Isolation of bacteriophages from air using vacuum filtration technique: an improved and novel method

PhageCocktail: An R package to design phage cocktails from experimental phage-bacteria infection networks

BACKGROUND AND OBJECTIVE

Phage therapy is a resurgent strategy used in medicine and the food industry to lyse bacteria that cause damage to health or spoil a food product. Frequently, phage-bacteria infection networks have a large size, making it impossible to manually study all possible phage cocktails. Thus, this article presents an R package called PhageCocktail to automatically design efficient phage cocktails from phage-bacteria infection networks.

METHODS

This R package includes four different methods for designing phage cocktails: ExhaustiveSearch, ExhaustivePhi, ClusteringSearch, and ClusteringPhi. These four methods are explained in detail and are evaluated using 13 empirical phage-bacteria infection networks. More specifically, runtime and expected success (fraction of lysed bacteria) are analyzed.

RESULTS

The four methods have variations in terms of runtime and quality of the results. ExhaustiveSearch always provides the best possible phage cocktail, but its runtime could be long. ExhaustivePhi only focuses on one cocktail size, the one estimated as the best; thus, its runtime is less than ExhaustiveSearch, but it can produce cocktails with more phages than necessary. ClusteringSearch and ClusteringPhi are very fast (generally, less than one millisecond), providing always immediate results due to clustering techniques, but their accuracies can be lower, yielding cocktails with lower expected successes.

CONCLUSIONS

The larger the phage-bacteria infection network is, the more complex its analysis is. Thus, this tool eases this task for scientists and other users while designing phage cocktails of good quality. This R package includes four different methods; therefore, users may choose among them, considering their preferences in speed and accuracy of results.

An Appraisal of Bacteriophage Isolation Techniques from Environment

Researchers have recently renewed interest in bacteriophages. Being valuable models for the study of eukaryotic viruses, and more importantly, natural killers of bacteria, bacteriophages are being tapped for their potential role in multiple applications. Bacteriophages are also being increasingly sought for bacteriophage therapy due to rising antimicrobial resistance among pathogens. Reports show that there is an increasing trend in therapeutic application of natural bacteriophages, genetically engineered bacteriophages, and bacteriophage-encoded products as antimicrobial agents. In view of these applications, the isolation and characterization of bacteriophages from the environment has caught attention. In this review, various methods for isolation of bacteriophages from environmental sources like water, soil, and air are comprehensively described. The review also draws attention towards a handful on-field bacteriophage isolation techniques and the need for their further rapid development.

Computational design of phage cocktails based on phage-bacteria infection networks

The misuse and overuse of antibiotics have boosted the proliferation of multidrug-resistant (MDR) bacteria, which are considered a major public health issue in the twenty-first century. Phage therapy may be a promising way in the treatment of infections caused by MDR pathogens, without the side effects of the current available antimicrobials. Phage therapy is based on phage cocktails, that is, combinations of phages able to lyse the target bacteria. In this work, we present and explain in detail two innovative computational methods to design phage cocktails taking into account a given phage-bacteria infection network. One of the methods (Exhaustive Search) always generates the best possible phage cocktail, while the other method (Network Metrics) always keeps a very reduced runtime (a few milliseconds). Both methods have been included in a Cytoscape application that is available for any user. A complete experimental study has been performed, evaluating and comparing the biological quality, runtime, and the impact when additional phages are included in the cocktail.

A New Pipeline for Designing Phage Cocktails Based on Phage-Bacteria Infection Networks

In recent years, the spread of antibiotic-resistant bacteria and efforts to preserve food microbiota have induced renewed interest in phage therapy. Phage cocktails, instead of a single phage, are commonly used as antibacterial agents since the hosts are unlikely to become resistant to several phages simultaneously. While the spectrum of activity might increase with cocktail complexity, excessive phages could produce side effects, such as the horizontal transfer of genes that augment the fitness of host strains, dysbiosis or high manufacturing costs. Therefore, cocktail formulation represents a compromise between achieving substantial reduction in the bacterial loads and restricting its complexity. Despite the abovementioned points, the observed bacterial load reduction does not increase significantly with the size of phage cocktails, indicating the requirement for a systematic approach to their design. In this work, the information provided by host range matrices was analyzed after building phage-bacteria infection networks (PBINs). To this end, we conducted a meta-analysis of 35 host range matrices, including recently published studies and new datasets comprising Escherichia coli strains isolated during ripening of artisanal raw milk cheese and virulent coliphages from ewes' feces. The nestedness temperature, which reflects the host range hierarchy of the phages, was determined from bipartite host range matrices using heuristic (Nestedness Temperature Calculator) and genetic (BinMatNest) algorithms. The latter optimizes matrix packing, leading to lower temperatures, i.e., it simplifies the identification of the phages with the broadest host range. The structure of infection networks suggests that generalist phages (and not specialist phages) tend to succeed in infecting less susceptible bacteria. A new metric (Φ), which considers some properties of the host range matrices (fill, temperature, and number of bacteria), is proposed as an estimator of phage cocktail size. To identify the best candidates, agglomerative hierarchical clustering using Ward's method was implemented. Finally, a cocktail was formulated for the biocontrol of cheese-isolated E. coli, reducing bacterial counts by five orders of magnitude.