TBpore cluster: A novel phylogenetic pipeline for tuberculosis transmission studies using nanopore next-generation sequencing data.
<h4>Background</h4>Molecular typing of Mycobacterium tuberculosis complex isolates enhances understanding of tuberculosis (TB) transmission dynamics, supporting public health efforts in outbreak investigations. This study aims to validate TBpore, a novel bioinformatic pipeline for cluste...
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| Format: | Article |
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Public Library of Science (PLoS)
2025-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0325914 |
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| author | Sophie Gagnon Emmanuelle Ametepe Floriane Point William Cloutier Charette Arpita Chakravarti Paul Rivest Pierre-Marie Akochy Hafid Soualhine Zamin Iqbal Michael B Hall Simon Grandjean Lapierre |
| author_facet | Sophie Gagnon Emmanuelle Ametepe Floriane Point William Cloutier Charette Arpita Chakravarti Paul Rivest Pierre-Marie Akochy Hafid Soualhine Zamin Iqbal Michael B Hall Simon Grandjean Lapierre |
| author_sort | Sophie Gagnon |
| collection | DOAJ |
| description | <h4>Background</h4>Molecular typing of Mycobacterium tuberculosis complex isolates enhances understanding of tuberculosis (TB) transmission dynamics, supporting public health efforts in outbreak investigations. This study aims to validate TBpore, a novel bioinformatic pipeline for clustering TB transmission isolates using Oxford Nanopore Technology (ONT) data and comparing it against conventional Mycobacterial Interspersed Repetitive-Unit Variable Number (MIRU-VNTR) typing and Illumina sequencing.<h4>Methodology/principal findings</h4>This retrospective case-control study included 58 clinical isolates from two TB outbreaks in Canada, previously characterized by public health investigations and MIRU-VNTR typing. DNA extraction and sequencing were performed on both Illumina and ONT platforms. Illumina data were processed using Clockwork and psdm, while Nanopore data were analyzed with TBpore. SNP distances were used to compare clustering results across methods, with clusters defined by SNP distance thresholds of ≤5 and ≤12. Both sequencing methods showed a high degree of concordance in clustering results. All isolates from the M. africanum outbreak clustered within the defined SNP thresholds, consistent with MIRU-VNTR and epidemiological data. In the M. tuberculosis outbreak, 20 out of 21 isolates clustered similarly across methods, with one exception. Within outbreak pairwise SNP distances were lower with Nanopore.<h4>Conclusion/significance</h4>ONT sequencing and the TBpore pipeline offer an accurate alternative to Illumina technology for TB molecular epidemiology. This study suggests potential increased clustering sensitivity with Nanopore technology, warranting further validation on larger datasets with robust epidemiological metadata. |
| format | Article |
| id | doaj-art-70c1292432bd4be89a136ef4acb0ac26 |
| institution | Kabale University |
| issn | 1932-6203 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-70c1292432bd4be89a136ef4acb0ac262025-08-20T03:30:48ZengPublic Library of Science (PLoS)PLoS ONE1932-62032025-01-01206e032591410.1371/journal.pone.0325914TBpore cluster: A novel phylogenetic pipeline for tuberculosis transmission studies using nanopore next-generation sequencing data.Sophie GagnonEmmanuelle AmetepeFloriane PointWilliam Cloutier CharetteArpita ChakravartiPaul RivestPierre-Marie AkochyHafid SoualhineZamin IqbalMichael B HallSimon Grandjean Lapierre<h4>Background</h4>Molecular typing of Mycobacterium tuberculosis complex isolates enhances understanding of tuberculosis (TB) transmission dynamics, supporting public health efforts in outbreak investigations. This study aims to validate TBpore, a novel bioinformatic pipeline for clustering TB transmission isolates using Oxford Nanopore Technology (ONT) data and comparing it against conventional Mycobacterial Interspersed Repetitive-Unit Variable Number (MIRU-VNTR) typing and Illumina sequencing.<h4>Methodology/principal findings</h4>This retrospective case-control study included 58 clinical isolates from two TB outbreaks in Canada, previously characterized by public health investigations and MIRU-VNTR typing. DNA extraction and sequencing were performed on both Illumina and ONT platforms. Illumina data were processed using Clockwork and psdm, while Nanopore data were analyzed with TBpore. SNP distances were used to compare clustering results across methods, with clusters defined by SNP distance thresholds of ≤5 and ≤12. Both sequencing methods showed a high degree of concordance in clustering results. All isolates from the M. africanum outbreak clustered within the defined SNP thresholds, consistent with MIRU-VNTR and epidemiological data. In the M. tuberculosis outbreak, 20 out of 21 isolates clustered similarly across methods, with one exception. Within outbreak pairwise SNP distances were lower with Nanopore.<h4>Conclusion/significance</h4>ONT sequencing and the TBpore pipeline offer an accurate alternative to Illumina technology for TB molecular epidemiology. This study suggests potential increased clustering sensitivity with Nanopore technology, warranting further validation on larger datasets with robust epidemiological metadata.https://doi.org/10.1371/journal.pone.0325914 |
| spellingShingle | Sophie Gagnon Emmanuelle Ametepe Floriane Point William Cloutier Charette Arpita Chakravarti Paul Rivest Pierre-Marie Akochy Hafid Soualhine Zamin Iqbal Michael B Hall Simon Grandjean Lapierre TBpore cluster: A novel phylogenetic pipeline for tuberculosis transmission studies using nanopore next-generation sequencing data. PLoS ONE |
| title | TBpore cluster: A novel phylogenetic pipeline for tuberculosis transmission studies using nanopore next-generation sequencing data. |
| title_full | TBpore cluster: A novel phylogenetic pipeline for tuberculosis transmission studies using nanopore next-generation sequencing data. |
| title_fullStr | TBpore cluster: A novel phylogenetic pipeline for tuberculosis transmission studies using nanopore next-generation sequencing data. |
| title_full_unstemmed | TBpore cluster: A novel phylogenetic pipeline for tuberculosis transmission studies using nanopore next-generation sequencing data. |
| title_short | TBpore cluster: A novel phylogenetic pipeline for tuberculosis transmission studies using nanopore next-generation sequencing data. |
| title_sort | tbpore cluster a novel phylogenetic pipeline for tuberculosis transmission studies using nanopore next generation sequencing data |
| url | https://doi.org/10.1371/journal.pone.0325914 |
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