Ann Lab Med.  2018 Mar;38(2):110-118. 10.3343/alm.2018.38.2.110.

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 JY
• Hwang Y
• Shin MH
• Park MS
• Lee SH
• Yong D
• Lee K

• KMID: 2403355
• DOI: http://doi.org/10.3343/alm.2018.38.2.110

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.

Keyword

Bronchoalveolar lavage; Microbiota; Matrix-assisted laser desorption-ionization mass spectrometry; Culture; Next generation sequencing

MeSH Terms

Actinomyces
Agar
Bacteria
Bifidobacterium
Bronchoalveolar Lavage Fluid*
Bronchoalveolar Lavage*
Bronchoscopy
Clostridium
Enterobacteriaceae
Fungi
Humans
Lactobacillus
Lung
Mass Spectrometry
Microbiota
Neisseria
Prevotella
Respiratory System
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Staphylococcus
Streptococcus
Veillonella
Agar

Figure

• 

  Fig. 1 Number of the operational taxonomic units and genera identified by culture and 16S rRNA next generation sequencing analysis.

• 

  Fig. 2 Bacterial genera identified using culture with/without sequencing and 16S rRNA next generation sequencing analysis.

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