A gene that turns bacteria into superbugs is spreading through hospitals and farms.

A team of scientists made an alarming discovery in the urine of a patient at a Japanese hospital in 2003: a strain of Escherichia coli bacteria with a previously unknown gene that rendered the microbe resistant to an entire group of antibiotics. The Japanese researchers named this disturbing fragment of genetic material npmA, which turned the microorganism into a superbug immune to aminoglycosides, a family of drugs that includes some well-known ones, such as streptomycin and gentamicin. Microbiologist Bruno González Zorn explains that since then, npmA has become "a ghost" that has been silently spreading. His team has analyzed two million bacterial genomes and has detected that a variant of the gene, npmA2, has spread through hospitals and farms and has reached at least six countries. This bacterial adaptation, combined with others, can make some infections "practically incurable," warns González Zorn.

The emergence of drug-resistant microbes is "one of the most urgent threats" facing humanity, warned the heads of state and government gathered at the United Nations headquarters in New York on September 9, 2024. Just over five years ago, the World Health Organization documented 1.3 million deaths directly attributable to drug-resistant bacteria. One in five of those killed were children under five. The npmA2 gene is a new weapon that can jump from microbe to microbe.

“We have detected the beginning of global dissemination,” explains González Zorn, a professor at the Faculty of Veterinary Medicine at the Complutense University of Madrid. His team has identified the gene in the United Kingdom, Germany, the United States, Australia, China, and France, primarily in the bacterium Clostridioides difficile , responsible for diarrhea that can be fatal in debilitated patients. “Normally, resistance mechanisms do not confer resistance to an entire family of antibiotics. There is no single resistance mechanism to all penicillins or all tetracyclines, but this mechanism does confer resistance to the entire family of aminoglycosides,” explains González Zorn, an advisor to the World Health Organization.

Their study analyzed genomes from the international database AllTheBacteria . The results show that the gene's presence is still "rare," with around 100 detections in Clostridioides difficile bacteria, 0.34% of those examined. The gene was also found in a Dutch hospital during an outbreak of Enterococcus faecium , a microbe that can cause fatal infections in hospitalized patients. Scientists from seven institutions, including the French Pasteur Institute and the British University of Cambridge, collaborated on the study, published Thursday in the journal Nature Communications .

“We need to act now to detect the gene early,” says González Zorn. “We often detect new genes after they’ve already appeared in many intensive care units in many countries , and it’s already too late . However, this time we’ve seen that it’s spreading silently and isn’t present in Spain. It’s a very good time to develop tools to detect it and prevent it from spreading. Or at least to be able to find it early to isolate patients and know what we’re fighting against,” adds the microbiologist. “If we had detected it in 20 or 30 Spanish ICUs, it would have been a disaster; it would have been too late. The good thing is that we still have time to fight it, but we have to act now.”

Rafael Cantón , head of Microbiology at Madrid's Ramón y Cajal Hospital, is well aware of the danger of superbugs. He began working there in 1988, when laboratory tests indicated that microbes were susceptible to a wide variety of antibiotics. Since then, the overuse of drugs has led to the emergence of resistant strains, even to all available medications . "Aminoglycosides are antibiotics that are widely used in combination with others, such as in the treatment of tuberculosis or for bacteria that cause ventilator-associated pneumonia in hospitals. I'm concerned [about the global spread of the npmA2 gene] because we continue to lose groups of antibiotic families," Cantón laments.