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Items: 1 to 20 of 108

1.

Development and Optimization of Metagenomic Next-Generation Sequencing Methods for Cerebrospinal Fluid Diagnostics.

Simner PJ, Miller HB, Breitwieser FP, Pinilla Monsalve G, Pardo CA, Salzberg SL, Sears CL, Thomas DL, Eberhart CG, Carroll KC.

J Clin Microbiol. 2018 Aug 27;56(9). pii: e00472-18. doi: 10.1128/JCM.00472-18. Print 2018 Sep.

2.

Depletion of Human DNA in Spiked Clinical Specimens for Improvement of Sensitivity of Pathogen Detection by Next-Generation Sequencing.

Hasan MR, Rawat A, Tang P, Jithesh PV, Thomas E, Tan R, Tilley P.

J Clin Microbiol. 2016 Apr;54(4):919-27. doi: 10.1128/JCM.03050-15. Epub 2016 Jan 13.

3.

Quality control implementation for universal characterization of DNA and RNA viruses in clinical respiratory samples using single metagenomic next-generation sequencing workflow.

Bal A, Pichon M, Picard C, Casalegno JS, Valette M, Schuffenecker I, Billard L, Vallet S, Vilchez G, Cheynet V, Oriol G, Trouillet-Assant S, Gillet Y, Lina B, Brengel-Pesce K, Morfin F, Josset L.

BMC Infect Dis. 2018 Oct 29;18(1):537. doi: 10.1186/s12879-018-3446-5.

4.

Oxford Screening CSF and Respiratory samples ('OSCAR'): results of a pilot study to screen clinical samples from a diagnostic microbiology laboratory for viruses using Illumina next generation sequencing.

Sharp C, Golubchik T, Gregory WF, McNaughton AL, Gow N, Selvaratnam M, Mirea A, Foster D, Andersson M, Klenerman P, Jeffery K, Matthews PC.

BMC Res Notes. 2018 Feb 9;11(1):120. doi: 10.1186/s13104-018-3234-8.

5.

Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples.

Lewandowska DW, Zagordi O, Geissberger FD, Kufner V, Schmutz S, Böni J, Metzner KJ, Trkola A, Huber M.

Microbiome. 2017 Aug 8;5(1):94. doi: 10.1186/s40168-017-0317-z. Erratum in: Microbiome. 2017 Oct 12;5(1):137.

6.

Limited Correlation of Shotgun Metagenomics Following Host Depletion and Routine Diagnostics for Viruses and Bacteria in Low Concentrated Surrogate and Clinical Samples.

Oechslin CP, Lenz N, Liechti N, Ryter S, Agyeman P, Bruggmann R, Leib SL, Beuret CM.

Front Cell Infect Microbiol. 2018 Oct 23;8:375. doi: 10.3389/fcimb.2018.00375. eCollection 2018.

7.

Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis.

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.

N Engl J Med. 2019 Jun 13;380(24):2327-2340. doi: 10.1056/NEJMoa1803396.

8.

Prospective Cohort Study of Next-Generation Sequencing as a Diagnostic Modality for Unexplained Encephalitis in Children.

Haston JC, Rostad CA, Jerris RC, Milla SS, McCracken C, Pratt C, Wiley M, Prieto K, Palacios G, Shane AL, McElroy AK.

J Pediatric Infect Dis Soc. 2019 May 20. pii: piz032. doi: 10.1093/jpids/piz032. [Epub ahead of print]

PMID:
31107955
9.

The diagnostic value of metagenomic next-generation sequencing for identifying Streptococcus pneumoniae in paediatric bacterial meningitis.

Zhang XX, Guo LY, Liu LL, Shen A, Feng WY, Huang WH, Hu HL, Hu B, Guo X, Chen TM, Chen HY, Jiang YQ, Liu G.

BMC Infect Dis. 2019 Jun 4;19(1):495. doi: 10.1186/s12879-019-4132-y.

10.

Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid.

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.

Genome Res. 2019 May;29(5):831-842. doi: 10.1101/gr.238170.118. Epub 2019 Apr 16.

11.

The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies.

Brooks JP, Edwards DJ, Harwich MD Jr, Rivera MC, Fettweis JM, Serrano MG, Reris RA, Sheth NU, Huang B, Girerd P; Vaginal Microbiome Consortium, Strauss JF 3rd, Jefferson KK, Buck GA.

