Table_3_Strengthening the genomic surveillance of Francisella tularensis by using culture-free whole-genome sequencing from biological samples.XLSX
Introduction Francisella tularensis is a highly infectious bacterium that causes the zoonotic disease tularemia. The development of genotyping methods, especially those based on whole-genome sequencing (WGS), has recently increased the knowledge on the epidemiology of this disease. However, due to t...
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ftfrontimediafig:oai:figshare.com:article/24946968 2024-02-04T10:02:06+01:00 Table_3_Strengthening the genomic surveillance of Francisella tularensis by using culture-free whole-genome sequencing from biological samples.XLSX Joana Isidro Raquel Escudero Juan José Luque-Larena Miguel Pinto Vítor Borges Rosa González-Martín-Niño Sílvia Duarte Luís Vieira François Mougeot Dolors Vidal Daniel Herrera-Rodríguez Ruth Rodríguez-Pastor Silvia Herrero-Cófreces Fernando Jubete-Tazo João Paulo Gomes Isabel Lopes de Carvalho 2024-01-05T04:51:04Z https://doi.org/10.3389/fmicb.2023.1277468.s004 https://figshare.com/articles/dataset/Table_3_Strengthening_the_genomic_surveillance_of_Francisella_tularensis_by_using_culture-free_whole-genome_sequencing_from_biological_samples_XLSX/24946968 unknown doi:10.3389/fmicb.2023.1277468.s004 https://figshare.com/articles/dataset/Table_3_Strengthening_the_genomic_surveillance_of_Francisella_tularensis_by_using_culture-free_whole-genome_sequencing_from_biological_samples_XLSX/24946968 CC BY 4.0 Microbiology Microbial Genetics Microbial Ecology Mycology Francisella tularensis WGS RNA oligonucleotide baits Microtus arvalis SureSelect Dataset 2024 ftfrontimediafig https://doi.org/10.3389/fmicb.2023.1277468.s004 2024-01-11T00:17:20Z Introduction Francisella tularensis is a highly infectious bacterium that causes the zoonotic disease tularemia. The development of genotyping methods, especially those based on whole-genome sequencing (WGS), has recently increased the knowledge on the epidemiology of this disease. However, due to the difficulties associated with the growth and isolation of this fastidious pathogen in culture, the availability of strains and subsequently WGS data is still limited. Methods To surpass these constraints, we aimed to implement a culture-free approach to capture and sequence F. tularensis genomes directly from complex samples. Biological samples obtained from 50 common voles and 13 Iberian hares collected in Spain were confirmed as positive for F. tularensis subsp. holarctica and subjected to a WGS target capture and enrichment protocol, using RNA oligonucleotide baits designed to cover F. tularensis genomic diversity. Results We obtained full genome sequences of F. tularensis from 13 animals (20.6%), two of which had mixed infections with distinct genotypes, and achieved a higher success rate when compared with culture-dependent WGS (only successful for two animals). The new genomes belonged to different clades commonly identified in Europe (B.49, B.51 and B.262) and subclades. Despite being phylogenetically closely related to other genomes from Spain, the detected clusters were often found in other countries. A comprehensive phylogenetic analysis, integrating 599 F. tularensis subsp. holarctica genomes, showed that most (sub)clades are found in both humans and animals and that closely related strains are found in different, and often geographically distant, countries. Discussion Overall, we show that the implemented culture-free WGS methodology yields timely, complete and high-quality genomic data of F. tularensis, being a highly valuable approach to promote and potentiate the genomic surveillance of F. tularensis and ultimately increase the knowledge on the genomics, ecology and epidemiology of this highly ... Dataset Microtus arvalis Frontiers: Figshare |
institution |
Open Polar |
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Frontiers: Figshare |
op_collection_id |
ftfrontimediafig |
language |
unknown |
topic |
Microbiology Microbial Genetics Microbial Ecology Mycology Francisella tularensis WGS RNA oligonucleotide baits Microtus arvalis SureSelect |
spellingShingle |
Microbiology Microbial Genetics Microbial Ecology Mycology Francisella tularensis WGS RNA oligonucleotide baits Microtus arvalis SureSelect Joana Isidro Raquel Escudero Juan José Luque-Larena Miguel Pinto Vítor Borges Rosa González-Martín-Niño Sílvia Duarte Luís Vieira François Mougeot Dolors Vidal Daniel Herrera-Rodríguez Ruth Rodríguez-Pastor Silvia Herrero-Cófreces Fernando Jubete-Tazo João Paulo Gomes Isabel Lopes de Carvalho Table_3_Strengthening the genomic surveillance of Francisella tularensis by using culture-free whole-genome sequencing from biological samples.XLSX |
