Microbial adhesion to surfaces and the consequent biofilm formation has been documented in many different environments. Biofilms constitute a protected mode of growth that allows microorganisms to survival in hostile environments, being their physiology and behavior significantly different from their planktonic counterparts. In dairy industry, biofilms may be a source of recalcitrant contaminations, causing food spoilage and are possible sources of public health problems such as outbreaks of foodborne pathogens. Biofilms are difficult to eradicate due to their resistant phenotype. However, conventional cleaning and disinfection regimens may also contribute to inefficient biofilm control and to the dissemination of resistance. Consequently, new control strategies are constantly emerging with main incidence in the use of biosolutions (enzymes, phages, interspecies interactions and antimicrobial molecules from microbial origin). The present review will focus on describing the mechanisms involved in biofilm formation and behavior, deleterious effects associated with their presence, and some of the current and emergent control strategies, providing new insight of concern for food industry.

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A review of current and emergent biofilm control strategies

Antibiotic resistance in Pseudomonas aeruginosa: mechanisms and alternative therapeutic strategies

https://onlinelibrary.wiley.com/doi/pdf/10.1111/1469-0691.12023

Microbial culturomics: paradigm shift in the human gut microbiome study

Surface-associated microbial communities, called biofilms, are present in all environments. Although biofilms play an important positive role in a variety of ecosystems, they also have many negative effects, including biofilm-related infections in medical settings. The ability of pathogenic biofilms to survive in the presence of high concentrations of antibiotics is called "recalcitrance" and is a characteristic property of the biofilm lifestyle, leading to treatment failure and infection recurrence. This review presents our current understanding of the molecular mechanisms of biofilm recalcitrance toward antibiotics and describes how recent progress has improved our capacity to design original and efficient strategies to prevent or eradicate biofilm-related infections.

https://hal-pasteur.archives-ouvertes.fr/pasteur-01370744/document

Biofilm-Related Infections: Bridging the Gap between Clinical Management and Fundamental Aspects of Recalcitrance toward Antibiotics

The intestinal tract of mammals is colonized by a large number of microorganisms including trillions of bacteria that are referred to collectively as the gut microbiota. These indigenous microorganisms have co-evolved with the host in a symbiotic relationship. In addition to metabolic benefits, symbiotic bacteria provide the host with several functions that promote immune homeostasis, immune responses, and protection against pathogen colonization. The ability of symbiotic bacteria to inhibit pathogen colonization is mediated via several mechanisms including direct killing, competition for limited nutrients, and enhancement of immune responses. Pathogens have evolved strategies to promote their replication in the presence of the gut microbiota. Perturbation of the gut microbiota structure by environmental and genetic factors increases the risk of pathogen infection, promotes the overgrowth of harmful pathobionts, and the development of inflammatory disease. Understanding the interaction of the microbiota with pathogens and the immune system will provide critical insight into the pathogenesis of disease and the development of strategies to prevent and treat inflammatory disease.

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Gut microbiota: Role in pathogen colonization, immune responses, and inflammatory disease.

Part I: Isolation of Bacteriophages 1. Isolation of Bacteriophages for Fastidious Bacteria Shigenobu Matsuzaki, Jumpei Uchiyama, Iyo Takemura-Uchiyama, Takako Ujihara, and Masanori Daibata 2. Isolation of Bacteriophages of the Anaerobic Bacteria Bacteroides Cristina Garcia-Aljaro, Maite Muniesa, and Juan Jofre 3. Isolation of Bacteriophages for Clinically Relevant Bacteria Sanna Sillankorva Part II: Characterization of Bacteriophages 4. In Vitro Activity against Planktonic and Biofilm Populations Assessed by Flow Cytometry Luis Melo, Diana Priscila Pires, and Joana Azeredo 5. Observation of Bacteriophage Ultrastructure by Cryo-electron Microscopy Ana Cuervo and Jose L. Carrascosa 6. Bacteriophage Taxonomy: an Evolving Discipline Igor Tolstoy, Andrew M. Kropinski, and J. Rodney Brister Part III: Bacteriophage Selection and Cocktail Formulation 7. Determination of the Bacteriophage Host Range - Culture Based Approach Andrey V. Letarov, and Eugene E. Kulikov 8. Recovery and Characterization of Bacteria Resisting Infection by Lytic Bacteriophage Libera Latino and Christine Pourcel 9. Guidelines to Compose an Ideal Bacteriophage Cocktail Maia Merabishvili, Jean-Paul Pirnay, and Daniel De Vos Part IV: Biodistribution, Host Interaction and Clinical Application 10. Interaction of Bacteriophages with Mammalian Cells Zuzanna Kazmierczak and Krystyna Dabrowska 11. In Vivo Bacteriophage Biodistribution Nicolas Dufour, Raphaelle Delattre, and Laurent Debarbieux 12. Interaction of Bacteriophages with the Immune System: Induction of Bacteriophage-specific Antibodies Krystyna Dabrowska & nbsp 13. Bacteriophage Treatment of Infected Diabetic Foot Ulcers Vera V. Morozova, Yulia N. Kozlova, Denis A. Ganichev, and Nina V. Tikunova 14. Compassionate Use of Bacteriophage Therapy for Foot Ulcer Treatment as an Effective Step for Moving Toward Clinical Trials Randolph Fisha, Elizabeth Kutter, Gordon Wheat, Bob Blasdel, Mzia Kutateladze, and Sarah Kuhl Part V: Production, Purification and Bacteriophage Storage 15. Bacteriophage Production in Bioreactors Maryam Agboluaje and Dominic Sauvage 16. Computational Modelling of Bacteriophage Production for Process Optimization Konrad Krysiak-Baltyn and Sally L. Gras 17. Methods for Bacteriophage Preservation Malgorzata B. Lobocka, Aleksandra Glowacka, and Piotr Golec Part VI: Safety and Regulation 18. Bacteriophage Production in Compliance with Regulatory Requirements Jean-Paul Pirnay, Maia Merabishvili, Hilde Van Raemdonck, Daniel De Vos, and Gilbert Verbeken 19. Guidelines for Bacteriophage Product Certification Alan Fauconnier Part VII: New Phage Therapy Approaches 20. Nano/micro Formulations for Bacteriophage Delivery Pilar Cortes, Mary Cano-Sarabia, Joan Colom, Jennifer Otero, Daniel Maspoch, and Montserrat Llagostera 21. Synthetic Biology to Engineer Bacteriophage Genomes Ana Rita Costa, Catarina Milho, Joana Azeredo, and Diana Priscila Pires

