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152. rapid Ultra-high Enrichment of Bacterial Pathogens at Low Concentration from Blood for Species ID and AMR Prediction Using Nanopore Sequencing

BACKGROUND: Each year in the United States there are over 1.7 million cases of sepsis that account for a third of hospital deaths. A key to reducing morbidity and mortality rates is early, appropriate antibiotic therapy. Most new diagnostic approaches still suffer from insufficient sensitivity to lo...

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Autores principales: Tsui, Chiahao, Cunden, Lisa S, Billings, Nicole, Nanayakkara, Imaly A, Herriott, Ian, Kumcu, Michael E, Martin, Rachel R, Chen, Michelle, Pangestu, Febriana, Knysh, Paul, Maddux, Cabell, Munro, Zachary, Huntley, Miriam
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
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Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7776437/
http://dx.doi.org/10.1093/ofid/ofaa439.462
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author Tsui, Chiahao
Cunden, Lisa S
Billings, Nicole
Nanayakkara, Imaly A
Herriott, Ian
Kumcu, Michael E
Martin, Rachel R
Chen, Michelle
Pangestu, Febriana
Knysh, Paul
Maddux, Cabell
Munro, Zachary
Huntley, Miriam
author_facet Tsui, Chiahao
Cunden, Lisa S
Billings, Nicole
Nanayakkara, Imaly A
Herriott, Ian
Kumcu, Michael E
Martin, Rachel R
Chen, Michelle
Pangestu, Febriana
Knysh, Paul
Maddux, Cabell
Munro, Zachary
Huntley, Miriam
author_sort Tsui, Chiahao
collection PubMed
description BACKGROUND: Each year in the United States there are over 1.7 million cases of sepsis that account for a third of hospital deaths. A key to reducing morbidity and mortality rates is early, appropriate antibiotic therapy. Most new diagnostic approaches still suffer from insufficient sensitivity to low bacterial loads in blood and limited sets of detection targets for bacterial species identification (ID) and antimicrobial resistance (AMR) determination. As such, blood culture remains the gold standard for diagnosing bacteremia despite limitations such as > 2-day turnaround time (TAT), incompatibility with fastidious organisms, and frequent inability to recover causative pathogens. METHODS: 31 clinically relevant bacterial pathogens, made up of 17 gram-positive and 14 gram-negative bacterial species, were spiked into 2 to 4 healthy donor blood samples at 1 to 5 CFU/mL. The samples were run through our proprietary Blood2Bac™ pipeline, sequenced on a nanopore platform, and data were passed through Keynome®, our proprietary machine learning algorithm to determine species ID and AMR. RESULTS: By assessing the efficiency of pathogen DNA enrichment and genome coverage post sequencing, we report high performance of 3 CFU/mL for 3 bacterial species and ≤ 2 CFU/mL for the 28 remaining species, which includes S. aureus, E. coli, and Streptococcus spp., three of the leading causes of sepsis. For all 31 bacterial species tested, Keynome called species ID with 100% accuracy. In addition, Keynome also predicted the AMR profile of pathogens with 100% accuracy for 19 drug/species AMR combinations, including ciprofloxacin for E. coli, clindamycin for S. aureus, and aztreonam for K. pneumoniae. CONCLUSION: Blood2Bac is able to enrich a wide range of bacterial pathogens directly from blood and enable bacterial whole genome sequencing with an estimated TAT of 12 hours. When coupled with Keynome, our process provides accurate species ID and AMR calls for key BSI pathogens even at single-digit CFU/mL concentrations. Our species-agnostic and culture-free process enables detection of a diverse range of bacterial species with high sensitivity, providing a robust and comprehensive diagnostic. DISCLOSURES: Chiahao Tsui, n/a, Day Zero Diagnostics (Employee, Shareholder) Lisa S. Cunden, PhD, Day Zero Diagnostics (Shareholder) Nicole Billings, PhD, Day Zero Diagnostics (Employee) Imaly A. Nanayakkara, PhD, Day Zero Diagnostics (Employee, Shareholder) Ian Herriott, BS, Day Zero Diagnostics (Employee, Shareholder) Rachel R. Martin, n/a, Day Zero DIagnostics (Employee) Michelle Chen, MS, Day Zero Diagnostics (Employee, Shareholder) Febriana Pangestu, n/a, Day Zero Diagnostics (Employee, Shareholder) Paul Knysh, PhD, Day Zero Diagnostics (Employee) Cabell Maddux, n/a, Day Zero Diagnostics (Employee, Shareholder) Zachary Munro, n/a, Day Zero Diagnostics Inc. (Employee, Shareholder) Miriam Huntley, PhD, Day Zero Diagnostics (Employee, Shareholder)
