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Strengthening the genomic surveillance of Francisella tularensis by using culture-free whole-genome sequencing from biological samples

2024-01-05Journal article Open access
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dc.contributor.authorIsidro, Joana
dc.contributor.authorEscudero, Raquel
dc.contributor.authorLuque-Larena, Juan José
dc.contributor.authorPinto, Miguel
dc.contributor.authorBorges, Vítor
dc.contributor.authorGonzález-Martín-Niño, Rosa
dc.contributor.authorDuarte, Sílvia
dc.contributor.authorVieira, Luís
dc.contributor.authorMougeot, François
dc.contributor.authorVidal, Dolors
dc.contributor.authorHerrera-Rodríguez, Daniel
dc.contributor.authorRodríguez-Pastor, Ruth
dc.contributor.authorHerrero-Cófreces, Silvia
dc.contributor.authorJubete-Tazo, Fernando
dc.contributor.authorGomes, João Paulo
dc.contributor.authorLopes de Carvalho, Isabel
dc.date.accessioned2025-01-29T17:12:01Z
dc.date.available2025-01-29T17:12:01Z
dc.date.issued2024-01-05
dc.description.abstractIntroduction: 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 infectious pathogen.eng
dc.description.sponsorshipThis work was supported by funding from the European Union EU4Health Programme under grant agreement No 101113460 (GENEO) and by the GenomePT project (POCI-01-0145-FEDER-022184), supported by COMPETE 2020 - Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by Fundação para a Ciência e a Tecnologia (FCT). The acquisition of WGS-related reagents was supported by the Ministerio de Economía y Competitividad, Government of Spain/FEDER, RESERTULA project (CLG2015-66962-C2-2-R). Fieldwork for sample collection was funded by the Ministerio de Economía y Competitividad, Government of Spain/FEDER ECOTULA project (CGL2015-66962-C2-1-R) and by the Ministerio de Ciencia, Innovación y Universidades BOOMRAT project (PID2019-109327RB-I00) from Spain.
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationFront Microbiol. 2024 Jan 5:14:1277468. doi: 10.3389/fmicb.2023.1277468. eCollection 2023
dc.identifier.doi10.3389/fmicb.2023.1277468pt_PT
dc.identifier.eissn1664-302X
dc.identifier.pmid38249473
dc.identifier.urihttp://hdl.handle.net/10400.18/10322
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.relation101113460
dc.relation.hasversionhttps://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1277468/full
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectFrancisella tularensis
dc.subjectMicrotus arvalis
dc.subjectRNA Oligonucleotide Baits
dc.subjectSureSelect
dc.subjectWGS
dc.titleStrengthening the genomic surveillance of Francisella tularensis by using culture-free whole-genome sequencing from biological samplespt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.citation.startPage1277468
oaire.citation.titleFrontiers in Microbiologypt_PT
oaire.citation.volume14pt_PT
oaire.versionhttp://purl.org/coar/version/c_970fb48d4fbd8a85
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT

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