Bacterial strain identification method and system

Abstract

Methods for identifying bacterial strains by using sets of distributed genes that are present in some but not all strains of a given species, associated methods for treating bacterial infections are disclosed. The methods may include examining a sample of a bacterial species, selecting a strain of interest based on possession of a unique genetic characteristic that is present in only the strain of interest and not in the other strains, examining the distributed genes possessed by the strain of interest, and detecting gene-possession variation in the distributed genes of the sample strains as compared to genes of known strains.

1 . A method of identifying and distinguishing a bacterial strain within a species from another bacterial strain in the same species, the method comprising:
 examining a sample of a bacterial species, the sample having a plurality of strains, the strains having a plurality of core genes that are common to all of the strains and a plurality of distributed genes that are not common to all strains of the species;   selecting a strain of interest based on possession of a unique genetic characteristic that is present in only the strain of interest and not in the other strains;   examining the distributed genes possessed by the strain of interest;   accessing a database of information corresponding to known strains of bacterial species;   comparing data gathered in the examining of the distributed genes with data from the database;   detecting gene-possession variation in the distributed genes of the sample strains as compared to genes of the known strains; and   identifying the bacterial strain of the sample strain based on the detected gene-possession variation.   
     
     
         2 . The method of  claim 1 , wherein the examining of the distributed genes in the sample strain comprises use of a gene array. 
     
     
         3 . The method of  claim 1 , wherein the examining of the distributed genes in the sample strain comprises mass spectrometry to provide base composition analysis based on molecular weight, or a combination thereof. 
     
     
         4 . The method of  claim 1 , wherein the examining of the distributed genes in the sample strain comprises DNA sequencing. 
     
     
         5 . The method of  claim 1  further comprising correlating the gene-possession variation with a phenotypic character change in a host eukaryotic organism. 
     
     
         6 . The method of  claim 5 , wherein the phenotypic character change is selected from pathogenesis, virulence, drug resistance, viability and combinations thereof. 
     
     
         7 . The method of  claim 1  wherein the bacterial species is selected from the group consisting of  Bacillus anthracis, Borrelia burgdorferi, Bacillus cereus, Burkholderia mallei, Clostridium botulinum, Clostridium difficile, Campylobacter jejuni, Clostridium perfringens, Escherichia coli, Haemophilus influenzae, Gardnerella vaginalis, Listeria monocytogenes, Moraxella catarrhalis, Mycobacterium tuberculosis, Pseudomonas aeruginosa, Streptococcus agalactiae, Staphylococcus aureus, Salmonella enterica, Shigella, Streptococcus pneumoniae, Yersinia pestis, Burkholderia pseudomallei, Streptococcus pyogenes  and combinations thereof. 
     
     
         8 . The method of  claim 1 , wherein the identity is also based on phenotypic potential. 
     
     
         9 . A method of identifying a bacterial strain within a species from a sample, comprising:
 examining a bacterial species sample comprising at least two strains, wherein the strains possess a plurality of core genes common to all of strains and a plurality of distributed genes that are not common to all of the strains;   depositing a first set of polynucleotide capture probes for less than half of the core genes at corresponding addresses on a substrate, each probe corresponding to an address of one of the core genes;   depositing a second set of polynucleotide capture probes corresponding to the set of distributed genes on the substrate;   examining, with the second set of probes, the set of distributed genes to detect gene-possession variation between genes in the set;   comparing data gathered in the examining of the distributed genes with data from a database of information corresponding to known strains of bacterial species; and   identifying the bacterial strain of the sample based on the detected gene-possession variation.   
     
     
         10 . The method of  claim 9  wherein said bacterial species is selected from the group consisting of  Bacillus anthracis, Borrelia burgdorferi, Bacillus cereus, Burkholderia mallei, Clostridium botulinum, Clostridium difficile, Campylobacter jejuni, Clostridium perfringens, Escherichia coli, Gardnerella vaginalis, Listeria monocytogenes, Moraxella catarrhalis, Mycobacterium tuberculosis, Haemophilus influenzae, Listeria monocytogenes, Mycobacterium tuberculosis, Pseudomonas aeruginosa, Streptococcus agalactiae, Staphylococcus aureus, Salmonella enterica, Shigella, Streptococcus pneumoniae, Yersinia pestis, Burkholderia pseudomallei, Streptococcus pyogenes  and combinations thereof. 
     
     
         11 . The method of  claim 9 , wherein the substrate comprises a pool of addressable particles on a two-dimensional solid surface. 
     
     
         12 . The method of  claim 9 , wherein the substrate is selected from the group consisting of a glass, a polymer or combinations thereof.