In recent years, the role of metabolomics has become increasingly more important in the advancement of many research fields including medical studies. Due to lack of metabolomics research in the area of infectious disease and the rise in antibiotic resistance, there is a need for further studies on the modes of antibiotic action and the mechanisms of resistance of pathogenic microorganisms at the metabolome level. This study aimed to investigate effects of DNA synthesis inhibitors on the metabolome of E. coli and to develop a workflow for discrimination between E. coli isolates down to the sub-species level using a variety of methods, which can inform the choice of analytical techniques in metabolomics research. A metabolomics-based approach was used to elucidate metabolic alterations in E. coli K-12 upon challenge with trimethoprim at two pH levels (5 and 7) which mimic human urine acidity. FT-IR spectroscopy was used as a preliminary experiment to produce bacterial fingerprints and GC-MS was applied to generate global metabolic profiles in each condition. At pH 7, as the drug molecules exhibited higher permeability, stronger direct effects of the antibiotic were observed, i.e. decreased levels of nucleotides. Trehalose, an osmoprotectant, was up-regulated in these stress conditions and this up-regulation was mirrored by a decrease in glucose levels. This also correlated with up-regulation of pyruvate-related products (e.g. alanine, citrate and malate). Other off-target related effects were observed such as alterations in the levels of various amino acids upon trimethoprim challenge. This study offered a wider view of drug action at pH levels similar to healthy human urine. A high throughput FT-IR spectroscopy method was developed to discriminate between pathogenic E. coli isolates based on sequence type. This method employed a Bioscreen as a micro-culture incubator instead of traditional sample preparation (shaking flasks), which can be labour intensive and time consuming. Excluding the washing step in the protocol enabled discrimination between isolates of different sequence types. Moreover, a reproducible workflow of lipid analysis based on LC-MS was developed and applied on four pathogenic isolates with different sequence type and susceptibility to ciprofloxacin. This workflow enabled detection of a wide range of lipid classes and determination of significant alterations in lipid levels related to susceptibility to ciprofloxacin. Stressed and control isolates were also analysed using the developed Bioscreen FT-IR approach to assess phenotypic fingerprint differences, which were in line with the LC-MS-ve class distribution. Further investigation by means of four analytical platforms (FT-IR, GC-MS, LC-MS-ve and LC-MS+ve) was applied on E. coli ST131 isolates characterised using classical microbiological tests (virulence factors and metabolic tests). Procrustes transformation was used to compare between the analytical methods and the microbiological tests in terms of their capacity to discriminate between the different isolates. As indicated above, the results from FT-IR and LC-MS-ve were comparable and in line with virulence tests, while GC-MS and metabolic tests were in agreement. Complementary information generated by different analytical techniques and microbiological tests may indicate the requirement for careful selection of the method of investigation and may suggest the need to continue using a combination of methods which are applied to study different features of bacterial physiology.

Magister Pharmaceuticae - MPharm / Antibiotic resistance (ABR) is a global healthcare burden complicating the treatment of various infections. The infectious diseases burden is heavy in primary care. Urinary tract infections (UTIs) are common outpatient infections. Miscommunication in healthcare may lead to non-adherence, adverse events and fuel ABR. Labelling antibiotics should be explicit and understood by patients. Treatment of UTIs in primary care in the Western Cape is not well defined. This study’s aim is to describe the treatment of UTIs in primary care in the Cape Metropole of the Western Cape province.

Background: Gram-negative bloodstream infections (BSI) are common complications after kidney transplantation. In this cohort study, we evaluated the long-term effect of Gram-negative BSI on allograft survival in kidney transplant recipients. Methods: Among a cohort of 1820 kidney recipients who were prospectively followed at the Mayo Clinic (Rochester, MN) from January 1, 1996, to December 31, 2007, we identified 120 patients with initial episodes of Gram-negative BSI before allograft failure. Multivariable Cox proportional hazard regression was used to examine the association between Gram-negative BSI, as a time-dependent covariate, and allograft and patient survival. Results: The median age of kidney recipients was 51 years (interquartile range, 39-61 years) and 58% were men. Among patients with Gram-negative BSI, 75% had a urinary tract source of infection and Escherichia coli was the most common microorganism (50%). Gram-negative BSI after transplantation was independently associated with allograft loss due to allograft failure or death (hazard ratio [HR], 2.52; 95% confidence intervals [CI], 1.83-3.47; P<0.001), allograft failure with death-censored (HR, 3.17; 95% CI, 2.11-4.76; P<0.001) and all-cause mortality (HR, 2.25; 95% CI, 1.55-3.26; P<0.001). Conclusions: Prevention and proper management of urinary tract infections in kidney recipients is essential to reduce the risk of more serious complications, including Gram-negative BSI, that are associated with reduced allograft and patient survival.

