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Optimization of cer...
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Olausson, Josefin,1983Gothenburg University,Göteborgs universitet,Wallenberg Centre for Molecular and Translational Medicine,Institutionen för biomedicin, avdelningen för infektionssjukdomar,Institute of Biomedicine, Department of Infectious Medicine
(author)
Optimization of cerebrospinal fluid microbial DNA metagenomic sequencing diagnostics
- Article/chapterEnglish2022
Publisher, publication year, extent ...
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2022-03-01
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Springer Science and Business Media LLC,2022
Numbers
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LIBRIS-ID:oai:gup.ub.gu.se/315084
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https://gup.ub.gu.se/publication/315084URI
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https://doi.org/10.1038/s41598-022-07260-xDOI
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Subject category:ref swepub-contenttype
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Subject category:art swepub-publicationtype
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Infection in the central nervous system is a severe condition associated with high morbidity and mortality. Despite ample testing, the majority of encephalitis and meningitis cases remain undiagnosed. Metagenomic sequencing of cerebrospinal fluid has emerged as an unbiased approach to identify rare microbes and novel pathogens. However, several major hurdles remain, including establishment of individual limits of detection, removal of false positives and implementation of universal controls. Twenty-one cerebrospinal fluid samples, in which a known pathogen had been positively identified by available clinical techniques, were subjected to metagenomic DNA sequencing. Fourteen samples contained minute levels of Epstein-Barr virus. The detection threshold for each sample was calculated by using the total leukocyte content in the sample and environmental contaminants found in the bioinformatic classifiers. Virus sequences were detected in all ten samples, in which more than one read was expected according to the calculations. Conversely, no viral reads were detected in seven out of eight samples, in which less than one read was expected according to the calculations. False positive pathogens of computational or environmental origin were readily identified, by using a commonly available cell control. For bacteria, additional filters including a comparison between classifiers removed the remaining false positives and alleviated pathogen identification. Here we show a generalizable method for identification of pathogen species using DNA metagenomic sequencing. The choice of bioinformatic method mainly affected the efficiency of pathogen identification, but not the sensitivity of detection. Identification of pathogens requires multiple filtering steps including read distribution, sequence diversity and complementary verification of pathogen reads.
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Brunet, S.
(author)
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Vracar, Diana,1988Gothenburg University,Göteborgs universitet,Wallenberg Centre for Molecular and Translational Medicine,Institutionen för biomedicin, avdelningen för infektionssjukdomar,Institute of Biomedicine, Department of Infectious Medicine(Swepub:gu)xvradi
(author)
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Tian, Yarong,1989Gothenburg University,Göteborgs universitet,Institutionen för biomedicin, avdelningen för infektionssjukdomar,Wallenberg Centre for Molecular and Translational Medicine,Institute of Biomedicine, Department of Infectious Medicine(Swepub:gu)xtiaya
(author)
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Abrahamsson, SannaGothenburg University,Göteborgs universitet,Wallenberg Centre for Molecular and Translational Medicine,Institutionen för biomedicin, avdelningen för infektionssjukdomar,Institute of Biomedicine, Department of Infectious Medicine(Swepub:gu)xabras
(author)
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Meghadri, Sri HarshaGothenburg University,Göteborgs universitet,Wallenberg Centre for Molecular and Translational Medicine,Institutionen för biomedicin, avdelningen för infektionssjukdomar,Institute of Biomedicine, Department of Infectious Medicine
(author)
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Sikora, P.
(author)
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Karlberg, M. L.
(author)
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Jakobsson, Hedvig EGothenburg University,Göteborgs universitet,Wallenberg Centre for Molecular and Translational Medicine,Institutionen för biomedicin, avdelningen för infektionssjukdomar,Institute of Biomedicine, Department of Infectious Medicine(Swepub:gu)xenhed
(author)
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Tang, Ka-Wei,1983Gothenburg University,Göteborgs universitet,Institutionen för biomedicin, avdelningen för infektionssjukdomar,Wallenberg Centre for Molecular and Translational Medicine,Institute of Biomedicine, Department of Infectious Medicine(Swepub:gu)xtanka
(author)
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Göteborgs universitetWallenberg Centre for Molecular and Translational Medicine
(creator_code:org_t)
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In:Scientific Reports: Springer Science and Business Media LLC12:12045-2322
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Sikora, P.
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