Prophage genomics of carbapenemase-producing Klebsiella pneumoniae from animal-derived food sources

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a globally disseminated pathogen of significant public health concern. Mobile genetic elements, including prophages, frequently drive their multidrug resistance and virulence. However, the contribution of prophages to the genetic landscape of food-derived CRKP remains poorly characterized. The study aimed to characterize the diversity, genetic features, and evolutionary relationships of prophages in CRKP isolates recovered from animal-derived food sources, and to evaluate their potential role in disseminating antimicrobial resistance (AMR) and virulence within the food chain. Whole-genome sequencing was performed on 23 CRKP isolates obtained from foods of animal origin in Egypt. Prophage mining and annotation were conducted to identify and classify prophage elements, detect resistance-and virulence-associated genes, and assess evolutionary relationships through phylogenetic analysis. Eighteen intact prophages were classified as members of the class Caudoviricetes. Based on structural protein analysis, 61.11% exhibited a Siphovirus-morphotype (long, non-contractile tails), while 38.88% were identified as Peduoviridae/Myovirus-morphotype (contractile tails). The bla_SHV resistance gene was detected in three incomplete prophages related to PHAGE_Escher_RCS47_NC_042128. Prophage regions also encoded lysozyme-like endolysins, suggesting potential use as lytic agents, and phylogenetic analysis revealed high prophage diversity, likely contributing to CRKP accessory genome evolution, fitness, and virulence. Animal-derived food may serve as a reservoir for CRKP that carry diverse prophages and other mobile genetic elements. Prophage-associated resistance, virulence, and lysis-related genes highlight the potential for dissemination of AMR and pathogenic traits through the food chain, underscoring the importance of surveillance of foodborne CRKP and their mobilome.