topic_facet |
Microbiology Microbial Genetics Microbial Ecology Mycology Francisella tularensis WGS RNA oligonucleotide baits Microtus arvalis SureSelect |
description |
Introduction Francisella tularensis is a highly infectious bacterium that causes the zoonotic disease tularemia. The development of genotyping methods, especially those based on whole-genome sequencing (WGS), has recently increased the knowledge on the epidemiology of this disease. However, due to the difficulties associated with the growth and isolation of this fastidious pathogen in culture, the availability of strains and subsequently WGS data is still limited. Methods To surpass these constraints, we aimed to implement a culture-free approach to capture and sequence F. tularensis genomes directly from complex samples. Biological samples obtained from 50 common voles and 13 Iberian hares collected in Spain were confirmed as positive for F. tularensis subsp. holarctica and subjected to a WGS target capture and enrichment protocol, using RNA oligonucleotide baits designed to cover F. tularensis genomic diversity. Results We obtained full genome sequences of F. tularensis from 13 animals (20.6%), two of which had mixed infections with distinct genotypes, and achieved a higher success rate when compared with culture-dependent WGS (only successful for two animals). The new genomes belonged to different clades commonly identified in Europe (B.49, B.51 and B.262) and subclades. Despite being phylogenetically closely related to other genomes from Spain, the detected clusters were often found in other countries. A comprehensive phylogenetic analysis, integrating 599 F. tularensis subsp. holarctica genomes, showed that most (sub)clades are found in both humans and animals and that closely related strains are found in different, and often geographically distant, countries. Discussion Overall, we show that the implemented culture-free WGS methodology yields timely, complete and high-quality genomic data of F. tularensis, being a highly valuable approach to promote and potentiate the genomic surveillance of F. tularensis and ultimately increase the knowledge on the genomics, ecology and epidemiology of this highly ... |
format |
Dataset |
author |
Joana Isidro Raquel Escudero Juan José Luque-Larena Miguel Pinto Vítor Borges Rosa González-Martín-Niño Sílvia Duarte Luís Vieira François Mougeot Dolors Vidal Daniel Herrera-Rodríguez Ruth Rodríguez-Pastor Silvia Herrero-Cófreces Fernando Jubete-Tazo João Paulo Gomes Isabel Lopes de Carvalho |
author_facet |
Joana Isidro Raquel Escudero Juan José Luque-Larena Miguel Pinto Vítor Borges Rosa González-Martín-Niño Sílvia Duarte Luís Vieira François Mougeot Dolors Vidal Daniel Herrera-Rodríguez Ruth Rodríguez-Pastor Silvia Herrero-Cófreces Fernando Jubete-Tazo João Paulo Gomes Isabel Lopes de Carvalho |
author_sort |
Joana Isidro |
title |
Table_3_Strengthening the genomic surveillance of Francisella tularensis by using culture-free whole-genome sequencing from biological samples.XLSX |
title_short |
Table_3_Strengthening the genomic surveillance of Francisella tularensis by using culture-free whole-genome sequencing from biological samples.XLSX |
title_full |
Table_3_Strengthening the genomic surveillance of Francisella tularensis by using culture-free whole-genome sequencing from biological samples.XLSX |
title_fullStr |
Table_3_Strengthening the genomic surveillance of Francisella tularensis by using culture-free whole-genome sequencing from biological samples.XLSX |
title_full_unstemmed |
Table_3_Strengthening the genomic surveillance of Francisella tularensis by using culture-free whole-genome sequencing from biological samples.XLSX |
title_sort |
table_3_strengthening the genomic surveillance of francisella tularensis by using culture-free whole-genome sequencing from biological samples.xlsx |
publishDate |
2024 |
url |
https://doi.org/10.3389/fmicb.2023.1277468.s004 https://figshare.com/articles/dataset/Table_3_Strengthening_the_genomic_surveillance_of_Francisella_tularensis_by_using_culture-free_whole-genome_sequencing_from_biological_samples_XLSX/24946968 |
genre |
Microtus arvalis |
genre_facet |
Microtus arvalis |
op_relation |
doi:10.3389/fmicb.2023.1277468.s004 https://figshare.com/articles/dataset/Table_3_Strengthening_the_genomic_surveillance_of_Francisella_tularensis_by_using_culture-free_whole-genome_sequencing_from_biological_samples_XLSX/24946968 |
op_rights |
CC BY 4.0 |
op_doi |
https://doi.org/10.3389/fmicb.2023.1277468.s004 |
_version_ |
1789968471325409280 |