Bacteriophage latent-period evolution as a response to resource availability

Isolation, characterization, and application of a novel Vibrio parahaemolyticus bacteriophage from retail shrimp in Sarawak, Malaysia

Shrimp farming, a highly profitable sector in global aquaculture, has seen remarkable growth in recent years. This increasing demand and the expansion of farming operations, including in Sarawak, Malaysia, highlight the sector's potential. However, the industry faces significant challenges, particularly the prevalence of vibriosis, a bacterial infection caused by Vibrio species. Contamination of food products has also increased the risk of vibriosis in humans. The widespread use of antibiotics to combat this disease has led to the rapid emergence of antimicrobial resistance (AMR) bacteria. This study specifically focuses on the isolation and characterization of phage EniLVP02, a novel bacteriophage with the potential to combat V. parahaemolyticus infections. EniLVP02 was successfully isolated from shrimp purchased at a retail market and exhibited strong lytic activity against V. parahaemolyticus strains. Structural analysis categorized EniLVP02 within the Straboviridae family, belonging to the class Caudoviricetes. The phage displayed a narrow host range and lytic nature only towards V. parahaemolyticus strains isolated from the Telaga Air shrimp farm. Phage EniLVP02 exhibited long latent period of 120 min and large burst size of 144 phages per infected cells. Stability studies revealed EniLVP02's resilience across various pH (pH 4.0-9.0) and temperature (28 °C-65 °C) conditions, particularly at physiological temperatures. Comparative genome analyses indicated its distinct evolutionary relationship and low homology with other Vibriophages, suggesting its novelty. EniLVP02 demonstrated significant potential in biofilm prevention and destruction, with absorbance (OD600 nm) reduction from 0.592 ± 0.055 to 0.204± 0.016 and from 0.843± 0.003 to 0.174± 0.026 respectively. Moreover, in the treatment of V. parahaemolyticus-contaminated shrimp meat, EniLVP02 effectively inhibit bacterial concentrations by 75.2 % at room temperature and 16.2 % at 4 °C after 24 h. Genomic sequencing revealed low similarity between EniLVP02 with other phages, suggesting its novelty. Importantly, the absence of lysogeny-related, antibiotic resistance, and virulence genes in its genome supports EniLVP02's safety for therapeutic use. This study underscores the importance of exploring phages from retail food products for therapeutic applications and highlights the promising attributes of phage EniLVP02 in combating V. parahaemolyticus infections in aquaculture. Further investigations on its compatibility with other phages and application in diverse food matrices are warranted to assess its full potential.

Eco-evolutionary dynamics of temperate phages in periodic environments

Bacteriophages (viruses that exclusively infect bacteria) exhibit a continuum of infection mechanisms, including lysis and lysogeny in interactions with bacterial hosts. Recent work has demonstrated the short-term advantages of lysogeny over lysis in conditions of low host availability. Hence, temperate phage which can switch between lytic and lysogenic strategies-both stochastically and responsively-are hypothesized to have an evolutionary advantage in a broad range of conditions. However, the long-term advantages of lysogeny are not well understood, particularly when environmental conditions vary over time. To examine generalized drivers of viral strategies over the short- and long-term, we explore the eco-evolutionary dynamics of temperate viruses in periodic environments with varying levels of host availability and viral mortality. We use a nonlinear system of ordinary differential equations to simulate periodically-forced dynamics that separate a 'within-growth' phase and a 'between-growth' phase, in which a (potentially unequal) fraction of virus particles and lysogens survive. Using this ecological model and invasion analysis, we show and quantify how conflicts can arise between strategies in the short term that may favour lysis and strategies in the long term that may favour lysogeny. In doing so, we identify a wide range of conditions in which temperate strategies can outperform obligately lytic or lysogenic strategies. Finally, we demonstrate that temperate strategies can mitigate against the potential local extinction of viruses in stochastically fluctuating environments, providing further evidence of the eco-evolutionary benefits of being temperate.

Infection and Genomic Properties of Single- and Double-Stranded DNA Cellulophaga Phages

Bacterial viruses (phages) are abundant and ecologically impactful, but laboratory-based experimental model systems vastly under-represent known phage diversity, particularly for ssDNA phages. Here, we characterize the genomes and infection properties of two unrelated marine flavophages-ssDNA generalist phage phi18:4 (6.5 Kbp) and dsDNA specialist phage phi18:1 (39.2 Kbp)-when infecting the same Cellulophaga baltica strain #18 (Cba18), of the class Flavobacteriia. Phage phi18:4 belongs to a new family of ssDNA phages, has an internal lipid membrane, and its genome encodes primarily structural proteins, as well as a DNA replication protein common to ssDNA phages and a unique lysis protein. Phage phi18:1 is a siphovirus that encodes several virulence genes, despite not having a known temperate lifestyle, a CAZy enzyme likely for regulatory purposes, and four DNA methyltransferases dispersed throughout the genome that suggest both host modulation and phage DNA protection against host restriction. Physiologically, ssDNA phage phi18:4 has a shorter latent period and smaller burst size than dsDNA phage phi18:1, and both phages efficiently infect this host. These results help augment the diversity of characterized environmental phage-host model systems by studying infections of genomically diverse phages (ssDNA vs. dsDNA) on the same host.

Phage cocktail against Vibrio parahaemolyticus causing acute hepatopancreatic necrosis disease (AHPND) in Penaeus vannamei: Genomic, biological, and pathological characterization

Phages vB_Pd_PDCC-1, vB_Vc_SrVc9, and vB_Vp_PvVp11 were found to be lytic against Vibrio parahaemolyticus acute hepatopancreatic necrosis disease (AHPND) and other pathogenic vibrios. The complete genomic and biological characterization of phage vB_Vp_PvVp1 was conducted, and a cocktail of these three phages was applied to juvenile Penaeus vannamei infected with V. parahaemolyticus AHPND. Water samples collected during the challenges were analyzed using metagenomics. At the end of the experimental infection, the phage cocktail did not improve shrimp survival compared to the positive control group (infected only with bacteria). This suggests the emergence of phage-resistant V. parahaemolyticus strains. However, a significantly lower mortality rate was observed 12 h post-infection, along with a shortening of the disease course in the phage therapy treatment. A phage-resistant strain of V. parahaemolyticus AHPND was in vitro isolated. For the first time, we report the identification of nucleotide variants in the glycosyltransferase gene of this mutant strain through genome sequencing. Although the phage cocktail was ineffective in controlling AHPND, some protective benefits of phage therapy were noted in P. vannamei during the acute phase-the most critical stage-compared to the positive control. Phage therapy decreased alpha diversity and altered the microbiota composition during the challenge, increasing V. parahaemolyticus. The Vibrio AHPND pathogen produces a potent PirAB toxin, making this disease difficult to manage. Further studies are needed to explore synergistic approaches as effective therapeutic tools.

A novel broad-spectrum bacteriophage cocktail against methicillin-resistant Staphylococcus aureus: Isolation, characterization, and therapeutic potential in a mastitis mouse model

Bovine mastitis is a considerable challenge within the dairy industry, causing significant financial losses and threatening public health. The increased occurrence of methicillin-resistant Staphylococcus aureus (MRSA) has provoked difficulties in managing bovine mastitis. Bacteriophage therapy presents a novel treatment strategy to combat MRSA infections, emerging as a possible substitute for antibiotics. This study evaluated the therapeutic potency of a novel bacteriophage cocktail against MRSA mastitis. Two new bacteriophages (vB_SauR_SW21 and vB_SauR_SW25) with potent lytic activity against MRSA were isolated and characterized. The one-step growth curve displayed a rapid latent period (20-35 min) and substantial burst size (418 and 316 PFU/ cell). In silico analyses have confirmed the absence of antimicrobial resistance or virulence factor-encoding genes within their genomes. According to the results, combining these phages augmented their host range and virulence. The phage cocktail significantly reduced bacterial burden in a BALB/c mastitis model, demonstrating efficacy comparable to antibiotic treatment. Moreover, its administration led to decreased concentrations of IL-1β and TNF-α compared to the negative control group. The bacteriophage cocktail (SW21-SW25) exhibits a promising profile for therapeutic applications and may represent a novel substitute to antibiotics for managing MRSA bovine mastitis.

Crossing the Chasm: How to Approach Translational Pharmacokinetic-Pharmacodynamic Modeling of Phage Dosing

Effectively treating multidrug-resistant bacterial infections remains challenging due to the limited drug development pipeline and a scarcity of novel agents effective against these highly resistant pathogens. Bacteriophages (phages) are a potential addition to the antimicrobial treatment arsenal. Though, phages are currently being tested in clinical trials for antibiotic-resistant infections, phages lack a fundamental understanding of optimal dosing in humans. Rationally designed preclinical studies using in vitro and in vivo infection models, allow us to assess clinically relevant phage +/- antibiotic exposure (pharmacokinetics), the resulting treatment impact on the infecting pathogen (pharmacodynamics) and host immune response (immunodynamics). A mechanistic modeling framework allows us to integrate this knowledge gained from preclinical studies to develop predictive models. We reviewed recently published mathematical models based on in vitro and/or in vivo data that evaluate the effects of varying bacterial or phage densities, phage characteristics (burst size, adsorption rate), phage pharmacokinetics, phage-antibiotic combinations and host immune responses. In our review, we analyzed study designs and the data used to inform the development of these mechanistic models. Insights gained from model-based simulations were reviewed as they help identify crucial phage parameters for determining effective phage dosing. These efforts contribute to bridging the gap between phage therapy research and its clinical translation.

Preclinical characterization and in silico safety assessment of three virulent bacteriophages targeting carbapenem-resistant uropathogenic Escherichia coli

Phage therapy has recently been revitalized in the West with many successful applications against multi-drug-resistant bacterial infections. However, the lack of geographically diverse bacteriophage (phage) genomes has constrained our understanding of phage diversity and its genetics underpinning host specificity, lytic capability, and phage-bacteria co-evolution. This study aims to locally isolate virulent phages against uropathogenic Escherichia coli (E. coli) and study its phenotypic and genomic features. Three obligately virulent Escherichia phages (øEc_Makalu_001, øEc_Makalu_002, and øEc_Makalu_003) that could infect uropathogenic E. coli were isolated and characterized. All three phages belonged to Krischvirus genus. One-step growth curve showed that the latent period of the phages ranged from 15 to 20 min, the outbreak period ~ 50 min, and the burst size ranged between 74 and 127 PFU/bacterium. Moreover, the phages could tolerate a pH range of 6 to 9 and a temperature range of 25-37 °C for up to 180 min without significant loss of phage viability. All phages showed a broad host spectrum and could lyse up to 30% of the 35 tested E. coli isolates. Genomes of all phages were approximately ~ 163 kb with a gene density of 1.73 gene/kbp and an average gene length of ~ 951 bp. The coding density in all phages was approximately 95%. Putative lysin, holin, endolysin, and spanin genes were found in the genomes of all three phages. All phages were strictly virulent with functional lysis modules and lacked any known virulence or toxin genes and antimicrobial resistance genes. Pre-clinical experimental and genomic analysis suggest these phages may be suitable candidates for therapeutic applications.

Spatial clustering of hosts can favor specialist parasites

Generalist parasites seem to enjoy the clear ecological advantage of a greater chance to find a host, and genetic trade-offs are therefore often invoked to explain why specialists can coexist with or outcompete generalists. Here we develop an alternative perspective based on optimal foraging theory to explain why spatial clustering can favor specialists even without genetic trade-offs. Using analytical and simulation models inspired by bacteriophage, we examine the optimal use of two hosts, one yielding greater reproductive success for the parasite than the other. We find that a phage may optimally ignore the worse host when the two hosts are clustered together in dense, ephemeral patches. We model conditions that enhance or reduce this selective benefit to a specialist parasite and show that it is eliminated entirely when the hosts occur only in separate patches. These results show that specialists can be favored even when trade-offs are weak or absent and emphasize the importance of spatiotemporal heterogeneity in models of optimal niche breadth.

Viral plasticity facilitates host diversity in challenging environments

The antagonistic coevolution of microbes and viruses influences fundamentally the diversity of microbial communities. Information on how environmental variables interact with emergent defense-counterdefense strategies and community composition is, however, still scarce. Following biological intuition, diversity should increase with improved growth conditions, which offset evolutionary costs; however, laboratory and regional data suggest that microbial diversity decreases in nutrient-rich conditions. Moreover, global oceanic data show that microbial and viral diversity decline for high latitudes, although the underlying mechanisms are unknown. This article addresses these gaps by introducing an eco-evolutionary model for bacteria-virus antagonistic coevolution. The theory presented here harmonizes the observations above and identifies negative density dependence and viral plasticity (dependence of virus performance on host physiological state) as key drivers: environmental conditions selecting for slow host growth also limit viral performance, facilitating the survival of a diverse host community; host diversity, in turn, enables viral portfolio effects and bet-hedging strategies that sustain viral diversity. From marine microbes to phage therapy against antibiotic-resistant bacteria or cancer cells, the ubiquity of antagonistic coevolution highlights the need to consider eco-evolutionary interactions across a gradient of growth conditions.

Accounting for cellular-level variation in lysis: implications for virus-host dynamics

Viral impacts on microbial populations depend on interaction phenotypes-including viral traits spanning the adsorption rate, latent period, and burst size. The latent period is a key viral trait in lytic infections. Defined as the time from viral adsorption to viral progeny release, the latent period of bacteriophage is conventionally inferred via one-step growth curves in which the accumulation of free virus is measured over time in a population of infected cells. Developed more than 80 years ago, one-step growth curves do not account for cellular-level variability in the timing of lysis, potentially biasing inference of viral traits. Here, we use nonlinear dynamical models to understand how individual-level variation of the latent period impacts virus-host dynamics. Our modeling approach shows that inference of the latent period via one-step growth curves is systematically biased-generating estimates of shorter latent periods than the underlying population-level mean. The bias arises because variability in lysis timing at the cellular level leads to a fraction of early burst events, which are interpreted, artefactually, as an earlier mean time of viral release. We develop a computational framework to estimate latent period variability from joint measurements of host and free virus populations. Our computational framework recovers both the mean and variance of the latent period within simulated infections including realistic measurement noise. This work suggests that reframing the latent period as a distribution to account for variability in the population will improve the study of viral traits and their role in shaping microbial populations.IMPORTANCEQuantifying viral traits-including the adsorption rate, burst size, and latent period-is critical to characterize viral infection dynamics and develop predictive models of viral impacts across scales from cells to ecosystems. Here, we revisit the gold standard of viral trait estimation-the one-step growth curve-to assess the extent to which assumptions at the core of viral infection dynamics lead to ongoing and systematic biases in inferences of viral traits. We show that latent period estimates obtained via one-step growth curves systematically underestimate the mean latent period and, in turn, overestimate the rate of viral killing at population scales. By explicitly incorporating trait variability into a dynamical inference framework that leverages both virus and host time series, we provide a practical route to improve estimates of the mean and variance of viral traits across diverse virus-microbe systems.

Physiochemical characterization of a potential Klebsiella phage MKP-1 and analysis of its application in reducing biofilm formation

The common intestinal pathogen Klebsiella pneumoniae (K. pneumoniae) is one of the leading causes of fatal superbug infections that can resist the effects of commonly prescribed medicines. The uncontrolled use or misuse of antibiotics has increased the prevalence of drug-resistant K. pneumoniae strains in the environment. In the quest to search for alternative therapeutics for treating these drug-resistant infections, bacteriophages (bacterial viruses) emerged as potential candidates for in phage therapy against Klebsiella. The effective formulation of phage therapy against drug-resistant Klebsiella infections demands thorough characterization and screening of many bacteriophages. To contribute effectively to the formulation of successful phage therapy against superbug infections by K. pneumoniae, this study includes the isolation and characterization of a novel lytic bacteriophage MKP-1 to consider its potential to be used as therapeutics in treating drug-resistant Klebsiella infections. Morphologically, having a capsid attached to a long non-contractile tail, it was found to be a siphovirus that belongs to the class Caudoviricetes and showed infectivity against different strains of the target host bacterium. Comparatively, this double-stranded DNA phage has a large burst size and is quite stable in various physiological conditions. More interestingly, it has the potential to degrade the tough biofilms formed by K. pneumoniae (Klebsiella pneumoniae subsp. pneumoniae (Schroeter) Trevisan [ATCC 15380]) significantly. Thus, the following study would contribute effectively to considering phage MKP-1 as a potential candidate for phage therapy against Klebsiella infection.

Bacteriophages isolated from mouse feces attenuates pneumonia mice caused by Pseudomonas aeruginosa

BACKGROUND

Most of the current bacteriophages (phages) are mostly isolated from environments. However, phages isolated from feces might be more specific to the bacteria that are harmful to the host. Meanwhile, some phages from the environment might affect non-pathogenic bacteria for the host.

METHODS

Here, bacteriophages isolated from mouse feces were intratracheally (IT) or intravenously (IV) administered in pneumonia mice caused by Pseudomonas aeruginosa at 2 hours post-intratracheal bacterial administration. As such, the mice with phage treatment, using either IT or IV administration, demonstrated less severe pneumonia as indicated by mortality, serum cytokines, bacteremia, bacterial abundance in bronchoalveolar lavage fluid (BALF), and neutrophil extracellular traps (NETs) in lung tissue (immunofluorescence of neutrophil elastase and myeloperoxidase).

