Taxonomic classification of strain PO100/5 shows a broader geographic distribution and genetic markers of the recently described Corynebacterium silvaticum

Abstract

The bacterial strain PO100/5 was isolated from a skin abscess taken from a pig (Sus scrofa domesticus) in the Alentejo region of southern Portugal. It was identified as Corynebacterium pseudotuberculosis using biochemical tests, multiplex PCR and Pulsed Field Gel Electrophoresis. After genome sequencing and rpoB phylogeny, the strain was classified as C. ulcerans. To better understand the taxonomy of this strain and improve identification methods, we compared strain PO100/5 to other publicly available genomes from C. diphtheriae group. Taxonomic analysis reclassified it and three others strains as the recently described C. silvaticum, which have been isolated from wild boar and roe deer in Germany and Austria. The results showed that PO100/5 is the first sequenced genome of a C. silvaticum strain from livestock and a different geographical region, has the unique sequence type ST709, and could be could produce the diphtheriae toxin, along with strain 05–13. Genomic analysis of PO100/5 showed four prophages, and eight conserved genomic islands in comparison to C. ulcerans. Pangenome analysis of 38 C. silvaticum and 76 C. ulcerans genomes suggested that C. silvaticum is a genetically homogeneous species, with 73.6% of its genes conserved and a pangenome near to be closed (α > 0.952). There are 172 genes that are unique to C. silvaticum in comparison to C. ulcerans. Most of these conserved genes are related to nutrient uptake and metabolism, prophages or immunity against them, and could be genetic markers for species identification. Strains PO100/5 (livestock) and KL0182T (wild boar) were predicted to be potential human pathogens. This information may be useful for identification and surveillance of this pathogen.

Proteomics of Toxigenic Corynebacteria

“…C. silvaticum is a new species comprising bacteria formerly described as untypical C. ulcerans strains isolated from roe deer and wild boars in Germany and Austria [ 50 ]. Later, a broader distribution of the species with strains isolated in Portugal was reported [ 51 ]. A phylogenetic analysis showed that the species has diverged into two clades.…”

In silico identification of vaccine and drug targets for Corynebacterium ulcerans and the recently described C. silvaticum

“…All the genomes were annotated in PATRIC using RASTtk (Brettin et al 2015). The taxonomy of the samples had previously been veri ed as C. ulcerans or C. silvaticum (Viana et al 2020) using FastANI (Jain et al 2018), and were additionally submitted to the Type Strain Genome Server (Meier-Kolthoff and Göker 2019) to con rm their taxonomy.…”

“…It is known so far that it is cytotoxic in humans (Möller et al 2021). Therefore, the bacterium has a zoonotic potential that leads to a potential economic loss in animal production (Dangel et al 2020;Viana et al 2020).…”

“…ulcerans was selected based on its emergence as a causative agent of diphtheria and the fact that It has a wide range of reservoir species (Hacker et al 2016;Tiwari et al 2008), which increases its threat potential. C. silvaticum was selected based on its ability to infect production animals and has a, as yet, unknown potential to cause zoonotic infections (Dangel et al 2020;Viana et al 2020). The current vaccine for diphtheria uses the toxoid from C. diphtheriae (Rappuoli and Malito 2014) and the lack of sequence diversity could lower the e ciency of the current vaccine and antitoxin against C. ulcerans tox + strains (Otsuji et al 2019) and could play a role in diphtheria cases in vaccinated individuals (Vandentorren et al 2014).…”

“…C. silvaticum is a recently described NTTB species close to C. ulcerans that causes caseous lymphadenitis in wild animals such as wild boar and roe deer, which are reservoirs, and domestic pigs(Dangel et al 2020). Its potential host range is unknown, and It could potentially cause zoonotic infections(Viana et al 2020).…”