Browsing by Author "Alan Tracey"

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    ’Candidatus Ornithobacterium hominis’: Insights gained from draft genomes obtained from nasopharyngeal swabs
    (2019-02-01) Susannah J. Salter; Paul Scott; Andrew J. Page; Alan Tracey; Marcus C. de Goffau; Claire Cormie; Bernardo Ochoa-Montaño; Clare L. Ling; Jiraporn Tangmanakit; Paul Turner; Julian Parkhill; University of Cambridge; Quadram Institute Bioscience; Mahidol University; Nuffield Department of Clinical Medicine; Wellcome Sanger Institute; Illumina Cambridge Ltd.; Angkor Hospital for Children
    © 2019 The Authors. ‘Candidatus Ornithobacterium hominis’ represents a new member of the Flavobacteriaceae detected in 16S rRNA gene surveys of people from South-East Asia, Africa and Australia. It frequently colonizes the infant nasopharynx at high proportional abundance, and we demonstrate its presence in 42 % of nasopharyngeal swabs from 12-month-old children in the Maela refugee camp in Thailand. The species, a Gram-negative bacillus, has not yet been cultured, but the cells can be identified in mixed samples by fluorescent hybridization. Here, we report seven genomes assembled from metagenomic data, two to improved draft standard. The genomes are approximately 1.9 Mb, sharing 62 % average amino acid identity with the only other member of the genus, the bird pathogen Ornithobacterium rhinotracheale. The draft genomes encode multiple antibiotic-resistance genes, competition factors, Flavobacterium johnsoniae-like gliding motility genes and a homologue of the Pasteurella multocida mitogenic toxin. Intra-and inter-host genome comparison suggests that colonization with this bacterium is both persistent and strain exclusive.
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    Programmed genome editing of the omega-1 ribonuclease of the blood fluke, Schistosoma mansoni
    (2019-01-15) Wannaporn Ittiprasert; Victoria H. Mann; Shannon E. Karinshak; Avril Coghlan; Gabriel Rinaldi; Geetha Sankaranarayanan; Apisit Chaidee; Toshihiko Tanno; Chutima Kumkhaek; Pannathee Prangtaworn; Margaret M. Mentink-Kane; Christina J. Cochran; Patrick Driguez; Nancy Holroyd; Alan Tracey; Rutchanee Rodpai; Bart Everts; Cornelis H. Hokke; Karl F. Hoffmann; Matthew Berriman; Paul J. Brindley; Institute of Biological, Environmental and Rural Sciences; Faculty of Medicine, Khon Kaen University; Leiden University Medical Center - LUMC; University of Maryland, Baltimore; Faculty of Medicine, Siriraj Hospital, Mahidol University; National Institutes of Health, Bethesda; The George Washington University; Research Institute
    CRISPR/Cas9-based genome editing has yet to be reported in species of the Platyhelminthes. We tested this approach by targeting omega-1 (ω1) of Schistosoma mansoni as proof of principle. This secreted ribonuclease is crucial for Th2 polarization and granuloma formation. Schistosome eggs were exposed to Cas9 complexed with guide RNA complementary to ω1 by electroporation or by transduction with lentiviral particles. Some eggs were also transfected with a single stranded donor template. Sequences of amplicons from gene-edited parasites exhibited Cas9-catalyzed mutations including homology directed repaired alleles, and other analyses revealed depletion of ω1 transcripts and the ribonuclease. Gene-edited eggs failed to polarize Th2 cytokine responses in macrophage/T-cell co-cultures, while the volume of pulmonary granulomas surrounding ω1-mutated eggs following tail-vein injection into mice was vastly reduced. Knock-out of ω1 and the diminished levels of these cytokines following exposure showcase the novel application of programmed gene editing for functional genomics in schistosomes.