The upper and lower airway microbiome in severe asthma

Introduction: Severe asthma is complex and immunologically heterogenous; airways infection and innate immune dysregulation may confer inhaled corticosteroid resistance and remains clinically challenging. We hypothesise that marked airway microbiome compositional shifts in severe asthma represent a ‘treatable trait’, with dominance of pathogenic species, warranting targeted therapy. Additionally, these changes are thought to be distinct in the paucibacillary lower airway vs. heavily colonised nasopharynx. Methods: We performed Oxford Nanopore metagenomic sequencing, and RT-qPCR of induced sputum (n=67), bronchoalveolar lavage (BAL;n=71) and nasal lavage (NL;n=28 paired with sputum) samples from the Wessex Severe Asthma Cohort encompassing mild/moderate/severe asthma and health. Findings were integrated with clinical and cytokine data. Key Results: A dominant pathogenic organism (H.influenzae, S.pneumoniae, M.catarrhalis) was identified in sputua of 21% of patients with severe asthma and accompanied by sputum neutrophilia and elevated type-1 cytokines (including IL-1β, IL-6, IL-8, TNF;p<0.01, unpaired t-test, Benjamini-Hochberg correction). From BAL, airways infection was identified infrequently (Severe asthma, n=1/21 H.influenzae; Mild-Moderate asthma,n=2/25 T.whipplei). Metagenomic analysis of NL demonstrated a distinct microbiome; presence of pathogenic organisms in the upper airways did not predict concurrent presence in sputum of severe asthmatics. Conclusion: Airways infection is reliably identified in sputum using metagenomic sequencing and is associated with neutrophilic inflammation. The microbiome in the upper and lower airway are distinct and ongoing work is exploring its impact on mucosal immune responses at these sites

Azithromycin versus standard care in patients with mild-to-moderate COVID-19 (ATOMIC2): an open-label, randomised trial

BACKGROUND: The antibacterial, anti-inflammatory, and antiviral properties of azithromycin suggest therapeutic potential against COVID-19. Randomised data in mild-to-moderate disease are not available. We assessed whether azithromycin is effective in reducing hospital admission in patients with mild-to-moderate COVID-19. METHODS: This prospective, open-label, randomised superiority trial was done at 19 hospitals in the UK. We enrolled adults aged at least 18 years presenting to hospitals with clinically diagnosed, highly probable or confirmed COVID-19 infection, with fewer than 14 days of symptoms, who were considered suitable for initial ambulatory management. Patients were randomly assigned (1:1) to azithromycin (500 mg once daily orally for 14 days) plus standard care or to standard care alone. The primary outcome was death or hospital admission from any cause over the 28 days from randomisation. The primary and safety outcomes were assessed according to the intention-to-treat principle. This trial is registered at ClinicalTrials.gov (NCT04381962) and recruitment is closed. FINDINGS: 298 participants were enrolled from June 3, 2020, to Jan 29, 2021. Three participants withdrew consent and requested removal of all data, and three further participants withdrew consent after randomisation, thus, the primary outcome was assessed in 292 participants (145 in the azithromycin group and 147 in the standard care group). The mean age of the participants was 45·9 years (SD 14·9). 15 (10%) participants in the azithromycin group and 17 (12%) in the standard care group were admitted to hospital or died during the study (adjusted OR 0·91 [95% CI 0·43-1·92], p=0·80). No serious adverse events were reported. INTERPRETATION: In patients with mild-to-moderate COVID-19 managed without hospital admission, adding azithromycin to standard care treatment did not reduce the risk of subsequent hospital admission or death. Our findings do not support the use of azithromycin in patients with mild-to-moderate COVID-19. FUNDING: National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford and Pfizer

Azithromycin versus standard care in patients with mild-to-moderate COVID-19 (ATOMIC2): an open-label, randomised trial.

BACKGROUND: The antibacterial, anti-inflammatory, and antiviral properties of azithromycin suggest therapeutic potential against COVID-19. Randomised data in mild-to-moderate disease are not available. We assessed whether azithromycin is effective in reducing hospital admission in patients with mild-to-moderate COVID-19. METHODS: This prospective, open-label, randomised superiority trial was done at 19 hospitals in the UK. We enrolled adults aged at least 18 years presenting to hospitals with clinically diagnosed, highly probable or confirmed COVID-19 infection, with fewer than 14 days of symptoms, who were considered suitable for initial ambulatory management. Patients were randomly assigned (1:1) to azithromycin (500 mg once daily orally for 14 days) plus standard care or to standard care alone. The primary outcome was death or hospital admission from any cause over the 28 days from randomisation. The primary and safety outcomes were assessed according to the intention-to-treat principle. This trial is registered at ClinicalTrials.gov (NCT04381962) and recruitment is closed. FINDINGS: 298 participants were enrolled from June 3, 2020, to Jan 29, 2021. Three participants withdrew consent and requested removal of all data, and three further participants withdrew consent after randomisation, thus, the primary outcome was assessed in 292 participants (145 in the azithromycin group and 147 in the standard care group). The mean age of the participants was 45·9 years (SD 14·9). 15 (10%) participants in the azithromycin group and 17 (12%) in the standard care group were admitted to hospital or died during the study (adjusted OR 0·91 [95% CI 0·43-1·92], p=0·80). No serious adverse events were reported. INTERPRETATION: In patients with mild-to-moderate COVID-19 managed without hospital admission, adding azithromycin to standard care treatment did not reduce the risk of subsequent hospital admission or death. Our findings do not support the use of azithromycin in patients with mild-to-moderate COVID-19. FUNDING: National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford and Pfizer

