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Direct Detection and Quantification of Bacterial Cell-free DNA in Patients with Bloodstream Infection (BSI) Using the Karius Plasma Next Generation Sequencing (NGS) Test
BACKGROUND: Blood cultures can have low sensitivity if a patient is pretreated with antibiotics. A molecular diagnostic for bloodstream infection (BSI) that can also quantitate pathogen DNA could be a useful tool in detecting and monitoring culture-negative infections. METHODS: We prospectively enro...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5631118/ http://dx.doi.org/10.1093/ofid/ofx163.1613 |
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author | Wanda, Lisa Ruffin, Felicia Hill-Rorie, Jonathan Hollemon, Desiree Seng, Hon Hong, David Blauwkamp, Tim Kertesz, Mickey Fowler, Vance |
author_facet | Wanda, Lisa Ruffin, Felicia Hill-Rorie, Jonathan Hollemon, Desiree Seng, Hon Hong, David Blauwkamp, Tim Kertesz, Mickey Fowler, Vance |
author_sort | Wanda, Lisa |
collection | PubMed |
description | BACKGROUND: Blood cultures can have low sensitivity if a patient is pretreated with antibiotics. A molecular diagnostic for bloodstream infection (BSI) that can also quantitate pathogen DNA could be a useful tool in detecting and monitoring culture-negative infections. METHODS: We prospectively enrolled 75 patients (50 with culture confirmed BSI due to Staphylococcus aureus [n = 21] or Gram-negative bacilli [n = 29] at baseline, and 25 with negative blood cultures) to evaluate the Karius plasma next generation sequencing (NGS) test to detect BSI. Blood samples from patients with confirmed BSI were collected for the study within one day of positive blood culture and then every 2–3 days. Cell-free DNA (cfDNA) was extracted from plasma and underwent NGS in the Karius CLIA/CAP laboratory (Redwood City, CA). After removal of human sequences, remaining reads were aligned against a curated pathogen database. Organisms present at a significance-level above a predefined threshold were reported. Quantity of cfDNA for each reported pathogen was expressed as molecules per microliter (MPM). RESULTS: When compared with baseline blood culture, the plasma NGS test had a positive agreement of 80% (40/50) and negative agreement of 84% (21/25). Overall, serially collected samples were positive by plasma NGS testing significantly longer than blood culture (mean 6.0 days vs. 2.4 days, respectively; P < 0.0001. Figure). Patients with BSI were positive longer by NGS testing than blood culture for both S. aureus (mean 6.9 days vs. 4.0 days, respectively; P < 0.005) and gram-negative bacilli (mean 5.4 days vs. 1.3 days, respectively; P < 0.001). Pathogen cfDNA in BSI patients, quantified as MPM, declined over time during treatment. S. aureus MPM declined more slowly than gram-negative MPM and was significantly higher than gram-negative MPM at day 6 (P < 0.001). CONCLUSION: The Karius plasma NGS test can directly detect pathogens in patients with BSI. Pathogen cfDNA signal in plasma remains positive longer than blood culture and combined with quantification of pathogen cfDNA, could be a useful biomarker to aid in diagnosis and monitoring of infections, particularly in those with sterile blood cultures. DISCLOSURES: L. Wanda, Karius, Inc: Collaborator and Employee, Salary; F. Ruffin, Karius, Inc.: Collaborator and Research Contractor, Salary; J. Hill-Rorie, Karius, Inc: Collaborator, Research support and Salary; D. Hollemon, Karius, Inc: Employee, Salary; H. Seng, Karius, Inc: Employee, Salary; D. Hong, Karius, Inc.: Employee, Salary;
T. Blauwkamp, Karius, Inc: Employee, Salary; M. Kertesz, Karius, Inc: Employee, Salary; V. Fowler Jr., Karius, Inc: Grant Investigator, Grant recipient Pfizer, Novartis, Galderma, Novadigm, Durata, Debiopharm, Genentech, Achaogen, Affinium, Medicines Co., Cerexa, Tetraphase, Trius, MedImmune, Bayer, Theravance, Cubist, Basilea, Affinergy, Janssen, xBiotech, Contrafect: Consultant, Consulting fee NIH, MedImmune, Cerexa/Forest/Actavis/Allergan, Pfizer, Advanced Liquid Logics, Theravance, Novartis, Cubist/Merck; Medical Biosurfaces; Locus; Affinergy; Basilea; Contrafect; Karius: Grant Investigator, Grant recipient Green Cross, Cubist, Cerexa, Durata, Theravance; Debiopharm: Consultant, Consulting fee UpToDate: Royalties, Royalties |
format | Online Article Text |
