Enhanced Virus Detection and Metagenomic Sequencing in Patients with Meningitis and Encephalitis
Meningitis and encephalitis are leading global causes of central nervous system (CNS) disability and mortality. Current diagnostic workflows remain inefficient, requiring costly pathogen-specific assays and sometimes invasive surgical procedures. Meningitis and encephalitis are leading causes of cen...
Saved in:
| Published in | mBio Vol. 12; no. 4; p. e0114321 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
American Society for Microbiology
31.08.2021
|
| Subjects | |
| Online Access | Get full text |
Cover
Loading…
| Abstract | Meningitis and encephalitis are leading global causes of central nervous system (CNS) disability and mortality. Current diagnostic workflows remain inefficient, requiring costly pathogen-specific assays and sometimes invasive surgical procedures.
Meningitis and encephalitis are leading causes of central nervous system (CNS) disease and often result in severe neurological compromise or death. Traditional diagnostic workflows largely rely on pathogen-specific tests, sometimes over days to weeks, whereas metagenomic next-generation sequencing (mNGS) profiles all nucleic acid in a sample. In this single-center, prospective study, 68 hospitalized patients with known (
n
= 44) or suspected (
n
= 24) CNS infections underwent mNGS from RNA and DNA to identify potential pathogens and also targeted sequencing of viruses using hybrid capture. Using a computational metagenomic classification pipeline based on KrakenUniq and BLAST, we detected pathogen nucleic acid in cerebrospinal fluid (CSF) from 22 subjects, 3 of whom had no clinical diagnosis by routine workup. Among subjects diagnosed with infection by serology and/or peripheral samples, we demonstrated the utility of mNGS to detect pathogen nucleic acid in CSF, importantly for the
Ixodes scapularis
tick-borne pathogens Powassan virus,
Borrelia burgdorferi
, and
Anaplasma phagocytophilum
. We also evaluated two methods to enhance the detection of viral nucleic acid, hybrid capture and methylated DNA depletion. Hybrid capture nearly universally increased viral read recovery. Although results for methylated DNA depletion were mixed, it allowed the detection of varicella-zoster virus DNA in two samples that were negative by standard mNGS. Overall, mNGS is a promising approach that can test for multiple pathogens simultaneously, with efficacy similar to that of pathogen-specific tests, and can uncover geographically relevant infectious CNS disease, such as tick-borne infections in New England. With further laboratory and computational enhancements, mNGS may become a mainstay of workup for encephalitis and meningitis.
IMPORTANCE
Meningitis and encephalitis are leading global causes of central nervous system (CNS) disability and mortality. Current diagnostic workflows remain inefficient, requiring costly pathogen-specific assays and sometimes invasive surgical procedures. Despite intensive diagnostic efforts, 40 to 60% of people with meningitis or encephalitis have no clear cause of CNS disease identified. As diagnostic uncertainty often leads to costly inappropriate therapies, the need for novel pathogen detection methods is paramount. Metagenomic next-generation sequencing (mNGS) offers the unique opportunity to circumvent these challenges using unbiased laboratory and computational methods. Here, we performed comprehensive mNGS from 68 prospectively enrolled patients with known (
n
= 44) or suspected (
n
= 24) CNS viral infection from a single center in New England and evaluated enhanced methods to improve the detection of CNS pathogens, including those not traditionally identified in the CNS by nucleic acid detection. Overall, our work helps elucidate how mNGS can become integrated into the diagnostic toolkit for CNS infections. |
|---|---|
| AbstractList | ABSTRACT Meningitis and encephalitis are leading causes of central nervous system (CNS) disease and often result in severe neurological compromise or death. Traditional diagnostic workflows largely rely on pathogen-specific tests, sometimes over days to weeks, whereas metagenomic next-generation sequencing (mNGS) profiles all nucleic acid in a sample. In this single-center, prospective study, 68 hospitalized patients with known (n = 44) or suspected (n = 24) CNS infections underwent mNGS from RNA and DNA to identify potential pathogens and also targeted sequencing of viruses using hybrid capture. Using a computational metagenomic classification pipeline based on KrakenUniq and BLAST, we detected pathogen nucleic acid in cerebrospinal fluid (CSF) from 22 subjects, 3 of whom had no clinical diagnosis by routine workup. Among subjects diagnosed with infection by serology and/or peripheral samples, we demonstrated the utility of mNGS to detect pathogen nucleic acid in CSF, importantly for the Ixodes scapularis tick-borne pathogens Powassan virus, Borrelia burgdorferi, and Anaplasma phagocytophilum. We also evaluated two methods to enhance the detection of viral nucleic acid, hybrid capture and methylated DNA depletion. Hybrid capture nearly universally increased viral read recovery. Although results for methylated DNA depletion were mixed, it allowed the detection of varicella-zoster virus DNA in two samples that were negative by standard mNGS. Overall, mNGS is a promising approach that can test for multiple pathogens simultaneously, with efficacy similar to that of pathogen-specific tests, and can uncover geographically relevant infectious CNS disease, such as tick-borne infections in New England. With further laboratory and computational enhancements, mNGS may become a mainstay of workup for encephalitis and meningitis. IMPORTANCE Meningitis and encephalitis are leading global causes of central nervous system (CNS) disability and mortality. Current diagnostic workflows remain inefficient, requiring costly pathogen-specific assays and sometimes invasive surgical procedures. Despite intensive diagnostic efforts, 40 to 60% of people with meningitis or encephalitis have no clear cause of CNS disease identified. As diagnostic uncertainty often leads to costly inappropriate therapies, the need for novel pathogen detection methods is paramount. Metagenomic next-generation sequencing (mNGS) offers the unique opportunity to circumvent these challenges using unbiased laboratory and computational methods. Here, we performed comprehensive mNGS from 68 prospectively enrolled patients with known (n = 44) or suspected (n = 24) CNS viral infection from a single center in New England and evaluated enhanced methods to improve the detection of CNS pathogens, including those not traditionally identified in the CNS by nucleic acid detection. Overall, our work helps elucidate how mNGS can become integrated into the diagnostic toolkit for CNS infections. Meningitis and encephalitis are leading causes of central nervous system (CNS) disease and often result in severe neurological compromise or death. Traditional diagnostic workflows largely rely on pathogen-specific tests, sometimes over days to weeks, whereas metagenomic next-generation sequencing (mNGS) profiles all nucleic acid in a sample. In this single-center, prospective study, 68 hospitalized patients with known ( = 44) or suspected ( = 24) CNS infections underwent mNGS from RNA and DNA to identify potential pathogens and also targeted sequencing of viruses using hybrid capture. Using a computational metagenomic classification pipeline based on KrakenUniq and BLAST, we detected pathogen nucleic acid in cerebrospinal fluid (CSF) from 22 subjects, 3 of whom had no clinical diagnosis by routine workup. Among subjects diagnosed with infection by serology and/or peripheral samples, we demonstrated the utility of mNGS to detect pathogen nucleic acid in CSF, importantly for the Ixodes scapularis tick-borne pathogens Powassan virus, Borrelia burgdorferi, and Anaplasma phagocytophilum. We also evaluated two methods to enhance the detection of viral nucleic acid, hybrid capture and methylated DNA depletion. Hybrid capture nearly universally increased viral read recovery. Although results for methylated DNA depletion were mixed, it allowed the detection of varicella-zoster virus DNA in two samples that were negative by standard mNGS. Overall, mNGS is a promising approach that can test for multiple pathogens simultaneously, with efficacy similar to that of pathogen-specific tests, and can uncover geographically relevant infectious CNS disease, such as tick-borne infections in New England. With further laboratory and computational enhancements, mNGS may become a mainstay of workup for encephalitis and meningitis. Meningitis and encephalitis are leading global causes of central nervous system (CNS) disability and mortality. Current diagnostic workflows remain inefficient, requiring