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Strain-level bacter...
Strain-level bacterial typing directly from patient samples using optical DNA mapping
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- Nyblom, My, 1995 (författare)
- Chalmers tekniska högskola,Chalmers University of Technology,Chalmers Univ Technol, Dept Life Sci, S-41296 Gothenburg, Sweden.
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- Johnning, Anna, 1985 (författare)
- Gothenburg University,Göteborgs universitet,CARe - Centrum för antibiotikaresistensforskning,Institutionen för matematiska vetenskaper,Centre for antibiotic resistance research, CARe,Department of Mathematical Sciences,Chalmers Univ Technol & Univ Gothenburg, Dept Math Sci, S-41296 Gothenburg, Sweden.;Fraunhofer Chalmers Ctr, Dept Syst & Data Anal, S-41288 Gothenburg, Sweden.;Ctr Antibiot Resistance Res Gothenburg CARe, S-40530 Gothenburg, Sweden.
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- Frykholm, Karolin, 1977 (författare)
- Chalmers tekniska högskola,Chalmers University of Technology,Chalmers Univ Technol, Dept Life Sci, S-41296 Gothenburg, Sweden.
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visa fler...
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- Wrande, Marie (författare)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi
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- Müller, Vilhelm, 1990 (författare)
- Chalmers tekniska högskola,Chalmers University of Technology,Chalmers Univ Technol, Dept Life Sci, S-41296 Gothenburg, Sweden.
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- Goyal, Gaurav, 1983 (författare)
- Karolinska Institutet
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- Robertsson, Miriam (författare)
- Chalmers Univ Technol, Dept Life Sci, S-41296 Gothenburg, Sweden.
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- Dvirnas, Albertas (författare)
- Lunds universitet,Lund University,Lund Univ, Dept Astron & Theoret Phys, S-22362 Lund, Sweden.
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- Sewunet, Tsegaye (författare)
- Karolinska Institutet
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- Kesarimangalam, Sriram, 1983 (författare)
- Chalmers tekniska högskola,Chalmers University of Technology,Chalmers Univ Technol, Dept Life Sci, S-41296 Gothenburg, Sweden.
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- Ambjornsson, Tobias (författare)
- Lunds universitet,Lund University,Lund Univ, Dept Astron & Theoret Phys, S-22362 Lund, Sweden.
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- Giske, Christian G. (författare)
- Karolinska Institutet,Karolinska universitetssjukhuset,Karolinska University Hospital
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- Sandegren, Linus (författare)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi
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- Kristiansson, Erik, 1978 (författare)
- Gothenburg University,Göteborgs universitet,CARe - Centrum för antibiotikaresistensforskning,Institutionen för matematiska vetenskaper,Centre for antibiotic resistance research, CARe,Department of Mathematical Sciences,Chalmers Univ Technol & Univ Gothenburg, Dept Math Sci, S-41296 Gothenburg, Sweden.;Ctr Antibiot Resistance Res Gothenburg CARe, S-40530 Gothenburg, Sweden.
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- Westerlund, Fredrik, 1978 (författare)
- Chalmers tekniska högskola,Chalmers University of Technology,Chalmers Univ Technol, Dept Life Sci, S-41296 Gothenburg, Sweden.;Ctr Antibiot Resistance Res Gothenburg CARe, S-40530 Gothenburg, Sweden.
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Kk, S (författare)
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Chalmers tekniska högskola Chalmers Univ Technol, Dept Life Sci, S-41296 Gothenburg, Sweden (creator_code:org_t)
- 2023-02-23
- 2023
- Engelska.
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Ingår i: COMMUNICATIONS MEDICINE. - : Springer Science and Business Media LLC. - 2730-664X. ; 3:31
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Abstract
Ämnesord
Stäng
- For bacterial infections, it is important to rapidly and accurately identify and characterize the type of bacteria involved so that optimal antibiotic treatment can be given quickly to the patient. However, current diagnostic methods are sometimes slow and cannot be used for mixtures of bacteria. We have, therefore, developed a method to identify bacteria directly from patient samples. The method was tested on two common species of disease-causing bacteria - Escherichia coli and Klebsiella pneumoniae - and it could correctly identify the bacterial strain or subtype in both urine samples and mixtures. Hence, the method has the potential to provide fast diagnostic information for choosing the most suited antibiotic, thereby reducing the risk of death and suffering. Nyblom, Johnning et al. develop an optical DNA mapping approach for bacterial strain typing of patient samples. They demonstrate rapid identification of clinically relevant E. coli and K. pneumoniae strains, without the need for cultivation. BackgroundIdentification of pathogens is crucial to efficiently treat and prevent bacterial infections. However, existing diagnostic techniques are slow or have a too low resolution for well-informed clinical decisions.MethodsIn this study, we have developed an optical DNA mapping-based method for strain-level bacterial typing and simultaneous plasmid characterisation. For the typing, different taxonomical resolutions were examined and cultivated pure Escherichia coli and Klebsiella pneumoniae samples were used for parameter optimization. Finally, the method was applied to mixed bacterial samples and uncultured urine samples from patients with urinary tract infections. 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.
Ämnesord
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Infektionsmedicin (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Infectious Medicine (hsv//eng)
- NATURVETENSKAP -- Biologi -- Mikrobiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Microbiology (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Mikrobiologi inom det medicinska området (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Microbiology in the medical area (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinsk bioteknologi -- Biomedicinsk laboratorievetenskap/teknologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Medical Biotechnology -- Biomedical Laboratory Science/Technology (hsv//eng)
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Nyblom, My, 1995
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Johnning, Anna, ...
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Frykholm, Karoli ...
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Wrande, Marie
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Müller, Vilhelm, ...
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Goyal, Gaurav, 1 ...
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Robertsson, Miri ...
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Dvirnas, Alberta ...
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Sewunet, Tsegaye
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Kesarimangalam, ...
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Ambjornsson, Tob ...
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Giske, Christian ...
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Sandegren, Linus
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Kristiansson, Er ...
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Westerlund, Fred ...
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Kk, S
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Chalmers tekniska högskola
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Göteborgs universitet
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Uppsala universitet
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Karolinska Institutet