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  • Journal article
    Saunders P, Wu Z, Fahy WA, Stewart ID, Saini G, Smith DJF, Braybrooke R, Stock C, Renzoni EA, Johnson SR, Jenkins RG, Belvisi MG, Smith JA, Maher TM, Molyneaux PLet al., 2023,

    The burden and impact of cough in patients with idiopathic pulmonary fibrosis: an analysis of the prospective observational PROFILE study

    , Annals of the American Thoracic Society, Vol: 20, Pages: 1267-1273, ISSN: 1546-3222

    RATIONALE: Cough is a commonly reported symptom in idiopathic pulmonary fibrosis (IPF) that negatively impacts patient-reported quality of life. However, both the burden of cough at diagnosis and the behaviour of cough over time have not been systematically described in patients with IPF. OBJECTIVES: By utilising data prospectively collected as part of the PROFILE study we sought to assess cough burden and the impact that this has on quality of life within a cohort of patients with newly diagnosed IPF. We also re-examined the previously described relationship between cough and mortality and the association of cough with the MUC5B promoter polymorphism. METHODS: The PROFILE study is a multicentre, prospective, observational, longitudinal cohort study of incident IPF. Leicester cough questionnaire (LCQ) scores were recorded at baseline in 632 subjects and then repeated 6 monthly in a subset (n=216) of the cohort. RESULTS: The median LCQ at diagnosis was 16.1 (inter-quartile range 6.5). LCQ scores remained stable over the subsequent year in the majority of patients. There was a weak association between LCQ score and baseline lung function with worse cough related quality of life associating with more severe physiological impairment. Cough scores were not associated with subsequent mortality after correcting for baseline lung function. Furthermore, there was no relationship between LCQ score and MUC5B promotor polymorphism status. CONCLUSION: The burden of cough in IPF is high. Although cough is weakly associated with disease severity at baseline, cough-specific QoL as measured by the LCQ, confers no prognostic value. Cough-specific QoL burden remains relatively stable over time and does not associate with MUC5B promotor polymorphism.

  • Journal article
    Yip AYG, King OG, Omelchenko O, Kurkimat S, Horrocks V, Mostyn P, Danckert N, Ghani R, Satta G, Jauneikaite E, Davies FJ, Clarke TB, Mullish BH, Marchesi JR, McDonald JAKet al., 2023,

    Antibiotics promote intestinal growth of carbapenem-resistant Enterobacteriaceae by enriching nutrients and depleting microbial metabolites

    , Nature Communications, Vol: 14, Pages: 1-20, ISSN: 2041-1723

    The intestine is the primary colonisation site for carbapenem-resistant Enterobacteriaceae (CRE) and serves as a reservoir of CRE that cause invasive infections (e.g. bloodstream infections). Broad-spectrum antibiotics disrupt colonisation resistance mediated by the gut microbiota, promoting the expansion of CRE within the intestine. Here, we show that antibiotic-induced reduction of gut microbial populations leads to an enrichment of nutrients and depletion of inhibitory metabolites, which enhances CRE growth. Antibiotics decrease the abundance of gut commensals (including Bifidobacteriaceae and Bacteroidales) in ex vivo cultures of human faecal microbiota; this is accompanied by depletion of microbial metabolites and enrichment of nutrients. We measure the nutrient utilisation abilities, nutrient preferences, and metabolite inhibition susceptibilities of several CRE strains. We find that CRE can use the nutrients (enriched after antibiotic treatment) as carbon and nitrogen sources for growth. These nutrients also increase in faeces from antibiotic-treated mice and decrease following intestinal colonisation with carbapenem-resistant Escherichia coli. Furthermore, certain microbial metabolites (depleted upon antibiotic treatment) inhibit CRE growth. Our results show that killing gut commensals with antibiotics facilitates CRE colonisation by enriching nutrients and depleting inhibitory microbial metabolites.

  • Journal article
    Yuzbashev T, Yuzbashev E, Melkina O, Patel D, Dietz H, Bubnov D, Ledesma Amaro Ret al., 2023,

    A DNA assembly toolkit to unlock the CRISPR/Cas9 potential for metabolic engineering

    , Communications Biology, Vol: 6, ISSN: 2399-3642

    CRISPR/Cas9-based technologies are revolutionising the way we engineer microbial cells. One of the key advantages of CRISPR in strain design is that it enables chromosomal integration of marker-free DNA, eliminating laborious and often inefficient marker recovery procedures. Despite the benefits, assembling CRISPR/Cas9 editing systems is still not a straightforward process, which may prevent its use and applications. In this work, we have identified some of the main limitations of current Cas9 toolkits and designed improvements with the goal of making CRISPR technologies easier to access and implement. These include 1) A system to quickly switch between marker-free and marker-based integration constructs using both a Cre-expressing and standard Escherichia coli strains, 2) the ability to redirect multigene integration cassettes into alternative genomic loci via Golden Gate-based exchange of homology arms, 3) a rapid, simple in-vivo method to assembly guide RNA sequences via recombineering between Cas9-helper plasmids and single oligonucleotides. We combine these methodologies with well-established technologies into a comprehensive toolkit for efficient metabolic engineering using CRISPR/Cas9. As a proof of concept, we developed the YaliCraft toolkit for Yarrowia lipolytica, which is composed of a basic set of 147 plasmids and 7 modules with different purposes. We used the toolkit to generate and characterize a library of 137 promoters and to build a de novo strain synthetizing 373.8 mg/L homogentisic acid.

  • Journal article
    McNally P, Linnane B, Williamson M, Elnazir B, Short C, Saunders C, Kirwan L, David R, Kemner-Van de Corput MPC, Tiddens HAWM, Davies JC, Cox DWet al., 2023,

    The clinical impact of Lumacaftor-Ivacaftor on structural lung disease and lung function in children aged 6-11 with cystic fibrosis in a real-world setting

    , Respiratory Research, Vol: 24, Pages: 1-9, ISSN: 1465-9921

    BACKGROUND: Data from clinical trials of lumacaftor-ivacaftor (LUM-IVA) demonstrate improvements in lung clearance index (LCI) but not in FEV1 in children with Cystic Fibrosis (CF) aged 6-11 years and homozygous for the Phe508del mutation. It is not known whether LUM/IVA use in children can impact the progression of structural lung disease. We sought to determine the real-world impact of LUM/IVA on lung structure and function in children aged 6-11 years. METHODS: This real-world observational cohort study was conducted across four paediatric sites in Ireland over 24-months using spirometry-controlled CT scores and LCI as primary outcome measures. Children commencing LUM-/IVA as part of routine care were included. CT scans were manually scored with the PRAGMA CF scoring system and analysed using the automated bronchus-artery (BA) method. Secondary outcome measures included rate of change of ppFEV1, nutritional indices and exacerbations requiring hospitalisation. RESULTS: Seventy-one participants were recruited to the study, 31 of whom had spirometry-controlled CT performed at baseline, and after one year and two years of LUM/IVA treatment. At two years there was a reduction from baseline in trapped air scores (0.13 to 0.07, p = 0.016), but an increase from baseline in the % bronchiectasis score (0.84 to 1.23, p = 0.007). There was no change in overall % disease score (2.78 to 2.25, p = 0.138). Airway lumen to pulmonary artery ratios (AlumenA ratio) were abnormal at baseline and worsened over the course of the study. In 28 participants, the mean annual change from baseline LCI2.5 (-0.055 (-0.61 to 0.50), p = 0.85) measurements over two years were not significant. Improvements from baseline in weight (0.10 (0.06 to 0.15, p < 0.0001), height (0.05 (0.02 to 0.09), p = 0.002) and BMI (0.09 (0.03 to 0.15) p = 0.005) z-scores were seen with LUM/IVA treatment. The mean annual

  • Journal article
    Cardenas PA, Cox MJ, Willis-Owen SA, Moffatt MF, Cookson WO, Cooper PJet al., 2023,

    Delayed acquisition of airway commensals in antibiotic naïve children and its relationship with wheezing in rural Ecuador

    , FRONTIERS IN ALLERGY, Vol: 4
  • Journal article
    Spagnolo P, Ryerson CJJ, Guler S, Feary J, Churg A, Fontenot APP, Piciucchi S, Udwadia Z, Corte TJJ, Wuyts WAA, Johannson KAA, Cottin Vet al., 2023,

