Method And System For Probabilistic Typing Of Microbial Strains

Abstract: The invention relates to a microbiological typing method, which comprises providing: a database of genetic profiles of microbial strains; and a phylogenetic tree of assignments of the genetic profiles to positions in the phylogenetic tree, and of frequencies of variation of the profiles in the tree. The typing of a microorganism comprises: measuring the genetic profile of the microorganism; determining a probability of variation of each genetic profile in the database with respect to the measured genetic profile, the probability of variation being calculated as a function of the frequencies of variation; and determining that the microorganism belongs to a taxon of the tree if at least the probability of variation for the taxon is greater than a threshold. According to the invention, the phylogenetic tree is constructed from a core genome of the microorganism species, and the predefined set of genetic markers is chosen from an accessory genome of the microorganism species.

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