Sökning: onr:"swepub:oai:gup.ub.gu.se/315084" > Optimization of cer...
Fältnamn | Indikatorer | Metadata |
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000 | 05366naa a2200445 4500 | |
001 | oai:gup.ub.gu.se/315084 | |
003 | SwePub | |
008 | 240528s2022 | |||||||||||000 ||eng| | |
024 | 7 | a https://gup.ub.gu.se/publication/3150842 URI |
024 | 7 | a https://doi.org/10.1038/s41598-022-07260-x2 DOI |
040 | a (SwePub)gu | |
041 | a eng | |
042 | 9 SwePub | |
072 | 7 | a ref2 swepub-contenttype |
072 | 7 | a art2 swepub-publicationtype |
100 | 1 | 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 |
245 | 1 0 | a Optimization of cerebrospinal fluid microbial DNA metagenomic sequencing diagnostics |
264 | c 2022-03-01 | |
264 | 1 | b 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 | 7 | a MEDICIN OCH HÄLSOVETENSKAPx Klinisk medicinx Infektionsmedicin0 (SwePub)302092 hsv//swe |
650 | 7 | a 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 | |
700 | 1 | a Brunet, S.4 aut |
700 | 1 | 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 |
700 | 1 | 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 |
700 | 1 | 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 |
700 | 1 | 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 |
700 | 1 | a Sikora, P.4 aut |
700 | 1 | a Karlberg, M. L.4 aut |
700 | 1 | 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 |
700 | 1 | 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 |
710 | 2 | a Göteborgs universitetb Wallenberg Centre for Molecular and Translational Medicine4 org |
773 | 0 | t Scientific Reportsd : Springer Science and Business Media LLCg 12:1q 12:1x 2045-2322 |
856 | 4 | u https://www.nature.com/articles/s41598-022-07260-x.pdf |
856 | 4 8 | u https://gup.ub.gu.se/publication/315084 |
856 | 4 8 | u https://doi.org/10.1038/s41598-022-07260-x |
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