Short-term genome stability of serial Clostridium difficile ribotype 027 isolates in an experimental gut model and recurrent human disease

Copyright: © 2013 Eyre et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are creditedClostridium difficile whole genome sequencing has the potential to identify related isolates, even among otherwise indistinguishable strains, but interpretation depends on understanding genomic variation within isolates and individuals.Serial isolates from two scenarios were whole genome sequenced. Firstly, 62 isolates from 29 timepoints from three in vitro gut models, inoculated with a NAP1/027 strain. Secondly, 122 isolates from 44 patients (2–8 samples/patient) with mostly recurrent/on-going symptomatic NAP-1/027 C. difficile infection. Reference-based mapping was used to identify single nucleotide variants (SNVs).Across three gut model inductions, two with antibiotic treatment, total 137 days, only two new SNVs became established. Pre-existing minority SNVs became dominant in two models. Several SNVs were detected, only present in the minority of colonies at one/two timepoints. The median (inter-quartile range) [range] time between patients’ first and last samples was 60 (29.5–118.5) [0–561] days. Within-patient C. difficile evolution was 0.45 SNVs/called genome/year (95%CI 0.00–1.28) and within-host diversity was 0.28 SNVs/called genome (0.05–0.53). 26/28 gut model and patient SNVs were non-synonymous, affecting a range of gene targets.The consistency of whole genome sequencing data from gut model C. difficile isolates, and the high stability of genomic sequences in isolates from patients, supports the use of whole genome sequencing in detailed transmission investigations.Peer reviewe

Comparison of equipment used to measure shear properties in equine arena surfaces

The design of a novel apparatus, the Glen Withy torque tester (GWTT), for measuring horizontal shear properties in equine sport surfaces is described. Previous research has considered the effect of vertical loading on equine performance and injury but only limited discussion has concerned the grip or horizontal motion of the hoof. The horizontal support of the hoof by the surface must be sufficient to avoid excess slip without overloading the limb. The GWTT measures the torque necessary to twist an artificial hoof that is being pushed into the surface under a consistently applied vertical load. Its output was validated using a steel surface, then was used to test two sand and fibre surfaces (waxed and non-waxed) through rotations of 40–140°, and vertical loads of 157–1138 N. An Orono biomechanical surface tester (OBST) measured longitudinal shear and vertical force, whilst a traction tester measured rotational shear after being dropped onto the surfaces. A weak, but significant, linear relationship was found between rotational shear measured using the GWTT and longitudinal shear quantified using the OBST. However, only the GWTT was able to detect significant differences in shear resistance between the surfaces. Future work should continue to investigate the strain rate and non-linear load response of surfaces used in equestrian sports. Measurements should be closely tied to horse biomechanics and should include information on the maintenance condition and surface composition. Both the GWTT and the OBST are necessary to adequately characterise all the important functional properties of equine sport surfaces

A “Learning Revolution”? Investigating Pedagogic Practices around Interactive Whiteboards in British Primary Classrooms

Interactive whiteboards have been rapidly introduced into all primary schools under UK Government initiatives. These large, touch-sensitive screens, which control a computer connected to a digital projector, seem to be the first type of educational technology particularly suited for whole-class teaching and learning. Strong claims are made for their value by manufacturers and policy makers, but there has been little research on how, if at all, they influence established pedagogic practices, communicative processes and educational goals. This study has been designed to examine this issue, using observations in primary (elementary) school classrooms. It is funded by the UK Economic and Social Research Council and builds on the authors’ previous research on ICT in educational dialogues and collaborative activities

Spatial proteomics defines the content of trafficking vesicles captured by golgin tethers.

Intracellular traffic between compartments of the secretory and endocytic pathways is mediated by vesicle-based carriers. The proteomes of carriers destined for many organelles are ill-defined because the vesicular intermediates are transient, low-abundance and difficult to purify. Here, we combine vesicle relocalisation with organelle proteomics and Bayesian analysis to define the content of different endosome-derived vesicles destined for the trans-Golgi network (TGN). The golgin coiled-coil proteins golgin-97 and GCC88, shown previously to capture endosome-derived vesicles at the TGN, were individually relocalised to mitochondria and the content of the subsequently re-routed vesicles was determined by organelle proteomics. Our findings reveal 45 integral and 51 peripheral membrane proteins re-routed by golgin-97, evidence for a distinct class of vesicles shared by golgin-97 and GCC88, and various cargoes specific to individual golgins. These results illustrate a general strategy for analysing intracellular sub-proteomes by combining acute cellular re-wiring with high-resolution spatial proteomics

Capsular Typing Method for Streptococcus agalactiae Using Whole-Genome Sequence Data.

