An excel macro for determining allelic and sequence types of bacterial clones in multilocus sequence typing

Yu Jin Park, Min Hyuk Choi, Dokyun Kim, Kwangjun Lee, Hyun Ok Kim, Seokhoon Jeong

Research output: Contribution to journalArticle

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.

LanguageEnglish
Pages183-189
Number of pages7
JournalAnnals of Laboratory Medicine
Volume39
Issue number2
DOIs
Publication statusPublished - 2019 Jan 1

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Multilocus Sequence Typing
Macros
Clone Cells
Genes
Sequence Analysis
Personnel
Molecular Typing
Information Storage and Retrieval
Essential Genes
Epidemiologic Studies

All Science Journal Classification (ASJC) codes

  • Clinical Biochemistry
  • Biochemistry, medical

Cite this

Park, Yu Jin ; Choi, Min Hyuk ; Kim, Dokyun ; Lee, Kwangjun ; Kim, Hyun Ok ; Jeong, Seokhoon. / An excel macro for determining allelic and sequence types of bacterial clones in multilocus sequence typing. In: Annals of Laboratory Medicine. 2019 ; Vol. 39, No. 2. pp. 183-189.
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An excel macro for determining allelic and sequence types of bacterial clones in multilocus sequence typing. / Park, Yu Jin; Choi, Min Hyuk; Kim, Dokyun; Lee, Kwangjun; Kim, Hyun Ok; Jeong, Seokhoon.

In: Annals of Laboratory Medicine, Vol. 39, No. 2, 01.01.2019, p. 183-189.

Research output: Contribution to journalArticle

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