RESULTS

Interestingly, the abundance of phages in BALF from the IT and IV injections was similar, supporting a flexible route of phage administration. With the incubation of bacteria with neutrophils, the presence of bacteriophages significantly improved bactericidal activity, but not NETs formation, with the elevated supernatant IL-6 and TNF-α, but not IL-1β. In conclusion, our findings suggest that bacteriophages against Pseudomonas aeruginosa can be discovered from feces of the host.

CONCLUSIONS

The phages attenuate pneumonia partly through an enhanced neutrophil bactericidal activity, but not via inducing NETs formation. The isolation of phages from the infected hosts themselves might be practically useful for future treatment. More studies are warranted.

High throughput platform technology for rapid target identification in personalized phage therapy

As bacteriophages continue to gain regulatory approval for personalized human therapy against antibiotic-resistant infections, there is a need for transformative technologies for rapid target identification through multiple, large, decentralized therapeutic phages biobanks. Here, we design a high throughput phage screening platform comprised of a portable library of individual shelf-stable, ready-to-use phages, in all-inclusive solid tablets. Each tablet encapsulates one phage along with luciferin and luciferase enzyme stabilized in a sugar matrix comprised of pullulan and trehalose capable of directly detecting phage-mediated adenosine triphosphate (ATP) release through ATP bioluminescence reaction upon bacterial cell burst. The tablet composition also enhances desiccation tolerance of all components, which should allow easier and cheaper international transportation of phages and as a result, increased accessibility to therapeutic phages. We demonstrate high throughput screening by identifying target phages for select multidrug-resistant clinical isolates of Pseudomonas aeruginosa, Salmonella enterica, Escherichia coli, and Staphylococcus aureus with targets identified within 30-120 min.

Therapeutics and prophylactic efficacy of novel lytic Escherichia phage vB_EcoS_PJ16 against multidrug-resistant avian pathogenic E. coli using in vivo study

Avian pathogenic Escherichia coli (APEC) is the causative agent of avian colibacillosis, which causes significant economic losses to the poultry industry. The growing resistance of bacteria to antibiotics is a major global public health concern. However, there is limited data on the efficacy of phage therapy in effectively controlling and treating APEC infections. In this study, a novel lytic Escherichia phage, vB_EcoS_PJ16, was isolated from poultry farm wastewater and characterized in both in vitro and in vivo conditions. Transmission electron microscopy analysis revealed the presence of an icosahedral head and a long non-contractile tail, classifying the phage under the Caudoviricetes class. Host range determination showed that Escherichia phage vB_EcoS_PJ16 exhibited lytic activity against multiple strains of pathogenic E. coli, while no significant signs of lysis for Klebsiella pneumoniae, Salmonella Typhimurium, Listeria monocytogenes, and Staphylococcus aureus. Biophysical characterization revealed that the isolated phage was sturdy, as it remained viable for up to 300 days at temperatures of 30 °C, 37 °C, and 42 °C and for up to 24 h at pH 5 to 11, with only minor changes in titer. Kinetic analysis at multiplicity of infection (MOI) 0.1 showed a latency period of about 20 min and a burst size of 26.5 phage particles per infected cell for phage vB_EcoS_PJ16. Whole genome sequencing unveiled that the phage vB_EcoS_PJ16 genome consists of a double-stranded linear DNA molecule with 57,756 bp and a GC content of 43.58%. The Escherichia phage vB_EcoS_PJ16 genome consisted of 98 predicted putative ORFs, with no transfer RNA identified in the genome. Among these 98 genes, 34 genes were predicted to have known functions. A significant reduction in APEC viability was observed at MOI 100 during in vitro bacterial challenge tests conducted at different MOIs (0.01, 1, and 100). In vivo oral evaluation of the isolated phage to limit E. coli infections in day-old chicks indicated a decrease in mortality within both the therapeutic (20%) and prophylactic (30%) groups, when compared to the control group. The findings of this study contribute to our current knowledge of Escherichia phages and suggest a potentially effective role of phages in the therapeutic and prophylactic control of antibiotic-resistant APEC strains.

Lytic/Lysogenic Transition as a Life-History Switch

The transition between lytic and lysogenic life cycles is the most important feature of the life-history of temperate viruses. To explain this transition, an optimal life-history model is offered based a discrete-time formulation of phage/bacteria population dynamics that features infection of bacteria by Poisson sampling of virions from the environment. The time step is the viral latency period. In this model, density-dependent viral absorption onto the bacterial surface produces virus/bacteria coexistence and density dependence in bacterial growth is not needed. The formula for the transition between lytic and lysogenic phases is termed the 'fitness switch'. According to the model, the virus switches from lytic to lysogenic when its population grows faster as prophage than as virions produced by lysis of the infected cells, and conversely for the switch from lysogenic to lytic. A prophage that benefits the bacterium it infects automatically incurs lower fitness upon exiting the bacterial genome, resulting in its becoming locked into the bacterial genome in what is termed here as a 'prophage lock'. The fitness switch qualitatively predicts the ecogeographic rule that environmental enrichment leads to microbialization with a concomitant increase in lysogeny, fluctuating environmental conditions promote virus-mediated horizontal gene transfer, and prophage-containing bacteria can integrate into the microbiome of a eukaryotic host forming a functionally integrated tripartite holobiont. These predictions accord more with the 'Piggyback-the-Winner' hypothesis than with the 'Kill-the-Winner' hypothesis in virus ecology.

Potential of an Isolated Bacteriophage to Inactivate Klebsiella pneumoniae: Preliminary Studies to Control Urinary Tract Infections

Urinary tract infections (UTIs) caused by resistant Klebsiella pneumoniae can lead to severe clinical complications and even death. An alternative treatment option for infected patients is using bacteriophages. In the present study, we isolated phage VB_KPM_KP1LMA (KP1LMA) from sewage water using a K. pneumoniae strain as a host. Whole-genome analysis indicated that the genome was a double-stranded linear 176,096-bp long DNA molecule with 41.8% GC content and did not contain virulence or antibiotic resistance genes. The inactivation potential of phage KP1LMA was assessed in broth at an MOI of 1 and 10, and a maximum inactivation of 4.9 and 5.4 log CFU/mL, respectively, was observed after 9 h. The efficacy at an MOI of 10 was also assessed in urine to evaluate the phage's performance in an acidic environment. A maximum inactivation of 3.8 log CFU/mL was observed after 9 h. The results suggest that phage KP1LMA could potentially control a UTI caused by this strain of K. pneumoniae, indicating that the same procedure can be used to control UTIs caused by other strains if new specific phages are isolated. Although phage KP1LMA has a narrow host range, in the future, efforts can be made to expand its spectrum of activity and also to combine this phage with others, potentially enabling its use against other K. pneumoniae strains involved in UTIs.

A new Rogue-like Escherichia phage UDF157lw to control Escherichia coli O157:H7

Introduction

Shiga toxin-producing Escherichia coli (STEC) O157:H7 is one of the notorious foodborne pathogens causing high mortality through the consumption of contaminated food items. The food safety risk from STEC pathogens could escalate when a group of bacterial cells aggregates to form a biofilm. Bacterial biofilm can diminish the effects of various antimicrobial interventions and enhance the pathogenicity of the pathogens. Therefore, there is an urgent need to have effective control measurements. Bacteriophages can kill the target bacterial cells through lytic infection, and some enzymes produced during the infection have the capability to penetrate the biofilm for mitigation compared to traditional interventions. This study aimed to characterize a new Escherichia phage vB_EcoS-UDF157lw (or UDF157lw) and determine its antimicrobial efficacy against E. coli O157:H7.

Methods

Phage characterization included biological approaches, including phage morphology, one-step growth curve, stability tests (pH and temperature), and genomic approaches (whole-genome sequencing). Later, antimicrobial activity tests, including productive infection against susceptible bacterial strains, in vitro antimicrobial activity, and anti-biofilm, were conducted.

Results

UDF157lw is a new member of the phages belonging to the Rogunavirus genus, comprising a long and non-contractile tail, isolated from bovine feces and shares close genomic evolutionary similarities with Escherichia phages vB_EcoS-BECP10 and bV_EcoS_AKS96. When used against E. coli O157:H7 (ATCC35150), phage UDF157lw exhibited a latent period of 14 min and a burst size of 110 PFU per infected cell. The phage remained viable in a wide range of pH values (pH 4-11) and temperatures (4-60°C). No virulence genes, such as stx, lysogenic genes, and antibiotic resistance genes, were found. Phage UDF157lw demonstrated high infection efficiencies against different E. coli O157:H7 and generic E. coli strains. In addition, UDF157lw encoded a unique major tail protein (ORF_26) with prominent depolymerase enzyme activity against various E. coli O157:H7 strains, causing large plaque sizes. In contrast to the phage without encoding depolymerase gene, UDF157lw was able to reduce the 24-h and 48-h E. coli O157:H7 biofilm after 1-h phage treatment.

