WEBVTT

00:00:00.000 --> 00:00:05.390 align:middle line:90%


00:00:05.390 --> 00:00:07.560 align:middle line:84%
I have with me here
Estee Torok, who's

00:00:07.560 --> 00:00:09.660 align:middle line:84%
going to be telling
us about her research

00:00:09.660 --> 00:00:11.760 align:middle line:84%
into how genome
sequencing can be

00:00:11.760 --> 00:00:14.700 align:middle line:90%
useful for medical microbiology.

00:00:14.700 --> 00:00:17.720 align:middle line:84%
So, Estee, tell us
about your research.

00:00:17.720 --> 00:00:18.600 align:middle line:90%
Hello, Josie.

00:00:18.600 --> 00:00:21.270 align:middle line:84%
As you know, I'm a Consultant in
Infectious Diseases and Medical

00:00:21.270 --> 00:00:24.030 align:middle line:84%
Microbiology at Addenbrooke's
Hospital in Cambridge.

00:00:24.030 --> 00:00:26.670 align:middle line:84%
And I spend most of
my time in research.

00:00:26.670 --> 00:00:30.030 align:middle line:84%
My research involves
using microbial genomics

00:00:30.030 --> 00:00:33.120 align:middle line:84%
to investigate outbreaks
of infection in hospital,

00:00:33.120 --> 00:00:36.944 align:middle line:84%
and also to rapidly diagnose
drug-resistant infections.

00:00:36.944 --> 00:00:38.610 align:middle line:84%
And this can be very
helpful, because it

00:00:38.610 --> 00:00:40.710 align:middle line:84%
can inform infection
control teams

00:00:40.710 --> 00:00:43.440 align:middle line:84%
and advise them as to whether
to escalate or de-escalate

00:00:43.440 --> 00:00:45.090 align:middle line:90%
infection control procedures.

00:00:45.090 --> 00:00:46.660 align:middle line:84%
And in terms of
patient management,

00:00:46.660 --> 00:00:48.960 align:middle line:84%
it can help us to target
antibiotic therapy.

00:00:48.960 --> 00:00:51.240 align:middle line:84%
Currently, how are
bacterial infections

00:00:51.240 --> 00:00:53.514 align:middle line:90%
tested for drug resistance?

00:00:53.514 --> 00:00:55.680 align:middle line:84%
So, what we normally do in
the diagnostic laboratory

00:00:55.680 --> 00:00:58.530 align:middle line:84%
is we plate the organisms
onto agar plates.

00:00:58.530 --> 00:01:02.280 align:middle line:84%
And then we put antibiotic
discs onto the agar plates

00:01:02.280 --> 00:01:04.030 align:middle line:90%
and incubate them overnight.

00:01:04.030 --> 00:01:06.780 align:middle line:84%
And if the organism is
sensitive to the antibiotics,

00:01:06.780 --> 00:01:09.330 align:middle line:84%
you get a zone of clearance
around the antibiotic disc.

00:01:09.330 --> 00:01:12.420 align:middle line:84%
But if the organism
is resistant,

00:01:12.420 --> 00:01:16.230 align:middle line:84%
then the organisms grow up
towards the antibiotic disc.

00:01:16.230 --> 00:01:21.330 align:middle line:84%
So, it's a method that is cheap
and relatively straightforward,

00:01:21.330 --> 00:01:24.720 align:middle line:84%
but can take 24 to 48
hours to give us a result.

00:01:24.720 --> 00:01:28.290 align:middle line:84%
What can genomics offer over
these traditional laboratory

00:01:28.290 --> 00:01:29.590 align:middle line:90%
methods?

00:01:29.590 --> 00:01:33.000 align:middle line:84%
So, in addition to giving us
antibiotics susceptibility

00:01:33.000 --> 00:01:36.150 align:middle line:84%
data, one of the advantages
is that the rapid methods

00:01:36.150 --> 00:01:37.570 align:middle line:90%
can do this much more quickly.

00:01:37.570 --> 00:01:41.680 align:middle line:84%
So, within a few hours, rather
than within 24 to 48 hours.

00:01:41.680 --> 00:01:44.250 align:middle line:84%
In addition to the antibiotic
susceptibility or resistance

00:01:44.250 --> 00:01:48.120 align:middle line:84%
data, it can give us organism
identity, and information

00:01:48.120 --> 00:01:50.970 align:middle line:84%
about virulence factors,
such as toxin genes.

