System and method for tracking and controlling infections
First Claim
1. A method of tracking the spread of infectious bacteria, comprising:
- obtaining a plurality of bacterium samples from a plurality of patients or objects at a plurality of different physical locations;
performing DNA sequencing on a first region of deoxyribonucleic acid from each bacterium sample;
storing in a database for each of the plurality of bacterium samples;
a) the nucleotide sequence data from the first sequenced region of each bacterium sample, and b) the physical location of the patient or object from which each bacterium sample was obtained;
comparing the nucleotide sequence data stored in the database of at least two of the plurality of samples on both a base pair level and a repeat motif level;
determining a measure of phylogenetic relatedness between the compared samples based upon differences between the compared nucleotide sequence data;
identifying patients infected or objects contaminated with phylogenetically related bacteria based on the phylogenetic relatedness determination;
tracking the spread over time of the bacteria based on;
a) the identified patients or contaminated objects, and b) the physical locations of the identified patients or objects stored in the database; and
providing a warning based on the tracking of the spread of the bacteria wherein the warning allows the recipient of the warning to control the further spread of the bacteria.
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Accused Products
Abstract
The present invention is a system and method for performing real-time infection control over a computer network. The method comprises obtaining a sample of a microorganism at a health care facility, sequencing a first region of a nucleic acid from the microorganism sample, comparing the first sequenced region with historical sequence data stored in a database, determining a measure of phylogenetic relatedness between the microorganism sample and historical samples stored in the database, and providing infection control information based on the phylogenetic relatedness determination to the health care facility, thereby allowing the health care facility to use the infection control information to control or prevent the spread of an infection.
16 Citations
41 Claims
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1. A method of tracking the spread of infectious bacteria, comprising:
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obtaining a plurality of bacterium samples from a plurality of patients or objects at a plurality of different physical locations; performing DNA sequencing on a first region of deoxyribonucleic acid from each bacterium sample; storing in a database for each of the plurality of bacterium samples;
a) the nucleotide sequence data from the first sequenced region of each bacterium sample, and b) the physical location of the patient or object from which each bacterium sample was obtained;comparing the nucleotide sequence data stored in the database of at least two of the plurality of samples on both a base pair level and a repeat motif level; determining a measure of phylogenetic relatedness between the compared samples based upon differences between the compared nucleotide sequence data; identifying patients infected or objects contaminated with phylogenetically related bacteria based on the phylogenetic relatedness determination; tracking the spread over time of the bacteria based on;
a) the identified patients or contaminated objects, and b) the physical locations of the identified patients or objects stored in the database; andproviding a warning based on the tracking of the spread of the bacteria wherein the warning allows the recipient of the warning to control the further spread of the bacteria. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9)
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10. A method of tracking the spread of infectious fungi, comprising:
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obtaining a plurality of fungus samples from a plurality of patients or objects at a plurality of different physical locations; performing DNA sequencing on a first region of deoxyribonucleic acid from each fungus sample, the first region consisting essentially of a variable number of tandem repeats (VNTRs) region; storing in a database for each of the plurality of fungus samples;
a) the nucleotide sequence data from the first sequenced region of each fungus sample, and b) the physical location of the patient or object from which each fungus sample was obtained;comparing the nucleotide sequence data stored in the database of at least two of the plurality of samples on both a base pair level and a repeat motif level; determining a measure of phylogenetic relatedness between the compared samples based upon differences between the compared nucleotide sequence data; identifying patients infected or objects contaminated with phylogenetically related fungi based on the phylogenetic relatedness determination; tracking the spread over time of the fungus based on;
a) the identified patients or contaminated objects, and b) the physical locations of the identified patients or objects stored in the database; andproviding a warning based on the tracking of the spread of the fungus wherein the warning allows the recipient of the warning to control the further spread of the fungus. - View Dependent Claims (11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26)
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25. A system for tracking the spread of infectious fungi, comprising:
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a computer network; a centralized database; a facility, connected to the computer network, where a plurality of fungus samples from a plurality of patients or objects at a plurality of different locations are obtained; a server connected to the computer network, the server receiving nucleotide sequence data for a first sequenced region of a deoxyribonucleic acid from each of the plurality of fungus samples and a physical location of a patient or object from which each fungus sample was obtained, the first sequenced region consisting essentially of a variable number of tandem repeats (VNTRs) region; storing in a database for each of the plurality of fungus samples;
a) the nucleotide sequence data from each of the plurality of fungus samples, and b) the physical location of the patient or object from which each fungus sample was obtained;accessing the centralized database and comparing the stored nucleotide sequence data of at least two of the plurality of fungus samples; determining a measure of phylogenetic relatedness between the compared samples; identifying patients infected or objects contaminated with phylogenetically related fungi based on the phylogenetic relatedness determination; tracking the spread over time of the fungus based on a) the identified patients or objects, and b) and the physical locations of the identified patients or objects stored in the database; and transmitting a warning over the computer network to the facility based on the tracking of the spread of the fungi, thereby allowing the facility to control further spread of the fungal infection.
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27. A method of tracking the spread of infectious viruses, comprising:
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obtaining a plurality of virus samples from a plurality of patients or objects at a plurality of different physical locations; performing DNA sequencing on a first region of deoxyribonucleic acid from each virus sample, the first region consisting essentially of a variable number of tandem repeats (VNTRs) region; storing in a database for each of the plurality of virus samples;
a) the nucleotide sequence data from the first sequenced region of each virus sample, and b) the physical location of the patient or object from which each virus sample was obtained;comparing the nucleotide sequence data stored in the database of at least two of the plurality of samples on both a base pair level and a repeat motif level; determining a measure of phylogenetic relatedness between the compared samples based upon differences between the compared nucleotide sequence data; identifying patients infected or objects contaminated with phylogenetically related viruses based on the phylogenetic relatedness determination; tracking the spread over time of the virus based on;
a) the identified patients or contaminated objects, and b) the physical locations of the identified patients or objects stored in the database; andproviding a warning based on the tracking of the spread of the virus wherein the warning allows the recipient of the warning to control the further spread of the virus. - View Dependent Claims (28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41)
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40. A system for tracking the spread of infectious viruses, comprising:
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a computer network; a centralized database; a facility, connected to the computer network, where a plurality of virus samples from a plurality of patients or objects at a plurality of different locations are obtained; a server connected to the computer network, the server receiving nucleotide sequence data for a first sequenced region of a deoxyribonucleic acid from each of the plurality of virus samples and a physical location of a patient or object from which each virus sample was obtained, the first sequenced region consisting essentially of a variable number of tandem repeats (VNTRs) region; storing in a database for each of the plurality of virus samples;
a) the nucleotide sequence data from each of the plurality of virus samples, and b) the physical location of the patient or object from which each virus sample was obtained;accessing the centralized database and comparing the stored nucleotide sequence data of at least two of the plurality of virus samples; determining a measure of phylogenetic relatedness between the compared samples; identifying patients infected or objects contaminated with phylogenetically related viruses based on the phylogenetic relatedness determination; tracking the spread over time of the virus based on a) the identified patients or objects, and b) and the physical locations of the identified patients or objects stored in the database; and transmitting a warning over the computer network to the facility based on the tracking of the spread of the virus, thereby allowing the facility to control further spread of the viral infection.
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Specification