Hello, and thank you for listening to the MicroBinFeed podcast. Here, we will be
discussing topics in microbial bioinformatics. We hope that we can give you some
insights, tips, and tricks along the way. There is so much information we all
know from working in the field, but nobody writes it down. There is no manual,
and it's assumed you'll pick it up. We hope to fill in a few of these gaps. My
co-hosts are Dr. Nabil Ali Khan and Dr. Andrew Page. I am Dr. Lee Katz. Both
Andrew and Nabil work in the Quadram Institute in Norwich, UK, where they work
on microbes in food and the impact on human health. I work at Centers for
Disease Control and Prevention and am an adjunct member at the University of
Georgia in the U.S. Hello and welcome to the MicroBinFeed podcast. Andrew and I
are your co-hosts today, and we're talking about Campylobacter. We're hoping we
can discuss some of the specific issues for bioinformaticians to keep in mind
when studying this organism. Our guest today is Dr. Ozan Gongadou. He leads the
Foodborne Enteric Pathogen Group at the London School of Hygiene and Tropical
Medicine, where they study the physiology and pathogenesis of Campylobacter and
other related enteric microorganisms like Listeria and Vibrio. He has a
background in microbiology and computer science. He completed his PhD at LSHTM
in 2011, and he's worked in a number of different projects continuing Campy
pathogenesis and some omics as well. And he started his position in early 2019
as an assistant professor and group leader. So Ozan, firstly, we normally ask
the question, who are you and what is a typical day for you? Yeah, so thanks for
having me on this podcast. So yeah, so my background is a microbiologist and
computer scientist, and I've been at the school at London School of Hygiene and
Tropical Medicine actually for a long time, since 2004. And I would say my first
decade at the school was studying really the pathogen and physiology of
Campylobacter, trying to understand the function of genes and their roles, often
related to survival. And really, a lot of my research in the last sort of five
years have moved from the sort of laboratory work to more applied work, because
it's a really important aspect of Campylobacter research and shifting more
towards next generation sequencing, whether that's whole genome sequence
transcriptomics or metagenomics microbiome work. So a typical day these days
involves doing, trying to find a little time to do some research, and that is
often bioinformatics research. I have very little time, unfortunately, to go
back in the lab. And currently, I have three PhD students and one postdoc, and
they are doing all of the laboratory work in terms of pathogenesis and
physiology. And yeah, the typical cycle of academia of trying to win, trying to
get some funding to continue this research. So can you tell me about
Campylobacter, right, because it's not a pathogen that is on the tip of your
tongue. If a common person thinks about foodborne pathogens, you know, he thinks
chicken, salmonella, that kind of thing. So where does Campy fit into that? In
the early 2000s, when I started, when I spoke to people about Campylobacter,
that I'm working on Campylobacter, most people hadn't heard of it. And you know,
especially when you compare it to something like Salmonella, that a lot of
people were aware of. And I think there's a few reasons for this. The disease,
Campylobacter is typically self-limiting. So most people would contract it
within two weeks. You may get diarrhea, you may get, you know, various symptoms
related to diarrhea and gastroenteritis, but it would pretty much clear and pass
out the system. The problem that we have is that there's a, first of all,
there's a distinction between what we see in high resource countries and what we
see in low resource, low middle income countries, low resource countries. So in
high resource countries, it's typically acute bloody diarrhea, and it's more
associated with an economic, economic implications of the disease. So a lot of
people take time off work. And for example, in 2019, it was estimated that it
cost the UK government 1 billion alone that year from people contracting
Campylobacter. However, elderly people, immunocompromised people, they can get,
they can die from it. And one of the issues is that most people don't go to
report the infection. So whereas we see cases in the UK of like 50,000, 60,000,
70,000 a year, it's generally believed that it's actually 10 times more than
this. So it's up to like half a million or more. So what are the main routes of
transmission then? So the main routes of transmission, pretty much in the
developing, in the high resource countries, it's from contaminated poultry,
contaminated avians, from food. However, just to, just to go back on the disease
profile in low resource countries is very different. It's watery diarrhea. And a
lot of children die from, from contracting Campylobacter. And just simply a case
of lack of fluids, probably due to pre-exposure and the regularity of exposure
in low resource countries. A lot of the time, it's much more environmental. It's
much more from things like just water contamination. People don't get acute
diarrhea. They would get what's acute bloody diarrhea. They would get more of a
watery diarrhea. And so the disease profiles, if you like from high income
countries and low income countries are different. And the sources of where you
actually contract the infection are varied. I would say in the last five years,
the UK government has definitely made a big push to educate people to be much
more aware of what Campylobacter is. So definitely speaking to people, you get