costly pathogen-specific assays and sometimes invasive surgical procedures. Despite intensive diagnostic efforts, 40 to 60% of people with meningitis or encephalitis have no clear cause of CNS disease identified. As diagnostic uncertainty often leads to costly inappropriate therapies, the need for novel pathogen detection methods is paramount. Metagenomic next-generation sequencing (mNGS) offers the unique opportunity to circumvent these challenges using unbiased laboratory and computational methods. Here, we performed comprehensive mNGS from 68 prospectively enrolled patients with known ( = 44) or suspected ( = 24) CNS viral infection from a single center in New England and evaluated enhanced methods to improve the detection of CNS pathogens, including those not traditionally identified in the CNS by nucleic acid detection. Overall, our work helps elucidate how mNGS can become integrated into the diagnostic toolkit for CNS infections. Meningitis and encephalitis are leading causes of central nervous system (CNS) disease and often result in severe neurological compromise or death. Traditional diagnostic workflows largely rely on pathogen-specific tests, sometimes over days to weeks, whereas metagenomic next-generation sequencing (mNGS) profiles all nucleic acid in a sample. In this single-center, prospective study, 68 hospitalized patients with known ( n = 44) or suspected ( n = 24) CNS infections underwent mNGS from RNA and DNA to identify potential pathogens and also targeted sequencing of viruses using hybrid capture. Using a computational metagenomic classification pipeline based on KrakenUniq and BLAST, we detected pathogen nucleic acid in cerebrospinal fluid (CSF) from 22 subjects, 3 of whom had no clinical diagnosis by routine workup. Among subjects diagnosed with infection by serology and/or peripheral samples, we demonstrated the utility of mNGS to detect pathogen nucleic acid in CSF, importantly for the Ixodes scapularis tick-borne pathogens Powassan virus, Borrelia burgdorferi , and Anaplasma phagocytophilum . We also evaluated two methods to enhance the detection of viral nucleic acid, hybrid capture and methylated DNA depletion. Hybrid capture nearly universally increased viral read recovery. Although results for methylated DNA depletion were mixed, it allowed the detection of varicella-zoster virus DNA in two samples that were negative by standard mNGS. Overall, mNGS is a promising approach that can test for multiple pathogens simultaneously, with efficacy similar to that of pathogen-specific tests, and can uncover geographically relevant infectious CNS disease, such as tick-borne infections in New England. With further laboratory and computational enhancements, mNGS may become a mainstay of workup for encephalitis and meningitis. Meningitis and encephalitis are leading global causes of central nervous system (CNS) disability and mortality. Current diagnostic workflows remain inefficient, requiring costly pathogen-specific assays and sometimes invasive surgical procedures. Meningitis and encephalitis are leading causes of central nervous system (CNS) disease and often result in severe neurological compromise or death. Traditional diagnostic workflows largely rely on pathogen-specific tests, sometimes over days to weeks, whereas metagenomic next-generation sequencing (mNGS) profiles all nucleic acid in a sample. In this single-center, prospective study, 68 hospitalized patients with known ( n = 44) or suspected ( n = 24) CNS infections underwent mNGS from RNA and DNA to identify potential pathogens and also targeted sequencing of viruses using hybrid capture. Using a computational metagenomic classification pipeline based on KrakenUniq and BLAST, we detected pathogen nucleic acid in cerebrospinal fluid (CSF) from 22 subjects, 3 of whom had no clinical diagnosis by routine workup. Among subjects diagnosed with infection by serology and/or peripheral samples, we demonstrated the utility of mNGS to detect pathogen nucleic acid in CSF, importantly for the Ixodes scapularis tick-borne pathogens Powassan virus, Borrelia burgdorferi , and Anaplasma phagocytophilum . We also evaluated two methods to enhance the detection of viral nucleic acid, hybrid capture and methylated DNA depletion. Hybrid capture nearly universally increased viral read recovery. Although results for methylated DNA depletion were mixed, it allowed the detection of varicella-zoster virus DNA in two samples that were negative by standard mNGS. Overall, mNGS is a promising approach that can test for multiple pathogens simultaneously, with efficacy similar to that of pathogen-specific tests, and can uncover geographically relevant infectious CNS disease, such as tick-borne infections in New England. With further laboratory and computational enhancements, mNGS may become a mainstay of workup for encephalitis and meningitis. IMPORTANCE Meningitis and encephalitis are leading global causes of central nervous system (CNS) disability and mortality. Current diagnostic workflows remain inefficient, requiring costly pathogen-specific assays and sometimes invasive surgical procedures. Despite intensive diagnostic efforts, 40 to 60% of people with meningitis or encephalitis have no clear cause of CNS disease identified. As diagnostic uncertainty often leads to costly inappropriate therapies, the need for novel pathogen detection methods is paramount. Metagenomic next-generation sequencing (mNGS) offers the unique opportunity to circumvent these challenges using unbiased laboratory and computational methods. Here, we performed comprehensive mNGS from 68 prospectively enrolled patients with known ( n = 44) or suspected ( n = 24) CNS viral infection from a single center in New England and evaluated enhanced methods to improve the detection of CNS pathogens, including those not traditionally identified in the CNS by nucleic acid detection. Overall, our work helps elucidate how mNGS can become integrated into the diagnostic toolkit for CNS infections. Meningitis and encephalitis are leading causes of central nervous system (CNS) disease and often result in severe neurological compromise or death. Traditional diagnostic workflows largely rely on pathogen-specific tests, sometimes over days to weeks, whereas metagenomic next-generation sequencing (mNGS) profiles all nucleic acid in a sample. In this single-center, prospective study, 68 hospitalized patients with known (n = 44) or suspected (n = 24) CNS infections underwent mNGS from RNA and DNA to identify potential pathogens and also targeted sequencing of viruses using hybrid capture. Using a computational metagenomic classification pipeline based on KrakenUniq and BLAST, we detected pathogen nucleic acid in cerebrospinal fluid (CSF) from 22 subjects, 3 of whom had no clinical diagnosis by routine workup. Among subjects diagnosed with infection by serology and/or peripheral samples, we demonstrated the utility of mNGS to detect pathogen nucleic acid in CSF, importantly for the Ixodes scapularis tick-borne pathogens Powassan virus, Borrelia burgdorferi, and Anaplasma phagocytophilum. We also evaluated two methods to enhance the detection of viral nucleic acid, hybrid capture and methylated DNA depletion. Hybrid capture nearly universally increased viral read recovery. Although results for methylated DNA depletion were mixed, it allowed the detection of varicella-zoster virus DNA in two samples that were negative by standard mNGS. Overall, mNGS is a promising approach that can test for multiple pathogens simultaneously, with efficacy similar to that of pathogen-specific tests, and can uncover geographically relevant infectious CNS disease, such as tick-borne infections in New England. With further laboratory and computational enhancements, mNGS may become a mainstay of workup for encephalitis and meningitis. IMPORTANCE Meningitis and encephalitis are leading global causes of central nervous system (CNS) disability and mortality. Current diagnostic workflows remain inefficient, requiring costly pathogen-specific assays and sometimes invasive surgical procedures. Despite intensive diagnostic efforts, 40 to 60% of people with meningitis or encephalitis have no clear cause of CNS disease identified. As diagnostic uncertainty often leads to costly inappropriate therapies, the need for novel pathogen detection methods is paramount. Metagenomic next-generation sequencing (mNGS) offers the unique opportunity to circumvent these challenges using unbiased laboratory and computational methods. Here, we performed comprehensive mNGS from 68 prospectively enrolled patients with known (n = 44) or suspected (n = 24) CNS viral infection from a single center in New England and evaluated enhanced methods to improve the detection of CNS pathogens, including those not traditionally identified in the CNS by nucleic acid