Description and whole genome sequencing ofEikenella exiguasp. nov., isolated from brain abscess and blood

Abstract

We herein describe the first novel species within the genus Eikenella since it was established in 1972 by the reclassification of “Bacteroides corrodens” to Eikenella corrodens. From a poly-microbial brain abscess, we encountered an Eikenella isolate PXX that could not validly be named E. corrodens. The isolate grew on blood agar with small, translucent, pitting colonies after 3 days of anaerobic incubation. By reviewing previously collected invasive isolates, we found an additional Eikenella strain EI_02 from a blood culture exhibiting the same properties as PXX. Phylogenetic analyses based on both whole genome and individual house-keeping genes confirmed that the two strains allocate in a phylogenetic cluster separate from E. corrodens.Using specific amplification and sequencing of the Eikenella nusG-gene as a method, we further detected the novel Eikenella species in six historic brain-abscesses previously reported to contain E. corrodens based on 16S metagenomics. Out of 24 Eikenella whole genome projects available in GenBank, eight cluster together with PXX and EI_02. These isolates were recovered from brain abscess (2), blood (1), bone/soft tissue (3), parotid gland (1) and unknown (1). It remains to be investigated whether the new species can be a cause of endocarditis.The average nucleotide identity (ANI) value between strain PXX and the E. corrodens type strain ATCC 23834 was 92.1% and the corresponding genome-to-genome distance value 47.1%, both supporting the classification of PXX as a novel species. For this species we propose the name Eikenella exigua. The E. exigua type strain is PXXT (DSM 109756T, NCTC 14318T).