Pathogen determination from clinical abscess fluids using metagenomic next-generation sequencing
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ORIGINAL ARTICLE
Pathogen determination from clinical abscess fluids using metagenomic next-generation sequencing Yuxi Zhao 1 & Jinlian Chen 1 & Bing Bai 1 & Yu Wang 1 & Jinxin Zheng 1 & Zhijian Yu 1 & Qiwen Deng 1 & Peiyu Li 2 Received: 4 June 2020 / Accepted: 7 October 2020 # Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i. 2020
Abstract 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.
Introduction Abscess formation is characterized by the accumulation of pus or necrotic tissue fluid in a confined space, which can be found in almost any organ or tissue of the human body. In most cases, the abscess formation is caused by the pathogen infection. Therefore, antibiotic treatment of purulent capsule disease caused by microbial agents is mandatory in clinical
Yuxi Zhao and Jinlian Chen contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12223-020-00829-x) contains supplementary material, which is available to authorized users. * Peiyu Li [email protected] 1
Department of Infectious Diseases and Shenzhen Key Laboratory for Endogenous Infection, Shenzhen Nanshan People’s Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
2
Department of Infectious Diseases and Shenzhen Key Laboratory for Endogenous Infection, Affiliated Shenzhen Sixth Hospital of Guangdong Medical University, Shenzhen, China
practice. According to clinical data and clinical trials
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