detection. Overall, our work helps elucidate how mNGS can become integrated into the diagnostic toolkit for CNS infections. Meningitis and encephalitis are leading causes of central nervous system (CNS) disease and often result in severe neurological compromise or death. Traditional diagnostic workflows largely rely on pathogen-specific tests, sometimes over days to weeks, whereas metagenomic next-generation sequencing (mNGS) profiles all nucleic acid in a sample. In this single-center, prospective study, 68 hospitalized patients with known (n = 44) or suspected (n = 24) CNS infections underwent mNGS from RNA and DNA to identify potential pathogens and also targeted sequencing of viruses using hybrid capture. Using a computational metagenomic classification pipeline based on KrakenUniq and BLAST, we detected pathogen nucleic acid in cerebrospinal fluid (CSF) from 22 subjects, 3 of whom had no clinical diagnosis by routine workup. Among subjects diagnosed with infection by serology and/or peripheral samples, we demonstrated the utility of mNGS to detect pathogen nucleic acid in CSF, importantly for the Ixodes scapularis tick-borne pathogens Powassan virus, Borrelia burgdorferi, and Anaplasma phagocytophilum. We also evaluated two methods to enhance the detection of viral nucleic acid, hybrid capture and methylated DNA depletion. Hybrid capture nearly universally increased viral read recovery. Although results for methylated DNA depletion were mixed, it allowed the detection of varicella-zoster virus DNA in two samples that were negative by standard mNGS. Overall, mNGS is a promising approach that can test for multiple pathogens simultaneously, with efficacy similar to that of pathogen-specific tests, and can uncover geographically relevant infectious CNS disease, such as tick-borne infections in New England. With further laboratory and computational enhancements, mNGS may become a mainstay of workup for encephalitis and meningitis. IMPORTANCE Meningitis and encephalitis are leading global causes of central nervous system (CNS) disability and mortality. Current diagnostic workflows remain inefficient, requiring costly pathogen-specific assays and sometimes invasive surgical procedures. Despite intensive diagnostic efforts, 40 to 60% of people with meningitis or encephalitis have no clear cause of CNS disease identified. As diagnostic uncertainty often leads to costly inappropriate therapies, the need for novel pathogen detection methods is paramount. Metagenomic next-generation sequencing (mNGS) offers the unique opportunity to circumvent these challenges using unbiased laboratory and computational methods. Here, we performed comprehensive mNGS from 68 prospectively enrolled patients with known (n = 44) or suspected (n = 24) CNS viral infection from a single center in New England and evaluated enhanced methods to improve the detection of CNS pathogens, including those not traditionally identified in the CNS by nucleic acid detection. Overall, our work helps elucidate how mNGS can become integrated into the diagnostic toolkit for CNS infections.Meningitis and encephalitis are leading causes of central nervous system (CNS) disease and often result in severe neurological compromise or death. Traditional diagnostic workflows largely rely on pathogen-specific tests, sometimes over days to weeks, whereas metagenomic next-generation sequencing (mNGS) profiles all nucleic acid in a sample. In this single-center, prospective study, 68 hospitalized patients with known (n = 44) or suspected (n = 24) CNS infections underwent mNGS from RNA and DNA to identify potential pathogens and also targeted sequencing of viruses using hybrid capture. Using a computational metagenomic classification pipeline based on KrakenUniq and BLAST, we detected pathogen nucleic acid in cerebrospinal fluid (CSF) from 22 subjects, 3 of whom had no clinical diagnosis by routine workup. Among subjects diagnosed with infection by serology and/or peripheral samples, we demonstrated the utility of mNGS to detect pathogen nucleic acid in CSF, importantly for the Ixodes scapularis tick-borne pathogens Powassan virus, Borrelia burgdorferi, and Anaplasma phagocytophilum. We also evaluated two methods to enhance the detection of viral nucleic acid, hybrid capture and methylated DNA depletion. Hybrid capture nearly universally increased viral read recovery. Although results for methylated DNA depletion were mixed, it allowed the detection of varicella-zoster virus DNA in two samples that were negative by standard mNGS. Overall, mNGS is a promising approach that can test for multiple pathogens simultaneously, with efficacy similar to that of pathogen-specific tests, and can uncover geographically relevant infectious CNS disease, such as tick-borne infections in New England. With further laboratory and computational enhancements, mNGS may become a mainstay of workup for encephalitis and meningitis. IMPORTANCE Meningitis and encephalitis are leading global causes of central nervous system (CNS) disability and mortality. Current diagnostic workflows remain inefficient, requiring costly pathogen-specific assays and sometimes invasive surgical procedures. Despite intensive diagnostic efforts, 40 to 60% of people with meningitis or encephalitis have no clear cause of CNS disease identified. As diagnostic uncertainty often leads to costly inappropriate therapies, the need for novel pathogen detection methods is paramount. Metagenomic next-generation sequencing (mNGS) offers the unique opportunity to circumvent these challenges using unbiased laboratory and computational methods. Here, we performed comprehensive mNGS from 68 prospectively enrolled patients with known (n = 44) or suspected (n = 24) CNS viral infection from a single center in New England and evaluated enhanced methods to improve the detection of CNS pathogens, including those not traditionally identified in the CNS by nucleic acid detection. Overall, our work helps elucidate how mNGS can become integrated into the diagnostic toolkit for CNS infections. |
| Author | Goldstein, Robert Ganesh, Vijay Goldberg, Marcia B. Freimark, Lisa M. Ye, Simon Cummins, Kaelyn C. Sabeti, Pardis Cho, Tracey A. Lemieux, Jacob Mukerji, Shibani S. Kanjilal, Sanjat Solomon, Isaac H. Ahmed, Asim A. Park, Daniel Frosch, Matthew P. Piantadosi, Anne Kinsella, Cormac M. Rosenberg, Eric Leone, Michael J. Thon, Jesse M. Adams, Gordon Ostrem, Bridget |
| Author_xml | – sequence: 1 givenname: Anne orcidid: 0000-0002-5942-1534 surname: Piantadosi fullname: Piantadosi, Anne organization: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA, Emory University School of Medicine, Atlanta, Georgia, USA – sequence: 2 givenname: Shibani S. surname: Mukerji fullname: Mukerji, Shibani S. organization: Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA, Harvard Medical School, Boston, Massachusetts, USA – sequence: 3 givenname: Simon surname: Ye fullname: Ye, Simon organization: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA, Harvard-MIT Program of Health Sciences and Technology, Cambridge, Massachusetts, USA – sequence: 4 givenname: Michael J. surname: Leone fullname: Leone, Michael J. organization: Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA – sequence: 5 givenname: Lisa M. surname: Freimark fullname: Freimark, Lisa M. organization: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA – sequence: 6 givenname: Daniel surname: Park fullname: Park, Daniel organization: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA – sequence: 7 givenname: Gordon surname: Adams fullname: Adams, Gordon organization: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA – sequence: 8 givenname: Jacob surname: Lemieux fullname: Lemieux, Jacob organization: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA, Harvard Medical School, Boston, Massachusetts, USA – sequence: 9 givenname: Sanjat orcidid: 0000-0002-1221-5725 surname: Kanjilal fullname: Kanjilal, Sanjat organization: Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA, Harvard Medical School, Boston, Massachusetts, USA, Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA – sequence: 10 givenname: Isaac H. surname: Solomon fullname: Solomon, Isaac H. organization: Harvard Medical School, Boston, Massachusetts, USA, Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA – sequence: 11 givenname: Asim A. surname: Ahmed fullname: Ahmed, Asim A. organization: Harvard Medical School, Boston, Massachusetts, USA, Department of Pediatrics, Harvard Medical School, Children’s Hospital, Boston, Massachusetts, USA – sequence: 12 givenname: Robert surname: Goldstein fullname: Goldstein, Robert organization: Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA, Harvard Medical School, Boston, Massachusetts, USA – sequence: 13 givenname: Vijay surname: Ganesh fullname: Ganesh, Vijay