Integrated genomic map from uropathogenic Escherichia coli J96

Draft Genome Sequence of Uropathogenic Escherichia coli Strain J96

Escherichia coli J96 (O4:K6) was isolated from a human pyelonephritis patient. Here, we report the draft genome sequence of E. coli J96, which contains virulence genes, including adhesion factors, alpha-hemolysins, and cytotoxic necrotizing factor. J96 infects the kidney and bladder, making it an important tool for studying E. coli pathogenesis.

Difference in the regulation of IL-8 expression induced by uropathogenic E. coli between two kinds of urinary tract epithelial cells

Bacterial adherence to epithelial cells is a key virulence trait of pathogenic bacteria. The type 1 fimbriae and the P-fimbriae of uropathogenic Escherichia coli (UPEC) have both been described to be important for the establishment of urinary tract infections (UTI). To explore the interactions between the host and bacterium responsible for the different environments of UPEC invasion, we examined the effect of pH and osmolarity on UPEC strain J96 fimbrial expression, and subsequent J96-induced interleukin-8 (IL-8) expression in different uroepithelial cells. The J96 strain grown in high pH with low osmolarity condition was favorable for the expression of type 1 fimbriae; whereas J96 grown in low pH with high osmolarity condition was beneficial for P fimbriae expression. Type 1 fimbriated J96 specifically invaded bladder 5637 epithelial cells and induced IL-8 expression. On the contrary, P fimbriated J96 invaded renal 786-O epithelial cells and induced IL-8 expression effectively. Type 1 fimbriated J96-induced IL-8 induction involved the p38, as well as ERK, JNK pathways, which leads to AP-1-mediated gene expression. P fimbriated J96-induced augmentation of IL-8 expression mainly involved p38-mediated AP-1 and NF-κB transcriptional activation. These results indicate that different expression of fimbriae in J96 trigger differential IL-8 gene regulation pathways in different uroepithelial cells.

Unique DNA sequences of avian pathogenicEscherichia coliisolates as determined by genomic suppression subtractive hybridization

Genomic suppression subtractive hybridization was carried out between an avian pathogenic Escherichia coli (APEC) and an E. coli isolate from apparently healthy poultry (avian fecal E. coli or AFEC) to understand the genomic differences between APEC and AFEC and to identify potential virulence genes. In an effort to ensure that the genes identified were novel, tester and driver strains were chosen by their similarities in certain known virulence genes. In total, 24 subtractive hybridization fragments specific for APEC were obtained. Eight of the fragments were phage or plasmid related, 13 matched to chromosomal regions and three did not show homology to any known genes. We further determined the association of APEC-specific fragments with virulence by screening a collection of APEC, AFEC and human uropathogenic E. coli (UPEC) using the PCR. Chromosomally located fragments that matched to the ireA iron-responsive element gene, the tia invasion determinant gene, the ibeA invasion gene, genes encoding P pili and a gene encoding aldo/keto reductase were present at significantly higher frequencies in APEC and UPEC than in AFEC, suggesting their contribution to the virulence of extraintestinal pathogenic E. coli. No genes were found to be specific to APEC alone.

Analysis of genome plasticity in pathogenic and commensal Escherichia coli isolates by use of DNA arrays

Genomes of prokaryotes differ significantly in size and DNA composition. Escherichia coli is considered a model organism to analyze the processes involved in bacterial genome evolution, as the species comprises numerous pathogenic and commensal variants. Pathogenic and nonpathogenic E. coli strains differ in the presence and absence of additional DNA elements contributing to specific virulence traits and also in the presence and absence of additional genetic information. To analyze the genetic diversity of pathogenic and commensal E. coli isolates, a whole-genome approach was applied. Using DNA arrays, the presence of all translatable open reading frames (ORFs) of nonpathogenic E. coli K-12 strain MG1655 was investigated in 26 E. coli isolates, including various extraintestinal and intestinal pathogenic E. coli isolates, 3 pathogenicity island deletion mutants, and commensal and laboratory strains. Additionally, the presence of virulence-associated genes of E. coli was determined using a DNA "pathoarray" developed in our laboratory. The frequency and distributional pattern of genomic variations vary widely in different E. coli strains. Up to 10% of the E. coli K-12-specific ORFs were not detectable in the genomes of the different strains. DNA sequences described for extraintestinal or intestinal pathogenic E. coli are more frequently detectable in isolates of the same origin than in other pathotypes. Several genes coding for virulence or fitness factors are also present in commensal E. coli isolates. Based on these results, the conserved E. coli core genome is estimated to consist of at least 3,100 translatable ORFs. The absence of K-12-specific ORFs was detectable in all chromosomal regions. These data demonstrate the great genome heterogeneity and genetic diversity among E. coli strains and underline the fact that both the acquisition and deletion of DNA elements are important processes involved in the evolution of prokaryotes.

Pathogenicity islands of uropathogenic E. coli and the evolution of virulence

Uropathogenic Escherichia coli (UPEC) are the most important group of microorganisms responsible for urinary tract infection. UPEC differ from non-pathogenic E. coli and from other E. coli pathotypes by the production of specific virulence factors, which enable the bacteria to adhere to uroepithelial cells and to establish urinary tract infections. Besides adherence factors, toxins, 'modulins', capsules, iron uptake systems and other bacterial products contribute to the virulence of the strains. The respective genes are frequently located on large pieces of DNA called 'pathogenicity islands' (PAIs). PAIs form (unstable) regions of the genome of UPECs, which are often associated with tRNA genes. Using various molecular techniques, the functions of PAI encoded gene products have been studied. The usage of DNA arrays give answers to questions on the distribution of PAIs among various enterobacteria and on the expression of the different genes under in vitro and in vivo conditions. In addition, assumptions can be made on the evolution of these important pathogens.

Virulence factors of uropathogens

Urinary tract infections are among the most frequent infections encountered in developed countries. The vast majority of community-acquired urinary tract infections are caused by Escherichia coli. However, other bacterial species play an important role in nosocomial urinary tract infections. All these species are equipped with a variety of virulence factors. The best characterized are those from Escherichia coli. Among the first virulence factors that come into play during establishment of a urinary tract infection are adhesins. Besides their primary function as adhesin molecules several other additional functions can now be attributed to these organelles. Adhesins may also function as invasins, promote biofilm formation and transmit signals to epithelial cells resulting in inflammation. Furthermore, subunit proteins of adhesins seem to be promising vaccines. Later in infection, toxins seem to enhance virulence. However, for cytotoxic necrotizing factor type 1 this is controversial. Many virulence factors of uropathogenic bacteria are encoded by foreign DNA stretches inserted into the core genome. These pathogenicity islands or islets were obviously acquired via horizontal gene transfer creating new pathotypes more efficient in establishing infection. The role of new virulence factors and the new functions of already known virulence factors will be discussed as well as the concept of the composite genome of uropathogenic Escherichia coli.