Purpose: Ultrasonically measured intravesical prostatic protrusion may be a promising noninvasive method of assessing bladder outlet obstruction. Previous investigations of this technique focused on patients with acute urinary retention and symptomatic men identified in urology clinics, which may not reflect the distribution of intravesical prostatic protrusion in community dwelling men. Materials and Methods: In 2006 a total of 322 white men residing in Olmsted County, Minnesota underwent transrectal ultrasound examination which permitted direct measurement of intravesical prostatic protrusion. Cross-sectional associations between lower urinary tract symptoms/benign prostatic enlargement and intravesical prostatic protrusion were measured. Rapid increases in lower urinary tract symptoms/benign prostatic enlargement measures as predictors of severe intravesical prostatic protrusion were also assessed. Results: Overall 10% of these men had an intravesical prostatic protrusion of 10 mm or greater. Greater intravesical prostatic protrusion was weakly correlated with greater prostate volume (rs = 0.28), higher obstructive symptoms (rs = 0.18) and lower peak urinary flow rate (rs = -0.18). Men with the most rapidly growing prostate before intravesical prostatic protrusion measurement were 3 times more likely to have an intravesical prostatic protrusion of 10 mm or greater. Men with an intravesical prostatic protrusion of 10 mm or greater were more likely to use medications for lower urinary tract symptoms/benign prostatic enlargement compared to those with an intravesical prostatic protrusion less than 10 mm (adjusted OR 2.95, 95% CI 1.23-7.06). Conclusions: These population based data provide reference ranges for future studies of intravesical prostatic protrusion as a predictor of adverse urological outcomes. Intravesical prostatic protrusion is significantly correlated with greater prostate volume, higher obstructive symptoms and lower peak urinary flow rate, suggesting that it may have clinical usefulness in predicting the need for treatment.

El texto completo de este trabajo no está disponible en el Repositorio Académico UPC por restricciones de la casa editorial donde ha sido publicado. / We analyzed the association between antibiotic resistance and recurrent urinary tract infection (rUTI) by Escherichia coli. Susceptibility levels to 14 antimicrobial agents and the presence of extended-spectrum β-lactamases (ESBL) were established using MicroScan. Incidences of multidrug resistant (MDR), extensively drug resistant (XDR), and ESBL-producer isolates as well as rUTIs were estimated. The time to recurrence was established adjusted for number of antibiotic-resistant families and MDR as predictors of interest, respectively. Overall, 8,553 urinary tract infection (UTI) cases related to E. coli, including 963 rITU, were analyzed with levels of resistance >30% in all cases, except for amikacin, nitrofurantoin, and carbapenems. The incidence of rUTI was of 11.3%, being 46.5%, 24.3%, and 42.5% for MDR, XDR, and ESBLs, respectively. Bivariate analysis showed that rUTI was associated with age, gender, resistance to specific antimicrobials, MDR, and XDR. The number of antibiotic families tested as resistant, MDR, XDR, gender, and age were associated with time to recurrence when adjusted for number of antibiotic families, and MDR, gender, and age were related when adjusted for MDR. High rates of antibiotic resistance to the usual antibiotics was observed in E. coli causing UTI, with female sex, age, and antibiotic resistance being risk factors for the development of rUTI. / Fondo Nacional de Desarrollo Científico, Tecnológico y de Innovación Tecnológica / Revisión por pares

This dissertation aims to explore the role of patient and family engagement in the context of two current health issues: catheter-associated urinary tract infections (CAUTI) and antibiotic resistance. Chapter One contains an introduction to patient and family engagement, CAUTI, and antibiotic resistance, followed by gaps in the science, a description of the theoretical framework, and specific aims addressed in this dissertation. Chapter Two is a systematic review of existing CAUTI prevention interventions that involve patient and family engagement. Chapter Three is a study designed to meet the learning needs of parents by developing a graphically-enhanced CAUTI-prevention educational resource using participatory design methods. Chapter Four is an environmental scan that summarizes the content and format of existing resources about antibiotic resistance and antibiotic use available from children’s hospital websites across the United States. Finally, Chapter Five contains an overall summary of the findings of this dissertation, a discussion of results within the guiding theoretical framework, practice and policy implications, and suggestions for future research.

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京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第18863号 / 医博第3974号 / 新制||医||1008(附属図書館) / 31814 / 京都大学大学院医学研究科医学専攻 / (主査)教授 渡邊 直樹, 教授 岩田 想, 教授 岩井 一宏 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Yes / The cocrystal of nitrofurantoin with urea (C8H6N4O5)·(CH4N2O), a non-ionic supramolecular complex, has been studied. Nitrofurantoin (NF) is a widely used antibacterial drug for the oral treatment of infections of the urinary tract. Characterization of the cocrystal of nitrofurantoin with urea (NF–urea) was performed spectroscopically by employing FT-IR, FT- and dispersive-Raman, and CP-MAS solid-state 13C NMR techniques, along with quantum chemical calculations. With the purpose of having a better understanding of H-bonding (inter- and intra-molecular), two different models (monomer and monomer + 3urea) of the NF–urea cocrystal were prepared. The fundamental vibrational modes were characterized depending on their potential energy distribution (PED). A combined experimental and theoretical wavenumber study proved the existence of the cocrystal. The presence and nature of H-bonds present in the molecules were ascertained using quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis. As the HOMO–LUMO gap defines the reactivity of a molecule, and this gap is more for the API than the cocrystal, this implies that the cocrystal is more reactive. Global descriptors were calculated to understand the chemical reactivity of the cocrystal and NF. Local reactivity descriptors such as Fukui functions, local softness and electrophilicity indices were analysed to determine the reactive sites within the molecule. The comparison between NF–urea (monomer) and NF showed that the cocrystal has improved overall reactivity, which is affected by the increased intermolecular hydrogen bond strength. The docking studies revealed that the active sites (C[double bond, length as m-dash]O, N–H, NO2, N–N) of NF showed best binding energies of −4.89 kcal mol−1 and −5.56 kcal mol−1 for MUL and 1EGO toxin, respectively, which are bacterial proteins of Escherichia coli. This cocrystal could potentially work as an exemplar system to understand H-bond interactions in biomolecules.

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