Abstract
BackgroundSwine brucellosis caused by B. suis biovar 2 is an emergent disease in domestic pigs in Europe. The emergence of this pathogen has been linked to the increase of extensive pig farms and the high density of infected wild boars (Sus scrofa). In Portugal and Spain, the majority of strains share specific molecular characteristics, which allowed establishing an Iberian clonal lineage. However, several strains isolated from wild boars in the North-East region of Spain are similar to strains isolated in different Central European countries.ResultsComparative analysis of five newly fully sequenced B. suis biovar 2 strains belonging to the main circulating clones in Iberian Peninsula, with publicly available Brucella spp. genomes, revealed that strains from Iberian clonal lineage share 74% similarity with those reference genomes. Besides the 210 kb translocation event present in all biovar 2 strains, an inversion with 944 kb was presented in chromosome I of strains from the Iberian clone. At left and right crossover points, the inversion disrupted a TRAP dicarboxylate transporter, DctM subunit, and an integral membrane protein TerC. The gene dctM is well conserved in Brucella spp. except in strains from the Iberian clonal lineage. Intraspecies comparative analysis also exposed a number of biovar-, haplotype- and strain-specific insertion-deletion (INDELs) events and single nucleotide polymorphisms (SNPs) that could explain differences in virulence and host specificities. Most discriminative mutations were associated to membrane related molecules (29%) and enzymes involved in catabolism processes (20%). Molecular identification of both B. suis biovar 2 clonal lineages could be easily achieved using the target-PCR procedures established in this work for the evaluated INDELs.ConclusionWhole-genome analyses supports that the B. suis biovar 2 Iberian clonal lineage evolved from the Central-European lineage and suggests that the genomic specialization of this pathogen in the Iberian Peninsula is independent of a specific genomic event(s), but instead driven by allopatric speciation, resulting in the establishment of a new ecovar.
Highlights
Swine brucellosis caused by B. suis biovar 2 is an emergent disease in domestic pigs in Europe
All B. suis isolates were previously subjected to polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) analysis of the omp2a and omp2b [22] and omp31 [23] genes, to assess the different haplotypes, and to target-PCR to confirm the presence of the large inversion in B. suis biovar 2 Iberian clonal lineage [11]
Phylogenomic relationships of B. suis biovar 2 To understand the genomic specialization observed in the Iberian Peninsula, the genetic structure and evolutionary relationships of the B. suis strains isolated in the Iberian Peninsula were assessed by three Whole-Genome based phylogenetic approaches: Multiple Sequence Alignment (WG-multiple sequence alignment (MSA)); Single Nucleotide Polymorphism distribution (WG-single nucleotide polymorphism (SNP)) and insertion and deletion events distribution (WG-INDEL)
Summary
Swine brucellosis caused by B. suis biovar 2 is an emergent disease in domestic pigs in Europe. Brucella suis is a facultative intracellular pathogen infecting a broad range of animals and humans This species comprises five biovars, denominated biovar 1 to 5, which infect specific hosts. Biovars 1, 2 and 3 infect suidae and are the etiological agents of swine brucellosis, but biovars 1 and Ferreira et al BMC Genomics (2017) 18:726 clonal lineage The latter has been described exclusively in the Iberian Peninsula, in pigs and wild boars, mainly south of the River Ebro, suggesting a genomic specialization and local adaptation [12]. The complete genome sequences of five B. suis biovar 2 strains representative of Iberian and Central-European clonal lineages, isolated from wild boars in Portugal and Spain, have been released [15, 16], and it was shown that the Iberian lineage is characterized by the presence of a large chromosomal inversion [11]. “atypical” Brucella strains were isolated from diverse animal sources, including cold-blooded hosts, such as frogs and fish [18,19,20] and are likely going to be proposed as new species in the future
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