An Investigation into the utilisation of ethanolamine by uropathogenic E. coli

Urinary tract infections (UTIs) are one of the most common bacterial infections worldwide with E. coli as the causal organism responsible for 75% of all cases. Uropathogenic E. coli (UPEC) naturally reside in the gastrointestinal tract (GI tract) and infect the urinary tract via migratory ascension of the urethra. Ethanolamine, an amino alcohol found naturally in phospholipids as phosphatidylethanolamine, can be metabolised by bacteria to be used as an alternate source of nitrogen and carbon. Within the GI tract ethanolamine provides pathogenic bacteria with a competitive advantage over the commensal bacteria. The ability of bacteria to utilise ethanolamine is dependent on the presence of the ethanolamine utilisation (eut) operon encoding enzymes and bacterial microcompartment packaging. Recent studies suggest the regulator of the eut operon, eutR, can modulate the expression of virulence factors in Enterohaemorrhagic E. coli (EHEC). Transcriptome analysis of UPEC in active UTIs has found that the eut operon is expressed within the urinary tract and confers a competitive advantage in the murine urinary tract, but the exact mechanism conferring this advantage is not known. The aim of this thesis was to investigate the utilisation of ethanolamine by UPEC. This thesis provides evidence that ethanolamine is present in the urine at concentrations of approximately 0.57mM and correlated with the expression of the eut operon in UPEC infected urine. Additionally, the ability to metabolise ethanolamine by the eut operon is conserved across UPEC in this cohort (Cork University Hospital, Cork). Ethanolamine provides UPEC with a growth advantage as a sole nitrogen source in modified M9 minimal medium and an artificial urine medium (AUM). Metabolite analysis shows that the growth advantage observed in both media correlates with ethanolamine metabolism. Expression of eut operon genes and electron microscopy evidence of bacterial microcompartment formation was found in UPEC strain U1 metabolising ethanolamine in AUM. Mutational analysis confirmed a requirement for a functional eut operon to metabolise ethanolamine and suggests that ethanolamine is utilised by UPEC as an additional carbon source. Ethanolamine provide U1 with a competitive growth advantage at 10mM concentrations in vitro. RT-PCR provides evidence that suggests ii ethanolamine regulated the expression of type 1 fimbriae in U1. In conclusion, this thesis supports the hypothesis that ethanolamine provides UPEC with a growth advantage in urine with a potential role in the pathogenicity of UTIs

Bacterial microcompartment-mediated ethanolamine metabolism in E. coli urinary tract infection

Urinary tract infections (UTIs) are common, in general caused by intestinal Uropathogenic E.coli (UPEC) ascending via the urethra. Microcompartment-mediated catabolism of ethanolamine, a host cell breakdown product, fuels competitive overgrowth of intestinal E. coli, both pathogenic enterohaemorrhagic E. coli and commensal strains. During UTI urease negative E. coli thrive, despite the comparative nutrient limitation in urine. The role of ethanolamine as a potential nutrient source during UTI is understudied. We evaluated the role of metabolism of ethanolamine as a potential nitrogen and carbon source for UPEC in the urinary tract. We analysed infected urine samples by culture, HPLC, qRT-PCR and genomic sequencing. Ethanolamine concentration in urine was comparable to the most abundant reported urinary amino acid D-serine. Transcription of the eut operon was detected in the majority of urine samples screened containing E. coli. All sequenced UPECs had conserved eut operons while metabolic genotypes previously associated with UTI (dsdCXA, metE) were mainly limited to phylogroup B2. In vitro ethanolamine was found to be utilised as a sole source of nitrogen by UPECs. Metabolism of ethanolamine in artificial urine medium (AUM) induced metabolosome formation and provided a growth advantage at the physiological levels found in urine. Interestingly, eutE (acetaldehyde dehydrogenase) was required for UPECs to utilise ethanolamine to gain a growth advantage in AUM, suggesting ethanolamine is also utilised as a carbon source. This data suggests urinary ethanolamine is a significant additional carbon and nitrogen source for infecting E. coli

BERENICE Final Analysis: Cardiac Safety Study of Neoadjuvant Pertuzumab, Trastuzumab, and Chemotherapy Followed by Adjuvant Pertuzumab and Trastuzumab in HER2-Positive Early Breast Cancer

