On the ability to extract MLVA profiles of Vibrio cholerae isolates from WGS data generated with Oxford Nanopore Technologies
Abstract Objective Multiple-Locus Variable Number of Tandem Repeats (VNTR) Analysis (MLVA) is widely used to subtype pathogens causing foodborne and waterborne disease outbreaks. The MLVAType shiny application was previously designed to extract MLVA profiles of Vibrio cholerae isolates from whole-ge...
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2025-01-01
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| Online Access: | https://doi.org/10.1186/s13104-025-07093-7 |
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| author | Jérôme Ambroise Bertrand Bearzatto Jean-Francois Durant Leonid M. Irenge Jean-Luc Gala |
| author_facet | Jérôme Ambroise Bertrand Bearzatto Jean-Francois Durant Leonid M. Irenge Jean-Luc Gala |
| author_sort | Jérôme Ambroise |
| collection | DOAJ |
| description | Abstract Objective Multiple-Locus Variable Number of Tandem Repeats (VNTR) Analysis (MLVA) is widely used to subtype pathogens causing foodborne and waterborne disease outbreaks. The MLVAType shiny application was previously designed to extract MLVA profiles of Vibrio cholerae isolates from whole-genome sequencing (WGS) data, and provide backward compatibility with traditional MLVA typing methods. The previous development and validation work was conducted using short (pair-end 300 and 150 nt long) reads from Illumina MiSeq and Hiseq sequencing. In this study, the MLVAType application was validated using long reads generated by Oxford Nanopore Technologies (ONT) sequencing platforms. In silico MLVA profiles of V. cholerae isolates (n = 9) from the Democratic Republic of the Congo were generated using the MLVAType application on Nanopore WGS data. The WGS-derived in silico MLVA profiles were extracted from Canu (v.2.2) assemblies obtained through MinION and GridION sequencing by ONT. The results were compared to those obtained from SPAdes assemblies (v3.13.0; k-mer 175) generated from short-read (pair-end 300-bp) reference data obtained by MiSeq sequencing, Illumina. Results For each isolate, the in silico MLVA profiles were concordant across all three sequencing methods, demonstrating that the MLVAType application can accurately predict the MLVA profiles from assembled genomes generated by long-reads ONT sequencers. |
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| institution | Kabale University |
| issn | 1756-0500 |
| language | English |
| publishDate | 2025-01-01 |
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| spelling | doaj-art-354c76130db240b085527cb632831f252025-01-19T12:08:40ZengBMCBMC Research Notes1756-05002025-01-011811510.1186/s13104-025-07093-7On the ability to extract MLVA profiles of Vibrio cholerae isolates from WGS data generated with Oxford Nanopore TechnologiesJérôme Ambroise0Bertrand Bearzatto1Jean-Francois Durant2Leonid M. Irenge3Jean-Luc Gala4Center for Applied Molecular Technologies (CTMA), Institute of Clinical and Experimental Research (IREC), Université catholique de Louvain (UCLouvain)Center for Applied Molecular Technologies (CTMA), Institute of Clinical and Experimental Research (IREC), Université catholique de Louvain (UCLouvain)Center for Applied Molecular Technologies (CTMA), Institute of Clinical and Experimental Research (IREC), Université catholique de Louvain (UCLouvain)Center for Applied Molecular Technologies (CTMA), Institute of Clinical and Experimental Research (IREC), Université catholique de Louvain (UCLouvain)Center for Applied Molecular Technologies (CTMA), Institute of Clinical and Experimental Research (IREC), Université catholique de Louvain (UCLouvain)Abstract Objective Multiple-Locus Variable Number of Tandem Repeats (VNTR) Analysis (MLVA) is widely used to subtype pathogens causing foodborne and waterborne disease outbreaks. The MLVAType shiny application was previously designed to extract MLVA profiles of Vibrio cholerae isolates from whole-genome sequencing (WGS) data, and provide backward compatibility with traditional MLVA typing methods. The previous development and validation work was conducted using short (pair-end 300 and 150 nt long) reads from Illumina MiSeq and Hiseq sequencing. In this study, the MLVAType application was validated using long reads generated by Oxford Nanopore Technologies (ONT) sequencing platforms. In silico MLVA profiles of V. cholerae isolates (n = 9) from the Democratic Republic of the Congo were generated using the MLVAType application on Nanopore WGS data. The WGS-derived in silico MLVA profiles were extracted from Canu (v.2.2) assemblies obtained through MinION and GridION sequencing by ONT. The results were compared to those obtained from SPAdes assemblies (v3.13.0; k-mer 175) generated from short-read (pair-end 300-bp) reference data obtained by MiSeq sequencing, Illumina. Results For each isolate, the in silico MLVA profiles were concordant across all three sequencing methods, demonstrating that the MLVAType application can accurately predict the MLVA profiles from assembled genomes generated by long-reads ONT sequencers.https://doi.org/10.1186/s13104-025-07093-7In silico MLVA profilesSequencingNanoporeLong readsWGS |
| spellingShingle | Jérôme Ambroise Bertrand Bearzatto Jean-Francois Durant Leonid M. Irenge Jean-Luc Gala On the ability to extract MLVA profiles of Vibrio cholerae isolates from WGS data generated with Oxford Nanopore Technologies BMC Research Notes In silico MLVA profiles Sequencing Nanopore Long reads WGS |
| title | On the ability to extract MLVA profiles of Vibrio cholerae isolates from WGS data generated with Oxford Nanopore Technologies |
| title_full | On the ability to extract MLVA profiles of Vibrio cholerae isolates from WGS data generated with Oxford Nanopore Technologies |
| title_fullStr | On the ability to extract MLVA profiles of Vibrio cholerae isolates from WGS data generated with Oxford Nanopore Technologies |
| title_full_unstemmed | On the ability to extract MLVA profiles of Vibrio cholerae isolates from WGS data generated with Oxford Nanopore Technologies |
| title_short | On the ability to extract MLVA profiles of Vibrio cholerae isolates from WGS data generated with Oxford Nanopore Technologies |
| title_sort | on the ability to extract mlva profiles of vibrio cholerae isolates from wgs data generated with oxford nanopore technologies |
| topic | In silico MLVA profiles Sequencing Nanopore Long reads WGS |
| url | https://doi.org/10.1186/s13104-025-07093-7 |
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