Method and system for microbiome-derived diagnostics and therapeutics infectious disease and other health conditions associated with antibiotic usage
AssigneeuBiome, Inc.
InventorsZachary Apte, Jessica Richman, Daniel Almonacid, Siavosh Rezvan Behbahani
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Abstract
Methods, compositions, and systems are provided for detecting one or more effects of antibiotic usage for an infectious disease or other health condition on the microbiome of an individual, monitoring such effects, and/or determining, displaying, or promoting a therapy for such an effect. Methods, compositions, and systems are also provided for generating and comparing microbiome composition and/or functional diversity datasets. Methods, compositions, and systems are also provided for generating a characterization model for antibiotic usage.
Claims36
A method of determining a classification of occurrence of a microbiome indicative of, or associated with, antibiotic usage or screening for the presence or absence of a microbiome indicative of antibiotic usage in an individual and/or determining a course of treatment for an individual human having a microbiome indicative of antibiotic usage, the method comprising,
- providing a sample comprising bacteria (or at least one of the following microorganisms including:
- bacteria, archaea, unicellular eukaryotic organisms and viruses, or the combinations thereof) from the individual human;
- determining an amount(s) of one or more of the following in the sample:
- bacterial taxon or gene sequence corresponding to gene functionality as set forth in Table A;
- comparing the determined amount(s) to a condition signature having cut-off or probability values for amounts of the bacterial taxon and/or gene sequence for an individual having a microbiome indicative of antibiotic usage or an individual not having a microbiome indicative of antibiotic usage or not or both;
- and
- determining a classification of the presence or absence of the microbiome indicative of antibiotic usage and/or determining the course of treatment for the individual human having the microbiome indicative of antibiotic usage based on the comparing.
A method for determining a classification of the presence or absence of a microbiome indicative of antibiotic usage and/or determine a course of treatment for an individual human having a microbiome indicative of antibiotic usage, the method comprising performing, by a computer system:
- receiving sequence reads of bacterial DNA obtained from analyzing a test sample from the individual human;
- mapping the sequence reads to a bacterial sequence database to obtain a plurality of mapped sequence reads, the bacterial sequence database including a plurality of reference sequences of a plurality of bacteria;
- assigning the mapped sequence reads to sequence groups based on the mapping to obtain assigned sequence reads assigned to at least one sequence group, wherein a sequence group includes one or more of the plurality of reference sequences;
- determining a total number of assigned sequence reads;
- for each sequence group of a condition signature set of one or more sequence groups selected from TABLE A:
- determining a relative abundance value of assigned sequence reads assigned to the sequence group relative to the total number of assigned sequence reads, the relative abundance values forming a test feature vector;
- comparing the test feature vector to calibration feature vectors generated from relative abundance values of calibration samples having a known status of antibiotic usage;
- and
- determining the classification of the presence or absence of the microbiome indicative of antibiotic usage and/or determining the course of treatment for the individual human having the microbiome indicative of antibiotic usage based on the comparing.
A method for at least one of characterizing, diagnosing, and treating an antibiotic usage issue in at least a subject, the method comprising:
- at a sample handling network, receiving an aggregate set of samples from a population of subjects;
- at a computing system in communication with the sample handling network, generating a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects upon processing nucleic acid content of each of the aggregate set of samples with a fragmentation operation, a multiplexed amplification operation using a set of primers, a sequencing analysis operation, and an alignment operation;
- at the computing system, receiving a supplementary dataset, associated with at least a subset of the population of subjects, wherein the supplementary dataset is informative of characteristics associated with antibiotic usage;
- at the computing system, transforming the supplementary dataset and features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset into a characterization model of the antibiotic usage;
- based upon the characterization model, generating a therapy model configured to correct the antibiotic usage issue;
- and
- at an output device associated with the subject and in communication with the computing system, promoting a therapy to the subject with the antibiotic usage issue, upon processing a sample from the subject with the characterization model, in accordance with the therapy model.
A method for characterizing an antibiotic usage issue, the method comprising:
- upon processing an aggregate set of samples from a population of subjects, generating at least one of a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects, the microbiome functional diversity dataset indicative of systemic functions present in the microbiome components of the aggregate set of samples;
- at the computing system, transforming at least one of the microbiome composition dataset and the microbiome functional diversity dataset into a characterization model of the antibiotic usage issue, wherein the characterization model is diagnostic of the antibiotic usage issue producing observed changes in health, quality of life, or behavior;
- and
- based upon the characterization model, generating a therapy model configured to improve a state of the antibiotic usage issue.
Dependencies are inferred from the claim text.