Group B streptococcus (GBS) capsular serotypes are major determinants of virulence and affect potential vaccine coverage. Here we report a whole-genome-sequencing-based method for GBS serotype assignment. This method shows strong agreement (kappa of 0.92) with conventional methods and increased serotype assignment (100%) to all 10 capsular types

Infection Inspection: using the power of citizen science for image-based prediction of antibiotic resistance in Escherichia coli treated with ciprofloxacin

Antibiotic resistance is an urgent global health challenge, necessitating rapid diagnostic tools to combat its threat. This study uses citizen science and image feature analysis to profile the cellular features associated with antibiotic resistance in Escherichia coli. Between February and April 2023, we conducted the Infection Inspection project, in which 5273 volunteers made 1,045,199 classifications of single-cell images from five E. coli strains, labelling them as antibiotic-sensitive or antibiotic-resistant based on their response to the antibiotic ciprofloxacin. User accuracy in image classification reached 66.8 ± 0.1%, lower than our deep learning model's performance at 75.3 ± 0.4%, but both users and the model were more accurate when classifying cells treated at a concentration greater than the strain’s own minimum inhibitory concentration. We used the users’ classifications to elucidate which visual features influence classification decisions, most importantly the degree of DNA compaction and heterogeneity. We paired our classification data with an image feature analysis which showed that most of the incorrect classifications happened when cellular features varied from the expected response. This understanding informs ongoing efforts to enhance the robustness of our diagnostic methodology. Infection Inspection is another demonstration of the potential for public participation in research, specifically increasing public awareness of antibiotic resistance

Depression, anxiety, and loneliness among adolescents and young adults with IBD in the UK: The role of disease severity, age of onset, and embarrassment of the condition

Purpose: Adolescents and young adults (AYA) with Inflammatory Bowel Disease (IBD) report higher depressive symptoms and anxiety compared to healthy controls, with disease severity and abdominal pain being important factors. In the current study, building on what young people had told us in our previous work, we examined whether embarrassment of the condition, social self-efficacy, and friendship quality mediated the relationship between abdominal pain and disease severity, and mental health/well-being. We also included loneliness as a component of well-being. Methods: Data on depression, anxiety, loneliness, friendship quality, social self-efficacy, and disease embarrassment were collected from 130 AYA with IBD ages 14–25years; data on disease severity and abdominal pain were taken from their medical records. Structural Equation Modeling (SEM) was used to test the relationships between the variables. Results: Using SEM, we established that higher IBD disease activity negatively impacted how AYA felt about their friendships and how embarrassed they were about their condition; embarrassment then influenced reports of mental health, including loneliness. Abdominal pain, disease onset, and social self-efficacy directly predicted internalising problems. Conclusion: In this sample of 14–25-year-old patients with IBD, specifics about the disease (severity and pain) predicted poorer mental health, suggesting discussion of mental health should be part of the clinical dialogue between patient and consultant. In addition, embarrassment about their condition increased depression, anxiety, and loneliness, mediating the relationship between disease severity and well-being. Thus, it is important to consider how perceived stigma affects those with chronic illness, and those issues should be explored in clinic

Sustaining, forming, and letting go of friendships for young people with Inflammatory Bowel Disease (IBD): A qualitative interview-based study

Inflammatory bowel disease (IBD) is an incurable, chronic, gastrointestinal condition that can constrain young people's social relationships. Few studies have specifically explored friendships of people with IBD. This qualitative, participatory study used interviews, photographs, and friendship maps to explore friendships and friendship networks of young people with IBD. An online Young Person's Advisory Group was actively engaged throughout the study. Thirty-one young people participated (n = 16 males, n = 15 female; n = 24 Crohn's disease, n = 6 ulcerative colitis, n = 1 IBD-unclassified; the mean age at study was 18.7 years; range 14-25 years). Findings present a metatheme "The importance and meaning of friendships" and three interwoven subthemes of "Sustaining friendships," "Forming new friendships," and "Letting go of friendships." Friendship was important to the young people with IBD, providing support, but associated with challenges such as disclosure. Such challenges could be mitigated by clearer conversations with clinicians about friendships and more extensive conversations about friendships and long-term conditions in education settings

