Antibiotic resistance genes are abundant in the environment, many in forms that could easily move into bacteria causing disease in people, according to a Swedish study.
The researchers trawled through thousands of genetic sequences seeking suspected antibiotic resistance genes (Microbiome, doi: 10.1186/s40168-023-01479-0).
Such research could allow scientists to identify resistance genes at risk of turning up in patients being treated in hospitals. ‘A lot of resistance genes that we see in pathogens have their origins in environmental bacteria,’ says Johan Bengtsson-Palme at Chalmers University of Technology in Sweden. ‘At some point, these genes have been able to jump from these harmless bacteria into disease-causing microorganisms.’
To identify potential problem genes, bioinformatician Juan Inda-Diaz at Chalmers University of Technology in Sweden analysed 10,000 metagenomic sequences for what the team termed ‘latent’ antibiotic resistance genes. Machine learning had been used to identify likely suspects for such a trawl.
A surprisingly large number of resistance genes were identified from wastewater and also from bird faeces, notes Bengtsson-Palme. Some genes were highly mobile, and already present in species found in people. These may represent emerging threats to human health, the study concluded.
‘For certain types of resistance genes, we actually seem to know most of the forms already,’ says Bengtsson-Palme. ‘For other classes, there is a huge diversity that we have not even begun to tap into and see what that could mean in terms of future resistance threats.’
Antimicrobial resistance (AMR) is termed a leading threat to global health by the World Health Organization. It is estimated that almost 5m deaths were linked to bacterial AMR in 2019, mostly caused by six types of bacteria.
The Swedish research group would like to set up a monitoring programme to track resistance in the environment that could act as an early warning tool for emerging resistance to important antimicrobials.
David Graham, an AMR researcher at the University of Newcastle, UK, says the research is conceptually interesting. He warns, however, that many presumed ‘resistance’ genes are not related to antibiotics, but to general stress responses in bacteria.
‘Chemical warfare is continuously occurring across the microbial world and bacteria intrinsically produce defence proteins, which are often not related to actual resistance [to our drugs],’ he says.
‘This kind of research will become more profound if you can use it to guide drug discovery – design new drugs that are more resilient to becoming resistant.’