organization: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA, Harvard Medical School, Boston, Massachusetts, USA, Department of Neurology, Brigham and Women’s Hospital, Boston, Massachusetts, USA – sequence: 14 givenname: Bridget surname: Ostrem fullname: Ostrem, Bridget organization: Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA, Harvard Medical School, Boston, Massachusetts, USA – sequence: 15 givenname: Kaelyn C. surname: Cummins fullname: Cummins, Kaelyn C. organization: Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA – sequence: 16 givenname: Jesse M. surname: Thon fullname: Thon, Jesse M. organization: Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA, Harvard Medical School, Boston, Massachusetts, USA – sequence: 17 givenname: Cormac M. surname: Kinsella fullname: Kinsella, Cormac M. organization: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA – sequence: 18 givenname: Eric surname: Rosenberg fullname: Rosenberg, Eric organization: Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA, Harvard Medical School, Boston, Massachusetts, USA, Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA – sequence: 19 givenname: Matthew P. surname: Frosch fullname: Frosch, Matthew P. organization: Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA, Harvard Medical School, Boston, Massachusetts, USA, Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA – sequence: 20 givenname: Marcia B. surname: Goldberg fullname: Goldberg, Marcia B. organization: Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA, Harvard Medical School, Boston, Massachusetts, USA – sequence: 21 givenname: Tracey A. surname: Cho fullname: Cho, Tracey A. organization: Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA, Harvard Medical School, Boston, Massachusetts, USA, University of Iowa, Department of Neurology, Iowa City, Iowa, USA – sequence: 22 givenname: Pardis surname: Sabeti fullname: Sabeti, Pardis organization: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA, Harvard Medical School, Boston, Massachusetts, USA, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA, Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/34465023$$D View this record in MEDLINE/PubMed |
| BookMark | eNp1kd1vFCEUxYmpsbX20Vczj8ZkKp8D-2KiddUmNZr48YoM3NllMwMrsBr_e5nd2rQm5QVyOPy4957H6CjEAAg9JficEKpeTm98PMeEcNZS8gCdUCJwKwUhR7fOx-gs5w2uizGiGH6EjhnnncCUnaAfy7A2wYJrvvu0y81bKGCLj6ExwTUfoZgVhDh523yBnzsI1odV40Pz2RQPoeTmty_r6gtV98Xn_bNlBW7XZpyFJ-jhYMYMZ9f7Kfr2bvn14kN79en95cXrq9ZwpUpreukcZ71ylggpLUg5SEPxYlaUqR2yBScwUOmA9FYyhXlvMMBC1EYHy07R5YHrotnobfKTSX90NF7vhZhW2qTi7QiaCukIk0pBZ7lwuO_EIAyr33ZD7_jMenVgbXf9BM7WRpMZ70Dv3gS_1qv4SyuOO8pIBTy_BqRYp5aLnny2MI4mQNzlWkGnqKjBLar1xcFq8kT1Ju5SqGPSBOs5YT0nrPcJazpzn90u7Kaif3lWQ3sw2BRzTjDcWO4Dsv_81hcz51_78uM9r_4CJBLEQQ |
| CitedBy_id | crossref_primary_10_1186_s12866_024_03416_z crossref_primary_10_1016_j_jceh_2024_102471 crossref_primary_10_1016_j_idc_2023_04_002 crossref_primary_10_1038_s41591_024_03275_1 crossref_primary_10_22207_JPAM_16_4_34 crossref_primary_10_1186_s12987_022_00400_5 crossref_primary_10_1016_j_rmcr_2024_102007 crossref_primary_10_2807_1560_7917_ES_2023_28_45_2200913 crossref_primary_10_1038_s41598_024_75120_x crossref_primary_10_3349_ymj_2023_0250 crossref_primary_10_1097_WCO_0000000000001155 crossref_primary_10_1371_journal_pone_0318805 crossref_primary_10_3390_diagnostics13020280 crossref_primary_10_1186_s13073_025_01447_3 crossref_primary_10_2217_fmb_2023_0107 crossref_primary_10_1016_j_spinee_2024_11_004 crossref_primary_10_3389_fped_2024_1259088 crossref_primary_10_1002_ccr3_9676 crossref_primary_10_3389_fneur_2023_1193834 crossref_primary_10_3389_fneur_2022_989280 crossref_primary_10_3389_fped_2022_923125 crossref_primary_10_3389_fcimb_2022_968135 crossref_primary_10_1093_ofid_ofac295 crossref_primary_10_3389_fmicb_2022_926240 crossref_primary_10_1099_mgen_0_001079 crossref_primary_10_1097_WNO_0000000000001455 crossref_primary_10_3390_v17030300 crossref_primary_10_1128_spectrum_02946_22 crossref_primary_10_1128_spectrum_02264_23 crossref_primary_10_1128_msystems_00581_23 crossref_primary_10_1017_S0266467423000019 crossref_primary_10_1080_20008686_2024_2441537 crossref_primary_10_1096_fj_202400792R crossref_primary_10_3390_v14122757 crossref_primary_10_3389_fmed_2025_1524783 crossref_primary_10_3389_fcimb_2023_1240283 crossref_primary_10_1080_01616412_2023_2265243 crossref_primary_10_1177_19418744241242957 crossref_primary_10_3389_fcimb_2022_943859 crossref_primary_10_3389_fcimb_2023_1169101 crossref_primary_10_1007_s40291_024_00727_9 crossref_primary_10_1016_j_mcpro_2024_100822 crossref_primary_10_31073_onehealthjournal2024_I_05 crossref_primary_10_1631_jzus_B2300029 crossref_primary_10_3389_fvets_2025_1540437 crossref_primary_10_1097_IPC_0000000000001448 crossref_primary_10_1007_s10096_024_05011_6 crossref_primary_10_1016_j_heliyon_2024_e35287 crossref_primary_10_2147_IDR_S450693 crossref_primary_10_3892_mmr_2024_13277 crossref_primary_10_1001_jamaneurol_2022_2287 crossref_primary_10_1089_hs_2023_0100 crossref_primary_10_3389_fcimb_2023_1104858 crossref_primary_10_1016_j_diagmicrobio_2023_116169 crossref_primary_10_3390_pathogens13040275 crossref_primary_10_1016_j_psj_2024_103592 crossref_primary_10_3390_v16111653 crossref_primary_10_1016_j_ebiom_2022_104287 |
| Cites_doi | 10.1016/j.ijid.2017.11.028 10.1212/01.wnl.0000191407.81333.00 10.1101/gr.213959.116 10.1038/s41598-019-52570-2 10.1007/s00277-016-2770-3 10.1111/j.1399-0012.2009.01044.x 10.1101/gr.238170.118 10.1007/s15010-017-1014-3 10.1086/509330 10.1056/NEJMoa1401268 10.1093/jpids/piz032 10.1016/j.cmi.2019.04.028 10.1016/S0022-2836(05)80360-2 10.1016/j.jcv.2018.04.017 10.1093/cid/ciaa035 10.1186/s13059-018-1568-0 10.1093/bioinformatics/btu170 10.1093/jpids/piw066 10.1111/ajt.14058 10.1093/bioinformatics/btn322 10.1212/WNL.0000000000000086 10.1093/cid/cix792 10.1038/ncomms11257 10.1056/NEJMoa1803396 10.1186/s13059-014-0519-7 10.15585/mmwr.mm6717e1 10.1038/nature20167 10.1056/NEJMcpc1707557 10.5858/arpa.2016-0539-RA 10.1038/s41564-018-0349-6 10.1016/S1474-4422(18)30499-X 10.1086/367841 10.1186/s12985-017-0764-y 10.1016/j.mimet.2016.05.022 10.2169/internalmedicine.56.8185 10.1038/s41587-018-0006-x 10.1146/annurev-pathmechdis-012418-012751 10.1017/S0950268815000850 10.1128/JCM.00472-18 10.1002/ana.24499 10.1128/jcm.30.8.2207-2210.1992 10.3201/eid0812.020532 10.1016/j.jinf.2017.12.014 10.1016/S1473-3099(18)30245-7 10.1007/s13365-019-00784-5 10.1128/JCM.03050-15 10.1126/science.1259657 10.1093/cid/cix881 10.1093/ofid/ofv136 10.1093/ofid/ofx121 10.1038/ncpneuro0401 10.4269/ajtmh.2011.10-0613 10.1038/s41587-019-0156-5 10.1080/14737159.2018.1487292 10.1038/s41576-019-0113-7 |
| ContentType | Journal Article |
| Copyright | Copyright © 2021 Piantadosi et al. Copyright © 2021 Piantadosi et al. 2021 Piantadosi et al. |
| Copyright_xml | – notice: Copyright © 2021 Piantadosi et al. – notice: Copyright © 2021 Piantadosi et al. 2021 Piantadosi et al. |
| DBID | AAYXX CITATION CGR CUY CVF ECM EIF NPM 7X8 5PM DOA |
| DOI | 10.1128/mBio.01143-21 |
| DatabaseName | CrossRef Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed MEDLINE - Academic PubMed Central (Full Participant titles) DOAJ Directory of Open Access Journals |
| DatabaseTitle | CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) MEDLINE - Academic |
| DatabaseTitleList | MEDLINE CrossRef MEDLINE - Academic |
| Database_xml | – sequence: 1 dbid: DOA name: DOAJ Directory of Open Access Journals url: https://www.doaj.org/ sourceTypes: Open Website – sequence: 2 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 3 dbid: EIF name: MEDLINE url: https://proxy.k.utb.cz/login?url=https://www.webofscience.com/wos/medline/basic-search sourceTypes: Index Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Biology |
| EISSN | 2150-7511 |
| Editor | Duggal, Nisha |
| Editor_xml | – sequence: 1 givenname: Nisha surname: Duggal fullname: Duggal, Nisha |
| ExternalDocumentID | oai_doaj_org_article_257d13788e6c45d0b65f5a35776fbd4c PMC8406231 mBio01143-21 34465023 10_1128_mBio_01143_21 |
| Genre | Research Support, Non-U.S. Gov't Journal Article Research Support, N.I.H., Extramural |
| GrantInformation_xml | – fundername: NIMH NIH HHS grantid: K23 MH115812 – fundername: NCATS NIH HHS grantid: KL2 TR002542 – fundername: NIAID NIH HHS grantid: K08 AI139348 – fundername: NHGRI NIH HHS grantid: T32 HG010464 – fundername: NIAID NIH HHS grantid: T32 AI007061 – fundername: NIAID NIH HHS grantid: P30 AI060354 – fundername: HHS | NIH | National Institute of Mental Health (NIMH) grantid: K23MH115812 funderid: https://doi.org/10.13039/100000025 – fundername: HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID) grantid: K08AI139348 funderid: https://doi.org/10.13039/100000060 – fundername: HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID) grantid: 5P30AI060354-16 funderid: https://doi.org/10.13039/100000060 – fundername: HHS | NIH | National Center for Advancing Translational Sciences (NCATS) grantid: KL2TR002542 funderid: https://doi.org/10.13039/100006108 – fundername: Harvard Medical School (HMS) grantid: Harvard University Eleanor and Miles Shore Fellowship Program funderid: https://doi.org/10.13039/100006691 – fundername: ; grantid: K08AI139348 – fundername: ; grantid: Harvard University Eleanor and Miles Shore Fellowship Program – fundername: ; grantid: K23MH115812 – fundername: ; grantid: KL2TR002542 – fundername: ; grantid: 5P30AI060354-16 |
