Active bacteriophage biocontrol and therapy on sub-millimeter scales towards removal of unwanted bacteria from foods and microbiomes

How Simple Maths Can Inform Our Basic Understanding of Phage Therapy

Phage therapy is the application of bacterial viruses to control and, ideally, to eliminate problematic bacteria from patients. Usually employed are so-called strictly lytic phages, which upon adsorption of a bacterium should give rise to both bacterial death and bacterial lysis. This killing occurs with single-hit kinetics, resulting in relatively simple ways to mathematically model organismal-level, phage-bacterium interactions. Reviewed here are processes of phage therapy as viewed from these simpler mathematical perspectives, starting with phage dosing, continuing through phage adsorption of bacteria, and then considering the potential for phage numbers to be enhanced through in situ phage population growth. Overall, I suggest that a basic working knowledge of the underlying "simple maths" of phage therapy can be helpful toward making dosing decisions and predicting certain outcomes. This especially is during controlled in vitro experimentation but is relevant to thinking about in vivo applications as well.

Automating Predictive Phage Therapy Pharmacology

Viruses that infect as well as often kill bacteria are called bacteriophages, or phages. Because of their ability to act bactericidally, phages increasingly are being employed clinically as antibacterial agents, an infection-fighting strategy that has been in practice now for over one hundred years. As with antibacterial agents generally, the development as well as practice of this phage therapy can be aided via the application of various quantitative frameworks. Therefore, reviewed here are considerations of phage multiplicity of infection, bacterial likelihood of becoming adsorbed as a function of phage titers, bacterial susceptibility to phages also as a function of phage titers, and the use of Poisson distributions to predict phage impacts on bacteria. Considered in addition is the use of simulations that can take into account both phage and bacterial replication. These various approaches can be automated, i.e., by employing a number of online-available apps provided by the author, the use of which this review emphasizes. In short, the practice of phage therapy can be aided by various mathematical approaches whose implementation can be eased via online automation.

Bacteriophage Adsorption: Likelihood of Virion Encounter with Bacteria and Other Factors Affecting Rates

For ideal gasses, the likelihood of collision of two molecules is a function of concentrations as well as environmental factors such as temperature. This too is the case for particles diffusing within liquids. Two such particles are bacteria and their viruses, the latter called bacteriophages or phages. Here, I review the basic process of predicting the likelihoods of phage collision with bacteria. This is a key step governing rates of phage-virion adsorption to their bacterial hosts, thereby underlying a large fraction of the potential for a given phage concentration to affect a susceptible bacterial population. Understanding what can influence those rates is very relevant to appreciating both phage ecology and the phage therapy of bacterial infections, i.e., where phages are used to augment or replace antibiotics; so too adsorption rates are highly important for predicting the potential for phage-mediated biological control of environmental bacteria. Particularly emphasized here, however, are numerous complications on phage adsorption rates beyond as dictated by the ideals of standard adsorption theory. These include movements other than due to diffusion, various hindrances to diffusive movement, and the influence of assorted heterogeneities. Considered chiefly are the biological consequences of these various phenomena rather than their mathematical underpinnings.

A Taxonomy-Agnostic Approach to Targeted Microbiome Therapeutics-Leveraging Principles of Systems Biology

The study of human microbiomes has yielded insights into basic science, and applied therapeutics are emerging. However, conflicting definitions of what microbiomes are and how they affect the health of the "host" are less understood. A major impediment towards systematic design, discovery, and implementation of targeted microbiome therapeutics is the continued reliance on taxonomic indicators to define microbiomes in health and disease. Such reliance often confounds analyses, potentially suggesting associations where there are none, and conversely failing to identify significant, causal relationships. This review article discusses recent discoveries pointing towards a molecular understanding of microbiome "dysbiosis" and away from a purely taxonomic approach. We highlight the growing role of systems biological principles in the complex interrelationships between the gut microbiome and host cells, and review current approaches commonly used in targeted microbiome therapeutics, including fecal microbial transplant, bacteriophage therapies, and the use of metabolic toxins to selectively eliminate specific taxa from dysbiotic microbiomes. These approaches, however, remain wholly or partially dependent on the bacterial taxa involved in dysbiosis, and therefore may not capitalize fully on many therapeutic opportunities presented at the bioactive molecular level. New technologies capable of addressing microbiome-associated diseases as molecular problems, if solved, will open possibilities of new classes and categories of targeted microbiome therapeutics aimed, in principle, at all dysbiosis-driven disorders.

