Turn-around-time for one sample / DNA extraction
Multiplex PCR
Migration
≈3h30 / DNA extraction
9 PCR
9 migrations
9 sequencing
Bioinformatic analysis and comparison to database
≈48h / DNA extraction
PCR
Migration
Sequencing
Bioinformatic analysis and comparison to database
≈24h / DNA extraction
PCR
Migration
Sequencing
Bioinformatic analysis and comparison to database
≈4-6 days
Cost per sample / ≈10€ / ≈120-150€ / ≈20€ / ≈150€
Indication / Screening of
C. acnes population phylogeny / Investigation of the main clusters circulating in
C. acnes population / Larger analysed C. acnes populations / Large population and possibility to investigate resistome/virulome data
Advantages / - The fastest method
- First-line typing method recommended (McDowell, 2018) / Uncomplicated and can be applied to bacterial isolates (Scholz et al 2014) / - Very rapid
- Applied both to bacterial isolates and to complex microbiomes (Scholz et al, 2014) / Comprehensive analysis
Drawbacks / - Only give phylotype information / - Time-consuming
- Expensive
- Not applicable to metagenomics studies because of requirement to combine sequences of usually seven gene loci
- Available sequencing platforms so far lacked sufficient resolution to disclose diversity beyond the species level.
(Scholz et al 2014) / - May reduce the resolution relative to MLST (except if applying a genome mining strategy as demonstrated previously, in order to resolve the vast majority of C. acnes clusters identified by MLST9 method, and in some cases, improved it) (Scholz et al 2014)
- SLST requires that the target species has a basically clonal population structure, because recombination may blur typing results based on a single locus. It was previously shown that C. acnes population meets this criterion (Scholz et al., 2014) / - Heaviness of the protocols
- High cost
- Technically demanding
- Specific skills needed (complex bioinformatic analyzes)
Supplementary data Table 2: Presentation of all existing molecular typing methods with the advantages and drawbacks for each of them.