| GroupedDBID | --- 0R~ 53G 5VS AAFWJ AAGFI AAUOK AAYXX ADBBV AENEX AFPKN ALMA_UNASSIGNED_HOLDINGS AOIJS BAWUL BCNDV BTFSW CITATION DIK E3Z EBS FRP GROUPED_DOAJ GX1 H13 HYE HZ~ KQ8 M48 O5R O5S O9- OK1 P2P PGMZT RHI RNS RPM RSF CGR CUY CVF ECM EIF NPM - 0R ADACO BXI HZ M~E RHF 7X8 5PM |
| ID | FETCH-LOGICAL-a488t-ab7dd43b8dc1577ce77f7a209b8dc8a1433941ef27de1bc73804ba0ee95215fc3 |
| IEDL.DBID | M48 |
| ISSN | 2150-7511 |
| IngestDate | Wed Aug 27 01:20:14 EDT 2025 Thu Aug 21 13:38:46 EDT 2025 Fri Jul 11 06:51:02 EDT 2025 Tue Dec 28 13:59:02 EST 2021 Thu Apr 03 07:07:22 EDT 2025 Thu Apr 24 23:10:13 EDT 2025 Tue Jul 01 01:52:49 EDT 2025 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 4 |
| Keywords | metagenomic sequencing hybrid capture encephalitis next-generation sequencing (NGS) meningitis methylated DNA depletion virus |
| Language | English |
| License | This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. https://creativecommons.org/licenses/by/4.0 This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-a488t-ab7dd43b8dc1577ce77f7a209b8dc8a1433941ef27de1bc73804ba0ee95215fc3 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Tracey A. Cho and Pardis Sabeti contributed equally. Present address: Kaelyn C. Cummins, Baylor College of Medicine, Houston, Texas, USA; Jesse M. Thon, Department of Neurology, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Cormac M. Kinsella, Amsterdam UMC, Amsterdam, The Netherlands. Anne Piantadosi, Shibani S. Mukerji, and Simon Ye all contributed equally to this work. Author order was determined by mutual agreement among first authors. |
| ORCID | 0000-0002-5942-1534 0000-0002-1221-5725 |
| OpenAccessLink | https://journals.asm.org/doi/10.1128/mBio.01143-21 |
| PMID | 34465023 |
| PQID | 2568250119 |
| PQPubID | 23479 |
| PageCount | 13 |
| ParticipantIDs | doaj_primary_oai_doaj_org_article_257d13788e6c45d0b65f5a35776fbd4c pubmedcentral_primary_oai_pubmedcentral_nih_gov_8406231 proquest_miscellaneous_2568250119 asm2_journals_10_1128_mBio_01143_21 pubmed_primary_34465023 crossref_primary_10_1128_mBio_01143_21 crossref_citationtrail_10_1128_mBio_01143_21 |
| ProviderPackageCode | CITATION AAYXX |
| PublicationCentury | 2000 |
| PublicationDate | 20210831 |
| PublicationDateYYYYMMDD | 2021-08-31 |
| PublicationDate_xml | – month: 8 year: 2021 text: 20210831 day: 31 |
| PublicationDecade | 2020 |
| PublicationPlace | United States |
| PublicationPlace_xml | – name: United States – name: 1752 N St., N.W., Washington, DC |
| PublicationTitle | mBio |
| PublicationTitleAbbrev | mBio |
| PublicationTitleAlternate | mBio |
| PublicationYear | 2021 |
| Publisher | American Society for Microbiology |
| Publisher_xml | – name: American Society for Microbiology |
| References | e_1_3_2_26_2 e_1_3_2_28_2 e_1_3_2_41_2 e_1_3_2_20_2 e_1_3_2_43_2 e_1_3_2_22_2 e_1_3_2_45_2 e_1_3_2_24_2 e_1_3_2_47_2 e_1_3_2_9_2 e_1_3_2_16_2 e_1_3_2_37_2 e_1_3_2_7_2 e_1_3_2_18_2 e_1_3_2_54_2 e_1_3_2_10_2 e_1_3_2_31_2 e_1_3_2_52_2 e_1_3_2_5_2 e_1_3_2_12_2 e_1_3_2_33_2 e_1_3_2_58_2 e_1_3_2_3_2 e_1_3_2_14_2 e_1_3_2_35_2 e_1_3_2_56_2 e_1_3_2_50_2 e_1_3_2_27_2 e_1_3_2_48_2 e_1_3_2_29_2 Fasolka MJ (e_1_3_2_49_2) 2017 e_1_3_2_40_2 Bennett JE (e_1_3_2_39_2) 2014 e_1_3_2_21_2 e_1_3_2_42_2 e_1_3_2_23_2 e_1_3_2_44_2 e_1_3_2_25_2 e_1_3_2_46_2 e_1_3_2_15_2 e_1_3_2_38_2 e_1_3_2_8_2 e_1_3_2_17_2 e_1_3_2_59_2 e_1_3_2_6_2 e_1_3_2_19_2 e_1_3_2_30_2 e_1_3_2_53_2 e_1_3_2_32_2 e_1_3_2_51_2 e_1_3_2_11_2 e_1_3_2_34_2 e_1_3_2_57_2 e_1_3_2_4_2 e_1_3_2_13_2 e_1_3_2_36_2 e_1_3_2_55_2 e_1_3_2_2_2 Fasolka, MJ (B48) 2017 Altschul, SF, Gish, W, Miller, W, Myers, EW, Lipman, DJ (B55) 1990; 215 Riva, N, Franconi, I, Meschiari, M, Franceschini, E, Puzzolante, C, Cuomo, G, Bianchi, A, Cavalleri, F, Genovese, M, Mussini, C (B28) 2017; 45 Charalampous, T, Kay, GL, Richardson, H, Aydin, A, Baldan, R, Jeanes, C, Rae, D, Grundy, S, Turner, DJ, Wain, J, Leggett, RM, Livermore, DM, O’Grady, J (B36) 2019; 37 Miller, S, Naccache, SN, Samayoa, E, Messacar, K, Arevalo, S, Federman, S, Stryke, D, Pham, E, Fung, B, Bolosky, WJ, Ingebrigtsen, D, Lorizio, W, Paff, SM, Leake, JA, Pesano, R, DeBiasi, R, Dominguez, S, Chiu, CY (B23) 2019; 29 Kupila, L, Vuorinen, T, Vainionpää, R, Hukkanen, V, Marttila, RJ, Kotilainen, P (B5) 2006; 66 Aburakawa, Y, Katayama, T, Saito, T, Sawada, J, Suzutani, T, Aizawa, H, Hasebe, N (B27) 2017; 56 Menzel, P, Ng, KL, Krogh, A (B58) 2016; 7 Asplund, M, Kjartansdóttir, KR, Mollerup, S, Vinner, L, Fridholm, H, Herrera, JAR, Friis-Nielsen, J, Hansen, TA, Jensen, RH, Nielsen, IB, Richter, SR, Rey-Iglesia, A, Matey-Hernandez, ML, Alquezar-Planas, DE, Olsen, PVS, Sicheritz-Pontén, T, Willerslev, E, Lund, O, Brunak, S, Mourier, T, Nielsen, LP, Izarzugaza, JMG, Hansen, AJ (B30) 2019; 25 Vareil, M, Wille, H, Kassab, S, Le-Cornec, C, Puges, M, Desclaux, A, Lafon, ME, Tumiotto, C, Cazanave, C, Neau, D (B32) 2018; 104 Morjaria, S, Arguello, E, Taur, Y, Sepkowitz, K, Hatzoglou, V, Nemade, A, Rosenblum, M, Cavalcanti, MS, Palomba, ML, Kaltsas, A (B43) 2015; 2 Morgulis, A, Coulouris, G, Raytselis, Y, Madden, TL, Agarwala, R, Schäffer, AA (B56) 2008; 24 Dunn, BE, Monson, TP, Dumler, JS, Morris, CC, Westbrook, AB, Duncan, JL, Dawson, JE, Sims, KG, Anderson, BE (B40) 1992; 30 Vora, NM, Holman, RC, Mehal, JM, Steiner, CA, Blanton, J, Sejvar, J (B25) 2014; 82 (B1) 2019; 18 Hogan, CA, Yang, S, Garner, OB, Green, DA, Gomez, CA, Dien Bard, J, Pinsky, BA, Banaei, N (B47) 2021; 72 Chiu, CY, Miller, SA (B9) 2019; 20 Thoendel, M, Jeraldo, PR, Greenwood-Quaintance, KE, Yao, JZ, Chia, N, Hanssen, AD, Abdel, MP, Patel, R (B33) 2016; 127 Wilson, MR, Zimmermann, LL, Crawford, ED, Sample, HA, Soni, PR, Baker, AN, Khan, LM, DeRisi, JL (B15) 2017; 17 Wilson, MR, Sample, HA, Zorn, KC, Arevalo, S, Yu, G, Neuhaus, J, Federman, S, Stryke, D, Briggs, B, Langelier, C, Berger, A, Douglas, V, Josephson, SA, Chow, FC, Fulton, BD, DeRisi, JL, Gelfand, JM, Naccache, SN, Bender, J, Dien Bard, J, Murkey, J, Carlson, M, Vespa, PM, Vijayan, T, Allyn, PR, Campeau, S, Humphries, RM, Klausner, JD, Ganzon, CD, Memar, F, Ocampo, NA, Zimmermann, LL, Cohen, SH, Polage, CR, DeBiasi, RL, Haller, B, Dallas, R, Maron, G, Hayden, R, Messacar, K, Dominguez, SR, Miller, S, Chiu, CY (B18) 2019; 380 Torres, SD, Jia, DT, Schorr, EM, Park, BL, Boubour, A, Boehme, A, Ankam, JV, Gofshteyn, JS, Tyshkov, C, Green, DA, Vargas, W, Zucker, J, Yeshokumar, AK, Thakur, KT (B45) 2020; 26 Gu, W, Miller, S, Chiu, CY (B8) 2019; 14 Mongkolrattanothai, K, Naccache, SN, Bender, JM, Samayoa, E, Pham, E, Yu, G, Dien Bard, J, Miller, S, Aldrovandi, G, Chiu, CY (B11) 2017; 6 Lyons, JL, Schaefer, PW, Cho, TA, Azar, MM (B41) 2017; 377 Glaser, CA, Honarmand, S, Anderson, LJ, Schnurr, DP, Forghani, B, Cossen, CK, Schuster, FL, Christie, LJ, Tureen, JH (B4) 2006; 43 Huang, C, Slater, B, Rudd, R, Parchuri, N, Hull, R, Dupuis, M, Hindenburg, A (B42) 2002; 8 Gire, SK, Goba, A, Andersen, KG, Sealfon, RSG, Park, DJ, Kanneh, L, Jalloh, S, Momoh, M, Fullah, M, Dudas, G, Wohl, S, Moses, LM, Yozwiak, NL, Winnicki, S, Matranga, CB, Malboeuf, CM, Qu, J, Gladden, AD, Schaffner, SF, Yang, X, Jiang, P-P, Nekoui, M, Colubri, A, Coomber, MR, Fonnie, M, Moigboi, A, Gbakie, M, Kamara, FK, Tucker, V, Konuwa, E, Saffa, S, Sellu, J, Jalloh, AA, Kovoma, A, Koninga, J, Mustapha, I, Kargbo, K, Foday, M, Yillah, M, Kanneh, F, Robert, W, Massally, JLB, Chapman, SB, Bochicchio, J, Murphy, C, Nusbaum, C, Young, S, Birren, BW, Grant, DS, Scheiffelin, JS, Lander, ES, Happi, C, Gevao, SM, Gnirke, A, Rambaut, A, Garry, RF, Khan, SH, Sabeti, PC (B49) 2014; 345 Haston, JC, Rostad, CA, Jerris, RC, Milla, SS, McCracken, C, Pratt, C, Wiley, M, Prieto, K, Palacios, G, Shane, AL, McElroy, AK (B19) 2020; 9 Quist-Paulsen, E, Ormaasen, V, Kran, A-MB, Dunlop, O, Ueland, PM, Ueland, T, Eikeland, R, Aukrust, P, Nordenmark, TH (B3) 2019; 9 McGill, F, Griffiths, MJ, Bonnett, LJ, Geretti, AM, Michael, BD, Beeching, NJ, McKee, D, Scarlett, P, Hart, IJ, Mutton, KJ, Jung, A, Adan, G, Gummery, A, Sulaiman, WAW, Ennis, K, Martin, AP, Haycox, A, Miller, A, Solomon, T (B2) 2018; 18 Glaser, CA, Gilliam, S, Schnurr, D, Forghani, B, Honarmand, S, Khetsuriani, N, Fischer, M, Cossen, CK, Anderson, LJ (B24) 2003; 36 