Genetic Characterization of Brucella spp.

Detalhes bibliográficos
Autor(a) principal: Pelerito, Ana
Data de Publicação: 2021
Outros Autores: Nunes, Alexandra, Grilo, Teresa, Isidro, Joana, Silva, Catarina, Ferreira, Ana Cristina, Valdezate, Sylvia, Núncio, Maria Sofia, Georgi, Enrico, Gomes, João Paulo
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10362/129671
Resumo: Funding Information: Funding: This work is a result of the GenomePT project (POCI-01- 0145-FEDER-022184), supported by the COMPETE 2020 – Operational Program for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Program (Lisboa2020), Algarve Portugal Regional Operational Program (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by the Fundação para a Ciência e a Tecnologia (FCT). The studies have arisen from the Project QUANDHIP (Chafea Grant Agreement no. 2010 21 02), which has been funded by the European Commission in the framework of the Health Program.
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spelling Genetic Characterization of Brucella spp.Whole Genome Sequencing-Based Approach for the Determination of Multiple Locus Variable Number Tandem Repeat ProfilesBrucellasppgenotypingMLVAPython scriptwhole-genome sequencingzoonosisMicrobiologyMicrobiology (medical)Funding Information: Funding: This work is a result of the GenomePT project (POCI-01- 0145-FEDER-022184), supported by the COMPETE 2020 – Operational Program for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Program (Lisboa2020), Algarve Portugal Regional Operational Program (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by the Fundação para a Ciência e a Tecnologia (FCT). The studies have arisen from the Project QUANDHIP (Chafea Grant Agreement no. 2010 21 02), which has been funded by the European Commission in the framework of the Health Program.Brucellosis is an important zoonosis that is emerging in some regions of the world, gaining increased relevance with the inclusion of the causing agent Brucella spp. in the class B bioterrorism group. Until now, multi-locus VNTR Analysis (MLVA) based on 16 loci has been considered as the gold standard for Brucella typing. However, this methodology is laborious, and, with the rampant release of Brucella genomes, the transition from the traditional MLVA to whole genome sequencing (WGS)-based typing is on course. Nevertheless, in order to avoid a disruptive transition with the loss of massive genetic data obtained throughout the last decade and considering that the transition timings will vary considerably among different countries, it is important to determine WGS-based MLVA alleles of the nowadays sequenced genomes. On this regard, we aimed to evaluate the performance of a Python script that had been previously developed for the rapid in silico extraction of the MLVA alleles, by comparing it to the PCR-based MLVA procedure over 83 strains from different Brucella species. The WGS-based MLVA approach detected 95.3% of all possible 1,328 hits (83 strains×16 loci) and showed an agreement rate with the PCR-based MLVA procedure of 96.4% for MLVA-16. According to our dataset, we suggest the use of a minimal depth of coverage of ~50x and a maximum number of ~200 contigs as guiding “boundaries” for the future application of the script. In conclusion, the evaluated script seems to be a very useful and robust tool for the in silico determination of MLVA profiles of Brucella strains, allowing retrospective and prospective molecular epidemiological studies, which are important for maintaining an active epidemiological surveillance of brucellosis.Centre for Toxicogenomics and Human Health (ToxOmics)NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM)RUNPelerito, AnaNunes, AlexandraGrilo, TeresaIsidro, JoanaSilva, CatarinaFerreira, Ana CristinaValdezate, SylviaNúncio, Maria SofiaGeorgi, EnricoGomes, João Paulo2021-12-22T23:25:59Z2021-11-122021-11-12T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10362/129671eng1664-302XPURE: 35418594https://doi.org/10.3389/fmicb.2021.740068info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-03-11T05:08:45Zoai:run.unl.pt:10362/129671Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:46:36.905281Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv Genetic Characterization of Brucella spp.
Whole Genome Sequencing-Based Approach for the Determination of Multiple Locus Variable Number Tandem Repeat Profiles
title Genetic Characterization of Brucella spp.
spellingShingle Genetic Characterization of Brucella spp.
Pelerito, Ana
Brucellaspp
genotyping
MLVA
Python script
whole-genome sequencing
zoonosis
Microbiology
Microbiology (medical)
title_short Genetic Characterization of Brucella spp.
title_full Genetic Characterization of Brucella spp.
title_fullStr Genetic Characterization of Brucella spp.
title_full_unstemmed Genetic Characterization of Brucella spp.
title_sort Genetic Characterization of Brucella spp.
author Pelerito, Ana
author_facet Pelerito, Ana
Nunes, Alexandra
Grilo, Teresa
Isidro, Joana
Silva, Catarina
Ferreira, Ana Cristina
Valdezate, Sylvia
Núncio, Maria Sofia
Georgi, Enrico
Gomes, João Paulo
author_role author
author2 Nunes, Alexandra
Grilo, Teresa
Isidro, Joana
Silva, Catarina
Ferreira, Ana Cristina
Valdezate, Sylvia
Núncio, Maria Sofia
Georgi, Enrico
Gomes, João Paulo
author2_role author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Centre for Toxicogenomics and Human Health (ToxOmics)
NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM)
RUN
dc.contributor.author.fl_str_mv Pelerito, Ana
Nunes, Alexandra
Grilo, Teresa
Isidro, Joana
Silva, Catarina
Ferreira, Ana Cristina
Valdezate, Sylvia
Núncio, Maria Sofia
Georgi, Enrico
Gomes, João Paulo
dc.subject.por.fl_str_mv Brucellaspp
genotyping
MLVA
Python script
whole-genome sequencing
zoonosis
Microbiology
Microbiology (medical)
topic Brucellaspp
genotyping
MLVA
Python script
whole-genome sequencing
zoonosis
Microbiology
Microbiology (medical)
description Funding Information: Funding: This work is a result of the GenomePT project (POCI-01- 0145-FEDER-022184), supported by the COMPETE 2020 – Operational Program for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Program (Lisboa2020), Algarve Portugal Regional Operational Program (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by the Fundação para a Ciência e a Tecnologia (FCT). The studies have arisen from the Project QUANDHIP (Chafea Grant Agreement no. 2010 21 02), which has been funded by the European Commission in the framework of the Health Program.
publishDate 2021
dc.date.none.fl_str_mv 2021-12-22T23:25:59Z
2021-11-12
2021-11-12T00:00:00Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10362/129671
url http://hdl.handle.net/10362/129671
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv 1664-302X
PURE: 35418594
https://doi.org/10.3389/fmicb.2021.740068
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
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reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
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