    Occupational interstitial lung diseases

    , JOURNAL OF INTERNAL MEDICINE, ISSN: 0954-6820
  • Conference paper
    Getino M, Stout R, Davies F, Jauneikaite Eet al., 2023,

    P14 Optimization of real-time sequencing for rapid detection of bacterial species and antimicrobial resistance in blood and urine infections

    , BSAC UTI Conference 2023, Publisher: Oxford University Press, ISSN: 2632-1823
  • Journal article
    Woodward RT, Bismarck A, 2023,

    Where porous polymers can make a difference

    , Express Polymer Letters, Vol: 17, Pages: 771-772, ISSN: 1788-618X
  • Journal article
    Woodward RT, Bismarck A, 2023,

    Where porous polymers can make a difference

    , EXPRESS POLYMER LETTERS, Vol: 17, Pages: 771-772, ISSN: 1788-618X
  • Journal article
    Jackson C, Stewart ID, Plekhanova T, Cunningham PS, Hazel AL, Al-Sheklly B, Aul R, Bolton CE, Chalder T, Chalmers JD, Chaudhuri N, Docherty AB, Donaldson G, Edwardson CL, Elneima O, Greening NJ, Hanley NA, Harris VC, Harrison EM, Ho L-P, Houchen-Wolloff L, Howard LS, Jolley CJ, Jones MG, Leavy OC, Lewis KE, Lone NI, Marks M, McAuley HJC, McNarry MA, Patel BV, Piper-Hanley K, Poinasamy K, Raman B, Richardson M, Rivera-Ortega P, Rowland-Jones SL, Rowlands AV, Saunders RM, Scott JT, Sereno M, Shah AM, Shikotra A, Singapuri A, Stanel SC, Thorpe M, Wootton DG, Yates T, Gisli Jenkins R, Singh SJ, Man WD-C, Brightling CE, Wain LV, Porter JC, Thompson AAR, Horsley A, Molyneaux PL, Evans RA, Jones SE, Rutter MK, Blaikley JF, PHOSP-COVID Study Collaborative Groupet al., 2023,

    Effects of sleep disturbance on dyspnoea and impaired lung function following hospital admission due to COVID-19 in the UK: a prospective multicentre cohort study

    , The Lancet Respiratory Medicine, Vol: 11, Pages: 673-684, ISSN: 2213-2600

    BACKGROUND: Sleep disturbance is common following hospital admission both for COVID-19 and other causes. The clinical associations of this for recovery after hospital admission are poorly understood despite sleep disturbance contributing to morbidity in other scenarios. We aimed to investigate the prevalence and nature of sleep disturbance after discharge following hospital admission for COVID-19 and to assess whether this was associated with dyspnoea. METHODS: CircCOVID was a prospective multicentre cohort substudy designed to investigate the effects of circadian disruption and sleep disturbance on recovery after COVID-19 in a cohort of participants aged 18 years or older, admitted to hospital for COVID-19 in the UK, and discharged between March, 2020, and October, 2021. Participants were recruited from the Post-hospitalisation COVID-19 study (PHOSP-COVID). Follow-up data were collected at two timepoints: an early time point 2-7 months after hospital discharge and a later time point 10-14 months after hospital discharge. Sleep quality was assessed subjectively using the Pittsburgh Sleep Quality Index questionnaire and a numerical rating scale. Sleep quality was also assessed with an accelerometer worn on the wrist (actigraphy) for 14 days. Participants were also clinically phenotyped, including assessment of symptoms (ie, anxiety [Generalised Anxiety Disorder 7-item scale questionnaire], muscle function [SARC-F questionnaire], dyspnoea [Dyspnoea-12 questionnaire] and measurement of lung function), at the early timepoint after discharge. Actigraphy results were also compared to a matched UK Biobank cohort (non-hospitalised individuals and recently hospitalised individuals). Multivariable linear regression was used to define associations of sleep disturbance with the primary outcome of breathlessness and the other clinical symptoms. PHOSP-COVID is registered on the ISRCTN Registry (ISRCTN10980107). FINDINGS: 2320 of 2468 participants in the PHOSP-COVID study attended

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