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Environment and sustainability

Combating antimicrobial resistance in global sewers

A Danish research project suggests that poverty and poor sanitary conditions may be a more important cause of the global problem of antimicrobial resistance than the excessive use of antibiotics.

The prevalence of antimicrobial resistance has never been higher and more relevant than in 2019. More multidrug-resistant bacteria are now lurking in the world’s hospitals than ever before, and worldwide, researchers are trying to find the next new antibiotic that can save the lives and limbs of people when everything else fails.

But perhaps the research world is approaching the problem incorrectly. At least, this is what a Danish researcher believes: that the battle against multidrug-resistant bacteria has become focused in the wrong direction.

“For many years, we have focused on the last part of the long chain that leads to the problem: the multidrug-resistant bacteria among critically ill people in hospitals. These are the people we are trying to help by developing new types of antibiotics, rapid diagnostic tests or infection control. Afterwards, we try to patch the system when things go wrong, instead of preventing and thereby ensuring that the problems do not arise. If we can instead reduce the general transmission of infection and ensure that antibiotics work the first time, we will not need to develop new antibiotics at all, because then we would not have any antimicrobial resistance,” explains Frank Møller Aarestrup, Professor, National Food Institute and Head, Research Group for Genomic Epidemiology, Technical University of Denmark, Lyngby.

In 2016, the Novo Nordisk Foundation awarded a Challenge Programme grant of DKK 60 million to Frank Møller Aarestrup to test his theories that the problem of antimicrobial resistance can be examined differently. The grant runs until 2023.

Focusing on far too few types of bacteria

Frank Møller Aarestrup believes that society, including the research community, has been incorrectly focusing for a long time on developing weapons to combat the transmission of antimicrobial resistance.

Globally, only 5–10% of antibiotics is used in hospitals, yet almost the entire focus is on individual cases of antimicrobial resistance that emerge in individual hospital locations. This could include multidrug-resistant gonorrhoea in England or vancomycin-resistant enterococci in Copenhagen.

Denmark, for example, focuses enormously on methicillin-resistant Streptococcus aureus (MRSA), with each of the few cases of MRSA being documented and analysed in minute detail. However, MRSA only represent about 0.5% of all cases of staphylococcal infection, and staphylococci only account for a fraction of all cases of bacterial infection.

Further, many people die from infectious diseases caused by non-resistant bacteria, but there is not much public focus on this.

According to Frank Møller Aarestrup, the problem is that the concept of resistance has taken on a life of its own in the public debate. There is a disconnect between the discussion and the actual problem, which is the transmission of infectious diseases.

“One of our collaboration partners has developed advanced computer models that show where to focus to minimize the number of deaths from infectious diseases. The models show very clearly that trying to control the transmission of infection and thus the development of resistance has a much greater effect in minimizing the total number of deaths than focusing on rare problems in hospitals. Unfortunately, the political focus is primarily on the rare cases of multidrug-resistant bacteria, which is probably because improving hygiene and the like, which we know really works, is not as sexy as the technological solutions of developing new types of antibiotics,” says Frank Møller Aarestrup.

We do not know where resistance develops

According to Frank Møller Aarestrup, solely focusing on the last part of the chain that leads to antimicrobial resistance also results in missed opportunities to intervene earlier to prevent antimicrobial resistance from occurring.

An example of this is where antimicrobial resistance is almost always discovered: in high-income countries, mainly Europe and the eastern United States. For example, MRSA was discovered in the United Kingdom.

Does this mean that the resistance problem in this case originated in the United Kingdom?

Probably not, but it is unclear where MRSA actually originated, because researchers first focus on the problem after it arrives in high-income countries: when multidrug-resistant bacteria are discovered in a hospital.

Nevertheless, the general consensus among researchers is that antimicrobial resistance most likely originates in Asia and that people on holiday in Asia get infected and bring the multidrug-resistant microbes home.

However, not everyone, including Frank Møller Aarestrup, agrees with this assumption.

“The problem is that we have not actually investigated whether this hypothesis is correct. We assume that, because Asia supposedly uses more broad-spectrum antibiotics than Europe, North America and Oceania, bacteria can more easily develop antimicrobial resistance there. However, we do not know whether this is true because we have not investigated this,” he says.

Antimicrobial resistance is exploding in Africa

In fact, Frank Møller Aarestrup’s research shows that many assumptions on the origins of the development of antimicrobial resistance are simply wrong.

As the first stage of this major research project based on a grant from the Novo Nordisk Foundation, Frank Møller Aarestrup and his research team from the Technical University of Denmark carried out a pilot study that took samples from sewage treatment plants in 60 countries and investigated the concentration of multidrug-resistant bacteria.

