Microbial Contamination in Next Generation Sequencing: Implications for Sequence-Based Analysis of Clinical Samples
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The high level of accuracy and sensitivity of next generation sequencing for quantifying genetic material across organismal boundaries gives it tremendous potential for pathogen discovery and diagnosis in human disease. Despite this promise, substantial bacterial contamination is routinely found in existing human-derived RNA-seq datasets that likely arises from environmental sources. This raises the need for stringent sequencing and analysis protocols for studies investigating sequence-based microbial signatures in clinical samples.
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A database of background microorganisms commonly detected in mNGS data from normal flora or laboratory contamination typically needs to be maintained for accurate mNGS analyses.
“A database of background microorganisms commonly detected in mNGS data and arising from normal flora or laboratory contamination101,104 typically needs to be maintained for accurate mNGS analyses.”
From Clinical metagenomics (2019) · cites this paper as [104]
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- Authors
- Strong, M. J., Xu, G., Morici, L., Splinter Bon-Durant, S., Baddoo, M., Lin, Z., Fewell, C., Taylor, C. M., & Flemington, E. K.
- Affiliations
- Tulane University (US)
- University of California San Diego (US)
- Louisiana State University (US)
- Corresponding author
- Flemington, Erik K.
- Venue
- PLoS Pathogens
- Publisher
- Public Library of Science (PLoS)
- Published
- 2014-11-20
- Volume
- 10
- Issue
- 11
- Pages
- e1004437
- ISSN
- 1553-7366 (ISSN-L)
- 1553-7374
- PMC
- PMC4239086
- OpenAlex
- W1974764034
- Cited by
- 186
- References
- 33
- Citations by year
- 2026: 3 · 2025: 5 · 2024: 15 · 2023: 6 · 2022: 14 · 2021: 12 · 2020: 23 · 2019: 30 · 2018: 25 · 2017: 13 · 2016: 27 · 2015: 9 · 2014: 4
- FWCI
- 7.24
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Pathogens (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- Funders
- National Institutes of Health
- National Cancer Institute (R01CA138268, F30CA177267)
- National Institute of General Medical Sciences (P20GM103518, U54GM104940)
- National Institute of Allergy and Infectious Diseases (R01AI101046, R01AI106676)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- microbial contamination, next-generation sequencing, RNA-seq, bacterial contamination, clinical samples, environmental contamination, pathogen discovery, pathogen diagnosis, sequencing protocols, microbial signatures
- MeSH terms
- Equipment Contamination, Humans, Infections, Databases, Nucleic Acid, High-Throughput Nucleotide Sequencing
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