Researchers in Denmark have analyzed sewage from over 100 countries to map global antimicrobial resistance genes and found evidence of greater transmission of these genes of concern than previously estimated. The resource will identify resistance earlier and aid in effective public health strategies.
Sewage analysis rose in prominence during the COVID-19 pandemic, where it was shown to be an effective method to monitor disease development in a specific area. Researchers at Denmark’s DTU National Food Institute, however, have been using sewage monitoring since 2016 as an effective and inexpensive tool for monitoring infectious diseases and antimicrobial resistance.
For the latest work, the team analyzed sewage samples received by Technical University of Denmark (DTU) from 243 cities in 101 countries between 2016 and 2019. The findings, published in Nature Communications, effectively map where in the world the occurrence of resistance genes is highest, how the genes are located, and in which types of bacteria they are found.
“We’ve found similar resistance genes in highly different bacterial types. We find it worrying when genes can pass from a very broad group of bacteria to a completely different group with which there is no resemblance. It’s rare for these gene transmissions to occur over such long distances. It’s a bit like very different animal species producing offspring,” says FTU Assistant Professor Patrick Munk. For genes in bacteria that don’t usually make people sick—such as lactic acid bacteria—it’s of less concern. However, if the resistance genes find their way into bacteria that are important to human health—such as salmonella—it’s a completely different story. "This makes it much more likely that the bacteria will actually kill people—for example in a hospital—because no treatment is available,” Munk adds.
In different areas of Sub-Saharan Africa, the researchers have found the same resistance gene in a number of different bacteria. “We interpret this to mean that we may be quite close to a transmission hotspot, where there is a gene transmission from one to another to a third bacterium. That’s why we’re seeing the gene in so many different contexts precisely there,” Munk says.
He adds that many of the surprising transmissions appear to occur in the Sub-Saharan Africa. These are also countries with the least developed programs for monitoring resistance, which means that there is very little data on the resistance situation. “We risk overlooking important trends because we don’t have data,” Munk says, stressing that solid data will help develop effective strategies for combating resistance. “Right now, we have huge knowledge about how resistance behaves in the West and—based on that knowledge—we plan how to combat resistance. It now turns out that if we look at some new locations, the resistance genes may behave very differently—presumably because they have more favorable transmission conditions. Therefore, the way in which you combat resistance must also be adjusted and tailored to the local conditions.”
Genomic analysis of wastewater is fast and fairly inexpensive relative to how many people you can cover. Wastewater analyses do not require ethical approval, as the sample material cannot be linked to individuals. The samples contain a very large number of microorganisms from different sources, including human feces.
The global sewage project—which is supported by the Novo Nordisk Foundation and the VEO research project—concludes in 2023. Early feedback suggests the efforts are a good supplement to existing monitoring initiatives, which mainly operate at national or regional level and measure resistance in bacteria from sick people.
The bacteria are then broken up and their collective DNA is broken into smaller pieces, which state-of-the-art DNA sequencing equipment can read all at once. A supercomputer can then compare the billions of recorded DNA sequences with known genes and construct larger pieces of the original genomes contained in the samples. This process provides insight into several areas such as in which bacteria and genetic neighborhoods the resistance genes are located.
Unlike data from conventional analysis methods, raw data from metagenomic studies can be reused to shed light on other problems. For example, the researchers in the sewage project have used their dataset to analyze the occurrence of other pathogenic microorganisms in the sewage.
As new resistance genes are discovered—even far into the future—researchers will be able to reuse raw data to quickly establish where they have first appeared and how they have spread. The whole dataset has also been made freely available to researchers worldwide and has also been used to detect many new viruses globally and to map the ethnic composition of different populations.