Determination of phage susceptibility as a clinical diagnostic tool: A routine perspective

As the global burden of disease caused by multidrug resistant bacteria is a major source of concern, credible clinical alternatives to antibiotic therapy, such as personalized phage therapy, are actively explored. Although phage therapy has been used for more than a century, the issue of an easy to implement diagnostic tool for determining phage susceptibility that meets current routine clinical needs is still open. In this Review, we summarize the existing methods used for determining phage activity on bacteria, including the three reference methods: the spot test, the double agar overlay plaque assay, and the Appelmans method. The first two methods rely on the principle of challenging the overnight growth of a lawn of bacteria in an agar matrix to a known relative phage to bacteria concentration and represent good screening tools to determine if the tested phage can be used for a “passive” and or “active” treatment. Beside these methods, several techniques, based on “real-time” growth kinetics assays (GKA) have been developed or are under development. They all monitor the growth of clinical isolates in the presence of phages, but use various detection methods, from classical optical density to more sophisticated techniques such as computer-assisted imagery, flow-cytometry, quantitative real-time polymerase chain reaction (qPCR) or metabolic indicators. Practical considerations as well as information provided about phage activity are reviewed for each technique. Finally, we also discuss the analytical and interpretative requirements for the implementation of a phage susceptibility testing tool in routine clinical microbiology.

Pathways to Phage Therapy Enlightenment, or Why I Have Become a Scientific Curmudgeon

Over the past decade I, with collaborators, have authored a number of publications outlining what in the first of these I described as "Phage therapy best practices"-phage therapy being the use of bacterial viruses (bacteriophages) to treat bacterial infections, such as clinically. More generally, this is phage-mediated biocontrol of bacteria, including of bacteria that can contaminate foods. For the sake of increasing accessibility, here I gather some of these suggestions, along with some frustrations, into a single place, while first providing by way of explanation where they, and I, come from scientifically. Although in my opinion phage therapy and phage-mediated biocontrol are both sound approaches toward combating unwanted bacteria, I feel at the same time that the practice of especially phage therapy research could be improved. I supply also, as supplemental material, a list of ∼100 English language 2000-and-later publications providing primary descriptions of phage application to humans.

Further Considerations on How to Improve Phage Therapy Experimentation, Practice, and Reporting: Pharmacodynamics Perspectives

Phage therapy uses bacterial viruses (bacteriophages) to infect and kill targeted pathogens. Approximately one decade ago, I started publishing on how possibly to improve upon phage therapy experimentation, practice, and reporting. Here, I gather and expand upon some of those suggestions. The issues emphasized are (1) that using ratios of antibacterial agents to bacteria is not how dosing is accomplished in the real world, (2) that it can be helpful to not ignore Poisson distributions as a means of either anticipating or characterizing phage therapy success, and (3) how to calculate a concept of 'inundative phage densities.' Together, these are issues of phage therapy pharmacodynamics, meaning they are ways of thinking about the potential for phage therapy treatments to be efficacious mostly independent of the details of delivery of phages to targeted bacteria. Much emphasis is placed on working with Poisson distributions to better align phage therapy with other antimicrobial treatments.

Phage Therapy in the 21st Century: Is There Modern, Clinical Evidence of Phage-Mediated Efficacy?

Many bacteriophages are obligate killers of bacteria. That this property could be medically useful was first recognized over one hundred years ago, with 2021 being the 100-year anniversary of the first clinical phage therapy publication. Here we consider modern use of phages in clinical settings. Our aim is to answer one question: do phages serve as effective anti-bacterial infection agents when used clinically? An important emphasis of our analyses is on whether phage therapy-associated anti-bacterial infection efficacy can be reasonably distinguished from that associated with often coadministered antibiotics. We find that about half of 70 human phage treatment reports-published in English thus far in the 2000s-are suggestive of phage-mediated anti-bacterial infection efficacy. Two of these are randomized, double-blinded, infection-treatment studies while 14 of those studies, in our opinion, provide superior evidence of a phage role in observed treatment successes. Roughly three-quarters of these potentially phage-mediated outcomes are based on microbiological as well as clinical results, with the rest based on clinical success. Since many of these phage treatments are of infections for which antibiotic therapy had not been successful, their collective effectiveness is suggestive of a valid utility in employing phages to treat otherwise difficult-to-cure bacterial infections.

