Targeted bacteriophage suppresses Salmonella Infantis while preserving the overall microbiome in a chicken gut model
Multidrug-resistant Salmonella enterica serovar Infantis (S. Infantis) is an emerging threat in poultry production and food safety, yet the broader microbiological effects of targeted bacteriophage therapies against this pathogen within complex gut microbial communities where it would typically reside have only been studied minimally. Here, we used a continuous-culture in vitro chicken gut model to examine microbiome responses to phage-mediated suppression of multidrug-resistant S. Infantis. A representative outbreak-associated UK isolate carrying a pESI-like megaplasmid and blaCTX-M-1 established stable colonisation within the model over 120 h. Following phage treatment, viable S. Infantis counts decreased by approximately 3-log within 24 h and remained suppressed throughout the experiment. Metagenomic analysis showed persistence of bacteriophages within treatment vessels and preservation of overall microbial diversity despite sustained pathogen suppression. Phage treatment was also associated with a reduction of an expanded Klebsiella population observed in Salmonella-inoculated vessels and recovery of commensal taxa towards baseline levels. These findings suggest that phage treatment can suppress pathogen-associated microbial networks and expansion while maintaining the broader gut microbial community, supporting the use of bacteriophage interventions for control of antimicrobial-resistant Salmonella in poultry.