Combining Ion Torrent next generation sequencing with qPCR facilitates real-time outbreak investigations

The 2011 Escherichia coli outbreak in Germany caused by the Shiga-toxin producing E. coli (STEC) with the O104:H4 serotype, claimed 50 lives and sickened more than a thousand1. The outbreak was a sobering reminder of the dangers of STEC infection, which in humans generates symptoms ranging from mild intestinal complications to more serious kidney problems that can be fatal.  

To identify the outbreak isolate, the genetic code of this deadly E. coli strain was sequenced in just three days by scientists in Germany and independently supported by a second research team in China. Because speed and accuracy mattered most, both teams used the Ion Personal Genome Machine® (PGM™) System. With 2.5-hour run times the Ion PGM™ System can generate whole-genome sequencing results from library prep to assembly in under a day whereas other methods may require weeks.  The rapid sequencing of the E. coli bacteria helped scientists locate the source of the outbreak, determine from which older strains the new bacteria evolved, and identify important features of the bacteria such as antibiotic resistance2.

The genetic information also led to the rapid development of a custom qPCR assay to accurately detect this E. coli isolate to screen food samples. The qPCR-based assay can determine the presence or absence of a pathogen in 10–24 hrs, depending on sample types and size, whereas traditional testing methods can take up to 10 days for results. The qPCR-based test from Life Technologies combines advances in sample preparation using Dynabeads®, a sensitive qPCR step, and sophisticated data analysis.   
In the anticipation of the next outbreak, when there’s no room for error, next generation sequencing followed with qPCR-based assay development offers many advantages over other molecular techniques.  Together their speed, accuracy, and sensitivity, with the capacity to identify and quantify the target organism, make these techniques promising tools to make the world a safer place.    

For more information on next generation sequencing solutions for outbreak investigation, check out our Ion PGM™ System bacterial typing page.  For more information on customized PCR assay and reagents to off-the-shelf food testing for Salmonella, Salmonella enteritidis, E. coli, Listeria, Cronobacter sakazakii, and Campylobacter jejuni, check out Life Technologies solutions to food safety.


  1. European Food Safety Authority (July 11, 2012)  “E.coli:  Rapid response in a crisis”  
  2. Mellmann A et al.  2011 Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology.  PLoS ONE 6(7):e22751
  3. Rohde H, et al. Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. New England Journal of Medicine. 10.1056/NEJMoa1107643 [doi]

For research use only. Not for use in diagnostic procedures.