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

Susannah J Salter,Paul Turner,Jiraporn Tangmanakit,Claire Cormie,Alan Tracey,Julian Parkhill,Bernardo Ochoa-Montaño,Paul Scott,Clare L Ling,Marcus C De Goffau,Andrew J Page

doi:10.1099/mgen.0.000247

Abstract

‘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.

Highlights

During previous work on the nasopharyngeal microbiota of children in the Maela refugee camp in Thailand, an abundant unclassified taxon was discovered through 16S rRNA gene sequencing [1]
We propose the name ‘Candidatus Ornithobacterium hominis’ and describe a screening protocol to detect its presence in samples
Despite significant loss of sequence coverage to human and other bacterial genomes, two samples assembled into 9 and 15 contigs from ‘Candidatus O. hominis’, yielding draft genomes predicted to be nearly complete based on the detection of all ribosomal protein genes and by intersample comparison

Summary

Introduction

During previous work on the nasopharyngeal microbiota of children in the Maela refugee camp in Thailand, an abundant unclassified taxon was discovered through 16S rRNA gene sequencing [1]. It was >99 % identical to other unclassified sequences reported in nasopharyngeal samples from the Gambia [2, 3], Kenya [4] and Australia [5], and the gene shared 93 % nucleotide identity with that of the avian respiratory pathogen Ornithobacterium rhinotracheale.

Methods

Results

Conclusion