Diversified repertoire of phage resistance in Klebsiella pneumoniae and bidirectional steering effects impacting antibiotic susceptibility

Bacteriophage (phage) therapy is rising as a promising anti-infective option to combat antimicrobial resistance; however, its clinical utilization is severely hindered by the potential emergence of phage resistance. Fortunately, certain phage resistance mechanisms can restore bacterial antibiotic susceptibility, making the combination of phages with antibiotics a potential strategic approach. Here, we demonstrated that phage resistance can also lead to increased antibiotic resistance and provided mechanistic insights into bacterial phage defense mechanisms. We discovered a repertoire of phage resistance mechanisms in Klebsiella pneumoniae , including the disruption of phage binding site ( fhuA ::Tn and tonB ::Tn), extension of phage latent period ( mnmE ::Tn and rpoN ::Tn) and increased mutation frequency ( mutS ::Tn and mutL ::Tn). Different from the prevailing view that phage resistance re-sensitizes antibiotic-resistant bacteria, we revealed a bidirectional steering effect on the bacterial antibiotic susceptibility. Specifically, it was uncovered that, while rpoN ::Tn became more susceptible to colistin, mutS ::Tn and mutL ::Tn caused increased resistance to rifampicin and colistin. Our findings highlight the diversified strategies utilized by K. pneumoniae to overcome phage infection and the parallel effect on the antibiotic susceptibility. Mechanism-guided phage steering represents a rational strategy that should be incorporated into phage therapy to better inform clinical decisions. ### Competing Interest Statement The authors have declared no competing interest.