New and more detailed map of antimicrobial resistance

Sewage sample collection in Tamale, Ghana – one of 101 countries involved in global surveillance of infectious diseases and antimicrobial resistance through sewage. Credit: Courage Kosi Setsoafia Saba

During the COVID-19 pandemic, the world realized the value of using sewage analyzes to monitor disease development in an area. However, a group of researchers at the DTU National Food Institute have been using sewage monitoring from around the world since 2016 as an effective and inexpensive tool to monitor infectious diseases and antimicrobial resistance.

By analyzing sewage samples taken by DTU from 243 cities in 101 countries between 2016 and 2019, the researchers mapped where in the world resistance genes are most common, how genes are located, and in which bacterial strains. .

Results of the new metagenomic study published recently Nature Communication– surprised researchers. In fact, the study shows that genes arise in many different genetic contexts and types of bacteria, suggesting more transmission than the researchers expected.

“We found similar resistance genes in quite different types of bacteria. We find it worrisome that genes move from a very large group of bacteria to a completely different group with no similarity. It’s a bit like very different animal species producing offspring,” explains Assistant Professor Patrick Munk.

This is less of a concern if the genes are found in bacteria that don’t usually make people sick, such as lactic acid bacteria. However, if resistance genes get into bacteria (like salmonella) that are important to human health, that’s a whole different story.

“This makes bacteria much more likely to actually kill people — in a hospital, for example — because no cure is available,” says Patrick Munk.

Like a complex puzzle

The Genomic Epidemiology Research Group at DTU’s National Food Institute has developed and maintains one of the world’s most comprehensive databases of resistance. It contains 3,134 currently known resistance genes.

The researchers used the database to map resistance genes in sewage samples in the new study.

The samples contain a large number of microorganisms from different sources, including human feces. Frozen sewage samples were sent to DTU, where lab technicians removed all bacteria from the thawed samples.

The bacteria are then fragmented and their bulk DNA is broken down into smaller pieces that state-of-the-art DNA sequencing equipment can read at once.

A supercomputer can then compare billions of recorded DNA sequences with known genes and create larger chunks of the original genomes found in the samples.

This process provides insights into various areas, such as in which bacteria and genetic neighborhoods the resistance genes are located.

New and more detailed map of antimicrobial resistance

The world map shows the genesis of resistance genes in different countries. The darker the color used for a country, the higher the frequency of resistance genes in bacteria. Gray countries did not provide sewage samples. Credit: Technical University of Denmark

Hotspots for the transfer of genes

In different parts of Sub-Saharan Africa, the researchers found the same resistance gene in several different bacteria.

“We interpret this to mean that we could be pretty close to a transmission point where there is gene transfer from one to the other to a third bacterium. So we see the gene right there in so many different contexts,” Patrick said. Munk explains.

He adds that many of the startling transmissions occurred in Sub-Saharan Africa. These are also the countries with the least developed programs to monitor resilience, which means there is little data on the resilience situation.

“We risk missing important trends because we don’t have data,” he says, emphasizing that solid data is exactly what is needed to develop effective strategies to combat resistance:

“Right now, we have tremendous knowledge of how resistance behaves in the West, and we plan how to fight resistance based on that knowledge. Now if we look at some new places, it turns out that resistance genes can behave very differently, probably because they have more favorable transmission conditions. The way you deal with resistance must also be adjusted and adapted to local conditions.”

Arrival

The global sewage project, supported by the Novo Nordisk Foundation and the VEO research project, ends in 2023. This has proven to be a good complement to existing monitoring initiatives that operate and measure mainly at the national or regional level, the researchers said. resistance in bacteria from sick people.

Therefore, they hope that the successor of the project will emerge so that the world can continue to benefit from the important information produced by the monitoring program. This also applies to countries with robust monitoring programs and control strategies.

“There are so many analogies with climate change that what’s going on on the other side of the world doesn’t matter to you. As we’ve seen over and over again, sooner or later the problem will come back to bite us.” Patrick Munk emphasizes.

Reusable data

Unlike data from traditional analysis methods, raw data from metagenomic studies can be reused to shed light on other issues. For example, researchers at the sewer project used their datasets to analyze the occurrence of other pathogenic microorganisms in sewage.

The entire dataset from sewer monitoring is freely available to researchers around the world. For example, it is already being used to detect many new viruses globally and to map the ethnic composition of different populations.

As new resistance genes are discovered, researchers will be able to quickly identify where they first appeared and how they spread by reusing raw data.

In the study, the researchers examined 757 sewage samples from 243 cities in 101 countries. Samples were collected and sent to DTU’s campus in Lyngby between 2016 and 2019.

Genomic analysis of wastewater is fast and fairly inexpensive given how many people you can cover. Wastewater analyzes do not require ethical approval as sample material cannot be associated with individuals.

More information:
Patrick Munk et al. Genomic analysis of sewage from 101 countries reveals the global landscape of antimicrobial resistance, Nature Communication (2022). DOI: 10.1038/s41467-022-34312-7

Provided by the Technical University of Denmark

Quotation: New and more detailed antimicrobial resistance map (2022, December 1), retrieved December 1, 2022 from https://phys.org/news/2022-12-antimicrobial-resistance.html.

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