Fusobacterium abscessus sp. nov., associated with brain abscess in humans

Recent genome-based phylogenetic investigations of the Fusobacterium nucleatum group have revealed that genomes currently annotated as F. nucleatum (sensu stricto) bifurcate into two separate phylogenetic groups: a large cluster containing the F. nucleatum type strain and a smaller cluster possibly representing a novel species. To further investigate this, we searched our strain archive for Fusobacterium isolates potentially representing the smaller cluster. A strain Vestland17^T, cultured from a polymicrobial brain abscess, had been found to share less than 99% similarity with the F. nucleatum type strain by partial 16S rRNA gene sequencing. The isolate grew on blood agar with dry whitish colonies (0.5-1 mm) after 24-48 h of anaerobic incubation. Genome-based phylogenetic analyses confirmed that it belonged to the smaller F. nucleatum outlier cluster. We further confirmed the presence of this outlier cluster in four additional historic brain abscess samples using specific amplification and sequencing of the dnaB gene directly from remnant extracted DNA stored in our diagnostic biobank. A core-genome phylogenetic tree including the novel strain Vestland17^T and several more recent GenBank whole-genome references reproduced the previously observed bifurcation within the F. nucleatum (sensu stricto) species. Average Nucleotide Identities (ANI) between the two clusters are in the range 94.7-95.2%, supporting that the smaller cluster represents a different species as per a 95-96% ANI threshold. This was further supported by alternative strategies based on the biological species concept. For this species, we propose the name Fusobacterium abscessus. The type strain of F. abscessus is Vestland17^T (DSM 121298^T, NCTC 15275^T).