Phage Henu12-resistant mutant derives fitness trade-offs in Shigella dysenteriae.

UNLABELLED: The rapid emergence of multidrug-resistant Shigella dysenteriae strains necessitates new therapeutic approaches, such as phage therapy. Phages are considered a promising adjunct to antibiotics. The rapid emergence of phage-resistant bacterial mutants represents a major challenge in clinical practice. Nevertheless, this sometimes comes with fitness trade-offs. Thus, understanding the fitness trade-offs is crucial prior to phage clinical application. In the present study, a new lytic S. dysenteriae phage, Henu12, was isolated. Henu12 was assigned to the Caudoviricetes class and demonstrated good thermal, pH, and chloroform stability. The phage genome comprises a 69,779 bp linear double-stranded DNA with 90 open reading frames and has the highest similarity with Shigella phage Sf15 and Escherichia phage vB_EcoM_3HA14. Interestingly, the genome did not contain integrases, virulence, or antibiotic resistance genes. A time-kill assay demonstrated synergistic effects with polymyxin B, tetracycline, and ceftazidime. The phage-resistant mutant demonstrated impaired adsorption, downregulation of the tested lipopolysaccharide biosynthetic genes, enhanced sensitivity to polymyxin B and tetracycline, and environmental stressors, impaired biofilm, and diminished in vivo colonization compared to the wild-type strain. The whole-genome resequencing of the phage-resistant mutant identified a multi-base insertion in the waaH gene involved in the lipopolysaccharide biosynthesis pathway, potentially responsible for the phage resistance phenotype, along with other mutations related to the associated trade-offs. Together, these findings provide new insights into the evolutionary interactions between phage resistance and bacterial fitness that could potentially offer a novel approach to treat resistant Shigella dysenteriae infections.

IMPORTANCE: Phage therapy is a promising approach to combat the rise of multidrug-resistant bacteria. The emergence of phage-resistant bacterial strains is a potential complication associated with the application of phages. In the current study, we demonstrated that the synergistic use of phage Henu12 in conjunction with antibiotics not only enhances the bactericidal efficacy but also postpones the development of resistant strains. In addition, we provide a better understanding of the fitness trade-off that might fill some gaps in the future success of phage therapies in combating resistant shigellosis in clinical settings.