Improving Phage-Biofilm In Vitro Experimentation

Bacteriophages or phages, the viruses of bacteria, are abundant components of most ecosystems, including those where bacteria predominantly occupy biofilm niches. Understanding the phage impact on bacterial biofilms therefore can be crucial toward understanding both phage and bacterial ecology. Here, we take a critical look at the study of bacteriophage interactions with bacterial biofilms as carried out in vitro, since these studies serve as bases of our ecological and therapeutic understanding of phage impacts on biofilms. We suggest that phage-biofilm in vitro experiments often may be improved in terms of both design and interpretation. Specific issues discussed include (a) not distinguishing control of new biofilm growth from removal of existing biofilm, (b) inadequate descriptions of phage titers, (c) artificially small overlying fluid volumes, (d) limited explorations of treatment dosing and duration, (e) only end-point rather than kinetic analyses, (f) importance of distinguishing phage enzymatic from phage bacteriolytic anti-biofilm activities, (g) limitations of biofilm biomass determinations, (h) free-phage interference with viable-count determinations, and (i) importance of experimental conditions. Toward bettering understanding of the ecology of bacteriophage-biofilm interactions, and of phage-mediated biofilm disruption, we discuss here these various issues as well as provide tips toward improving experiments and their reporting.

Safety and Efficacy of a Phage, kpssk3, in an in vivo Model of Carbapenem-Resistant Hypermucoviscous Klebsiella pneumoniae Bacteremia

Antimicrobial resistance (AMR) is one of the most significant threats to global public health. As antibiotic failure is increasing, phages are gradually becoming important agents in the post-antibiotic era. In this study, the therapeutic effects and safety of kpssk3, a previously isolated phage infecting carbapenem-resistant hypermucoviscous Klebsiella pneumoniae (CR-HMKP), were evaluated in a mouse model of systemic CR-HMKP infection. The therapeutic efficacy experiment showed that intraperitoneal injection with a single dose of phage kpssk3 (1 × 10⁷ PFU/mouse) 3 h post infection protected 100% of BALB/c mice against bacteremia induced by intraperitoneal challenge with a 2 × LD₁₀₀ dose of NY03, a CR-HMKP clinical isolate. In addition, mice were treated with antibiotics from three classes (polymyxin B, tigecycline, and ceftazidime/avibactam plus aztreonam), and the 7 days survival rates of the treated mice were 20, 20, and 90%, respectively. The safety test consisted of 2 parts: determining the cytotoxicity of kpssk3 and evaluating the short- and long-term impacts of phage therapy on the mouse gut microbiota. Phage kpssk3 was shown to not be cytotoxic to mammalian cells in vitro or in vivo. Fecal samples were collected from the phage-treated mice at 3 time points before (0 day) and after (3 and 10 days) phage therapy to study the change in the gut microbiome via high-throughput 16S rDNA sequence analysis, which revealed no notable alterations in the gut microbiota except for decreases in the Chao1 and ACE indexes.

Evaluation of Phage Delivery Systems on Induced Motile Aeromonas Septicemia in Oreochromis niloticus

Background: The success of phage therapy is affected by the method of treatment delivery. This study focused on comparing different phage delivery routes, specifically oral (phage-impregnated feed), intraperitoneal (IP), and bath (immersion), in treatment of induced motile Aeromonas septicemia (MAS). Materials and Methods: The efficacy of Aeromonas hydrophila phage cocktail in treating MAS-infected Oreochromis niloticus through different delivery routes was assessed by challenging the fish with 100% lethal dose of A. hydrophila and conducting a 15-day treatment regimen. Blood and kidney samples were analyzed for bacterial and phage concentrations. Results: All routes exhibited reduction of disease symptoms, significant (p < 0.05) decrease in bacterial count, and increase in phage count. Notably, IP route showed significant activity in reducing bacterial load. Conclusions: Phage therapy through IP route is the most effective yet invasive in controlling MAS infection in O. niloticus. The efficacy of oral route depends on the fish's intake of feeds, whereas the bath route was the least effective.

Bacteriophage treatment of carbapenemase-producing Klebsiella pneumoniae in a multispecies biofilm: a potential biocontrol strategy for healthcare facilities

The p-traps of hospital handwashing sinks represent a potential reservoir for antimicrobial-resistant organisms of major public health concern, such as carbapenemase-producing KPC+ Klebsiella pneumoniae (CPKP). Bacteriophages have reemerged as potential biocontrol agents, particularly against biofilm-associated, drug-resistant microorganisms. The primary objective of our study was to formulate a phage cocktail capable of targeting a CPKP strain (CAV1016) at different stages of colonization within polymicrobial drinking water biofilms using a CDC biofilm reactor (CBR) p-trap model. A cocktail of four CAV1016 phages, all exhibiting depolymerase activity, were isolated from untreated wastewater using standard methods. Biofilms containing Pseudomonas aeruginosa, Micrococcus luteus, Stenotrophomonas maltophilia, Elizabethkingia anophelis, Cupriavidus metallidurans, and Methylobacterium fujisawaense were established in the CBR p-trap model for a period of 28 d. Subsequently, CAV1016 was inoculated into the p-trap model and monitored over a period of 21 d. Biofilms were treated for 2 h at either 25 °C or 37 °C with the phage cocktail (109 PFU/ml) at 7, 14, and 21 d post-inoculation. The effect of phage treatment on the viability of biofilm-associated CAV1016 was determined by plate count on m-Endo LES agar. Biofilm heterotrophic plate counts (HPC) were determined using R2A agar. Phage titers were determined by plaque assay. Phage treatment reduced biofilm-associated CAV1016 viability by 1 log10 CFU/cm2 (p < 0.05) at 7 and 14 d (37 °C) and 1.4 log10 and 1.6 log10 CFU/cm2 (p < 0.05) at 7 and 14 d, respectively (25 °C). No significant reduction was observed at 21 d post-inoculation. Phage treatment had no significant effect on the biofilm HPCs (p > 0.05) at any time point or temperature. Supplementation with a non-ionic surfactant appears to enhance phage association within biofilms. The results of this study suggest the potential of phages to control CPKP and other carbapenemase-producing organisms associated with microbial biofilms in the healthcare environment.

Use of phage therapy to treat long-standing, persistent, or chronic bacterial infections

Viruses of bacteria - known as bacteriophages or phages - have been used clinically as antibacterial agents for nearly 100 years. Often this phage therapy is of long-standing, persistent, or chronic bacterial infections, and this can be particularly so given prior but insufficiently effective infection treatment using standard antibiotics. Such infections, in turn, often have a biofilm component. Phages in modern medicine thus are envisaged to serve especially as anti-biofilm/anti-persistent infection agents. Here I review the English-language literature concerning in vivo experimental and clinical phage treatment of longer-lived bacterial infections. Overall, published data appears to be supportive of a relatively high potential for phages to cure infections which are long standing and which otherwise have resisted treatment with antibieiotics.

Basic Phage Mathematics

Basic mathematical descriptions are useful in phage ecology, applied phage ecology such as in the course of phage therapy, and also toward keeping track of expected phage-bacterial interactions as seen during laboratory manipulation of phages. The most basic mathematical descriptor of phages is their titer, that is, their concentration within stocks, experimental vessels, or other environments. Various phenomena can serve to modify phage titers, and indeed phage titers can vary as a function of how they are measured. An important aspect of how changes in titers can occur results from phage interactions with bacteria. These changes tend to vary in degree as a function of bacterial densities within environments, and particularly densities of those bacteria that are susceptible to or at least adsorbable by a given phage type. Using simple mathematical models one can describe phage-bacterial interactions that give rise particularly to phage adsorption events. With elaboration one can consider changes in both phage and bacterial densities as a function of both time and these interactions. In addition, phages along with their impact on bacteria can be considered as spatially constrained processes. In this chapter we consider the simpler of these concepts, providing in particular detailed verbal explanations toward facile mathematical insight. The primary goal is to stimulate a more informed use and manipulation of phages and phage populations within the laboratory as well as toward more effective phage application outside of the laboratory, such as during phage therapy. More generally, numerous issues and approaches to the quantification of phages are considered along with the quantification of individual, ecological, and applied properties of phages.

Phage Therapy: Various Perspectives on How to Improve the Art

Use of phages as antibacterial agents has a long and, even, storied history. During that time much has been learned but, to a degree, also forgotten. As a consequence, today we experience a largely preclinical development of a field which already has been subject to substantial clinical practice. This development, as well, is now occurring within a much more rigorously regulated environment than previously had been the case. The consequence is not only a need to reinvent standards of practice but to do so within a more explicitly pharmacological context. Of particular concern is that the application of phages to bacterial infections does not always result in control of the latter, necessitating ongoing thought on how to refine treatment protocols. Here I consider a number of issues relevant to such refinement, focusing on areas which, in my opinion, phage therapy researchers-perhaps especially those new to the field-might struggle with. In order of presentation, I consider how best to describe phage therapy within publications toward achieving a more coherent literature, the importance of Poisson distributions along with killing titers toward understanding phage dosing, the associated importance of establishing sufficient phage numbers in situ to achieve adequate bacteria killing, various problems with the use of multiplicity of infection (MOI) as a description of phage dosing, how to anticipate the basic kinetics of phage-bacteria absorptive interactions, how to distinguish passive from active treatments, and basic approaches toward addressing disappointing efficacy outcomes.