Rapid typing and subtyping of Staphylococcus aureus clonal complex 8 (CC8) strains


Researchers at TGen and the United States Centers Disease Control and Prevention (CDC) have collaboratively developed a panel of assays for rapidly and consistently typing Staphylococcus aureus strains, and subtyping the strains within clonal complex 8 (CC8).  The developed technology is an improvement over previously used typing methods and can be used as a method for source tracking of the bacteria within a facility (e.g., hospitals, medical service centers) to perform surveillance of infections and determine the origin of the infections.  The efficient typing system allows for wide use in clinical laboratories for robust tracking of both methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) infections to help focus resources effectively, assess the possibility of an outbreak or transmission event, and inform infection prevention and control. 


CC8 strains of S. aureus are prevalent pathogens in the United States causing infection in both immunocompromised and healthy persons, and in both healthcare and community settings.  Unfortunately, typing strains of S. aureus is not a routine practice in clinical microbiology laboratories, in part because of the cost, time, and expertise required, as well as the frequent inconclusiveness of results.  Typing by pulse field gel electrophoresis (PFGE), the method by which the “USA” strains were originally defined, is laborious and determination of a strain type can be subjective. Additionally, sequencing and interpretation of the spa gene is relatively expensive, and spa types aren’t always consistent with evolutionary lineages.  Furthermore, PFGE and spa typing alone are often not able to distinguish among lineages within CC8, as well as other clonal complexes.  Imprecision of these current tools for typing MRSA and the lack of tools for typing MSSA make surveillance and source tracing difficult and sometimes misleading.


The developed technology uses real time polymerase chain reactions (PCR) targeting single nucleotide polymorphisms (SNPs) based on whole genome sequencing to detect and identify S. aureus strains as belonging to CC8 or other clonal complexes and distinguish strain types within CC8.  Additionally, different SNPs provide different scales of resolution for identifying particular strains (e.g., a CC8-specific SNP versus a USA300-specific SNP) or even species in a given set of samples.  A canonical SNP-based approach eliminates the lineage confusion seen with PFGE, spa typing, and mobile genetic marker typing, as SNPs are inherently stable and quantify relatedness among strains, and thus provides a scalable, affordable, and reliable means of distinguishing the various strain types in CC8.


Link to Issued US Patent 11,572,591


Patent Information:
For Information, Contact:
Katie Bray
Intellectual Property Counsel
The Translational Genomics Research Institute
Elizabeth Driebe
Jolene Bowers
David Engelthaler
Paul Keim
Brandi Limbago
James Rasheed
Linda McDougal
Valerie Albrecht