PLoS Biology: Building a "Wikipedia" for drug-resistant bacteria

In the future, even small infections could threaten human lives
if pathogenic bacteria become resistant to traditional antibiotic treatments.

Based on 214,000 microbiome samples, DTU researchers have created a freely accessible platform that shows where and how many
different types of drug-resistant bacteria are found in the world.

In order to understand how antibiotic resistance spreads around the world, it is important to know where, which and how many resistance genes are found
in all the environments around us.
Genes that provide resistance can be transmitted
between animals, humans and the environment.

Today, there is a wealth of data in various online repositories, and there are limited
datasets on the occurrence of drug-resistant bacteria in sewage, soil, animals, or humans.
But this data is not being actively used because, so far, it has been difficult to access, process, and especially utilize these large data sets
due to the computing power required.

"Such a large amount of data is interesting because we can discover new patterns and links
between disease-causing microbes and antibiotic resistance.
For example, we can see that the prevalence of certain types of antibiotic resistance varies very differently
in different parts of the world.
Hannah-Marie Martiny, a PhD student at DTU's National Food Research Institute and one of the driving forces behind the new database, says we can use this knowledge to develop guidelines
on how to fight drug resistance in different parts of the world.

The link between bacteria and drug resistance

Researchers at DTU's National Food Research Institute analyzed 214,000 samples from animals, humans, and soil, among others, and organized them to make them available
to others.
The goal is to create a directory
of drug-resistant bacteria that spans countries, populations and environments.

"You can compare it to a large encyclopedia like Wikipedia, which gathers knowledge from many different sources and organizes
it in a way that everyone can access.
In the same way, we collect data on bacterial antibiotic resistance and share
it with everyone.
She said
.

The 214,000 samples add up to about 300 terabytes, which can take months to analyze on a high-performance computer

"By taking the initial very resource-intensive analysis and making it available to everyone, we have a better opportunity for researchers around the world to come up with new solutions
that help reduce antibiotic resistance.
" This is in line with the principles of making data work in open science and equity," said Frank Möller Aarestrup, professor at DTU's National Food Research Institute, one of
the pioneers of resistance monitoring.

The development of drug-resistant bacterial types varies
from country to country.
However, drug-resistant bacteria in places such as Egypt can quickly spread around the world and cause Danish patients to contract bacteria
that are resistant to traditional treatments.

Frank Möller Aarestrup said: "The experience of the coronavirus disease 2019 pandemic has shown us the value of global surveillance data, for example, when a disease has the potential to spread beyond a country's borders, it can be used to respond to the disease
.
"

The development of the database is described in a curated data resource on the characteristics of the global antimicrobial resistance group of the 214K metagenome published in the scientific paper PLoS Biology

The project is supported by the Novo Nordisk Foundation as part of the Multifunctional Observatory for Emerging Infectious Diseases (VEO), which is supported
by the European Union's Horizon 2020 research and innovation programme.
The Genetic Epidemiology Research Group conducts targeted research with a view to predicting and preventing infectious diseases between humans and animals and supports global detection and control, with a particular focus on antibiotic resistance
.
More information about the work of the organization can be found on the Institute's website
.

For more information, visit the DTU Food Institute website to learn about the Institute's research in DNA sequencing technology, which helps set international standards
for detecting, monitoring and studying the global spread of pathogenic microorganisms and antibiotic-resistant bacteria.