The Regional Danish Scientific Ethics Committee (N-20120050) approved the study, and written informed consent was obtained from the subject.

A phylogenetic reference tree was constructed using shared core sequences of 86 P. acnes genomes of the 188 strains used in this study (Table S1). The core of the 86 genomes was obtained by splitting the genome sequence of the reference strain P. acnes KPA171202 into 500 bp fragments and aligning each fragment against all other genomes using blastn v. 2.2.28+ [21] with the following cut-off parameters: coverage > 90% and identity > 80%. Any fragment that did not yield a hit from all genomes was discarded, and the rest were aligned using Muscle v. 3.8.31[22] and concatenated into a 1,964,522 bp-sequence, hereafter referred to as the core genome. Using MEGA v. 5.2.2[23] we identified 107,397 single nucleotide polymorphisms (SNPs) and 8,100 gaps. A reference phylogenetic tree (Figure 1) was built in MEGA [23] using the Minimal evolution algorithm and 500 replication in the bootstrap test with the “complete deletion” option to exclude gaps from the analysis.

The strategy aimed at scanning the entire genome to identify an approximately 500 bp DNA fragment suitable for SLST. This sequence length was chosen to ensure that overlapping reads from forward and reverse Sanger sequencing would result in high quality sequences.

A sliding window of 500 bp running along the genome (step size +1 bp) ensured that all possible candidates were evaluated. For each base pair step an alignment of the fragment to the rest of the genomes was done. The corresponding sequences from the other genomes were identified by blastn in the BLAST+ suite [21] and aligned with Muscle [22]. These blastn searches were made in batches of 100 candidates to speed up the process (2,500×600 bp instead of 2,500,000×500 bp). After the sequences were aligned, 500 bp windows from these 600 bp fragment alignments were extracted. Altogether, 2,558,882 fragment alignments were checked for their resolution capacity, i.e. usability in a SLST scheme for P. acnes.

The initial pool of fragments was 2,558,882, covering the complete genome. We then filtered the alignments of each of these fragments with a custom-made Python script. This filtering first removed all fragments with less than 86 aligned sequences. The remaining 1,923,100 fragments corresponded to the core genome (Figure 2). These were then tested for inconsistencies between the three major clades of P. acnes (types I, II, III). A total of 1,480,343 windows were then tested against strains clustering in the subtypes IA₁, IA₂, IB, or IC of type I, i.e.. This subtype filtering reduced the number of usable fragments to 19,018. Next, differentiation of six clusters within type IA in the reference tree was introduced as a requirement for an acceptable typing scheme. These clusters correspond to the designated letters A, B, C, D, E and F in the resulting SLST scheme (all traditionally typed IA). After this filtering, 917 SLST candidate fragments that could resolve the major clades, the subtypes of type I strains, and the six clusters within type IA remained. A substantial proportion of the 917 fragments were overlapping. All overlapping sequences (seen as three spikes in Figure 2) were merged into the final three candidates of which one was selected based on manual inspection.

To test the applicability of the final SLST candidate, primers targeting conserved regions flanking the target sequence were developed. The forward and reverse primer sequences used to target the SLST fragment were 5'-CAGCGGCGCTGCTAAGAACTT-3' and 5'-CCGGCTGGCAAATGAGGCAT-3', respectively.

A total of 77 strains covering the known diversity of P. acnes were used for validation of the primer pair (Table S1). DNA was extracted from isolates grown on 5% blood agar (Statens Serum Institut, Copenhagen, Denmark) for 48 hours in an anaerobic chamber. Using a 1-µl inoculation loop, colonies were collected from the agar plate and suspended in PCR-grade water. A volume of 20 µl of this suspension was mixed with 80 µl of 0.05 M NaOH and incubated for 45 minutes at 60°C. After incubation, 9.2 µl of 1 M Tris-HCl, pH 7, was added. This crude DNA preparation was diluted 100 times for PCR analysis. All PCR reactions were carried out in a 25 µl volume containing 10 µl 5′-PRIME Hotmastermix (5 PRIME, Hamburg, Germany), 3 µl of each primer (10 µM), 4 µl of PCR grade H₂O, and 5 µl of diluted DNA. Amplification was achieved with an initial cycle of 40 seconds of denaturation at 96°C and 35 cycles of 35 seconds at 94°C for denaturation, 40 seconds at 55°C for annealing, and 40 seconds at 72°C for extension with a final extension step at 72°C for 7 minutes. Purified PCR products were Sanger sequenced from both directions at GATC Biotech, Konstanz, Germany, using standard procedures. Data analyses were carried out using MEGA.

