An expanded multilocus sequence typing scheme for propionibacterium acnes: investigation of 'pathogenic', 'commensal' and antibiotic resistant strains

Abstract

The Gram-positive bacterium Propionibacterium acnes is a member of the normal human skin microbiota and is associated with various infections and clinical conditions. There is tentative evidence to suggest that certain lineages may be associated with disease and others with health. We recently described a multilocus sequence typing scheme (MLST) for P. acnes based on seven housekeeping genes (http://pubmlst.org/pacnes). We now describe an expanded eight gene version based on six housekeeping genes and two 'putative virulence' genes (eMLST) that provides improved high resolution typing (91eSTs from 285 isolates), and generates phylogenies congruent with those based on whole genome analysis. When compared with the nine gene MLST scheme developed at the University of Bath, UK, and utilised by researchers at Aarhus University, Denmark, the eMLST method offers greater resolution. Using the scheme, we examined 208 isolates from disparate clinical sources, and 77 isolates from healthy skin. Acne was predominately associated with type IA(1) clonal complexes CC1, CC3 and CC4; with eST1 and eST3 lineages being highly represented. In contrast, type IA(2) strains were recovered at a rate similar to type IB and II organisms. Ophthalmic infections were predominately associated with type IA(1) and IA(2) strains, while type IB and II were more frequently recovered from soft tissue and retrieved medical devices. Strains with rRNA mutations conferring resistance to antibiotics used in acne treatment were dominated by eST3, with some evidence for intercontinental spread. In contrast, despite its high association with acne, only a small number of resistant CC1 eSTs were identified. A number of eSTs were only recovered from healthy skin, particularly eSTs representing CC72 (type II) and CC77 (type III). Collectively our data lends support to the view that pathogenic versus truly commensal lineages of P. acnes may exist. This is likely to have important therapeutic and diagnostic implications.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1. eBURST population snapshot of the eMLST database.

A total of eight clonal complexes, where isolates share 7/8 loci with at least one other eST in the group, and 21 singletons were identified. The frequency of each eST is indicated by the area of each circle. Type IA1 isolates are represented by CC1, CC3, CC4 and 11 singletons; type IA2 by CC2 and two singletons, type IB by CC5 and one singleton; type II by CC6, CC69 and six singletons; type III by CC77 and one singleton. Founding genotypes are highlighted in blue and sub-founders in yellow. eSTs only isolated from healthy skin are circled in green. Note, the spacing between singletons and clonal complexes is not related to the genetic distance between them. Culture collection strain NCTC737 (type IA1) is represented by eST1 (ST18, Arahus), KPA171202 by eST5 (ST36, Arahus), CCUG32901 by eST5 (ST36, Arahus) and ATCC11828 by eST27 (novel ST, Arahus).

Figure 2. Neighbour-net splits graph of allelic profiles from all 91 P. acnes eSTs.

Parallelogram structures indicative of recombination are clearly present within the major divisions I, II and III. Overall levels of recombination within the population were statistically significant (phi test; p = 0.021).

Figure 3. Minimum evolution phylogenetic tree of concatenated gene sequences from all 91 P. acnes eSTs.

The tree was constructed using concatenated sequences (4253 bp) from each eST. The sequence input order was randomized, and bootstrapping resampling statistics were performed using 500 data sets. Bootstrap values are shown on the arms of the tree. Horizontal bar represents genetic distance. Coloured vertical bars on the right relate to eBURST groupings or clonal complexes. The colour scheme relating to each eBURST group is described, with singletons highlighted in red. Culture collection strain NCTC737 (type IA1) is represented by eST1 (ST18, Arahus), KPA171202 by eST5 (ST36, Arahus), CCUG32901 by eST5 (ST36, Arahus) and ATCC11828 by eST27 (novel ST, Arahus).