Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii

We acknowledge the Broad Institute Sequencing Platform and Imperial College London for generating the DNA sequence described here (and R265 Illumina sequences described previously [4]). We thank Sinéad Chapman for coordinating sequencing at the Broad Institute and Margaret Priest for assistance in submitting assemblies to NCBI. This project was supported by the National Human Genome Research Institute, grant no. U54HG003067. R.A.F. is supported by the Wellcome Trust. R.C.M. is supported by the Lister Institute for Preventive Medicine, the Medical Research Council UK, and the European Research Council.Peer reviewedPublisher PD

Genomics of Loa loa, a Wolbachia-free filarial parasite of humans

Loa loa, the African eyeworm, is a major filarial pathogen of humans. Unlike most filariae, Loa loa does not contain the obligate intracellular Wolbachia endosymbiont. We describe the 91.4 Mb genome of Loa loa, and the genome of the related filarial parasite Wuchereria bancrofti, and predict 14,907 Loa loa genes based on microfilarial RNA sequencing. By comparing these genomes to that of another filarial parasite, Brugia malayi, and to several other nematode genomes, we demonstrate synteny among filariae but not with non-parasitic nematodes. The Loa loa genome encodes many immunologically relevant genes, as well as protein kinases targeted by drugs currently approved for humans. Despite lacking Wolbachia, Loa loa shows no new metabolic synthesis or transport capabilities compared to other filariae. These results suggest that the role played by Wolbachia in filarial biology is more subtle than previously thought and reveal marked differences between parasitic and non-parasitic nematodes

Emergence of Epidemic Multidrug-Resistant Enterococcus faecium from Animal and Commensal Strains

Peer reviewe

Tracing Genetic Exchange and Biogeography of Cryptococcus neoformans var. grubii at the Global Population Level

Cryptococcus neoformans var. grubii is the causative agent of cryptococcal meningitis, a significant source of mortality in immunocompromised individuals, typically human immunodeficiency virus/AIDS patients from developing countries. Despite the worldwide emergence of this ubiquitous infection, little is known about the global molecular epidemiology of this fungal pathogen. Here we sequence the genomes of 188 diverse isolates and characterize the major subdivisions, their relative diversity, and the level of genetic exchange between them. While most isolates of C. neoformans var. grubii belong to one of three major lineages (VNI, VNII, and VNB), some haploid isolates show hybrid ancestry including some that appear to have recently interbred, based on the detection of large blocks of each ancestry across each chromosome. Many isolates display evidence of aneuploidy, which was detected for all chromosomes. In diploid isolates of C. neoformans var. grubii (serotype AA) and of hybrids with C. neoformans var. neoformans (serotype AD) such aneuploidies have resulted in loss of heterozygosity, where a chromosomal region is represented by the genotype of only one parental isolate. Phylogenetic and population genomic analyses of isolates from Brazil reveal that the previously “African” VNB lineage occurs naturally in the South American environment. This suggests migration of the VNB lineage between Africa and South America prior to its diversification, supported by finding ancestral recombination events between isolates from different lineages and regions. The results provide evidence of substantial population structure, with all lineages showing multi-continental distributions; demonstrating the highly dispersive nature of this pathogen

The Dynamic Genome and Transcriptome of the Human Fungal Pathogen Blastomyces and Close Relative Emmonsia

