Poultry-associated nitrofurantoin-resistant and pre-resistant Escherichia coli clones are found in multiple countries and one-health compartments

Escherichia coli is the most common cause of urinary tract infection (UTI) in humans. The nitrofuran-class antibacterial drug nitrofurantoin is a frequent UTI therapy, with resistance rarely observed. Here we show that nitrofurantoin resistant (NFT-R) E. coli are sometimes excreted by dogs fed a raw meat diet in the city of Bristol, United Kingdom, and that NFT-R and pre-resistant (one mutation away from NFT-R) E. coli can be found contaminating chicken meat sold for human consumption and chicken-based raw dog food in the same city. Using whole genome sequencing, we identified multiple NFT-R or pre-resistant E. coli clones spanning several phylogroups. These clones were dominated by isolates from poultry farms and poultry meat in Europe, Canada, the United States and Japan, and we identified instances where closely related NFT-R and pre-resistant isolates have colonised humans and caused UTIs. The origins of these poultry-associated NFT-R and pre-resistant E. coli clones are uncertain, but nitrofuran-class antibacterials (particularly furazolidone, furaltadone, and nitrofurazone) were used in poultry production during the 1970s and 80s, though this practice has been banned since the 1990s. It is possible, therefore, that this caused an initial selective pressure for the emergence of NFT-R and pre-resistant E. coli clones on poultry farms. Our findings have potentially important implications for domestic hygiene, particularly among people receiving nitrofurantoin therapy.