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An Excel Macro for Determining Allelic and Sequence Types of Bacterial Clones in Multilocus Sequence Typing

Authors
 Yu Jin Park  ;  Min Hyuk Choi  ;  Dokyun Kim  ;  Kwangjun Lee  ;  Hyun Ok Kim  ;  Seok Hoon Jeong 
Citation
 ANNALS OF LABORATORY MEDICINE, Vol.39(2) : 183-189, 2019 
Journal Title
ANNALS OF LABORATORY MEDICINE
ISSN
 2234-3806 
Issue Date
2019
MeSH
Databases, Factual ; Multilocus Sequence Typing/methods* ; Software*
Keywords
Automatic data processing ; Macro ; Microsoft Excel ; Molecular epidemiology ; Multilocus sequence typing ; Software
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.
Files in This Item:
T201904441.pdf Download
DOI
10.3343/alm.2019.39.2.183
Appears in Collections:
1. College of Medicine (의과대학) > Dept. of Laboratory Medicine (진단검사의학교실) > 1. Journal Papers
Yonsei Authors
Kim, Dokyun(김도균) ORCID logo https://orcid.org/0000-0002-0348-5440
Kim, Hyun Ok(김현옥) ORCID logo https://orcid.org/0000-0002-4964-1963
Jeong, Seok Hoon(정석훈) ORCID logo https://orcid.org/0000-0001-9290-897X
URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/173292
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