Bacteriophage therapy : from lab to clinical practice

Soon after their discovery in the early 20th century, bacteriophages were recognized to have great potential as antimicrobial agents, a potential that has yet to be fully realized. The nascent field of phage therapy was adversely affected by inadequately controlled trials and the discovery of antibiotics. Although the study of phages as anti-infective agents slowed, phages played an important role in the development of molecular biology. In recent years, the increase in multidrug-resistant bacteria has renewed interest in the use of phages as antimicrobial agents. With the wide array of possibilities offered by genetic engineering, these bacterial viruses are being modified to precisely control and detect bacteria and to serve as new sources of antibacterials. In applications that go beyond their antimicrobial activity, phages are also being developed as vehicles for drug delivery and vaccines, as well as for the assembly of new materials. This review highlights advances in techniques used to engineer phages for all of these purposes and discusses existing challenges and opportunities for future work.

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Genetically Engineered Phages: a Review of Advances over the Last Decade

Bacteriophages (phages), natural enemies of bacteria, can encode enzymes able to degrade polymeric substances. These substances can be found in the bacterial cell surface, such as polysaccharides, or are produced by bacteria when they are living in biofilm communities, the most common bacterial lifestyle. Consequently, phages with depolymerase activity have a facilitated access to the host receptors, by degrading the capsular polysaccharides, and are believed to have a better performance against bacterial biofilms, since the degradation of extracellular polymeric substances by depolymerases might facilitate the access of phages to the cells within different biofilm layers. Since the diversity of phage depolymerases is not yet fully explored, this is the first review gathering information about all the depolymerases encoded by fully sequenced phages. Overall, in this study, 160 putative depolymerases, including sialidases, levanases, xylosidases, dextranases, hyaluronidases, peptidases as well as pectate/pectin lyases, were found in 143 phages (43 Myoviridae, 47 Siphoviridae, 37 Podoviridae, and 16 unclassified) infecting 24 genera of bacteria. We further provide information about the main applications of phage depolymerases, which can comprise areas as diverse as medical, chemical, or food-processing industry.

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Bacteriophage-encoded depolymerases: their diversity and biotechnological applications

The interest for natural antimicrobial compounds has increased due to alterations in consumer positions towards the use of chemical preservatives in foodstuff and food processing surfaces. Bacteriophages fit in the class of natural antimicrobial and their effectiveness in controlling bacterial pathogens in agro-food industry has led to the development of different phage products already approved by USFDA and USDA. The majority of these products are to be used in farm animals or animal products such as carcasses, meats and also in agricultural and horticultural products. Treatment with specific phages in the food industry can prevent the decay of products and the spread of bacterial diseases and ultimately promote safe environments in animal and plant food production, processing, and handling. This is an overview of recent work carried out with phages as tools to promote food safety, starting with a general introduction describing the prevalence of foodborne pathogens and bacteriophages and a more detailed discussion on the use of phage therapy to prevent and treat experimentally induced infections of animals against the most common foodborne pathogens, the use of phages as biocontrol agents in foods, and also their use as biosanitizers of food contact surfaces.

/pdf/bacteriophages-and-their-role-in-food-safety-t8ukdxgpe2.pdf

Bacteriophages and Their Role in Food Safety

https://repositorium.sdum.uminho.pt/bitstream/1822/46544/1/document_46988_1.pdf

Sanna Sillankorva

Papers

Bacteriophage therapy : from lab to clinical practice

Genetically Engineered Phages: a Review of Advances over the Last Decade

Bacteriophage-encoded depolymerases: their diversity and biotechnological applications

Bacteriophages and Their Role in Food Safety

Phage therapy as an alternative or complementary strategy to prevent and control biofilm-related infections.