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Front. Mol. Biosci.
Sec. Molecular Diagnostics and Therapeutics
Volume 11 - 2024 | doi: 10.3389/fmolb.2024.1419213

Multiplex detection and identification of viral, bacterial and protozoan pathogens in human blood and plasma using an expanded high-density resequencing microarray platform Provisionally Accepted

Moussa Kourout1, 2  Scott Espich1, 2  Carolyn Fisher1, 2 Irina Tiper1, 2 Anjan Purkayastha3 Sean Smith1, 2  Luis Santana-Quintero1, 2  Robert Duncan1, 2*
  • 1United States Food and Drug Administration, United States
  • 2Center for Drug Evaluation and Research, United States Food and Drug Administration, United States
  • 3Independent researcher, United States

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Nucleic acid tests for blood donor screening have improved the safety of the blood supply; however, increasing numbers of emerging pathogen tests are burdensome. Multiplex testing platforms are a potential solution.The Blood Borne Pathogen Resequencing Microarray Expanded (BBP-RMAv.2) can perform multiplex detection and identification of 80 viruses, bacteria and parasites.This study evaluated pathogen detection in human blood or plasma. Samples spiked with selected pathogens, each with one of 6 viruses, 2 bacteria and 5 protozoans were tested on this platform. The nucleic acids were extracted, amplified using multiplexed sets of primers, and hybridized to a microarray. The reported sequences were aligned to a database to identify the pathogen. To directly compare the microarray to an emerging molecular approach, the amplified nucleic acids were also submitted to nanopore next generation sequencing (NGS).The BBP-RMAv.2 detected viral pathogens at a concentration as low as 100 copies/ml and a range of concentrations from 1,000 to 100,000 copies/ml for all the spiked some concentration and as low as 100 copies/ml for viral pathogens. Coded specimens were identified correctly demonstrating the effectiveness of the platform. The nanopore sequencing correctly identified most samples and the results of the two platforms were compared.These results indicated that the BBP-RMAv.2 could be employed for multiplex detection with potential for use in blood safety or disease diagnosis. The NGS was nearly as effective at identifying pathogens in blood and performed better than BBP-RMAv.2 at identifying pathogen-negative samples.

Keywords: Microarray, Blood-Borne Pathogens, Multiplex detection, targeted sequencing, Resequencing microarray

Received: 17 Apr 2024; Accepted: 23 May 2024.

Copyright: © 2024 Kourout, Espich, Fisher, Tiper, Purkayastha, Smith, Santana-Quintero and Duncan. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Robert Duncan, United States Food and Drug Administration, Silver Spring, United States