Department of Respiratory Medicine, Haining People's Hospital, Haining, China.
Haining People's Hospital, Haining, China.
Medicine (Baltimore). 2022 Dec 23;101(51):e32423. doi: 10.1097/MD.0000000000032423.
Lower respiratory tract infection (LRTI) is still a threat to human health. Metagenomics next-generation sequencing (NGS) provides an efficient and unbiased way to identify LRTI pathogens, and has been shown to have several advantages over traditional methods. However, its application is currently limited in low-resource settings. Our aim was to collect and analyze data on LRTI cases at a county-level community hospital in Eastern China over one year, in order to compare the efficiency of NGS and traditional methods including culture, nucleic acid amplification and antibody techniques. We performed NGS of bronchoalveolar lavage fluid (BALF) for pathogen identification in 71 patients with LRTI. We compared the detection rates, identified pathogens, and turnaround time of NGS with traditional methods. Pathogens were detected using traditional methods in 19 cases, and the results were compared with those obtained with the NGS technique in 60 cases. The pathogen detection rate of NGS (84.5%) was much higher than that of the traditional methods (26.8%). Moreover, with the traditional methods considered the gold standard, the consistency rate between NGS and traditional methods was 68.4%. For the 19 cases in which the traditional method was used, the main pathogens included invasive Aspergillus (5 cases), Pseudomonas aeruginosa (3 cases), Candida albicans (3 cases), and Staphylococcus aureus (2 cases). Among the 60 cases detected by NGS, the main pathogens included Mycobacterium (12 cases), Streptococcus pneumoniae (5 cases), Klebsiella pneumoniae (3 cases), P. aeruginosa (3 cases), Haemophilus influenzae (3 cases), and S. aureus (3 cases), Aspergillus (9 cases), Pneumocystis jiroveci (5 cases), C. albicans (3 cases), Human Papilloma Virus (9 cases), Epstein-Barr virus (8 cases), and parvovirus (6 cases). In addition, 2 cases of chlamydia and 1 case of mycoplasma infection were detected by NGS. The time taken to perform the NGS tests was significantly shorter than that taken with the traditional method. NGS analysis of bronchoalveolar lavage fluid, in combination with traditional pathogen detection methods, can improve the efficiency of pathogen detection. More attention should be paid to the regional epidemic characteristics of infectious pathogens in LRTI.
下呼吸道感染（LRTI）仍然是威胁人类健康的因素。宏基因组下一代测序（NGS）为鉴定 LRTI 病原体提供了一种高效且无偏倚的方法，并且已被证明优于传统方法。然而，其在资源有限的环境中的应用目前受到限制。本研究的目的是收集和分析中国东部一家县级社区医院一年来的 LRTI 病例数据，以比较 NGS 与包括培养、核酸扩增和抗体技术在内的传统方法的效率。我们对 71 例 LRTI 患者的支气管肺泡灌洗液（BALF）进行了 NGS 以鉴定病原体。我们比较了 NGS 与传统方法的检测率、鉴定出的病原体和周转时间。传统方法检测出 19 例病例，将结果与 60 例使用 NGS 技术的结果进行了比较。NGS 的病原体检测率（84.5%）明显高于传统方法（26.8%）。此外，以传统方法为金标准，NGS 与传统方法的一致性率为 68.4%。在使用传统方法的 19 例病例中，主要病原体包括侵袭性曲霉（5 例）、铜绿假单胞菌（3 例）、白色念珠菌（3 例）和金黄色葡萄球菌（2 例）。在通过 NGS 检测的 60 例病例中，主要病原体包括分枝杆菌（12 例）、肺炎链球菌（5 例）、肺炎克雷伯菌（3 例）、铜绿假单胞菌（3 例）、流感嗜血杆菌（3 例）、金黄色葡萄球菌（3 例）、曲霉（9 例）、卡氏肺孢子虫（5 例）、白色念珠菌（3 例）、人乳头瘤病毒（9 例）、EB 病毒（8 例）和细小病毒（6 例）。此外，通过 NGS 检测到 2 例衣原体感染和 1 例支原体感染。NGS 检测的时间明显短于传统方法。对支气管肺泡灌洗液进行 NGS 分析，并结合传统的病原体检测方法，可以提高病原体检测的效率。应更加关注 LRTI 中传染性病原体的区域性流行特征。