an impression that they are much more aware of this. A classic example they gave
is there was a government campaign to say, don't wash your chicken. Don't wash
your poultry when you get it out, when you take it out of the bag. And most
people actually were a bit confused by that because naturally one would think
you'd wash it to make it clean. The problem is, is that on the surface of the
actual avian, the poultry Campylobacter resides heavily in numbers. And so there
was a risk of it splashing around, you know, to utensils, to surrounding
vegetables or tables, equipment and things like that. And so you actually were
increasing the risk of Campylobacter passing, getting to humans. And so it was
the advice was take it out of the bag and directly put this in the oven and cook
the thing properly. And that does go a long way to actually minimizing the
contraction of Campylobacter infection. So yeah, I would say definitely more
people are aware of Campylobacter these days. I mean, how often would you expect
to see Campy on a store-bought chicken? The problem we have, okay, a little bit
is why is Campylobacter present in chickens in such high numbers? So it can
actually be found up to 10 to the 9 CFU, that's a hell of a lot of, you know,
bacteria colonies within chickens. And it doesn't necessarily cause avians and
chicken harm. This is a, this is a bit of a conundrum. So there is a discussion
point about whether is Campylobacter a commensal, you know, is it actually there
happily residing? There has been some research in the last five years that have
shown, depending on the strain of Campylobacter, the, you know, the genomics of
the Campylobacter, what genes are present in the genome, the type of chicken and
the environmental conditions, it, you know, Campylobacter within chickens may
actually cause a similar disease or a disease profile within chickens. And so
there's a discussion point as to whether it's classified as a commensal, but the
reality is it's there in high numbers. So is there any difference between like
organic chicken or free range chicken or just, you know, barren hens, that kind
of thing? So that's a good question. The short answer is very difficult to
answer that in a yes or no response. What I would say is that some of the
research that actually we've been doing the last five years have shown that
actually if you manipulate the environmental parameters, if you manipulate, for
example, stocking density, which is the amount of chickens in a space, you do
change, you do have a knock-on effect on the chicken gut microbiome in terms of
microbial population structure and potentially also impact the levels of
Campylobacter within the chickens. So it's very difficult to definitively say,
you know, you need to do this or you need to do that. I mean, in terms of in
terms of poultry welfare and things like that, it's obviously very important to
have, you know, low stocking density and all of these welfare issues come into
play. And obviously that has downstream effects on Campylobacter within the
actual avians. So my understanding of the way chickens are reared for eating
broiler chickens, they get an empty, like a chicken, I don't know what you call
it, a barn. And then they shove in some new, you know, baby chicks, they grow
them up. And then a few weeks later, they kill them all and then it's empty
again. So how does Campy persist? You know, how does it get in there and spread
and then keep spreading all the time? It's the sort of $64,000 question. So
we've done some research where we've looked, and many other groups, when do you
see Campy appearing in the chicken gut microbiome? Why do you see it? You know,
why is it coming in there? There is some anecdotal information that says
typically it appears within the two weeks of the chicken life cycle. And you're
right. Typically, these chickens would be, for example, killed at day 35 for
meat production. Now, a lot of the time.  What definitely has happened is, you
know, in terms of controlling Campylobacter infections, yes, we need to study it
within the laboratory in terms of pathogenesis and physiology, and then link
that information to more applied research because what's happening in the
laboratory isn't always what's happening in the farm. Yes, government policy
needs to come into place to try to minimize Campylobacter coming into these
farms. And I can definitely say from visiting some of the UK's leading poultry
suppliers, I mean, just to get into these facilities, it was like going through,
you know, a NASA system of security. It was incredible. And so then you start to
question where is the Campylobacter coming from? Now, Campylobacter, one of its
most interesting attributes is it is omnipresent. It is present throughout the
environment. You can find it everywhere. And so this is a problem because even
though it's got a relatively small genome, I think roughly 1.64 megabases in
size, it's incredibly compact. There's very free space of, you know, it's all
open reading frames throughout the genome. And it must have good genetic
regulatory mechanisms to survive in non-ideal conditions. It's classified as
microaerophilic, which means ideally it likes five to 10% oxygen. And we have in
the environment approximately 19.2% oxygen. How is it able to survive in these
conditions? This is the great Campylobacter conundrum. I would also touch on a
little bit on Campylobacter in terms of why we've had difficulties studying it
over the years. Why is it, you know, a lot of scientists, when they think of
Campylobacter, it's a really fussy pedantic bacteria. And some of the reasons
for this is because when you compare it to other bacteria like Bacillus or E.
