Bird's-eye MApping of plasmids (BeMAp) for visualization and comparison of genomic structures of different plasmids by mapping antimicrobial resistance genes on spreadsheets

• Published in: Journal of microbiological methods Vol. 204; p. 106645
• Main Authors: Tsuda, Yusuke, Suzuki, Masahiro, Wachino, Jun-ichi, Kimura, Kouji, Arakawa, Yoshichika
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.01.2023
• Subjects: Anti-Bacterial Agents - pharmacology; Anti-Bacterial Agents - therapeutic use; Antimicrobial resistance gene; beta-Lactamases - genetics; blaIMP-6; blaIMPs; Drug Resistance, Bacterial - genetics; Genomics; Microbial Sensitivity Tests; Plasmids; Plasmids - genetics; CDS; Antimicrobial resistance gene; Plasmids; MBL; BeMAp; blaIMPs; blaIMP-6; Inc; bla(IMPs); bla(IMP-6)
• ISSN: 0167-7012; 1872-8359
• DOI: 10.1016/j.mimet.2022.106645

Effective classification and visualization of multiple antimicrobial resistance plasmids can be challenging, and few tools to analyze similarities among plasmids depending on the location of genes are available. We created a new plasmid mapping program called Bird's-eye MApping of plasmids (BeMAp) to map antimicrobial resistance genes across multiple plasmids onto a spreadsheet and visualize their similarities based on gene types, locations, alignments, and organization. We analyzed plasmids containing various antimicrobial resistance genes, together with genes coding for IMP-type metallo-β-lactamases. Moreover, the mapping of plasmids with antimicrobial resistance genes and Incompatibility (Inc) groups showed that clustered plasmids with a similar organization of antimicrobial resistance genes were not always classified into the same Inc groups, indicating that the program displays multiple plasmids regardless of the Inc group classification. Our results showed that this calculation protocol and mapping strategy could provide a valuable tool for the practical and convenient visualization and comparison of the genomic structure of multiple plasmids in parallel. •Multiple plasmids carrying blaIMPs, including blaIMP-6, were analyzed.•BeMAp visualizes genomic structural similarities among multiple plasmids.•Relation between antimicrobial resistance genes and features of plasmids was visualized.