Emendation of Propionibacterium acnes subsp. acnes (Deiko et al. 2015) and proposal of Propionibacterium acnes type II as Propionibacterium acnes subsp. defendens subsp. nov

Abstract

Recently, it has been proposed that strains of Propionibacterium acnes from the type III genetic division should be classified as P. acnessubsp. elongatum subsp. nov., with strains from the type I and II divisions collectively classified as P. acnessubsp. acnes subsp. nov. Under such a taxonomic re-appraisal, we believe that types I and II should also have their own separate rank of subspecies. In support of this, we describe a polyphasic taxonomic study based on the analysis of publicly available multilocus and whole-genome sequence datasets, alongside a systematic review of previously published phylogenetic, genomic, phenotypic and clinical data. Strains of types I and II form highly distinct clades on the basis of multilocus sequence analysis (MLSA) and whole-genome phylogenetic reconstructions. In silico or digital DNA-DNA similarity values also fall within the 70-80 % boundary recommended for bacterial subspecies. Furthermore, we see important differences in genome content, including the presence of an active CRISPR/Cas system in type II strains, but not type I, and evidence for increasing linkage equilibrium within the separate divisions. Key biochemical differences include positive test results for β-haemolytic, neuraminidase and sorbitol fermentation activities with type I strains, but not type II. We now propose that type I strains should be classified as P. acnessubsp. acnes subsp. nov., and type II as P. acnessubsp. defendens subsp. nov. The type strain of P. acnessubsp. acnes subsp. nov. is NCTC 737T (=ATCC 6919T=JCM 6425T=DSM 1897T=CCUG 1794T), while the type strain of P. acnessubsp. defendens subsp. nov. is ATCC 11828 (=JCM 6473=CCUG 6369).

Fig. 1.

Minimum evolution phylogenetic tree (mega v7.0) (Kumar et al., 2016) of concatenated gene sequences (4253 bp) from all STs currently represented in the MLST₈ database (http://pubmlst.org/pacnes/), and covering all major genetic divisions. Sequence input order was randomized, and bootstrapping resampling statistics were performed using 500 data sets. Bootstrap values (≥70 %) are shown on the arms of the tree. Horizontal bar represents genetic distance. CC, Clonal complex.

Fig. 2.

Neighbour-net split graph (SplitsTree v4.14.4) of allelic profiles from all STs currently represented in the MLST₈ database (http://pubmlst.org/pacnes/), and covering all major genetic divisions (Huson & Bryant, 2006). A distance matrix was generated from the allelic profile data and saved in NEXUS format for input to SplitsTree. Parallelogram formations indicative of recombination/ reticulation events are evident within the major type I and II divisions.