Ahmed, Nada

Abstract Background Candidatus Ornithobacterium hominis (O. hominis), which was identified in nasopharyngeal swabs from Egypt, has been associated with respiratory disorders in humans. O. hominis, a recently identified member of the Flavobacteriaceae family, belongs to the largest family within the Bacteroidetes phylum. This family includes hundreds of species and 90 genera, including major human pathogens such as Capnocytophaga canimorsus and Elizabethkingia meningoseptica. Herein, we presented two draft genome assemblies of O. hominis that were extracted from metagenomic data using the Illumina sequencing method. The alignment of reads against the O. hominis genome was accomplished using BLASTN, and the reads with significant hits were extracted using Seqtk and assembled using SPAdes. The primary goal of this study was to obtain a more profound understanding of the genomic landscape of O. hominis, with an emphasis on identifying the associated virulence, antimicrobial genes, and distinct defense mechanisms to shed light on the potential role of O. hominis in human respiratory infections. Results The genome size was estimated to be 1.84 Mb, including 1,931,660 base pairs (bp), with 1,837 predicted coding regions and a G+C content of 35.62%. Genes encoding gliding motility, antibiotic resistance (20 genes), and the toxA gene were all included in the genome assembly. Gliding motility lipoproteins (GldD, GldJ, GldN, and GldH) and the gliding motility-associated ABC transporter substrate-binding protein, which acts as a crucial virulence mechanism in Flavobacterium species, were identified. The genome contained unique genes encoding proteins, such as the ParE1 toxin that defend against the actions of quinolone and other antibiotics. The cobalt-zinc-cadmium resistance gene encoding the protein CzcB, which is necessary for metal resistance, urease regulation, and colonization, was also detected. Several multidrug resistance genes encoding proteins were identified, such as MexB, MdtK, YheI, and VanC. Conclusion Our study focused on identifying virulence factors, and antimicrobial resistance genes present in the core genome of O. hominis. These findings provide valuable insights into the potential pathogenicity and antibiotic susceptibility of O. hominis.

Abstract Background Candidatus Ornithobacterium hominis (O. hominis), which was found in Egyptian nasopharyngeal swabs but remains unidentified, has been associated with respiratory disorders in humans. Herein, we presented two draft genome assemblies of O. hominis that were extracted from metagenomic data using the Illumina sequencing method. The primary goal of this study was to present the first O. hominis genome sequence from Egyptian populations. Results The genome size was estimated to be 1,931,660 base pairs (bp), with 1,837 predicted coding regions and a G + C content of 35.62%. The toxA gene, 20 antibiotic resistance genes, and gliding motility genes were found in the genome assembly. Gliding motility lipoproteins (GldD, GldJ, GldN, and GldH) and the gliding motility-associated ABC transporter substrate-binding protein, which acts as a crucial virulence mechanism in Flavobacterium species, were identified. The genome contained unique proteins, such as the ParE1 toxin, that exhibit a defense mechanism against quinolone and other antibiotic actions. The cobalt-zinc-cadmium resistance protein CzcB, which is necessary for metal resistance, urease regulation, and colonization, was also detected. Several multidrug resistance proteins were identified, such as MexB, mdtK, yheI, and VanC. Conclusion Numerous virulence factors such as toxA and gliding motility genes, were present in the core O. hominis genome. Additionally, the draft genome contains several antibiotic-resistance genes. These findings may contribute to a better understanding of the genomic landscape of O. hominis and the identification of genes involved in virulence and antibiotic resistance.