Characterization of genomic diversity in extraintestinal pathogenic Escherichia coli (ExPEC) and development of a diagnostic DNA microarray for the differentiation of ExPEC isolates causing urinary tract infections

Extraintestinal pathogenic Escherichia coli (ExPEC) represent a diverse group of strains of E. coli, which infect extraintestinal sites, such as the urinary tract, the bloodstream, the meninges, the peritoneal cavity, and the lungs. Urinary tract infections (UTIs) caused by uropathogenic E. coli (UPEC), the major subgroup of ExPEC, are among the most prevalent microbial diseases world wide and a substantial burden for public health care systems. UTIs are responsible for serious morbidity and mortality in the elderly, in young children, and in immune-compromised and hospitalized patients. ExPEC strains are different, both from genetic and clinical perspectives, from commensal E. coli strains belonging to the normal intestinal flora and from intestinal pathogenic E. coli strains causing diarrhea. ExPEC strains are characterized by a broad range of alternate virulence factors, such as adhesins, toxins, and iron accumulation systems. Unlike diarrheagenic E. coli, whose distinctive virulence determinants evoke characteristic diarrheagenic symptoms and signs, ExPEC strains are exceedingly heterogeneous and are known to possess no specific virulence factors or a set of factors, which are obligatory for the infection of a certain extraintestinal site (e. g. the urinary tract). The ExPEC genomes are highly diverse mosaic structures in permanent flux. These strains have obtained a significant amount of DNA (predictably up to 25% of the genomes) through acquisition of foreign DNA from diverse related or non-related donor species by lateral transfer of mobile genetic elements, including pathogenicity islands (PAIs), plasmids, phages, transposons, and insertion elements. The ability of ExPEC strains to cause disease is mainly derived from this horizontally acquired gene pool; the extragenous DNA facilitates rapid adaptation of the pathogen to changing conditions and hence the extent of the spectrum of sites that can be infected. However, neither the amount of unique DNA in different ExPEC strains (or UPEC strains) nor the mechanisms lying behind the observed genomic mobility are known. Due to this extreme heterogeneity of the UPEC and ExPEC populations in general, the routine surveillance of ExPEC is exceedingly difficult. In this project, we presented a novel virulence gene algorithm (VGA) for the estimation of the extraintestinal virulence potential (VP, pathogenicity risk) of clinically relevant ExPECs and fecal E. coli isolates. The VGA was based on a DNA microarray specific for the ExPEC phenotype (ExPEC pathoarray). This array contained 77 DNA probes homologous with known (e.g. adhesion factors, iron accumulation systems, and toxins) and putative (e.g. genes predictably involved in adhesion, iron uptake, or in metabolic functions) ExPEC virulence determinants. In total, 25 of DNA probes homologous with known virulence factors and 36 of DNA probes representing putative extraintestinal virulence determinants were found at significantly higher frequency in virulent ExPEC isolates than in commensal E. coli strains. We showed that the ExPEC pathoarray and the VGA could be readily used for the differentiation of highly virulent ExPECs both from less virulent ExPEC clones and from commensal E. coli strains as well. Implementing the VGA in a group of unknown ExPECs (n=53) and fecal E. coli isolates (n=37), 83% of strains were correctly identified as extraintestinal virulent or commensal E. coli. Conversely, 15% of clinical ExPECs and 19% of fecal E. coli strains failed to raster into their respective pathogenic and non-pathogenic groups. Clinical data and virulence gene profiles of these strains warranted the estimated VPs; UPEC strains with atypically low risk-ratios were largely isolated from patients with certain medical history, including diabetes mellitus or catheterization, or from elderly patients. In addition, fecal E. coli strains with VPs characteristic for ExPEC were shown to represent the diagnostically important fraction of resident strains of the gut flora with a high potential of causing extraintestinal infections. Interestingly, a large fraction of DNA probes associated with the ExPEC phenotype corresponded to novel DNA sequences without any known function in UTIs and thus represented new genetic markers for the extraintestinal virulence. These DNA probes included unknown DNA sequences originating from the genomic subtractions of four clinical ExPEC isolates as well as from five novel cosmid sequences identified in the UPEC strains HE300 and JS299. The characterized cosmid sequences (pJS332, pJS448, pJS666, pJS700, and pJS706) revealed complex modular DNA structures with known and unknown DNA fragments arranged in a puzzle-like manner and integrated into the common E. coli genomic backbone. Furthermore, cosmid pJS332 of the UPEC strain HE300, which carried a chromosomal virulence gene cluster (iroBCDEN) encoding the salmochelin siderophore system, was shown to be part of a transmissible plasmid of Salmonella enterica. Taken together, the results of this project pointed towards the assumptions that first, (i) homologous recombination, even within coding genes, contributes to the observed mosaicism of ExPEC genomes and secondly, (ii) besides en block transfer of large DNA regions (e.g. chromosomal PAIs) also rearrangements of small DNA modules provide a means of genomic plasticity. The data presented in this project supplemented previous whole genome sequencing projects of E. coli and indicated that each E. coli genome displays a unique assemblage of individual mosaic structures, which enable these strains to successfully colonize and infect different anatomical sites.

