2024-03-28T08:26:16Zhttp://repisalud.isciii.es/oai/requestoai:repisalud.isciii.es:20.500.12105/143242023-05-03T12:45:25Zcom_20.500.12105_2060com_20.500.12105_2052com_20.500.12105_2051col_20.500.12105_2061
Repisalud
author
Pelerito, Ana
author
Nunes, Alexandra
author
Grilo, Teresa
author
Isidro, Joana
author
Silva, Catarina
author
Ferreira, Ana Cristina
author
Valdezate, Sylvia
author
Núncio, Maria Sofia
author
Georgi, Enrico
author
Gomes, João Paulo
funder
Unión Europea. Fondo Europeo de Desarrollo Regional (FEDER/ERDF)
funder
Fundação para a Ciência e Tecnologia (Portugal)
funder
Unión Europea. Comisión Europea
2022-05-09T09:37:02Z
2022-05-09T09:37:02Z
2021-11
Front Microbiol. 2021 Nov 12;12:740068.
1664-302X
http://hdl.handle.net/20.500.12105/14324
34867857
10.3389/fmicb.2021.740068
Frontiers in Microbiology
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.
eng
Brucella spp.
MLVA
Python script
Genotyping
Whole-genome sequencing
Zoonosis
Genetic Characterization of Brucella spp.: Whole Genome Sequencing-Based Approach for the Determination of Multiple Locus Variable Number Tandem Repeat Profiles
journal article
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URL
https://repisalud.isciii.es/bitstream/20.500.12105/14324/1/GeneticCharacterizationOfBrucella_2021.pdf
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https://repisalud.isciii.es/bitstream/20.500.12105/14324/6/GeneticCharacterizationOfBrucella_2021.pdf.txt
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GeneticCharacterizationOfBrucella_2021.pdf.txt