Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt.
Biomedical Research Department, Armed Force College of Medicine, Cairo, Egypt.
BMC Microbiol. 2024 Feb 2;24(1):47. doi: 10.1186/s12866-023-03172-6.
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.
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.
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.
在埃及鼻咽拭子中发现的鸟分枝杆菌（O. hominis）与人类呼吸道疾病有关。O. hominis 是黄杆菌科的一个新成员，属于拟杆菌门最大的家族。该家族包括数百个种和 90 个属，包括主要的人类病原体，如嗜沫卡他菌和脑膜败血伊丽莎白菌。本文介绍了从宏基因组数据中使用 Illumina 测序方法提取的 O. hominis 的两个基因组草案组装。使用 BLASTN 将读取序列与 O. hominis 基因组进行比对，使用 Seqtk 提取具有显著命中的读取，并使用 SPAdes 进行组装。本研究的主要目的是更深入地了解 O. hominis 的基因组景观，重点是识别相关的毒力、抗微生物基因和独特的防御机制，以阐明 O. hominis 在人类呼吸道感染中的潜在作用。
基因组大小估计为 1.84 Mb，包括 1,931,660 个碱基对（bp），预测有 1,837 个编码区，G+C 含量为 35.62%。基因组中包含编码滑行运动、抗生素耐药性（20 个基因）和 toxA 基因的基因。鉴定了滑行运动脂蛋白（GldD、GldJ、GldN 和 GldH）和滑行运动相关 ABC 转运体底物结合蛋白，该蛋白是黄杆菌属物种中重要的毒力机制。基因组中还包含编码 ParE1 毒素等蛋白的独特基因，这些基因可以抵御喹诺酮类和其他抗生素的作用。还检测到编码 CzcB 蛋白的钴锌镉抗性基因，该基因对于金属抗性、脲酶调节和定植是必需的。鉴定了多个编码蛋白的多药耐药基因，如 MexB、MdtK、YheI 和 VanC。
本研究重点是鉴定 O. hominis 核心基因组中存在的毒力因子和抗微生物耐药基因。这些发现为 O. hominis 的潜在致病性和抗生素敏感性提供了有价值的见解。
