Thorpe: Welcome to Beyond the Data.
I'm Dr. Phoebe Thorpe and here
with me today is Alicia Cronquist a food epidemiologist
with the state of Colorado.
Thank you very much for joining us.
Cronquist: Thank you.
Thorpe: You have a very interesting job
at the state of Colorado.
Tell me what you get to do.
Cronquist: I coordinate the surveillance
and outbreak investigation for foodborne and enteric pathogens.
Thorpe: So when somebody gets sick you get
to figure out what caused it.
Cronquist: We should certainly try to, yes.
Thorpe: Our session today talks about CIDT's,
culture-independent diagnostic testing.
Tell me what that is.
Cronquist: Culture-independent diagnostic testing is any sort
of laboratory test that detects the antigen or the nucleic acid
for the pathogen in question.
It's different from culture
in which you're growing the bacteria on an agar plate.
Thorpe: It tests for small bit of the bacteria rather
than actually growing the whole bacteria?
Cronquist: Yes, that's an important distinction.
Thorpe: And that's been helpful because it makes it faster?
Cronquist: There are quite a few advantages to CIDT,
or culture-independent diagnostic testing.
And the first one, from the patient perspective,
and the provider perspective,
and the public health perspective is
that culture-independent diagnostic testing is faster.
You can have results in the same day.
Whereas culture can take two,
three or sometimes even longer days.
Thorpe: And sometimes you can't culture things.
Cronquist: Right.
Another huge advantage
of culture-independent diagnostic testing is
that it can test for a wider range of pathogens
than you can test for with culture.
This has been incredibly important
with some pathogens already such as Shiga toxin-producing E. coli
where it's revolutionized how we detect investigative control
Shiga toxin-producing E. coli, or STEC.
Thorpe: So, but it came out in our presentation
that there's some disadvantages
to using CIDTs instead of cultures.
What, what, some of the problems there?
Cronquist: There are several challenges
from a public health perspective with CIDT.
One of the challenges is
that you can't distinguish whether the organism is alive
or dead.
And so it can detect organisms that have died.
So it can't tell you if the patient is still infectious.
This is important to us when we're trying to decide
if somebody needs to be kept home from school or child care
or kept out of work
until they're cleared by public health.
Thorpe: And then there was also some mention about,
what if you wanted to connect one person's infection
to another infection to figure out where the source is...
Cronquist: Right.
One of the biggest challenges with CIDT is
that it doesn't produce an isolate, or a tiny piece
of the bacteria that made somebody ill.
And these isolates are very, very important to us for a range
of public health, public health uses.
For example, Pulsenet, which we talked about in the presentation
as well, but Pulsenet helps us to detect infections
that might be spread around the country.
That is still an isolate-based system.
We also do routine subtyping and serotyping in speciation
which helps us to monitor trends by subtype or species over time.
So for example if we launch an intervention to,
to control Salmonella enteritidis in one part
of the food supply, we need isolates
to track the Salmonella enteritidis,
not just general Salmonella.
Thorpe: And it also is important
for antibiotic resistance tracking too?
Cronquist: Yes.
At this point we need isolates
to do antimicrobial susceptibility testing.
This is important at the patient level to direct patient care.
But it's also very important at the population level
so we know what type
of antibiotic susceptibility we're seeing
in foodborne pathogens.
Thorpe: And you, you mentioned Pulsenet.
Pulsenet is been around 20 years this year,
and it has really thrived because of partnerships.
Can you tell me some of what the partnerships are doing
to work on these challenges?
Cronquist: Pulsenet has been a roaring success.
So one of the reasons for that is the clinical laboratories
around the country submit isolates, or little pieces
of the bacteria to state public health labs,
where public health labs use pulsed-field gel
electrophoresis, or PFGE,
and upload those sequences to Pulsenet.
It, it's all worked so well
because clinical labs have submitted the isolates to us.
What we're working on now is making sure clinical labs
continue to submit isolates or the clinical material,
which is generally stool, to the state public health labs
so that we can do the culture
and then the pulsed-field gel electrophoresis .
Thorpe: And that helps them, you figure out what,
what isolates are going around and who might've been infected
with them and how else is that also used, the isolates?
Cronquist: The isolates are used
for a really wide range of things.
The number one reason is exactly what you say, isolates are used
to detect outbreaks and without it we won't have Pulsenet
working so well to detect foodborne outbreaks.
It won't help us to prevent as much disease.
Isolates are also used
for antimicrobial susceptibility testing so that
at a population level we can make recommendations
about what antibiotics are effective
and what trends we're seeing, and then it also helps us
to track serotype specific surveillance data.
So it's not enough for us to say all E. coli is going up
or going down, or all Salmonella is going up or going down,
we need to monitor a little bit more finely.
Thorpe: There's some technologies that are coming
and the partnership is, are working together
to make the technologies and have a plan.
Can you tell me a little bit more about that, where the,
where you're going in the future?
Cronquist: With whole genome sequencing we can,
we can detect an even finer level of distinction
between the various strains of bacteria that we're tracking.
But whole genome sequencing still requires isolates.
So while we're taking a great leap forward
with whole genome sequencing, we still need isolates
and we still need partnerships with clinical labs
and state public health labs to receive isolates
or clinical material from them.
Thorpe: And then they mention some other technologies
that are being explored and so this is kind of a plan
to go forward of how to get from, the,
incorporate both the CID technology
and other technologies that are coming up.
Is that what's going on?
Cronquist: That's exactly right.
Right now we're in a phase when we still need isolates
in the setting of CIDT.
We still need to have isolates to do PFGE
and whole genome sequencing
and antimicrobial susceptibility testing.
However there is quite a lot of work going
on to generate the next, the next level of testing
where we don't believe we will need isolates anymore.
So are in an interim stage where we're using a lot of resources
and we're thinking hard about how to make sense
of our CIDT data and how to still obtain isolates
for all the testing we need to do.
But we know that there is plans in the future
that will move us away from that. We're very excited about that.
Thorpe: This all sounds really exciting and thank you
so much for joining us.
Cronquist: Thank you!
Thorpe: And if you want to know more about it,
please see our public health grand rounds
and thank you for joining us