Combating Antimicrobial Resistance Spread in Food and Drinks Using Bacteriophage Technologies

A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Bacteriophages".

Deadline for manuscript submissions: 31 March 2026 | Viewed by 1873

Special Issue Editor

Centre for Epidemiology and Planetary Health, Department of Veterinary and Animal Science, Scotland's Rural College, Inverness IV2 5NA, UK
Interests: phage therapy; biofilms; zoonoses; prophage; bacterial pathogenicity; virulence factors; Galleria mellonella; cell lines; antimicrobial resistance; phage formulation; fermentation model; cloning; RNA seq; qPCR
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Special Issue Information

Dear Colleagues,

The rising prevalence of antimicrobial resistance (AMR) is negatively impacting treatment outcomes and posing a serious threat to human health, agriculture, and the environment. If left unchecked, AMR could lead to devastating global health and economic consequences. To mitigate this crisis, precise detection and effective control of pathogenic bacteria in key sources of infection such as agriculture, raw and processed foods, beverages, and relevant environments are crucial.

Bacteriophages (phages) are highly specialised parasitic bacterial viruses. Lytic phages infect and lyse their hosts, while temperate phages can integrate into their bacterial host chromosomes or co-exist independently as plasmids intracellularly. Harnessing phage technologies offers a promising approach to the detection and control of pathogenic bacteria. This strategy will complement existing methods, limit the spread of AMR, and enhance microbial safety in food and beverages.   

In this Special Issue, we aim to publish manuscripts covering:

  • Phage-based strategies as biocontrol agents of pathogenic bacteria in food and beverages (including water)
  • Phage–host interactions in foodborne and waterborne bacteria in relevant infection models
  • Regulatory frameworks for phage applications in food and beverages.
  • Engineering, synthetic biology, and formulation strategies for optimal phage delivery, activity, and stability in agriculture, raw and processed food products, and beverages.
  • Industrial and commercial applications of phages in agriculture and food processing units.
  • Harnessing artificial intelligence, machine learning, and computational biology to explore the role of phages in AMR gene carriage and spread through foodborne and waterborne pathogens.
  • Phage-based biosensors for pathogen detection in food products.

Dr. Janet Nale
Guest Editor

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Keywords

  • bacteriophage
  • phage therapy
  • antimicrobial resistance
  • food
  • drink
  • water
  • agriculture
  • pathogenic bacteria
  • lytic phages
  • lysogens
  • prophages
  • temperate phage

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Published Papers (2 papers)

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16 pages, 2594 KB  
Article
The Potential Roles of Prophages in the Pathogenicity of Klebsiella pneumoniae Strains from Kenya
by Juliah K. Akhwale, Ivy J. Mutai and Janet Y. Nale
Antibiotics 2025, 14(11), 1145; https://doi.org/10.3390/antibiotics14111145 - 12 Nov 2025
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Abstract
Background/Objectives: Antimicrobial resistance (AMR) in Klebsiella pneumoniae poses a serious threat to healthcare, especially in sub-Saharan Africa (SSA). To complement AMR infection control in Kenya, here, clinical and environmental genomes were investigated to determine the potential roles prophages play in K. pneumoniae pathogenicity. [...] Read more.
Background/Objectives: Antimicrobial resistance (AMR) in Klebsiella pneumoniae poses a serious threat to healthcare, especially in sub-Saharan Africa (SSA). To complement AMR infection control in Kenya, here, clinical and environmental genomes were investigated to determine the potential roles prophages play in K. pneumoniae pathogenicity. Methods: Prophages were extracted from 89 Kenyan K. pneumoniae genomes. The intact prophages were examined for virulence genes carriage, and their phylogenetic relationships were established. Results: Eighty-eight (~99%) of the genomes encode at least a single prophage, and there is an average of four prophages and 2.8% contributory genomes per bacterial strain. From the 364 prophages identified, 250 (68.7%) were intact, while 58 (15.9%) and 57 (15.7%) were questionable and incomplete, respectively. Approximately, 30% of the intact prophages encode 38 virulence genes that are linked to iron uptake (8), regulation (6), adherence (5), secretion system (4), antiphagocytosis (4), autotransporter (4), immune modulation (3), invasion (2), toxin (1) and cell surface/capsule (1). Phylogenetic analyses revealed three distinct clades of the intact prophages irrespective of their hosts, sources and locations, which support the plasticity of the genomes and potential to mediate horizontal gene transfer. Conclusions: This study provides first evidence showing the diverse prophages that are encoded in K. pneumoniae from SSA with particular focus on Kenyan strains. This also shows the potential roles these prophages play in the pathogenicity and success of K. pneumoniae and could improve knowledge and complement control strategies in the region and across the globe. Further work is needed to show the expression of these genes through lysogenisation. Full article
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Review

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33 pages, 739 KB  
Review
A Comprehensive Review of the Application of Bacteriophages Against Enteric Bacterial Infection in Poultry: Current Status, Challenges, and Future Prospects
by Muhammad Muneeb, Ehsaan Ullah Khan, Sohail Ahmad, Ijaz Hussain, Shumaila Batool, Arooj Fatima, Elham Assadi Soumeh, Ali R. Al Sulaiman and Ala E. Abudabos
Antibiotics 2025, 14(12), 1207; https://doi.org/10.3390/antibiotics14121207 - 1 Dec 2025
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Abstract
The poultry industry plays a major role in the emergence and spread of foodborne zoonotic diseases, particularly those associated with antibiotic-resistant bacteria. These diseases pose substantial global public health challenges, and the increasing development of antimicrobial resistance further intensifies these concerns. In response, [...] Read more.
The poultry industry plays a major role in the emergence and spread of foodborne zoonotic diseases, particularly those associated with antibiotic-resistant bacteria. These diseases pose substantial global public health challenges, and the increasing development of antimicrobial resistance further intensifies these concerns. In response, scientific efforts have expanded to develop and implement innovative technologies capable of mitigating the rising prevalence of multidrug-resistant (MDR) microorganisms. Therapeutic bacteriophage supplementation has regained significant attention because it can selectively lyse specific bacteria, is cost-effective to produce, offers environmentally favorable characteristics, and provides several advantages over conventional antibiotics. Experimental studies have demonstrated that phage therapy is both safe and effective for controlling poultry-associated enteric pathogens. Phages can be applied at various stages of the poultry production chain, from rearing to processing and distribution, using multiple delivery strategies. Despite certain limitations, the targeted and well-regulated application of phage cocktails offers considerable potential as an alternative to antibiotics for managing MDR infections. The success of bacteriophage therapy depends on several factors, including the timing of administration, dosage, delivery method, and its integration with other therapeutic approaches. Therefore, developing a comprehensive understanding of bacteriophage utilization in poultry production is both timely and necessary. This review examines the applications, constraints, and future opportunities of phage therapy within the commercial poultry industry, with particular emphasis on the mechanisms through which bacteriophages control bacterial infections. Full article
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