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LIBRIS Formathandbok  (Information om MARC21)
FältnamnIndikatorerMetadata
00005366naa a2200445 4500
001oai:gup.ub.gu.se/315084
003SwePub
008240528s2022 | |||||||||||000 ||eng|
0247 a https://gup.ub.gu.se/publication/3150842 URI
0247 a https://doi.org/10.1038/s41598-022-07260-x2 DOI
040 a (SwePub)gu
041 a eng
042 9 SwePub
072 7a ref2 swepub-contenttype
072 7a art2 swepub-publicationtype
1001 a Olausson, Josefin,d 1983u Gothenburg University,Göteborgs universitet,Wallenberg Centre for Molecular and Translational Medicine,Institutionen för biomedicin, avdelningen för infektionssjukdomar,Institute of Biomedicine, Department of Infectious Medicine4 aut0 (Swepub:gu)xolajo
2451 0a Optimization of cerebrospinal fluid microbial DNA metagenomic sequencing diagnostics
264 c 2022-03-01
264 1b Springer Science and Business Media LLC,c 2022
520 a 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.
650 7a MEDICIN OCH HÄLSOVETENSKAPx Klinisk medicinx Infektionsmedicin0 (SwePub)302092 hsv//swe
650 7a MEDICAL AND HEALTH SCIENCESx Clinical Medicinex Infectious Medicine0 (SwePub)302092 hsv//eng
653 a meningitis
653 a infections
653 a england
653 a Science & Technology - Other Topics
7001 a Brunet, S.4 aut
7001 a Vracar, Diana,d 1988u Gothenburg University,Göteborgs universitet,Wallenberg Centre for Molecular and Translational Medicine,Institutionen för biomedicin, avdelningen för infektionssjukdomar,Institute of Biomedicine, Department of Infectious Medicine4 aut0 (Swepub:gu)xvradi
7001 a Tian, Yarong,d 1989u Gothenburg University,Göteborgs universitet,Institutionen för biomedicin, avdelningen för infektionssjukdomar,Wallenberg Centre for Molecular and Translational Medicine,Institute of Biomedicine, Department of Infectious Medicine4 aut0 (Swepub:gu)xtiaya
7001 a Abrahamsson, Sannau Gothenburg University,Göteborgs universitet,Wallenberg Centre for Molecular and Translational Medicine,Institutionen för biomedicin, avdelningen för infektionssjukdomar,Institute of Biomedicine, Department of Infectious Medicine4 aut0 (Swepub:gu)xabras
7001 a Meghadri, Sri Harshau Gothenburg University,Göteborgs universitet,Wallenberg Centre for Molecular and Translational Medicine,Institutionen för biomedicin, avdelningen för infektionssjukdomar,Institute of Biomedicine, Department of Infectious Medicine4 aut
7001 a Sikora, P.4 aut
7001 a Karlberg, M. L.4 aut
7001 a Jakobsson, Hedvig Eu Gothenburg University,Göteborgs universitet,Wallenberg Centre for Molecular and Translational Medicine,Institutionen för biomedicin, avdelningen för infektionssjukdomar,Institute of Biomedicine, Department of Infectious Medicine4 aut0 (Swepub:gu)xenhed
7001 a Tang, Ka-Wei,d 1983u Gothenburg University,Göteborgs universitet,Institutionen för biomedicin, avdelningen för infektionssjukdomar,Wallenberg Centre for Molecular and Translational Medicine,Institute of Biomedicine, Department of Infectious Medicine4 aut0 (Swepub:gu)xtanka
7102 a Göteborgs universitetb Wallenberg Centre for Molecular and Translational Medicine4 org
7730 t Scientific Reportsd : Springer Science and Business Media LLCg 12:1q 12:1x 2045-2322
8564 u https://www.nature.com/articles/s41598-022-07260-x.pdf
8564 8u https://gup.ub.gu.se/publication/315084
8564 8u https://doi.org/10.1038/s41598-022-07260-x

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