Comparative genomics of a novel clade shed light on the evolution of the genus Erysipelothrix and characterise an emerging species

Abstract

Erysipelothrix sp. isolates obtained from a deadly outbreak in farmed turkeys were sequenced and compared to representatives of the genus. Phylogenetic trees—supported by digital DNA:DNA hybridization and Average Nucleotide Identity—revealed a novel monophyletic clade comprising isolates from pigs, turkeys, and fish, including isolates previously described as E. sp. Strain 2. Genes coding for the SpaC protein, typically found in E. sp. Strain 2, were detected in all isolates of the clade. Therefore, we confirm E. sp. Strain 2 represents a unique species that may be isolated from a broad host range, and the name “Erysipelothrix takahashiae” is suggested. Core genome analysis showed that the pathogenic species of this genus, E. rhusiopathiae and the clade E. sp. Strain 2, are enriched in core functionalities related to nutrient uptake and transport, but not necessarily homologous pathways. For instance, whereas the aerobic DctA transporter may uptake C4-dicarboxylates in both species, the anaerobic DcuC transporter is exclusive of the E. sp. Strain 2. Remarkably, the pan-genome analysis uncovered that genes related to transport and metabolism, recombination and repair, translation and transcription in the fish isolate, within the novel clade, have undergone a genomic reduction through pseudogenization. This reflects distinct selective pressures shaping the genome of species and strains within the genus Erysipelothrix while adapting to their respective niches.

Genomic characterisation of a novel species of Erysipelothrix associated with mortalities among endangered seabirds

“…This included 106 genomes: a) the 16 isolates from this study; b) 86 previously sequenced E. rhusiopathiae isolates, representing a diversity of geographic and host origins and spanning the clades described for this species (Clade 1 (n = 7), Clade 2 (n = 14), intermediate clade (n = 8), Clade 3 (n = 57)) [36]; c) two genomes of Erysipelothrix piscisicarius (formerly referred to as E. sp. strain 2) [37,38]: the type strain 15TAL0474 T (GCA_003931795.1) [39], and EsS2-7-Brazil (GCA_016617655.1). E. piscisicarius is the most closely-related species to E. rhusiopathiae currently known; d) a recently deposited Erysipelothrix genome, reported as a new species, Erysipelothrix sp.…”

Erysipelothrix anatis sp. nov., Erysipelothrix aquatica sp. nov. and Erysipelothrix urinaevulpis sp. nov., three novel species of the genus, and emended description of Erysipelothrix

“…For a more detailed understanding of the phylogenetic relationship of the novel strains among other Erysipelothrix species, the criteria of Pomaranski et al [10,11] and Grazziotin et al [7,8] were considered. Phylogenetic analyses based on the partial nucleotide and amino acid sequences of two representative housekeeping genes, gyrB and rpoB, were performed to also check Table 1.…”

“…Low sequence similarities (<97 %) to type strains of known Erysipelothrix species indicated clearly that all novel strains represented new species [25]. The high 16S rRNA gene sequence similarities (>99 %) among seven of the studied strains did not mean that the strains represent the same species [7, 15]. Genome sequence based comparisons including DNA–DNA hybridization (DDH) and average nucleotide identity (ANI) are required for the species assignment of the seven strains, which had high 16S rRNA gene sequence similarities [17].…”

“…[10, 11] and Grazziotin et al . [7, 8] were considered. Phylogenetic analyses based on the partial nucleotide and amino acid sequences of two representative housekeeping genes, gyrB and rpoB , were performed to also check non-synonymous substitutions [26].…”

“…Furthermore, Erysipelothrix inopinata and Erysipelothrix larvae were isolated from vegetable broth and the larval gut of rhinoceros beetle [4,5]. A number of publications present novel species of Erysipelothrix that infect pigs, poultry and fish [2,[6][7][8][9], of which Erysipelothrix piscisicarius has recently been described. Despite its name, this species has proven to cause deadly outbreaks not only in fish, but also in pigs and poultry [10][11][12][13][14].…”