BERENICE (NCT02132949) assessed the cardiac safety of the neoadjuvant–adjuvant pertuzumab–trastuzumab-based therapy for high-risk, HER2-positive early breast cancer (EBC). We describe key secondary objectives at final analysis. Eligible patients received dose-dense doxorubicin and cyclophosphamide q2w × 4 ➝ paclitaxel qw × 12 (Cohort A) or 5-fluorouracil, epirubicin, cyclophosphamide q3w × 4 ➝ docetaxel q3w × 4 (B) as per physician’s choice. Pertuzumab–trastuzumab (q3w) was initiated from the taxane start and continued post-surgery to complete 1 year. Median follow-up: 64.5 months. There were no new cardiac issues and a low incidence of Class III/IV heart failure (Cohort B only: one patient (0.5%) in the adjuvant and treatment-free follow-up (TFFU) periods). Fourteen patients (7.7%) had LVEF declines of ≥10% points from baseline to <50% in Cohort A, as did 20 (10.5%) in B during the adjuvant period (12 (6.2%) in A and 7 (3.6%) in B during TFFU). The five-year event-free survival rates in Cohorts A and B were 90.8% (95% CI: 86.5, 95.2) and 89.2% (84.8, 93.6), respectively. The five-year overall survival rates were 96.1% (95% CI: 93.3, 98.9) and 93.8% (90.3, 97.2), respectively. The final analysis of BERENICE further supports pertuzumab–trastuzumab-based therapies as standard of care for high-risk, HER2-positive EBC

Identification of extracolonic pathologies by computed tomographic colonography in colorectal cancer symptomatic patients

BACKGROUND & AIMS: Symptoms suggestive of colorectal cancer may originate outside the colorectum. Computed tomographic colonography (CTC) is used to examine the colorectum and abdominopelvic organs simultaneously. We performed a prospective randomized controlled trial to quantify the frequency, nature, and consequences of extracolonic findings. METHODS: We studied 5384 patients from 21 UK National Health Service hospitals referred by their family doctor for the investigation of colorectal cancer symptoms from March 2004 through December 2007. The patients were assigned randomly to groups that received the requested test (barium enema or colonoscopy, n = 3574) or CTC (n = 1810). We determined the frequency and nature of extracolonic findings, subsequent investigations, ultimate diagnosis, and extracolonic cancer diagnoses 1 and 3 years after testing patients without colorectal cancer. RESULTS: Extracolonic pathologies were detected in 959 patients by CTC (58.7%), in 42 patients by barium enema analysis (1.9%), and in no patients by colonoscopy. Extracolonic findings were investigated in 142 patients (14.2%) and a diagnosis was made for 126 patients (88.1%). Symptoms were explained by extracolonic findings in 4 patients analyzed by barium enema (0.2%) and in 33 patients analyzed by CTC (2.8%). CTC identified 72 extracolonic neoplasms, however, barium enema analysis found only 3 (colonoscopy found none). Overall, CTC diagnosed extracolonic neoplasms in 72 of 1634 patients (4.4%); 26 of these were malignant (1.6%). There were significantly more extracolonic malignancies detected than expected 1 year after examination, but these did not differ between patients evaluated by CTC (22.2/1000 person-years), barium enema (26.5/1000 person-years; P = .43), or colonoscopy (32.0/1000 person-years; P = .88). CONCLUSIONS: More than half of the patients with symptoms of colorectal cancer are found to have extracolonic pathologies by CTC analysis. However, the proportion of patients found to have extracolonic malignancies after 1 year of CTC examination is not significantly greater than after barium enema or colonoscopy examinations. International Standard Randomised Controlled Trials no: 95152621.isrctn.com

Identifying the consequences of ocean sprawl for sedimentary habitats

Extensive development and construction in marine and coastal systems is driving a phenomenon known as “ocean sprawl”. Ocean sprawl removes or transforms marine habitats through the addition of artificial structures and some of the most significant impacts are occurring in sedimentary environments. Marine sediments have substantial social, ecological, and economic value, as they are rich in biodiversity, crucial to fisheries productivity, and major sites of nutrient transformation. Yet the impact of ocean sprawl on sedimentary environments has largely been ignored. Here we review current knowledge of the impacts to sedimentary ecosystems arising from artificial structures. Artificial structures alter the composition and abundance of a wide variety of sediment-dependent taxa, including microbes, invertebrates, and benthic-feeding fishes. The effects vary by structure design and configuration, as well as the physical, chemical, and biological characteristics of the environment in which structures are placed. The mechanisms driving effects from artificial structures include placement loss, habitat degradation, modification of sound and light conditions, hydrodynamic changes, organic enrichment and material fluxes, contamination, and altered biotic interactions. Most studies have inferred mechanism based on descriptive work, comparing biological and physical processes at various distances from structures. Further experimental studies are needed to identify the relative importance of multiple mechanisms and to demonstrate causal relationships. Additionally, past studies have focused on impacts at a relatively small scale, and independently of other development that is occurring. There is need to quantify large-scale and cumulative effects on sedimentary ecosystems as artificial structures proliferate. We highlight the importance for comprehensive monitoring using robust survey designs and outline research strategies needed to understand, value, and protect marine sedimentary ecosystems in the face of a rapidly changing environment