Cargando…
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
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 cultur...
Autores principales: | , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The Korean Society for Laboratory Medicine
2018
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5736669/ https://www.ncbi.nlm.nih.gov/pubmed/29214754 http://dx.doi.org/10.3343/alm.2018.38.2.110 |
_version_ | 1783287402667704320 |
---|---|
author | Sung, Ji Yeon Hwang, Younjee Shin, Mi Hwa Park, Moo Suk Lee, Sang Hoon Yong, Dongeun Lee, Kyungwon |
author_facet | Sung, Ji Yeon Hwang, Younjee Shin, Mi Hwa Park, Moo Suk Lee, Sang Hoon Yong, Dongeun Lee, Kyungwon |
author_sort | Sung, Ji Yeon |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-5736669 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | The Korean Society for Laboratory Medicine |
record_format | MEDLINE/PubMed |
spelling | pubmed-57366692018-03-01 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 Sung, Ji Yeon Hwang, Younjee Shin, Mi Hwa Park, Moo Suk Lee, Sang Hoon Yong, Dongeun Lee, Kyungwon Ann Lab Med Original Article 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. The Korean Society for Laboratory Medicine 2018-03 2017-12-04 /pmc/articles/PMC5736669/ /pubmed/29214754 http://dx.doi.org/10.3343/alm.2018.38.2.110 Text en © The Korean Society for Laboratory Medicine http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Article Sung, Ji Yeon Hwang, Younjee Shin, Mi Hwa Park, Moo Suk Lee, Sang Hoon Yong, Dongeun Lee, Kyungwon 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 |
title | 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 |
title_full | 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 |
title_fullStr | 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 |
title_full_unstemmed | 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 |
title_short | 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 |
title_sort | 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 |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5736669/ https://www.ncbi.nlm.nih.gov/pubmed/29214754 http://dx.doi.org/10.3343/alm.2018.38.2.110 |
work_keys_str_mv | AT sungjiyeon utilityofconventionalcultureandmalditofmsforidentificationofmicrobialcommunitiesinbronchoalveolarlavagefluidincomparisonwiththegsjuniornextgenerationsequencingsystem AT hwangyounjee utilityofconventionalcultureandmalditofmsforidentificationofmicrobialcommunitiesinbronchoalveolarlavagefluidincomparisonwiththegsjuniornextgenerationsequencingsystem AT shinmihwa utilityofconventionalcultureandmalditofmsforidentificationofmicrobialcommunitiesinbronchoalveolarlavagefluidincomparisonwiththegsjuniornextgenerationsequencingsystem AT parkmoosuk utilityofconventionalcultureandmalditofmsforidentificationofmicrobialcommunitiesinbronchoalveolarlavagefluidincomparisonwiththegsjuniornextgenerationsequencingsystem AT leesanghoon utilityofconventionalcultureandmalditofmsforidentificationofmicrobialcommunitiesinbronchoalveolarlavagefluidincomparisonwiththegsjuniornextgenerationsequencingsystem AT yongdongeun utilityofconventionalcultureandmalditofmsforidentificationofmicrobialcommunitiesinbronchoalveolarlavagefluidincomparisonwiththegsjuniornextgenerationsequencingsystem AT leekyungwon utilityofconventionalcultureandmalditofmsforidentificationofmicrobialcommunitiesinbronchoalveolarlavagefluidincomparisonwiththegsjuniornextgenerationsequencingsystem |