System and method for tracking and controlling infections

• US 8,046,172 B2
• Filed: 11/05/2007
• Issued: 10/25/2011
• Est. Priority Date: 09/06/2000
• Status: Active Grant

• Current Assignee: eGenomics, Inc.
• Original Assignee: eGenomics, Inc.
• Inventors: Kreiswirth, Barry N., Naidich, Steven M.
• Primary Examiner(s): ZEMAN, MARY K
• Application Number:
  US11/979,500
• Publication Number:
  US 20080206767A1
• Time in Patent Office: 1,450 Days
• Field of Search: None
• US Class Current: 702/19
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: G16B 10/00 ICT specially adapted for evolutionary bioinformatics, e.g. phylogenetic tree construction or analysis
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16H 10/40 for data related to laboratory analysis, e.g. patient specimen analysis
• CPC Class Codes: G16H 10/60 for patient-specific data, e.g. for electronic patient records
• CPC Class Codes: G16H 50/30 for calculating health indices; for individual health risk assessment
• CPC Class Codes: G16H 70/60 relating to pathologies

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.

Claims

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;

determining the DNA sequence of a first region of deoxyribonucleic acid from each bacterium sample, wherein said first region has a clock speed that is suitable for tracking the spread of infectious bacteria;

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.

2. The method of claim 1, wherein each bacterium sample is obtained from a patient as the patient is admitted to a health care facility and prior to being exposed to patients in the health care facility.

3. The method of claim 1, further comprising:

obtaining a medical history from a patient from which at least one of the plurality of bacterium samples was taken;

determining an infection risk factor based on the patient'"'"'s medical history, the infection risk factor being a measure of the patient'"'"'s risk of acquiring an infection; and

taking appropriate infection control measures in accordance with the infection risk factor.

4. The method of claim 1, wherein the step of determining the DNA sequence comprises either

a) sequencing the first region at a physically separate facility and transmitting the resulting nucleotide sequence data to the database via a computer network;

or

b) sending each of the plurality of bacterium samples to an infection control facility that has access to the database, sequencing the first region at the infection control facility, and storing the nucleotide sequence data in the database.

5. The method of claim 1, wherein the step of determining the phylogenetic relatedness between at least two compared samples comprises at least one of:

comparing a first bacterium sample to other samples obtained from the same location as where the first bacterium sample was taken, thereby determining a local phylogenetic relatedness;

comparing the first bacterium sample to other samples obtained from the same geographical region as where the first bacterium sample was taken, thereby determining a regional phylogenetic relatedness; and

comparing the first bacterium sample to other samples obtained globally, thereby determining a global phylogenetic relatedness.

6. The method of claim 1, further comprising:

determining drug resistance and treatment information of the bacterium by retrieving drug information data of identical or similar bacteria from the database; and

transmitting over a computer network the drug information data to a location where the bacterium sample was obtained.

7. The method of claim 1, wherein providing a warning comprises:

determining whether a location where each bacterium was obtained has an outbreak problem; and

transmitting over a computer network an outbreak warning to each location having an outbreak problem.

8. The method of claim 1, further comprising:

determining the DNA sequence of a second region of deoxyribonucleic acid of each bacterium sample;

storing the nucleotide sequence data from the second region of the deoxyribonucleic acid of each bacterium sample in a database;

comparing the nucleotide sequence data from the second sequenced region to nucleotide sequence data already stored in the database; and

determining a measure of phylogenetic relatedness based on the comparison of the first and second sequenced regions.

9. The method of claim 8, wherein the determination of relatedness based on the second sequenced region is used to verify the determination of relatedness based on the first sequenced region.