Strain-Level Typing of Streptococcus pyogenes Using Optical DNA Mapping
Journal article, 2025
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.
diagnostics
opticalDNA mapping
bacterial typing
genomics
nanofluidics
Streptococcus pyogenes
Author
Radhika Nambannor Kunnath
Center for Antibiotic Resistance Research in Gothenburg (CARe)
Chalmers, Life Sciences, Chemical Biology
Zahra Abbaspour
Chalmers, Life Sciences, Chemical Biology
Anna Johnning
Chalmers, Mathematical Sciences, Applied Mathematics and Statistics
University of Gothenburg
Fraunhofer-Chalmers Centre
Center for Antibiotic Resistance Research in Gothenburg (CARe)
Karolin Frykholm
Center for Antibiotic Resistance Research in Gothenburg (CARe)
Chalmers, Life Sciences, Chemical Biology
Marie Wrande
Uppsala University
Albertas Dvirnas
Chalmers, Life Sciences, Chemical Biology
Lund University
Sriram Kesarimangalam
Center for Antibiotic Resistance Research in Gothenburg (CARe)
Chalmers, Life Sciences, Chemical Biology
Christian G. Giske
Karolinska Institutet
Karolinska University Hospital
Tobias Ambjornsson
Lund University
Linus Sandegren
Uppsala University
Erik Kristiansson
University of Gothenburg
Fredrik Westerlund
Chalmers, Life Sciences, Chemical Biology
Center for Antibiotic Resistance Research in Gothenburg (CARe)
ACS Infectious Diseases
2373-8227 (eISSN)
Vol. 11 11 3085-3092IDAR-Neo - Identification and characterization of fecal carriage of antimicrobial resistant bacteria in neonates in low-resource settings
Swedish Research Council (VR) (2022-03490), 2023-01-01 -- 2025-12-31.
Subject Categories (SSIF 2025)
Infectious Medicine
Microbiology in the Medical Area
Microbiology
Infrastructure
Myfab (incl. Nanofabrication Laboratory)
DOI
10.1021/acsinfecdis.5c00430
PubMed
41091517