Abstract
Microarrays have proven to be useful in rapid detection of many viruses and bacteria. Pathogen detection microarrays have been used 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 determine 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.
Highlights
Rapid detection and characterization of bacterial and viral pathogens is important for clinical microbiological diagnostics, public health, veterinary diagnostics, drug and food safety, environmental monitoring and biodefense
S. flexneri was positively detected at 100 genome copies and above, but not at 10 genome copies
The Axiom Microbiome Array presents a new opportunity for screening of thousands of microbial species at a fraction of the cost of metagenomic sequencing
Summary
Rapid detection and characterization of bacterial and viral pathogens is important for clinical microbiological diagnostics, public health, veterinary diagnostics, drug and food safety, environmental monitoring and biodefense. Various detection technologies based on nucleic acid signatures have emerged in the past few years, including TaqMan PCR [1] and Luminex bead-based systems [2, 3] The Axiom Microbiome Array is commercialized by Affymetrix/ Thermo Fisher under a license from LLNL and the LLNL authors receive royalties. This does not alter our adherence to PLOS ONE policies on sharing data and materials
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