Biomerieux, Inc.

Institut Pasteur

Assistance Publique-hopitaux De Paris

Université Paris Diderot-paris 7

Etienne Ruppe

Patrice Courvalin

Pierre Mahe

Antoine Andremont

Maud Tournoud

Stéphane Schicklin

Ghislaine Guigon

Sylvie Bremont

A method for identifying a pathogen contained in a metagenomic sample and for identifying pathogenic markers in the genome of the pathogen includes: processing the sample to extract DNA from pathogens, sequencing the extracted DNA, thereby producing a set of reads, comparing the reads to a database of genomes of known pathogens to assign reads to the pathogens; producing a pool of reads and assembling them to produce contigs, comparing the contigs to a second database of markers to check whether they contain a marker. The method further includes the step of comparing the reads to the second database to assign reads to the markers, a read being assigned to a marker if it falls entirely into or is astride the marker, and the pool also includes the reads assigned to the markers, the contigs thereby being assembled from reads assigned to a pathogen and reads assigned to markers.

Identification and antibiotic characterization of pathogens in metagenomic sample

Growing community of inventors

Paris, France

Etienne Ruppe