Comparison of in silico predicted Mycobacterium tuberculosis spoligotypes and lineages from whole genome sequencing data
Abstract Bacterial strain-types in the Mycobacterium tuberculosis complex underlie tuberculosis disease, and have been associated with drug resistance, transmissibility, virulence, and host–pathogen interactions. Spoligotyping was developed as a molecular genotyping technique used to determine strai...
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| Format: | Article |
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Nature Portfolio
2023-07-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-38384-3 |
| _version_ | 1797778941272915968 |
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| author | Gary Napier David Couvin Guislaine Refrégier Christophe Guyeux Conor J. Meehan Christophe Sola Susana Campino Jody Phelan Taane G. Clark |
| author_facet | Gary Napier David Couvin Guislaine Refrégier Christophe Guyeux Conor J. Meehan Christophe Sola Susana Campino Jody Phelan Taane G. Clark |
| author_sort | Gary Napier |
| collection | DOAJ |
| description | Abstract Bacterial strain-types in the Mycobacterium tuberculosis complex underlie tuberculosis disease, and have been associated with drug resistance, transmissibility, virulence, and host–pathogen interactions. Spoligotyping was developed as a molecular genotyping technique used to determine strain-types, though recent advances in whole genome sequencing (WGS) technology have led to their characterization using SNP-based sub-lineage nomenclature. Notwithstanding, spoligotyping remains an important tool and there is a need to study the congruence between spoligotyping-based and SNP-based sub-lineage assignation. To achieve this, an in silico spoligotype prediction method (“Spolpred2”) was developed and integrated into TB-Profiler. Lineage and spoligotype predictions were generated for > 28 k isolates and the overlap between strain-types was characterized. Major spoligotype families detected were Beijing (25.6%), T (18.6%), LAM (13.1%), CAS (9.4%), and EAI (8.3%), and these broadly followed known geographic distributions. Most spoligotypes were perfectly correlated with the main MTBC lineages (L1-L7, plus animal). Conversely, at lower levels of the sub-lineage system, the relationship breaks down, with only 65% of spoligotypes being perfectly associated with a sub-lineage at the second or subsequent levels of the hierarchy. Our work supports the use of spoligotyping (membrane or WGS-based) for low-resolution surveillance, and WGS or SNP-based systems for higher-resolution studies. |
| first_indexed | 2024-03-12T23:24:47Z |
| format | Article |
| id | doaj.art-fcafc4a52ea941b0a4dbdda8c79a94e7 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-12T23:24:47Z |
| publishDate | 2023-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-fcafc4a52ea941b0a4dbdda8c79a94e72023-07-16T11:16:37ZengNature PortfolioScientific Reports2045-23222023-07-011311710.1038/s41598-023-38384-3Comparison of in silico predicted Mycobacterium tuberculosis spoligotypes and lineages from whole genome sequencing dataGary Napier0David Couvin1Guislaine Refrégier2Christophe Guyeux3Conor J. Meehan4Christophe Sola5Susana Campino6Jody Phelan7Taane G. Clark8Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical MedicineInstitut Pasteur de la GuadeloupeUniversité Paris-SaclayDISC Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Univ. Bourgogne Franche-Comté (UBFC)Nottingham Trent UniversityUniversité Paris-SaclayFaculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical MedicineFaculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical MedicineFaculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical MedicineAbstract Bacterial strain-types in the Mycobacterium tuberculosis complex underlie tuberculosis disease, and have been associated with drug resistance, transmissibility, virulence, and host–pathogen interactions. Spoligotyping was developed as a molecular genotyping technique used to determine strain-types, though recent advances in whole genome sequencing (WGS) technology have led to their characterization using SNP-based sub-lineage nomenclature. Notwithstanding, spoligotyping remains an important tool and there is a need to study the congruence between spoligotyping-based and SNP-based sub-lineage assignation. To achieve this, an in silico spoligotype prediction method (“Spolpred2”) was developed and integrated into TB-Profiler. Lineage and spoligotype predictions were generated for > 28 k isolates and the overlap between strain-types was characterized. Major spoligotype families detected were Beijing (25.6%), T (18.6%), LAM (13.1%), CAS (9.4%), and EAI (8.3%), and these broadly followed known geographic distributions. Most spoligotypes were perfectly correlated with the main MTBC lineages (L1-L7, plus animal). Conversely, at lower levels of the sub-lineage system, the relationship breaks down, with only 65% of spoligotypes being perfectly associated with a sub-lineage at the second or subsequent levels of the hierarchy. Our work supports the use of spoligotyping (membrane or WGS-based) for low-resolution surveillance, and WGS or SNP-based systems for higher-resolution studies.https://doi.org/10.1038/s41598-023-38384-3 |
| spellingShingle | Gary Napier David Couvin Guislaine Refrégier Christophe Guyeux Conor J. Meehan Christophe Sola Susana Campino Jody Phelan Taane G. Clark Comparison of in silico predicted Mycobacterium tuberculosis spoligotypes and lineages from whole genome sequencing data Scientific Reports |
| title | Comparison of in silico predicted Mycobacterium tuberculosis spoligotypes and lineages from whole genome sequencing data |
| title_full | Comparison of in silico predicted Mycobacterium tuberculosis spoligotypes and lineages from whole genome sequencing data |
| title_fullStr | Comparison of in silico predicted Mycobacterium tuberculosis spoligotypes and lineages from whole genome sequencing data |
| title_full_unstemmed | Comparison of in silico predicted Mycobacterium tuberculosis spoligotypes and lineages from whole genome sequencing data |
| title_short | Comparison of in silico predicted Mycobacterium tuberculosis spoligotypes and lineages from whole genome sequencing data |
| title_sort | comparison of in silico predicted mycobacterium tuberculosis spoligotypes and lineages from whole genome sequencing data |
| url | https://doi.org/10.1038/s41598-023-38384-3 |
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