Three closely related thermally dimorphic pathogens are causal agents of major fungal diseases affecting humans in the Americas: blastomycosis, histoplasmosis and paracoccidioidomycosis. Here we report the genome sequence and analysis of four strains of the etiological agent of blastomycosis, Blastomyces, and two species of the related genus Emmonsia, typically pathogens of small mammals. Compared to related species, Blastomyces genomes are highly expanded, with long, often sharply demarcated tracts of low GC-content sequence. These GC-poor isochore-like regions are enriched for gypsy elements, are variable in total size between isolates, and are least expanded in the avirulent B. dermatitidis strain ER-3 as compared with the virulent B. gilchristii strain SLH14081. The lack of similar regions in related species suggests these isochore-like regions originated recently in the ancestor of the Blastomyces lineage. While gene content is highly conserved between Blastomyces and related fungi, we identified changes in copy number of genes potentially involved in host interaction, including proteases and characterized antigens. In addition, we studied gene expression changes of B. dermatitidis during the interaction of the infectious yeast form with macrophages and in a mouse model. Both experiments highlight a strong antioxidant defense response in Blastomyces, and upregulation of dioxygenases in vivo suggests that dioxide produced by antioxidants may be further utilized for amino acid metabolism. We identify a number of functional categories upregulated exclusively in vivo, such as secreted proteins, zinc acquisition proteins, and cysteine and tryptophan metabolism, which may include critical virulence factors missed before in in vitro studies. Across the dimorphic fungi, loss of certain zinc acquisition genes and differences in amino acid metabolism suggest unique adaptations of Blastomyces to its host environment. These results reveal the dynamics of genome evolution and of factors contributing to virulence in Blastomyces.Author SummaryDimorphic fungal pathogens including Blastomyces are the cause of major fungal diseases in North and South America. The genus Emmonsia includes species infecting small mammals as well as a newly emerging pathogenic species recently reported in HIV-positive patients in South Africa. Here, we synthesize both genome sequencing of four isolates of Blastomyces and two species of Emmonsia as well as deep sequencing of Blastomyces RNA to draw major new insights into the evolution of this group and the pathogen response to infection. We investigate the trajectory of genome evolution of this group, characterizing the phylogenetic relationships of these species, a remarkable genome expansion that formed large isochore-like regions of low GC content in Blastomyces, and variation of gene content, related to host interaction, among the dimorphic fungal pathogens. Using RNA-Seq, we profile the response of Blastomyces to macrophage and mouse pulmonary infection, identifying key pathways and novel virulence factors. The identification of key fungal genes involved in adaptation to the host suggests targets for further study and therapeutic intervention in Blastomyces and related dimorphic fungal pathogens

Convalescent plasma in patients admitted to hospital with COVID-19 (RECOVERY): a randomised controlled, open-label, platform trial

SummaryBackground Azithromycin has been proposed as a treatment for COVID-19 on the basis of its immunomodulatoryactions. We aimed to evaluate the safety and efficacy of azithromycin in patients admitted to hospital with COVID-19.Methods In this randomised, controlled, open-label, adaptive platform trial (Randomised Evaluation of COVID-19Therapy [RECOVERY]), several possible treatments were compared with usual care in patients admitted to hospitalwith COVID-19 in the UK. The trial is underway at 176 hospitals in the UK. Eligible and consenting patients wererandomly allocated to either usual standard of care alone or usual standard of care plus azithromycin 500 mg once perday by mouth or intravenously for 10 days or until discharge (or allocation to one of the other RECOVERY treatmentgroups). Patients were assigned via web-based simple (unstratified) randomisation with allocation concealment andwere twice as likely to be randomly assigned to usual care than to any of the active treatment groups. Participants andlocal study staff were not masked to the allocated treatment, but all others involved in the trial were masked to theoutcome data during the trial. The primary outcome was 28-day all-cause mortality, assessed in the intention-to-treatpopulation. The trial is registered with ISRCTN, 50189673, and ClinicalTrials.gov, NCT04381936.Findings Between April 7 and Nov 27, 2020, of 16 442 patients enrolled in the RECOVERY trial, 9433 (57%) wereeligible and 7763 were included in the assessment of azithromycin. The mean age of these study participants was65·3 years (SD 15·7) and approximately a third were women (2944 [38%] of 7763). 2582 patients were randomlyallocated to receive azithromycin and 5181 patients were randomly allocated to usual care alone. Overall,561 (22%) patients allocated to azithromycin and 1162 (22%) patients allocated to usual care died within 28 days(rate ratio 0·97, 95% CI 0·87–1·07; p=0·50). No significant difference was seen in duration of hospital stay (median10 days [IQR 5 to >28] vs 11 days [5 to >28]) or the proportion of patients discharged from hospital alive within 28 days(rate ratio 1·04, 95% CI 0·98–1·10; p=0·19). Among those not on invasive mechanical ventilation at baseline, nosignificant difference was seen in the proportion meeting the composite endpoint of invasive mechanical ventilationor death (risk ratio 0·95, 95% CI 0·87–1·03; p=0·24).Interpretation In patients admitted to hospital with COVID-19, azithromycin did not improve survival or otherprespecified clinical outcomes. Azithromycin use in patients admitted to hospital with COVID-19 should be restrictedto patients in whom there is a clear antimicrobial indication

