Cultivation-Free Typing of Bacteria Using Optical DNA Mapping
Artikel i vetenskaplig tidskrift, 2020
A variety of pathogenic bacteria can infect humans, and rapid species identification is crucial for the correct treatment. However, the identification process can often be time-consuming and depend on the cultivation of the bacterial pathogen(s). Here, we present a stand-alone, enzyme-free, optical DNA mapping assay capable of species identification by matching the intensity profiles of large DNA molecules to a database of fully assembled bacterial genomes (>10 000). The assay includes a new data analysis strategy as well as a general DNA extraction protocol for both Gram-negative and Gram-positive bacteria. We demonstrate that the assay is capable of identifying bacteria directly from uncultured clinical urine samples, as well as in mixtures, with the potential to be discriminative even at the subspecies level. We foresee that the assay has applications both within research laboratories and in clinical settings, where the time-consuming step of cultivation can be minimized or even completely avoided.
diagnostics
nanofluidics
UTI
optical DNA mapping
bacteria
Författare
Vilhelm Müller
Chalmers, Biologi och bioteknik, Kemisk biologi
My Nyblom
Chalmers, Biologi och bioteknik, Kemisk biologi
Anna Johnning
Göteborgs universitet
Chalmers, Matematiska vetenskaper, Tillämpad matematik och statistik
Stiftelsen Fraunhofer-Chalmers Centrum för Industrimatematik
Marie Wrande
Uppsala universitet
Albertas Dvirnas
Lunds universitet
Sriram Kesarimangalam
Chalmers, Biologi och bioteknik, Kemisk biologi
Christian G. Giske
Karolinska universitetssjukhuset
Karolinska Institutet
Tobias Ambjörnsson
Lunds universitet
L. Sandegren
Uppsala universitet
Erik Kristiansson
Chalmers, Matematiska vetenskaper, Tillämpad matematik och statistik
Göteborgs universitet
Fredrik Westerlund
Chalmers, Biologi och bioteknik, Kemisk biologi
ACS Infectious Diseases
2373-8227 (eISSN)
Vol. 6 5 1076-1084Ämneskategorier
Mikrobiologi
DOI
10.1021/acsinfecdis.9b00464
PubMed
32294378