Repository logo
 
Publication

Genetic Characterization of Brucella spp.: Whole Genome Sequencing-Based Approach for the Determination of Multiple Locus Variable Number Tandem Repeat Profiles

2021-11-12Journal article Open access
Simple item page
dc.contributor.authorPelerito, Ana
dc.contributor.authorNunes, Alexandra
dc.contributor.authorGrilo, Teresa
dc.contributor.authorIsidro, Joana
dc.contributor.authorSilva, Catarina
dc.contributor.authorFerreira, Ana Cristina
dc.contributor.authorValdezate, Sylvia
dc.contributor.authorNúncio, Maria Sofia
dc.contributor.authorGeorgi, Enrico
dc.contributor.authorGomes, João Paulo
dc.date.accessioned2022-07-03T16:22:17Z
dc.date.available2022-07-03T16:22:17Z
dc.date.issued2021-11-12
dc.description.abstractBrucellosis 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.pt_PT
dc.description.sponsorshipThis 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.pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationFront Microbiol. 2021 Nov 12;12:740068. doi: 10.3389/fmicb.2021.740068. eCollection 2021.bpt_PT
dc.identifier.doi10.3389/fmicb.2021.740068pt_PT
dc.identifier.issn1664-302X
dc.identifier.urihttp://hdl.handle.net/10400.18/8053
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherFrontiers Mediapt_PT
dc.relation.publisherversionhttps://www.frontiersin.org/articles/10.3389/fmicb.2021.740068/fullpt_PT
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.subjectBrucella spp.pt_PT
dc.subjectMLVApt_PT
dc.subjectPython scriptpt_PT
dc.subjectGenotypingpt_PT
dc.subjectWhole-genome Sequencingpt_PT
dc.subjectZoonosispt_PT
dc.titleGenetic Characterization of Brucella spp.: Whole Genome Sequencing-Based Approach for the Determination of Multiple Locus Variable Number Tandem Repeat Profilespt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.citation.startPage740068pt_PT
oaire.citation.titleFrontiers in Microbiologypt_PT
oaire.citation.volume12pt_PT
rcaap.embargofctAcesso de acordo com política editorial da revista.pt_PT
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT

Files

Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
Pelerito et al_2021_MLVA.pdf
Size:
951.97 KB
Format:
Adobe Portable Document Format
Download

Collections

DDI - Artigos em revistas internacionais
DGH - Artigos em revistas internacionais