Ann Lab Med 2019; 39(6): 530-536  https://doi.org/10.3343/alm.2019.39.6.530
Application of the Whole Genome-Based Bacterial Identification System, TrueBac ID, Using Clinical Isolates That Were Not Identified With Three Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) Systems
Sung-Min Ha, M.Sc.1,2*, Chang Ki Kim, M.D., Ph.D.3,4*, Juhye Roh, M.D.5, Jung-Hyun Byun, M.D.4,5,6, Seung-Jo Yang, Ph.D.1, Seon-Bin Choi, M.Sc.1, Jongsik Chun, Ph.D.1,2, and Dongeun Yong, M.D., Ph.D.4,5,7
1ChunLab, Inc., Seoul, Korea; 2School of Biological Sciences & Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea; 3Seoul Clinical Laboratories, Yongin, Korea; 4Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea; 5Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea; 6Department of Laboratory Medicine, Gyeongsang National University Hospital, and Gyeongsang National University College of Medicine, Jinju, Korea; 7Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
Corresponding author: Dongeun Yong, M.D., Ph.D.
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: +82-2-2228-2802 Fax: +82-2-364-1583 E-mail: deyong@yuhs.ac

*These authors contributed equally to this work.
Received: October 14, 2018; Revised: January 8, 2019; Accepted: May 22, 2019; Published online: November 1, 2019.
© 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/4.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
Background: Next-generation sequencing is increasingly used for taxonomic identification of pathogenic bacterial isolates. We evaluated the performance of a newly introduced whole genome-based bacterial identification system, TrueBac ID (ChunLab Inc., Seoul, Korea), using clinical isolates that were not identified by three matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems and 16S rRNA gene sequencing.
Methods: Thirty-six bacterial isolates were selected from a university-affiliated hospital and a commercial clinical laboratory. Species was identified by three MALDI-TOF MS systems: Bruker Biotyper MS (Bruker Daltonics, Billerica, MA, USA), VITEK MS (bioMérieux, Marcy l’Étoile, France), and ASTA MicroIDSys (ASTA Inc., Suwon, Korea). Whole genome sequencing was conducted using the Illumina MiSeq system (Illumina, San Diego, CA, USA), and genome-based identification was performed using the TrueBac ID cloud system (www.truebacid.com).
Results: TrueBac ID assigned 94% (34/36) of the isolates to known (N=25) or novel (N=4) species, genomospecies (N=3), or species group (N=2). The remaining two were identified at the genus level.
Conclusions: TrueBac ID successfully identified the majority of isolates that MALDI-TOF MS failed to identify. Genome-based identification can be a useful tool in clinical laboratories, with its superior accuracy and database-driven operations.
Keywords: Next generation sequencing, Genome-based identification, TrueBac ID, Performance

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