coli, it's not classified as a model organism. It hasn't had a very good
convenient animal model over the years, and it's very difficult to grow. It can
be quite fussy. And these attributes actually led us, it was one of the first
bacteria to have its whole genome sequence. This was in 1999, 2000 at the Sanger
Institute. And it was really interesting because it, again, we found a compact
genome. It did not have classic secretion systems like type three secretion
system, which was missing. More recently, our group has started studying, we
found strains that have the type six secretion system. So we've looked into
that. And it has, you know, I'll give you one story, one, you know, anecdote. A
lot of people pre-2000 did not believe Campylobacter had a capsule. They were
really adamant that it did not have a capsule around the actual bacteria. And
scientists at the NSHTM actually showed that it does have a capsule. And I
remember people apparently were speaking in a conference and the audience
members were shouting and saying, I've worked on Campylobacter for 30 years and
I've never seen a capsule. This is horrific. I'm leaving this presentation. Lo
and behold, the genome sequence came out. There's your 25, 30 gene loci encoding
for the capsule. Nobody said anything after that. It's clear, it's definitive.
And some other key attributes that came out from that genome sequence was things
like lipo oligosaccharide on the outer surface, you know, things like O-link
glycosylation, addition of sugars on the flagella to help evasion of the immune
system. And really interestingly, N-link glycosylation, periplasmic proteins,
outer surface protein, which sugars being added to help functionality
traditionally only found in eukaryotes. So this was something quite novel to
Campylobacter. So really that genome sequencing did spawn a new era, I would
say, of pathogenesis physiology research from 2000 onwards. So when you're
talking about Campy, do you mean the entire genus or are you talking more about
Jejuni? That's a good point. Yeah, so typically we're referring to Campylobacter
jejuni. And the reason for that is that's the species that causes about 80%, 85%
of infections within humans. There are some really other important species like
Campylobacter coli, Campylobacter foetus and various other ones. But yeah, so
typically we're talking about Jejuni. Is there any vaccines or anything or
treatments for it that you can give to chickens to stop it in its tracks before
it gets to humans? That's a really good question. And the vaccine discussion
point is really interesting. I think there are some vaccines out there at early
phase. I noticed that there's some research going on at NSHTM, for example, that
look at animals zoonotic type vaccines. I think a lot of the time it comes down,
it's two issues. First of all, it comes down to cost. There's no way to justify
giving a vaccine to, for example, putting it in the chicken feed or the poultry
feed to an animal that you're gonna sacrifice or kill in 35 days. So there has
to be a real cost. A lot of these things come down to cost. But the other side
is what I mentioned earlier. This is the interesting point. You only need 100 to
500 colonies to come into contact with a human and that human will contract an
infection. Can a vaccine work efficiently when there is 10 to the nine colonies
within a chicken? So even if you did bring that, even if the vaccine was
efficient and you did bring that number down to like 10 to the five or 10 to the
four, it's still there and it's still potentially giving issues to humans. And
so when we look at really dealing with campylobacter, I think maybe like almost
a one health approach is needed. So you need that laboratory pathogenesis
physiology and you need the vaccine potentially, you need government policy and
you need education to customers and consumers to cook the chicken properly. So
is campy present in like wild birds and things like that? So if you vaccinated
all the chickens, would you still have major problems then with just wild birds
flying around causing issues? Exactly, that is the case. Campylobacter is
omnipresent within the environment it is present in wild birds as well. And
there's been a number of studies on this and this links to what happens in low
resource countries because in low resource countries, you don't always get that
state of the art high throughput manufacturing process for chicken even poultry
production. You do backyard markets, you do get peri-urban type markets and
these all have a role in the zoonosis process. Yeah, I'm curious following on
