Skip to main content

Lund University Publications

LUND UNIVERSITY LIBRARIES

Strain-Level Typing of Streptococcus pyogenes Using Optical DNA Mapping

Kunnath, Radhika N. ; Abbaspour, Zahra ; Johnning, Anna ; Frykholm, Karolin ; Wrande, Marie ; Dvirnas, Albertas LU ; KK, Sriram ; Giske, Christian G. ; Ambjörnsson, Tobias LU and Sandegren, Linus , et al. (2025) In ACS Infectious Diseases 11(11). p.3085-3092
Abstract

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... (More)

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.

(Less)
Please use this url to cite or link to this publication:
author
; ; ; ; ; ; ; ; and , et al. (More)
; ; ; ; ; ; ; ; ; ; and (Less)
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
bacterial typing, diagnostics, genomics, nanofluidics, optical DNA mapping, Streptococcus pyogenes
in
ACS Infectious Diseases
volume
11
issue
11
pages
8 pages
publisher
The American Chemical Society (ACS)
external identifiers
  • pmid:41091517
  • scopus:105021846234
ISSN
2373-8227
DOI
10.1021/acsinfecdis.5c00430
language
English
LU publication?
yes
additional info
Publisher Copyright: © 2025 The Authors. Published by American Chemical Society
id
5e76d430-6d6a-4a66-9564-ee86ec490514
date added to LUP
2026-01-22 11:22:43
date last changed
2026-01-23 03:00:08
@article{5e76d430-6d6a-4a66-9564-ee86ec490514,
  abstract     = {{<p>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 &gt;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.</p>}},
  author       = {{Kunnath, Radhika N. and Abbaspour, Zahra and Johnning, Anna and Frykholm, Karolin and Wrande, Marie and Dvirnas, Albertas and KK, Sriram and Giske, Christian G. and Ambjörnsson, Tobias and Sandegren, Linus and Kristiansson, Erik and Westerlund, Fredrik}},
  issn         = {{2373-8227}},
  keywords     = {{bacterial typing; diagnostics; genomics; nanofluidics; optical DNA mapping; Streptococcus pyogenes}},
  language     = {{eng}},
  month        = {{11}},
  number       = {{11}},
  pages        = {{3085--3092}},
  publisher    = {{The American Chemical Society (ACS)}},
  series       = {{ACS Infectious Diseases}},
  title        = {{Strain-Level Typing of Streptococcus pyogenes Using Optical DNA Mapping}},
  url          = {{http://dx.doi.org/10.1021/acsinfecdis.5c00430}},
  doi          = {{10.1021/acsinfecdis.5c00430}},
  volume       = {{11}},
  year         = {{2025}},
}