Discussion

The findings of this study provide insights into a new member of the Rogunavirus phages and demonstrate its antimicrobial potential against E. coli O157:H7 in vitro.

Genome analysis of triple phages that curtails MDR E. coli with ML based host receptor prediction and its evaluation

Infections by multidrug resistant bacteria (MDR) are becoming increasingly difficult to treat and alternative approaches like phage therapy, which is unhindered by drug resistance, are urgently needed to tackle MDR bacterial infections. During phage therapy phage cocktails targeting different receptors are likely to be more effective than monophages. In the present study, phages targeting carbapenem resistant clinical isolate of E. coli U1007 was isolated from Ganges River (U1G), Cooum River (CR) and Hospital waste water (M). Capsid architecture discerned using TEM identified the phage families as Podoviridae for U1G, Myoviridae for CR and Siphoviridae for M phage. Genome sequencing showed the phage genomes varied in size U1G (73,275 bp) CR (45,236 bp) and M (45,294 bp). All three genomes lacked genes encoding tRNA sequence, antibiotic resistant or virulent genes. A machine learning (ML) based multi-class classification model using Random Forest, Logistic Regression, and Decision Tree were employed to predict the host receptor targeted by receptor binding protein of all 3 phages and the best performing algorithm Random Forest predicted LPS O antigen, LamB or OmpC for U1G; FhuA, OmpC for CR phage; and FhuA, LamB, TonB or OmpF for the M phage. OmpC was validated as receptor for U1G by physiological experiments. In vivo intramuscular infection study in zebrafish showed that cocktail of dual phages (U1G + M) along with colsitin resulted in a significant 3.5 log decline in cell counts. Our study highlights the potential of ML tool to predict host receptor and proves the utility of phage cocktail to restrict E. coli U1007 in vivo.

A novel lytic phage exhibiting a remarkable in vivo therapeutic potential and higher antibiofilm activity against Pseudomonas aeruginosa

BACKGROUND

Pseudomonas aeruginosa is a nosocomial bacterium responsible for variety of infections. Inappropriate use of antibiotics could lead to emergence of multidrug-resistant (MDR) P. aeruginosa strains. Herein, a virulent phage; vB_PaeM_PS3 was isolated and tested for its application as alternative to antibiotics for controlling P. aeruginosa infections.

METHODS

Phage morphology was observed using transmission electron microscopy (TEM). The phage host range and efficiency of plating (EOP) in addition to phage stability were analyzed. One-step growth curve was performed to detect phage growth kinetics. The impact of isolated phage on planktonic cells and biofilms was assessed. The phage genome was sequenced. Finally, the therapeutic potential of vB_PaeM_PS3 was determined in vivo.

RESULTS

Isolated phage has an icosahedral head and a contractile tail and was assigned to the family Myoviridae. The phage vB_PaeM_PS3 displayed a broad host range, strong bacteriolytic ability, and higher environmental stability. Isolated phage showed a short latent period and large burst size. Importantly, the phage vB_PaeM_PS3 effectively eradicated bacterial biofilms. The genome of vB_PaeM_PS3 consists of 93,922 bp of dsDNA with 49.39% G + C content. It contains 171 predicted open reading frames (ORFs) and 14 genes as tRNA. Interestingly, the phage vB_PaeM_PS3 significantly attenuated P. aeruginosa virulence in host where the survival of bacteria-infected mice was markedly enhanced following phage treatment. Moreover, the colonizing capability of P. aeruginosa was markedly impaired in phage-treated mice as compared to untreated infected mice.

CONCLUSION

Based on these findings, isolated phage vB_PaeM_PS3 could be potentially considered for treating of P. aeruginosa infections.

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.

Bacteriophages for the Targeted Control of Foodborne Pathogens

Foodborne illness is exacerbated by novel and emerging pathotypes, persistent contamination, antimicrobial resistance, an ever-changing environment, and the complexity of food production systems. Sporadic and outbreak events of common foodborne pathogens like Shiga toxigenic E. coli (STEC), Salmonella, Campylobacter, and Listeria monocytogenes are increasingly identified. Methods of controlling human infections linked with food products are essential to improve food safety and public health and to avoid economic losses associated with contaminated food product recalls and litigations. Bacteriophages (phages) are an attractive additional weapon in the ongoing search for preventative measures to improve food safety and public health. However, like all other antimicrobial interventions that are being employed in food production systems, phages are not a panacea to all food safety challenges. Therefore, while phage-based biocontrol can be promising in combating foodborne pathogens, their antibacterial spectrum is generally narrower than most antibiotics. The emergence of phage-insensitive single-cell variants and the formulation of effective cocktails are some of the challenges faced by phage-based biocontrol methods. This review examines phage-based applications at critical control points in food production systems with an emphasis on when and where they can be successfully applied at production and processing levels. Shortcomings associated with phage-based control measures are outlined together with strategies that can be applied to improve phage utility for current and future applications in food safety.

Newly Isolated Virulent Salmophages for Biocontrol of Multidrug-Resistant Salmonella in Ready-to-Eat Plant-Based Food

Due to irrational antibiotic stewardship, an increase in the incidence of multidrug resistance of bacteria has been observed recently. Therefore, the search for new therapeutic methods for pathogen infection treatment seems to be necessary. One of the possibilities is the utilization of bacteriophages (phages)—the natural enemies of bacteria. Thus, this study is aimed at the genomic and functional characterization of two newly isolated phages targeting MDR Salmonella enterica strains and their efficacy in salmonellosis biocontrol in raw carrot–apple juice. The Salmonella phage vB_Sen-IAFB3829 (Salmonella phage strain KKP 3829) and Salmonella phage vB_Sen-IAFB3830 (Salmonella phage strain KKP 3830) were isolated against S. I (6,8:l,-:1,7) strain KKP 1762 and S. Typhimurium strain KKP 3080 host strains, respectively. Based on the transmission electron microscopy (TEM) and whole-genome sequencing (WGS) analyses, the viruses were identified as members of tailed bacteriophages from the Caudoviricetes class. Genome sequencing revealed that these phages have linear double-stranded DNA and sizes of 58,992 bp (vB_Sen-IAFB3829) and 50,514 bp (vB_Sen-IAFB3830). Phages retained their activity in a wide range of temperatures (from −20 °C to 60 °C) and active acidity values (pH from 3 to 11). The exposure of phages to UV radiation significantly decreased their activity in proportion to the exposure time. The application of phages to the food matrices significantly reduced the level of Salmonella contamination compared to the control. Genome analysis showed that both phages do not encode virulence or toxin genes and can be classified as virulent bacteriophages. Virulent characteristics and no possible pathogen factors make examined phages feasible to be potential candidates for food biocontrol.

The balance between fitness advantages and costs drives adaptation of bacteriophage Qβ to changes in host density at different temperatures

Introduction

Host density is one of the main factors affecting the infective capacity of viruses. When host density is low, it is more difficult for the virus to find a susceptible cell, which increases its probability of being damaged by the physicochemical agents of the environment. Nevertheless, viruses can adapt to variations in host density through different strategies that depend on the particular characteristics of the life cycle of each virus. In a previous work, using the bacteriophage Qβ as an experimental model, we found that when bacterial density was lower than optimal the virus increased its capacity to penetrate into the bacteria through a mutation in the minor capsid protein (A1) that is not described to interact with the cell receptor.

Results

Here we show that the adaptive pathway followed by Qβ in the face of similar variations in host density depends on environmental temperature. When the value for this parameter is lower than optimal (30°C), the mutation selected is the same as at the optimal temperature (37°C). However, when temperature increases to 43°C, the mutation selected is located in a different protein (A2), which is involved both in the interaction with the cell receptor and in the process of viral progeny release. The new mutation increases the entry of the phage into the bacteria at the three temperatures assayed. However, it also considerably increases the latent period at 30 and 37°C, which is probably the reason why it is not selected at these temperatures.

Conclusion

The conclusion is that the adaptive strategies followed by bacteriophage Qβ, and probably other viruses, in the face of variations in host density depend not only on their advantages at this selective pressure, but also on the fitness costs that particular mutations may present in function of the rest of environmental parameters that influence viral replication and stability.

