Ann Lab Med 2019; 39(2): 183-189  https://doi.org/10.3343/alm.2019.39.2.183
An Excel Macro for Determining Allelic and Sequence Types of Bacterial Clones in Multilocus Sequence Typing
Yu Jin Park, M.D.1,2, Min Hyuk Choi, M.D.1,2, Dokyun Kim, M.D.1,2, Kwangjun Lee, Ph.D.3, Hyun Ok Kim, M.D., Ph.D.1,
and Seok Hoon Jeong, M.D., Ph.D.1,2
1Department of Laboratory Medicine, 2Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea; 3Division of Antimicrobial Resistance, National Institute of Health, Centers for Disease Control and Prevention, Cheongju, Korea
Corresponding author: Dokyun Kim, M.D. https://orcid.org/0000-0002-0348-5440
Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Gangnam Severance Hospital, Yonsei University College of Medicine, 211 Eonju-ro, Gangnam-gu, Seoul 06273, Korea
Tel: +82-2-2019-3532
Fax: +82-2-2057-8926
E-mail: kyunsky@yuhs.ac
Received: March 29, 2018; Revised: July 9, 2018; Accepted: October 16, 2018; Published online: March 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: Multilocus sequence typing (MLST) was designed to overcome the low discriminatory power and poor reproducibility of previous molecular typing schemes, and it is useful for inter-laboratory, inter-regional, and inter-national comparison of pathogenic clones. MLST includes labor-intensive sequencing processes and meticulous allelic/sequence type (ST) determination processes, often prone to error. We developed a free automated MLST determination program (MLST typer) based on the Visual Basic for Applications macro, which runs on Microsoft Excel.
Methods: MLST typer imports sequence data in the FASTA format, converts reverse-complement counterparts of the reverse sequences, assembles forward and reverse-complement converted sequences, and returns allelic numbers for each gene and ST of each isolate. To evaluate the performance of MLST typer, we tested the sequence data from 200 clinical isolates, each consisting of seven housekeeping gene sequences, with a total of 1,400 allelic number determinations. The results were compared with manual assessment.
Results: MLST typer comprises three worksheets: the Main page, Result page, and Summary page. The Main page console operates the process according to user-specified parameters. The Result and Summary pages provide the allelic type and ST determinations. It took approximately 12 minutes to analyze the sequence data from 200 clinical isolates. Compared with manual assessment, the rate of correct identification was 97.2% (1,361/1,400).
Conclusions: MLST typer can be widely used for epidemiological studies owing to its thoroughness in repetitive functions, good compatibility with FASTA type data files, and easy-to-understand outputs for allelic and ST determinations.
Keywords: Multilocus sequence typing, Microsoft Excel, Macro, Software, Automatic data processing, Molecular epidemiology



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