Development and evaluation of a core genome multilocus sequence typing (cgMLST) scheme for Brucella spp.

Sankarasubramanian, Jagadesan; Vishnu, Udayakumar S.; Gunasekaran, Paramasamy; Rajendhran, Jeyaprakash

doi:10.1016/j.meegid.2018.10.021

Cited by 31 publications

(22 citation statements)

References 32 publications

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“…For comparative purposes with the described wgMLST-based approach, in parallel we also evaluated the genetic relatedness among the 36 PT strains with three distinct strategies, namely with: i) the traditional MLST schemas based on 9 and 21 loci [32;33]; ii) the freely available genus-specific cgMLST schema [16] based on 164 loci (comprising~6% of the loci panel used in this study); and iii) a core-genome SNV-based approach that is also largely used worldwide. In general, similar genotype associations were achieved with the three approaches, but with different discriminatory power.…”

Section: Comparison With Loci-based and Other Genome-based Approachesmentioning

confidence: 99%

“…Phylogenetic analysis of Brucella melitensis loci [16], and the other runs on a pay-per-use platform (RIDOM SeqSphere) despite involving a wider core gene set of 2704 targets [17].…”

Section: Plos Onementioning

confidence: 99%

“…Molecular epidemiological studies provide information about genetic grounds and origin of bacterial isolates, but such trace back studies in Brucella species can be challenging as genomes are generally quite conserved. With the technological advances and decreased cost of whole genome sequencing, new methods of pathogen typing, including gene-by-gene comparison using core genome multilocus sequence typing (cgMLST), as well as single-nucleotide polymorphism (SNP) calling based on a reference sequence analysis, are considered to be a suitable and more informative replacement of the gold standard typing schemes [16]. Although the SNP-based analysis may constitute a better option for phylogenetic analyses of conserved genomes (because this approach covers the entire genome, including the intergenic regions) [17], very recently, efforts to develop cgMLST schemes for Brucella have been done [16,17].…”

Section: Introductionmentioning

confidence: 99%

“…With the technological advances and decreased cost of whole genome sequencing, new methods of pathogen typing, including gene-by-gene comparison using core genome multilocus sequence typing (cgMLST), as well as single-nucleotide polymorphism (SNP) calling based on a reference sequence analysis, are considered to be a suitable and more informative replacement of the gold standard typing schemes [16]. Although the SNP-based analysis may constitute a better option for phylogenetic analyses of conserved genomes (because this approach covers the entire genome, including the intergenic regions) [17], very recently, efforts to develop cgMLST schemes for Brucella have been done [16,17]. One of these schemes involves 2704 genes and is based on a pay-per-use platform [17], whereas the other involves a strikingly low number of genes (n = 164) for differentiating purposes [16].…”

Section: Introductionmentioning

confidence: 99%

“…Although the SNP-based analysis may constitute a better option for phylogenetic analyses of conserved genomes (because this approach covers the entire genome, including the intergenic regions) [17], very recently, efforts to develop cgMLST schemes for Brucella have been done [16,17]. One of these schemes involves 2704 genes and is based on a pay-per-use platform [17], whereas the other involves a strikingly low number of genes (n = 164) for differentiating purposes [16].…”

Section: Introductionmentioning

confidence: 99%

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Genome–scale approach to study the genetic relatedness among Brucella melitensis strains

et al. 2020

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Brucellosis is an important zoonotic disease that affects both humans and animals. To date, laboratory surveillance is still essentially based on the traditional MLVA-16 methodology and the associated epidemiological information is frequently scarce. Our goal was to contribute to the improvement of Brucella spp. surveillance through the implementation of a whole genome sequencing (WGS) approach. We created a curated ready-to-use speciesspecific wgMLST scheme enrolling a panel of 2656 targets (http://doi.org/10.5281/zenodo. 3575026) and used this schema to perform a retrospective analysis of the genetic relatedness among B. melitensis strains causing human infection in Portugal (a country where brucellosis is an endemic disease) from 2010 to 2018. The strains showed a phylogenetic clustering within genotype II (25 out of 36) and IV (4 out of 36), and shared clades with strains isolated from countries with which Portugal has intense food trading, tourism and similar eating habits, such as Spain, Italy and Greece. In addition, our results point to the identification of strong associations between B. melitensis strains, likely underlying missed "outbreaks" as 22 out of the 36 strains showed genetic linkage with others. In fact, the applied gene-by-gene approach grouped these strains into six genetic clusters each one containing putative epidemiological links. Nevertheless, more studies will be needed in order to define the appropriate range of cut-offs (probable non-static cut-offs) that best illustrate the association between genetic linkage and epidemiological information and may serve as alerts for the health authorities. The release of this freely available and scalable schema contributes to the required technological transition for laboratorial surveillance of brucellosis and will facilitate the assessment of ongoing and future outbreaks in order to prevent the transmission spread.

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Section: Comparison With Loci-based and Other Genome-based Approachesmentioning

confidence: 99%

“…Phylogenetic analysis of Brucella melitensis loci [16], and the other runs on a pay-per-use platform (RIDOM SeqSphere) despite involving a wider core gene set of 2704 targets [17].…”

Section: Plos Onementioning

confidence: 99%