The human gut virome: composition, colonization, interactions, and impacts on human health

The gut virome is an incredibly complex part of the gut ecosystem. Gut viruses play a role in many disease states, but it is unknown to what extent the gut virome impacts everyday human health. New experimental and bioinformatic approaches are required to address this knowledge gap. Gut virome colonization begins at birth and is considered unique and stable in adulthood. The stable virome is highly specific to each individual and is modulated by varying factors such as age, diet, disease state, and use of antibiotics. The gut virome primarily comprises bacteriophages, predominantly order Crassvirales, also referred to as crAss-like phages, in industrialized populations and other Caudoviricetes (formerly Caudovirales). The stability of the virome's regular constituents is disrupted by disease. Transferring the fecal microbiome, including its viruses, from a healthy individual can restore the functionality of the gut. It can alleviate symptoms of chronic illnesses such as colitis caused by Clostridiodes difficile. Investigation of the virome is a relatively novel field, with new genetic sequences being published at an increasing rate. A large percentage of unknown sequences, termed 'viral dark matter', is one of the significant challenges facing virologists and bioinformaticians. To address this challenge, strategies include mining publicly available viral datasets, untargeted metagenomic approaches, and utilizing cutting-edge bioinformatic tools to quantify and classify viral species. Here, we review the literature surrounding the gut virome, its establishment, its impact on human health, the methods used to investigate it, and the viral dark matter veiling our understanding of the gut virome.

In Search of Proximate Triggers of Anthrax Outbreaks in Wildlife: A Hypothetical Individual-Based Model of Plasmid Transfer within Bacillus Communities

Bacillus anthracis, the causative agent of anthrax in humans, livestock, and wildlife, exists in a community with hundreds of other species of bacteria in the environment. Work on the genetics of these communities has shown that B. anthracis shares a high percentage of chromosomal genes with both B. thuringiensis and B. cereus, and that phenotypic differences among these bacteria can result from extra-chromosomal DNA in the form of plasmids. We developed a simple hypothetical individual-based model to simulate the likelihood of detecting plasmids with genes encoding anthrax toxins within bacterial communities composed of B. anthracis, B. thuringiensis, and B. cereus, and the surrounding matrix of extra-cellular polymeric substances. Simulation results suggest the horizontal transfer of plasmids with genes encoding anthrax toxins among Bacillus species persisting outside the host could function as a proximate factor triggering anthrax outbreaks.

Characterization of a novel Jerseyvirus phage T102 and its inhibition effect on biofilms of multidrug-resistant Salmonella

Biofilm, as a complex microbial community, is a serious and major safety concern in the food industry. Interestingly, some phages could effectively disrupt biofilms. This study characterized a novel isolated Salmonella bacteriophage T102, and its ability to control and remove biofilm produced by multidrug-resistant Salmonella. Phage T102 exhibited a broad host range within the Salmonella genus, especially drug-resistant Salmonella. The genome of phage T102 was comprised of 41,941 bp with 49.7% G + C composition, and with no genes associated with antibiotic resistance or virulence factors. The structural protein profile of phage T102 was subjected to SDS-PAGE and UPLC-MS/MS analysis, among them, 34 peptides were consistent with the hypothetical protein sequences annotated in the genome of T102. The biofilm inhibition assay revealed that phage T102 inhibited the formation of 6 h biofilms by two multidrug-resistant S. Typhimurium strains by 43.17 and 32.42%, respectively. 24 h biofilms formed by S. Typhimurium decreased by 54.94 and 53.67%, respectively, after 2 h of exposure to phage T102. Microscopic observation confirmed the inhibition effect of phage T102 on biofilm formation on spiked lettuce. Overall, our results support new research into the application of bacteriophage for biofilm reduction.

Single-Cell Approach Reveals Intercellular Heterogeneity in Phage-Producing Capacities

Bacteriophage burst size is the average number of phage virions released from infected bacterial cells, and its magnitude depends on the duration of an intracellular progeny accumulation phase. Burst size is often measured at the population level, not the single-cell level, and consequently, statistical moments are not commonly available. In this study, we estimated the bacteriophage lambda (λ) single-cell burst size mean and variance following different intracellular accumulation period durations by employing Escherichia coli lysogens bearing lysis-deficient λ prophages. Single lysogens can be isolated and chemically lysed at desired times following prophage induction to quantify progeny intracellular accumulation within individual cells. Our data showed that λ phage burst size initially increased exponentially with increased lysis time (i.e., period between induction and chemical lysis) and then saturated at longer lysis times. We also demonstrated that cell-to-cell variation, or "noise," in lysis timing did not contribute significantly to burst size noise. The burst size noise remained constant with increasing mean burst size. The most likely explanation for the experimentally observed constant burst size noise was that cell-to-cell differences in burst size originated from intercellular heterogeneity in cellular capacities to produce phages. The mean burst size measured at different lysis times was positively correlated to cell volume, which may determine the cellular phage production capacity. However, experiments controlling for cell size indicated that there are other factors in addition to cell size that determine this cellular capacity. IMPORTANCE Phages produce offspring by hijacking a cell's replicative machinery. Previously, it was noted that the variation in the number of phages produced by single infected cells far exceeded cell size variation. It was hypothesized that this variation is a consequence of variation in the timing of host cell lysis. Here, we show that cell-to-cell variation in lysis timing does not significantly contribute to the burst size variation. We suggest that the constant burst size variation across different host lysis times results from cell-to-cell differences in capacity to produce phages. We found that the mean burst size measured at different lysis times was positively correlated to cell volume, which may determine the cellular phage production capacity. However, experiments controlling for cell size indicated that there are other factors in addition to cell size that determine this cellular capacity.

Characteristics of Environmental Klebsiella pneumoniae and Klebsiella oxytoca Bacteriophages and Their Therapeutic Applications

In recent years, multidrug-resistant (MDR) strains of Klebsiella pneumoniae have spread globally, being responsible for the occurrence and severity of nosocomial infections. The NDM-1-kp, VIM-1 carbapenemase-producing isolates as well as extended-spectrum beta lactamase-producing (ESBL) isolates along with Klebsiella oxytoca strains have become emerging pathogens. Due to the growing problem of antibiotic resistance, bacteriophage therapy may be a potential alternative to combat such multidrug-resistant Klebsiella strains. Here, we present the results of a long-term study on the isolation and biology of bacteriophages active against K. pneumoniae, as well as K. oxytoca strains. We evaluated biological properties, morphology, host specificity, lytic spectrum and sensitivity of these phages to chemical agents along with their life cycle parameters such as adsorption, latent period, and burst size. Phages designated by us, vB_KpnM-52N (Kpn52N) and VB_KpnM-53N (Kpn53N), demonstrated relatively broad lytic spectra among tested Klebsiella strains, high burst size, adsorption rates and stability, which makes them promising candidates for therapeutic purposes. We also examined selected Klebsiella phages from our historical collection. Notably, one phage isolated nearly 60 years ago was successfully used in purulent cerebrospinal meningitis in a new-born and has maintained lytic activity to this day. Genomic sequences of selected phages were determined and analyzed. The phages of the sequenced genomes belong to the Slopekvirus and Jiaodavirus genus, a group of phages related to T4 at the family level. They share several features of T4 making them suitable for antibacterial therapies: the obligatorily lytic lifestyle, a lack of homologs of known virulence or antibiotic resistance genes, and a battery of enzymes degrading host DNA at infection.

Phenotypic characterization of phage vB_vcM_Kuja

Bacteriophage therapy targeting the increasingly resistant Vibrio cholerae is highly needed. Hence, studying the phenotypic behavior of potential phages under different conditions is a prerequisite to delivering the phage in an active infective form. The objective of this study was to characterize phage VP4 (vB_vcM_Kuja), an environmental vibriophage isolated from River Kuja in Migori County, Kenya in 2015. The phenotypic characteristics of the phage were determined using a one-step growth curve, restriction digestion profile, pH, and temperature stability tests. The results revealed that the phage is stable through a wide range of temperatures (20-50°C) and maintains its plaque-forming ability at pH ranging from 6 to 12. The one-step growth curve showed a latent period falling between 40 and 60 min, while burst size ranged from 23 to 30 plaque-forming units/10 µl at the same host strain. The restriction digestion pattern using EcoRI, SalI, HindIII, and XhoI enzymes showed that HindIII could cut the phage genome. The phage DNA could not be restricted by the other three enzymes. The findings of this study can be used in future studies to determine phage-host interactions.

A New Kayfunavirus-like Escherichia Phage vB_EcoP-Ro45lw with Antimicrobial Potential of Shiga Toxin-Producing Escherichia coli O45 Strain

Lytic bacteriophages are re-considered as a solution to resolve antibiotic-resistant rampage. Despite frequent foodborne outbreaks caused by the top six non-O157 Shiga-toxin-producing Escherichia coli (STEC), the current interventions are not sufficiently effective against each serogroup, particularly O45. Therefore, this study aimed to characterize a new short-tailed phage, vB_EcoP-Ro45lw (or Ro45lw), as an alternative antimicrobial agent for STEC O45 strains. Phage Ro45lw belongs to the Kayfunavirus genus within the Autographiviridae family and shares no close evolutionary relationship with any reference phages. Ro45lw contains a tail structure composed of a unique tail fiber and tail tubular proteins A and B, likely to produce enzymatic activity against the target bacterial cells besides structural function. Additionally, the phage genome does not contain virulent, antibiotic-resistant, or lysogenic genes. The phage has a latent period of 15 min with an estimated burst size of 55 PFU/CFU and is stable at a wide range of pH (pH4 to pH11) and temperatures (30 °C to 60 °C). Regardless of the MOIs (MOI = 0.1, 1, and 10) used, Ro45lw has a strong antimicrobial activity against both environmental (E. coli O45:H-) and clinical (E. coli O45:H2) strains at 25 °C. These findings indicate that phage Ro45lw has antimicrobial potential in mitigating pathogenic STEC O45 strains.

