Next Generation Sequencing:
READY FOR
PRIME TIME PRIME TIME
READY FOR
by Nancy Maddox, writer
May 2011 was a bad month for german health officials. an unusually virulent strain of E. coli was running amok in the country, sickening thousands of people and
ultimately killing 53. authorities initially identified spanish
cucumbers as the source of the outbreak, but—after causing
spanish exporters to lose hundreds of millions of dollars in sales—
cucumbers were exonerated.
Now what?
Enter the Ion Torrent, one of Life Technologies
next-generation sequencing (NGS) platforms.
Two teams of scientists used the Ion Torrent to lay
bare the bacterium’s entire genome in three days
flat. The detailed molecular information enabled the
development of a real-time PCR test to distinguish
among the outbreak strain of E. coli O104:H4 and
closely related strains. That test, in turn, enabled
laboratory scientists to effectively screen the food
supply. Not long thereafter, the true culprit was
fingered: bean sprouts grown in Lower
Saxony, Germany.
The resolution of that outbreak is just one example of
the power of NGS technology. The Ion Torrent and its
competitors—Illumina’s MiSeq, Roche’s Junior GS,
and others—are the cutting edge in microbiology
test platforms, delivering orders of magnitudes more
information than any previous technology.
Yet although NGS has been used in some high-profile
disease investigations—for example, tracing the chain
of transmission of Klebsiella pneumoniae during an
outbreak at the National Institutes of Health (NIH)
Clinical Center—it has mostly been confined to
high-end research laboratories, like those at NIH.
With smaller, cheaper test platforms now on the
market, the technology is making its way into the
public health arena.
Kelly Wroblewski, MPH, MT(ASCP), director of APHL’s
infectious disease program, estimates that “a handful
to a large handful” of public health laboratories (PHLs)
have capability for NGS. Although, even at these
laboratories, most “next-gen” projects are still
spinning up.
John Fontana, PhD, head of the Connecticut Public
Health Laboratory, said, “One of the things I think
should be said about [NGS] is it’s not that easy to use
so far. There’s no standard way of analyzing the data.
I think the information you get from the sequencer is
the easy part. The hardest part is doing the analysis.
That’s where resources are thin.”
Fontana has an Ion Torrent in house, but is relying
on interns from the University of Connecticut professional science master’s program to “get it going.”
The Connecticut laboratory, like most PHLs, has no
dedicated research unit. Said Fontana, “We’re waiting
for people to develop [best practices] and give us some
help to do the analysis.”
