Development of a physical activity programme for people with recently diagnosed rheumatoid arthritis

Background People with rheumatoid arthritis (RA) are less physically active (PA) than the general population and lower PA levels are associated with work disability, reduced physical function and co-morbidities. This suggests an urgent need to identify programmes that effectively promote sustainable PA to improve physical function in RA.Objectives The purpose of this research was to seek patient's views in relation to a range of potential PA programmes.Methods Focus groups were carried out with adults with RA with participants purposefully sampled to reflect a range of age and gender. Prior to commencing the research a draft interview guide was reviewed by the study Patient Research Partner and a pilot interview conducted. The interview guide was designed to explore PA support needs and experiences since diagnosis as well as motivators and facilitators to support engagement in PA. Each focus group was subsequently provided with information regarding potential PA programmes and invited to comment upon their suitability for people with a recent diagnosis of RA. Focus groups were audio recorded, transcribed and anonymised. Ethics approval for the study was obtained. Written informed consent was obtained from all participants. Thematic analysis was used to identify the main themes across the groups. Emerging themes were verified through discussion and a coding framework based on these themes developed. Themes and sub-themes were subsequently reviewed and the interpretation and analysis discussed and agreed.Results Three focus groups were conducted with 19 patients in total (15 female, 4 male); mean age (SD) 60 (±10) years; mean time (SD) since diagnosis 44 (±34) months. There was strong support for a PA programme with four key themes garnered from the focus groups:Recruitment and adherence included programme endorsement from peers and PA endorsement from health professionals; the need for support to overcome barriers to PA, such as pain and fatigue; and prompts such as text messages to improve adherence.Programme scheduling included timing with most suggesting six to 12 months following diagnosis, once a stable drug regime was established; afternoon sessions were preferred; views on frequency of sessions and duration of the programme were disparate.Programme content included support for education on relaxation and coping strategies, medication, flare, fatigue and pain; supervised exercise sessions; home exercise training; and expert physiotherapy input. Goal setting received mixed opinions with emphasis on the need to be patient-led.Programme delivery suggested group sessions were preferred by most, but not all; individual sessions in addition to the group were positively received; telephone support polarised opinion; but an accessible location was an agreed priority.Conclusions Participants supported development of a PA programme delivered at an accessible location, by physiotherapists within six to 12 months of diagnosis. Mixed views relating to delivery suggests a flexible approach may need to be developed.Disclosure of Interest None declare

Impact of early initiation versus national standard of care of antiretroviral therapy in Swaziland's public sector health system : study protocol for a stepped-wedge randomized trial

Background: There is robust clinical evidence to support offering early access to antiretroviral treatment (ART) to all HIV-positive individuals, irrespective of disease stage, to both improve patient health outcomes and reduce HIV incidence. However, as the global treatment guidelines shift to meet this evidence, it is still largely unknown if early access to ART for all (also referred to as "treatment as prevention" or " universal test and treat") is a feasible intervention in the resource-limited countries where this approach could have the biggest impact on the course of the HIV epidemics. The MaxART Early Access to ART for All (EAAA) implementation study was designed to determine the feasibility, acceptability, clinical outcomes, affordability, and scalability of offering early antiretroviral treatment to all HIV-positive individuals in Swaziland's public sector health system. Methods: This is a three-year stepped-wedge randomized design with open enrollment for all adults aged 18 years and older across 14 government-managed health facilities in Swaziland's Hhohho Region. Primary endpoints are retention and viral suppression. Secondary endpoints include ART initiation, adherence, drug resistance, tuberculosis, HIV disease progression, patient satisfaction, and cost per patient per year. Sites are grouped to transition two at a time from the control (standard of care) to intervention (EAAA) stage at each four-month step. This design will result in approximately one half of the total observation time to accrue in the intervention arm and the other half in the control arm. Our estimated enrolment number, which is supported by conservative power calculations, is 4501 patients over the course of the 36-month study period. A multidisciplinary, mixed-methods approach will be adopted to supplement the randomized controlled trial and meet the study aims. Additional study components include implementation science, social science, economic evaluation, and predictive HIV incidence modeling. Discussion: A stepped-wedge randomized design is a causally strong and robust approach to determine if providing antiretroviral treatment for all HIV-positive individuals is a feasible intervention in a resource-limited, public sector health system. We expect our study results to contribute to health policy decisions related to the HIV response in Swaziland and other countries in sub-Saharan Africa

Species classifier choice is a key consideration when analysing low-complexity food microbiome data

