis showed that this strain carried multiple virulence genes including sfa, aer cnf and an intact polyketide synthase (pks) island.

ABU strains, in contrast, lack essential virulence factors like P fimbriae. ABU was suggested to be caused by strains of low virulence, which do not provoke a host response and therefore cause no symptoms. Genotypic analyses contradicted this notion however, as many ABU strains carry virulence genes but fail to express them suggesting that these strains may have arisen from virulent UPEC strains but achieved long-term persistence by attenuation of virulence factors that provoke a host response [22] and the genes encoding putative virulence determinants are nonfunctional and in various states of genomic decay. [9] Successful colonization of the urinary tract by ABU requires UPEC adaptation to different nutrient availability, osmolarity, or host response; manifested as stable genomic changes resulting from genome plasticity and selection. [24] Global gene expression profiling of asymptomatic E. coli strains 83972 (prototype ABU strain that lacks defined O and K surface antigens; OR: K5: H) and VR50 (OR:K1:H) during biofilm growth in human urine by DNA microarray revealed that 417 and 355 genes were up- and down-regulated, respectively (genes involved in transcription and stress were up-regulated while the down-regulated genes were mainly involved in translation, metabolism and energy production). [16]

Although, UPEC strains differ considerably in the range and expression levels of virulence factors that can affect bacterial growth and persistence within the urinary tract, data regarding virulence characteristics of UPEC isolates from patients with different clinical manifestations of UTI like cystitis, ABU, or pyelonephritis is sparse. Aerobactin is shown to be strongly associated with pyelonephritis, cystitis and bacteraemia as opposed to ABU or faecal strains. [6] The entire length of the urinary tract is iron limiting, but anatomical variations from urethra to kidneys possibly offer considerable differences in iron source availability. Garcia et al. suggested that iron receptors of UPEC possibly provide niche specificity to colonize distinct sites within the urinary tract. [25] Haeme uptake, for example, is important consistently for kidney colonization and only rarely for bladder infection. In contrast, IutA-mediated aerobactin utilization may contribute more significantly to bladder colonization than kidney infection.

Moreno et al. have shown some factors such as P fimbriae (especially allele II of papG) to be critical for reaching the kidney and toxins cnf1 and S and/or FIC fimbriae for producing urosepsis; whereas both the uroseptic and the pyelonephritic isolates exhibited similar prevalence of the malX, papA, fimH and kpsMTII genes. [26]

Pathogenesis of urinary tract infection

It is believed that primary reservoir of UPEC isolates is within the human intestinal tract, as the isolate responsible for UTI in a given individual on clonal analysis often matches rectal isolates from the same person. Two important routes by which bacteria can invade and spread within the urinary tract are the ascending and haematogenous pathways, while lymphatic spread of infection to the urinary tract with any regularity has little evidence to support. [27]

Haematogenous route

Infection of the renal parenchyma by blood-borne organisms in humans is less common as compared to the ascending route. In patient with bacteraemia or endocarditis caused by a Gram-positive organism, abscess can be present in kidneys. Infection of the kidney with Gram-negative bacilli though is uncommon by the haematogenous route.

Ascending route

The widely accepted paradigm of infection is the ascension of bacteria from the gut microbiota to the vagina and then the bladder i.e. the faecal-perineal-urethral pathway and rectal flora serving as reservoir for the strains infecting the urinary tract. [28],[29] Colonization of the vaginal introitus and periuretheral area with E. coli seems to be one of the critical initial steps in the pathogenesis. [27],[30] The short urethra in females and its proximity to the vulvar and perineal areas makes faecal contamination likely. Uropathogens gain entry into the bladder, by means of the urethral massage that may accompany sexual intercourse. Once the bacteria ascend into the bladder, they may multiply and pass up the ureter, particularly if vesicoureteral reflux is present, and then to the renal parenchyma. The subsequent development of infection depends upon the particular organism, the inoculum size and the adequacy of host defences.

The majority of recent research on the pathogenesis of uncomplicated UTI points to the 'special pathogenicity' of UTI-causing E. coli, i.e. the role of putative virulence genes on UPEC. [6],[29] Researchers have demonstrated that intestinal colonization with UPEC is critical to the development of a UTI. [28],[30],[31] A competing, 'prevalence' hypothesis suggests that UTI occurs when ordinary faecal E. coli are in the right place at the right time in sufficient numbers to enter the urinary tract and cause infection by simple mass action. [29],[31] A pathotypic and phenotypic comparison of concurrent urinary and rectal isolates however favoured former. [32] Moreno et al. [29] suggest that special pathogenicity is the primary force underlying UTI, but in some women, high prevalence of relatively low virulence E. coli strains in the faecal reservoir may cause UTI.

