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Volume 26, Number 2—February 2020
Dispatch

Rapid Nanopore Whole-Genome Sequencing for Anthrax Emergency Preparedness

Heather P. McLaughlinComments to Author , Julia V. Bugrysheva, Andrew B. Conley, Christopher A. Gulvik, Blake Cherney, Cari B. Kolton, Chung K. Marston, Elke Saile, Erin Swaney, David Lonsway, Amy S. Gargis, Thiphasone Kongphet-Tran, Christine Lascols, Pierre Michel, Julie Villanueva, Alex R. Hoffmaster, Jay E. Gee, and David Sue
Author affiliations: Centers for Disease Control and Prevention, Atlanta, Georgia, USA (H.P. McLaughlin, J.V. Bugrysheva, C.A. Gulvik, B. Cherney, C.B. Kolton, C.K. Marston, E. Saile, D. Lonsway, A.S. Gargis, T. Kongphet-Tran, C. Lascols, P. Michel, J. Villanueva, A.R. Hoffmaster, J.E. Gee, D. Sue); IHRC–Georgia Tech Applied Bioinformatics Laboratory, Atlanta (A.B. Conley); Texas Department of State Health Services Laboratory, Austin, Texas, USA (E. Swaney)

Main Article

Figure 1

Time required to detect antimicrobial resistance markers in Bacillus anthracis strain Ba0914 by using WGS and summary of assembly results. A) Comparison of time to complete rapid nanopore (MinION) and short-read (iSeq) sequencing laboratory workflows. Workflows include DNA extraction, library preparation, WGS, and bioinformatics analysis. B) Comparison of nanopore-based and short-read sequencing–based data used to assemble the B. anthracis chromosome and plasmid sequences and to detect known AMR

Figure 1. Time required to detect antimicrobial resistance markers in Bacillus anthracis strain Ba0914 by using WGS and summary of assembly results. A) Comparison of time to complete rapid nanopore (MinION) and short-read (iSeq) sequencing laboratory workflows. Workflows include DNA extraction, library preparation, WGS, and bioinformatics analysis. B) Comparison of nanopore-based and short-read sequencing–based data used to assemble the B. anthracis chromosome and plasmid sequences and to detect known AMR mutations and genes. Mutations associated with fluoroquinolone resistance in B. anthracis are located within the quinolone resistance–determining regions of gyrA, gyrB, parC, and parE genes. AMR genes contained in the Resfinder database (https://cge.cbs.dtu.dk) were queried against the assemblies. The rsiP mutation associated with penicillin resistance was not included. The nanopore assembly was generated by using the first 120,000 basecalled reads. AMR, antimicrobial resistance; WGS, whole-genome sequencing.

Main Article

Page created: January 20, 2020
Page updated: January 20, 2020
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