One pot RNA:DNA assembly for ribosomal RNA detection of pathogenic bacteria with single-molecule sensitivity Article Swipe
Filip Bošković
,
Sarah E. Sandler
,
Simon Brauburger
,
Yuan Shui
,
B. V. Vijaya Kumar
,
Joana Pereira Dias
,
Plamena Naydenova
,
Jinbo Zhu
,
Stephen Baker
,
Ulrich F. Keyser
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1101/2024.08.15.608086
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1101/2024.08.15.608086
Effective treatment of infectious diseases hinges on timely and accurate diagnosis. Current methods face challenges in distinguishing between pathogens that cause a similar symptom and where appropriate treatment may be hindered by antimicrobial resistance (AMR). Here, we introduce a PCR-free system that identifies and quantifies ribosomal RNA transcripts (rRNA) in pathogenic bacteria instead of DNA-encoding rRNA genes. Our method leverages the potential of >1 million rRNAs found in replicating bacterial cells in comparison to the limited number of rRNA DNA copies per cell. We combined nanopores with RNA nanotechnology to identify rRNA from bacteria and other cells. We developed a simultaneous protocol for rRNA isolation, assembly and enrichment with assembled RNA identifiers (IDs), which prevents heat degradation and eliminates background RNA. Our method detects multiple bacterial species, including AMR variants of Salmonella enterica and Acinetobacter baumannii, and coinfection. This approach offers unmatched specificity, with the ability to identify a single bacterium without amplification. The integration of CRISPR-dCas9 binding to RNA IDs leads to serovar-specific identification and opens new avenues in identifying pathogens up to their variants using abundant rRNAs.
Related Topics
Concepts
RNA
Ribosomal RNA
Biology
Salmonella enterica
Pathogenic bacteria
DNA
Computational biology
Bacteria
Gene
Microbiology
Genetics
Salmonella
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2024.08.15.608086
- https://www.biorxiv.org/content/biorxiv/early/2024/08/17/2024.08.15.608086.full.pdf
- OA Status
- green
- References
- 52
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4401670305
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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- DOI
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https://doi.org/10.1101/2024.08.15.608086Digital Object Identifier
- Title
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One pot RNA:DNA assembly for ribosomal RNA detection of pathogenic bacteria with single-molecule sensitivityWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2024Year of publication
- Publication date
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2024-08-17Full publication date if available
- Authors
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Filip Bošković, Sarah E. Sandler, Simon Brauburger, Yuan Shui, B. V. Vijaya Kumar, Joana Pereira Dias, Plamena Naydenova, Jinbo Zhu, Stephen Baker, Ulrich F. KeyserList of authors in order
- Landing page
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https://doi.org/10.1101/2024.08.15.608086Publisher landing page
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https://www.biorxiv.org/content/biorxiv/early/2024/08/17/2024.08.15.608086.full.pdfDirect link to full text PDF
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greenOpen access status per OpenAlex
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https://www.biorxiv.org/content/biorxiv/early/2024/08/17/2024.08.15.608086.full.pdfDirect OA link when available
- Concepts
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0Total citation count in OpenAlex
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52Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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