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

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.

Ornithobacterium rhinotracheale: MALDI-TOF MS and Whole Genome Sequencing Confirm That Serotypes K, L and M Deviate from Well-Known Reference Strains and Numerous Field Isolates

“…Ornithobacterium rhinotracheale is a gram-negative rod-shaped bacterium firstly described in 1994 [ 1 ], and it was the only species in its genus until 2019 when Salter et al [ 2 ] proposed a new species, Ornithobacterium hominis, isolated from humans. O. rhinotracheale is an economically important bacterial pathogen of turkeys and chickens worldwide [ 3 ], and it is ranked among the most important bacterial agents of poultry respiratory diseases [ 4 ].…”

<p>Trends and Development in the Antibiotic-Resistance of <em>Acinetobacter baumannii</em>: A Scientometric Research Study (1991–2019)</p>

“…47 Some studies have proposed using the CRISPR system to combat antibiotic resistance and achieved certain research results. [48][49][50] Now the focus of the research is to solve the limitation of therapy in clinical treatment, then apply it to the clinical widely. The combination of antibiotics and phages is based on the treatment of antibiotic-resistant A. baumannii, while the study of biofilm is based on the control of the transmission of antibiotic-resistant A. baumannii.51 Both of them are to solve the problem of antibiotic-resistance of A. baumannii, but the control of transmission is to prevent the problem at the source, which is more effective to solve the problem.…”

Antimicrobial resistance in enteric bacteria: current state and next-generation solutions

“…128 Long-read sequencing is also an emerging and increasingly cost-effective strategy to achieve better resolution on plasmid vs. chromosomal elements, and can assist with covering genomic sites that do not always attain adequate coverage such as repeated DNA elements at insertion sequence sites found upstream of the cfiA carbapenemase in BFG. 129 These and other emerging technologies will likely prove essential in identifying elements beyond strict ARG sequences that can have a substantial impact on the extent of AMR in genomes or metagenomes.…”