By Donald Zuhn --
Earlier this month, eGenomics, Inc. announced that the U.S. Patent and Trademark Office has issued U.S. Patent No. 7,349,808, which is directed to a method for performing real-time infection control by determining the phylogenetic relatedness between sequence data obtained from a microorganism sample isolated in a health care facility with historical sequence data in a database and providing infection control information based on that phylogenetic relatedness. The '808 patent is the first U.S. patent to be awarded to eGenomics, which is also named as an assignee on U.S. Patent Application Publication No. 2008/0206767.
According to the New York-based biotechnology company's press release, the '808 patent covers eGenomics' proprietary warning system for hospital infection control in which "fingerprints" for infection-causing bacteria are determined by automated DNA sequencing and then stored in a central database containing over 6,000 analyzed Staphylococcus aureus strains (as well as sequence data from other infectious organisms). These fingerprints are then analyzed using proprietary algorithms, thereby allowing hospital infection control teams to monitor the spread of specific harmful pathogens in "real time." The eGenomics system, which differentiates clusters of related microorganism strains in order to identify a source or transmission vector, is currently being used in active surveillance programs at Beth Israel Medical Center in New York, Newark Beth Israel Medical Center, and the VA Medical Center in East Orange, NJ, and by researchers at the Centers for Disease Control and Prevention, Rockefeller University, Duke University Medical Center, Purdue University, and The Institute for Genomic Research (TIGR).
Dr. Barry Kreiswirth (at left), who founded eGenomics with Steve Naidich, believes that the system "should be a major component of every hospitals' effort to monitor and prevent methycillin-resistant strains of Staphylococcus aureus (MRSA) infections," and noted that eGenomics was in the process of expanding its system to track other common nosocomial, or hospital-acquired, infections. Dr. Kreiswirth also noted that the eGenomics' system could be used to reduce the chance of acquiring a nosocomial infection; identify outbreaks and their sources before they become endemic; identify non-outbreaks, allowing hospitals to avoid costly infection control measures; direct more appropriate antibiotic usage, thereby extending the effectiveness of existing antibiotics; lower the costs to control infections; and provide faster and more accurate information than other comparable techniques.
The '808 patent issued from U.S. Application No. 09/656,084, filed September 6, 2000. Independent claims 1 and 25 of the '808 patent recite:
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, the first region consisting essentially of a variable number of tandem repeats (VNTRs) region;
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.25. A system for tracking the spread of infectious bacteria, comprising:
a computer network;
a centralized database;
a facility, connected to the computer network, where a plurality of bacterium 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 bacterium samples and a physical location of a patient or object from which each bacterium 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 bacterium samples: a) the nucleotide sequence data from each of the plurality of bacterium samples, and b) the physical location of the patient or object from which each bacterium sample was obtained;
accessing the centralized database and comparing the stored nucleotide sequence data of at least two of the plurality of bacterium samples;
determining a measure of phylogenetic relatedness between the compared samples;
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 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 bacteria, thereby allowing the facility to control further spread of the bacterial infection.
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