from that, is there evidence of carriage in water for campy? Yes, big time. So
here's another anecdotal story. In high income, high resource countries, we do
see a peak in the summer of campylobacter. Now, there's a few hypotheses going
around for this. One that, you know, it could be due to lifestyle. So for
example, people do more barbecues, they may not be cooking their chicken
properly, there may be some contamination at that point. But you also see in
terms of, you know, humidity, water droplets, swimming pools, this kind of
thing, puddles even having campylobacter. So in the U.S. there was an outbreak
of campylobacter infections of people doing a, I'm not sure what the exact name
is, it wasn't a triathlon, but it was something like tough mother or something
like that. Iron man? No, tough mother's the thing, yeah, yeah. Tough mother? I
can't remember the exact name. And there was an outbreak, or a number of people
contracted campylobacter that was believed to be because there were a number of
puddles around this course or whatever it was that had campylobacter within the
water. And so this is the kind of thing that can happen. And it's quite
interesting because that's definitely linked more to sort of a lifestyle type
aspect. I don't think we have a clear definitive answer as to why the numbers
are increasing in the summer, in high resource countries at least, but I know a
lot of people are looking into that kind of research. Yeah, I'll just clarify
with the tough mother thing. That's quite, that makes sense because the tough
mother thing I think is, it's sort of that bootcamp obstacle course where you're
climbing over stuff or you're jumping over things with ropes and the water pits
behind it for you to fall into. So yeah, that would be very muddy and very wet
and people would be jumping in and out of water. Exactly. What about vaccinating
humans? You know, if we can't do chickens to humans, is there any vaccine
candidates out there, particularly for low resource countries? I'm not sure how
close we are to that if I'm honest with you. I know people are working on this,
but again, it comes down to cost. It's not an area that I have expertise. Okay,
maybe I'll tell you the answer. I think the vaccine candidates they've had so
far cause Guillain-Barre disease. Apart from gastroenteritis, one of the issues
that can happen if you contract campylobacter there is approximately, I think
the numbers are like one in a thousand chance that you could get post-infectious
neuropathy. So those are where the bacteria outer surface mimics the human
gangliosides within the human. And so you actually get an autoimmune illness. So
your body attacks yourself and you can get paralysis. And there's a variant of
this Miller-Fisher syndrome which is paralysis of the eyes. One in a thousand
doesn't sound a lot, but when you see the numbers globally of how many people
contract this, this is an issue. And there were famous stories about famous
footballers that were contracting it. I think the one I remember is Marcus Babel
was a famous German international playing for Liverpool that contracted it and
he was paralyzed for nine months. And so if the vaccine is causing potential
risk of GBS, Guillain-Barre syndrome, then that's definitely a problem and a no-
go area. And I think that's, from my understanding,  one of the reasons that the
strategy up to now and the cheapest strategy was potentially to give this to the
poultry in terms of potentially lowering the numbers within the chickens. There
is an interesting discussion point there actually about the poultry in that some
researchers have actually said that maybe the presence of Campylobacter does
actually lead to a, I wouldn't say necessarily healthier, but metrics of the
chicken look better when Campylobacter is present. There's been some conflicting
reports about that, but some people with a huge sample size, huge N, have
actually observed this. So it comes back to the point of, is Campylobacter a
commensal? And that is a question that at the moment is not answered, is
unanswered. Okay, so that's all the time we have for today. We've been talking
about Campylobacter and just giving a brief overview of this organism. And we'll
be discussing specifics that bioinformaticians need to keep in mind when
studying this organism. Our guest today was Dr. Ozengongadu. He leads the food
enteric pathogen group at the London School of Hygiene and Tropical Medicine.
And we're really happy to have him on the show and we'll see you next time.
Thank you so much for listening to us at home. If you like this podcast, please
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