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

被引:9
|
作者
Lin, Jyun-Hong [1 ]
Wu, Zong-Yen [2 ]
Gong, Liang [3 ]
Wong, Chee-Hong [3 ]
Chao, Wen-Cheng [4 ]
Yen, Chun-Ming [5 ,6 ]
Wang, Ching-Ping [7 ]
Wei, Chia-Lin [3 ]
Huang, Yao-Ting [1 ]
Liu, Po-Yu [5 ,8 ]
机构
[1] Natl Chung Cheng Univ, Dept Comp Sci & Informat Engn, Chiayi 62102, Taiwan
[2] Natl Chung Hsing Univ, Dept Vet Med, Taichung 40227, Taiwan
[3] Jackson Lab Genom Med, Genome Technol, Farmington, CT 06032 USA
[4] Taichung Vet Gen Hosp, Dept Med Res, Taichung 40705, Taiwan
[5] Natl Chung Hsing Univ, Program Translat Med, Taichung 40227, Taiwan
[6] Taichung Vet Gen Hosp, Dept Neurosurg, Taichung 40705, Taiwan
[7] Taichung Vet Gen Hosp, Dept Otolaryngol Head & Neck Surg, Taichung 40705, Taiwan
[8] Taichung Vet Gen Hosp, Div Infect Dis, Dept Internal Med, Taichung 40705, Taiwan
来源
JOURNAL OF CLINICAL MEDICINE | 2019年 / 8卷 / 03期
关键词
metagenomics; whole genome sequencing; genomics; brain abscess; Streptococcus constellatus; Prevotella; CENTRAL-NERVOUS-SYSTEM; METAGENOMIC IDENTIFICATION; ANTIBIOTIC-RESISTANCE; PATHOGENS; EXPANSION; BIAS;
D O I
10.3390/jcm8030351
中图分类号
R5 [内科学];
学科分类号
1002 ; 100201 ;
摘要
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.
引用
收藏
页数:11
相关论文
共 50 条
  • [21] Complex microbiota of a Chinese "Fen" liquor fermentation starter (Fen-Daqu), revealed by culture-dependent and culture-independent methods
    Zheng, Xiao-Wei
    Yan, Zheng
    Han, Bei-Zhong
    Zwietering, Marcel H.
    Samson, Robert A.
    Boekhout, Teun
    Nout, M. J. Robert
    [J]. FOOD MICROBIOLOGY, 2012, 31 (02) : 293 - 300
  • [22] Microbial Diversity of Wild Bird Feathers Revealed throughCulture-Based and Culture-Independent Techniques
    Matthew D. Shawkey
    Kimberly L. Mills
    Colin Dale
    Geoffrey E. Hill
    [J]. Microbial Ecology, 2005, 50 : 40 - 47
  • [23] A New Whole Genome Culture-Independent Diagnostic Test (WG-CIDT) for Rapid Detection of Salmonella in Lettuce
    Ogunremi, Dele
    Dupras, Andree Ann
    Naushad, Sohail
    Gao, Ruimin
    Duceppe, Marc-Olivier
    Omidi, Katayoun
    Marquez, Imelda Galvan
    Huang, Hongsheng
    Goodridge, Lawrence
    Levesque, Roger C.
    Hasan, Nur A.
    Dadlani, Manoj
    Dixon, Brent
    Magierowski, Sebastian
    Masson, Luke
    [J]. FRONTIERS IN MICROBIOLOGY, 2020, 11
  • [24] Culture-based and culture-independent assessment of the impact of mixed and single plant treatments on rhizosphere microbial communities in hydrocarbon contaminated flare-pit soil
    Phillips, Lori A.
    Greer, Charles W.
    Germida, James J.
    [J]. SOIL BIOLOGY & BIOCHEMISTRY, 2006, 38 (09): : 2823 - 2833
  • [25] Sources and Persistence of Fecal Indicator Bacteria and Bacteroidales in Sand as Measured by Culture-Based and Culture-Independent Methods: a Case Study at Santa Monica Pier, California
    Mika, Kathryn B.
    Chavarria, Karina A.
    Imamura, Greg
    Tang, Chay
    Torres, Robert
    Jay, Jennifer A.
    [J]. WATER AIR AND SOIL POLLUTION, 2017, 228 (04):
  • [26] Unveiling the microbial communities and metabolic pathways of Keem, a traditional starter culture, through whole-genome sequencing
    Babita Rana
    Renu Chandola
    Pankaj Sanwal
    Gopal Krishna Joshi
    [J]. Scientific Reports, 14
  • [27] Whole-Genome Sequencing Identifies Genetic Variances in Culture-Expanded Human Mesenchymal Stem Cells
    Cai, Jun
    Miao, Xuexia
    Li, Yueying
    Smith, Cory
    Tsang, Kitman
    Cheng, Linzhao
    Wang, Qian-fei
    [J]. STEM CELL REPORTS, 2014, 3 (02): : 227 - 233
  • [28] Unveiling the microbial communities and metabolic pathways of Keem, a traditional starter culture, through whole-genome sequencing
    Rana, Babita
    Chandola, Renu
    Sanwal, Pankaj
    Joshi, Gopal Krishna
    [J]. SCIENTIFIC REPORTS, 2024, 14 (01)
  • [29] Microfluidic Capture of Mycobacterium tuberculosis from Clinical Samples for Culture-Free Whole-Genome Sequencing
    Ismail, Nabila
    Dippenaar, Anzaan
    Morgan, George
    Grobbelaar, Melanie
    Wells, Felicia
    Caffry, Jessica
    Morais, Cristiana
    Gizynski, Krzysztof
    McGurk, David
    Boada, Eduardo
    Murton, Heather
    Warren, Robin M.
    Van Rie, Annelies
    [J]. MICROBIOLOGY SPECTRUM, 2023, 11 (04):
  • [30] Sources and Persistence of Fecal Indicator Bacteria and Bacteroidales in Sand as Measured by Culture-Based and Culture-Independent Methods: a Case Study at Santa Monica Pier, California
    Kathryn B. Mika
    Karina A. Chavarria
    Greg Imamura
    Chay Tang
    Robert Torres
    Jennifer A. Jay
    [J]. Water, Air, & Soil Pollution, 2017, 228