Untrimmed sequences of approximately 600 bp were edited, aligned, and trimmed according to SLST sequences extracted from available P. acnes genomes. The trimmed sequences were assigned to SLST type according to the typing scheme.

One sample from eight different sites of the facial skin and oral mucosa were collected from a healthy 26-year-old male with no history of acne or recent antibiotic treatment. Using a sterile cotton swap soaked in PCR grade water, symmetric samples were collected from a 2×2 cm area from the left and right side of the forehead, cheek, nose, and the buccal oral mucosa. Swabs were immediately transferred to a 1.5 ml Eppendorf tube containing 750 µl PowerLyzer PowerSoil Bead Solution (MO-BIO, Carlsbad, CA). Samples were vortexed for 2 minutes to ensure the release of bacteria to the suspension, which was then transferred to a PowerLyzer Glass Bead Tube (MO-BIO, Carlsbad, CA). DNA was extracted with the PowerLyzer PowerSoil DNA Isolation Kit (MO-BIO, Carlsbad, CA) according to the manufacturer's instructions. The SLST target sequence was amplified using fusion primers for the lib-L kit with barcodes attached to the forward primer (Table S3). PCR reaction mixtures were made in a total volume of 25 µl and comprised of 5 µl of DNA sample, 2.5 µl AccuPrime PCR Buffer II (Invitrogen), 1.5 µl of each primer (10 µM) (DNA Technology), 0.15 µl AccuPrime Taq DNA Polymerase High Fidelity (Invitrogen), and 14.35 µl of PCR grade water. PCR was performed using the following cycle conditions: an initial denaturation at 95°C for 2 minutes, followed by 30 cycles of denaturation at 95°C for 20 seconds, annealing at 55°C for 20 seconds, elongation at 72°C for 15 seconds, and then a final elongation step at 72°C for 3 minutes. Two PCR reactions were performed for all samples. The PCR products were verified on an agarose gel, pooled, and purified using the NucleoSpin Extract Kit (Macherey-Nagel). The concentration of the purified PCR product was measured with a NanoDrop 2000 spectrophotometer (Thermo Scientific). The SLST amplicons were sequenced unidirectionally from the forward primer end on a 454 Genome Sequencer FLX+ platform at GATC Biotech AG (Konstanz, Germany).

The initial processing of the data was made with the pyronoise (shhh.flows) implementation in Mothur v. 1.33.0 [24]. The reads were then assigned to STs using the best hit in a blastn comparison to the SLST database (Figure 3). The best hit was evaluated on the average of coverage and identity, and all hits lower than 99.5% were discarded as unassigned (< 9% of reads). Reads with two or more identical best hits, remained unassigned.

A swab of facial skin collected in parallel with the samples used for DNA extraction was suspended in sterile 0.85% saline and plated in 2-fold dilutions on 5% blood agar. After anaerobic incubation for four days 100 P. acnes-suspect colonies were subcultivated to purity and their identity tested using bacteriological procedures [15]. A total of 74 isolated confirmed as P. acnes were then subjected to SLST as described above.

The genome mining strategy resulted in the identification of three genomic loci suitable for SLST. The three regions are all found within a stretch of 600 Kb in the genome (Figure 1). Region 1 spans 881 bp and is found at nucleotide positions 2,025,740 – 2,026,621 (coordinates according to the KPA171202 genome sequence). This region partially overlaps with a coding sequence, PPA1871, annotated as 2',3'-cyclic-nucleotide 2'-phosphodiesterase precursor. Region 2 spans 719 bp and is found at nucleotide positions 1,867,701 – 1,868,420. This is upstream of the gene PPA1715, annotated as a hypothetical protein. Region 3 spans 819 bp and is found at nucleotide positions 1,462,788 – 1,463,607, immediately upstream of the gene PPA1340 encoding the CAMP factor 1, and partially overlapping with the flanking hypothetical gene PPA2385 specific to P. acnes.