BMC Microbiol. 2015 Mar 21;15:66. doi: 10.1186/s12866-015-0351-6.

12.

Comparing Viral Metagenomic Extraction Methods.

Klenner J, Kohl C, Dabrowski PW, Nitsche A.

Curr Issues Mol Biol. 2017;24:59-70. doi: 10.21775/cimb.024.059. Epub 2017 Jul 6.

PMID:
28686568
13.

Chronic Meningitis Investigated via Metagenomic Next-Generation Sequencing.

Wilson MR, O'Donovan BD, Gelfand JM, Sample HA, Chow FC, Betjemann JP, Shah MP, Richie MB, Gorman MP, Hajj-Ali RA, Calabrese LH, Zorn KC, Chow ED, Greenlee JE, Blum JH, Green G, Khan LM, Banerji D, Langelier C, Bryson-Cahn C, Harrington W, Lingappa JR, Shanbhag NM, Green AJ, Brew BJ, Soldatos A, Strnad L, Doernberg SB, Jay CA, Douglas V, Josephson SA, DeRisi JL.

JAMA Neurol. 2018 Aug 1;75(8):947-955. doi: 10.1001/jamaneurol.2018.0463.

14.

Assessment of REPLI-g Multiple Displacement Whole Genome Amplification (WGA) Techniques for Metagenomic Applications.

Ahsanuddin S, Afshinnekoo E, Gandara J, Hakyemezoğlu M, Bezdan D, Minot S, Greenfield N, Mason CE.

J Biomol Tech. 2017 Apr;28(1):46-55. doi: 10.7171/jbt.17-2801-008. Epub 2017 Mar 21. Erratum in: J Biomol Tech. 2017 Jul;28(2):96.

15.

Detection of Pulmonary Infectious Pathogens From Lung Biopsy Tissues by Metagenomic Next-Generation Sequencing.

Li H, Gao H, Meng H, Wang Q, Li S, Chen H, Li Y, Wang H.

Front Cell Infect Microbiol. 2018 Jun 25;8:205. doi: 10.3389/fcimb.2018.00205. eCollection 2018.

16.

Viral Surveillance in Serum Samples From Patients With Acute Liver Failure By Metagenomic Next-Generation Sequencing.

Somasekar S, Lee D, Rule J, Naccache SN, Stone M, Busch MP, Sanders C, Lee WM, Chiu CY.

Clin Infect Dis. 2017 Oct 16;65(9):1477-1485. doi: 10.1093/cid/cix596.

17.

Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection.

Schlaberg R, Chiu CY, Miller S, Procop GW, Weinstock G; Professional Practice Committee and Committee on Laboratory Practices of the American Society for Microbiology; Microbiology Resource Committee of the College of American Pathologists.

Arch Pathol Lab Med. 2017 Jun;141(6):776-786. doi: 10.5858/arpa.2016-0539-RA. Epub 2017 Feb 7.

PMID:
28169558
18.

Comparing viral metagenomics methods using a highly multiplexed human viral pathogens reagent.

Li L, Deng X, Mee ET, Collot-Teixeira S, Anderson R, Schepelmann S, Minor PD, Delwart E.

J Virol Methods. 2015 Mar;213:139-46. doi: 10.1016/j.jviromet.2014.12.002. Epub 2014 Dec 11.

19.

Rapid Metagenomic Next-Generation Sequencing during an Investigation of Hospital-Acquired Human Parainfluenza Virus 3 Infections.

Greninger AL, Zerr DM, Qin X, Adler AL, Sampoleo R, Kuypers JM, Englund JA, Jerome KR.

J Clin Microbiol. 2016 Dec 28;55(1):177-182. doi: 10.1128/JCM.01881-16. Print 2017 Jan.

20.

Direct Detection and Identification of Prosthetic Joint Infection Pathogens in Synovial Fluid by Metagenomic Shotgun Sequencing.

Ivy MI, Thoendel MJ, Jeraldo PR, Greenwood-Quaintance KE, Hanssen AD, Abdel MP, Chia N, Yao JZ, Tande AJ, Mandrekar JN, Patel R.

J Clin Microbiol. 2018 Aug 27;56(9). pii: e00402-18. doi: 10.1128/JCM.00402-18. Print 2018 Sep.

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