Strain-Level Typing of <i>Streptococcus pyogenes</i> Using Optical DNA Mapping

<i>Streptococcus pyogenes</i>, also known as group A <i>Streptococcus</i> (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 <i>S. pyogenes</i>. 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 <i>S. pyogenes</i> at both the species level and at even higher taxonomic resolutions with high accuracy. Our typing scheme also shows a high correlation with standard <i>emm</i> subtyping for the analyzed samples. We conclude that ODM has the potential to deliver timely and cost-efficient strain-level bacterial identification.