Identification of Highly Similar Microbial Strains and Pathogens

January 29, 2014

Distinguishing different microbial strains is a frequent issue with respect to human health and safety.  Strains that vary only slightly from each other may be difficult to distinguish with frequently used typing methods such as restriction mapping or 16S rRNA sequencing.  These methods may be insensitive to modest changes in genome sequence that have a profound impact on whether a strain impacts human health.  For this reason, next-generation sequencing of whole genomes has been more recently employed to allow more precise identification of different microbes in a sample.  While more powerful than older methods, it is not ideal with respect to the time it takes to complete the assay and also its ability to include structural information that may be critical among related strains.  
To circumvent these issues, we have developed a method that generates results more quickly than whole genome NGS yet can provide long-range structural information and sufficient sequence information for identifying many strains, including highly similar strains, through genetic signatures.  Single-molecule, solid-state nanodetectors are used to analyze multiple tags on DNAs longer than 50 kb.  When the DNAs are long enough with many tags, unique signatures are generated that distinguish even closely related strains.  The electronic detection on the semiconductor-based chips provides much higher resolution than can be obtained using optical methods.  Furthermore, this process is scalable and rapid with the ability to generate data within hours rather than days.  The small size of the genome mapping instrument makes it feasible that it could eventually become field deployable.