1) Thermo Fisher Scientific developed improvements to targeted and whole genome sequencing workflows that dramatically decrease overall time from sample to data/answer. 2) For a targeted bacterial identification panel, sequencing and analysis can now be completed in approximately 6.5 hours compared to standard times of 2.5 hours for sequencing and 1 hour for analysis. 3) For whole genome sequencing of bacterial isolates, the entire workflow from library preparation to data can now be finished in approximately 11 hours, compared to standard times of 1.5-3.5 hours for library prep, 2-7 hours for sequencing, and 1 hour for analysis.

1. Colin Davidson1, Mindy Landes2, Rongsu Qi1, Chaitali Parikh1, David Mandelman2, Haythem Latif2, Adam Harris2 , Nur Hasan3, Poorani Subramanian3, and Srinka Ghosh1 1Thermo Fisher
Scientific, 200 Oyster Point Blvd, South San Francisco, CA 94080; 2Thermo Fisher Scientific, 5781 Van Allen Way, Carlsbad, CA 92008; 3CosmosID, 155 Gibbs St #436, Rockville, MD 20850
Figure 3
Transposon-based library preparation. Each transposon complex consists of a tetramer of MuA
transposase and two double-stranded transposon end oligonucleotides. The complexes insert
the transposon ends into target gDNA, resulting in fragmentation and simultaneous tagging with
the transposon sequence. Those sequences are used as priming sites for introduction of
sequencing adapters during amplification by PCR.
Figure 4
Observed read length distribution at 200 flows is similarto
standard 500 flows and with the expected amplicon insert
length distribution The majority of the amplicons for the
targeted sequencing libraries have a mean insert length of
95 bp; it was estimated that the minimum number of flows
needed was 200. Analysis of Ion S5 XL runs (with 500
flows) at 300, 250, 200 and 180 flows demonstrated that at
200 flows, the read length distribution is still comparable to
500 flows. Whereas at 180 flows, read length distribution is
starting to be compromised.
Decreasing overall sequencing workflow times on the Ion S5™ XL sequencing system. Improvements in library preparation, template preparation (clonal amplificationof library molecules onto capture beads) and optimizing sequencing reagent flows on the S5 system provide a dramatic decrease in overall sequencing workflow
time. For Ion AmpliSeq™-based libraries such as the pan-bacterial ID panel sequencing and data analysis can be completed in about 6.5 hrs. For whole genome sequencing libraries produced from bacterial isolates, the sequencing workflow (from library preparation to data) can be completed in approximately 11 hrs.
Figure 1
Figure 5
Figure 6 Figure 7
Figure 8
INTRODUCTION
At this time next generation sequencing (NGS) is hindered by slow and often
manual workflow procedures. Decreasing overall workflow times is critical for the
widespread adoption of targeted and whole genome sequencing (WGS) for many
time-sensitive applications, in particular for infectious disease analysis. To this
end, we describe improvements to the four main steps of the NGS workflow: i)
library preparation; ii) template preparation, iii) sequencing; iv) and data analysis.
Together, these advances dramatically decrease the overall turnaround times.
Ion Torrent semiconductor-based sequencing instruments utilities flow
sequencing with speed largely dependent on and the number of nucleotide flows
(one flow produces ~0.5 base) and the speed of the flows (Figure 2).
CONCLUSIONS
For the targeted assays described, the total turnaround time could be completed in a
standard workday
ACKNOWLEDGEMENTS
Bacterial ID AmpliSeq™ assay: Kunal Banjara, Jamsheed Ghadiri, Andrew
Hutchison, Peter Vander Horn, Karen Clyde, Nisha Mulakken, Rajesh Gottimukkala,
Diana Jeon, and Simon Cawley. Torrent Suite Software: Dominique Belhachemi,
Christian Koller, and Mohit Gupta
TRADEMARKS/LICENSING
© 2016 Thermo Fisher Scientific, Inc. All rights reserved. All trademarks are the
property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified.
TT01: Speeding up sequencing: Sequencing in an hour enables sample to answer in a workday
Thermo Fisher Scientific • 5791 Van Allen Way • Carlsbad, CA 92008 • www.lifetechnologies.com
A sequencing run on the Ion S5™ XL System is started by inserting an Ion S5 chip preloaded with
templated beads containing clonal amplified library molecules. Nucleotides are flowed across the
chip with the addition of bases by the DNA polymerase resulting in the production of hydrogen
ions, changing the pH which is converted to a sequencing signal through ion-sensitive wells that
hold the templated beads. Read lengths of up to 400 bp can be produced with three available
semiconductorchips that produce up to 5, 20, or 80 million reads per chip
Figure 2
Whole Genome and Targeted Sequencing: Sample-to-data in ~6.5 to 11 hr
Bacterial Nucleic acid Manual Isothermal
Amplification (2 hr)
Sample Template Preparation Rapid Ion S5 XL Sequencing CosmosID
200 flows (55 min)
300 flows (80 min)
N/A
~ 1 hr
Targeted AmpliSeq panel (3.5 hr)
WGS with MuSeek (1.5 hr)
Library Preparation
1.5 - 3.5 hr 2 - 7 hr 1 hr55 - 80 min
Total time
~ 6.5 hr
~ 11.0 hr
MATERIALS AND METHODS
The new rapid workflow innovations were applied to two different library
preparation protocols: i) targeted libraries created using a highly-multiplexed PCR
approach consisting of 1200 amplicons targeting the 16S rRNA gene as well as
species-specific identification targets and antimicrobial resistance determinants;
and ii) an unbiased WGS approach using a MuA transposon-based library
preparation method. (Figure 3).
