The Effects of Freezing on Faecal Microbiota as Determined Using MiSeq Sequencing and Culture-Based Investigations

peer-reviewedBackground High-throughput sequencing has enabled detailed insights into complex microbial environments, including the human gut microbiota. The accuracy of the sequencing data however, is reliant upon appropriate storage of the samples prior to DNA extraction. The aim of this study was to conduct the first MiSeq sequencing investigation into the effects of faecal storage on the microbiota, compared to fresh samples. Culture-based analysis was also completed. Methods Seven faecal samples were collected from healthy adults. Samples were separated into fresh (DNA extracted immediately), snap frozen on dry ice and frozen for 7 days at -80°C prior to DNA extraction or samples frozen at -80°C for 7 days before DNA extraction. Sequencing was completed on the Illumina MiSeq platform. Culturing of total aerobes, anaerobes and bifidobacteria was also completed. Results No significant differences at phylum or family levels between the treatment groups occurred. At genus level only Faecalibacterium and Leuconostoc were significantly different in the fresh samples compared to the snap frozen group (p = 0.0298; p = 0.0330 respectively). Diversity analysis indicated that samples clustered based on the individual donor, rather than by storage group. No significant differences occurred in the culture-based analysis between the fresh, snap or -80°C frozen samples. Conclusions Using the MiSeq platform coupled with culture-based analysis, this study highlighted that limited significant changes in microbiota occur following rapid freezing of faecal samples prior to DNA extraction. Thus, rapid freezing of samples prior to DNA extraction and culturing, preserves the integrity of the microbiota.Jennifer Deane is in receipt of a Teagasc Walsh Fellowship. The authors and their work were supported by the Science Foundation Ireland and funded by the Centre for Science, Engineering and Technology (SFI-CSET) grant 02/CE/B124 and by FP7 funded CFMATTERS (Cystic Fibrosis Microbiome-determined Antibiotic Therapy Trial in Exacerbations: Results Stratified, Grant Agreement no. 603038). The Alimentary Pharmabiotic Centre is a research centre funded by Science Foundation Ireland (SFI). This publication has emanated from research supported in part by a research grant from Science Foundation Ireland (SFI) under Grant Number SFI/12/RC/2273

Choosing a College Major: A Prototype Decision Support System

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Designing Heterogeneous-mHealth Apps for Cystic Fibrosis Adults

In this chapter, we will discuss the design and development of a patient passport mHealth application for Cystic Fibrosis adults from ideation to app-store release. By allowing the patients access to their own unique data, it is anticipated that it will be of benefit when travelling abroad and between CF centres. The design process followed a pipeline we developed that is informed by patient and healthcare professional input. The app structure resembles an Irish patient file and is divided into three categories: “My CF Info”, “My Medical History”, and “My Clinical Appointments”. My CF Info allows the patient to store personal information such genotype, medical team contact information, physiotherapy, allergies, and medications. My Medical History allows the user to record information such as CF renal disease, CF diabetes, and the insertion/removal of a portacath/gastrostomy tube. My Clinical Appointments allows the user to record the type of appointment (annual assessment, clinic, other) and all information that would ordinarily be inserted into a patient file such as weight, height, spirometry and other comments. Weight and lung function are also displayed in a plot graph. The app has undergone pilot testing with five CF adults before being rolled out onto the Google Play Store

Symptomatic Recovery in Miller Fisher Syndrome Parallels Vestibular–Perceptual and not Vestibular–Ocular Reflex Function

Unpleasant visual symptoms including oscillopsia and dizziness may occur when there is unexpected motion of the visual world across the subject's retina (“retinal slip”) as in an acute spontaneous nystagmus or on head movement with an acute ophthalmoplegia. In contrast, subjects with chronic ocular dysmotility, e.g., congenital nystagmus or chronic progressive external ophthalmoplegia, are typically symptom free. The adaptive processes that render chronic patients asymptomatic are obscure but may include a suppression of oscillopsia perception as well as an increased tolerance to perceived oscillopsia. Such chronic asymptomatic patients display an attenuation of vestibular-mediated angular velocity perception, implying a possible contributory role in the adaptive process. In order to assess causality between symptoms, signs (i.e., eye movements), and vestibular–perceptual function, we prospectively assessed symptom ratings and ocular-motor and perceptual vestibular function, in a patient with acute but transient ophthalmoplegia due to Miller Fisher Syndrome (as a model of visuo-vestibular adaptation). The data show that perceptual measures of vestibular function display a significant attenuation as compared to ocular-motor measures during the acute, symptomatic period. Perhaps significantly, both symptomatic recovery and normalization of vestibular–perceptual function were delayed and then occurred in a parallel fashion. This is the first report showing that symptomatic recovery of visuo-vestibular symptoms is better paralleled by vestibular–perceptual testing than vestibular–ocular reflex (VOR) measures. The findings may have implications for the understanding of patients with chronic vestibular symptoms where VOR testing is often unhelpful

Trouble in Paradise - A disabled person's right to the satisfaction of a self-defined need:Some conceptual and practical problems