Experimental studies on UPEC in murine models show that type I fimbriae, capped by adhesin fimH, promote bacterial binding with superficial bladder epithelial cells (facet cells). [33],[34] The binding seems to get tighter when subjected to the shear forces of urine; [35] later, UPEC invade the facet cells. Once inside, UPEC are trafficked into membrane-bound, acidic compartments with features similar to late endosome or lysosomes. [34] In their intracellular niche, UPEC avoid the clearing actions of immune cells and antibiotics. Blango and Mulvey [36] effectively demonstrated that antibiotics concentrations far exceeding minimal inhibitory doses in the urine specimens were ineffective in eradicating UPEC reservoirs from bladder tissues. Inside the facet cells, UPEC activates an intricate cascade (elucidated using scanning and transmission electron microscopy, immune-histochemistry and time-lapse video-microscopy in a murine model). [7],[37],[38] This includes interaction of type 1 pili with uroplakins, zippering of facet cells around invading UPEC and formation of intracellular bacterial community (IBC). Anderson et al., in murine model demonstrated the requirement for K1 polysaccharide in IBC development; aberrant sialic acid accumulation, resulting from disruption of K1 capsule assembly, produced defect in intracellular proliferation and IBC development. [39] Thus, demonstrating the complex but important role of UPEC capsular polysaccharide and sialic acid signalling during multiple stages of UTI pathogenesis.

During IBC development, fast-growing, rod-shaped bacteria mature into slower growing, highly organized biofilm-like communities consisting of several thousands of coccoid bacteria, filling most of the facet cell cytoplasm and causing luminal protrusions termed pods. Bacteria later switch to a motile rod-shaped phenotype and those on the periphery get detached and flux out spreading within the urinary tract. Re-entry of these fluxed bacteria into the IBC developmental cascade is associated with slower kinetics. Ultimately, bacteria stops replicating and a dormant reservoir is established in the bladder tissue that, in response to unknown signals can re-activate and produce recurrent infection. [7],[37],[40]

Host risk factors in urinary tract infection

Several defence mechanisms are employed by the host to eliminate microbes that gain entry to the bladder including high urine flow rate, voiding frequency, urine osmolality, pH and organic acids. Urine has several inhibitors of bacterial adherence (bladder mucopolysaccharides, secretory immunoglobulin A; secreted proteins that bind to fimbrial adhesins on the bacterial wall, prostatic secretions) and inflammatory response mediated by PMNs and cytokines help in bacterial elimination. [27]

Some factors which predispose young women to UTI include short urethra, sexual intercourse, lack of post-coital voiding, diaphragm use (manipulation involved in its placement on the cervix may promote bacterial colonization) and spermicide use (increases vaginal pH and is toxic to the lactobacilli) by increasing adherence of E. coli to vaginal epithelial cells. [41] Estrogen deficiency is recognized as a risk factor for recurrent UTIs in postmenopausal women because vaginal flora changes and protective lactobacilli are replaced by E. coli and other uropathogens. [42]

Host immune response to infection by uropathogenic E. coli

A vital step in pathogenesis of UTI is the activation of host immune response leading to the effector phase involved in bacterial clearance. [43],[44] Host innate immune response is triggered in reaction to the breach by UPEC into the normally sterile urinary tract. It is a rapid and highly potent process often involving Toll like receptors (TLRs) which recognize various microbial products and launch signalling pathways eventually leading to pathogen clearance from the host and establishing a memory response for future attacks. [44]

Cirl et al. [45] have reported a secreted toxin (Tcps) in uropathogenic E. coli CFT073, containing a Toll/IL1 like receptor domain that inhibits MyD88 (key TLR signalling adaptor)-dependent cytokine secretion in uroepithelial cell culture. This weakens the innate immune responses leading to an increase in the severity of UTIs in humans. The effector phase depends on CXCL8/ CXCR1-directed migration of neutrophils, cytokine production, exfoliation of infected bladder epithelial cells and removal of remaining inflammatory cells and bacteria. UPEC evades recognition of 'pattern recognition receptors', thus decreasing innate immune response by uroepithelial cells. This results in inhibition of the proinflammatory and prosurvival NF-κB pathway that directs cytokine production. [10],[46] During the course, reactive nitrogen and oxygen species generated as part of host response also contribute in limiting the infection. [10],[46] NO-detoxifying enzyme flavohaemoglobin produced by UPEC helps protect it from nitrosative stress and may form an attractive target for newer therapeutic strategies for UTI. [47] Li et al. showed that a component of the DNA damage repair regulon, SulA, is essential for UPEC virulence in a mouse model for human UTI, since epithelial cells produce sufficient levels of DNA damaging agents. [48] LexA and RecA coordinate various operons for repair of DNA damage in UPEC.

Infection of the urinary tract by UPEC also induces adaptive immune responses, though existing knowledge regarding this is limited. Severe combined immunodeficient mice exhibit increased susceptibility to infection with UPEC, indicating that T- and B-cell-mediated immunity contributes considerably to the clearance of infecting bacteria (19). Factors involved in host response to UPEC and the mechanisms by which UPEC influences these responses have been reviewed in detail by Sivick and Mobley. [49]

 ~ Conclusion and Future Prospects Top

Recent achievements in large-scale genome sequencing, comparative genomics and molecular epidemiology have helped unravel current challenges of E. coli pathogenomics and to achieve insight into the in vivo significance of genome dynamics.

A few fundamental questions though, still linger. Large number of genes in the CFT073 genome, particularly those shown to be UPEC specific, well suggest that many urovirulence factors remain uncharacterized; besides, information on specific urovirulent genetic profile of UPEC isolates from patients with different clinical manifestations of UTI or the association between particular determinants and invasiveness in clinical condition is limited. [21],[50],[51] Most of the information on pathogenomics is derived from murine models, and it is unclear how gene expression of UPEC in these animal models compares with that during UTI in humans. [5] It would also be interesting to have more UPEC-specific genomic data from Indian isolates and study geographical variation if any. [52][59]

 ~ References Top

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