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Utility of Conventional Culture and MALDI-TOF MS for Identification of Microbial Communities in Bronchoalveolar Lavage Fluid in Comparison with the GS Junior Next Generation Sequencing System

Authors
 Ji Yeon Sung  ;  Younjee Hwang  ;  Mi Hwa Shin  ;  Moo Suk Park  ;  Sang Hoon Lee  ;  Dongeun Yong  ;  Kyungwon Lee 
Citation
 Annals of Laboratory Medicine, Vol.38(2) : 110-118, 2018 
Journal Title
 Annals of Laboratory Medicine 
ISSN
 2234-3806 
Issue Date
2018
MeSH
Bacteria/*genetics/isolation & purification ; Bronchoalveolar Lavage Fluid/*microbiology ; Fungi/genetics/isolation & purification ; *High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota ; Ribosomal RNA, 16S/chemistry/genetics/metabolism ; Respiratory Tract Infections/diagnosis/metabolism ; DNA Sequence Analysis ; Mass *Spectrometry, Matrix-Assisted Laser Desorption-Ionization
Keywords
Bronchoalveolar lavage ; Culture ; Matrix-assisted laser desorption-ionization mass spectrometry ; Microbiota ; Next generation sequencing
Abstract
BACKGROUND: Diverse microbiota exist in the lower respiratory tract. Although next generation sequencing (NGS) is the most widely used microbiome analysis technique, it is difficult to implement NGS in clinical microbiology laboratories. Therefore, we evaluated the performance of conventional culture methods together with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in identifying microbiota in bronchoalveolar lavage (BAL) fluid. METHODS: BAL fluid samples (n=27) were obtained from patients undergoing diagnostic bronchoscopy for lung mass evaluation. Bacterial and fungal culture was performed with conventional media used in clinical microbiology laboratories. On an average, 20 isolated colonies were picked from each agar plate and identified by MALDI-TOF MS. Microbiome analysis using 16S rRNA NGS was conducted for comparison. RESULTS: Streptococcus spp. and Neisseria spp. were most frequently cultured from the BAL fluid samples. In two samples, Enterobacteriaceae grew predominantly on MacConkey agar. Actinomyces and Veillonella spp. were commonly identified anaerobes; gut bacteria, such as Lactobacillus, Bifidobacterium, and Clostridium, and fungi were also isolated. NGS revealed more diverse bacterial communities than culture, and Prevotella spp. were mainly identified solely by NGS. Some bacteria, such as Staphylococcus spp., Clostridium spp., and Bifidobacterium spp., were identified solely by culture, indicating that culture may be more sensitive for detecting certain bacteria. CONCLUSIONS: Culture and NGS of BAL fluid samples revealed common bacteria with some different microbial communities. Despite some limitations, culture combined with MALDI-TOF MS might play a complementary role in microbiome analysis using 16S rRNA NGS.
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DOI
10.3343/alm.2018.38.2.110
Appears in Collections:
1. College of Medicine (의과대학) > Dept. of Internal Medicine (내과학교실) > 1. Journal Papers
1. College of Medicine (의과대학) > Dept. of Laboratory Medicine (진단검사의학교실) > 1. Journal Papers
Yonsei Authors
박무석(Park, Moo Suk) ORCID logo https://orcid.org/0000-0003-0820-7615
신미화(Shin, Mi Hwa) ORCID logo https://orcid.org/0000-0003-2215-8629
용동은(Yong, Dong Eun) ORCID logo https://orcid.org/0000-0002-1225-8477
이경원(Lee, Kyungwon) ORCID logo https://orcid.org/0000-0003-3788-2134
이상훈(Lee, Sang Hoon) ORCID logo https://orcid.org/0000-0002-7706-5318
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URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/162069
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