First Multilocus Sequence Typing scheme to study Propionibacterium freudenreichii population structure

Propionibacterium freudenreichii is used as a ripening culture in Swiss cheese manufacture. Despite its predominance in cheese, P. freudenreichii can survive in different habitats. In this study, the molecular diversity and the population structure, specifically the relationships between P. freudenreichii strains, were investigated using multilocus sequence typing (MLST). Internal fragments of seven genes were amplified by PCR and sequenced for 113 strains of different subspecies and from various origins, including 10 countries and a variety of dairy and vegetal habitats. The MLST scheme resolved 46 sequence types (STs) with occurrence frequencies ranging from 1 to 11. Our results indicate a low level of nucleotide polymorphism in the core genome of the species: single nucleotide polymorphisms accounted for only 2.28% of the concatenated sequence, and the average polymorphism rate in pairwise comparison was 0.46%. The results also show that recombination played a significant role in the distribution of this polymorphism among isolates. Remarkably, the lineages defined by the STs exhibited little if any strain origin specialization. Furthermore, subspecies identification of the strains, based on their aptitude to use lactose and nitrate, revealed considerable phenotypic heterogeneity of the lineages. Namely, some strains of different countries and habitats, and of different subspecies displayed the same STs whereas strains of the same origin or subspecies were disseminated over the phylogenetic tree. This study brings new insights into the population structure and the mode of evolution of P. freudenreichii. It also constitutes the first development of MLST, an effective molecular typing tool, for this specie