Identification of bacteria and spores

• US 20070003996A1
• Filed: 02/09/2006
• Published: 01/04/2007
• Est. Priority Date: 02/09/2005
• Status: Abandoned Application

• Current Assignee: Vermillion, Inc.
• Original Assignee: Vermillion, Inc.
• Inventors: Yip, Ping, Mansfield, Brian, Hitt, Ben
• Application Number:
  US11/350,269
• Publication Number:
  US 20070003996A1
• Time in Patent Office: Days
• US Class Current: 435/34
• CPC Class Codes: C12Q 1/04 Determining presence or kind of microorganism; Use of selective media for testing antibiotics or bacteriocides; Compositions containing a chemical indicator therefor C12Q1/6897 takes precedence
• CPC Class Codes: G01N 27/624 Differential mobility spectrometry [DMS]; Field asymmetric-waveform ion mobility spectrometry [FAIMS]
• CPC Class Codes: G01N 33/497 of gaseous biological material, e.g. breath

Abstract

Bacteria can be identified by analyzing a data stream that is obtained by processing a sample containing the bacteria, where the data stream has been abstracted to produce a sample vector that characterizes the data stream in a predetermined vector space containing at least one diagnostic cluster, the diagnostic cluster being associated with bacteria of known type, and by determining whether the sample vector rests with the diagnostic cluster, and if the sample rests within the diagnostic cluster, an indication that the bacteria are of the known type can be provided. Similarly, spores can be identified by analyzing a data stream that is obtained by processing a sample containing the spores, where the data stream has been abstracted to produce a sample vector that characterizes the data stream in a predetermined vector space containing at least one diagnostic cluster, the diagnostic cluster being associated with spores of known type, and by determining whether the sample vector rests with the diagnostic cluster, and if the sample rests within the diagnostic cluster, an indication that the spores are of the known type can be provided.

Claims

1. A method of identifying bacteria by analyzing a data stream that is obtained by processing a sample containing the bacteria, wherein the data stream has been abstracted to produce a sample vector that characterizes the data stream in a predetermined vector space containing at least one diagnostic cluster, the diagnostic cluster being associated with bacteria of known type, comprising:

determining whether the sample vector rests with the diagnostic cluster; and

if the sample rests within the diagnostic cluster, providing an indication that the bacteria are of the known type.

2. The method of claim 1, wherein the bacteria are selected from the group of genera consisting of Bacillus, Clostridium and Mycobacterium.

3. The method of claim 2, wherein the bacteria are selected from the group of species consisting of B. subtilis, B. cereus, B. thuringiensis, B. anthrasis), C. perfingens, C. tetani, C. sordellii, C. difficile, M smegmatis and M tuberculosis.

4. The method of claim 1, wherein the data stream is produced by a technique selected from the group consisting of mass spectrometry and high-field asymmetric waveform ion mobility spectrometry.

5. The method of claim 4, wherein the data stream is produced by a micromachined differential mobility spectrometer.

6. The method of claim 1, wherein the sample is selected from the group of sources consisting of headspace gas collected from a bacterial culture, bacterial culture fluid, and sputum, blood, urine, saliva, or breath collected from an animal or human patient.

7. A method of identifying bacterial spores by analyzing a data stream that is obtained by processing a sample containing the spores, wherein the data stream has been abstracted to produce a sample vector that characterizes the data stream in a predetermined vector space containing at least one diagnostic cluster, the diagnostic cluster being associated with spores of known type, comprising:

determining whether the sample vector rests with the diagnostic cluster; and

if the sample rests within the diagnostic cluster, providing an indication that the spores are of the known type.

8. The method of claim 7, wherein the sample containing spores is processed by pyrolosis.

9. The method of claim 7, wherein the spores are produced by bacteria selected from the group of genera consisting of Bacillus, Clostridium and Mycobacterium.

10. The method of claim 9, wherein the bacteria are selected from the group of species consisting of B. subtilis, B. cereus, B. thuringiensis, B. anthrasis, C. perfingens, C. tetani, C. sordellii, C. difficile, M. smegmatis and M tuberculosis.

11. The method of claim 7, wherein the data stream is produced by a technique selected from the group consisting of mass spectrometry and high-field asymmetric waveform ion mobility spectrometry.

12. The method of claim 11, wherein the data stream is produced by a micromachined differential mobility spectrometer.

13. A computer system containing a sample vector abstracted from a data stream that is obtained by processing a sample containing bacteria, the sample vector characterizing the data stream in a predetermined vector space containing at least one diagnostic cluster, the diagnostic cluster being associated with bacteria of known type.

14. A computer system containing a sample vector abstracted from a data stream that is obtained by processing a sample containing spores, the sample vector characterizing the data stream in a predetermined vector space containing at least one diagnostic cluster, the diagnostic cluster being associated with spores of known type.

15. A machine readable medium containing a sample vector abstracted from a data stream that is obtained by processing a sample containing bacteria, the sample vector characterizing the data stream in a predetermined vector space containing at least one diagnostic cluster, the diagnostic cluster being associated with bacteria of known type.

16. A machine readable medium containing a sample vector abstracted from a data stream that is obtained by processing a sample containing spores, the sample vector characterizing the data stream in a predetermined vector space containing at least one diagnostic cluster, the diagnostic cluster being associated with spores of known type.

17. A portable device for detecting one or more predetermined bacteria or bacterial spores in a sample, comprising:

a microfabricated differential mobility spectrometer configured to process the sample and output a data stream;

means for abstracting the data stream to produce a sample vector characterizing the data stream in a predetermined vector space containing at least one diagnostic cluster, the diagnostic cluster being associated with the predetermined bacteria or bacterial spores; and

means for determining whether the sample vector rests with the diagnostic cluster and, if the sample rests within the diagnostic cluster, for providing an indication that the sample contains the predetermined bacteria or bacterial spores.