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.

Application Notes & Publications

Read application notes and peer-reviewed publications to learn how the Ion PGM™ System has been used for bacterial and viral typing.

Data Set

Download a data set generated on the Ion PGM™ System and see the results for yourself.

Informatics Solutions

Learn about bacterial identification informatics solutions for the fastest way to get to your biological results.

Bacterial Typing Workflow for the Ion PGM™ System

1 Construct

The Ion Plus Fragment Library Kit or Ion Xpress™ Plus Fragment Library kit provides low-cost sample preparation in as little as 2 hours...Read more

2 Prepare

The Ion Chef™ System† provides simple, high-throughput template preparation with only minutes of hands-on time....Read more

3 Run

The Ion PGM™ Sequencer enables rapid sequencing with 400 or 200 bp sequencing. Runs are completed in just 3.7 hours...Read more

4 Analyze

Primary data analysis is performed using Torrent Suite™ Software. The Ridom™ SeqSphere+ software...Read more

Bacterial Typing Application Notes, Literature and Publications

Application Notes and Literature

Bacterial Typing Application Note

Microbial Solutions Brochure

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.

Ion PGM™ Hi-Q™ Sequencing Kit
Ion 16S™ Metagenomics Solution