Kimura Hirokazu, Hayashi Yuriko, Kitagawa Masanari, Yoshizaki Miwa, Saito Kensuke, Harada Kazuhiko, Okayama Kaori, Miura Yusuke, Kimura Ryusuke, Shirai Tatsuya, Fujita Kiyotaka, Machida Suguru, Ito Kazuto, Kurosawa Isao
Department of Health Science, Gunma Paz University Graduate School of Health Sciences, Takasaki-shi 370-0006, Gunma, Japan.
Advanced Medical Science Research Center, Gunma Paz University Research Institute, Shibukawa-shi 377-0008, Gunma, Japan.
Microorganisms. 2023 Aug 24;11(9):2142. doi: 10.3390/microorganisms11092142.
The identification of pathogens associated with respiratory symptoms other than the novel coronavirus disease 2019 (COVID-19) can be challenging. However, the diagnosis of pathogens is crucial for assessing the clinical outcome of patients. We comprehensively profiled pathogens causing non-COVID-19 respiratory symptoms during the 7th prevalent period in Gunma, Japan, using deep sequencing combined with a next-generation sequencer (NGS) and advanced bioinformatics technologies. The study included nasopharyngeal swabs from 40 patients who tested negative for severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) using immuno-chromatography and/or quantitative reverse transcription polymerase chain reaction (qRT-PCR) methods. Comprehensive pathogen sequencing was conducted through deep sequencing using NGS. Additionally, short reads obtained from NGS were analyzed for comprehensive pathogen estimation using MePIC (Metagenomic Pathogen Identification Pipeline for Clinical Specimens) and/or VirusTap. The results revealed the presence of various pathogens, including respiratory viruses and bacteria, in the present subjects. Notably, human adenovirus (HAdV) was the most frequently detected virus in 16 of the 40 cases (40.0%), followed by coryneforms, which were the most frequently detected bacteria in 21 of the 40 cases (52.5%). Seasonal human coronaviruses (NL63 type, 229E type, HKU1 type, and OC43 type), human bocaviruses, and human herpesviruses (human herpesvirus types 1-7) were not detected. Moreover, multiple pathogens were detected in 50% of the subjects. These results suggest that various respiratory pathogens may be associated with non-COVID-19 patients during the 7th prevalent period in Gunma Prefecture, Japan. Consequently, for an accurate diagnosis of pathogens causing respiratory infections, detailed pathogen analyses may be necessary. Furthermore, it is possible that various pathogens, excluding SARS-CoV-2, may be linked to fever and/or respiratory infections even during the COVID-19 pandemic.
识别与2019年新型冠状病毒病（COVID-19）以外的呼吸道症状相关的病原体可能具有挑战性。然而，病原体的诊断对于评估患者的临床结局至关重要。我们使用深度测序结合下一代测序仪（NGS）和先进的生物信息学技术，全面分析了日本群马县第7流行期导致非COVID-19呼吸道症状的病原体。该研究纳入了40例使用免疫层析和/或定量逆转录聚合酶链反应（qRT-PCR）方法检测严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）呈阴性的患者的鼻咽拭子。通过使用NGS的深度测序进行全面的病原体测序。此外，使用MePIC（临床标本宏基因组病原体鉴定管道）和/或VirusTap对从NGS获得的短读段进行分析，以进行全面的病原体估计。结果显示，本研究对象中存在多种病原体，包括呼吸道病毒和细菌。值得注意的是，人腺病毒（HAdV）是40例中的16例（40.0%）中最常检测到的病毒，其次是棒状杆菌，是40例中的21例（52.5%）中最常检测到的细菌。未检测到季节性人类冠状病毒（NL63型、229E型、HKU1型和OC43型）、人博卡病毒和人类疱疹病毒（人类疱疹病毒1-7型）。此外，50%的研究对象中检测到多种病原体。这些结果表明，在日本群马县第7流行期，各种呼吸道病原体可能与非COVID-19患者有关。因此,为准确诊断引起呼吸道感染的病原体，可能需要进行详细的病原体分析。此外，即使在COVID-19大流行期间，除SARS-CoV-2外的各种病原体也可能与发热和/或呼吸道感染有关。
