Antimicrobial resistance (AMR) is an urgent and expanding threat, with AMR bacteria expected to kill as many as 10 million people annually by 2050. The most common culprit, AMR E. coli, was associated with over 600,000 deaths globally in 2019. E. coli is also the main cause of urinary tract infections (UTIs), which affect 1 in 2 women and killed 230,000 people globally in 2019. Many antibiotics used for treating UTIs, including the fluroquinolone ciprofloxacin, have seen increasing levels of resistance. New methods to combat AMR are needed.

One promising tool in the fight against AMR is phage therapy – the use of lytic phage to treat bacterial infections. Phage are ubiquitous and diverse, specific for their targets, and cause fewer off-target effects than antibiotics. Most importantly, phage can evolve in response to bacteria and are safe for human consumption. There are currently no FDA-approved phage therapies, but dozens of compassionate use cases have shown favorable results. In the U.S., phage is generally co-administered with antibiotics; this can result in synergistic, additive, or antagonistic interactions. However, there are currently no rules that predict these interactions.

Ciprofloxacin (CPFX) is a fluroquinolone antibiotic that targets bacterial topoisomerases and has previously shown antagonism with phage at some concentrations.  E. coli and other bacteria can encode a variety of CPFX resistance mechanisms including efflux pumps, target site (DNA gyrase and topoisomerase IV) mutations, porin changes, and proteins that modify CPFX or block its access to topoisomerase. Different resistance mechanisms could alter the intracellular CPFX concentration and affect phage-antibiotic interactions; however, this has not yet been investigated. We hypothesize that bacterial CPFX resistance genes can predict patterns of phage-CPFX interactions.

To test this, we are conducting phage-CPFX interaction screenings on multiple strains of Extraintestinal Pathogenic E. coli (ExPEC) at a wide range of phage and antibiotic concentrations, with a focus on uropathogenic E. coli. The phage used for screening include ΦHP3 and ΦHP3.1, two genetically similar T4-like phage that encode a topoisomerase. We are also identifying each ExPEC strain’s specific CPFX resistance mechanisms through hits to AMR gene databases. This research aims to determine the mechanisms by which bacterial AMR genes impact phage-antibiotic interactions and develop the first rules predicting phage-antibiotic pairings. This could inform rational selection of phage for therapeutic use and help make phage therapy feasible on a larger scale.