Multilocus sequence typing and phylogenetic analysis of Propionibacterium acnes

Abstract

Propionibacterium acnes is a commensal of human skin but is also implicated in the pathogenesis of acne vulgaris, in biofilm-associated infections of medical devices and endophthalmitis, and in infections of bone and dental root canals. Recent studies associate P. acnes with prostate cancer. As the species includes evolutionary lineages with distinct association with health and disease, there is a need for a high-resolution typing scheme. Recently, two multilocus sequence typing (MLST) schemes were reported, one based on nine and one based on seven housekeeping genes. In the present study, the two schemes were compared with reference to a phylogenetic tree based on 78 P. acnes genomes and their gene contents. Further support for a basically clonal population structure of P. acnes and a scenario of the global spread of epidemic clones of P. acnes was obtained. Compared to the Belfast scheme, the Aarhus MLST scheme (http://pacnes.mlst.net/), which is based on nine genes, offers significantly enhanced resolution and phylogenetic inferences more concordant with analyses based on a comprehensive sampling of the entire genomes, their gene contents, and their putative pathogenic potential.

Fig 1

Map of the P. acnes genome with the location of the nine genes used in the Aarhus MLST scheme and seven genes used in the Belfast MLST scheme.

Fig 2

Phylogenetic tree of 75 strains of P. acnes constructed by the minimum evolution algorithm in MEGA version 5 and based on a 92,577-bp concatemer of complete sequences of 76 housekeeping genes evenly distributed across the entire genome. For each strain the ET and CC determined according to the Aarhus MLST scheme and the Belfast scheme are indicated. Bootstrap values exceeding 50 are shown. The phylogenetic analysis identified seven clades that corresponded to CCs identified by eBURST analysis based on data generated according to the Aarhus scheme.

Fig 3

Population snapshots of P. acnes generated by eBURST analysis of MLST allele profiles determined according to the Aarhus and Belfast MLST schemes. The analysis was based on data sets that include all STs in the two MLST databases supplemented with data retrieved from 75 genome-sequenced strains. Clonal clusters (CCs) are named after the assumed founding ST, which are indicated by blue dots. Note that ST numbers in the two schemes do not correspond to each other.