Streptomyces sanguinis sp. nov., a Ceftriaxone‐Resistant Strain Obtained From Human Blood and Reclassification of Streptomyces thermospinosisporus as Streptomyces thermocarboxydovorans subsp. thermospinosisporus subsp. nov

Abstract

The taxonomic position of an actinomycete, strain 15‐116AT, isolated from a blood culture of a 31‐year‐old male from the United States was determined using polyphasic taxonomic analysis. Genome‐based phylogeny showed that the strain was closely related to Streptomyces composti, Streptomyces thermocarboxydovorans, and Streptomyces thermospinosisporus species. Digital DNA–DNA (dDDH) relatedness and average nucleotide identity (ANI) between the draft genome sequence of the strain and those of its closest phylogenomic neighbors listed above were between 35.9% and 37.3% (< 70%) and 88.5%, 88.1%, and 88.6% (95%–96.7%), respectively. However, the dDDH and ANI values between the genome sequence of S. thermocarboxydovorans JCM 10367T and S. thermospinosisporus JCM 11756T were 72.3% and 96.7%, respectively. These values are above the defined thresholds for prokaryotic species demarcation (70% dDDH and 95%–96.7% ANI) and fall within the dDDH range of 70%–79% for subspecies designation. Based on these findings and in accordance with the priority rule in nomenclature, S. thermospinosisporus is considered a later heterotypic synonym of S. thermocarboxydovorans and is classified as a subspecies of S. thermocarboxydovorans, for which the name S. thermocarboxydovorans subsp. thermospinosisporus subsp. nov. is proposed. Consequently, S. thermocarboxydovorans subsp. thermocarboxydovorans is created. Strain 15‐116AT was characterized by the presence of LL‐diaminopimelic acid in its peptidoglycan; diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylinositol as the major phospholipids; MK‐9(H8) and MK‐9(H6) as the predominant menaquinones (> 10%); and iso-C15:0, anteiso‐C15:0, iso-C16:0, and anteiso-C17:0 as the major fatty acids (> 10%). Morphological, phenotypic, and genomic traits distinguished strain 15‐116AT from its closest phylogenetic neighbors and highlighted the assignment of strain 15‐116AT (= DSM 106436T = ATCC BAA‐2935T) to a novel species of the genus Streptomyces, for which the name Streptomyces sanguinis sp. nov. is proposed. Genome screening for virulence factor‐associated genes showed that the strain harbored a gene encoding isocitrate lyase, which is required for persistent infection of Mycobacterium tuberculosis (YP_177728), as well as gene clusters associated with phenazine biosynthesis (NP_252902), unlike its close relatives. Moreover, strain 15‐116AT possessed a gene encoding elongation factor Tu (WP_003028672), which plays an important role in the bacterium′s ability to adhere to host cells. However, further experimental studies are required to evaluate the pathogenic potential of this strain.