00:01:50.970 --> 00:01:53.190 align:middle line:84%
So, are you using these
genomic methods routinely

00:01:53.190 --> 00:01:55.120 align:middle line:90%
at Addenbrooke's Hospital?

00:01:55.120 --> 00:01:55.904 align:middle line:90%
We're not quite.

00:01:55.904 --> 00:01:57.570 align:middle line:84%
This is something
that we've been trying

00:01:57.570 --> 00:01:58.839 align:middle line:90%
to do for a little while.

00:01:58.839 --> 00:01:59.880 align:middle line:90%
And we're in the process.

00:01:59.880 --> 00:02:02.910 align:middle line:84%
We've done a number of
proof-of-concept studies.

00:02:02.910 --> 00:02:07.040 align:middle line:84%
But at the moment, we're not
able to do this in real time.

00:02:07.040 --> 00:02:08.550 align:middle line:84%
However, there is
a project that's

00:02:08.550 --> 00:02:10.940 align:middle line:84%
about start at Addenbrooke's
in the new year, which will

00:02:10.940 --> 00:02:12.690 align:middle line:90%
aim to do this in real time.

00:02:12.690 --> 00:02:15.180 align:middle line:84%
And obviously, within
Public Health England,

00:02:15.180 --> 00:02:18.940 align:middle line:84%
it's being done for organisms
such as tuberculosis.

00:02:18.940 --> 00:02:21.690 align:middle line:84%
So it's not quite in
everyday clinical practise,

00:02:21.690 --> 00:02:22.990 align:middle line:90%
but it's on its way.

00:02:22.990 --> 00:02:25.110 align:middle line:84%
So what are the
challenges associated

00:02:25.110 --> 00:02:27.120 align:middle line:84%
with using these
methods routinely

00:02:27.120 --> 00:02:28.920 align:middle line:90%
in a health care setting?

00:02:28.920 --> 00:02:30.820 align:middle line:84%
OK, so, there are a
number of challenges.

00:02:30.820 --> 00:02:33.330 align:middle line:84%
First of all, not every
diagnostic microbiology

00:02:33.330 --> 00:02:35.220 align:middle line:84%
laboratory has
sequencing machine,

00:02:35.220 --> 00:02:37.050 align:middle line:90%
because they're quite expensive.

00:02:37.050 --> 00:02:40.330 align:middle line:84%
Secondly, people need to
be trained to use them.

00:02:40.330 --> 00:02:42.870 align:middle line:84%
Thirdly, we need to have
expertise to analyse the genome

00:02:42.870 --> 00:02:46.410 align:middle line:84%
sequence data and report it
back to clinical, and people.

00:02:46.410 --> 00:02:48.160 align:middle line:84%
So, there are a
number of challenges.

00:02:48.160 --> 00:02:51.240 align:middle line:84%
First of all, cost, secondly,
expertise, and thirdly,

00:02:51.240 --> 00:02:52.449 align:middle line:90%
availability.

00:02:52.449 --> 00:02:54.240 align:middle line:84%
And things are being
changed at the moment.

00:02:54.240 --> 00:02:56.640 align:middle line:84%
So, bioinformatic pipelines
are being developed

00:02:56.640 --> 00:03:00.000 align:middle line:84%
that will become more automated,
and will enable us to use

00:03:00.000 --> 00:03:01.560 align:middle line:90%
this in clinical practice.

00:03:01.560 --> 00:03:03.570 align:middle line:90%
And is it expensive?

00:03:03.570 --> 00:03:06.580 align:middle line:84%
To buy a machine is, I
think, about £80,000.

00:03:06.580 --> 00:03:09.480 align:middle line:84%
So it's too expensive
for most laboratories

00:03:09.480 --> 00:03:11.550 align:middle line:90%
to afford them by themselves.

00:03:11.550 --> 00:03:13.920 align:middle line:84%
The costs of the actual tests,
I think you can sequence

00:03:13.920 --> 00:03:16.510 align:middle line:84%
a bacterial genome for
between £50 and £100,

00:03:16.510 --> 00:03:20.770 align:middle line:90%
depending on economies of scale.

00:03:20.770 --> 00:03:22.690 align:middle line:90%
Thank you very much, Estee.

00:03:22.690 --> 00:03:24.590 align:middle line:90%
My pleasure, Josie.

00:03:24.590 --> 00:03:27.638 align:middle line:90%