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Candidatus Ornithobacterium hominis sp. nov.: insights gained from draft genomes obtained from nasopharyngeal swabs

View ORCID ProfileSusannah J Salter, Paul Scott, Andrew J Page, Alan Tracey, Marcus C de Goffau, Bernardo Ochoa-Montaño, Clare L Ling, Jiraporn Tangmanakit, Paul Turner, Julian Parkhill
doi: https://doi.org/10.1101/326074
Susannah J Salter
1Pathogen Genomics, Wellcome Sanger Institute, Hinxton, United Kingdom
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  • For correspondence: sb18@sanger.ac.uk
Paul Scott
1Pathogen Genomics, Wellcome Sanger Institute, Hinxton, United Kingdom
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Andrew J Page
1Pathogen Genomics, Wellcome Sanger Institute, Hinxton, United Kingdom
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Alan Tracey
1Pathogen Genomics, Wellcome Sanger Institute, Hinxton, United Kingdom
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Marcus C de Goffau
1Pathogen Genomics, Wellcome Sanger Institute, Hinxton, United Kingdom
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Bernardo Ochoa-Montaño
2Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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Clare L Ling
3Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
4Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Jiraporn Tangmanakit
3Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
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Paul Turner
4Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
5Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
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Julian Parkhill
1Pathogen Genomics, Wellcome Sanger Institute, Hinxton, United Kingdom
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ABSTRACT

Candidatus Ornithobacterium hominis sp. nov. represents a new member of the Flavobacteriaceae detected in 16S rRNA gene surveys from Southeast Asia, Africa and Australia. It frequently colonises 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 hybridisation. Here we report seven genomes assembled from metagenomic data, two to improved draft standard. The genomes are approximately 1.9Mb, 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 homolog of the Pasteurella multocida mitogenic toxin. Intra- and inter-host genome comparison suggests that colonisation with this bacterium is both persistent and strain exclusive.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted May 18, 2018.
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Candidatus Ornithobacterium hominis sp. nov.: insights gained from draft genomes obtained from nasopharyngeal swabs
Susannah J Salter, Paul Scott, Andrew J Page, Alan Tracey, Marcus C de Goffau, Bernardo Ochoa-Montaño, Clare L Ling, Jiraporn Tangmanakit, Paul Turner, Julian Parkhill
bioRxiv 326074; doi: https://doi.org/10.1101/326074
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Candidatus Ornithobacterium hominis sp. nov.: insights gained from draft genomes obtained from nasopharyngeal swabs
Susannah J Salter, Paul Scott, Andrew J Page, Alan Tracey, Marcus C de Goffau, Bernardo Ochoa-Montaño, Clare L Ling, Jiraporn Tangmanakit, Paul Turner, Julian Parkhill
bioRxiv 326074; doi: https://doi.org/10.1101/326074

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