Abstract
Numerous techniques are currently available with different principles, costs, and levels of resolution to understand the transmission dynamics of brucellosis worldwide. We aimed to compare the B. abortus population structure of 53 Brazilian genomes using eight different genotyping methods [multiple-locus variable-number tandem-repeat analysis (MLVA8, MLVA11, MLVA16), multilocus sequence typing (MLST9, MLST21), core genome MLST (cgMLST) and two techniques based on single nucleotide polymorphisms (SNP) detection (parSNP and NASP)]. The strains were isolated from six different states between 1977 and 2008 and were previously analysed using MLVA8, MLVA11, and MLVA16. Then, their whole genomes were sequenced, assembled, and submitted to MSLT9 MLST21, cgMLST, and SNP analyses, using the mlst,chewbbaca, parSNP, and NASP programs, respectively. All the genotypes were compared in the R program (dendextend package). MLST9 and MLST21 were the two techniques with the lowest level of resolution, both presenting 4 genotypes. MLVA8, MLVA11, and MLVA16 showed a progressive level of resolution as more loci were analysed, with 6, 16, and 44 genotypes, respectively. The cgMLST showed the highest level of resolution, depicting 45 genotypes, followed by the SNPs methods, both with 44 genotypes. Hierarchical grouping by the mean distance among the correlation of the techniques showed clustering of MLST9 and MLST21, the second clustering of MLVA8, MLVA11, and MLVA 16 and a third clustering grouping parSNP, NASP, and cgMLST. In the assessed population, MLVA was more discriminatory than MLST and was more practical and cheaper to perform. Furthermore, SNP techniques and cgMLST provided the highest levels of resolution, showing high agreement with each other, which could be explained by the high clonality of B. abortus genomes (90% of its gene repertoire belongs to the core genome). In conclusion, it was observed that different techniques might be more indicated depending on available resources. It investigated epidemiological scenarios, with MLVA being a simpler and ideal technique for countries that are still in the diseasecontrol phase, and SNP and cgMLST techniques would be better choices for outbreak investigations and for surveillance in countries in the eradication or where brucellosis is already eradicated.