We decided to use fragment 3, as only single nucleotide gaps were observed in some genomes, whereas alignments of the other two fragments showed gaps of up to 10 bp. By stepwise removal of nucleotides from both ends we identified a DNA sequence of 484 bp that was able to resolve all the phylogenetic clades found in our reference tree. In the following, this sequence is designated the “SLST target sequence”.

Two conserved flanking regions 85 bp downstream and 45 bp upstream of the SLST target sequence were identified as suitable PCR primers (Table S3), which resulted in an amplicon of 612 bp.

Reference sequences for alignment and trimming are found at the web-interface typing tool at http://medbac.dk/slst/pacnes. The interface allows any number of strains to be typed in batches. The sequences do not have to be trimmed, as long as the sequence is complete, and may be in reverse complement form.

Among 187 strains previously typed with MLST9 to represent 75 ST, 41 SLST types were identified (Table S1). A total of 80 polymorphic sites were observed in these 41 SLSTs. Phylogenetic analysis of the 41 distinct sequences revealed clustering concordant with that of the core genome reference tree (Figures 4 and 1). The chosen naming of the sequence types includes a number combined with a letter reflecting the phylogenetic relationship of strains (Figure 1). To make the transition from older schemes to the SLST scheme easier, we have appended the corresponding MLST9 type to the SLST type designations.

Overall, there is congruency between MLST9 types and the new SLST types (Figure 1). The clonal clusters (CCs) identified by eBurst analysis of MLST9 allelic profiles [17] are congruent with the letters assigned by the SLST, except for CC28 (HL025PA1 and 30.2.L1), which spans both D1 (IA) and F1-F6 (IA) (Figure 1). This phylogenetic ambiguity of CC28 is resolved neither by the MLST9 scheme nor by the MLST8 scheme reported by [19], which includes the two strains in CC-4. From the reference tree it is evident that D1 (IA) strains belong to a distinct cluster, which is detected only by the SLST.

Alignment of the SLST target locus against the NCBI database using blastn identified 90 P. acnes genomes that contained this sequence, and consequently could be assigned to an SLST type (Table S1). Homologous sequences were not detected in any other bacteria represented in the NCBI database. A total of 12 of the 90 P. acnes genomes identified by the blastn search were not included in our phylogenetic analysis. Two were recently added to the P. acnes databases, i.e. the strains HL042PA3 [25] and DSM 1897. The following strains were previously identified as P. acnes by [19]: 409-HC1, 434-HC2, 5U42AFAA and CC003-HC2. The remaining six strains have not been assigned to species level: KPL1847, KPL1849, KPL1854, KPL2003, KPL2008, KPL2009. All of these strains cluster with P. acnes in a tree based on concatamers of the MLST9 genes (data not shown).

To test if the SLST scheme presented here is applicable to analysis of the population diversity of P. acnes in metagenomic studies, samples from eight different skin and mucosal sites (symmetric samples from the left and right side of the forehead, cheek, nose, and mouth) were collected and used to map the diversity of the P. acnes population. After processing, a total of 183,786 high quality reads were obtained. SLST analysis of the sequences showed that each sample contained from 4 to 13 SLTS types. Overall, the skin sample sites were dominated by P. acnes SLST type A1 (IA), followed by types D1 (IA), C1 (IA) and E3 (IA). Combined, these four SLSTs represented approximately 95% of the population (Figure 3). In contrast, the oral mucosal samples were characterised by more SLSTs representing clusters H, K and L (corresponding to phylotypes IB, II and III, respectively) and small proportions of C1 (IA). Comparison of the four anatomical sites sampled from the left and right sides of the same face show a clear symmetric distribution of clones. A total of 5,408 (3%) reads had two or more identical best hits and remained unassigned. Another 21,356 (11.6%) reads were unassigned due to low hit scores.

To test if reads that remained unassigned due to low hit scores represented sequence errors or new STs, 74 P. acnes isolates collected in parallel from the same cheek as the samples analysed by sequence-based analysis were subjected to SLST analysis. The results did not identify new types and confirmed the type distribution obtained in the sequence-based population analysis (Figure 3). Thus, it is conceivable that the unassigned reads represented sequence errors.

The sequence data have been submitted to the EMBL databases under accession No. PRJEB5434.