Summary Molecular Epidemiology
1. INTRODUCTION
A. WHAT IS MOLECULAR EPIDEMIOLOGY?
Epidemiology = Study of the relationships existing between diseases and factors (environmental, behavioral, social...) prone
to influence their frequency, distribution, and evolution.
- Factors can be abiotic and biotic
o Fe abiotic: economic status
o Fe biotic
- Pathogens can also cause asymptomatic infections
Molecular epidemiology is an integration between molecular biology and traditional epidemiologic research. Molecular
biologists look close at the reality, they look at the DNA of a given pathogen in a test tube, while the epidemiologist look at it
from a higher distance to the reality. Epidemiology looks at the bigger picture, molecular epidemiology only focuses on the
details.
The richness and major challenges in molecular epidemiology are that molecular biologists and epidemiologists often have a
different vision of the reality, ‘myopia’ and ‘presbyopia’ respectively.
- Presbyopia: can’t distinguish
- Myopia: makes more sense, but still can’t recognize what it is
- When we look at the right distance we recognize what it is
Waiting for sufficient hybrids between these two scientists, communication needs to be optimal among them.
Epidemiology is the basic science of public health. It answers several questions like:
• What causes disease?
• How does disease spread?
• What prevents disease?
• What works in controlling disease?
Molecular epidemiology will use molecular tools to answer these questions. You must distinguish infection from disease. An
infection is caused by a pathogen, but this is not necessarily a disease. Only when the individual is experiencing symptoms,
we call it a disease.
WHY MOLECULAR EPIDEMIOLOGY? WHAT FOR?
1) Provide the scientific basis to prevent disease & injury and promote health.
This is the rapid evolution of HIV in a SINGLE patient. A phylogenetic analysis
is made on the sequence of HIV on different timepoints. You see that over 13
years the HIV strain has already evolved very quickly and that it drifted away
from the initial transmitted virus. The virus is hyperviable and changes very
rapidly, here they are similar to and different from the virus that caused the
infection, during evolution multiple things can occur.
1
,2) Determine relative importance to establish priorities for research & action.
Here you see a risk mapping of Cutaneous Leishmania in Iran from 2009 and 2013. You see
an evolution in the places where you have a high risk of Leishmania infection. When you
know this, you can for example just target a region instead of the whole country.
Program of elimination worked well but were now present in the west of the country,
change in the distribution of the parasite.
3) Identify sections of the population at greatest risk to target interventions.
In molecular epidemiology they are often using molecular tools to identify transmission chain. In the picture you see a patient
that is infected. With sequencing you identify it as a green pathogen. In molecular epidemiology you would like to know
where this person got infected with the pathogen. This can be done by trying to find some possible sources: bore, river,
swamp, infected neighbour. You see here that the swamp is the source and caused the transmission to the patient.
Transmission chain studies are often used for nosocomial infection in hospitals to try to identify the source of the infection:
nurse, doctor, airco, water, .... Once you know the source you can have a targeted intervention to cut the transmission
chain/spread.
We want to determine where the infection is coming from, based on this we will know where to attack to solve the infection.
4) Evaluate effectiveness of programs in improving the health of the population.
Safety and effectiveness of mass drug administration (MDA) to accelerate elimination of artemisinin- resistant falciparum
malaria:
Leishmania causes leishmaniasis: visceral, mucocutaneous and cutaneous. Evolution of the number of cases is shown, at the
beginning of the 90s a lot of people were dying – intervention was launched. To monitor the success = classical
epidemiological approach.
This MDA was safe and feasible and could accelerate elimination of P. falciparum in addition to EDT and LLINs when
community participation was sufficient.
2
,5) Study natural history of disease from precursor states through clinical course
This is a study that was done in 2010 in a village in Nepal. They wanted to know what the natural history was of Leishmania
infection in that region. All the dots are houses and there they took samples of humans and animals. They wanted to know if
animals could play a role in the natural history of leishmania. They found that a lot of animals were positive (PCR) which mean
that they were infected with leishmania. These animals were living in close proximity to the positive humans (= close contact).
The boxes are places where we found positive humans and animals. This really suggested that there was really a transmission
between animals and humans, but they did not know if the animals were the reservoir.
Conclusion: with molecular tools they really found an epidemiological link between the animals and humans.
6) Conduct surveillance of disease and injury occurrence in populations (humans or animals or ...)
Surveillance is obviously one of the most
important applications of molecular
epidemiology. In the figure you see the
spread of the different variances of HIV
throughout the world.
Epidemiology of an infectious disease is
dynamic. Here you see all the flights
around the world during the day. Imagine
that in each of this flight is a person that is
infected with a dangerous disease, you
can see how easy it is nowadays to have a
propagation of a pathogen. This picture
shows how weak we are in front of the
pathogen.
3
, 7) Investigate disease outbreaks
Here you see the spread of HIV around the world and the origin is the Congo River Basin. This picture could be replaced with
Coronavirus. The origin would than not be the same (China). Molecular epidemiology has the tools to investigate this.
Epidemiology is highly dynamic!
Epidemiology of an infectious disease is dynamic. On the slide you see all the flights around the world during the day. Imagine
that in each of this flight is a person that is infected with a dangerous disease, you can see how easy it is nowadays to have a
propagation of a pathogen. This picture shows how weak we are in front of the pathogen.
Take home message:
• Get a broad view (reality is not only at the bottom of a test tube)
• Do not work alone
• Remind that epidemiology is not static
B. KEY EPIDEMIOLOGICAL CONCEPTS AND POSSIBLE BOTTLENECKS
Caution: Often you only know the number of notified cases in a year. The incidence is estimated but what proportion of the
incident cases are detected and notified?
4
1. INTRODUCTION
A. WHAT IS MOLECULAR EPIDEMIOLOGY?
Epidemiology = Study of the relationships existing between diseases and factors (environmental, behavioral, social...) prone
to influence their frequency, distribution, and evolution.
- Factors can be abiotic and biotic
o Fe abiotic: economic status
o Fe biotic
- Pathogens can also cause asymptomatic infections
Molecular epidemiology is an integration between molecular biology and traditional epidemiologic research. Molecular
biologists look close at the reality, they look at the DNA of a given pathogen in a test tube, while the epidemiologist look at it
from a higher distance to the reality. Epidemiology looks at the bigger picture, molecular epidemiology only focuses on the
details.
The richness and major challenges in molecular epidemiology are that molecular biologists and epidemiologists often have a
different vision of the reality, ‘myopia’ and ‘presbyopia’ respectively.
- Presbyopia: can’t distinguish
- Myopia: makes more sense, but still can’t recognize what it is
- When we look at the right distance we recognize what it is
Waiting for sufficient hybrids between these two scientists, communication needs to be optimal among them.
Epidemiology is the basic science of public health. It answers several questions like:
• What causes disease?
• How does disease spread?
• What prevents disease?
• What works in controlling disease?
Molecular epidemiology will use molecular tools to answer these questions. You must distinguish infection from disease. An
infection is caused by a pathogen, but this is not necessarily a disease. Only when the individual is experiencing symptoms,
we call it a disease.
WHY MOLECULAR EPIDEMIOLOGY? WHAT FOR?
1) Provide the scientific basis to prevent disease & injury and promote health.
This is the rapid evolution of HIV in a SINGLE patient. A phylogenetic analysis
is made on the sequence of HIV on different timepoints. You see that over 13
years the HIV strain has already evolved very quickly and that it drifted away
from the initial transmitted virus. The virus is hyperviable and changes very
rapidly, here they are similar to and different from the virus that caused the
infection, during evolution multiple things can occur.
1
,2) Determine relative importance to establish priorities for research & action.
Here you see a risk mapping of Cutaneous Leishmania in Iran from 2009 and 2013. You see
an evolution in the places where you have a high risk of Leishmania infection. When you
know this, you can for example just target a region instead of the whole country.
Program of elimination worked well but were now present in the west of the country,
change in the distribution of the parasite.
3) Identify sections of the population at greatest risk to target interventions.
In molecular epidemiology they are often using molecular tools to identify transmission chain. In the picture you see a patient
that is infected. With sequencing you identify it as a green pathogen. In molecular epidemiology you would like to know
where this person got infected with the pathogen. This can be done by trying to find some possible sources: bore, river,
swamp, infected neighbour. You see here that the swamp is the source and caused the transmission to the patient.
Transmission chain studies are often used for nosocomial infection in hospitals to try to identify the source of the infection:
nurse, doctor, airco, water, .... Once you know the source you can have a targeted intervention to cut the transmission
chain/spread.
We want to determine where the infection is coming from, based on this we will know where to attack to solve the infection.
4) Evaluate effectiveness of programs in improving the health of the population.
Safety and effectiveness of mass drug administration (MDA) to accelerate elimination of artemisinin- resistant falciparum
malaria:
Leishmania causes leishmaniasis: visceral, mucocutaneous and cutaneous. Evolution of the number of cases is shown, at the
beginning of the 90s a lot of people were dying – intervention was launched. To monitor the success = classical
epidemiological approach.
This MDA was safe and feasible and could accelerate elimination of P. falciparum in addition to EDT and LLINs when
community participation was sufficient.
2
,5) Study natural history of disease from precursor states through clinical course
This is a study that was done in 2010 in a village in Nepal. They wanted to know what the natural history was of Leishmania
infection in that region. All the dots are houses and there they took samples of humans and animals. They wanted to know if
animals could play a role in the natural history of leishmania. They found that a lot of animals were positive (PCR) which mean
that they were infected with leishmania. These animals were living in close proximity to the positive humans (= close contact).
The boxes are places where we found positive humans and animals. This really suggested that there was really a transmission
between animals and humans, but they did not know if the animals were the reservoir.
Conclusion: with molecular tools they really found an epidemiological link between the animals and humans.
6) Conduct surveillance of disease and injury occurrence in populations (humans or animals or ...)
Surveillance is obviously one of the most
important applications of molecular
epidemiology. In the figure you see the
spread of the different variances of HIV
throughout the world.
Epidemiology of an infectious disease is
dynamic. Here you see all the flights
around the world during the day. Imagine
that in each of this flight is a person that is
infected with a dangerous disease, you
can see how easy it is nowadays to have a
propagation of a pathogen. This picture
shows how weak we are in front of the
pathogen.
3
, 7) Investigate disease outbreaks
Here you see the spread of HIV around the world and the origin is the Congo River Basin. This picture could be replaced with
Coronavirus. The origin would than not be the same (China). Molecular epidemiology has the tools to investigate this.
Epidemiology is highly dynamic!
Epidemiology of an infectious disease is dynamic. On the slide you see all the flights around the world during the day. Imagine
that in each of this flight is a person that is infected with a dangerous disease, you can see how easy it is nowadays to have a
propagation of a pathogen. This picture shows how weak we are in front of the pathogen.
Take home message:
• Get a broad view (reality is not only at the bottom of a test tube)
• Do not work alone
• Remind that epidemiology is not static
B. KEY EPIDEMIOLOGICAL CONCEPTS AND POSSIBLE BOTTLENECKS
Caution: Often you only know the number of notified cases in a year. The incidence is estimated but what proportion of the
incident cases are detected and notified?
4