WGS libraries: Purified Escherichia coli (balanced G:C content),
Rhodopseudomonas palustris (high G:C content), and Staphylococcus aureus
(low G:C content) gDNA was used as input into the MuSeek™ library preparation
protocol (Figure 3).
Targeted libraries: Total nucleic acids from six bacterial cultures (Acinetobacter
baumannii, Enterobacter cloacae, Enterococcus faecium, Klebsiella pneumoniae,
Pseudomonas aeruginosa, Staphylococcus aureus) were extracted as input for
into the Ion AmpliSeq™ Library Kit 2.0, except thermocycling were optimized by
reducing anneal/extend time from 4min to 1min.
Template preparation: Targeted libraries were clonally amplified using an
isothermal amplification approach using the Ion PGM™ Template IA 500 Kit.
Template preparation for WGS libraries was performed using an automated and
rapid an isothermal amplification approach on the Ion Chef™ System
Sequencing: Sequencing was performed on the Ion S5™ XL Sequencer using
an Ion 520™ Chip. Sequencing times were improved by reducing flow times and
the total number of flows. The implementation of On-Instrument Analysis (OIA)
enabled near real-time base calling reducing the total primary analysis time.
Bioinformatic Analysis: Unassembled WGS data were analyzed by CosmosID
MetaGenID Bioinformatics package using curated GenBook databases of
Bacteria, Virus, Fungi, Parasite, Antibiotic Resistance, and Virulence Factors.
RESULTS
Targeted and WGS libraries were generated, sequenced, and analyzed in ≤6.5 – 11 hours with targeted sequencing and analysis taking as little as 50 minutes compared to 2.5 hours and 1 hour for standard sequencing and analysis, respectively. Analysis of sequencing
accuracy for targeted libraries revealed a raw read accuracy >99.5%, comparable to data from the standard workflow (Figure 4). The read length distribution for the targeted libraries was similar to standard workflow (Figure 5) with 100% specificity for species identification
and ,at flows greater than 200, mapping to 16S rRNA families for targeted libraries indicating rapid sequencing without compromising detection accuracy (Figure 6). Sequencing times on the Ion S5TM XL were vastly improved by the combination of reduced flow times, total
number of flows, and the implementation of On-Instrument Analysis (OIA), in which phase estimation prior to base calling was moved on instrument (Figure 7). The modifications for rapid sequencing were found to be robust and highly reproducible (Figure 8). Sequencing
libraries prepared from bacterial genomes representing a range of GC content demonstrated that the resulting shortened average read lengths did not adversely affect species identification (Figure 9). Antimicrobial resistance determinant identification from WGS libraries
was robust to 300 flows (Figure 10)
Read quality of Ion S5 XL with reduced flow number numbers
is comparable to that of standard Ion PGM flow numbers.
Decreased flow numbers demonstrate a raw read accuracy
>99.5% with Ion S5 XL at 300 and 200 flows
Performance of S5 XL Sequencing with modified parameters is
highly reproducible (n=3) for targeted sequencing using the
AmpliSeq panel
Sequencing times on the Ion S5 XL were improved by reducing
flow times, the total number of flows, and the implementation of
On-Instrument Analysis (OIA)
Reducing flow number to 200 does not reduce total number of
reads nor the accuracy of species ID amplicon alignment nor
16S rRNA amplicon assignment. ~100% specificitywith species
ID targets were observed 180 flows. However, 16S rRNA
identification specificitywas affected at 180 flows. Based the
above results, a 200 flow minimum could be used for targeted
sequencing using this AmpliSeq panel without compromising
detection accuracy using universal and species-specific
amplicons.
Reducing the flows number (400, 300, 200, 150) shortened the
average read length for WGS libraries (reads subsampled to
1.1 million)but did not adversely affect species identification by
percent matching of total unique k-mers at ≥300 flows
Figure 10
Figure 9
Reducing flow number to 300 does not reduce identification (percent matching of total
unique k-mers) of antimicrobial resistance determinants and virulence factors in WGS
libraries
Isothermal Amplification
on Ion Chef (7 hr)
For Research Use Only. Not for use in diagnostic applications