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spelling pubmed-77764372021-01-07 152. rapid Ultra-high Enrichment of Bacterial Pathogens at Low Concentration from Blood for Species ID and AMR Prediction Using Nanopore Sequencing Tsui, Chiahao Cunden, Lisa S Billings, Nicole Nanayakkara, Imaly A Herriott, Ian Kumcu, Michael E Martin, Rachel R Chen, Michelle Pangestu, Febriana Knysh, Paul Maddux, Cabell Munro, Zachary Huntley, Miriam Open Forum Infect Dis Poster Abstracts BACKGROUND: Each year in the United States there are over 1.7 million cases of sepsis that account for a third of hospital deaths. A key to reducing morbidity and mortality rates is early, appropriate antibiotic therapy. Most new diagnostic approaches still suffer from insufficient sensitivity to low bacterial loads in blood and limited sets of detection targets for bacterial species identification (ID) and antimicrobial resistance (AMR) determination. As such, blood culture remains the gold standard for diagnosing bacteremia despite limitations such as > 2-day turnaround time (TAT), incompatibility with fastidious organisms, and frequent inability to recover causative pathogens. METHODS: 31 clinically relevant bacterial pathogens, made up of 17 gram-positive and 14 gram-negative bacterial species, were spiked into 2 to 4 healthy donor blood samples at 1 to 5 CFU/mL. The samples were run through our proprietary Blood2Bac™ pipeline, sequenced on a nanopore platform, and data were passed through Keynome®, our proprietary machine learning algorithm to determine species ID and AMR. RESULTS: By assessing the efficiency of pathogen DNA enrichment and genome coverage post sequencing, we report high performance of 3 CFU/mL for 3 bacterial species and ≤ 2 CFU/mL for the 28 remaining species, which includes S. aureus, E. coli, and Streptococcus spp., three of the leading causes of sepsis. For all 31 bacterial species tested, Keynome called species ID with 100% accuracy. In addition, Keynome also predicted the AMR profile of pathogens with 100% accuracy for 19 drug/species AMR combinations, including ciprofloxacin for E. coli, clindamycin for S. aureus, and aztreonam for K. pneumoniae. CONCLUSION: Blood2Bac is able to enrich a wide range of bacterial pathogens directly from blood and enable bacterial whole genome sequencing with an estimated TAT of 12 hours. When coupled with Keynome, our process provides accurate species ID and AMR calls for key BSI pathogens even at single-digit CFU/mL concentrations. Our species-agnostic and culture-free process enables detection of a diverse range of bacterial species with high sensitivity, providing a robust and comprehensive diagnostic. DISCLOSURES: Chiahao Tsui, n/a, Day Zero Diagnostics (Employee, Shareholder) Lisa S. Cunden, PhD, Day Zero Diagnostics (Shareholder) Nicole Billings, PhD, Day Zero Diagnostics (Employee) Imaly A. Nanayakkara, PhD, Day Zero Diagnostics (Employee, Shareholder) Ian Herriott, BS, Day Zero Diagnostics (Employee, Shareholder) Rachel R. Martin, n/a, Day Zero DIagnostics (Employee) Michelle Chen, MS, Day Zero Diagnostics (Employee, Shareholder) Febriana Pangestu, n/a, Day Zero Diagnostics (Employee, Shareholder) Paul Knysh, PhD, Day Zero Diagnostics (Employee) Cabell Maddux, n/a, Day Zero Diagnostics (Employee, Shareholder) Zachary Munro, n/a, Day Zero Diagnostics Inc. (Employee, Shareholder) Miriam Huntley, PhD, Day Zero Diagnostics (Employee, Shareholder) Oxford University Press 2020-12-31 /pmc/articles/PMC7776437/ http://dx.doi.org/10.1093/ofid/ofaa439.462 Text en © The Author 2020. 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 Poster Abstracts
Tsui, Chiahao
Cunden, Lisa S
Billings, Nicole
Nanayakkara, Imaly A
Herriott, Ian
Kumcu, Michael E
Martin, Rachel R
Chen, Michelle
Pangestu, Febriana
Knysh, Paul
Maddux, Cabell
Munro, Zachary
Huntley, Miriam
152. rapid Ultra-high Enrichment of Bacterial Pathogens at Low Concentration from Blood for Species ID and AMR Prediction Using Nanopore Sequencing
title 152. rapid Ultra-high Enrichment of Bacterial Pathogens at Low Concentration from Blood for Species ID and AMR Prediction Using Nanopore Sequencing
title_full 152. rapid Ultra-high Enrichment of Bacterial Pathogens at Low Concentration from Blood for Species ID and AMR Prediction Using Nanopore Sequencing
title_fullStr 152. rapid Ultra-high Enrichment of Bacterial Pathogens at Low Concentration from Blood for Species ID and AMR Prediction Using Nanopore Sequencing
title_full_unstemmed 152. rapid Ultra-high Enrichment of Bacterial Pathogens at Low Concentration from Blood for Species ID and AMR Prediction Using Nanopore Sequencing
title_short 152. rapid Ultra-high Enrichment of Bacterial Pathogens at Low Concentration from Blood for Species ID and AMR Prediction Using Nanopore Sequencing
title_sort 152. rapid ultra-high enrichment of bacterial pathogens at low concentration from blood for species id and amr prediction using nanopore sequencing
topic Poster Abstracts
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7776437/
http://dx.doi.org/10.1093/ofid/ofaa439.462
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