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: A computer-implemented method for detecting a genome sequence in digital form in a genome of a microorganism in digital form, including:—storing, in a computer memory, a set of digital genome sequences of constant length k, or ‘k-mers’, the set being obtained by sliding, at a constant pitch, a window of length k over the genome sequence;—for each k-mer, determining its absence or presence in the genome;—determining that the genome sequence is present in the genome if the percentage of k-mers detected as present in the genome is higher than a predetermined threshold.

Abstract: A method for detecting a biological species of interest (SOI) potentially present in an analysis sample, the biological species of interest having a known or partially known genome, the analysis sample comprising a mixture of various biological species, the method comprising (a) extracting nucleic acids from the analysis sample; (b) sequencing nucleotide sequences extracted, (c) on the basis of the sequencing result, (i) assigning the sequences resulting from the sequencing, based on a reference database of sequences; (i) assigning sequences; (ii) determining a quantity (RSOI, RNSOI) of sequences assigned to the biological species of interest; and, prior to the sequencing, adding a calibrator, the calibrator being a biological species added in a known concentration, to the analysis sample, the calibrator having a known genome, and on the basis of the sequencing result, determining a quantity (RCAL) of sequences assigned to the calibrator; (d) on the basis of the quantities of sequences estimated in the det

Abstract: A method for detecting a biological species of interest (SOI) present in an analysis sample, the biological species of interest having a known genome, the analysis sample comprising a mixture of various biological species, the method comprising (a) extracting nucleotide sequences from the analysis sample; (b) sequencing the nucleotide sequences extracted in the extracting; (c) on the basis of the sequencing, obtaining normalized sequences assigned to the biological species of interest and to the control species; and (d) comparing the normalized sequences respectively assigned to the biological species of interest and to the control species to detection thresholds respectively associated with the biological species of interest and with the control species.

Abstract: A method for determining a quantity Ginhib quantifying the inhibitory capacity of a molecule on a type of microorganism includes: preparing a plurality of samples, including microorganisms of the type, a nutrient medium for the microorganism and an initial amount of the molecule per microorganism increasing in a range [Qmin,Qmax] as a function of a classification of the samples; measuring the growth of the microorganisms in the samples as a function of time; and determining the quantity Ginhib as a function of the measurements of the growth. Determination of the quantity Ginhib includes: for each sample, calculating a value reflecting the growth of the microorganism of said type based on measurements of growth; classifying the values calculated for the samples as a function of the classification of the samples; and determining the quantity Ginhib as a function of the variation of the classified values.

Abstract: The subject of the invention is a method for making an in vitro prognosis of severity for a patient in septic shock, including the following steps: (i) the level of expression of the expression product of at least one gene chosen from the lilrb2 and lilrb1 genes is measured in vitro on the basis of a biological sample taken from the patient, (ii) the level of expression of the expression product of the at least one gene is compared with a control level of expression, of the expression product of the same gene, with a good prognosis of severity, in which a level of expression of the expression product of the at least one gene below the control level of expression indicates a poor prognosis of severity for the patient, and also a kit for implementing the method.

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: A method for determining a quantity Ginhib quantifying the inhibitory capacity of a molecule on a type of microorganism includes: preparing a plurality of samples, including microorganisms of the type, a nutrient medium for the microorganism and an initial amount of the molecule per microorganism increasing in a range [Qmin, Qmax] as a function of a classification of the samples; measuring the growth of the microorganisms in the samples as a function of time; and determining the quantity Ginhib as a function of the measurements of the growth. Determination of the quantity Ginhib includes: for each sample, calculating a value reflecting the growth of the microorganism of said type based on measurements of growth; classifying the values calculated for the samples as a function of the classification of the samples; and determining the quantity Ginhib as a function of the variation of the classified values.

Abstract: The subject of the invention is a method for making an in vitro prognosis of severity for a patient in septic shock, including the following steps: (i) the level of expression of the expression product of at least one gene chosen from the lilrb2 and lilrb1 genes is measured in vitro on the basis of a biological sample taken from the patient, (ii) the level of expression of the expression product of the at least one gene is compared with a control level of expression, of the expression product of the same gene, with a good prognosis of severity, in which a level of expression of the expression product of the at least one gene below the control level of expression indicates a poor prognosis of severity for the patient, and also a kit for implementing the method.