Ann Lab Med.  2019 Mar;39(2):183-189. 10.3343/alm.2019.39.2.183.

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

• Park YJ
• Choi MH
• Kim D
• Lee K
• Kim HO
• Jeong SH

• KMID: 2425974
• DOI: http://doi.org/10.3343/alm.2019.39.2.183

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.

Keyword

Multilocus sequence typing; Microsoft Excel; Macro; Software; Automatic data processing; Molecular epidemiology

MeSH Terms

Automatic Data Processing
Clone Cells*
Complement System Proteins
Epidemiologic Studies
Genes, Essential
Information Storage and Retrieval
Molecular Epidemiology
Molecular Typing
Multilocus Sequence Typing*
Complement System Proteins

Figure

• 

  Fig. 1 Schematic process of MLST typer: detailed schematic processes (A) from importing 308 data to allelic typing and (B) from sorting to sequence typing. The software and example files are freely available at: http://medicine.yonsei.ac.kr/en/Research/research_inst/Research_Bacterial/Research_papers/index.asp (article #109) or upon request from the authors at [e-mail] or [e-mail]: Contig, contiguous DNA sequence; MLST, multilocus sequence typing; ST, sequence type; RC, reverse-complement.

• 

  Fig. 2 Composition of the MLST typer console.Abbreviations: MLST, multilocus sequence typing; RC, reverse-complement; ST, sequence type.

• 

  Fig. 3 Example of the Results and Summary worksheet. (A) Example of Results worksheet with assembled sequence and allele typing results. The Result worksheet columns are color-indexed according to each process: importing the DNA sequence (blue), reverse complement (RC) conversion of reverse sequences (yellow), assembling the contig according to consensus sequences (green), and allelic typing (red). (B) Example of Summary worksheet with sorted allelic types and sequence types (ST) results. The Summary worksheet columns are color-indexed according to each process: sort matched allelic types according to isolate names (blue) and find STs queried from the database (green).

• 

  Fig. 4 The “R-F Assembly” process. This is an optional process that can be performed after the main workflow is completed. (A) Ideal assembly provides the longest possible forward-reverse assembled contig. (B) When forward and reverse sequences are incorrectly named, it can result in a shorter than expected contig. (C) The “R-F Assembly” process elongates the assembled contig through reverse-forward order assembly.

• 

  Fig. 5 Evaluation of the accuracy of MLST typer compared with manual assessment.Abbreviation: MLST, multilocus sequence typing.

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