Logo do repositório
 
Publicação

Incorporating the genomic signature of environmental Mycobacterium bovis into transmission models of animal tuberculosis under a phylodynamics conceptual framework

datacite.subject.fosCiências Naturais::Ciências Biológicaspt_PT
dc.contributor.advisorCunha, Mónica Vieira
dc.contributor.advisorSalvador, Liliana
dc.contributor.authorPereira, André C.
dc.date.accessioned2025-02-24T17:29:25Z
dc.date.embargo2028-02
dc.date.issued2024-04
dc.date.submitted2023-10
dc.description.abstractAnimal tuberculosis (TB) remains an impacting animal and public health problem worldwide. This disease, affecting a wide range of mammal species, is primarily caused by Mycobacterium bovis. National authorities tackle animal TB mainly through culling programmes focused on cattle, overlooking transmission in wildlife and infection via the environment. This dissertation thus aimed at improving our understanding of the transmission processes of M. bovis/M. caprae at interfaces, via the development, application, and integration of novel tools to support data-driven intervention. We developed eco-phylodynamic frameworks informed by pathogen whole genome sequencing (WGS) data, representing a multi-host transmission system in Portugal, at the livestock-wildlife interface. We found evidence for the co-circulation of M. bovis Eu1, Eu2, and Eu3 clonal complexes, enlightening Eu2 emergence and spread processes, showing most host transitions are intraspecific, while interspecific transmission between wildlife species, and between wild boar and cattle, are highly supported. We report the first phylodynamic analysis of Eu3 in Iberia and, via ecological modelling, we show most host transitions occurred toward higher temperature and precipitation and lower agriculture, road, and host density. Phylogeographic reconstruction evidenced frequent transmission between two ecological clusters, representing an ecological corridor of unrecognised importance. Due to the historic inability to isolate environmental M. bovis, in this dissertation, an innovative single-cell workflow was developed, enabling quantification and sorting of viable and dormant M. bovis cells from natural substrates, showing widespread environmental contamination in animal aggregation spots. Whole genome enrichment and WGS enabled assessment, for the first time, of phylogenomic relatedness of environmental and animal M. bovis strains, showing these genomes are highly intertwined, with data supporting environmental contamination by shedding animals and pointing the environment as source of new infections. This dissertation offers ground-breaking insights, with implications for animal TB policy formulation, advocating the inclusion of genomic and environmental surveillance in control programmes.pt_PT
dc.identifier.tid101768478pt_PT
dc.identifier.urihttp://hdl.handle.net/10400.5/98680
dc.language.isoengpt_PT
dc.relationIncorporating the genomic signature of environmental Mycobacterium bovis into transmission models of animal TB under a phylodynamics conceptual framework
dc.relationCentre for Ecology, Evolution and Environmental Changes
dc.subjectAnimal tuberculosispt_PT
dc.subjectMycobacterium bovispt_PT
dc.subjectMulti-host systempt_PT
dc.subjectEnvironmental surveillancept_PT
dc.subjectGenomic surveillancept_PT
dc.subjectTuberculose animalpt_PT
dc.subjectMycobacterium bovispt_PT
dc.subjectSistema multi-hospedeiropt_PT
dc.subjectVigilância ambientalpt_PT
dc.subjectVigilância genómicapt_PT
dc.titleIncorporating the genomic signature of environmental Mycobacterium bovis into transmission models of animal tuberculosis under a phylodynamics conceptual frameworkpt_PT
dc.typedoctoral thesis
dspace.entity.typePublication
oaire.awardTitleIncorporating the genomic signature of environmental Mycobacterium bovis into transmission models of animal TB under a phylodynamics conceptual framework
oaire.awardTitleCentre for Ecology, Evolution and Environmental Changes
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/PDQI/SFRH%2FBD%2F136557%2F2018/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT//COVID%2FBD%2F153206%2F2023/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDB%2F00329%2F2020/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/Concurso de avaliação no âmbito do Programa Plurianual de Financiamento de Unidades de I&D (2017%2F2018) - Financiamento Base/UIDB%2F04046%2F2020/PT
oaire.fundingStreamPDQI
oaire.fundingStream6817 - DCRRNI ID
oaire.fundingStreamConcurso de avaliação no âmbito do Programa Plurianual de Financiamento de Unidades de I&D (2017/2018) - Financiamento Base
person.familyNameConceição Pereira
person.givenNameAndré
person.identifier.ciencia-id591C-25AD-F68B
person.identifier.orcid0000-0003-4112-4037
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.rightsembargoedAccesspt_PT
rcaap.typedoctoralThesispt_PT
relation.isAuthorOfPublication9543b330-7ae9-4088-8b70-c43f7202e504
relation.isAuthorOfPublication.latestForDiscovery9543b330-7ae9-4088-8b70-c43f7202e504
relation.isProjectOfPublication922c9c92-c12f-46df-a57b-f3d44c6eacce
relation.isProjectOfPublicationc16b4504-b1c4-4fef-8449-0275ef4ca569
relation.isProjectOfPublicatione6d2c5ff-9af2-4726-9821-7bcf881e9e2d
relation.isProjectOfPublication5fc6b146-0cfc-4509-be9f-39ead93c7eb1
relation.isProjectOfPublication.latestForDiscoveryc16b4504-b1c4-4fef-8449-0275ef4ca569
thesis.degree.nameTese de doutoramento, Biologia (Microbiologia), Universidade de Lisboa, Faculdade de Ciências, 2024pt_PT

Ficheiros

Principais
A mostrar 1 - 1 de 1
Miniatura indisponível
Nome:
scnd990026354741912_td_André_Pereira.pdf
Tamanho:
18.56 MB
Formato:
Adobe Portable Document Format
Licença
A mostrar 1 - 1 de 1
Miniatura indisponível
Nome:
license.txt
Tamanho:
1.2 KB
Formato:
Item-specific license agreed upon to submission
Descrição: