MOOC CERTIFICATION

UNIVERSITY OF GENEVA
Global Health at the Human-Animal-Ecosystem
Interface

A PROJECT REPORT
Submitted in partial fulfillment of the requirements for the award of
degree of

BACHELOR OF TECNOLOGY

IN

Computer Science and Engineering

Submitted to

LOVELY PROFESSIONAL UNIVERSITY

PHAGWARA, PUNJAB

From 04/27/20 to 05/29/20

Submitted By
Name of student: Satyam Tripathi
Registration Number: 11903767
Signature of the student: Satyam Tripathi

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 Student Declaration

To whom so ever it may concern

I, Satyam Tripathi, 11903767 hereby declare that the work done

by me on “Global Health at the Human-Animal-Ecosystem
Interface” from APRIL, 2020 to APRIL, 2020, is a record of
original work for the partial fulfillment of the requirements for the
award of the degree, Bachelor Of Technology in Computer
Science and Engineering.

SATYAM TRIPATHI (11903767)

Satyam Tripathi

Dated: 29 Apr 2020

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CERTIFICATE by University of Geneva

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 ACKNOWLEDGEMENT

I would like to express my deepest appreciation to all those who

provided me the possibility to complete this report.  A special gratitude
I give to our course mentor Dr. Isabelle Bolon, whose contribution in
stimulating suggestions and encouragement, helped me to coordinate
my course especially in writing this report.

Furthermore I would also like to acknowledge with much appreciation

the crucial role of the other participants who enrolled in this course,
because of whom I could present my ideas and suggestions on “How to
deal with Zoonotic Diseases”.  I have to appreciate the guidance given
by other supervisor as well as the panels especially in our idea
presentation that has improved my knowledge and presentation skills
thanks to their comment and advices.

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List of Figures/Charts

Fig 2.1 (Consumption of bushmeat in Ghana before and

during spread of Ebola)

https://journals.plos.org/plosntds/article?
id=10.1371/journal.pntd.0005450
(Pg. no. 13)

Fig 3.1 (Spread of TB all over the world)

https://singularityhub.com/2011/12/19/cdc-issues-new-guidelines-for-
tuberculosis-as-drug-resistant-forms-spread/ (Pg. no. 17)

Fig 4.1 (Countries reporting anti-microbial resistance)

https://journals.plos.org/plosmedicine/article?
id=10.1371/journal.pmed.1002344
(Pg. no. 19)

Fig 5.1 (Consumption of Rice all over the world)

http://chartsbin.com/view/9116 (Pg. no. 26)

Fig 5.2 (Consumption of Seafood all over the world)

https://ourworldindata.org/seafood-production (Pg. no. 30)

Fig 5.3 (Effect of diseases on the base of gender)

https://www.thelancet.com/journals/lancet/article/PIIS0140-
6736(20)31561-0/fulltext (Pg. no. 32)
INTRODUCTION OF THE PROJECT UNDERTAKEN

Objectives of the work undertaken

To learn about some of the major and current Global Health

Challenges at the Human-Animal-Ecosystem Interface: zoonotic
emerging infections (e.g. Ebola, Nipah, MERS, Avian Influenza),
antimicrobial resistance, neglected tropical diseases (e.g. rabies,
leishmaniasis, zoonotic TB), snakebite and other human-animal
conflicts etc. And learn new concepts from the field of epidemiology,
social anthropology, disease ecology, veterinary sciences, global health
policy etc. Also, learn about innovative tools and frameworks used to
study and tackle some of these Global Health challenges of the
Sustainable Development Goals era.

Scope of the Work

To gain a rational understanding of the various diseases and virus

forms that are spread all over the world and how the health
organizations deal with it. The actions taken by various health
organizations in order to stop the spread of diseases and viruses.

Importance and Applicability

This allows you to identify one of the most important work that saves
billions of lives every year, and the hard work that have been put by
the health workers in order to save these lives.

Learning Outcomes

Learnt about the process and work through which a vaccine or a cure
for a disease is created. And how does these health organizations track
the origin of diseases and find a cure for it.

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INTRODUCTION OF THE COMPANY

Company’s Vision and Mission

Coursera envision a world where anyone, anywhere can transform

their life by accessing the world’s best learning experience.

Origin and growth of company

Coursera was founded by Daphne Koller and Andrew Ng with a vision

of providing life-transforming learning experiences to anyone,
anywhere. It is now a leading online learning platform for higher
education, where 73 million learners from around the world come to
learn skills of the future.

Various departments and their functions

More than 200 of the world’s top universities and industry educators’

partner with Coursera to offer courses, Specializations, certificates, and
degree programs. Thousands of companies trust the company’s
enterprise platform Coursera for Business to transform their talent. 

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Brief description of the work done

Introduction to the Project

This MOOC is based on how the health of both humans and animals
gets affected due to the interdependence in this ecosystem that we live
in. And how do we as humans deal with the various life-threatening
diseases and viruses.
Activities/ equipment handled
I interacted with the other participants of this course through the
chatting facility that was a part of this MOOC in which we shared our
ideas with the panel members and other participants on how we can do
to control the spread of animal borne diseases.

Challenges faced and how those were tackled

One of the major challenges in making a cure for these diseases is to
track the source of it. And in order to track the source of the diseases,
scientists sometimes have to spend years in countries in Africa to get
this job done.

Learning outcomes

Learnt about the various steps taken by the health organization in order
to help humans and animal from the diseases that are originated and
spread due to their interaction and interdependence.

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CHAPTER 2: EMERGING INFECTIOUS DISEASES

This chapter focuses on the current global threat posed by zoonotic*

emerging infections and the tools and challenges for studying and
controlling them.

When talking about global health, we immediately think about

emerging zoonotic infections. The number of emerging infections has
been increasing over the last decades. And most of them have an
animal origin, they are zoonosis. Let us think about SARS back in
2003, avian influenza, or more recently, MERS or Ebola.
What are the key issues for a new virus to infect humans?
First you need a naive population, you need hosts that have not been
exposed previously to the given virus, to be susceptible to the disease.
The second key point that a virus needs to fulfill, to create a new
emerging disease, is to be transmitted from one human to another
human to assure the chain of transmission and there is different ways
to do this. 
Let us start again with HIV 35 years ago, that is a spillover from
chimps to humans. 
What HIV has done is not only to adapt to humans, but to create a
chronic infection for many years, so that it could offer opportunities for
transmission from one human to human through sexual contact.
They use a large number of vectors* to assure human transmission
from one human to a human. Like it's the case for the Zika virus,
no one is immune to this disease and the density of the vectors is very
high and the density of the population is very high. So this provides
opportunities of transmission for a virus to adapt to human, 
A key issue for these viruses is that they need to be adapted to the
human receptors that you will find at the surface of the different human
mucosa. A good example is influenza we know that influenza can
infect humans. In nature you have approximately 16 different or 
18 different types of influenza circulating in animals. 

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Still only three, really manage to cause big pandemics in humans, H1,
H2, H3. This helps us to understand that there is, what we call a barrier
of species.
All influenza viruses are not really dangerous for humans. They’re not
adapted to the receptors at the surface of the respiratory tract of
humans. We know that it can infect humans, we know that it infects
animals but still it fails to cause pandemics. 
Since more than 15 years we know that H5N1 has caused several
hundreds of human cases, but still it failed to cause a pandemic, why? 
Because the virus is not really adapted to humans and it is not able to
cause human to human transmission. 
We also know that the viruses are still evolving in the animal world,
and could one day possibly, to be really adapted to human receptors. 
So it's really very difficult to predict what are the requirements of the
different viruses to cause a new pandemic.
Ebola is transmitted by close contact, MERS coronavirus is an airborne
disease, mainly by droplets, but also possibly by aerosols, Zika is
transmitted by a vector and Chikungunya is also transmitted by a
vector. You just read three different types of transmission in humans, 
and different types of constrains to a given virus to be adapted to
human, and to be able to be transmitted from one case to another.

Zoonotic viruses and how to investigate when new viruses emerge.

Some estimate that around 70 to 75% of emerging viruses come from
animals. And so, we are interested in studying those animal
populations, but also studying the human populations that come in very
close contact with those animals. So that we can very quickly detect
whether or not those viruses jump between the animals and the
humans, and if they cause diseases in humans.
So, over the last 30 years or so, the number of emerging infections or 
new infections, new viruses, has increased significantly. 
But there's a number of reasons for that. Surveillance has improved
and so we are much more quickly able to detect these viruses. 
We've had changes in land use, so for example, some damns are built. 

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So, there populations have to move around from certain areas.
Our behavior has changed and we have had massive changes in food
and agriculture systems over the last several decades. So, there's
differences in the way that we live. So, we're coming in contact with
animals more. 
And therefore, we need to look in animal populations, we need to look
in the human populations, but we also need to look in the environment
of where the humans and the animals come together. So, avian
influenza subtype H5N1. This is a highly pathogenic avian influenza. 
It was first detected in humans in 1997 in Hong Kong. During that
outbreak, there were 18 human cases that were detected. And there was
a massive effort to stamp out the virus, a massive 
Culling* occurred in Hong Kong, removing the virus from the animal
population.
How that person became infected, and to try to evaluate the risk
factors, or the types of exposures that led to the transmission between
the animal and the human. So the types of investigations that we do
for H5N1 include looking specifically in the poultry populations. 
Trying to understand when mortality happened, how many of the birds
were infected, which species of the birds were infected. 
Looking in the human populations to find the extent of infection,
through serology*. Basically, you're taking blood samples. And you're
looking for antibodies which will indicate whether or not the person
has been infected with the virus. So when you look in the environment,
you take samples. If the outbreak occurred in a market, and you'll see
some pictures, the market environment provides an incredible
environment for these viruses to survive. And you can take swabs from
certain areas. If it's a poultry market, for example, you can swab the
areas where the birds reside. 
And all of this information will really help you to better understand
where the virus is and how that will potentially allow for the virus to
move from the birds to the people. 
We can do disinfection or close the market and clean it thoroughly that
will help stop transmission. 

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One more such virus is Nipah virus, that comes from the bats, so we
need to collect information about the virus, about the bats and about
the humans and their domestic animals. So one of the key actor of our
system is the bats. 
In Cambodia in term of population size we have estimates ranging
from 4 to 6,000 bats at a single place, depending on the season. 
So at this roost*, we've been monitoring the population for 
several years.
 Monthly census is done because population directly impacts the
spread of Nipah virus. And in particular, the different phases of the
reproduction cycle of the bats is important. And we've observed that
we have here a highly synchronized reproduction. 
And most of the pups will arrive at the same time. Leading to a pulse
of naive individuals in the population with no immunity to the virus at
some point of the year. And this can lead to a peak in the circulation of
the virus. 
Surveys are done understand the perception of the bats by the local
peoples. To also to understand the practices, and the agricultural
practices of these people and how that could put them in contact with
the bats, direct or indirect contact. And what would be the risk of
transmission and spill over of the virus from the bats to the humans.
 People are tested for Nipah Virus antibodies. And this gives a first
information on past spill overs of the virus to the human population
living around this area. 
Questions are asked by locals, if they know about zoonosis? 
And actually there are only a few zoonosis that are known by locals. 
That include rabies, they know that mad dogs can transmit a disease to
humans. Avian influenza that can be transmitted from ducks, in
particular. And malaria, that can be transmitted from mosquitoes. 
Those three diseases that are well known by locals. Have in particular,
have been highly advertised by national campaigns. 
A popular mode of transmission is consumption of bushmeat. 
As we know, all of Africa and especially in Central Africa, 
bushmeat is an important source of proteins.

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And this phenomenon is growing fast due to new encroachments, 
such as mining or logging, which push people further into the forest. 
As we know, bushmeat is a great vector for infectious diseases, notably
Ebola. But, also for other potential viruses. 
Transportation is also a great risk for dissemination. Marketplaces are
finally a potential bomb for germ transmission. 
It's about awareness-raising in school or communities, law
enforcement on the ground, creation of sanctuaries for some species, 
development of alternatives to feed people, and sometimes local-
breeding programs for these species. Therefore, by diminishing the
trade and the consumption of red meat, conservation indirectly
contributes to better health for the communities. And that would in turn
prevent the contamination of people who interact with them. The
reverse is true. Using tuberculosis prevention to limit close contact
with gorillas would certainly contribute to their ultimate conservation. 

FIG 2.1

(In the above graph, it is clearly shown that the consumption of

bushmeat was highest before the spread of Ebola, which makes it the

primary cause for Ebola spread. And as soon as people were aware
about the vector, the bushmeat consumption declined sharply.)

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CHAPTER 3: ZOONOTIC NEGLECTED DISEASES
There are infectious diseases that receive far less attention by the
media and the public typically because they affect poor and rural
communities of the world. These are the so-called neglected tropical
diseases, and particularly we will be talking about zoonotic neglected
tropical diseases. 
There is just a lack of coordination and a lack of committment that is
still needed for the elimination of some of these diseases. Many of the
actions that she points are actions that imply an intervention on the
animal health. Also intervention on the environment. For example, by
ensuring access to safe water and sanitation, we could eliminate many
of these diseases.
Places where underserved populations live with limited access to 
health services, to other services including water and sanitation.
This is a place where neglected tropical diseases thrive. If you look a
little bit more deeply at that image, what do you see? There will be
animals. Animals are a source of livelihoods for people. And these
populations live very closely with their animals. 
So what are neglected tropical diseases? 
NTDs, neglected tropical diseases are actually a proxy to describe
underserved populations, to describe poverty. They are diseases that
affect populations but these diseases do not cause media outcry. They
also do not travel widely, they're not influenzas but they cause stigma
for example, think of leprosy, think of epilepsy caused by pig tape
worm. Think of elephantiasis caused by lymphatic filariasis. So they
have an important impact on morbidity, mortality, but are neglected
also by research. Until development, until services, until water
sanitation reach these people we can start with programs to have
people confronted with these neglected tropical diseases having access
to care.
So, the neglected tropical diseases were coined to bring a bunch of 
endemic diseases onto the landscape of global health, of health. 
We had to prioritize, so there are currently 18 diseases on this list. 

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There are five intervention methods to approach these diseases. 
One is going at population level, preventive chemotherapy. 
The second one is, treating the case. Treating the patient in innovative
and integrated disease management. We have veterinary public health
looking at the problems from a more holistic point of view. How can
we have better health in animals that will affect better health in
humans. Vector ecology and management of vectors and 
also water sanitation and hygiene. This is really a big center of
attention for improvement in neglected tropical disease. 
From a research we found out that about a fifth of all infectious
diseases was due to neglected tropical diseases. That is compared to
about 50% compared to malaria, tuberculosis, and HIV. 
About 70% of all the countries were affected by these Neglected
Tropical Diseases and those were in the tropical belt and that's why
we're calling it Neglected Tropical Diseases.
And 100% of all these diseases were located in low income countries.
70% Of these poor people, keep animals for their livelihoods. So that
sets the scene for the Neglected Zoonotic Diseases. 
Animals are source of food for these people and they're a source of
income, they're a piggy bank. When a child is sick, there's quick
money by selling an animal. They're used for transport. 
They're used for many, many reasons even for manure and for 
cooking fuel so and if you look a little bit further away from the
livestock. They're used for security. Dogs, you think in a place like
Africa, well dogs are sort of just vectors, just sort of parasitic diseases. 
They actually have a role, they have a role in fishing, in herding, in
security.
We have to be thinking a little bit more holistically, so not separating
epidemic diseases for endemic diseases, Neglected Tropical Disease do
not have as much epidemic potential. So when we're looking at the
One Health paradigm, we should be looking at the Neglected Zoonotic
Diseases as building that platform to be the alarm 
system in rural populations that will indicate 
that something might be going to happen, or going wrong or emerging 

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out of the wild, or out of different environments. 
Let’s take rabies, for example, in 2015, we assembled, countries and 
different actors in rabies elimination, to come together and agree on. 
a plan, a framework to eliminate rabies, to reach zero rabies stats by
2030. So together the community is looking at where can they provide 
leadership in their area of expertise, in their area of competence? 
WHO is looking of course at the public health aspects most
importantly. And then the animal health sectors is looking at how to
scale up vaccination of dogs as big prevention part of rabies control. 
There are other parts looking at the awareness raising in communities. 
We're looking to see how to make vaccines better, more available. 
And so we're looking at working with partners, not just the public
sector partners, private sector partners. Looking at vaccine
manufacturers, how can they scale up if we are really serious about
reaching 2030 targets. (No rabies by 2030)
We're working in countries, looking at opportunities to catalyze
activities. Just by starting something small generating the evidence
and then scaling up to reach a programmatic control program. 
So basically the point is think big have a strategy starts small, 
show your evidence and then scale up. 
So, let's take the example of the pig tapeworm. Who would ever
imagine that 30% of epilepsy in Africa for example is caused by the
pig tape worm and this is due to bad hygiene? And sanitation and due
to bad food preparation behaviors. So we have interventions that can
be done in animals, look at vaccination of pigs. Look at meat
inspection, that could eventually have a very large public health
impact. And this is a double, we have a double outcome. Not only an
increased public health impact, If we have improved pig health, the
revenues from sales of meat would also be increased for these
populations that raise pigs.
Zoonotic tuberculosis, it's an emerging problem simply because we
have neglected it for many years.
What do we mean by Zoonotic TB? 
Infection of cattle populations with the Mycobacterium bovis 

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organism which is transmitted to people mainly through consumption 
of unpasteurized dairy products. So during the last century in most
high income countries, pasteurization became widespread. 
But in many parts of the world, consumption of unpasteurized dairy
products remains common.
So, any strategy that use to control bovine TB and cattle has to take
into account the wildlife reservoir.

FIG 3.1
(You can see that actually in bovis infection,  Mycobacterium bovis
infection in cattle exists throughout the world. You can also see that
highest spread is in poor countries where living conditions are not
good like in AFRICAN countries.) 
The other problem is that in fact the diagnostics methods that we use
for tuberculosis, do not distinguish between Mycobacterium
tuberculosis and Mycobacterium bovis. 
This has obviously implications because we know that Mycobacterium
bovis, that is the one transfer from the animals to humans, is almost
always resistant to pyrazinamide. And pyrazinamide is one of the four
drugs that we use to treat tuberculosis. 
Mycobacterium bovis causes sometimes and oftentimes, extra-
pulmonary forms of tuberculosis. Not the common forms of TB
thataffect the lung but in fact, there are forms of TB that affect the
lymph nodes, for instance in the neck here or in the gastrointestinal
tract. 
Within, therefore, this context we have placed this End TB strategy, 
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which contains three essential pillars. The first one deals with good
patient care, the second one with the bold policies in the system that
we need, and the third one with research. So all of these in a way or
another are also applicable to zoonotic TB. In fact, if we want really at
a certain point to end tuberculosis then we really need to find, to
diagnose, to treat all cases of tuberculosis. 
So the three main areas that we need to strengthen for controlling
zoonotic TB. Firstly we need to improve the scientific based evidence
that we have available. So we need to strengthen surveillance data we
have for both disease in people and disease in livestock. Secondly, we
need to reduce transmission at the animal, human interface.
So, this means controlling disease in livestock but not just the cattle 
populations but also the wildlife reservoirs. We need to identify the
key populations at risk and target those populations for 
intervention such as groups with a close contact with livestock or 
consuming unpasteurized dairy products.
And finally, we have to strengthen intersectoral approaches to
controlling the disease. So, we really need to make an effort to raise
awareness among the stakeholders, engage the stakeholders and
encourage intersectoral collaboration.
CHAPTER 4: ANTIMICROBIAL RESISTANCE &
ZOONOTIC FOODBORNE INFECTIOUS DISEASES
Antimicrobial resistance has become, today, a major urgency in the
global health agenda. And it exemplifies, very well, the need for 
cross-sectoral and multi-disciplinary approaches to health. It requires
for tackling this major issue actions at the level of the health system, 
including the animal. But also, of course, the human side. Actions also
in the agri-food systems. 
Antimicrobial resistant, or drug resistant, infections is a natural
phenomenon. We found resistant bacteria in glaciers in the Ice Age.
But the more we use antibiotics, the quicker the bugs develop
resistance and the quicker the problems emerge. And there are
different types of antibiotic resistance. There's resistance to antibiotics
and that's bacteria. But also antiviral resistance to drugs like HIV
drugs. Parasitic resistance, for example to malaria. And then also
resistance to fungal drugs.At the beginning of this century if you got a
bloodstream infection your chances of dying were about 90%. And
when and then penicillin came along, that changed to about a 10%
chance of dying. But now we know we have global problem.

FIG 4.1
(The above map shows countries reporting anti-microbial resistance.
Asian countries are most affected by these problem where population
is high.)

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The data for Africa and Asia is much more patchy. We do know we
have a global problem.And we also know that although we've been
worrying about this, things have been getting worse. 
So why is this happening?.
Basically, we are using too many antibiotics inappropriately, both in
the animal sector where they used to promote growth as a substitute for
poor hygiene. And also in the human sector where very often use of
antibiotics is unregulated. Sold over the counter. People take them as a
strong medicine for viruses, headaches all sorts of things. And this
really is global threat. The O Neill Report has just been produced this
year and they've made some assumptions and estimates on the burden.
And are suggesting that at least 700, 000 deaths occur currently,
making it in line with many of the major problems. 
So what does this really mean?. 
In essence, infections are going to be much more difficult to treat. That
means longer stays, more treatment failures, more people living with
chronic infections and higher costs. It also means that having your joint
replacement surgery, your c-section, your cancer treatment will
become much more risky, potentially prohibitively risky. And it also
means that they'll be decreased productivity, more time off work, more
people unable to work.
To give you an example about treatment failure, here you see the data 
from an old study published about 15 years ago in a very high impact
medical journal. Showing that if you had a population of patients with
urinary tract infection, called pyelonephritis and you compare two
different antibiotics, one is ciprofloxacin, the other one is
cotrimoxazole. If the bacteria are susceptible to both antibiotics, then
the treatment success is almost 100%. However, if the bacteria is
resistant to cotrimoxazole then suddenly the success rate decreases to
lower than 40%. So it's very easy, those women, they will not improve
and at some point they may have to go to the hospital and 
receive an intravenous antibiotics because of antibiotic resistant
bacteria. But more importantly of course, antibiotic resistance, 

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as I mentioned before, can harm patients and even kill them. 
This is a threat that has been mention on many times that for 
some of the multiresistant superbugs that may really become pan-
resistant. 
What does this mean? 
That they are not treatable anymore with any commonly available
antibiotics so this is, for instance, the case for pan-resistant
tuberculosis or pan-resistant acinetobacter. These are bugs that
fortunately enough in many countries they are not frequent but they are
already some countries where you may encounter these kind of bugs
and this is certainly for us as clinicians, a nightmare scenario. But we
have to highlight that of course, antibiotic resistance, per se is not
killing, it's the bugs that are killing. And to distinguish what the
microorganism cause, what harm they cause and distinguish from the
resistant bugs, it's not always easy. Then of course, patients who
acquire resistant infections, they may have co-morbidities, they have
other underlying diseases. And then also a third very important
confounder is of course, the adequacy of antibiotic treatment. 
You may have a patient infected with a resistant bug but if he or 
she gets the right antibiotic right on time, there may be no additional
harm. So these are the kind of challenges we are facing at just as an
example of a very good high quality study that looked at these kind of
issues in a very detail passion. 
And here, very importantly the message that antimicrobial
resistance contributed only a relatively small contribution to the
overall burden of healthcare associated infections in intensive care
units. So to make it very simple, it's not good for your health to get
infected in intensive care unit because you have lots of underlying,
other diseases. Resistance complicates further but the part of resistance
on extending the length of stay of excess mortality was not as large as
it was previously reported. 
The term of foodborne disease includes all risks associated with food 
along the entire food chain as well as microorganisms, some chemical
agents contamination. 

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So, reducing human foodborne infections will required the reduction
of pathogens in animals and limitation of transmission from the
environment. Clearly, food safety provides a compelling example of
the One Health paradigm. And to clarify my thinking, I would like to
share my experience about the global spread of multidrug-resistant
Salmonella Kentucki. So yes, superbugs are comming in our food.
Thanks to our laboratory-based surveillance system in travellers we
have identified here, at Institut Pasteur, a type of multi-drug resistant
Salmonella named Salmonella Kentucky that originated in Egypt and
then has spread across the globe. Africa, Middle East, South Asia,
South East of Asia and now in Europe in the space of a few years. 
The principal reservoir of bacteria was found to be poultry, chickens
and turkeys, but secondary vehicles have been found like seafood,
spices and pigs. Hundreds of imported cases of Salmonella Kentucky
infections are now detected, each year in France, thousands in Europe.
Recently we even detected a number of isolates from the
Mediterranean region that had acquired resistance to all 
antibiotics including the last resort ones, carbapenems. 
So, the questions are, how this strain has been selected, 
accumulated resistance genes step by step, and disseminated? 
And what are the control measures we have taken from a One Health
perspective? So we need to say first that Egypt has the largest
aquaculture industry in Africa. And it is probably in this aquatic
environment that Salmonella Kentucky acquired its first antibiotic
resistances. Actually, large amounts of antibiotics are added to
waterways in fish feed. And integrated-culture as poultry, or rice were
also developed in close proximity by the farmers. That probably helped
to lead genetic transfer between environmental bacteria and
salmonella. Then we know that fluoroquinolones is a common
antibiotic used in chicken and turkey production and that may have
contributed to its rapid spread in the whole Africa and then
successively spot by spot, acquired new resistance determinants.
It is not unlikely that this bacteria strain may soon be established 
to biggest poultry farms like in Europe with a risk of increased and 

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potentially untreatable infections via the food industry.So clearly
Salmonella Kentucky, this story, is therefore a paradigm for epidemic
antibiotic resistance, and from a One Health perspective should recall
us these main messages:
Firstly, that the non-regulated and excessive use of 
antibiotics on farm-raised livestock presents a major health risk.
We know that rates of antibiotic resistance in bacteria from food
animals are reduced when antibiotic use is banned or decreased. 
We need to respect national and international guidelines and 
standards designed for intensive agriculture.
Secondly, that is clearly important to monitor these emerging
pathogens on both international and national fronts.In France, the
presence of this bacterium in the poultry industry is now tested in the
frame of national salmonella control programs.We can access reliable
updated information on the incidence of foodborne disease, occurence
of food contamination to evaluate the amplitude of this emergence and 
to evaluate the effectiveness of the controlled measures we have taken.
Thirdly, new technologies are coming, and in particular the genomics
era offers opportunity for a better understanding of the success story of
this strain. And we are working on its weakness, its possible Achilles
heel, providing science-based evidence in order to make good public
health decisions. So in summary, I would like to say that we need
attention to pay to the bacteria linked human, animal, and biosphere
ecosystems. Spread of resistant bacteria needs to be stopped.
And timely transparent information is needed about the types, 
quantities of antibiotic use in agriculture or along the food chain.
One Health is a global concept that must be translated at each level. 
Locally, nationally, internationally from the farm to the table

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CHAPTER 5: MANAGEMENT OF ECOSYSTEMS
UNDER GLOBAL CHANGES
The air you breathe, the water you drink, the food you eat, and the
medicines you take. All of these are by-products of our planet. Healthy
communities rely on the diversity of life or planet supports. But today,
the world that is losing its ability to keep humans healthy. Climate
change, deforestation, water crisis, pollution, draining of wetlands,
globalization, and other aspects of modern life are wiping out species, 
damaging ecosystems, and contributing to the spread of disease. 
Think of just two diseases, Ebola and Lyme disease. Largest scale
human transformation of the environment has brought humans in 
closer contact with animals that harbor this disease with tragic
consequences. It's urgent that we not only adapt to these change but
mitigate them. Now, this knowledge must be built into national plans. 
But our conversations around health, biodiversity, and climate change
cannot stop with us. It requires the involvement of every sector of
every government.
Scientific evidence of the direct and indirect impacts of biodiversity
loss on health outcomes is increasingly well established. And the need
to find common ground to confront these challenges is undeniable.
Ranging from increased vulnerability to natural disasters, disease
outbreaks, and nutritional insecurity. And the erosion of many other
ecosystem services. By demonstrating how the sustainable
management of biodiversity in agricultural landscapes and seascapes. 
And how climate, nutrition, and gender-sensitive strategies can jointly
support the transition toward healthy diets and sustainable
consumption, and production practices. Not only as a means to
supporting nutritional outcomes, but 
also as a vital building block, for social and ecological resilience and 
a tool for the mitigation and adaptation to climate change.
What biodiversity is, and why it is important for 
human health, particularly in the context of agricultural systems? 
>> Biodiversity's simply the variety of life on Earth, 

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the huge number of plants, animals, and microorganisms, but also the
genes, the genetic diversity within those species. And then finally, the
different habitats, different ecological complexes that we have on
Earth, and all of these are really important for health. 
And how can agricultural systems, in particular, be made more
sustainable in ways that mutually support biodiversity and human
health? 
>> So essentially, we could make better and more use of biodiversity
in agriculture. Firstly, we have a vast range of plants and animals, and 
we only use a proportion of them. We could be using a broader range
of those, and that would enable us to develop more nutritious crops,
but also adapt to changing circumstances. 
As well, though, we have to look at the way biodiversity supports the
functioning of the agroecosystem as a whole. So at the moment, in
many of our systems, we rely, probably far too much, on pesticides, for
instance, to control pests. We could be relying and making better use
of the natural enemies of pests of plants by nurturing those, so through
practices such as integrated pest management. Also, many of our crops
that are pollinator-dependent. And in many agricultural production
systems, pollinators are not present, in terms of the diversity and the
abundance that would give maximum yields. 
As you know, there is a growing burden of noncommunicable
diseases,which is responsible for up to 63% of the global burden of
disease, the majority of which is actually linked to poor lifestyle
choices. 
So how does biodiversity fit into all this? 
>> Diversity of food is good for people, and of course, that diversity of
foods, and therefore of nutrition is dependent on biodiversity in a very
straightforward way, but also physical activity. We're more likely to
engage in physical activity if we have green spaces in our 
environments. So there's more and more attention now to how can we 
encourage people to eat in ways that are not only good for 
their health, but good for the environment in reducing impacts on
biodiversity. 