Characterization of polyvalent Escherichia phage Sa157lw for the biocontrol potential of Salmonella Typhimurium and Escherichia coli O157:H7 on contaminated mung bean seeds

Seeds are one of the primary sources of contamination with foodborne pathogens, such as pathogenic Escherichia coli, and various Salmonella serovars, for produce, particularly sprouts. Due to the susceptibility of sprout growth to chemical-based antimicrobials and the rising issue of antimicrobial resistance, developing innovative antimicrobial interventions is an urgent need. Therefore, the objective of this study was to characterize Escherichia phage Sa157lw (or Sa157lw) for the biocontrol potential of Salmonella Typhimurium and E. coli O157:H7 on contaminated mung bean seeds. Phage Sa157lw was subjected to whole-genome sequencing and biological characterization, including morphology, one-step growth curve, and stress stability tests. Later, antimicrobial activity was determined in vitro and upon application on the mung bean seeds artificially contaminated with E. coli O157:H7 or Salmonella Typhimurium. Sa157lw possessed a contractile tail and belonged to the Kuttervirus genus under the Ackermannviridae family, sharing a close evolutionary relationship with E. coli phage ECML-4 and Kuttervirus ViI; however, tail spike genes (ORF_102 and ORF_104) were the primary region of difference. Comparative genomics showed that Sa157lw encoded a cluster of tail spike genes—including ORF_101, ORF_102, and ORF_104—sharing high amino acid similarity with the counterfeits of various Salmonella phages. Additionally, Sa157lw harbored a unique tail fiber (ORF_103), possibly related to the receptors binding of O157 strains. The genomic evidence accounted for the polyvalent effects of Sa157lw against E. coli O157:H7 and various Salmonella serovars (Typhimurium, Enteritidis, Agona, Saintpaul, and Heidelberg). Furthermore, the phage did not contain any virulence, antibiotic-resistant, or lysogenic genes. Sa157lw had a 30-min latent period on both E. coli O157:H7 and Salmonella Typhimurium, with an estimated burst size of 130 and 220 PFU/CFU, respectively, and was stable at a wide range of temperatures (4–60°C) and pH (pH4 to pH10). The phage application demonstrated a strong anti-E. coli O157:H7 and anti-Salmonella Typhimurium effects in 1.1 and 1.8 log reduction on the contaminated mung bean seeds after overnight storage at 22°C. These findings provide valuable insights into the polyvalent Sa157lw as a potential biocontrol agent of Salmonella Typhimurium and E. coli O157:H7 on sprout seeds.

Bacteriophage as a potential therapy to control antibiotic-resistant Pseudomonas aeruginosa infection through topical application onto a full-thickness wound in a rat model

Background

Antibiotic-resistant Pseudomonas aeruginosa (P. aeruginosa) is one of the most critical pathogens in wound infections, causing high mortality and morbidity in severe cases. However, bacteriophage therapy is a potential alternative to antibiotics against P. aeruginosa. Therefore, this study aimed to isolate a novel phage targeting P. aeruginosa and examine its efficacy in vitro and in vivo.

Results

The morphometric and genomic analyses revealed that ZCPA1 belongs to the Siphoviridae family and could infect 58% of the tested antibiotic-resistant P. aeruginosa clinical isolates. The phage ZCPA1 exhibited thermal stability at 37 °C, and then, it decreased gradually at 50 °C and 60 °C. At the same time, it dropped significantly at 70 °C, and the phage was undetectable at 80 °C. Moreover, the phage ZCPA1 exhibited no significant titer reduction at a wide range of pH values (4–10) with maximum activity at pH 7. In addition, it was stable for 45 min under UV light with one log reduction after 1 h. Also, it displayed significant lytic activity and biofilm elimination against P. aeruginosa by inhibiting bacterial growth in vitro in a dose-dependent pattern with a complete reduction of the bacterial growth at a multiplicity of infection (MOI) of 100. In addition, P. aeruginosa-infected wounds treated with phages displayed 100% wound closure with a high quality of regenerated skin compared to the untreated and gentamicin-treated groups due to the complete elimination of bacterial infection.

Conclusion

The phage ZCPA1 exhibited high lytic activity against MDR P. aeruginosa planktonic and biofilms. In addition, phage ZCPA1 showed complete wound healing in the rat model. Hence, this research demonstrates the potential of phage therapy as a promising alternative in treating MDR P. aeruginosa.

E. coli biofilm formation and its susceptibility towards T4 bacteriophages studied in a continuously operating mixing - tubular bioreactor system

A system consisting of a connected mixed and tubular bioreactor was designed to study bacterial biofilm formation and the effect of its exposure to bacteriophages under different experimental conditions. The bacterial biofilm inside silicone tubular bioreactor was formed during the continuous pumping of bacterial cells at a constant physiological state for 2 h and subsequent washing with a buffer for 24 h. Monitoring bacterial and bacteriophage concentration along the tubular bioreactor was performed via a piercing method. The presence of biofilm and planktonic cells was demonstrated by combining the piercing method, measurement of planktonic cell concentration at the tubular bioreactor outlet, and optical microscopy. The planktonic cell formation rate was found to be 8.95 × 10-3  h-1 and increased approximately four-fold (4×) after biofilm exposure to an LB medium. Exposure of bacterial biofilm to bacteriophages in the LB medium resulted in a rapid decrease of biofilm and planktonic cell concentration, to below the detection limit within < 2 h. When bacteriophages were supplied in the buffer, only a moderate decrease in the concentration of both bacterial cell types was observed. After biofilm washing with buffer to remove unadsorbed bacteriophages, its exposure to the LB medium (without bacteriophages) resulted in a rapid decrease in bacterial concentration: again below the detection limit in < 2 h.

The Life Cycle Transitions of Temperate Phages: Regulating Factors and Potential Ecological Implications

Phages are viruses that infect bacteria. They affect various microbe-mediated processes that drive biogeochemical cycling on a global scale. Their influence depends on whether the infection is lysogenic or lytic. Temperate phages have the potential to execute both infection types and thus frequently switch their infection modes in nature, potentially causing substantial impacts on the host-phage community and relevant biogeochemical cycling. Understanding the regulating factors and outcomes of temperate phage life cycle transition is thus fundamental for evaluating their ecological impacts. This review thus systematically summarizes the effects of various factors affecting temperate phage life cycle decisions in both culturable phage-host systems and natural environments. The review further elucidates the ecological implications of the life cycle transition of temperate phages with an emphasis on phage/host fitness, host-phage dynamics, microbe diversity and evolution, and biogeochemical cycles.

Minimizing Foaming and Bulking in Activated Sludge with Bacteriophage Treatment: A Review of Mathematical Modeling

The interest in the ability of phages to control bacterial populations has extended from medical applications into the fields of agriculture, aquaculture, and the food industry. In particular, several authors have proposed using bacteriophages as an alternative method to control foaming and bulking in wastewater treatment. This strategy has shown successful results at the laboratory scale. However, this technology is still in development, and there are several challenges to overcome before bacteriophages can be widely used to control foaming and bulking in pilot or larger-scale treatment plants. Several models of the infection mechanisms in individual bacteria–phage pairs have been reported, i.e., for controlled systems with only one bacterium species in the presence of one phage species. However, activated sludge treatment systems largely differ from this situation, which opens a large horizon for future research. Mathematical models will play a key role in this development process, and this review offers an overview of the proposed models: their applications, potential, and challenges. A particular focus is placed on the model properties, such as parameter identifiability and states’ observability, which are essential for process prediction, monitoring, or dynamic optimization.

Hypoxia Increases the Tempo of Phage Resistance and Mutational Bottlenecking of Pseudomonas aeruginosa

Viruses that infect bacteria (i.e., phages) are abundant and widespread in the human body, and new anti-infective approaches such as phage therapy are essential for the future of effective medicine. Our understanding of microenvironmental factors such as tissue oxygen availability at the site of phage-bacteria interaction remains limited, and it is unknown whether evolved resistance is sculpted differentially under normoxia vs. hypoxia. We, therefore, analyzed the phage-bacteria interaction landscape via adsorption, one-step, time-kill dynamics, and genetic evolution under both normoxia and hypoxia. This revealed that adsorption of phages to Pseudomonas aeruginosa decreased under 14% environmental oxygen (i.e., hypoxia), but phage time-kill and one-step growth kinetics were not further influenced. Tracking the adaptation of P. aeruginosa to phages uncovered a higher frequency of phage resistance and constrained types of spontaneous mutation under hypoxia. Given the interest in developing phage therapies, developing our understanding of the phage-pathogen interaction under microenvironmental conditions resembling those in the body offers insight into possible strategies to overcome multidrug-resistant (MDR) bacteria.