Matranga, CB, Andersen, KG, Winnicki, S, Busby, M, Gladden, AD, Tewhey, R, Stremlau, M, Berlin, A, Gire, SK, England, E, Moses, LM, Mikkelsen, TS, Odia, I, Ehiane, PE, Folarin, O, Goba, A, Kahn, SH, Grant, DS, Honko, A, Hensley, L, Happi, C, Garry, RF, Malboeuf, CM, Birren, BW, Gnirke, A, Levin, JZ, Sabeti, PC (B50) 2014; 15 Piantadosi, A, Kanjilal, S, Ganesh, V, Khanna, A, Hyle, EP, Rosand, J, Bold, T, Metsky, HC, Lemieux, J, Leone, MJ, Freimark, L, Matranga, CB, Adams, G, McGrath, G, Zamirpour, S, Telford, S, Rosenberg, E, Cho, T, Frosch, MP, Goldberg, MB, Mukerji, SS, Sabeti, PC (B17) 2018; 66 Greninger, AL (B46) 2018; 18 Brown, JR, Bharucha, T, Breuer, J (B20) 2018; 76 Nesher, L, Hadi, CM, Salazar, L, Wootton, SH, Garey, KW, Lasco, T, Luce, AM, Hasbun, R (B6) 2016; 144 Wilson, MR, Naccache, SN, Samayoa, E, Biagtan, M, Bashir, H, Yu, G, Salamat, SM, Somasekar, S, Federman, S, Miller, S, Sokolic, R, Garabedian, E, Candotti, F, Buckley, RH, Reed, KD, Meyer, TL, Seroogy, CM, Galloway, R, Henderson, SL, Gern, JE, DeRisi, JL, Chiu, CY (B10) 2014; 370 Schlaberg, R, Chiu, CY, Miller, S, Procop, GW, Weinstock, G (B21) 2017; 141 Nurk, S, Meleshko, D, Korobeynikov, A, Pevzner, PA (B54) 2017; 27 Breitwieser, FP, Baker, DN, Salzberg, SL (B53) 2018; 19 Blauwkamp, TA, Thair, S, Rosen, MJ, Blair, L, Lindner, MS, Vilfan, ID, Kawli, T, Christians, FC, Venkatasubrahmanyam, S, Wall, GD, Cheung, A, Rogers, ZN, Meshulam-Simon, G, Huijse, L, Balakrishnan, S, Quinn, JV, Hollemon, D, Hong, DK, Vaughn, ML, Kertesz, M, Bercovici, S, Wilber, JC, Yang, S (B22) 2019; 4 Rosenberg, R, Lindsey, NP, Fischer, M, Gregory, CJ, Hinckley, AF, Mead, PS, Paz-Bailey, G, Waterman, SH, Drexler, NA, Kersh, GJ, Hooks, H, Partridge, SK, Visser, SN, Beard, CB, Petersen, LR (B37) 2018; 67 Levi, ME, Quan, D, Ho, JT, Kleinschmidt-Demasters, BK, Tyler, KL, Grazia, TJ (B44) 2010; 24 Murkey, JA, Chew, KW, Carlson, M, Shannon, CL, Sirohi, D, Sample, HA, Wilson, MR, Vespa, P, Humphries, RM, Miller, S, Klausner, JD, Chiu, CY (B16) 2017; 4 Hasan, MR, Rawat, A, Tang, P, Jithesh, PV, Thomas, E, Tan, R, Tilley, P (B35) 2016; 54 Dahlgren, FS, Mandel, EJ, Krebs, JW, Massung, RF, McQuiston, JH (B39) 2011; 85 Simner, PJ, Miller, S, Carroll, KC (B7) 2018; 66 Christopeit, M, Grundhoff, A, Rohde, H, Belmar-Campos, C, Grzyska, U, Fiehler, J, Wolschke, C, Ayuk, F, Kröger, N, Fischer, N (B13) 2016; 95 Fan, S, Ren, H, Wei, Y, Mao, C, Ma, Z, Zhang, L, Wang, L, Ge, Y, Li, T, Cui, L, Wu, H, Guan, H (B12) 2018; 67 Metsky, HC, Siddle, KJ, Gladden-Young, A, Qu, J, Yang, DK, Brehio, P, Goldfarb, A, Piantadosi, A, Wohl, S, Carter, A, Lin, AE, Barnes, KG, Tully, DC, Corleis, B, Hennigan, S, Barbosa-Lima, G, Vieira, YR, Paul, LM, Tan, AL, Garcia, KF, Parham, LA, Odia, I, Eromon, P, Folarin, OA, Goba, A, Simon-Lorière, E, Hensley, L, Balmaseda, A, Harris, E, Kwon, DS, Allen, TM, Runstadler, JA, Smole, S, Bozza, FA, Souza, TML, Isern, S, Michael, SF, Lorenzana, I, Gehrke, L, Bosch, I, Ebel, G, Grant, DS, Happi, CT, Park, DJ, Gnirke, A, Sabeti, PC, Matranga, CB (B51) 2019; 37 Wilson, MR, Shanbhag, NM, Reid, MJ, Singhal, NS, Gelfand, JM, Sample, HA, Benkli, B, O’Donovan, BD, Ali, IKM, Keating, MK, Dunnebacke, TH, Wood, MD, Bollen, A, DeRisi, JL (B14) 2015; 78 Tomkins-Tinch, C, Park, DJ, Ye, S (B57) 2016 Bennett, JE, Dolin, R, Blaser, MJ (B38) 2014 Bolger, AM, Lohse, M, Usadel, B (B52) 2014; 30 Parra, M, Alcala, A, Amoros, C, Baeza, A, Galiana, A, Tarragó, D, García-Quesada, MÁ, Sánchez-Hellín, V (B29) 2017; 14 Gilden, DH, Mahalingam, R, Cohrs, RJ, Tyler, KL (B26) 2007; 3 Simner, PJ, Miller, HB, Breitwieser, FP, Pinilla Monsalve, G, Pardo, CA, Salzberg, SL, Sears, CL, Thomas, DL, Eberhart, CG, Carroll, KC (B34) 2018; 56 Shi, M, Lin, X-D, Tian, J-H, Chen, L-J, Chen, X, Li, C-X, Qin, X-C, Li, J, Cao, J-P, Eden, J-S, Buchmann, J, Wang, W, Xu, J, Holmes, EC, Zhang, Y-Z (B31) 2016; 540 |
| References_xml | – ident: e_1_3_2_13_2 doi: 10.1016/j.ijid.2017.11.028 – ident: e_1_3_2_6_2 doi: 10.1212/01.wnl.0000191407.81333.00 – ident: e_1_3_2_55_2 doi: 10.1101/gr.213959.116 – ident: e_1_3_2_4_2 doi: 10.1038/s41598-019-52570-2 – ident: e_1_3_2_14_2 doi: 10.1007/s00277-016-2770-3 – ident: e_1_3_2_45_2 doi: 10.1111/j.1399-0012.2009.01044.x – ident: e_1_3_2_24_2 doi: 10.1101/gr.238170.118 – ident: e_1_3_2_29_2 doi: 10.1007/s15010-017-1014-3 – ident: e_1_3_2_5_2 doi: 10.1086/509330 – ident: e_1_3_2_11_2 doi: 10.1056/NEJMoa1401268 – ident: e_1_3_2_20_2 doi: 10.1093/jpids/piz032 – ident: e_1_3_2_31_2 doi: 10.1016/j.cmi.2019.04.028 – ident: e_1_3_2_56_2 doi: 10.1016/S0022-2836(05)80360-2 – ident: e_1_3_2_33_2 doi: 10.1016/j.jcv.2018.04.017 – ident: e_1_3_2_48_2 doi: 10.1093/cid/ciaa035 – ident: e_1_3_2_54_2 doi: 10.1186/s13059-018-1568-0 – ident: e_1_3_2_53_2 doi: 10.1093/bioinformatics/btu170 – ident: e_1_3_2_12_2 doi: 10.1093/jpids/piw066 – ident: e_1_3_2_16_2 doi: 10.1111/ajt.14058 – ident: e_1_3_2_57_2 doi: 10.1093/bioinformatics/btn322 – ident: e_1_3_2_26_2 doi: 10.1212/WNL.0000000000000086 – ident: e_1_3_2_18_2 doi: 10.1093/cid/cix792 – ident: e_1_3_2_59_2 doi: 10.1038/ncomms11257 – volume-title: Mandell, Douglas, and Bennett’s principles and practice of infectious diseases year: 2014 ident: e_1_3_2_39_2 – ident: e_1_3_2_19_2 doi: 10.1056/NEJMoa1803396 – ident: e_1_3_2_51_2 doi: 10.1186/s13059-014-0519-7 – ident: e_1_3_2_38_2 doi: 10.15585/mmwr.mm6717e1 – ident: e_1_3_2_32_2 doi: 10.1038/nature20167 – ident: e_1_3_2_58_2 – ident: e_1_3_2_42_2 doi: 10.1056/NEJMcpc1707557 – ident: e_1_3_2_22_2 doi: 10.5858/arpa.2016-0539-RA – ident: e_1_3_2_23_2 doi: 10.1038/s41564-018-0349-6 – ident: e_1_3_2_2_2 doi: 10.1016/S1474-4422(18)30499-X – ident: e_1_3_2_25_2 doi: 10.1086/367841 – ident: e_1_3_2_30_2 doi: 10.1186/s12985-017-0764-y – ident: e_1_3_2_34_2 doi: 10.1016/j.mimet.2016.05.022 – ident: e_1_3_2_28_2 doi: 10.2169/internalmedicine.56.8185 – ident: e_1_3_2_52_2 doi: 10.1038/s41587-018-0006-x – ident: e_1_3_2_9_2 doi: 10.1146/annurev-pathmechdis-012418-012751 – ident: e_1_3_2_7_2 doi: 10.1017/S0950268815000850 – ident: e_1_3_2_35_2 doi: 10.1128/JCM.00472-18 – ident: e_1_3_2_15_2 doi: 10.1002/ana.24499 – ident: e_1_3_2_41_2 doi: 10.1128/jcm.30.8.2207-2210.1992 – ident: e_1_3_2_43_2 doi: 10.3201/eid0812.020532 – ident: e_1_3_2_21_2 doi: 10.1016/j.jinf.2017.12.014 – ident: e_1_3_2_3_2 doi: 10.1016/S1473-3099(18)30245-7 – ident: e_1_3_2_46_2 doi: 10.1007/s13365-019-00784-5 – ident: e_1_3_2_36_2 doi: 10.1128/JCM.03050-15 – ident: e_1_3_2_50_2 doi: 10.1126/science.1259657 – ident: e_1_3_2_8_2 doi: 10.1093/cid/cix881 – ident: e_1_3_2_44_2 doi: 10.1093/ofid/ofv136 – ident: e_1_3_2_17_2 doi: 10.1093/ofid/ofx121 – ident: e_1_3_2_27_2 doi: 10.1038/ncpneuro0401 – ident: e_1_3_2_40_2 doi: 10.4269/ajtmh.2011.10-0613 – volume-title: DNA sequence library for external RNA controls year: 2017 ident: e_1_3_2_49_2 – ident: e_1_3_2_37_2 doi: 10.1038/s41587-019-0156-5 – ident: e_1_3_2_47_2 doi: 10.1080/14737159.2018.1487292 – ident: e_1_3_2_10_2 doi: 10.1038/s41576-019-0113-7 – volume: 66 start-page: 75 year: 2006 end-page: 80 ident: B5 article-title: Etiology of aseptic meningitis and encephalitis in an adult population publication-title: Neurology doi: 10.1212/01.wnl.0000191407.81333.00 – volume: 345 start-page: 1369 year: 2014 end-page: 1372 ident: B49 article-title: Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak publication-title: Science doi: 10.1126/science.1259657 – year: 2017 ident: B48 publication-title: DNA sequence library for external RNA controls ;National Institute of Standards and Technology ;Gaithersburg, MD – volume: 24 start-page: 1757 year: 2008 end-page: 1764 ident: B56 article-title: Database indexing for production MegaBLAST searches publication-title: Bioinformatics doi: 10.1093/bioinformatics/btn322 – volume: 37 start-page: 783 year: 2019 end-page: 792 ident: B36 article-title: Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection publication-title: Nat Biotechnol doi: 10.1038/s41587-019-0156-5 – volume: 72 start-page: 239 year: 2021 end-page: 245 ident: B47 article-title: Clinical impact of metagenomic next-generation sequencing of plasma cell-free DNA for the diagnosis of infectious diseases: a multicenter retrospective cohort study publication-title: Clin Infect Dis doi: 10.1093/cid/ciaa035 – volume: 4 start-page: ofx121 year: 2017 ident: B16 article-title: Hepatitis E virus-associated meningoencephalitis in a lung transplant recipient diagnosed by clinical metagenomic sequencing publication-title: Open Forum Infect Dis doi: 10.1093/ofid/ofx121 – volume: 141 start-page: 776 year: 2017 end-page: 786 ident: B21 article-title: Validation of metagenomic next-generation sequencing tests for universal pathogen detection publication-title: Arch Pathol Lab Med doi: 10.5858/arpa.2016-0539-RA – volume: 37 start-page: 160 year: 2019 end-page: 168 ident: B51 article-title: Capturing sequence diversity in metagenomes with comprehensive and scalable probe design publication-title: Nat Biotechnol doi: 10.1038/s41587-018-0006-x – volume: 