peer-reviewedBackground The use of shotgun metagenomics to analyse low-complexity microbial communities in foods has the potential to be of considerable fundamental and applied value. However, there is currently no consensus with respect to choice of species classification tool, platform, or sequencing depth. Here, we benchmarked the performances of three high-throughput short-read sequencing platforms, the Illumina MiSeq, NextSeq 500, and Ion Proton, for shotgun metagenomics of food microbiota. Briefly, we sequenced six kefir DNA samples and a mock community DNA sample, the latter constructed by evenly mixing genomic DNA from 13 food-related bacterial species. A variety of bioinformatic tools were used to analyse the data generated, and the effects of sequencing depth on these analyses were tested by randomly subsampling reads. Results Compositional analysis results were consistent between the platforms at divergent sequencing depths. However, we observed pronounced differences in the predictions from species classification tools. Indeed, PERMANOVA indicated that there was no significant differences between the compositional results generated by the different sequencers (p = 0.693, R2 = 0.011), but there was a significant difference between the results predicted by the species classifiers (p = 0.01, R2 = 0.127). The relative abundances predicted by the classifiers, apart from MetaPhlAn2, were apparently biased by reference genome sizes. Additionally, we observed varying false-positive rates among the classifiers. MetaPhlAn2 had the lowest false-positive rate, whereas SLIMM had the greatest false-positive rate. Strain-level analysis results were also similar across platforms. Each platform correctly identified the strains present in the mock community, but accuracy was improved slightly with greater sequencing depth. Notably, PanPhlAn detected the dominant strains in each kefir sample above 500,000 reads per sample. Again, the outputs from functional profiling analysis using SUPER-FOCUS were generally accordant between the platforms at different sequencing depths. Finally, and expectedly, metagenome assembly completeness was significantly lower on the MiSeq than either on the NextSeq (p = 0.03) or the Proton (p = 0.011), and it improved with increased sequencing depth. Conclusions Our results demonstrate a remarkable similarity in the results generated by the three sequencing platforms at different sequencing depths, and, in fact, the choice of bioinformatics methodology had a more evident impact on results than the choice of sequencer did.This research was funded by Science Foundation Ireland in the form of a centre grant (APC Microbiome Institute grant number SFI/12/RC/2273). Research in the Cotter laboratory is also funded by Science Foundation Ireland through the PI award “Obesibiotics” (11/PI/1137). Orla O’Sullivan is funded by Science Foundation Ireland through a Starting Investigator Research Grant award (13/SIRG/2160)

Knowledge co-production for Indigenous adaptation pathways: transform post-colonial articulation complexes to empower local decision-making

Co-production between scientific and Indigenous knowledge has been identified as useful to generating adaptation pathways with Indigenous peoples, who are attached to their traditional lands and thus highly exposed to the impacts of climate change. However, ignoring the complex and contested histories of nation-state colonisation can result in naïve adaptation plans that increase vulnerability. Here, through a case study in central Australia, we investigate the conditions under which co-production between scientific and Indigenous knowledge can support climate change adaptation pathways among place-attached Indigenous communities. A research team including scientists, Ltyentye Apurte Rangers and other staff from the Central Land Council first undertook activities to co-produce climate change presentations in the local Arrernte language; enable community members to identify potential adaptation actions; and implement one action, erosion control. Second, we reflected on the outcomes of these activities in order to unpack deeper influences. Applying the theory of articulation complexes, we show how ideologies, institutions and economies have linked Indigenous societies and the establishing Australian nation-state since colonisation. The sequence of complexes characterised as frontier, mission, pastoral, land-rights, community-development and re-centralisation, which is current, have both enabled and constrained adaptation options. We found knowledge co-production generates adaptation pathways when: (1) effective methods for knowledge co-production are used, based on deeply respectful partnerships, cultural governance and working together through five co-production tasks—prepare, communicate, discuss, bring together and apply; (2) Indigenous people have ongoing connection to their traditional territories to maintain their Indigenous knowledge; (3) the relationship between the Indigenous people and the nation-state empowers local decision-making and learning, which requires and creates consent, trust, accountability, reciprocity, and resurgence of Indigenous culture, knowledge and practices. These conditions foster the emergence of articulation complexes that enable the necessary transformative change from the colonial legacies. Both these conditions and our approach are likely to be relevant for place-attached Indigenous peoples across the globe in generating climate adaptation pathways

Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir

peer-reviewedKefir is a putatively health-promoting dairy beverage that is produced when a kefir grain, consisting of a consortium of microorganisms, is added to milk to initiate a natural fermentation. Here, a detailed analysis was carried out to determine how the microbial population, gene content, and flavor of three kefirs from distinct geographic locations change over the course of 24-h fermentations. Metagenomic sequencing revealed that Lactobacillus kefiranofaciens was the dominant bacterial species in kefir during early stages of fermentations but that Leuconostoc mesenteroides became more prevalent in later stages. This pattern is consistent with an observation that genes involved in aromatic amino acid biosynthesis were absent from L. kefiranofaciens but were present in L. mesenteroides. Additionally, these shifts in the microbial community structure, and associated pathways, corresponded to changes in the levels of volatile compounds. Specifically, Acetobacter spp. correlated with acetic acid; Lactobacillus spp. correlated with carboxylic acids, esters and ketones; Leuconostoc spp. correlated with acetic acid and 2,3-butanedione; and Saccharomyces spp. correlated with esters. The correlation data suggest a causal relationship between microbial taxa and flavor that is supported by observations that addition of L. kefiranofaciens NCFB 2797 increased the levels of esters and ketones whereas addition of L. mesenteroides 213M0 increased the levels of acetic acid and 2,3-butanedione. Finally, we detected genes associated with probiotic functionalities in the kefir microbiome. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein and can be applied to optimize the fermentation processes, flavors, and health-related attributes of this and other fermented foods. IMPORTANCE Traditional fermented foods represent relatively low-complexity microbial environments that can be used as model microbial communities to understand how microbes interact in natural environments. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein. In the process, the link between individual species, and associated pathways, with flavor compounds is revealed and several genes that could be responsible for the purported gut health-associated benefits of consuming kefir are identified. Ultimately, in addition to providing an important fundamental insight into microbial interactions, this information can be applied to optimize the fermentation processes, flavors, and health-related attributes of this and other fermented foods