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Title: Axiom Microbiome Array, the next generation microarray for high-throughput pathogen and microbiome analysis

Abstract

Microarrays have proven to be useful in rapid detection of many viruses and bacteria. Pathogen detection microarrays have been utilized to diagnose viral and bacterial infections in clinical samples and to evaluate the safety of biological drug materials. In this study, the Axiom Microbiome Array was evaluated to discover its sensitivity, specificity and utility in microbiome analysis of veterinary clinical samples. The array contains probes designed to detect more than 12,000 species of viruses, bacteria, fungi, protozoa and archaea, yielding the most comprehensive microbial detection platform built to date. The array was able to detect Shigella and Aspergillus at 100 genome copies, and vaccinia virus DNA at 1,000 genome copies. The Axiom Microbiome Array made correct species-level calls in mock microbial community samples. When tested against serum, tissue, and fecal samples from pigs experimentally co-infected with porcine reproductive and respiratory syndrome virus and porcine circovirus type 2, the microarray correctly detected these two viruses and other common viral and bacterial microbiome species. This cost-effective and high-throughput microarray is an efficient tool to rapidly analyze large numbers of clinical and environmental samples for the presence of multiple viral and bacterial pathogens.

Authors:
ORCiD logo [1];  [1];  [1];  [1];  [2];  [2];  [3];  [1]; ORCiD logo [1];  [4]
  1. Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
  2. Thermo Fisher Scientific, Santa Clara, CA, (United States)
  3. Kansas State Univ., Manhattan, KS (United States)
  4. Hokkaido Univ., Sapporo (Japan)
Publication Date:
Research Org.:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE National Nuclear Security Administration (NNSA)
OSTI Identifier:
1512638
Report Number(s):
LLNL-JRNL-757463
Journal ID: ISSN 1932-6203; 945267
Grant/Contract Number:  
AC52-07NA27344
Resource Type:
Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 14; Journal Issue: 2; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Thissen, James B., Be, Nicholas A., McLoughlin, Kevin, Gardner, Shea, Rack, Paul G., Shapero, Michael H., Rowland, Raymond R. R., Slezak, Tom, Jaing, Crystal J., and Sawabe, Tomoo. Axiom Microbiome Array, the next generation microarray for high-throughput pathogen and microbiome analysis. United States: N. p., 2019. Web. doi:10.1371/journal.pone.0212045.
Thissen, James B., Be, Nicholas A., McLoughlin, Kevin, Gardner, Shea, Rack, Paul G., Shapero, Michael H., Rowland, Raymond R. R., Slezak, Tom, Jaing, Crystal J., & Sawabe, Tomoo. Axiom Microbiome Array, the next generation microarray for high-throughput pathogen and microbiome analysis. United States. doi:10.1371/journal.pone.0212045.
Thissen, James B., Be, Nicholas A., McLoughlin, Kevin, Gardner, Shea, Rack, Paul G., Shapero, Michael H., Rowland, Raymond R. R., Slezak, Tom, Jaing, Crystal J., and Sawabe, Tomoo. Fri . "Axiom Microbiome Array, the next generation microarray for high-throughput pathogen and microbiome analysis". United States. doi:10.1371/journal.pone.0212045. https://www.osti.gov/servlets/purl/1512638.
@article{osti_1512638,
title = {Axiom Microbiome Array, the next generation microarray for high-throughput pathogen and microbiome analysis},
author = {Thissen, James B. and Be, Nicholas A. and McLoughlin, Kevin and Gardner, Shea and Rack, Paul G. and Shapero, Michael H. and Rowland, Raymond R. R. and Slezak, Tom and Jaing, Crystal J. and Sawabe, Tomoo},
abstractNote = {Microarrays have proven to be useful in rapid detection of many viruses and bacteria. Pathogen detection microarrays have been utilized to diagnose viral and bacterial infections in clinical samples and to evaluate the safety of biological drug materials. In this study, the Axiom Microbiome Array was evaluated to discover its sensitivity, specificity and utility in microbiome analysis of veterinary clinical samples. The array contains probes designed to detect more than 12,000 species of viruses, bacteria, fungi, protozoa and archaea, yielding the most comprehensive microbial detection platform built to date. The array was able to detect Shigella and Aspergillus at 100 genome copies, and vaccinia virus DNA at 1,000 genome copies. The Axiom Microbiome Array made correct species-level calls in mock microbial community samples. When tested against serum, tissue, and fecal samples from pigs experimentally co-infected with porcine reproductive and respiratory syndrome virus and porcine circovirus type 2, the microarray correctly detected these two viruses and other common viral and bacterial microbiome species. This cost-effective and high-throughput microarray is an efficient tool to rapidly analyze large numbers of clinical and environmental samples for the presence of multiple viral and bacterial pathogens.},
doi = {10.1371/journal.pone.0212045},
journal = {PLoS ONE},
number = 2,
volume = 14,
place = {United States},
year = {2019},
month = {2}
}

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