Cargando…

Complex Microbiome in Brain Abscess Revealed by Whole-Genome Culture-Independent and Culture-Based Sequencing

Brain abscess is a severe infectious disease with high mortality and mobility. Although culture-based techniques have been widely used for the investigation of microbial composition of brain abscess, these approaches are inherent biased. Recent studies using 16S ribosomal sequencing approaches revea...

Descripción completa

Detalles Bibliográficos
Autores principales: Lin, Jyun-Hong, Wu, Zong-Yen, Gong, Liang, Wong, Chee-Hong, Chao, Wen-Cheng, Yen, Chun-Ming, Wang, Ching-Ping, Wei, Chia-Lin, Huang, Yao-Ting, Liu, Po-Yu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6462986/
https://www.ncbi.nlm.nih.gov/pubmed/30871085
http://dx.doi.org/10.3390/jcm8030351
_version_ 1783410675184304128
author Lin, Jyun-Hong
Wu, Zong-Yen
Gong, Liang
Wong, Chee-Hong
Chao, Wen-Cheng
Yen, Chun-Ming
Wang, Ching-Ping
Wei, Chia-Lin
Huang, Yao-Ting
Liu, Po-Yu
author_facet Lin, Jyun-Hong
Wu, Zong-Yen
Gong, Liang
Wong, Chee-Hong
Chao, Wen-Cheng
Yen, Chun-Ming
Wang, Ching-Ping
Wei, Chia-Lin
Huang, Yao-Ting
Liu, Po-Yu
author_sort Lin, Jyun-Hong
collection PubMed
description Brain abscess is a severe infectious disease with high mortality and mobility. Although culture-based techniques have been widely used for the investigation of microbial composition of brain abscess, these approaches are inherent biased. Recent studies using 16S ribosomal sequencing approaches revealed high complexity of the bacterial community involved in brain abscess but fail to detect fungal and viral composition. In the study, both culture-independent nanopore metagenomic sequencing and culture-based whole-genome sequencing using both the Illumina and the Nanopore platforms were conducted to investigate the microbial composition and genomic characterization in brain abscess. Culture-independent metagenomic sequencing revealed not only a larger taxonomic diversity of bacteria but also the presence of fungi and virus communities. The culture-based whole-genome sequencing identified a novel species in Prevotella and reconstructs a Streptococcus constellatus with a high GC-skew genome. Antibiotic-resistance genes CfxA and ErmF associated with resistance to penicillin and clindamycin were also identified in culture-based and culture-free sequencing. This study implies current understanding of brain abscess need to consider the broader diversity of microorganisms.
format Online
Article
Text
id pubmed-6462986
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-64629862019-04-19 Complex Microbiome in Brain Abscess Revealed by Whole-Genome Culture-Independent and Culture-Based Sequencing Lin, Jyun-Hong Wu, Zong-Yen Gong, Liang Wong, Chee-Hong Chao, Wen-Cheng Yen, Chun-Ming Wang, Ching-Ping Wei, Chia-Lin Huang, Yao-Ting Liu, Po-Yu J Clin Med Article Brain abscess is a severe infectious disease with high mortality and mobility. Although culture-based techniques have been widely used for the investigation of microbial composition of brain abscess, these approaches are inherent biased. Recent studies using 16S ribosomal sequencing approaches revealed high complexity of the bacterial community involved in brain abscess but fail to detect fungal and viral composition. In the study, both culture-independent nanopore metagenomic sequencing and culture-based whole-genome sequencing using both the Illumina and the Nanopore platforms were conducted to investigate the microbial composition and genomic characterization in brain abscess. Culture-independent metagenomic sequencing revealed not only a larger taxonomic diversity of bacteria but also the presence of fungi and virus communities. The culture-based whole-genome sequencing identified a novel species in Prevotella and reconstructs a Streptococcus constellatus with a high GC-skew genome. Antibiotic-resistance genes CfxA and ErmF associated with resistance to penicillin and clindamycin were also identified in culture-based and culture-free sequencing. This study implies current understanding of brain abscess need to consider the broader diversity of microorganisms. MDPI 2019-03-12 /pmc/articles/PMC6462986/ /pubmed/30871085 http://dx.doi.org/10.3390/jcm8030351 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Lin, Jyun-Hong
Wu, Zong-Yen
Gong, Liang
Wong, Chee-Hong
Chao, Wen-Cheng
Yen, Chun-Ming
Wang, Ching-Ping
Wei, Chia-Lin
Huang, Yao-Ting
Liu, Po-Yu
Complex Microbiome in Brain Abscess Revealed by Whole-Genome Culture-Independent and Culture-Based Sequencing
title Complex Microbiome in Brain Abscess Revealed by Whole-Genome Culture-Independent and Culture-Based Sequencing
title_full Complex Microbiome in Brain Abscess Revealed by Whole-Genome Culture-Independent and Culture-Based Sequencing
title_fullStr Complex Microbiome in Brain Abscess Revealed by Whole-Genome Culture-Independent and Culture-Based Sequencing
title_full_unstemmed Complex Microbiome in Brain Abscess Revealed by Whole-Genome Culture-Independent and Culture-Based Sequencing
title_short Complex Microbiome in Brain Abscess Revealed by Whole-Genome Culture-Independent and Culture-Based Sequencing
title_sort complex microbiome in brain abscess revealed by whole-genome culture-independent and culture-based sequencing
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6462986/
https://www.ncbi.nlm.nih.gov/pubmed/30871085
http://dx.doi.org/10.3390/jcm8030351
work_keys_str_mv AT linjyunhong complexmicrobiomeinbrainabscessrevealedbywholegenomecultureindependentandculturebasedsequencing
AT wuzongyen complexmicrobiomeinbrainabscessrevealedbywholegenomecultureindependentandculturebasedsequencing
AT gongliang complexmicrobiomeinbrainabscessrevealedbywholegenomecultureindependentandculturebasedsequencing
AT wongcheehong complexmicrobiomeinbrainabscessrevealedbywholegenomecultureindependentandculturebasedsequencing
AT chaowencheng complexmicrobiomeinbrainabscessrevealedbywholegenomecultureindependentandculturebasedsequencing
AT yenchunming complexmicrobiomeinbrainabscessrevealedbywholegenomecultureindependentandculturebasedsequencing
AT wangchingping complexmicrobiomeinbrainabscessrevealedbywholegenomecultureindependentandculturebasedsequencing
AT weichialin complexmicrobiomeinbrainabscessrevealedbywholegenomecultureindependentandculturebasedsequencing
AT huangyaoting complexmicrobiomeinbrainabscessrevealedbywholegenomecultureindependentandculturebasedsequencing
AT liupoyu complexmicrobiomeinbrainabscessrevealedbywholegenomecultureindependentandculturebasedsequencing