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<i>Brucella</i> sp. are the causative agents of brucellosis. One of the main characteristics of the <i>Brucella</i> genus concerns its very high genetic homogeneity. To date, classical bacteriology typing is still considered as the gold standard assay for direct diagnosis of <i>Brucella</i>. Molecular approaches are routinely used for the identification of <i>Brucella</i> at the genus level. However, genotyping is more complex, and to date, no method exists to quickly assign a strain into species and biovar levels, and new approaches are required. Next generation sequencing (NGS) opened a new era into the diagnosis of bacterial diseases. In this study, we designed a high-resolution melting (HRM) method for the rapid screening of DNA and direct assignment into one of the 12 species of the <i>Brucella</i> genus. This method is based on 17 relevant single nucleotide polymorphisms (SNPs), identified and selected from a whole genome SNP (wgSNP) analysis based on 988 genomes (complete and drafts). These markers were tested against the collection of the European Reference Laboratory (EU-RL) for brucellosis (1440 DNAs extracted from <i>Brucella</i> strains). The results confirmed the reliability of the panel of 17 SNP markers, allowing the differentiation of each species of <i>Brucella</i> together with biovars 1, 2, and 3 of <i>B. suis</i> and vaccine strain Rev1 (<i>B. melitensis</i>) within 3 h, which is a considerable gain of time for brucellosis diagnosis. Therefore, this genotyping tool provides a new and quick alternative for <i>Brucella</i> identification based on SNPs with the HRM-PCR assay.