IDENTIFICATION AND ANTIBIOTIC CHARACTERIZATION OF PATHOGENS IN METAGENOMIC SAMPLE

摘要

A method for identifying a pathogen contained in a metagenomic sample and for identifying pathogenic markers in the genome of said pathogen comprises: - processing (12) the sample to extract DNA from pathogens, - sequencing (14) the extracted DNA, thereby producing a set of reads, - comparing (22) the set of reads to a database of genomes of known pathogens in order to assign reads to said pathogens; - producing (26) a pool of reads comprising the reads assigned to a pathogen and assembling (28) the pooled reads to produce contigs, - comparing (30) the contigs to a second database of markers to check whether the produced contigs contain a marker, The method further comprise the step of comparing (24) the reads to the second database to assign reads to the markers, a read being assigned to a marker if it falls entirely into said marker or if it is astride said marker, and the pool also comprises the reads assigned to the markers, the contigs being thereby being assembled from reads assigned to a pathogen and reads assigned to the markers.