The results showed that China and India did not have the highest prevalence of antimicrobial resistance, as researchers in Europe and North America have always believed. Africa had a high prevalence of antimicrobial resistance, despite limited access to antibiotics in many parts of Africa.

According to Frank Møller Aarestrup, the difference between the assumptions of the research community and the new observations may be that China and India have far more researchers and publish much more scientific literature on the subject than the other Asian countries. These researchers actually write more about the prevalence and transmission of antimicrobial resistance in China and India, but this does not necessarily reflect the real picture.

“These initial results also surprised us because they contradicted what many other researchers thought. I was also very surprised that Africa has so much antimicrobial resistance and that we may be wrong about China and India,” says Frank Møller Aarestrup.

Investigated sewage in 60 countries

The researchers simply collected samples from wastewater treatment plants in 60 countries and sent them to Denmark, where researchers extracted all the DNA. They then sequenced uniform fragments of the DNA and matched it against a database of gene sequences for known antimicrobial resistance genes.

This gave the researchers an overview of the number of multidrug-resistant bacteria in a given sewage sample and insight into which antibiotic resistance genes they have.

Taking sewage samples has several advantages.

• Getting stool samples from a random population sample is very difficult because of concerns about privacy, including personal data protection. However, once the stool has been flushed down the toilet, it is no longer connected to the person and becomes an environmental sample that researchers can scrutinize fully.

• Second, it is much easier to take a sample from a wastewater treatment plant, in which bacteria from thousands of people are already mixed together, to get a representative sample of the prevalence of antimicrobial resistance in an often large catchment area that empties its toilets into the same sewerage system.

“We work very closely with the World Health Organization (WHO) because it gives us both legitimacy and access to healthcare systems around the world. This makes our research much easier,” says Frank Møller Aarestrup.

The computer for analysing the data is being developed

Performing this type of analysis may sound very simple, but it is not. Analysing and comparing the quantity of data in the various databases and in the sewage samples from the researchers’ next project requires the total capacity of Denmark’s most advanced supercomputer, Computerome, for a whole month.

In fact, the computer has not been completely finished and will not be ready until early summer 2019. Frank Møller Aarestrup has been given exclusive rights to use the computer in the first month to analyse his data.

If he could not use this computer, analysing each sample would have taken about 22 days, and in the follow-up research, which aims to confirm the results of the pilot project, he has 268 samples from 103 countries. Figure out how long that would take?

Two global groups in the prevalence of resistance

The researchers have already obtained quite interesting results from the pilot project.

First, the prevalence of antimicrobial resistance varies considerably by region.

Africa, Asia and South America are one group, and North America, Europe and Oceania (Australia and New Zealand) are the other. Antimicrobial resistance is very uniformly distributed in South America, Asia and Africa, which means that the bacteria have developed resistance uniformly to all types of antibiotics, whereas in North America, Europe and Oceania, the bacteria are mainly resistant to macrolide antibiotics.

Some places deviate, however. These include the Galápagos Islands, with a resistance profile similar to that in Europe, North America and Oceania, and Malta, with a profile similar to that in Africa.

“The explanations for this may be that many tourists from high-income countries visit the Galápagos Islands and that Malta is relatively close to Africa,” says Frank Møller Aarestrup.

The study was published in Nature Communications.

Tenuous link between use of antibiotics and the prevalence of antimicrobial resistance

In analysing the results, the researchers from the Technical University of Denmark tried to explain the findings for the prevalence and distribution of antimicrobial resistance.

One thing they examined is whether the total use of antibiotics in a country is associated with the prevalence of antimicrobial resistance. They also investigated whether antibiotic resistance genes in sewage samples can be linked to people travelling between two specific countries. Thus, is the prevalence of specific antibiotic resistance genes higher among countries that have many direct flights between them?

• The researchers found no association between antimicrobial resistance and air travel, which is one of the main arguments for the dominant theory of how antimicrobial resistance is transmitted from Asia to the Western Hemisphere.

• Even more interesting perhaps is that the researchers found the prevalence of antimicrobial resistance is very weakly associated with the use of antibiotics in countries.

“We really had to struggle to find any association. It was very weak even though the entire research world suggests that this pathway is the villain in developing antimicrobial resistance. This is rather worrying that the association that everyone is certain exists is so difficult to find. This can keep researchers awake at night, including me,” explains Frank Møller Aarestrup.