2 start-page: ofv136 year: 2015 ident: B43 article-title: West Nile virus central nervous system infection in patients treated with rituximab: implications for diagnosis and prognosis, with a review of literature publication-title: Open Forum Infect Dis doi: 10.1093/ofid/ofv136 – volume: 370 start-page: 2408 year: 2014 end-page: 2417 ident: B10 article-title: Actionable diagnosis of neuroleptospirosis by next-generation sequencing publication-title: N Engl J Med doi: 10.1056/NEJMoa1401268 – volume: 377 start-page: 1878 year: 2017 end-page: 1886 ident: B41 article-title: Case 34-2017. A 76-year-old man with fever, weight loss, and weakness publication-title: N Engl J Med doi: 10.1056/NEJMcpc1707557 – volume: 14 start-page: 97 year: 2017 ident: B29 article-title: Encephalitis associated with human herpesvirus-7 infection in an immunocompetent adult publication-title: Virol J doi: 10.1186/s12985-017-0764-y – volume: 54 start-page: 919 year: 2016 end-page: 927 ident: B35 article-title: Depletion of human DNA in spiked clinical specimens for improvement of sensitivity of pathogen detection by next-generation sequencing publication-title: J Clin Microbiol doi: 10.1128/JCM.03050-15 – volume: 8 start-page: 1367 year: 2002 end-page: 1371 ident: B42 article-title: First isolation of West Nile virus from a patient with encephalitis in the United States publication-title: Emerg Infect Dis doi: 10.3201/eid0812.020532 – volume: 36 start-page: 731 year: 2003 end-page: 742 ident: B24 article-title: In search of encephalitis etiologies: diagnostic challenges in the California Encephalitis Project, 1998-2000 publication-title: Clin Infect Dis doi: 10.1086/367841 – volume: 4 start-page: 663 year: 2019 end-page: 674 ident: B22 article-title: Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease publication-title: Nat Microbiol doi: 10.1038/s41564-018-0349-6 – volume: 67 start-page: 496 year: 2018 end-page: 501 ident: B37 article-title: Vital signs: trends in reported vectorborne disease cases—United States and territories, 2004-2016 publication-title: MMWR Morb Mortal Wkly Rep doi: 10.15585/mmwr.mm6717e1 – volume: 127 start-page: 141 year: 2016 end-page: 145 ident: B33 article-title: Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing publication-title: J Microbiol Methods doi: 10.1016/j.mimet.2016.05.022 – volume: 3 start-page: 82 year: 2007 end-page: 94 ident: B26 article-title: Herpesvirus infections of the nervous system publication-title: Nat Clin Pract Neurol doi: 10.1038/ncpneuro0401 – volume: 144 start-page: 189 year: 2016 end-page: 197 ident: B6 article-title: Epidemiology of meningitis with a negative CSF gram stain: under-utilization of available diagnostic tests publication-title: Epidemiol Infect doi: 10.1017/S0950268815000850 – volume: 30 start-page: 2114 year: 2014 end-page: 2120 ident: B52 article-title: Trimmomatic: a flexible trimmer for Illumina sequence data publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu170 – volume: 56 year: 2018 ident: B34 article-title: Development and optimization of metagenomic next-generation sequencing methods for cerebrospinal fluid diagnostics publication-title: J Clin Microbiol doi: 10.1128/JCM.00472-18 – volume: 9 start-page: 326 year: 2020 end-page: 333 ident: B19 article-title: Prospective cohort study of next-generation sequencing as a diagnostic modality for unexplained encephalitis in children publication-title: J Pediatric Infect Dis Soc doi: 10.1093/jpids/piz032 – volume: 215 start-page: 403 year: 1990 end-page: 410 ident: B55 article-title: Basic local alignment search tool publication-title: J Mol Biol doi: 10.1016/S0022-2836(05)80360-2 – volume: 380 start-page: 2327 year: 2019 end-page: 2340 ident: B18 article-title: Clinical metagenomic sequencing for diagnosis of meningitis and encephalitis publication-title: N Engl J Med doi: 10.1056/NEJMoa1803396 – volume: 15 start-page: 519 year: 2014 ident: B50 article-title: Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples publication-title: Genome Biol doi: 10.1186/s13059-014-0519-7 – year: 2016 ident: B57 publication-title: et al viral-ngs v1.25.0. https://github.com/broadinstitute/viral-ngs/releases/tag/v1.25.0 – volume: 540 start-page: 539 year: 2016 end-page: 543 ident: B31 article-title: Redefining the invertebrate RNA virosphere publication-title: Nature doi: 10.1038/nature20167 – year: 2014 ident: B38 publication-title: Mandell, Douglas, and Bennett’s principles and practice of infectious diseases ;8th ed ;Elsevier Health Sciences ;Philadelphia, PA – volume: 66 start-page: 778 year: 2018 end-page: 788 ident: B7 article-title: Understanding the promises and hurdles of metagenomic next-generation sequencing as a diagnostic tool for infectious diseases publication-title: Clin Infect Dis doi: 10.1093/cid/cix881 – volume: 85 start-page: 124 year: 2011 end-page: 131 ident: B39 article-title: Increasing incidence of Ehrlichia chaffeensis and Anaplasma phagocytophilum in the United States, 2000-2007 publication-title: Am J Trop Med Hyg doi: 10.4269/ajtmh.2011.10-0613 – volume: 18 start-page: 459 year: 2019 end-page: 480 ident: B1 article-title: Global, regional, and national burden of neurological disorders, 1990–2016: a systematic analysis for the Global Burden of Disease Study 2016 publication-title: Lancet Neurol doi: 10.1016/S1474-4422(18)30499-X – volume: 66 start-page: 789 year: 2018 end-page: 792 ident: B17 article-title: Rapid detection of Powassan virus in a patient with encephalitis by metagenomic sequencing publication-title: Clin Infect Dis doi: 10.1093/cid/cix792 – volume: 27 start-page: 824 year: 2017 end-page: 834 ident: B54 article-title: metaSPAdes: a new versatile metagenomic assembler publication-title: Genome Res doi: 10.1101/gr.213959.116 – volume: 95 start-page: 1919 year: 2016 end-page: 1921 ident: B13 article-title: Suspected encephalitis with Candida tropicalis and Fusarium detected by unbiased RNA sequencing publication-title: Ann Hematol doi: 10.1007/s00277-016-2770-3 – volume: 67 start-page: 20 year: 2018 end-page: 24 ident: B12 article-title: Next-generation sequencing of the cerebrospinal fluid in the diagnosis of neurobrucellosis publication-title: Int J Infect Dis doi: 10.1016/j.ijid.2017.11.028 – volume: 17 start-page: 803 year: 2017 end-page: 808 ident: B15 article-title: Acute West Nile virus meningoencephalitis diagnosed via metagenomic deep sequencing of cerebrospinal fluid in a renal transplant patient publication-title: Am J Transplant doi: 10.1111/ajt.14058 – volume: 14 start-page: 319 year: 2019 end-page: 338 ident: B8 article-title: Clinical metagenomic next-generation sequencing for pathogen detection publication-title: Annu Rev Pathol doi: 10.1146/annurev-pathmechdis-012418-012751 – volume: 9 start-page: 16158 year: 2019 ident: B3 article-title: Encephalitis and aseptic meningitis: short-term and long-term outcome, quality of life and neuropsychological functioning publication-title: Sci Rep doi: 10.1038/s41598-019-52570-2 – volume: 76 start-page: 225 year: 2018 end-page: 240 ident: B20 article-title: Encephalitis diagnosis using metagenomics: application of next generation sequencing for undiagnosed cases publication-title: J Infect doi: 10.1016/j.jinf.2017.12.014 – volume: 82 start-page: 443 year: 2014 end-page: 451 ident: B25 article-title: Burden of encephalitis-associated hospitalizations in the United States, 1998–2010 publication-title: Neurology doi: 10.1212/WNL.0000000000000086 – volume: 104 start-page: 56 year: 2018 end-page: 60 ident: B32 article-title: Clinical and biological features of enteroviral meningitis among adults and children and factors associated with severity and length of stay publication-title: J Clin Virol doi: 10.1016/j.jcv.2018.04.017 – volume: 18 start-page: 605 year: 2018 end-page: 615 ident: B46 article-title: The challenge of diagnostic metagenomics publication-title: Expert Rev Mol Diagn doi: 10.1080/14737159.2018.1487292 – volume: 43 start-page: 1565 year: 2006 end-page: 1577 ident: B4 article-title: Beyond viruses: clinical profiles and etiologies associated with encephalitis publication-title: Clin Infect Dis doi: 10.1086/509330 – volume: 78 start-page: 722 year: 2015 end-page: 730 ident: B14 article-title: Diagnosing Balamuthia mandrillaris encephalitis with metagenomic deep sequencing publication-title: Ann Neurol doi: 10.1002/ana.24499 – volume: 26 start-page: 14 year: 2020 end-page: 22 ident: B45 article-title: Central nervous system (CNS) enterovirus infections: a single center retrospective study on clinical features, diagnostic studies, and outcome publication-title: J Neurovirol doi: 10.1007/s13365-019-00784-5 – volume: 29 start-page: 831 year: 2019 end-page: 842 ident: B23 article-title: Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid publication-title: Genome Res doi: 10.1101/gr.238170.118 – volume: 56 start-page: 