Strain-Level Typing of Streptococcus pyogenes Using Optical DNA Mapping

Streptococcus
pyogenes, also known
as group A Streptococcus (GAS), is
a Gram-positive bacterial pathogen responsible for approximately 500,000
deaths globally per year. Therefore, surveillance of invasive GAS
infections is of critical importance in understanding societal transmission.
In this study, we propose an optical DNA mapping (ODM)-based assay
for strain-level typing of S. pyogenes. Fluorescently labeled DNA molecules of lengths >150 kbp are
stretched
in nanochannels and imaged to reveal genomic information. A core genome
alignment-based typing scheme is then utilized for identification
at the strain level. Although our technique lacks the nucleotide-level
resolution of whole-genome sequencing, it excels at detecting patterns
across long stretches of DNA that remain inaccessible to short-read
sequencing methods. Using clinical isolates, we demonstrate that the
ODM assay can identify S. pyogenes at
both the species level and at even higher taxonomic resolutions with
high accuracy. Our typing scheme also shows a high correlation with
standard emm subtyping for the analyzed samples.
We conclude that ODM has the potential to deliver timely and cost-efficient
strain-level bacterial identification.