| Title: |
Field-based detection of bacteria using nanopore sequencing: Method evaluation for biothreat detection in complex samples |
| Authors: |
Tyler, Andrea D.; McAllister, Jane; Stapleton, Helen; Gauci, Penny; Antonation, Kym; Thirkettle-Watts, David; Corbett, Cindi R. |
| Contributors: |
Al-Marzooq, Farah; Canadian Safety and Security Program |
| Source: |
PLOS ONE ; volume 18, issue 11, page e0295028 ; ISSN 1932-6203 |
| Publisher Information: |
Public Library of Science (PLoS) |
| Publication Year: |
2023 |
| Collection: |
PLOS Publications (via CrossRef) |
| Description: |
From pathogen detection to genome or plasmid closure, the utility of the Oxford Nanopore Technologies (ONT) MinION for microbiological analysis has been well documented. The MinION’s small footprint, portability, and real-time analytic capability situates it well to address challenges in the field of unbiased pathogen detection, as a component of a security investigation. To this end, a multicenter evaluation of the effect of alternative analytical approaches on the outcome of MinION-based sequencing, using a set of well-characterized samples, was explored in a field-based scenario. Three expert scientific response groups evaluated known bacterial DNA extracts as part of an international first responder (Chemical, Biological, Radiological) training exercise. Samples were prepared independently for analysis using the Rapid and/or Rapid PCR sequencing kits as per the best practices of each of the participating groups. Analyses of sequence data were in turn conducted using varied approaches including ONTs What’s in my pot (WIMP) architecture and in-house computational pipelines. Microbial community composition and the ability of each approach to detect pathogens was compared. Each group demonstrated the ability to detect all species present in samples, although several organisms were detected at levels much lower than expected with some organisms even falling below 1% abundance. Several ‘contaminant’ near neighbor species were also detected, at low abundance. Regardless of the sequencing approach chosen, the observed composition of the bacterial communities diverged from the input composition in each of the analyses, although sequencing conducted using the rapid kit produced the least distortion when compared to PCR-based library preparation methods. One of the participating groups generated drastically lower sequencing output than the other groups, likely attributed to the limited computer hard drive capacity, and occasional disruption of the internet connection. These results provide further consideration for ... |
| Document Type: |
article in journal/newspaper |
| Language: |
English |
| DOI: |
10.1371/journal.pone.0295028 |
| Availability: |
https://doi.org/10.1371/journal.pone.0295028; https://dx.plos.org/10.1371/journal.pone.0295028 |
| Rights: |
http://creativecommons.org/licenses/by/4.0/ |
| Accession Number: |
edsbas.9F3CEDC |
| Database: |
BASE |