Pathogen determination from clinical abscesses fluids using Metagenomic Next-Generation Sequencing

Abscesses can be manifested as local necrotic tissue of many organs or systems in human body, which is often caused by pathogen infection. Rapid and accurate identification of pathogenic bacteria would have a great significance in guiding clinical abscess patients to choose the correct antimicrobial treatment. The purpose of this study is to explore the application of metagenomic next-generation sequencing (mNGS) in the detection of clinical abscess pathogens. Nine patients with abscesses from different sources were enrolled in this study. The conventional bacterial culture and mNGS were used to detect the pathogenic bacteria in abscess fluid and compared the result. The dominant microflora of abscess in 8 cases can be found directly by mNGS, which suggests their reads abundance in the microbiome was over 80%. The pathogens from 6 cases detected by mNGS were utterly consistent with that from the conventional bacteria culture method, but the fastidious obligate anaerobic bacteria in 2 cases detected by mNGS were not found by the conventional culture method, which indicated that mNGS could be used as a supplement for determining the microbial pathogens. One sample was negative in traditional culture, but it was detected by the mNGS method of complex polymicrobial infection containing Parvimonas micra. The mNGS method can directly reflect the formation of abscesses and its diversity of microbial ecology in different parts of the patient's body, indicating that mNGS can be used as a supplement to the microbiological detection methods ignored by traditional microbiological methods.