One health clones of multidrug-resistant Escherichia coli carried by synanthropic animals in Brazil

WHO priority pathogens have disseminated beyond hospital settings and are now being detected in urban and wild animals worldwide. In this regard, synanthropic animals such as urban pigeons (Columba livia) and rodents (Rattus rattus, Rattus norvegicus and Mus musculus) are of interest to public health due to their role as reservoirs of pathogens that can cause severe diseases. These animals usually live in highly contaminated environments and have frequent interactions with humans, domestic animals, and food chain, becoming sentinels of anthropogenic activities. In this study, we report genomic data of Escherichia coli strains selected for ceftriaxone and ciprofloxacin resistance, isolated from pigeons and black rats. Genomic analysis revealed the occurrence of international clones belonging to ST10, ST155, ST224 and ST457, carrying a broad resistome to beta-lactams, aminoglycosides, trimethoprim/sulfamethoxazole, fluoroquinolones, tetracyclines and/or phenicols. SNP-based phylogenomic investigation confirmed clonal relatedness with high-risk lineages circulating at the humananimal-environmental interface globally. Our results confirm the dissemination of WHO priority CTX-Mpositive E. coli in urban rodents and pigeons in Brazil, highlighting potential of these animals as infection sources and hotspot for dissemination of clinically relevant pathogens and their resistance genes, which is a critical issue within a One Health perspective.

Automated summary

WHO priority pathogens have spread to urban and wild animals, including urban pigeons and rodents, which can serve as reservoirs for severe diseases. Genomic analysis of ceftriaxone and ciprofloxacin resistant Escherichia coli strains isolated from pigeons and rats revealed the presence of international clones carrying a broad range of resistance genes. These findings confirm the dissemination of clinically relevant pathogens and their resistance genes in urban animals, posing a critical issue in One Health perspective.