Strain-Level Typing of Streptococcus pyogenes Using Optical DNA Mapping
Artikel i vetenskaplig tidskrift, 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
Författare
Radhika Nambannor Kunnath
Center for Antibiotic Resistance Research in Gothenburg (CARe)
Chalmers, Life sciences, Kemisk biologi
Zahra Abbaspour
Chalmers, Life sciences, Kemisk biologi
Anna Johnning
Chalmers, Matematiska vetenskaper, Tillämpad matematik och statistik
Göteborgs universitet
Stiftelsen Fraunhofer-Chalmers Centrum för Industrimatematik
Center for Antibiotic Resistance Research in Gothenburg (CARe)
Karolin Frykholm
Center for Antibiotic Resistance Research in Gothenburg (CARe)
Chalmers, Life sciences, Kemisk biologi
Marie Wrande
Uppsala universitet
Albertas Dvirnas
Chalmers, Life sciences, Kemisk biologi
Lunds universitet
Sriram Kesarimangalam
Center for Antibiotic Resistance Research in Gothenburg (CARe)
Chalmers, Life sciences, Kemisk biologi
Christian G. Giske
Karolinska Institutet
Karolinska universitetssjukhuset
Tobias Ambjornsson
Lunds universitet
Linus Sandegren
Uppsala universitet
Erik Kristiansson
Göteborgs universitet
Fredrik Westerlund
Chalmers, Life sciences, Kemisk biologi
Center for Antibiotic Resistance Research in Gothenburg (CARe)
ACS Infectious Diseases
2373-8227 (eISSN)
Vol. 11 11 3085-3092IDAR-Neo - Identifikation och karaktärisering av tarmbärarskap med antibiotikaresistenta bakterier hos nyfödda i låginkomstländer
Vetenskapsrådet (VR) (2022-03490), 2023-01-01 -- 2025-12-31.
Ämneskategorier (SSIF 2025)
Infektionsmedicin
Mikrobiologi inom det medicinska området
Mikrobiologi
Infrastruktur
Myfab (inkl. Nanotekniklaboratoriet)
DOI
10.1021/acsinfecdis.5c00430
PubMed
41091517