Identification of bacterial pathogens in brain abscesses by metagenomic approach using nanopore 16S amplicon sequencing

Hyoshin Son; Jangsup Moon; Eun Jin Ha; Narae Kim; Eun-Young Kim; Han Sang Lee; Eun Jung Koh; Ji Hoon Phi; Chul-Kee Park; Jeong Eun Kim; Seung-Ki Kim; Soon-Tae Lee; Keun-Hwa Jung; Sang Kun Lee; Won-Sang Cho; Kon Chu

doi:10.1016/j.diagmicrobio.2023.116041

Identification of bacterial pathogens in brain abscesses by metagenomic approach using nanopore 16S amplicon sequencing

Diagn Microbiol Infect Dis. 2023 Dec;107(4):116041. doi: 10.1016/j.diagmicrobio.2023.116041. Epub 2023 Jul 28.

Authors

Hyoshin Son¹, Jangsup Moon², Eun Jin Ha³, Narae Kim⁴, Eun-Young Kim⁵, Han Sang Lee⁶, Eun Jung Koh⁷, Ji Hoon Phi⁸, Chul-Kee Park³, Jeong Eun Kim³, Seung-Ki Kim⁸, Soon-Tae Lee⁴, Keun-Hwa Jung⁴, Sang Kun Lee⁴, Won-Sang Cho³, Kon Chu⁹

Affiliations

¹ Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, College of Medicine Seoul National University, Seoul National University Hospital, Seoul, South Korea; Department of Neurology, Eunpyeong St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea.
² Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, College of Medicine Seoul National University, Seoul National University Hospital, Seoul, South Korea; Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea.
³ Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, South Korea.
⁴ Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, College of Medicine Seoul National University, Seoul National University Hospital, Seoul, South Korea.
⁵ Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, College of Medicine Seoul National University, Seoul National University Hospital, Seoul, South Korea; Department of Neurology, Chungnam National University Sejong Hospital, Sejong, Korea.
⁶ Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, College of Medicine Seoul National University, Seoul National University Hospital, Seoul, South Korea; Center of Hospital Medicine, Seoul National University Hospital, Seoul, South Korea.
⁷ Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, South Korea; Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, South Korea; Center of Hospital Medicine, Seoul National University Hospital, Seoul, South Korea.
⁸ Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, South Korea; Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, South Korea.
⁹ Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, College of Medicine Seoul National University, Seoul National University Hospital, Seoul, South Korea. Electronic address: stemcell.snu@gmail.com.

PMID: 37741170
DOI: 10.1016/j.diagmicrobio.2023.116041

Abstract

Brain abscess is medically challenging. In this study, we applied nanopore sequencing for 16S rRNA analysis and investigated its efficacy and diagnostic value for patients with brain abscesses. Genomic DNA was extracted from the pus samples (n = 27) of brain abscess, and 16S rRNA genes were amplified by PCR. Sequencing libraries were generated using a rapid barcoding kit, and the generated reads were analyzed using the EPI2ME16S workflow. A conventional culture study was performed. More sensitive identification of pathogens was made by 16S sequencing, faster than the culture study. The proportion of anaerobic bacteria identified by 16S sequencing was higher (75%) than that obtained by culturing (32%). Polymicrobial infections were identified in 10 cases (40%) by 16S sequencing, while the culture study identified multiple bacteria in only 2 cases (8%). 16S sequencing was useful for identifying the composition of polymicrobial infections, including rare pathogens, and for the initial diagnosis of space-occupying lesions.

Keywords: 16S ribosomal DNA; Bacteria; Brain abscess; Central nervous system infection; Metagenomics; Nanopore sequencing.

MeSH terms

Bacteria / genetics
Brain Abscess* / diagnosis
Brain Abscess* / microbiology
Coinfection*
DNA, Bacterial / analysis
DNA, Bacterial / genetics
High-Throughput Nucleotide Sequencing
Humans
Nanopore Sequencing*
Nanopores*
RNA, Ribosomal, 16S / genetics

Substances

RNA, Ribosomal, 16S
DNA, Bacterial