Identification and antibiotic characterization of pathogens in metagenomic sample

A metagenomics, pathogen technology, applied in the field of metagenomics, which can solve problems such as misleading clinicians and failing to characterize pathogen antibiotic susceptibility

Active Publication Date: 2019-06-21
BIOMERIEUX SA
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

At least for the first time when a clinician is confronted with a new pathogen, state-of-the-art metagenomic analysis fails to characterize the antibiotic susceptibility of the pathogen and, worse, may mislead the clinician by producing spurious results, such as species k as Resistant pathogens instead of species 1

Method used

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  • Identification and antibiotic characterization of pathogens in metagenomic sample
  • Identification and antibiotic characterization of pathogens in metagenomic sample
  • Identification and antibiotic characterization of pathogens in metagenomic sample

Examples

Experimental program
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Embodiment Construction

[0065] Embodiments of the invention are now described in connection with the characterization of pathogens contained in (small) bronchoalveolar lavage (BAL) of intensive care unit (ICU) patients, in particular respiratory acquired pneumonia (VAP). The goal is to list all pathogens present in the sample, along with antibiotic resistance determinants and, if possible, associate ARDs with pathogens.

[0066] refer to image 3 , a BAL sample is collected from a patient at 10 and then processed at 12 to extract nucleic acid from pathogens contained in the sample. This preparation in turn includes, for example, the following:

[0067] - a host cell removal step by means of a saponin preparation, as described in document US 2015 / 0337362;

[0068] - a lysis step, such as mechanical, enzymatic or osmotic lysis, which disrupts the membranes of the cells in the sample, thereby releasing their acidic nucleic acid content, destroys proteins by adding proteases and destroys RNA by adding ...

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Abstract

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 apathogen and reads assigned to the markers.

Description

technical field [0001] The present invention relates to the field of metagenomics and in particular the characterization of antibiotic susceptibility of pathogens in metagenomic samples by asserting the presence of antibiotic resistance markers in their genomes. Background technique [0002] Currently, identification of pathogens in clinical samples by classical microbiological techniques and antibiotic susceptibility testing (AST) profiling requires extensive testing and / or much prior knowledge about the pathogen. For example, microbiology workflows involve the growth of pathogens (e.g., on Petri dishes) to isolate them and obtain the critical biomass needed for subsequent testing. However, different bacteria may require different culture conditions (eg aerobic versus anaerobic bacteria), and if the culture conditions are not selected in an appropriate manner, may compete during the culture, or may even not grow at all. Therefore, the choice of media is often based on assu...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/689G16B40/00G16B30/00G16B20/20G16B20/00G16B30/20
CPCC12Q1/6869C12Q1/6888C12Q1/689G16B20/00G16B30/00G16B30/20G16B20/20C12Q2600/156C12Q2537/165G16B40/20C12Q2600/106C12Q2600/158
Inventor P·马埃M·图尔努德S·斯奇克林G·贵贡E·鲁佩
Owner BIOMERIEUX SA
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