Strain-level bacterial typing directly from patient samples using optical DNA mapping
Artikel i vetenskaplig tidskrift, 2023
Results
We demonstrate that optical DNA mapping of single DNA molecules can identify Escherichia coli and Klebsiella pneumoniae at the strain level directly from patient samples. At a taxonomic resolution corresponding to E. coli sequence type 131 and K. pneumoniae clonal complex 258 forming distinct groups, the average true positive prediction rates are 94% and 89%, respectively. The single-molecule aspect of the method enables us to identify multiple E. coli strains in polymicrobial samples. Furthermore, by targeting plasmid-borne antibiotic resistance genes with Cas9 restriction, we simultaneously identify the strain or subtype and characterize the corresponding plasmids.
Conclusion
The optical DNA mapping method is accurate and directly applicable to polymicrobial and clinical samples without cultivation. Hence, it has the potential to rapidly provide comprehensive diagnostics information, thereby optimizing early antibiotic treatment and opening up for future precision medicine management.
Författare
My Nyblom
Chalmers, Life sciences, Kemisk biologi
Anna Johnning
Göteborgs universitet
Chalmers, Matematiska vetenskaper
Chalmers, Matematiska vetenskaper, Tillämpad matematik och statistik
Centre for Antibiotic Resistance Research in Gothenburg (CARe)
Stiftelsen Fraunhofer-Chalmers Centrum för Industrimatematik
Karolin Frykholm
Chalmers, Life sciences, Kemisk biologi
Marie Wrande
Uppsala universitet
Vilhelm Müller
Chalmers, Life sciences, Kemisk biologi
Gaurav Goyal
Chalmers, Life sciences, Kemisk biologi
Miriam Robertsson
Albertas Dvirnas
Lunds universitet
Tsegaye Sewunet
Karolinska Institutet
Sriram Kesarimangalam
Chalmers, Life sciences, Kemisk biologi
Tobias Ambjornsson
Lunds universitet
Christian G. Giske
Karolinska Institutet
Karolinska universitetssjukhuset
Linus Sandegren
Uppsala universitet
Erik Kristiansson
Chalmers, Matematiska vetenskaper
Centre for Antibiotic Resistance Research in Gothenburg (CARe)
Göteborgs universitet
Fredrik Westerlund
Chalmers, Life sciences, Kemisk biologi
COMMUNICATIONS MEDICINE
2730-664X (ISSN)
Vol. 3 31 31Styrkeområden
Nanovetenskap och nanoteknik
Hälsa och teknik
Ämneskategorier
Infektionsmedicin
Mikrobiologi
Mikrobiologi inom det medicinska området
DOI
10.1038/s43856-023-00259-z
PubMed
36823379