This paper questions the usefulness of the rights-based approach to ameliorating the social situation of disabled people in Britain and advances two criticisms. First, that rights and self-de? ned needs have been under-theorised by disability theorists to the extent that they have insuf? ciently appreciated the problems that these approaches pose. The paper suggests that rights to appropriate resources to satisfy self-de? ned needs will generate vast numbers of competing rights claims and that the resulting tendency of rights to con? ict has been under-appreciated. Secondly, that there has been little consideration of how these con? icts might be reconciled. The ? rst two sections of the paper look at the concepts of ascribed and self-de? ned needs, respectively, whilst the ? nal one looks at some of the problems of the rights approach and some of the dif? culties of making self-de? ned need the basis of rights claims

Virtual monitoring in CF – the importance of continuous monitoring in a multi-organ chronic condition

Cystic Fibrosis (CF) is a chronic life-limiting condition that affects multiple organs within the body. Patients must adhere to strict medication regimens, physiotherapy, diet, and attend regular clinic appointments to manage their condition effectively. This necessary but burdensome requirement has prompted investigations into how different digital health technologies can enhance current care by providing the opportunity to virtually monitor patients. This review explores how virtual monitoring has been harnessed for assessment or performance of physiotherapy/exercise, diet/nutrition, symptom monitoring, medication adherence, and wellbeing/mental-health in people with CF. This review will also briefly discuss the potential future of CF virtual monitoring and some common barriers to its current adoption and implementation within CF. Due to the multifaceted nature of CF, it is anticipated that this review will be relevant to not only the CF community, but also those investigating and developing digital health solutions for the management of other chronic diseases

Radiologic imaging in cystic fibrosis: cumulative effective dose and changing trends over 2 decades

Objective: With the increasing life expectancy for patients with cystic fibrosis (CF), and a known predisposition to certain cancers, cumulative radiation exposure from radiologic imaging is of increasing significance. This study explores the estimated cumulative effective radiation dose over a 17-year period from radiologic procedures and changing trends of imaging modalities over this period. Methods: Estimated cumulative effective dose (CED) from all thoracic and extrathoracic imaging modalities and interventional radiology procedures for both adult and pediatric patients with CF, exclusively attending a nationally designated CF center between 1992-2009 for > 1 year, was determined. The study period was divided into three equal tertiles, and estimated CED attributable to all radiologic procedures was estimated for each tertile. Results: Two hundred thirty patients met inclusion criteria (2,240 person-years of follow-up; 5,596 radiologic procedures). CED was > 75 mSv for one patient (0.43%), 36 patients (15.6%) had a CED between 20 and 75 mSv, 56 patients (24.3%) had a CED between 5 and 20 mSv, and in 138 patients (60%) the CED was estimated to be between 0 and 5 mSv over the study period. The mean annual CED per patient increased consecutively from 0.39 mSv/y to 0.47 mSv/y to 1.67 mSv/y over the tertiles one to three of the study period, respectively (P < .001). Thoracic imaging accounted for 46.9% of the total CED and abdominopelvic imaging accounted for 42.9% of the CED, respectively. There was an associated 5.9-fold increase in the use of all CT scanning per patient (P < .001). Conclusions: This study highlights the increasing exposure to ionizing radiation to patients with CF as a result of diagnostic imaging, primarily attributable to CT scanning. Increased awareness of CED and strategies to reduce this exposure are needed

The altered gut microbiota in adults with cystic fibrosis

peer-reviewedBackground Cystic Fibrosis (CF) is an autosomal recessive disease that affects the function of a number of organs, principally the lungs, but also the gastrointestinal tract. The manifestations of cystic fibrosis transmembrane conductance regulator (CFTR) dysfunction in the gastrointestinal tract, as well as frequent antibiotic exposure, undoubtedly disrupts the gut microbiota. To analyse the effects of CF and its management on the microbiome, we compared the gut microbiota of 43 individuals with CF during a period of stability, to that of 69 non-CF controls using 454-pyrosequencing of the 16S rRNA gene. The impact of clinical parameters, including antibiotic therapy, on the results was also assessed. Results The CF-associated microbiome had reduced microbial diversity, an increase in Firmicutes and a reduction in Bacteroidetes compared to the non-CF controls. While the greatest number of differences in taxonomic abundances of the intestinal microbiota was observed between individuals with CF and the healthy controls, gut microbiota differences were also reported between people with CF when grouped by clinical parameters including % predicted FEV1 (measure of lung dysfunction) and the number of intravenous (IV) antibiotic courses in the previous 12 months. Notably, CF individuals presenting with severe lung dysfunction (% predicted FEV1 ≤ 40%) had significantly (p < 0.05) reduced gut microbiota diversity relative to those presenting with mild or moderate dysfunction. A significant negative correlation (−0.383, Simpson’s Diversity Index) was also observed between the number of IV antibiotic courses and gut microbiota diversity. Conclusions This is one of the largest single-centre studies on gut microbiota in stable adults with CF and demonstrates the significantly altered gut microbiota, including reduced microbial diversity seen in CF patients compared to healthy controls. The data show the impact that CF and it's management have on gut microbiota, presenting the opportunity to develop CF specific probiotics to minimise microbiota alterations.The authors and their work were supported by the Science Foundation of Ireland and funded by the Centre for Science, Engineering and Technology (SFI-CSET) grant 02/CE/B124 and by FP7 funded CFMATTERS (Cystic Fibrosis Microbiome-determined Antibiotic Therapy Trial in Exacerbations: Results Stratified, Grant Agreement no. 603038)