Poor sanitary conditions may enable antimicrobial resistance to be transmitted

To find another explanation for how antimicrobial resistance develops, Frank Møller Aarestrup used the Human Development Index of the United Nations Development Programme, which indicates the state of development of countries. It is based on World Bank data, which describes the infrastructure investment, wage levels and investment in sewage and healthcare for each country.

“It is probably the closest we can get to the original data from and situation of individual countries,” says Frank Møller Aarestrup.

When the researchers linked the prevalence of antimicrobial resistance with the Human Development Index in various countries, they found a very clear association that was much stronger than the association with the use of antibiotics.

The researchers subsequently extracted 1503 subcomponents of the World Bank data and linked them directly with the prevalence of antimicrobial resistance. They found very strong associations with investment in hospital services and investment in sewerage systems, but none for such parameters as the number of copper mines, forested areas and the like.

“This showed very clearly that investment in sanitary conditions is much more strongly associated with the development of antimicrobial resistance than the use of antibiotics,” explains Frank Møller Aarestrup.

Antibiotics in high-income countries disappear into the toilet

According to Frank Møller Aarestrup, it makes sense that sanitary conditions are a much stronger cause of antimicrobial resistance than antibiotic use.

The problem of antimicrobial resistance arises only when multidrug-resistant bacteria are transmitted. In a low-income country where many people still have to defecate on the streets, bacteria with newly acquired antimicrobial resistance can much more easily be transmitted, infect other people and become a problem than in a high-income country such as Denmark, for example, where antimicrobial resistance has greater difficulty in being transmitted because of higher hygiene standards and better sanitary conditions.

In almost all cases, multidrug-resistant bacteria are flushed down the toilet, never to be seen again.

“The World Bank is very pleased with the result and therefore now has an investment objective of slowing down the transmission of multidrug-resistant bacteria. Investing in restricting the use of antibiotics is difficult, but improving sanitary conditions in low-income countries is easier to invest in,” says Frank Møller Aarestrup.

Monitoring pathogenic bacteria in real time

In addition to studying sewage samples from various parts of the world, Frank Møller Aarestrup is launching several projects aimed at supporting these new and, for some, controversial conclusions.

• One project the researchers have created will examine the development of resistance over time from one wastewater treatment plant. The researchers will then investigate whether this is associated with the findings from hospitals in the region during the same period: that is, whether the overall development of resistance in society is associated with the specific problems of hospitals.

• Second, the researchers will also collect samples from socioeconomically diverse places in the same country, including in the United States. Here the researchers will determine whether the prevalence of antimicrobial resistance is higher in areas with low income than in areas with high income and thereby confirm the findings from the comparison with data from the World Bank.

“This is linked with another project that stemmed from the project funded by the Novo Nordisk Foundation. Here we will take samples from 14 locations in the United States and 10 African countries. Ideally we would have liked to carry out a study to determine the effect of implementing better sanitary conditions, but it is not easy to take samples from a country, ask them to invest DKK 3 billion in better sanitary infrastructure and then take samples again. This is the second best option,” says Frank Møller Aarestrup.

WHO may take over the project

Linked to the whole project of discovering the primary source of development of resistance is a project in which the researchers investigate the prevalence of various pathogenic bacteria in sewage samples.

Here, the researchers want to identify the prevalence of cholera bacteria, Salmonella, Campylobacter and others so that they can monitor the disease situation in a specific area in real time.

For example, if the number of cholera bacteria increases in sewage samples separated by 2 weeks, this indicates that an outbreak may be on the way, and through appropriate measures, public health authorities can mitigate the severity of the outbreak.

“The purpose of the projects is that we can transfer them to others in 5 years, so that a large international organization such as WHO can monitor the prevalence of bacteria and antimicrobial resistance in many countries. This will give use a much better overview of the factors involved when antimicrobial resistance develops, and we can put this into a general context of disease development and thus make data much more relevant to the population – and not only hospitals and researchers,” explains Frank Møller Aarestrup.

Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage” has been published in Nature Communications. In 2016, the Novo Nordisk Foundation awarded a Challenge Programme grant of DKK 60 million to Frank Møller Aarestrup for the project Global Surveillance of Antimicrobial Resistance.

Frank Møller Aarestrup
Professor, Head of Research Group
Global monitoring of antibiotic resistance Effectively reducing the prevalence of antibiotic resistance and using the best antibiotics requires knowledge based on continually monitoring the prevalence and spread of different types of antibiotic resistance globally. To increase this knowledge, the project will collect and analyse wastewater from cities throughout the world and make the results universally available, including for the public authorities, researchers and citizens. The project will use whole-genome sequencing, a technique that reveals the full DNA profile of bacteria. This will enable the prevalence of all known genes that produce antibiotic resistance to be determined in one operation.