Table 1.
Loci characteristics and discriminatory power of MLST schemes based on four (MLST4) and eight (MLST8) genes.
Figure 1.
Sliding window analysis of nucleotide diversity (π) within the concatenated sequence of all eight MLST loci (4253 bp).
Analysis was carried out using a window size of 200(aroE, guaA, sodA, tly and camp2) selected for further analysis are indicated.
Figure 2.
Neighbour-net splits graph of allelic profiles from all 38 STs identified upon MLST analysis of 87 P. acnes isolates.
STs representing all phylogroups were identified from this cohort of isolates. Parallelogram structures indicative of recombination events are evident within the major type I and II divisions.
Table 2.
Summary of phylogroups and their source for 87 isolates analysed by MLST in this study.
Table 3.
MLST results generated for 87 P. acnes isolates upon analysis with the four (MLST4) and eight (MLST8) gene schemes.
Figure 3.
Association of P. acnes phylogroups with different clinical conditions and normal skin.
Data was obtained from MLST analysis of 372 isolates.
Figure 4.
eBURST population snapshot of the current P. acnes MLST database.
To date, a total of nine clonal complexes, where the isolates share 7/8 loci with at least one other ST in the group, and 21 singletons have been identified. The frequency of each ST within the isolate database is indicated by the size of each circle. Founding genotypes are highlighted in blue and sub-founders in yellow. The previously described separate complexes CC1 and CC4 now form a large single complex with ST1 as the founder (100% bootstrap) and ST4 (98% bootstrap) as a sub-founder; these two clusters are linked via ST105. Note, the spacing between the singletons and clonal complexes is not related to the genetic distance between them.
Table 4.
Roles of mutation and recombination events in the generation of SLV alleles within P. acnes.
Table 5.
IA values for isolates and STs from the whole P. acnes population and major phylogroups (IA, IB, II & III).
Figure 5.
Alignment of CAMP factor 2 amino acid sequences from P. acnes type strain NCTC737 (type IA1; ST1; CC1) and P. humerusii strains HL044PA1, HL037PA2, HL037PA3 and P08.
Overall identity between the homologues from these two species based on their protein sequence is 92%. The N-terminal putative signal sequence cleavage site occurs at the AHA-VE sequence (start residue position, 26).
Figure 6.
MAUVE visualisation of synteny between P. acnes, P. avidum and P. humerusii genomes.
Pairwise alignments of genomes were generated using the progressive MAUVE algorithm (v2.3.1). The sequence similarity in the pairwise alignment of P. acnes (6609, type IB ST5, CC5) and P. avidum (ATCC25577) was 53.2%. The similarity between P. acnes (6609) and P. humerusii (P08) was 69.3%, and between P. avidum (ATCC25577) and P. humerusii (P08) 52.7%.