Ann Lab Med 2018; 38(2): 110-118  
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
Ji Yeon Sung, M.D.1, Younjee Hwang, B.S.2, Mi Hwa Shin, B.S.3, Moo Suk Park, M.D.3, Sang Hoon Lee, M.D.4, Dongeun Yong, M.D.1, and Kyungwon Lee, M.D.1
Research Institute of Bacterial Resistance and Department of Laboratory Medicine1, Yonsei University College of Medicine, Seoul; Brain Korea 21 PLUS Project for Medical Science2, Yonsei University, Seoul; Division of Pulmonary and Critical Care Medicine3, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul; Department of Internal Medicine4, Seoul National University College of Medicine, Division of Pulmonary and Critical Care Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
Correspondence to: Dongeun Yong
Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
Tel: +82-2-2228-2442
Fax: +82-2-364-1583
E-mail: DEYONG@yuhs.ac
Received: February 14, 2017; Revised: April 14, 2017; Accepted: October 10, 2017; Published online: March 1, 2018.
© The Korean Society for Laboratory Medicine. All rights reserved.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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.
Keywords: Bronchoalveolar lavage, Microbiota, Matrix-assisted laser desorption-ionization mass spectrometry, Culture, Next generation sequencing



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