Diversified repertoire of phage resistance inKlebsiella pneumoniaeand bidirectional steering effects impacting antibiotic susceptibility

Abstract

Phage therapy is a promising alternative treatment for multidrug-resistant bacterial infections. Unfortunately, phage resistance represents a major barrier hindering the clinical utility. Mechanistic insights into bacterial phage defense mechanisms are critical to optimize phages therapy. Here, we discovered a repertoire of phage resistance mechanisms in a model strainKlebsiella pneumoniaeMKP103, including the disruption of phage binding site (fhuA::Tn andtonB::Tn), extension of phage latent period (mnmE::Tn andrpoN::Tn) and increased mutation frequency (mutS::Tn andmutL::Tn). Different from the prevailing view that phage resistance re-sensitizes antibiotic-resistant bacteria, we demonstrated a bi-directional steering effect on antibiotic susceptibility. Specifically, it was uncovered that, whilerpoN::Tn became more susceptible to colistin,mutS::Tn andmutL::Tn caused increased resistance to rifampicin and the last-line colistin. Our findings highlight the diversified strategies utilized byK. pneumoniaeto overcome phage infection. Overall, mechanism-guided phage steering represents a vital strategy to maximize the success of phage therapy.