AP-1 Is Required For CMX-8933-Induced SOD Upregulation And Is Translocated In Response To A Human EPN Mimetic

Ependymin (EPN) is a neurotrophic factor (NTF) that functions in goldfish long-term memory formation and optic nerve elongation (Shashoua, 1976; Shashoua, 1977; Shashoua, 1985). Goldfish EPN, or CMX-8933 (a short goldfish EPN mimetic studied by our lab), surprisingly have several demonstrated effects on mammalian cells, including neuroregenerative effects in a rat stroke model (Shashoua et al, 2003), and the activation of therapeutic superoxide dismutase (SOD) (Parikh, 2003) and transcription factor AP-1 (Adams et al, 2003) in mouse neuroblastoma cells or rat primary cortical neuronal cultures. Among its various functions, AP-1 can function as a master switch in long-term memory consolidation (Sanyal et al, 2002), so it may be a key event in EPN’s mechanism of action. AP-1 activation is also a characteristic associated with other full-sized neurotrophic factors, including nerve growth factor and brain-derived nerve growth factor. This thesis was divided into three parts. The purpose of part I was to determine whether our previously observed upregulation of SOD by CMX-8933 is dependent upon (or merely concurrent with) AP-1 activation. Four independent SOD immunoblot experiments demonstrated that pre-treatment of rat primary cortical cultures with trifluoromethyl pyrimidine carboxylate (TFPC), a specific inhibitor of AP-1, significantly (p = 0.0004) decreased cellular levels of SOD by 67% at its IC50 concentration of 1 ìM, and completely inhibited the upregulation at 10 and 100 ìM concentrations. Thus, the CMX-8933-induced upregulation of SOD appears to depend (directly or indirectly) on AP-1 activation. Part II of this thesis included the use of bioinformatics to re-verify exciting recent observations that EPN-like proteins exist in mammals, termed mammalian-ependymin-related proteins or MERPs (Apostolopoulos et al, 2001). If our analyses were convincing, human EPN mimetics would then be designed and tested for AP-1 activation. Computer alignments and hydropathy plots performed with EPN amino acid sequences deduced from gene entries in GenBank verified the existence of mammalian homologs containing highly conserved domains with fish EPN’s, suggesting the possibilities of similar protein conformation and function. Two human EPN mimetics were designed, hEPN-1 (8 aa long, corresponding to the same region as CMX-8933) and hEPN-2 (14 aa long, containing CMX-8933 and 6 upstream aa). Several mimetic doses were tested on mouse Neuro-2a cultures for nuclear translocation of c-Jun and c-Fos proteins (comprising the AP-1 particle upregulated by fish CMX-8933). Seven independent c-Jun immunoblot experiments, and five c-Fos experiments, demonstrated a strong (as high as 25-fold) dose-dependent increase in the nuclear titers of the AP-1 proteins. Both peptides had statistically equivalent effects. Thus, human EPN appears to exist, and two mimetics derived from its sequence appear to be biologically active against mouse neuroblastoma cells. Since hEPN-1 and -2 have only a few residues in common with CMX-8933, we hypothesize that the mimetic shape rather than sequence may be important for biological activity. In part III of this thesis, the biological effects of hEPN-1 and hEPN-2 on mouse Neuro-2a cells were studied further using RT-PCR to analyze potential increases in specific mRNAs. mRNAs related to growth, energy production, and protein translation were tested since previous data in our lab (Kaska, 2003) indicated mRNAs for translational elongation factor-2 (EF-2), and ribosomal proteins L19 and S12 were upregulated in rat primary cortical cultures by fish mimetic CMX-8933 (Kaska, 2003). Treatment of Neuro-2a cells with 1.0 ìg/ml hEPN-1 (the highest dose tested for the AP-1 translocation experiments) for 24 hrs appeared to increase (N = 1) mRNAs for ATP Synthase-C, ribosomal protein L19, and translational EF-2, relative to the levels of housekeeper polyubiquitin. Thus hEPN-1 may be involved in processes related to growth. Altogether, the data from this thesis extends our knowledge of fish EPN mimetic CMX-8933 (showing that its induction of SOD requires AP-1), demonstrates that human EPN may exist (bioinformatics), shows that two human EPN mimetics are biologically active (induce AP-1 translocation), and shows that one mimetic hEPN-1 may activate several mRNAs related to growth in mouse Neuro-2a cells