WeFaceNano: a user-friendly pipeline for complete ONT sequence assembly and detection of antibiotic resistance in multi-plasmid bacterial isolates.

Autor: Heikema AP; Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center (Erasmus MC), Rotterdam, the Netherlands. a.heikema@erasmusmc.nl., Jansen R; Department of Pathology, Clinical Bioinformatics Unit, Erasmus University Medical Center (Erasmus MC), Rotterdam, The Netherlands., Hiltemann SD; Department of Pathology, Clinical Bioinformatics Unit, Erasmus University Medical Center (Erasmus MC), Rotterdam, The Netherlands., Hays JP; Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center (Erasmus MC), Rotterdam, the Netherlands., Stubbs AP; Department of Pathology, Clinical Bioinformatics Unit, Erasmus University Medical Center (Erasmus MC), Rotterdam, The Netherlands.
Jazyk: angličtina
Zdroj: BMC microbiology [BMC Microbiol] 2021 Jun 07; Vol. 21 (1), pp. 171. Date of Electronic Publication: 2021 Jun 07.
DOI: 10.1186/s12866-021-02225-y
Abstrakt: Background: Bacterial plasmids often carry antibiotic resistance genes and are a significant factor in the spread of antibiotic resistance. The ability to completely assemble plasmid sequences would facilitate the localization of antibiotic resistance genes, the identification of genes that promote plasmid transmission and the accurate tracking of plasmid mobility. However, the complete assembly of plasmid sequences using the currently most widely used sequencing platform (Illumina-based sequencing) is restricted due to the generation of short sequence lengths. The long-read Oxford Nanopore Technologies (ONT) sequencing platform overcomes this limitation. Still, the assembly of plasmid sequence data remains challenging due to software incompatibility with long-reads and the error rate generated using ONT sequencing. Bioinformatics pipelines have been developed for ONT-generated sequencing but require computational skills that frequently are beyond the abilities of scientific researchers. To overcome this challenge, the authors developed 'WeFaceNano', a user-friendly Web interFace for rapid assembly and analysis of plasmid DNA sequences generated using the ONT platform. WeFaceNano includes: a read statistics report; two assemblers (Miniasm and Flye); BLAST searching; the detection of antibiotic resistance- and replicon genes and several plasmid visualizations. A user-friendly interface displays the main features of WeFaceNano and gives access to the analysis tools.
Results: Publicly available ONT sequence data of 21 plasmids were used to validate WeFaceNano, with plasmid assemblages and anti-microbial resistance gene detection being concordant with the published results. Interestingly, the "Flye" assembler with "meta" settings generated the most complete plasmids.
Conclusions: WeFaceNano is a user-friendly open-source software pipeline suitable for accurate plasmid assembly and the detection of anti-microbial resistance genes in (clinical) samples where multiple plasmids can be present.
Databáze: MEDLINE
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