An Optimal Lysis Time Maximizes Bacteriophage Fitness in Quasi-Continuous Culture

Optimality models have a checkered history in evolutionary biology. While optimality models have been successful in providing valuable insight into the evolution of a wide variety of biological traits, a common objection is that optimality models are overly simplistic and ignore organismal genetics. We revisit evolutionary optimization in the context of a major bacteriophage life history trait, lysis time. Lysis time refers to the period spanning phage infection of a host cell and its lysis, whereupon phage progenies are released. Lysis time, therefore, directly determines phage fecundity assuming progeny assembly does not exhaust host resources prior to lysis. Noting that previous tests of lysis time optimality rely on batch culture, we implemented a quasi-continuous culture system to observe productivity of a panel of isogenic phage λ genotypes differing in lysis time. We report that under our experimental conditions, λ phage productivity is maximized around optimal lysis times ranging from 60 to 100 min, and λ wildtype strain falls within this range. It would appear that natural selection on phage λ lysis time uncovered a set of genetic solutions that optimized progeny production in its ecological milieu relative to alternative genotypes. We discuss this finding in light of recent results that lysis time variation is also minimized in the strains with lysis times closer to the λ wild-type strain. IMPORTANCE Optimality theory presents the idea that natural selection acts on organismal traits to produce genotypes that maximize organismal survival and reproduction. As such, optimality theory is a valuable tool in guiding our understanding of the genetic constraints and tradeoffs organisms experience as their genotypes are selected to produce optimal solutions to biological problems. However, optimality theory is often critiqued as being overly simplistic and ignoring the roles of chance and history in the evolution of organismal traits. We show here that the wild-type genotype of a popular laboratory model organism, the bacteriophage λ, produces a phenotype for a major life history trait, lysis time, that maximizes the reproductive success of bearers of that genotype relative to other possible genotypes. This result demonstrates, as is rarely shown experimentally, that natural selection can achieve optimal solutions to ecological challenges.

Isolation and Characterization of Lytic Proteus Virus 309

Proteus mirabilis is frequently associated with complicated urinary tract infections (UTIs) and is the main cause of catheter-associated urinary tract infections (CAUTIs). Treatment of such infections is complicated and challenging due to the biofilm forming abilities of P. mirabilis. If neglected or mistreated, infections may lead to life-threating conditions such as cystitis, pyelonephritis, kidney failure, and bacteremia that may progress to urosepsis. Treatment with antibiotics, especially in cases of recurring and persistent infections, leads to the development of resistant strains. Recent insights into phage therapy and using phages to coat catheters have been evaluated with many studies showing promising results. Here, we describe a highly lytic bacteriophage, Proteus_virus_309 (41,740 bp), isolated from a wastewater treatment facility in Cape Town, South Africa. According to guidelines of the International Committee on Taxonomy of Viruses (ICTV), bacteriophage 309 is a species within the genus Novosibovirus. Similar to most members of the genus, bacteriophage 309 is strain-specific and lyse P. mirabilis in less than 20 min.

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.

Genomic and Biological Profile of a Novel Bacteriophage, Vibrio phage Virtus, Which Improves Survival of Sparus aurata Larvae Challenged with Vibrio harveyi

Due to the emergence of multidrug-resistant bacteria, commonly known as “superbugs”, phage therapy for the control of bacterial diseases rose in popularity. In this context, the use of phages for the management of many important bacterial diseases in the aquaculture environment is auspicious. Vibrio harveyi, a well-known and serious bacterial pathogen, is responsible for many disease outbreaks in aquaculture, resulting in huge economic and production losses. We isolated and fully characterized a novel bacteriophage, Vibrio phage Virtus, infecting V. harveyi strain VH2. Vibrio phage Virtus can infect a wide spectrum of Vibrio spp., including strains of V. harveyi, V. owensii, V. campbellii, V. parahaemolyticus, and V. mediterranei. It has a latent period of 40 min with an unusually high burst size of 3200 PFU/cell. Vibrio phage Virtus has a double-stranded DNA of 82,960 base pairs with 127 predicted open reading frames (ORFs). No virulence, antibiotic resistance, or integrase-encoding genes were detected. In vivo phage therapy trials in gilthead seabream, Sparus aurata, larvae demonstrated that Vibrio phage Virtus was able to significantly improve the survival of larvae for five days at a multiplicity of infection (MOI) of 10, which suggests that it can be an excellent candidate for phage therapy.

Phage–Antibiotic Therapy as a Promising Strategy to Combat Multidrug-Resistant Infections and to Enhance Antimicrobial Efficiency

Infections caused by multidrug-resistant (MDR) bacteria have highlighted the importance of the development of new antimicrobial agents. While bacteriophages (phages) are widely studied as alternative agents to antibiotics, combined treatments using phages and antibiotics have exhibited Phage–Antibiotic Synergy (PAS), in which antibiotics promote phage replication and extraordinary antimicrobial efficacy with reduced development of bacterial resistance. This review paper on the current progress of phage–antibiotic therapy includes aspects of the mechanisms of PAS and the therapeutic performance of PAS in combating multidrug-resistant bacterial infections. The choice of phages and antibiotics, the administration time and sequence, and the concentrations of the two agents impact the bacterial inhibitory effects to different extents.

A Novel Phage Indirectly Regulates Diatom Growth by Infecting a Diatom-Associated Biofilm-Forming Bacterium

Algae and heterotrophic bacteria have close and intricate interactions, which are regulated by multiple factors in the natural environment. Phages are the major factor determining bacterial mortality rates. However, their impacts on the alga-associated bacteria and thus on the alga-bacterium interactions are poorly understood. Here, we obtained a diatom-associated bacterium, Stappia indica SNL01, that could form a biofilm and had an inhibitory effect on the growth of the diatom Thalassiosira pseudonana. Meanwhile, phage SI01, with a double-stranded circular DNA genome (44,247 bp), infecting S. indica SNL01 was isolated. Phylogenetic analysis revealed that phage SI01 represents a novel member of the Podoviridae family. The phage contained multiple lysis genes encoding cell wall-lysing muramidase and spore cortex-lysing SleB, as well as depolymerase-like tail spike protein. By lysing the host bacterium and inhibiting the formation of biofilm, this phage could indirectly promote the growth of the diatom. Our results provide new insights into how phages indirectly regulate algal growth by infecting bacteria that are closely associated with algae or in the phycosphere. IMPORTANCE The impact of phage infection on the alga-bacterium relationship in the ocean is poorly understood. Here, a novel phage infecting the diatom-associated bacterium Stappia indica SNL01 was isolated. This bacterium could form a biofilm and had a negative effect on diatom growth. We revealed that this phage contained multiple lysis genes and could inhibit the formation of the bacterial biofilm, thus indirectly promoting diatom growth. This study suggests that phages not only are important regulators of bacteria but also have substantial indirect effects on algae and the alga-bacterium relationship.

Population Dynamics of a Two Phages-One Host Infection System Using Escherichia coli Strain ECOR57 and Phages vB_EcoP_SU10 and vB_EcoD_SU57

In this study, we looked at the population dynamics of a two phages-one host system using phages vB_EcoP_SU10 (SU10) and vB_EcoD_SU57 (SU57) and the bacteria Escherichia coli, strain ECOR57. Phage-specific growth curves were observed where infections by SU10 resulted in a moderate production of phages and infections by SU57 resulted in a fast and extensive production of phage progeny. Sequentially adding SU10 followed by SU57 did not produce a significant change in growth rates, whereas adding SU57 followed by SU10 resulted in a decrease in SU10 titer The efficiency of the plating assays showed that ECOR57 exhibited a resistance spectrum after infection by both the single and combined phages. Phage-resistant bacteria exhibited four different morphotypes (i.e., normal, slimy, edgy, and pointy). The normal and edgy morphotypes had a high frequency of developing resistance. Bacterial growth and biofilm assays indicated that the edgy and pointy morphotypes reached a stationary phase faster and produced more biofilm compared to the wild type. These findings suggest that the dynamic structure of phage-bacteria communities dictate resistance evolution and development. Understanding when and how resistances arise and phage(s)-hosts interactions could aid in the design of phage therapy treatments.