“I don’t like to make a big thing out of It”: A qualitative interview-based study exploring factors affecting whether young people tell or do not tell their friends about their IBD

Inflammatory Bowel Disease (IBD) describes a group of conditions that includes Crohn’s disease and ulcerative colitis. Unlike some chronic conditions, to a greater or lesser extent, IBD is hidden from or invisible to others which enables concealment of the condition, especially when stigma is associated with the condition. Concealment or nondisclosure allows a means of identity management. Disclosure of a chronic condition is not a single event, and it is dependent on many factors. There is little literature that specifically addresses stigma and/or disclosure in relation to children and young people with IBD. An in-depth qualitative study was undertaken, framed by Interpretive Description and using interviews, friendship maps, and photographs within a participatory framework. Public and patient involvement and engagement (PPIE) was undertaken throughout (inception to dissemination) the study. Young people aged 14-25 years with IBD who had participated in the survey phase of the larger study self-selected to participate in interviews that focused broadly on friendship and feelings of social connectedness. Data were analysed using an iterative, interpretive approach. Preliminary themes were developed and these were explored further, and then tentative theoretical connections about friendship were developed. One superordinate theme focused on disclosure. Thirty-one young people (16 males, 15 females, mean age 18.7 years; 24 Crohn’s, 7 colitis) participated in the interviews (of these, five created friendship maps and six utilised photographs). Three discrete, but interlinked, themes were generated, revealing young people’s experiences of disclosure: to tell or not to tell; controlling the flow: the who, when, what, and how of telling; and reactions and responses to telling: anticipated and actual. Decisions about telling friends about having IBD are challenging for many young people. Having control over disclosure is not always possible, and the potential consequences can feel risky. However, most young people had positive experiences of disclosure and gained support from friends and romantic partners. Most young people downplayed the seriousness of their IBD, revealing some facets of their condition, aiming to sustain their self-identity. Only one young person had been given professional support to disclose. Provision of support and opportunities to discuss whether, when, who, and how to tell friends and what the risks and benefits may be is something that could be woven into an ongoing and wider person-centred dialogue between young people and health professionals within routine clinic visits

Depression, anxiety, and loneliness among adolescents and young adults with IBD in the UK: the role of disease severity, age of onset, and embarrassment of the condition

From Springer Nature via Jisc Publications RouterHistory: registration 2020-09-24, accepted 2020-09-24, online 2020-09-30, pub-electronic 2020-09-30, pub-print 2021-02Publication status: PublishedFunder: Crohn's and Colitis UK; doi: http://dx.doi.org/10.13039/501100003522; Grant(s): SP2017-2Funder: University of ManchesterAbstract: Purpose: Adolescents and young adults (AYA) with Inflammatory Bowel Disease (IBD) report higher depressive symptoms and anxiety compared to healthy controls, with disease severity and abdominal pain being important factors. In the current study, building on what young people had told us in our previous work, we examined whether embarrassment of the condition, social self-efficacy, and friendship quality mediated the relationship between abdominal pain and disease severity, and mental health/well-being. We also included loneliness as a component of well-being. Methods: Data on depression, anxiety, loneliness, friendship quality, social self-efficacy, and disease embarrassment were collected from 130 AYA with IBD ages 14–25 years; data on disease severity and abdominal pain were taken from their medical records. Structural Equation Modeling (SEM) was used to test the relationships between the variables. Results: Using SEM, we established that higher IBD disease activity negatively impacted how AYA felt about their friendships and how embarrassed they were about their condition; embarrassment then influenced reports of mental health, including loneliness. Abdominal pain, disease onset, and social self-efficacy directly predicted internalising problems. Conclusion: In this sample of 14–25-year-old patients with IBD, specifics about the disease (severity and pain) predicted poorer mental health, suggesting discussion of mental health should be part of the clinical dialogue between patient and consultant. In addition, embarrassment about their condition increased depression, anxiety, and loneliness, mediating the relationship between disease severity and well-being. Thus, it is important to consider how perceived stigma affects those with chronic illness, and those issues should be explored in clinic