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So a broad set of actions to deliver on the core concept which is a
healthy diet sustainably produced. The issue of sustainability is critical,
because diet is one of the important contributors to the greenhouse gas
emissions, but also is relying on planetary resources in a major way, 
particularly water, and land use. 
Agricultural practices are increasingly moving towards intensified
monocultures which may improve short-term grain yields, but limit the
biological diversity needed for high quality diet. For example, did you
know that of the 250,000 plant species known to humans, more that
30,000 plant species are edible, yet only 7,000 have been used for food
through human history.And of the 120 plants that are cultivated for our
consumption today, 9 provide more than 75% of our food, and 3 of
them, rice, maize and wheat, provide more than 50% of calories for
humans. Therefore, let me go into discussing a number of
international nutrition related processes and commitments taken by
nations. 

FIG 5.1
(The above map shows the consumption of main staple food: RICE. It
is mostly consumed in ASIAN countries such as CHINA, JAPAN,
PHILLIPENES, TAIWAN etc)
The estimates are that whereas right now between capture fisheries and
mariculture, we get about 130 maybe 140 million metric tons of food. 

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We need another 90 million by 2050 to break even. Here are a number
of examples around the world where cleaning up sources of
contamination usually land based runoff or port contamination has led
to cleaner seafood, better nutrition, healthier babies because 
fetuses are particularly vulnerable to accumulated contaminants that
mothers eat. 
And so, in certain parts of Africa, people have lost 50 to 75% of their 
livestock, which then, is essentially their whole livelihood. So people
have actually lost the ability to generate money or to even have money
to buy food. And the animals themselves are no longer producing
milk. So they really have lost a significant amount of value. When we
look at the pressures on the pastoralist communities besides the change
in the climactic conditions, besides the drought, besides the lack of
food resources for the animals or the crops for people to eat, the other
thing that we see is that range lands and grazing areas are shrinking. 
Urbanization, the conversion of forest to fuel and firewood, or 
the conversion of rain forest to agricultural land and many more. 
Planetary health scientists are interested in documenting and
characterizing the relationship between these types of ecosystem
transformations and human health outcomes, such as nutrition.
Throughout much of the developing world and particularly in sub-
sahara in Africa, many people rely on wildlife, often termed bush meat,
for food consumption. And today, the world is facing the sixth mass
extinction event with steep trajectories in wildlife declines, none
perhaps as dire as the one in Madagascar. Where lemurs are viewed as
the most endangered taxa of animals on Earth, and yet, in Northeastern
Madagascar, a place where I've lived and worked for nearly 20 years,
more than 90% of the Malagasy population rely on wildlife for food. 
From a nutritional perspective, more than 50% of the Malagasy
population is stunted, and more than 40% of the population is anemic,
and thus those two things come into conflict. In a place like
Madagascar, wild life is really important for human nutrition. 
I am suggesting however, that we understand this reliance on bush

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meat to adequately position development and public health specialists
to solve this arising conflict.
After having done this type of research for more than a decade in
Madagascar I began seeing these types of headlines. The world is
running out of fish faster than we thought, death of coral reefs could
devastate nations, global warming could cause fishing to decline by
millions of tons each year.
We became more and more interested in understanding the extent to
which the work we were doing in the rural, remote rainforest of
Madagascar, was parallel to the crisis we were facing with global
fisheries declines. We know that the global fisheries catch peaked in
1996 and has since been declining by 1 million metric tons per year. 
Specifically, what we wanted to know was how declining fish catch
would lead particular human populations toward alternative foods. 
And how these dietary changes would present specific nutritional 
vulnerabilities in different geographical and cultural contexts. 
Finally, we wanted to explore how aquaculture and fisheries
management might be able to alleviate this tension between fishery
decline and human food insecurity.
First, let's focus on declining fish catch. Harnessing data from the Sea
Around Us project. We were able to use estimates of fish catch data, 
beginning in 1950 and produced annually up until the present, 
to map changes in fish catch potential.These data were disaggregated
by four fishing sectors, industrial, artisanal, subsistence and
recreational fish catch. This allowed our team to understand which fish
would stay local for consumption and which fish would be exported
into the market. What this data also allowed us to do, 
was to observe the impacts of climate change on fish catch. 
Climate change will increase sea temperature and 
dry fish populations from the equator to the poles. 
It will also increase ocean acidification and reduce oxygenation of the
sea, causing fish to be smaller in size and schools to have fewer fish. 
You can see the dark red area highlighting where fish catch is expected
to decrease by 50% by 2050. As a public health specialist, I actually

