First Draft Genome Sequences of Neisseria sp. Strain 83E34 and Neisseria sp. Strain 74A18, Previously Identified as CDC Eugonic Fermenter 4b Species.

We report the first draft genome sequences of two isolates previously classified as CDC EF-4b species, Neisseria sp. 83E34 and Neisseria sp. 74A18. Both strains were isolated from patients with animal bites and likely constitute novel genomospecies with average nucleotide identities of <95% to other sequenced strains.

GENOME ANNOUNCEMENT

CDC eugonic fermenter 4b (EF-4b) is a designation of Gram-negative bacteria that are members of animal oral flora and are typically isolated from animal bite wounds in humans (1). In 2006, this group was identified as Neisseria zoodegmatis based on 16S sequence and biochemical testing (1–3). Only five isolates from human infections have been reported since the taxonomical classification of Neisseria zoodegmatis, while >30 isolates have been collected from CDC EF-4b bacteria (1, 4, 5). CDC EF-4b has also been cultured from a case of infectious tenosynovitis due to a Siberian tiger bite (6). To date, the 16S sequence is the only available nucleotide sequence for Neisseria zoodegmatis.

We sequenced the first draft genomes of two bacterial isolates that had been identified as CDC group EF-4b from the University of California, San Francisco (UCSF) microbiology lab. Isolate 74A18 was isolated from a right-hand index finger culture of a patient with flexor tenosynovitis following a dog bite. Isolate 83E34 was isolated from a left-lateral-hand culture of a patient with cellulitis following a cate bite. Both patients also had Pasteurella multocida isolated concurrently from the wound cultures.

DNA was extracted using the Qiagen EZ1 DNA tissue kit. Nextera XT paired-end and Nextera mate-pair libraries were sequenced at 250/350 bp and 2 × 80 bp on an Illumina MiSeq, respectively, and on an Oxford Nanopore MinION sequencer. Illumina sequences were adapter and quality (Q20) trimmed using cutadapt or NxTrim, de novo assembled using SPAdes version 3.5, metagenomically screened for contaminating sequence with SURPI, and annotated via Prokka version 1.1 (7–12). A total of 6,878,276 (74A18) and 9,380,478 (83E34) paired-end reads and 4,052,930 (74A18) and 5,428,958 (83E34) mate-pair reads were recovered after trimming. De novo assembly yielded 40 contigs totaling 2,419,010 bp, with an N50 of 233,412 bp for Neisseria sp. 83E34, while Neisseria sp. 74A18 yielded 88 contigs totaling 2,572,932 bp, with an N50 of 53,927 bp.

BLASTN analysis of the 16S sequence from Neisseria sp. 74A18 showed 98.6% identity to Neisseria shayeganii clone TM092 (accession no. KM462144) and 98.1% identity to Neisseria zoodegmatis strain N15a (accession no. JQ979306). BLASTN analysis of the 16S sequence from Neisseria sp. 83E34 demonstrated 99.3% identity to Neisseria canis oral taxon 137 (accession no. JN713302), 98.2% identity to Neisseria shayeganii clone TM092 (accession no. KM462144), and 96.7% identity to Neisseria zoodegmatis strain N15a (accession no. JQ979306). However, alignment of Neisseria sp. 83E34 to Neisseria canis housekeeping genes revealed poor alignment (84.7% for rpoB [accession no. KM438030] and 88.4% for cpn60 [accession no. KJ872773]), suggesting it may not be a strain of Neisseria canis. Pairwise whole-genome alignment by LASTZ revealed 89.3% identity between our two sequenced species and 93.9% identity between Neisseria sp. 83E34 and Neisseria wadsworthii 9715 (WGS AGAZ01), the closest whole genome available (13). These data are consistent with a high degree of genomic variability within related Neisseria spp. and isolates previously identified as CDC EF-4 members (14). Further sequencing of EF-4b species, including Neisseria zoodegmatis, will be needed to fully classify these species.

Accession number(s).

These whole-genome shotgun projects have been deposited at DDBJ/ENA/GenBank under the accession numbers LGYH00000000 (Neisseria sp. 83E34) and LGZA00000000 (Neisseria sp. 74A18).