We have all heard about the increasing use of point of care
testing in physician’s offices, etc. where rapid molecular
tests are used to screen a patient for multiple pathogens
at one time, providing an immediate result to help the
physician decide what the pathogen is and what drug
might be the best to treat the patient. While this is good for
the patient, public health labs will face a new challenge in
terms of surveillance, as there may no longer be a clinical
isolate of this infectious organism submitted to the public
health lab for further studies to look for changes in the
organism or development of resistance to certain drugs.
The only option may be to obtain the genetic material
from the initial patient specimen and analyze this using
bioinformatics expertise to determine more complete
information about the organism.
Do you foresee public health laboratories
(pHls) generating whole genomes for
surveillance purposes, or a more targeted
approach based on whole genome
information?
I think PHLs will have a role in both. They will need to use
NGS, for example, to sequence whole genomes of E. coli or
Salmonella to determine the sources of outbreaks—the
more complete genomes that are available to be shared and
analyzed, the more we will begin to understand how the
organism evolves and interacts in its host environment.
You may think this is all research that is probably being
performed in a university setting somewhere; however,
while researchers may be looking at the genetics of an
organism to develop a drug to target it, public health may
be looking at this genetic information to better understand
how the organism interacts during an outbreak in different populations. Computer programs now exist that can
predict how that organism might evolve in the future and
how current vaccines may become ineffective against it.
PHLs may not always need to sequence the full genome of
an organism, as specific gene regions could be targeted and
sequenced to identify an organism.
Do you think the world of classical bacteriol-
ogy/virology will totally disappear with these
new emerging technologies? What will a
public health laboratory look like in 20 years?
No, I think it will be very important to keep classical
bacteriology and virology skills in our laboratories so we
can identify new emerging organisms. Our big challenges
will be to maintain and continue to train the appropriate
laboratory staff in these important areas. I think in 20
years, PHL’s will look quite different; I envision a lot more
automated systems that can process samples and generate
vast amounts of data. I expect scientists in PHLs will spend
a lot more time in front of a computer making sense of
all this data; developing skills in bioinformatics will
be essential.
What are the challenges of bioinformatics
(using computers to manage biological
information)?
The vast amount of data produced by NGS platforms, which
produce dozens of terabytes of data (the average server
holds between 4 – 12 terabytes). Storing this data in a
cloud-based system may be the best solution in the near
future, but there are still concerns with privacy and
security. Analysis of the data also requires significant
computing power; data can be sent to powerful and fast
supercomputers to be analyzed and returned. Challenges
for PHLs will be obtaining and training staff with knowledge in bioinformatics; they will play a key role in
addressing quality issues with the sequence data.
Currently, approximately half the costs of NGS are in
bioinformatics (i.e., software costs and skilled scientists).
What does all this mean for the average,
non-laboratory, person?
I believe NGS will lead to better treatment through personalized medicine. The abilities to look for genetic markers
of disease (or markers that may predispose an individual
to disease) will help people decide on necessary lifestyle
changes to reduce their chances of getting a disease. Use
of personalized medicine would have applications in
pharmacogenetics (the study of how genes influence an
individual’s response to drugs) and preventative medicine,
screening for mutations before a person gets a disease in
the first place.
is there anything else you would like to add?
What we do know is that as more sequencing is performed,
more variants of unknown significance will be discovered;
and it will be up to the laboratory and the clinician to
interpret this data to know which sequence data have real
consequences and which are artifacts due to the technology. I think it is a good time for PHLs to start looking at the
future applications of NGS (if they are not already doing
this) such as newborn screening both pre and postnatal,
and outbreak detection in clinical, environmental and food
samples, etc.u
