ESBL-EC gut colonization in dogs is associated with a distinct microbiota and resistome composition

The gut microbiota of humans and animals acts as a reservoir of extended-spectrum beta-lactamase producing Escherichia coli (ESBL-EC). Dutch companion dogs show high prevalence of ESBL-EC (45%) and over time continuously shift between states of ESBL-EC carriage. Since the microbiota could be a factor of ESBL-EC susceptibility, we here assessed whether ESBL-EC carriage in dogs is associated with changes in the gut microbiota and resistome composition. Faecal samples were longitudinally collected from 57 companion dogs in the Netherlands every two weeks for a total of six weeks. Faecal samples were used to determine carriage of ESBL-EC by culture-based PCR and MALDITOF. The gut microbiota and gut resistome composition were determined by 16s rRNA gene sequencing and ResCap targeted sequencing, respectively. In line with previous studies, we observed that ESBL-EC carriage was highly prevalent in dogs, with 68% of the dogs found positive for ESBL-EC at least once over the course of six weeks. We furthermore found associations between carriage of ESBL-EC and the increased abundance of Clostridium sensu stricto 1, Enterococcus, Lactococcus and the shared genera of Escherichia-Shigella. Nanopore metagenomic sequencing revealed that these genera may include opportunistic pathogens such as Clostridium perfringens, Enterococcus hirae, Lactococcus garvieae and Shigella flexneri. When focussing on the resistome, we identified associations between ESBL carriage and the increased abundance of the antibiotic resistance genes: cmlA, dfrA, dhfR, floR and sul3. In summary, our study showed that ESBL-EC carriage is associated with a distinct microbiota and resistome.