title: MinION as part of a biomedical rapidly deployable laboratory.
abstract: Fast turnaround times are of utmost importance for biomedical reconnaissance, particularly regarding dangerous pathogens. Recent advances in sequencing technology and its devices allow sequencing within a short time frame outside stationary laboratories close to the epicenter of the outbreak. In our study, we evaluated the portable sequencing device MinION as part of a rapidly deployable laboratory specialized in identification of highly pathogenic agents. We tested the device in the course of a NATO live agent exercise in a deployable field laboratory in hot climate conditions. The samples were obtained from bio-terroristic scenarios that formed part of the exercise and contained unknown bacterial agents. To simulate conditions of a resource-limited remote deployment site, we operated the sequencer without internet access. Using a metagenomic approach, we were able to identify the causative agent in the analyzed samples. Furthermore, depending on the obtained data, we were able to perform molecular typing down to strain level. In our study we challenged the device and discuss advances as well as remaining limitations for sequencing biological samples outside of stationary laboratories. Nevertheless, massive parallel sequencing as a non-selective methodology yields important information and is able to support outbreak investigation - even in the field.
authors.affiliation: Bundeswehr Institute of Microbiology, Neuherbergstr. 11, 80937 Munich, Germany.
authors.forename: Mathias C
authors.initials: MC
authors.lastname: Walter
authors.affiliation: Bundeswehr Institute of Microbiology, Neuherbergstr. 11, 80937 Munich, Germany.
authors.forename: Katrin
authors.initials: K
authors.lastname: Zwirglmaier
authors.affiliation: Bundeswehr Institute of Microbiology, Neuherbergstr. 11, 80937 Munich, Germany.
authors.forename: Philipp
authors.initials: P
authors.lastname: Vette
authors.affiliation: Defense Research and Development Canada, Suffield Research Centre, PO Box 4000 Stn Main, Medicine Hat, Alberta, T1A 8K6, Canada.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Holowachuk
authors.affiliation: Bundeswehr Institute of Microbiology, Neuherbergstr. 11, 80937 Munich, Germany.
authors.forename: Kilian
authors.initials: K
authors.lastname: Stoecker
authors.affiliation: Bundeswehr Institute of Microbiology, Neuherbergstr. 11, 80937 Munich, Germany.
authors.forename: Gelimer H
authors.initials: GH
authors.lastname: Genzel
authors.affiliation: Bundeswehr Institute of Microbiology, Neuherbergstr. 11, 80937 Munich, Germany. Electronic address: markusantwerpen@instmikrobiobw.de.
authors.forename: Markus H
authors.initials: MH
authors.lastname: Antwerpen
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000302:isolation & purification*; D004196:Disease Outbreaks / Q000517:prevention & control*; D004867:Equipment Design; D019544:Equipment Failure Analysis; D059014:High-Throughput Nucleotide Sequencing / Q000295:instrumentation*; D007753:Laboratories / Q000458:organization & administration*; D011159:Population Surveillance / Q000379:methods; D017422:Sequence Analysis, DNA / Q000295:instrumentation*
keywords: MinION; Nanopore sequencing; Outbreak investigation