PathoLive—Real-Time Pathogen Identification from Metagenomic Illumina Datasets Article Swipe
Simon H. Tausch
,
Tobias P. Loka
,
Jakob M. Schulze
,
Andreas Andrusch
,
Jeanette Klenner
,
Piotr Wojciech Dąbrowski
,
Martin Lindner
,
Andreas Nitsche
,
Bernhard Y. Renard
·
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.3390/life12091345
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.3390/life12091345
Over the past years, NGS has become a crucial workhorse for open-view pathogen diagnostics. Yet, long turnaround times result from using massively parallel high-throughput technologies as the analysis can only be performed after sequencing has finished. The interpretation of results can further be challenged by contaminations, clinically irrelevant sequences, and the sheer amount and complexity of the data. We implemented PathoLive, a real-time diagnostics pipeline for the detection of pathogens from clinical samples hours before sequencing has finished. Based on real-time alignment with HiLive2, mappings are scored with respect to common contaminations, low-entropy areas, and sequences of widespread, non-pathogenic organisms. The results are visualized using an interactive taxonomic tree that provides an easily interpretable overview of the relevance of hits. For a human plasma sample that was spiked in vitro with six pathogenic viruses, all agents were clearly detected after only 40 of 200 sequencing cycles. For a real-world sample from Sudan, the results correctly indicated the presence of Crimean-Congo hemorrhagic fever virus. In a second real-world dataset from the 2019 SARS-CoV-2 outbreak in Wuhan, we found the presence of a SARS coronavirus as the most relevant hit without the novel virus reference genome being included in the database. For all samples, clinically irrelevant hits were correctly de-emphasized. Our approach is valuable to obtain fast and accurate NGS-based pathogen identifications and correctly prioritize and visualize them based on their clinical significance: PathoLive is open source and available on GitLab and BioConda.
Related Topics
Concepts
Metagenomics
Computational biology
Turnaround time
Computer science
Identification (biology)
Genome
Massive parallel sequencing
DNA sequencing
Biology
Data mining
Genetics
Gene
Botany
Operating system
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.3390/life12091345
- https://www.mdpi.com/2075-1729/12/9/1345/pdf?version=1661854346
- OA Status
- gold
- Cited By
- 9
- References
- 64
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4293773382
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4293773382Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.3390/life12091345Digital Object Identifier
- Title
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PathoLive—Real-Time Pathogen Identification from Metagenomic Illumina DatasetsWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2022Year of publication
- Publication date
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2022-08-30Full publication date if available
- Authors
-
Simon H. Tausch, Tobias P. Loka, Jakob M. Schulze, Andreas Andrusch, Jeanette Klenner, Piotr Wojciech Dąbrowski, Martin Lindner, Andreas Nitsche, Bernhard Y. RenardList of authors in order
- Landing page
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https://doi.org/10.3390/life12091345Publisher landing page
- PDF URL
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https://www.mdpi.com/2075-1729/12/9/1345/pdf?version=1661854346Direct link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
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https://www.mdpi.com/2075-1729/12/9/1345/pdf?version=1661854346Direct OA link when available
- Concepts
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Metagenomics, Computational biology, Turnaround time, Computer science, Identification (biology), Genome, Massive parallel sequencing, DNA sequencing, Biology, Data mining, Genetics, Gene, Botany, Operating systemTop concepts (fields/topics) attached by OpenAlex
- Cited by
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9Total citation count in OpenAlex
- Citations by year (recent)
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2025: 4, 2024: 1, 2021: 1, 2020: 1, 2019: 2Per-year citation counts (last 5 years)
- References (count)
-
64Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.turnaround | 16 |
| abstract_inverted_index.visualized | 103 |
| abstract_inverted_index.coronavirus | 182 |
| abstract_inverted_index.diagnostics | 63 |
| abstract_inverted_index.hemorrhagic | 160 |
| abstract_inverted_index.implemented | 59 |
| abstract_inverted_index.interactive | 106 |
| abstract_inverted_index.low-entropy | 92 |
| abstract_inverted_index.widespread, | 97 |
| abstract_inverted_index.diagnostics. | 13 |
| abstract_inverted_index.technologies | 24 |
| abstract_inverted_index.Crimean-Congo | 159 |
| abstract_inverted_index.interpretable | 113 |
| abstract_inverted_index.significance: | 230 |
| abstract_inverted_index.de-emphasized. | 207 |
| abstract_inverted_index.interpretation | 37 |
| abstract_inverted_index.non-pathogenic | 98 |
| abstract_inverted_index.contaminations, | 45, 91 |
| abstract_inverted_index.high-throughput | 23 |
| abstract_inverted_index.identifications | 219 |
| cited_by_percentile_year.max | 98 |
| cited_by_percentile_year.min | 89 |
| corresponding_author_ids | https://openalex.org/A5049164396 |
| countries_distinct_count | 1 |
| institutions_distinct_count | 9 |
| corresponding_institution_ids | https://openalex.org/I24359323, https://openalex.org/I2801133538 |
| citation_normalized_percentile.value | 0.61519432 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |