Abscesses are often clinically manifested as local necrotic tissues in various organs or systems of the human body, which is commonly caused by microbial infection. Rapid and accurate identification of pathogens from clinical abscetic samples would greatly guide a clinician to make the precise choices of the antimicrobial treatment. Here, this study aimed to investigate the application of metagenomic next-generation sequencing (mNGS) in the microbial detection of clinical samples of abscess fluids from various organs or systems. Nine patients with abscess from various organs or systems were enrolled in this study. The pathogenic bacteria in abscess fluid were detected and compared by the conventional bacterial culture and mNGS respectively. The dominant pathogens of abscess fluids in 8 cases can be found directly from mNGS, dominating over 80% of the total reads abundance of the microbiome. Although the pathogens from 6 cases detected by mNGS were consistent with that from the conventional bacteria culture method, the fastidious obligate anaerobic bacteria in 2 cases additionally detected by mNGS were not found by the conventional culture method. Moreover, complex polymicrobial infection containing Parvimonas micra in one case negatively with conventional bacterial culture were demonstrated by the mNGS method. And the mNGS method can directly reflect the diversity of microbial ecology in the abscess fluids from the different parts of the human body. Conclusively, mNGS can be used as a supplemental method for the pathogen detection of clinically abscess fluids.

脓肿临床上常表现为人体各器官或系统局部坏死组织，多由微生物感染所致。从临床脓肿样本中快速准确地鉴定病原体将极大地指导临床医生做出抗菌治疗的精确选择。在这里，本研究旨在研究宏基因组下一代测序 (mNGS) 在微生物检测来自各种器官或系统的脓肿液临床样本中的应用。9 名来自不同器官或系统的脓肿患者参加了这项研究。分别采用常规细菌培养和mNGS对脓肿液中的病原菌进行检测和比较。8例脓肿液的优势病原体可直接从mNGS中找到，占微生物组总读数丰度的 80% 以上。尽管mNGS检测的6例病原菌与常规细菌培养方法一致，但常规培养方法未发现mNGS额外检测的2例苛刻的专性厌氧菌。此外，复杂的多种微生物感染含有mNGS方法证明了在一个案例中对常规细菌培养呈阴性的微小微单胞菌。而mNGS方法可以直接反映人体不同部位脓肿液中微生物生态的多样性。最后，mNGS 可作为临床脓肿液病原体检测的补充方法。