Earth Sciences Division (ESD) Department of Energy (DOE) Lawrence Berkeley National Laboratory (LBNL)

Genotyping Arrays

In epidemiological surveillance, pathogen forensics, and phylogenetic studies, discriminatory markers that can track the spread of particular strains, are needed to subdivide bacterial isolates.

Molecular typing that survey the whole genome is valuable to distinguish highly related strains.  Genetic diversity among bacterial species can ultimately explain a variety of epidemiologic parameters, including geographic distribution and virulence.  Whole-genome sequencing represents the most powerful method for assessing genetic variability within a bacterial species, however it remains expensive and labor intensive, and is therefore limited to comparisons with only small numbers of strains within a bacterial species.  High-density microarray analysis of whole genome SNPs (tens of thousands of SNPs, each SNP is determined by 12 oligonucleotide probes) represents a new unbiased methodology which can be used to type large numbers of bacterial strains, provide accurate phylogenies and even resolve individual strains of genetically monomorphic pathogens.

Application of genotyping arrays:

  1. Yesinia pestis geographical distribution in central Asia:
    Yersinia pestis, the causative agents of plague, has been extensively studied through decades. Caucasus region is located on the crossroad between Europe and Asia. It was one of the chains of the Great Silk Road. It always was a vivid transition point for voyagers, thus, it was not protected from spread of different epidemics, and, among them, plague. In this study we genotyped isolates from Georgia, from Armenia, Azerbaijan and the North-Caucasian region of the Russian Federation using SNP microarrays.
    Our data revealed new populations not described before.
  2. Fransicella tularensis diversity:
    Francisella tularensis is the etiological agent of tularemia, a disease of humans acquired by contacting with infected mammals, such as rodents and rabbits, arthropod bite, ingestion of contaminated food or water or inhalation of infective aerosols.  It is a highly virulent, facultative intracellular bacterium, with as few as 10 bacterial cells capable of causing disease.  F. tularensis is considered a Category A bioterrorism agent due to its high level of infectivity, able to cause severe disease and to be inhaled. Naturally-occurring infections are reported throughout the Northern Hemisphere annually.
    We designed and validated a high density Francisella tularensis genotyping microarray that captured 43,324 single nucleotide variations throughout the entire genome.  This genotyping microarray has been validated with multiple typing experiments of 168 unique isolates.  Total of 30,849 SNPs passed stringent concordance and call rate filtering. These high forming SNPs will be an invaluable resources for studies of phylogeny, epidemics and/or virulence. As few as 187 SNPs were needed to detect current strain diversity, while provided internal replication to guard against assay failure. These smaller set of SNPs are premier candidates for clinical or filed applications.