Acidification of lakes in Finland : regional estimates of lake chemistry and critical loads

Yhteenveto: Järvien happamoituminen Suomessa: Alueellinen vedenlaatu ja kriittinen kuormitus

Mid-urethral slings for treatment of stress urinary incontinence : long- and mid-term follow-up

Urinary incontinence is a common problem, affecting one third of the women at least at some time during their lives. The prevalence of urinary incontinence increases with advancing age, and the everyday impact of incontinence on women and on health services is enormous. Urinary incontinence is usually divided into three different subtypes, of which stress urinary incontinence (SUI) is the most common. Surgical treatment is often needed to cure SUI, and modern mid-urethral sling procedures give the possibility to cure this condition with a low risk of adverse events, a problem often associated with the so-called traditional incontinence operations. Life expectancy among women in Western countries has grown beyond 80 years of age. Long-term efficacy of treatment options for urinary incontinence therefore becomes an important issue in a world with limited eco-nomic resources. The purpose of the present study was to prospectively evaluate the long-term efficacy and safety of the first minimally invasive mid-urethral tape procedure, the Tension-free Vaginal Tape (TVT) procedure. The long-term (5-year) follow-up results of the TVT procedure as a repeat operation af-ter an unsuccessful mid-urethral tape operation were studied and the reasons for failure of the first operation were analyzed. Another purpose was to compare the original TVT procedure with a newer modification, the Tension-free Vaginal Tape Obturator (TVT-O) procedure within a multi-centre, randomized context in order to find out possible differences between these procedures re-garding efficacy and complications and the effects on symptoms of urgency. The first study of the present thesis is a prospective, Nordic, three-centre follow-up study of 90 women suffering from SUI, who were treated by means of the TVT procedure. The mean follow-up time was more than eleven years, and the study is the first to be published in connection with more than ten years of follow-up. The second study is a retrospective analysis of 26 women who were treated with a repeat TVT procedure after an unsuccessful primary mid-urethral tape procedure. The third and fourth studies concern 273 women in seven centres in Finland who were ran-domly assigned to the TVT and TVT-O procedures, the 3-year follow-up results of which are pre-sented in this thesis. After eleven years of follow-up, 90% of the women had a negative cough stress test result and a negative 24-h pad test result. The subjective cure rate measured as the women s global impression of cure was 77%, the rate of improvement 20%, and only 3% thought that the treatment had failed. No late-onset adverse effects were found. The repeat TVT procedure was successful in 75% of the cases when women who were cured and women who were significantly improved were included. The reasons for failure of the first operation could be separated into four different groups: tape material-related, operation technique-related, concomitant illness-related and a group with no identifiable reason. There were no intra-operative complications during the repeat operation. In the randomized trial comparing the TVT with the TVT-O procedure a cough stress test results were negative in 94.6% and 89.5% of the women in the two groups, respectively, after a 3-year follow-up period. There were no statistical differences in the cure rate or the rate of complications be-tween the two procedures. Symptoms of urgency were analyzed more closely and the main finding was that the prevalence of urgency symptoms decreased significantly after both mid-urethral sling procedures. The TVT operation was found to be an effective and safe procedure even after eleven years of follow-up. Long-term follow-up after a repeat TVT procedure revealed that the TVT procedure can well be considered after an unsuccessful mid-urethra tape procedure, because 75% of the patients showed significantly improvement of their incontinence. The TVT and TVT-O procedures showed no statistically significant differences in efficacy and rate of complications after three years of follow-up. In most cases these procedures alleviate preoperative symptoms of urgency and the risk of developing de novo urgency is low.

Airborne sulphur and lake water acidification in Finland.

Tiivistelmä: Ilman rikkilaskeuma ja järvien happamoituminen Suomessa.