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see a map highlighting where food insecurity and malnutrition will be
the worst.
So, with decreasing fish catch along the equator, what will people eat?
My basic answer to this question, is that if you stop eating fish, 
almost any other food you move into will be nutritionally inferior. 
Key nutrients, the rich, long-chain fatty acids, vitamin B12, iron, 
zinc, and other minerals are in very high concentrations in seafood. 
Losing this rich nutritional resources will have consequences.
What types of nutritional consequences arise will depend on the dietary
change experienced.We expect that there will be three typologies of
countries affected by fish catch declines. 
They will be the wealthy unaffected nations, like the U.S., Japan, 
New Zealand etc. 
Where a local collapse in the fisheries will lead to slight price shift or 
specie shifts in the markets, but those who are eating fish before, 
will continue to eat fish. 
And those who were not eating fish before will continue to not eat fish.
Next, there will also be countries where undernutrition will increase. 
Places like Madagascar, Gabon, Surinam and others. These are places
where a local collapse of the fisheries will increase a reliance on 
tubers or staples or vegetarian foods, driving increases in micro-
nutrient deficiencies. Finally in countries like Indonesia, 
Brazil, Mexico and Islands of the South Pacific, a local collapse of the
fisheries will accelerate the nutrition transition. Where reductions in
fisheries will cause a decline in traditional diets accompanied 
by increases in western diets. Fast foods, processed foods, and a rise in
metabolic disease. So where exactly do we anticipate there to be 
peaks in nutritional vulnerability from undernutrition? We overlaid
these climate models of the impacts of sea temperature rise on 
fish catch and predicted the nutritional vulnerability of every coastal
nation of Earth, by looking at what they were currently consuming. 
This allowed us to predict the nutritional impacts of a decline in fish
catch. Highlighted are the countries that have the highest seafood

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dependency. And are at a threshold for nutritional deficiencies with
their current diet. You can see that Southeast Asia and 
Western Central Africa appear to be the most vulnerable to
undernutrition. So how do we fix this?

FIG 5.2
(The above map shows the consumption of sea food all over the word.
You can see that the consumption is higher in Asian countries like
China, Japan, India etc.)
Aquaculture will help but will not fix it alone. Agriculture production
outpaced Wild Fish Catch production a few years ago. However,
agriculture is not currently oriented to support the nutrition of 
vulnerable populations in the developing world. In looking at the 40
most nutritionally vulnerable nations on earth, with respect to seafood,
we noticed three different typologies of countries. First, in the dark red,
we have countries that produce little to no aquaculture. These countries
won't benefit nutritionally from aquaculture because they are not
producing it, and the market will not deliver it to them. Secondly in
yellow, we have countries that are producing a lot of aquaculture, but 
it's export oriented. It would rely on the economic benefits to trickle
down and benefit local people who are nutritionally vulnerable, which
is very unlikely to happen.
And finally, we have the countries in green, who are large aquaculture 

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producers, who are retaining aquaculture in domestic products. 
The problem here is that very often the fish are still not going to
nutritionally vulnerable people. Often landing in mega cities or at
wealthier households. Aquaculture will not deliver nutritional benefits 
unless it is designed that way from the outside. This is the case in
Cambodia and Bangladesh, where they have seen major 
successes in mixed rice, fish farming that can deliver nutritional
benefits. Finally we also need to consider improvements in fisheries
management. Currently, 60% of fisheries are either over exploited or
fully collapses, and additional 35% are fully exploited. We need to
reframe fisheries management toward new goals. Providing nutritional
benefits, allowing fisheries to recover and delivering sea food to local
populations. This then targets environmental conservation as a key
strategy in nutritional interventions. This is a positive outcome where a
healthy marine ecosystem causes an increase in fishery productivity,
and sustainably stabilizes human food security. 
It's evident that the environment in which we live is changing. 
And at very large and global scale, environmental changes posing
hazards to health include Ozone depletion, climate change, biodiversity
loss, land degradation and desertification. Stresses to food-producing
systems, urbanization, hydrological changes, and also the depletion
and contamination of freshwater sources.
The second thing that is important to have in mind is that, 
it is evident that human action and its current patterns of consumption
and production including the use of fossil fuels, are responsible for 
these environmental changes and ecosystem impairment. If we think
about the health examples of health impacts posed by these global
environmental changes, we may think of direct impacts, such as those
posed by flood, heat waves, and water shortages. Then those impacts
mediated through ecosystem. For example, changes in infectious
diseases, reduced food yields with consequent malnutrition and
stunting, Depletion of natural medicines, mental health, in personal,
cultural, for example the consistent services now we have less services
provided. 

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Gender should be considered in the assessment of vulnerability. To do
so we have to perform a gender analysis, which basically looks at how
different groups of the population, men, women and children will be
impacted by those changes. And then when it comes to management of
the risk already identified by conducting a gender analysis, we need to
understand the different impacts and then how different solutions can
be designed to tackle these impacts. As well as impacts of the
interventions that we're implementing to protect the health of the
populations. 

FIG 5.3

(From the above charts it is evident that the male gender are more
affected by some of the most lethal diseases than the female gender,
after the problem is identified a solution is formulated)

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 CONCLUSION

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