MR1 (in Mouse and Man)

MR1 (major histocompatibility complex (MHC)-related protein 1) is a nonpolymorphic class Ib antigen presenting molecule recognized by the innate-like mucosal-associated invariant T cell subset. MR1 is highly conserved across all mammals, implying an essential role in host defense. It presents nonprotein antigens which include precursors and derivatives from highly conserved microbial biosynthetic pathways of riboflavin and folic acid metabolism. MR1 was identified in 1995 by degenerate PCR on human chromosome 1q25. MR1 is ubiquitously expressed across tissues, at relatively high abundance, but with virtually no detectable constitutive surface expression. MR1 has a standard MHC-I fold, with α1 and α2 helices forming an exposed antigen-binding cleft, held open by several bulky side chains, with a β-sheet floor. MR1 ligands include formylpterins, naturally occurring photodegradation products of folic acid (vitamin B9), and ribityllumazines, precursors and derivatives of vitamin B2. MR1 predominantly exists in the late endoplasmic reticulum (ER), trafficking through the late endosomal and lysosomal compartments where it binds ligand, facilitated by chaperones from the MHC-II pathway: the invariant chain and HLA-DM. Diseases associated with MR1 deficiencies or polymorphisms are yet to be described, but are likely to produce predisposition to multisystem invasive infections, or chronic autoimmune inflammatory diseases

Azithromycin in viral infections

Azithromycin (AZM) is a synthetic macrolide antibiotic effective against a broad range of bacterial and mycobacterial infections. Due to an additional range of anti‐viral and anti‐inflammatory properties, it has been given to patients with the coronaviruses SARS‐CoV or MERS‐CoV. It is now being investigated as a potential candidate treatment for SARS‐CoV‐2 having been identified as a candidate therapeutic for this virus by both in vitro and in silico drug screens. To date there are no randomised trial data on its use in any novel coronavirus infection, although a large number of trials are currently in progress. In this review, we summarise data from in vitro, murine and human clinical studies on the anti‐viral and anti‐inflammatory properties of macrolides, particularly AZM. AZM reduces in vitro replication of several classes of viruses including rhinovirus, influenza A, Zika virus, Ebola, enteroviruses and coronaviruses, via several mechanisms. AZM enhances expression of anti‐viral pattern recognition receptors and induction of anti‐viral type I and III interferon responses. Of relevance to severe coronavirus‐19 disease (COVID‐19), which is characterised by an over‐exuberant innate inflammatory response, AZM also has anti‐inflammatory properties including suppression of IL‐1beta, IL‐2, TNF and GM‐CSF. AZM inhibits T cells by inhibiting calcineurin signalling, mammalian target of rapamycin activity and NFκB activation. AZM particularly targets granulocytes where it concentrates markedly in lysosomes, particularly affecting accumulation, adhesion, degranulation and apoptosis of neutrophils. Given its proven safety, affordability and global availability, tempered by significant concerns about antimicrobial stewardship, there is an urgent mandate to perform well‐designed and conducted randomised clinical trials

Biological functions of MAIT cells in tissues

Mucosal associated invariant T (MAIT) cells have a recognised innate-like capacity for antibacterial host defence, consequent on the specificity of their T cell receptor (TCR) for small molecule metabolites produced by a range of prokaryotic and fungal species, their effector memory phenotype, and their expression of cytotoxic molecules. However, recent studies have identified at least two other important functions of MAIT cells in antiviral immunity and in tissue homeostasis and repair. Each are related to distinct transcriptional programmes, which are activated differentially according to the specific immune context. Here we discuss these diverse functions, we review the evidence for the newly identified role of MAIT cells in promoting tissue repair, and we discuss emerging data pointing to the future directions of MAIT cell research including roles in cancer, in antiviral immunity and recent studies in the immune response to SARS-CoV-2 infection. Overall these studies have made us aware of the potential for pleiotropic roles of MAIT cells and related cell populations in micee and humans, and have created a simple and attractive new paradigm for regulation in barrier tissues, where antigen and tissue damage are sensed, integrated and interpreted