Phylogeny and virulence determinant detection of Fusobacterium necrophorum strains isolated at the UK Anaerobe Reference Unit between 1982 and 2019.

Abstract

Objectives: Explore the presence, or absence, of virulence genes and the phylogeny of a multi-decade UK collection of clinical and reference Fusobacterium necrophorum isolates.

Methods: Three hundred and eighty-five F. necrophorum strains (1982-2019) were recovered from storage (-80°C). Illumina whole genome sequencing (WGS) was undertaken with 374/385 genomes available for examination after quality checking. Sequences were analysed, using BioNumerics (bioMérieux; v 8.1), for the presence of known virulence genes. Strain phylogeny was investigated using a bespoke Fusobacterium spp. whole genome multi-locus sequence typing (wgMLST) method and single nucleotide polymorphism (SNP) analysis.

Results: F. necrophorum ssp. necrophorum and F. necrophorum ssp. funduliforme phylogeny showed clear separation of the two subspecies and clustering of F. necrophorum ssp. funduliforme into three distinct clades. Congruence between SNP and wgMLST analysis was high (99.3%) and indistinguishable clusters were observed with wgMLST (n=3) and SNP (n=1) analysis of isolates derived from different students attending the same education setting. There was no grouping of strains by disease state or decade of isolation. No association was demonstrated with specific virulence gene detection although conspicuous virulence gene patterns were seen amongst the different subspecies and clades.

Conclusions: There was no evidence that the pathogenesis of F. necrophorum infection was associated with the presence of the virulence determinants investigated. Host-pathogen interactions should, therefore, be a focus of future research. Person-to-person transmission is a feature of this important pathogen.