Cultivation-Free Typing of Bacteria Using Optical DNA Mapping
Open Access
- 15 April 2020
- journal article
- research article
- Published by American Chemical Society (ACS) in ACS Infectious Diseases
- Vol. 6 (5), 1076-1084
- https://doi.org/10.1021/acsinfecdis.9b00464
Abstract
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 standalone, enzyme-free, optical DNA mapping assay capable of species identification by matching 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 labs and in clinical settings, where the time-consuming step of cultivation can be minimized or even completely avoided.Keywords
Funding Information
- Vetenskapsr?det (2014-4305)
- Crafoordska Stiftelsen (20180675)
- Horizon 2020 Framework Programme (634890)
- Familjen Erling-Perssons Stiftelse
This publication has 44 references indexed in Scilit:
- Beyond sequencing: optical mapping of DNA in the age of nanotechnology and nanoscopyCurrent Opinion in Biotechnology, 2013
- Comparative Whole-Genome Mapping To Determine Staphylococcus aureus Genome Size, Virulence Motifs, and ClonalityJournal of Clinical Microbiology, 2012
- Deploying whole genome sequencing in clinical practice and public health: Meeting the challenge one bin at a timeGenetics in Medicine, 2011
- Optical mapping of DNA: Single‐molecule‐based methods for mapping genomesPeptide Science, 2011
- Single molecule linear analysis of DNA in nano-channel labeled with sequence specific fluorescent probesNucleic Acids Research, 2010
- Use of optical mapping to sort uropathogenic Escherichia coli strains into distinct subgroupsMicrobiology, 2010
- Optical maps distinguish individual strains of Escherichia coli O157 : H7Microbiology, 2007
- A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteriaJournal of Microbiological Methods, 2007
- A single-molecule barcoding system using nanoslits for DNA analysisProceedings of the National Academy of Sciences of the United States of America, 2007
- Subtractive hybridization and optical mapping of the enterotoxigenic Escherichia coli H10407 chromosome: isolation of unique sequences and demonstration of significant similarity to the chromosome of E. coli K-12Microbiology, 2006