Previously unknown antibiotic resistance is widespread among bacteria

Bacteriologist taking a bacterial culture from a Petri dish. Image: Tim Sandle

Genes that make bacteria resistant to antibiotics appear to be far more widespread in the environment than previous studies suggest. This is according to a new study, from Chalmers University of Technology and the University of Gothenburg in Sweden. The findings show that bacteria in almost all environments carry resistance genes.

This finding carries the risk of these genes being spread and hence aggravating the problem of bacterial infections that become untreatable with antibiotics.

According to lead scientist, Erik Kristiansson: “We have identified new resistance genes in places where they have remained undetected until now. These genes can constitute an overlooked threat to human health.”

The World Health Organisation states that antibiotic resistance is one of the greatest threats to global health. According to the UN Interagency Coordination Group on Antimicrobial Resistance, 700,000 people die each year from infections caused by antibiotic-resistant bacteria.

The genes that make bacteria resistant have long been studied. However, the focus is with identifying those resistance genes that are already prevalent in pathogenic bacteria. In contrast, the new study from Sweden looked at large quantities of DNA sequences from bacteria to analyse new forms of resistance genes. This was undertaken to understand how common these genes are.

By tracing the genes in thousands of different bacterial samples from different environments (including people, soil and from sewage treatment plants), the study analysed 630 billion DNA sequences in total by using metagenomics.

The researchers used DNA from two public databases. The first database, ResFinder, contains a couple of thousand previously known antibiotic resistance genes in bacteria. The researchers expanded these with a large number of new resistance genes that they had found through an analysis of bacterial DNA. The known and new resistance genes amounted to 20,000 in total. The second database, MGnify, contains large quantities of bacterial DNA from different sources such as bacteria living on and in people, in sewage treatment plants and from the soil and water.

The research found that antibiotic resistance genes are present in bacteria in almost all environments. This also includes the human microbiome and with pathogenic bacteria.

To put the findings into context, resistance genes in bacteria that live on and in humans and in the environment were ten times more abundant than those previously known. This leads the researchers to stress the need for more knowledge about the problem of antibiotic resistance.

The research team is working on integrating the new data into the international EMBARK project (Establishing a Monitoring Baseline for Antibiotic Resistance in Key environments). Thus, the project is seeking greater insight on how antibiotic resistance is spreading between humans and the environment.

The research appears in the journal Microbiome, titled “Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes.”