1919 year: 2017 end-page: 1923 ident: B27 article-title: Limbic encephalitis associated with human herpesvirus-7 (HHV-7) in an immunocompetent adult: the first reported case in Japan publication-title: Intern Med doi: 10.2169/internalmedicine.56.8185 – volume: 45 start-page: 385 year: 2017 end-page: 388 ident: B28 article-title: Acute human herpes virus 7 (HHV-7) encephalitis in an immunocompetent adult patient: a case report and review of literature publication-title: Infection doi: 10.1007/s15010-017-1014-3 – volume: 25 start-page: 1277 year: 2019 end-page: 1285 ident: B30 article-title: Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries publication-title: Clin Microbiol Infect doi: 10.1016/j.cmi.2019.04.028 – volume: 7 start-page: 11257 year: 2016 ident: B58 article-title: Fast and sensitive taxonomic classification for metagenomics with Kaiju publication-title: Nat Commun – volume: 20 start-page: 341 year: 2019 end-page: 355 ident: B9 article-title: Clinical metagenomics publication-title: Nat Rev Genet doi: 10.1038/s41576-019-0113-7 – volume: 18 start-page: 992 year: 2018 end-page: 1003 ident: B2 article-title: Incidence, aetiology, and sequelae of viral meningitis in UK adults: a multicentre prospective observational cohort study publication-title: Lancet Infect Dis doi: 10.1016/S1473-3099(18)30245-7 – volume: 19 start-page: 198 year: 2018 ident: B53 article-title: KrakenUniq: confident and fast metagenomics classification using unique k-mer counts publication-title: Genome Biol doi: 10.1186/s13059-018-1568-0 – volume: 30 start-page: 2207 year: 1992 end-page: 2210 ident: B40 article-title: Identification of Ehrlichia chaffeensis morulae in cerebrospinal fluid mononuclear cells publication-title: J Clin Microbiol doi: 10.1128/jcm.30.8.2207-2210.1992 – volume: 6 start-page: 393 year: 2017 end-page: 398 ident: B11 article-title: Neurobrucellosis: unexpected answer from metagenomic next-generation sequencing publication-title: J Pediatric Infect Dis Soc doi: 10.1093/jpids/piw066 – volume: 24 start-page: 223 year: 2010 end-page: 228 ident: B44 article-title: Impact of rituximab-associated B-cell defects on West Nile virus meningoencephalitis in solid organ transplant recipients publication-title: Clin Transplant doi: 10.1111/j.1399-0012.2009.01044.x |
| SSID | ssj0000331830 |
| Score | 2.547233 |
| Snippet | Meningitis and encephalitis are leading global causes of central nervous system (CNS) disability and mortality. Current diagnostic workflows remain... Meningitis and encephalitis are leading causes of central nervous system (CNS) disease and often result in severe neurological compromise or death. Traditional... ABSTRACT Meningitis and encephalitis are leading causes of central nervous system (CNS) disease and often result in severe neurological compromise or death.... |
| SourceID | doaj pubmedcentral proquest asm2 pubmed crossref |
| SourceType | Open Website Open Access Repository Aggregation Database Index Database Enrichment Source |
| StartPage | e0114321 |
| SubjectTerms | Adult Aged Central Nervous System Viral Diseases - cerebrospinal fluid Central Nervous System Viral Diseases - diagnosis Central Nervous System Viral Diseases - virology encephalitis Encephalitis - cerebrospinal fluid Encephalitis - diagnosis Encephalitis - virology Female High-Throughput Nucleotide Sequencing - methods Humans hybrid capture Male meningitis Meningitis - cerebrospinal fluid Meningitis - diagnosis Meningitis - virology Metagenome metagenomic sequencing Metagenomics - methods Middle Aged next-generation sequencing (NGS) Prospective Studies Research Article Virology virus Viruses - classification Viruses - genetics Viruses - isolation & purification Viruses - pathogenicity |
| SummonAdditionalLinks | – databaseName: American Society for Microbiology Open Access dbid: AAUOK link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwjV1Zi9RAEG6WXQRfxNt40aL4ZNakj3TyOKuzLMqqoCP7FvtkAk5GNpkH_71VnQNnccHXTnUSvq7qqj7qK0JeOQFrDKNNmvsipOAhQqpdHlLHpClYCNwITHA-_1ScrcSHC3lxQNiUCzMi2B3rbhMP8mfLZuXbzUmzPcYInqeYO34kWSXAGI8Wi9Xnj_POSsZRT7OJUPNqP5h74d1szw9Fuv5_xZhXr0r-5XtOb5NbY9BIF8Mo3yEHvr1LbgxlJH_fIz-W7Toe5NPvzeWuo-99Hy9YtVS3jp77XiMT66ax9OtwcRrcFW1a-mXgVO0obsaC3FC8qOlityWmM64xSm-6-2R1uvz27iwdKyekGgyyT7VRzgluSmdzqZT1SgWlWVZhS6kBCA7I-cCU87mxipeZMDrzvgJvLoPlD8hhu239I0JFxbUrTGHAsQsL8aS0oULGFulZWWqdkJcIZz0NXB1XFaysEfQ6gl6zPCFvJrRrO5KPYw2Mn9eJv57Ffw2sG9cJnuDQzUJIlh0bQHXq0fZqmJVcjrz5vrBCuswUMkjNAZgiGCdsQl5MA1-DceGJiW79dtdBzwJW0EiLl5CHgyLMn-JINQcRT0LUnors_cv-k7ZZRwJvWFRD1Jk__i_onpCbDO_RxH3sp-Swv9z5ZxAI9eb5qPl_ANYUBdc priority: 102 providerName: American Society for Microbiology – databaseName: DOAJ Directory of Open Access Journals dbid: DOA link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV1LixQxEA4yIHgRdX20jyWieLLd6by657jrzrIIK4Ku7C3myTTs9Mh2z8F_b1XSM8yIixev6QodvlRSVUnlK0LeegExhjW2rIKKJViIWBpfxdIzaRWLkVuBD5wvPqvzS_HpSl7tlPrCnLBMD5yBOwKV8hWSngflhPRTq2SUhsu6VtF64XD3BZu3E0ylPZijrk43pJqsOVqetKsP6P3zEnlBJ6Zfsj1blCj7_-Zn_pkuuWN_zh6Q-6PjSI_zgB-SO6F7RO7mUpK_DsiPebdIl_n0e3uz7ulpGFKSVUdN5-lFGAyysS5bR7_m5GkwWbTt6JfMq9pTPJAFuVzAqO1Ttzk-aVygp972j8nl2fzbx_NyrJ5QGliUQ2ls7b3gtvGuArRcqOtYG8AKWxoDQPCZqEJktQ-VdTVvpsKaaQgzsOgyOv6ETLpVF54RKmbceGWVBeMuHPiU0sUZsrbIwJrGmIK8QTj1qP69TpEFazSCrhPomlUFeb9BW7uRgBzrYFzfJv5uK_4zM2_cJniCU7cVQsLs1ABqpEc10v9So4K83ky8hgWGtyamC6t1Dz0VRNFIjVeQp1kRtr_iSDcHXk9B6j0V2RvL_peuXSQSbwiswfOsnv-Pwb8g9xim2qSj7pdkMtyswyvwlQZ7mJbFbxVIEho priority: 102 providerName: Directory of Open Access Journals |
| Title | Enhanced Virus Detection and Metagenomic Sequencing in Patients with Meningitis and Encephalitis |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/34465023 https://journals.asm.org/doi/10.1128/mBio.01143-21 https://www.proquest.com/docview/2568250119 https://pubmed.ncbi.nlm.nih.gov/PMC8406231 https://doaj.org/article/257d13788e6c45d0b65f5a35776fbd4c |
| Volume | 12 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwjV1Lb9NAEF6hVkhcEOVpKNEiECdcbO_aax8QStuUChRAgqDczD6JpcZpY0ei_56ZtRNI1UpcfFjP-jG7s_PNPr4h5JXhEGMoqcLYZi4ED-FCaWIXmiRVWeIcUxwPOI8_Z6cT_nGaTv9SCvUKbK4N7TCf1GR5dvD74vI9GPy77gBM_nZ-WC0OENizEI-U74JTEpjMYNwjfT8oM-y8OOMCPi4KBeCMNePm1SfA4CybebLlqDyf_3Ug9Opeyn-c08k9crdHlXTYdYM9csvW98ntLs_k5QPyc1TP_Eo__VEtVw09tq3fgVVTWRs6tq1EqtZ5pem3bmc1-DNa1fRrR7raUJytBbkuu1HV-GojPO84QxhfNQ_J5GT0_eg07FMrhBIstg2lEsZwpnKj41QIbYVwQiZRgSW5BEWwgsfWJcLYWGnB8ogrGVlbgLtPnWaPyE69qO0TQnnBpMlUpsDzcw2AM9WuQEqX1CZ5LmVAXqI6y3XTlj7sSPISlV56pZdJHJA3a22XumcnxyQZZzeJv96In3e0HDcJHmLTbYSQTdsXLJa_yt44Sxi2TIzE-jbTPDWRylKXSgaKyZwyXAfkxbrhS7A-XFKRtV2sGqiZQYiNvHkBedx1hM2rGHLRASQKiNjqIlvfsn2nrmae4RuiboCl8dP__ctn5E6Ce238XPc-2WmXK_scwFKrBmR3OJx8-TTwkw1w_TCNB940_gCwAxSx |
| linkProvider | Scholars Portal |
| linkToHtml | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwjV1Lb9QwELaqVgguiDehPIxAnEhJYsdJjlvYaqHdgkQX9Wb81AZ1s1WTPfDvmXGyK7aiEldnLEfjGc_Dnm8IeWs5xBha6Th1wsdgIXysbOpjm-VaZN4zzbHAeXoqJjP-5Tw_3yFiXQvzC_vyXrQHql2Ee3xUbExED_0Iyw-Lw3p5gF48i7F-fA_vDSHo2huNZl-PN9mVhKGsJmtQzevz4PyFBbItWxQg-__lZ15_LvmX_Tm6R-4OjiMd9Tt9n-y45gG51beS_P2Q_Bw383CZT3_UV6uWfnJdeGTVUNVYOnWdQjTWRW3o9_7xNJgsWjf0W4-r2lJMyAJd38CobsO0MZY0ztFTr9tHZHY0Pvs4iYfuCbECpexipQtrOdOlNWleFMYVhS9UllQ4UipgBKt46nxWWJdqU7Ay4VolzlVg0XNv2GOy2ywb95RQXjFlhRYajDs34FPmxleI2pK7rCyVisgbZKccxL-VIbLISolMl4HpMksj8n7NbWkGAHLsg3FxE_m7Dfllj7xxE-Ehbt2GCAGzwwDIjxz0T8LJZFPEznfC8NwmWuQ-VwwYI7y23ETk9XrjJSgY3pqoxi1XLcwUEEUjNF5EnvSCsFmKIdwceD0RKbZEZOtftr809TyAeENgDZ5n-uy_WPeK3J6cTU_kyefT431yJ8N3NSGv_Zzsdlcr9wIco06_HLTgD0imCjo |
| linkToPdf | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwjV1Lb9QwELaqrUBcEG_S8jACcSIliR0nOW7prgqlpRIs6s31UxuJzVZN9sC_Z8bJrtiKSlydcRJ94_GM7fE3hLyzHNYYWuk4dcLH4CF8rGzqY5vlWmTeM83xgvPpmTie8S8X-cUOEeu7MAOC7YFqF-EgHy37yvqhHmH5cXFYLw8wimcx3h_fDQdVI7I7Hs--nWx2VxKGYzVZk2re7AfzL7w_2_JFgbL_X3HmzXTJv_zP9AG5PwSOdNxr-iHZcc0jcqcvJfn7MbmcNPNwmE9_1terlh65LiRZNVQ1lp66TiEb66I29HufPA0ui9YNPe95VVuKG7Ig1xcwqtvQbYJXGucYqdftEzKbTn58Oo6H6gmxAqPsYqULaznTpTVpXhTGFYUvVJZU2FIqAIJVPHU-K6xLtSlYmXCtEucq8Oi5N-wpGTXLxj0nlFdMWaGFBufODcSUufEVsrbkLitLpSLyFuGUa-XJsLLISomgywC6zNKIfFijLc1AQI51MH7dJv5-I37VM2_cJniIqtsIIWF2aIDhIwf7kzAz2RS5850wPLeJFrnPFQNghNeWm4i8WStegoHhqYlq3HLVQk8Bq2ikxovIs34gbD7FkG4Oop6IFFtDZOtftp809TyQeMPCGiLPdO-_oHtN7p4fTeXXz2cn--Rehmk1YVv7BRl11yv3EuKiTr8ajOAPIZ4J1g |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Enhanced+Virus+Detection+and+Metagenomic+Sequencing+in+Patients+with+Meningitis+and+Encephalitis&rft.jtitle=mBio&rft.au=Piantadosi%2C+Anne&rft.au=Mukerji%2C+Shibani+S.&rft.au=Ye%2C+Simon&rft.au=Leone%2C+Michael+J.&rft.date=2021-08-31&rft.issn=2150-7511&rft.eissn=2150-7511&rft.volume=12&rft.issue=4&rft_id=info:doi/10.1128%2FmBio.01143-21&rft.externalDBID=n%2Fa&rft.externalDocID=10_1128_mBio_01143_21 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=2150-7511&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=2150-7511&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=2150-7511&client=summon |