Implication of a gene deletion on a Salmonella Enteritidis phage growth parameters

Synthetic biology has been applied countless times for the modification and improvement of bacterial strains and for the synthesis of products that do not exist in nature. Phages are natural predators of bacteria controlling their population levels; however, their genomes carry several genes with unknown functions. In this work, Bacteriophage Recombineering of Electroporated DNA was used to assess the influence of deletion of a single gene with unknown function in the overall replication parameters of Salmonella phage PVP-SE2. Deletion of ORF_01, transcribed immediately after infection, reduced both the latent and rise periods by 5 min in PVP-SE2ΔORF_01 compared to the wild-type phage. A direct consequence of the deletion led to a smaller progeny release per infected cell by the mutant compared to the wild-type phage. Despite the difference in growth characteristics, the mutant phage remained infective towards exponentially growing cells. The mutation engineered endured for at least ten passages, showing that there is no reversion back to the wild-type sequence. This study provides proof of concept that methodologies used for phage engineering should always be complemented by phage growth characterization to assess whether a mutation can trigger undesirable characteristics.

Characterization of a novel, biofilm dispersing, lytic bacteriophage against drug-resistant Enterobacter cloacae

AIM

To characterize a novel bacteriophage, En5822, isolated from the environment against Enterobacter cloacae and exploring its application as an alternate antimicrobial.

METHODS AND RESULTS

Bacteriophage was isolated from sewage sample by membrane-filtration immobilization technique. It was purified and studied for its various physical properties like microscopic structure, thermal and pH stability, latent period and burst time, antimicrobial and anti-biofilm activity as well as molecular aspects by genome sequencing and analysis. En5822 is a myovirus with relative pH and thermal stability. En5822 shows a notable reduction of host bacterial biofilm as well as planktonic cultures. Whole genome sequence analysis revealed that the En5822 genome does not contain undesirable temperate lifestyle genes, antibiotic resistance genes and toxin-encoding genes.

CONCLUSIONS

En5822 displays high lytic activity, specificity and biofilm reduction capability. It has a short latent period and high burst size that aid faster activity. Its genomic and physical attributes offer possibilities for its as an alternative antimicrobial for the treatment of drug-resistant E. cloacae infections.

SIGNIFICANCE AND IMPACT OF STUDY

The study describes a novel, naturally virulent bacteriophage from environment capable of lysing multi-drug resistant E. cloacae effectively. The phage could potentially serve as an alternative strategy for treating antibiotic-resistant infections.

Isolation, Characterization, and Efficacy of Three Lytic Phages Infecting Multidrug-Resistant Salmonella Serovars from Poultry Farms in Egypt

Multidrug-resistant (MDR) Salmonella serovars are considered a significant threat to veterinary and public health. Developing new antimicrobial compounds that can treat the infection caused by these notorious pathogens is a big challenge. Bacteriophages can be adsorbed on and inhibit the growth of bacteria, providing optimal and promising alternatives to chemical antimicrobial compounds against foodborne pathogens due to their abundance in nature and high host specificity. The objective of the current study was to isolate and characterize new phages from poultry farms and sewage and to evaluate their efficacy against S. Enteritidis isolates. The study reports three lytic phages designated as ϕSET1, ϕSET2, and ϕSET3 isolated from poultry carcasses and sewage samples in Qalubiya governorate Egypt. The effectiveness of phages was evaluated against multidrug-resistant S. Enteritidis strains. Electron microscopy showed that these phages belong to the Siphoviridae family. Phages were tested against 13 bacterial strains to determine their host range. They could infect four S. Enteritidis and one S. Typhimurium; however, they did not infect other tested bacterial species, indicating their narrow infectivity. The bacteriophage's single-step growth curves revealed a latent period of 20 min for ϕSET1 and 30 min for ϕSET2 and ϕSET3. The isolated Salmonella phages prevented the growth of S. Enteritidis for up to 18 hrs. The findings revealed that Salmonella phages could be used as alternative natural antibacterial compounds to combat infection with MDR S. Enteritidis in the poultry industry and represent a step forward to using large panels of phages for eliminating Salmonella from the food chain.

Nanotechnology Based Approaches in Phage Therapy: Overcoming the Pharmacological Barriers

With the emergence and spread of global antibiotic resistance and the need for searching safer alternatives, there has been resurgence in exploring the use of bacteriophages in the treatment of bacterial infections referred as phage therapy. Although modern phage therapy has come a long way as demonstrated by numerous efficacy studies but the fact remains that till date, phage therapy has not received regulatory approval for human use (except for compassionate use).Thus, to hit the clinical market, the roadblocks need to be seriously addressed and gaps mended with modern solution based technologies. Nanotechnology represents one such ideal and powerful tool for overcoming the pharmacological barriers (low stability, poor in-vivo retention, targeted delivery, neutralisation by immune system etc.) of administered phage preparations.In literature, there are many review articles on nanotechnology and bacteriophages but these are primarily focussed on highlighting the use of lytic and temperate phages in different fields of nano-medicine such as nanoprobes, nanosensors, cancer diagnostics, cancer cell targeting, drug delivery through phage receptors, phage display etc. Reviews specifically focused on the use of nanotechnology driven techniques strictly to improve phage therapy are however limited. Moreover, these review if present have primarily focussed on discussing encapsulation as a primary method for improving the stability and retention of phage(s) in the body.With new advances made in the field of nanotechnology, approaches extend from mere encapsulation to recently adopted newer strategies. The present review gives a detailed insight into the more recent strategies which include 1) use of lipid based nano-carriers (liposomes, transfersomes etc.) 2) adopting microfluidic based approach, surface modification methods to further enhance the efficiency and stability of phage loaded liposomes 3) Nano- emulsification approach with integration of microfluidics for producing multiple emulsions (suitable for phage cocktails) with unique control over size, shape and drop morphology 4) Phage loaded nanofibers produced by electro-spinning and advanced core shell nanofibers for immediate, biphasic and delayed release systems and 5) Smart release drug delivery platforms that allow superior control over dosing and phage release as and when required. All these new advances are aimed at creating a suitable housing system for therapeutic bacteriophage preparations while targeting the multiple issues of phage therapy i.e., improving phage stability and titers, improving in-vivo retention times, acting as suitable delivery systems for sustained release at target site of infection, improved penetration into biofilms and protection from immune cell attack. The present review thus aims at giving a complete insight into the recent advances (2010 onwards) related to various nanotechnology based approaches to address the issues pertaining to phage therapy. This is essential for improving the overall therapeutic index and success of phage therapy for future clinical approval.

Lytic Bacteriophages Against Bacterial Biofilms Formed by Multidrug-Resistant Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus Isolated from Burn Wounds

Background: Use of bacteriophages as antibiofilm agents to tackle multidrug-resistant bacteria has gained importance in recent years. Materials and Methods: In this study, biofilm formation by Staphylococcus aureus, Pseudomona aeruginosa, Klebsiella pneumoniae, and Escherichia coli under different growth conditions was studied. Furthermore, the ability of bacteriophages to inhibit biofilm formation was analyzed. Results: Under dynamic growth condition, wherein the medium is renewed for every 12 h, the amount of biomass produced and log₁₀ colony-forming unit counts of all bacterial species studied was highest when compared with other growth conditions tested. Biomass of biofilms produced was drastically reduced when incubated for 2 or 4 h with bacteriophages vB_SAnS_SADP1, vB_PAnP_PADP4, vB_KPnM_KPDP1, and vB_ECnM_ECDP3. Scanning electron microscopy and confocal laser scanning microscopy analyses indicated that the reduction in biomass was due to the lytic action of the bacteriophages. Conclusions: Results of our study reinforce the concept of developing bacteriophages as alternatives to antibiotics to treat bacterial infections.

A Rapid Method for Performing a Multivariate Optimization of Phage Production Using the RCCD Approach

Bacteriophages can be used in various applications, from the classical approach as substitutes for antibiotics (phage therapy) to new biotechnological uses, i.e., as a protein delivery vehicle, a diagnostic tool for specific strains of bacteria (phage typing), or environmental bioremediation. The demand for bacteriophage production increases daily, and studies that improve these production processes are necessary. This study evaluated the production of a T4-like bacteriophage vB_EcoM-UFV09 (an E. coli-infecting phage with high potential for reducing environmental biofilms) in seven types of culture media (Luria-Bertani broth and the M9 minimal medium with six different carbon sources) employing four cultivation variables (temperature, incubation time, agitation, and multiplicity of infection). For this purpose, the rotatable central composite design (RCCD) methodology was used, combining and comparing all parameters to determine the ideal conditions for starting to scale up the production process. We used the RCCD to set up the experimental design by combining the cultivation parameters in a specific and systematic way. Despite the high number of conditions evaluated, the results showed that when specific conditions were utilized, viral production was effective even when using a minimal medium, such as M9/glucose, which is less expensive and can significantly reduce costs during large-scale phage production.