Fast and affordable for routine monitoring and outbreak investigation
The Ion PGM™ System has been critical in facilitating a rapid response during disease surveillance and outbreak investigations, and for disease etiology determination.
Read application notes and peer-reviewed publications to learn how the Ion PGM™ System has been used for bacterial and viral typing.
Download a data set generated on the Ion PGM™ System and see the results for yourself.
Learn about bacterial identification informatics solutions for the fastest way to get to your biological results.
Bacterial Typing Workflow for the Ion PGM™ System
Bacterial Typing Application Notes, Literature and Publications
Application Notes and Literature
Discover how German scientists leveraged the Ion PGM™ Sequencer to get answers when faced with a serious public health outbreak (shiga toxin-producing E. coli outbreak in northern Germany). Learn more
The Ion PGM™ System is cited in more than 40 peer-reviewed publications about small genome sequencing, making it the leading system for de novo assembly of small genomes.
Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology. PLoS One 6(7):e22751. Mellmann A, Harmsen D, Cummings CA, et al. (2011)
Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4 N Eng J Med. 10.1056/NEJMoa1107643 [doi] Rohde H, et al. (2011)
Ion Torrent Personal Genome Machine sequencing for genomic typing of Neisseria meningitidis for rapid determination of multiple layers of typing information. J Clin Microbiol JCM.00038-12 [pii];10.1128/JCM.00038-12 [doi]. Vogel U, et al. (2012)
Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol. JCM.06094-11 [pii];10.1128/JCM.06094-11 [doi]. Larsen et al. (2012).
Bacterial Typing Informatics Solutions
Torrent Suite™ Software provides the tools that take you from raw sequence data to informative results, including optimized signal processing, base calling, sequence alignment, and variant analysis. Post run, sequencing data are available for download with a simple right-click. Reports are also easily browsed, with expandable analysis plots and straightforward tables that summarize key results to help ensure that sequencing runs are of high quality.
Bacterial and viral typing specific workflows in third-party software packages such as the Ridom® SeqSphere+ software package automate downstream analysis. SeqSphere+ enables your lab to employ whole genome microbial typing (MLST+), traditional MLST, or 16S rDNA sequencing projects. This software is designed for individual or distributed work-groups (client/server model) to enable easy data sharing.
Learn more about how this software can simplify your data analysis.
Microbial Sequencing videos
On Top of Outbreaks
Hear Dag Harmsen, M.D. from the University of Münster discuss how the Ion PGM™ System provides fast and accurate whole-genome “shotgun” sequencing of microbes for disease research on retrospective samples from outbreaks.
For Research Use Only. Not for use in diagnostic procedures.
The Ion Plus Fragment Library Kit or Ion Xpress™ Plus Fragment Library kit provides low-cost sample preparation in as little as 2 hours for gDNA and amplicon libraries.
The Ion Chef™ System® provides simple, high-throughput template preparation with only minutes of hands-on time. The Ion OneTouch™ 2 System provides simple, 15-minute template preparation for 400 or 200 bp sequencing runs.
The Ion PGM™ System enables rapid sequencing with 400 or 200 bp sequencing. Runs are completed in just 3.7 hours and 7.3 hours for the Ion 314™ Chip and Ion 318™ Chip, respectively.
Primary data analysis is performed using Torrent Suite™ Software. The Ridom™ SeqSphere+ software package provides a follow-on solution for bacterial typing.
Multilocus sequence typing of total-genome-sequenced bacteria.
J Clin Microbiol 50(4):1355–1361. Larsen MV, Cosentino S, Rasmussen S, et al. (2012)
Ion torrent personal genome machine sequencing for genomic typing of Neisseria meningitidis for rapid determination of multiple layers of typing information.
J Clin Microbiol 50(6):1889–1894. Vogel U, Szczepanowski R, Claus H, et al. (2012)
J Bacteriol 194(10):2759–2760. Amaral GR, Silva BS, Santos EO, et al. (2012)
Genome sequences for six Rhodanobacter strains, isolated from soils and the terrestrial subsurface, with variable denitrification capabilities.
J Bacteriol 194(16):4461–4462. Kostka JE, Green SJ, Rishishwar L, et al. (2012)
Next-generation Ion Torrent sequencing of drug resistance mutations in Mycobacterium tuberculosis strains.
J Clin Microbiol 50(12)3831–3837. Daum LT, Rodriguez JD, Worthy SA, et al. (2012)
Draft genome sequence of Staphylococcus vitulinus F1028, a strain isolated from a block of fermented soybean.
J Bacteriol 194(21):5961–5962. Nam YD, Chung WH, Seo MJ, et al. (2012)
Molecular evidence for interspecies transmission of H3N2pM/H3N2v influenza A viruses at an Ohio agricultural fair, July 2012.
Emerg Microbes and Infec 1: e33. 10. Bowman AS, Sreevatsan S, Killian ML, et al. (2012
Isolation of a novel swine influenza virus from Oklahoma in 2011 which is distantly related to human influenza C viruses.
PLoS Pathog 9(2):e1003176. Hause BM, Ducatez M, Collin EA, et al. (2013)
Outbreak investigation using high-throughput genome sequencing within a diagnostic microbiology laboratory.
J Clin Microbiol [Epub ahead of print]. Sherry NL, Porter JL, Seemann T, et al. (2013)