id | pubmed-5631118 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-56311182017-11-07 Direct Detection and Quantification of Bacterial Cell-free DNA in Patients with Bloodstream Infection (BSI) Using the Karius Plasma Next Generation Sequencing (NGS) Test Wanda, Lisa Ruffin, Felicia Hill-Rorie, Jonathan Hollemon, Desiree Seng, Hon Hong, David Blauwkamp, Tim Kertesz, Mickey Fowler, Vance Open Forum Infect Dis Abstracts BACKGROUND: Blood cultures can have low sensitivity if a patient is pretreated with antibiotics. A molecular diagnostic for bloodstream infection (BSI) that can also quantitate pathogen DNA could be a useful tool in detecting and monitoring culture-negative infections. METHODS: We prospectively enrolled 75 patients (50 with culture confirmed BSI due to Staphylococcus aureus [n = 21] or Gram-negative bacilli [n = 29] at baseline, and 25 with negative blood cultures) to evaluate the Karius plasma next generation sequencing (NGS) test to detect BSI. Blood samples from patients with confirmed BSI were collected for the study within one day of positive blood culture and then every 2–3 days. Cell-free DNA (cfDNA) was extracted from plasma and underwent NGS in the Karius CLIA/CAP laboratory (Redwood City, CA). After removal of human sequences, remaining reads were aligned against a curated pathogen database. Organisms present at a significance-level above a predefined threshold were reported. Quantity of cfDNA for each reported pathogen was expressed as molecules per microliter (MPM). RESULTS: When compared with baseline blood culture, the plasma NGS test had a positive agreement of 80% (40/50) and negative agreement of 84% (21/25). Overall, serially collected samples were positive by plasma NGS testing significantly longer than blood culture (mean 6.0 days vs. 2.4 days, respectively; P < 0.0001. Figure). Patients with BSI were positive longer by NGS testing than blood culture for both S. aureus (mean 6.9 days vs. 4.0 days, respectively; P < 0.005) and gram-negative bacilli (mean 5.4 days vs. 1.3 days, respectively; P < 0.001). Pathogen cfDNA in BSI patients, quantified as MPM, declined over time during treatment. S. aureus MPM declined more slowly than gram-negative MPM and was significantly higher than gram-negative MPM at day 6 (P < 0.001). CONCLUSION: The Karius plasma NGS test can directly detect pathogens in patients with BSI. Pathogen cfDNA signal in plasma remains positive longer than blood culture and combined with quantification of pathogen cfDNA, could be a useful biomarker to aid in diagnosis and monitoring of infections, particularly in those with sterile blood cultures. DISCLOSURES: L. Wanda, Karius, Inc: Collaborator and Employee, Salary; F. Ruffin, Karius, Inc.: Collaborator and Research Contractor, Salary; J. Hill-Rorie, Karius, Inc: Collaborator, Research support and Salary; D. Hollemon, Karius, Inc: Employee, Salary; H. Seng, Karius, Inc: Employee, Salary; D. Hong, Karius, Inc.: Employee, Salary;
T. Blauwkamp, Karius, Inc: Employee, Salary; M. Kertesz, Karius, Inc: Employee, Salary; V. Fowler Jr., Karius, Inc: Grant Investigator, Grant recipient Pfizer, Novartis, Galderma, Novadigm, Durata, Debiopharm, Genentech, Achaogen, Affinium, Medicines Co., Cerexa, Tetraphase, Trius, MedImmune, Bayer, Theravance, Cubist, Basilea, Affinergy, Janssen, xBiotech, Contrafect: Consultant, Consulting fee NIH, MedImmune, Cerexa/Forest/Actavis/Allergan, Pfizer, Advanced Liquid Logics, Theravance, Novartis, Cubist/Merck; Medical Biosurfaces; Locus; Affinergy; Basilea; Contrafect; Karius: Grant Investigator, Grant recipient Green Cross, Cubist, Cerexa, Durata, Theravance; Debiopharm: Consultant, Consulting fee UpToDate: Royalties, Royalties Oxford University Press 2017-10-04 /pmc/articles/PMC5631118/ http://dx.doi.org/10.1093/ofid/ofx163.1613 Text en © The Author 2017. Published by Oxford University Press on behalf of Infectious Diseases Society of America. http://creativecommons.org/licenses/by-nc-nd/4.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence (http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Abstracts Wanda, Lisa Ruffin, Felicia Hill-Rorie, Jonathan Hollemon, Desiree Seng, Hon Hong, David Blauwkamp, Tim Kertesz, Mickey Fowler, Vance Direct Detection and Quantification of Bacterial Cell-free DNA in Patients with Bloodstream Infection (BSI) Using the Karius Plasma Next Generation Sequencing (NGS) Test |
title | Direct Detection and Quantification of Bacterial Cell-free DNA in Patients with Bloodstream Infection (BSI) Using the Karius Plasma Next Generation Sequencing (NGS) Test |
title_full | Direct Detection and Quantification of Bacterial Cell-free DNA in Patients with Bloodstream Infection (BSI) Using the Karius Plasma Next Generation Sequencing (NGS) Test |
title_fullStr | Direct Detection and Quantification of Bacterial Cell-free DNA in Patients with Bloodstream Infection (BSI) Using the Karius Plasma Next Generation Sequencing (NGS) Test |
title_full_unstemmed | Direct Detection and Quantification of Bacterial Cell-free DNA in Patients with Bloodstream Infection (BSI) Using the Karius Plasma Next Generation Sequencing (NGS) Test |
title_short | Direct Detection and Quantification of Bacterial Cell-free DNA in Patients with Bloodstream Infection (BSI) Using the Karius Plasma Next Generation Sequencing (NGS) Test |
title_sort | direct detection and quantification of bacterial cell-free dna in patients with bloodstream infection (bsi) using the karius plasma next generation sequencing (ngs) test |
topic | Abstracts |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5631118/ http://dx.doi.org/10.1093/ofid/ofx163.1613 |
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