Abstract: 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.

Abstract: The method for detecting and monitoring a bacterial outbreak includes predicting that a collected bacterial strain and a bacterial strain from a database belong to the bacterial outbreak if their genomic distance is less than a first predetermined threshold, do not belong to the bacterial outbreak if their genomic distance is greater than a second predetermined threshold strictly greater than the first threshold, or may belong to the bacterial outbreak if their genetic distance is in-between. The first threshold is greater than or equal to a third threshold, such that a prediction that two bacterial strains with a genomic distance less than the third threshold belong to the outbreak has maximum specificity. The second threshold is less than or equal to a fourth threshold, such that a prediction that two bacterial strains with a genomic distance greater than the fourth threshold do not belong to the outbreak has maximum sensitivity.

Abstract: 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.