Description of Eikenella halliae sp. nov. and Eikenella longinqua sp. nov., derived from human clinical materials, emendation of Eikenella exigua Stormo et al. 2019 and emendation of the genus Eikenella to include species which are strict anaerobes

Abstract

<jats:p>The <jats:italic>Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella</jats:italic> (HACEK) group genus <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.1961" xlink:type="simple">Eikenella</jats:ext-link> </jats:named-content> </jats:italic> contained a single species, <jats:italic>Eikenella corrodens,</jats:italic> for many years. In November 2019, <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.36739" xlink:type="simple">Eikenella exigua</jats:ext-link> </jats:named-content> </jats:italic> was described after recovery from a brain abscess and blood culture in Norway. Coincidentally, characterization of 22 Gram-negative bacteria resembling <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.1961" xlink:type="simple">Eikenella</jats:ext-link> </jats:named-content> </jats:italic> from 17 Canadian patients had been underway. Seven isolates from five patients were conclusively identifiable as <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.1962" xlink:type="simple">E. corrodens</jats:ext-link> </jats:named-content> </jats:italic>. One (NML 120819) was deemed to represent a species of the genus <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.1961" xlink:type="simple">Eikenella</jats:ext-link> </jats:named-content> </jats:italic> most closely related to <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.1962" xlink:type="simple">E. corrodens</jats:ext-link> </jats:named-content> </jats:italic>. Fourteen isolates had 97.6 to 98.8% similarities to <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.1962" xlink:type="simple">E. corrodens</jats:ext-link> </jats:named-content> </jats:italic> by 16S rRNA gene sequencing, forming three distinct groups by genome analyses. The largest contained ten anaerobic isolates from eight patients recovered from blood, brain, bone and other abscesses; upon re-evaluation, this group was found to be most consistent with <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.36739" xlink:type="simple">E. exigua</jats:ext-link> </jats:named-content> </jats:italic>. A second facultatively anaerobic clade consisted of two ocular isolates from one patient and a sinus isolate from a second patient. The third taxon consisted of a single strictly anaerobic blood culture isolate. The novel taxa, like <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.1962" xlink:type="simple">E. corrodens</jats:ext-link> </jats:named-content> </jats:italic>, were poorly reactive biochemically and difficult to discern from each other phenotypically and chemotaxonomically, including by cellular fatty acids. MALDI-TOF (Bruker) and whole-genome sequencing were used to further characterize isolates. Draft genomes for the strains had similar DNA G+C contents (55.38–58.53 mol%) while sizes varied from 1.82 Mb to 2.54 Mb. We propose here emendations of the genus <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.1961" xlink:type="simple">Eikenella</jats:ext-link> </jats:named-content> </jats:italic> and the species <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.36739" xlink:type="simple">Eikenella exigua</jats:ext-link> </jats:named-content> </jats:italic>, as well as describing <jats:italic>Eikenella halliae</jats:italic> sp. nov. NML 130454<jats:sup>T</jats:sup> (=LMG 30894<jats:sup>T</jats:sup>=NCTC 14180<jats:sup>T</jats:sup>) and <jats:italic>Eikenella longinqua</jats:italic> sp. nov. NML 02-A-017<jats:sup>T</jats:sup> (=LMG 30896<jats:sup>T</jats:sup>=NCTC 14179<jats:sup>T</jats:sup>), on the basis of these findings.</jats:p>

Eikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic species

“…The G+C content of the genomic DNA of strain S3360 T was 58.4 mol%, as determined from the draft genome assembly using quast (4.4). This value lies within the range of 55.3-58.8 % for the other validly published species of the genus Eikenella, and it is most similar to the G+C content of the most closely genetically related species, E. longinqua, with 58.8 mol% [4].…”

“…Based on type species of all genera within the family Neisseriaceae for which wholegenome sequences were available and GcvT proteins could be annotated, we could demonstrate that this CSI is not specific for Neisseria and Eikenella any more, in contrast to when the work of Adeolu and Gupta was published in 2013 (Fig. S3): Firstly, two Eikenella species which have been published since [E. halliae [4] and Eikenella species KCOM 3110 (GCF_003990355. for growth of strain S3360 T was pH 7.0, with good growth also observed at pH 8.0, but considerably reduced growth at pH 4.0, 5.0 and 6.0, and slightly reduced growth at pH 9.0.…”

“…The selection of Eikenella sequences included all validly published species of this genus (sequences of type strains; n =4), plus an additional hitherto undescribed Eikenella species (KCOM 3110) and a strain described as ‘most like E. corrodens ’ and referred to as ‘ E. corrodens- like’ by Bernard et al (NML 120819) [4]. These species ( n =6) are hereafter referred to as ‘all recognized Eikenella species’.…”

“…S3): Firstly, two Eikenella species which have been published since [ E. halliae [4] and Eikenella species KCOM 3110 (GCF_003990355.1)] have a different two amino acid insertion (serine and glutamate, SE) at positions 107 and 108 of the GcvT sequence. Secondly, several non- Neisseria and non- Eikenella species included in our analysis ( Alysiella filiformis, Bergeriella denitrificans , Conchiformibius steedae , Morococcus cerebrosus , Snodgrassella acetivorans and Uruburuella suis share the CSI described to have been specific for Neisseria and Eikenella as of 2013.…”

“…Differential biochemical and atmospheric growth characteristics of strain S3360 T in comparison with all currently validly published Eikenella species Strains: 1, S3360 T (data from this study, determined in duplicate by Vitek 2 NH and GN cards); 2, Eikenella corrodens ATCC BAA-1152 (data from this study, determined in duplicate by Vitek 2 NH and GN cards); 3, Eikenella exigua PXX T (data from[3]); 4, Eikenella halliae NML 130454 T (data from[4]); 5, Eikenella longinqua NML 02-A-017 T (data from[4]). NH, Vitek 2 NH card; GN, Vitek 2 GN card; x, included in Vitek 2 NH or GN card; /, not included in Vitek 2 GN card; +, positive or growth; v, variable (mostly positive); -, negative or no growth; nd, not determined.…”