Bacteria are increasingly resistant to antibiotics, threatening the treatment of bacterial infections. Antibiotic resistance (ABR) is encoded in the DNA of the bacteria. ABR is spreading rapidly in human and animal populations because resistant bacteria are transmitted or because bacteria can transfer DNA encoding ABR to other bacteria, which then also become resistant.

Escherichia coli (E. coli), which is resistant to specific antibiotics, is considered a high-priority risk. Transfer of such E. coli between animals, such as livestock and humans, may contribute to the spread of ABR.

The HECTOR project set out to understand if certain E. coli are adapted to certain host species (human or animal) and how this adaptation is encoded by the DNA. Through genome comparison of 1198 E. coli strains, we found which E. coli strains are associated with the human host and which parts of their DNA aid in this adaptation.

We discovered that the DNA encodes metabolic activities allowing E. coli to potentially survive better in the human gut.

In addition, we studied the survival, and ABR transfer of E. coli adapted to different host species in live pigs and calves and in laboratory experiments imitating the chicken gut. We identified E. coli strains which are better able to survive in these models than other strains. However, our findings highlight the complexity of host adaptation, as we could not identify E. coli types surviving and growing well in either model. Furthermore, we observed that the transfer of DNA encoding ABR is rare in such experimental conditions.

The research of HECTOR has advanced our understanding of why some bacteria are able to spread between animal and human populations, thus contributing to the spread of ABR, and why others cannot. This can be helpful for risk assessment.

Whole-genome sequencing data of 1198 strains, together with metadata: NCBI BioProject