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Draft genome sequence data and comparative analysis of Erysipelothrix Rhusiopathiae vaccine strain VR-2.

ABSTRACT: Erysipelothrix rhusiopathiae VR-2 is a commercially available live attenuated vaccine strain widely used in Russia, Kazakhstan, and a number of European countries for immunization of pigs against swine erysipelas. The draft genome sequence of E. rhusiopathiae strain VR-2 reported in this paper is 1,704,727 bp in length, has CG content of 36.5%, and contains 1680 genes, including 51 tRNA, 3 rRNA, and 1408 protein-coding genes. Comparative sequence analysis between Fujisawa (serovar 1a), VR-2 and six other serovar N strains of E. rhusiopathiae revealed wide genetic variability of the chromosomal region essential for serovar-specific antigenicity and virulence of E. rhusiopathiae strains. We have performed a BLAST search and found 12 genomic loci potentially specific for the E. rhusiopathiae VR-2 strain. These data could be helpful for developing genetic assays for differentiation of field isolates and this live attenuated vaccine strain, which is especially important for epizootical monitoring of swine erysipelas in countries, where the live vaccine strain E. rhusiopathiae VR-2 is used for pig immunization, as well as for the design of recombinant vaccines against swine erysipelas. The genome of E. rhusiopathiae VR-2 has been submitted in GenBank under accession number RJTK00000000.1.

SUBMITTER: Kovalchuk SN

PROVIDER: S-EPMC7524903 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundErysipelothrix rhusiopathiae is the causative agent of animal erysipelas and, to a fewer occurrences, human erysipeloid. It is ubiquitous in nature and commensal in diverse species of animals, wild or domestic, from mammals and birds to reptiles and fish. Mechanisms of its virulence and pathogenicity are poorly understood.ResultsMaking use of the complete genome sequencing of E. rhusiopathiae strain SY1027 and comparative genome analysis between the three highly pathogenic strains (SY1027, Fujisawa and ATCC19414), the genomic structure and putative functional elements, such as pathogenicity island (PAI)-like regions, potential virulence factors and horizontal transferring genes of the bacteria are identified. Strain SY1027 genome is 1,752,910 base pairs long, just 30 kilobases smaller than strain Fujisawa, with the same GC level of 36.36%. It contains 1,845 open reading frames (ORF) predicted by GLIMMER 3.02, of which 1,775 were annotated by PGAAP, 1,757 (~95.23%) were annotated by NCBI nr blast, 1,209 by COG database and 1,076 by KEGG database. 37 potential virulence factors were annotated in strain SY1027 by VFDB, while 19 (~51.35%) of them are common in the 2 strains, 7 of which are potentially related to antibiotic resistance and highly conserved (~98-100% match identity (ID)) amongst the three strains of E. rhusiopathiae and modestly homologous to other gastrointestinal tract-inhabiting Firmicutes (~40% match ID), e.g. Clostridium spp., Enterococcus spp. Genomic island- and pathogenicity island-like regions were also predicted, in which some showed association with tRNA and potential virulence factors.ConclusionComplete genome sequencing of Erysipelothrix rhusiopathiae, the causative agent of animal erysipelas, was performed. Molecular identification of various genomic elements pave the way to the better understanding of mechanisms underlying metabolic capabilities, pathogenicity of swine erysipelas and prospective vaccine targets besides the widely used SpaA antigens.

Project description:Haemaphysalis longicornis Neumann, 1901 is one of the most well-known hard ticks because of its medical and veterinary importance. Haemaphysalis longicornis transmit a wide range of pathogens among vertebrates, affecting humans and animals in Asia and Oceania. In Japan, the tick species is a major pest of cattle because it can spread a protozoan parasite Theileria orientalis, which causes theileriosis and produces economic losses to the livestock industry (Yokoyama et al. 2012 [1]). Apart from bovine theileriosis, H. longicornis is a vector of bovine babesiosis caused by Babesia ovata, canine babesiosis caused by Babesia gibsoni, and rickettsiosis and viral diseases in humans. Its habitats are mainly Japan, Australia, New Zealand, New Caledonia, the Fiji Islands, Korea, China, and Russia (Oliver et al. 1973 [2]). In the United States, heavy H. longicornis infestations on cattle and white-tailed deer were reported in 2019, making it now one of the tick species to be an increasing threat to livestock animals and humans globally. Ticks reproduce offspring after mating with female and male ticks, however, interestingly, there are two races of H. longicornis: bisexual (diploid) and parthenogenetic (triploid) races [2]. Parthenogenetic H. longicornis is distributed throughout Japan, while the northern limit of the bisexual race is believed to be Fukushima Prefecture on Honshu Island (Fujita et al. 2013 and Kitaoka et al. 1961 [3,4]). This tick species is also considered to be of great scientific importance, and the parthenogenetic race collected in Okayama prefecture has been reared since 1961, while the bisexual race collected in Oita prefecture has been reared since 2008 under laboratory conditions in Japan (Boldbaatar et al. 2010 and Fujisaki et al. 1976 [5,6]). Namely, the "Okayama strain" and "Oita strain" of H. longicornis have been maintained for more than six decades and 15 years, respectively, stably under laboratory conditions. To obtain reference data of bisexual H. longicornis, we sequenced unfed females with haploid genomes using Illumina and MinION Q20 kit then obtained a draft genome consisting of 2.48 Gbp. The number of the contig was 98,529 and N50 was 46.5 Kb. Genome information derived from our laboratory colony of bisexual H. longicornis ticks would provide fundamental insight into understanding how different reproductive lineages occur within the same species of the tick.

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Draft genome sequence data and comparative analysis of Erysipelothrix Rhusiopathiae vaccine strain VR-2.

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