Bacteriophages--potential for application in wastewater treatment processes

The role of identified and characterized bacteriophage ZCEC13 in controlling pathogenic and multidrug-resistant Escherichia coli in wastewater: in vitro study

The spread and development of Multi-Drug Resistant (MDR) bacteria in wastewater became beyond control and a global public health concern. The conventional disinfectants used in wastewater treatment methods have been becoming increasingly ineffective against a range of pathogenic and MDR bacteria. Bacteriophages are considered a novel approach to microbial control. Therefore, this study aims to explore the possibility of using phages against pathogenic and MDR Escherichia coli strains isolated from wastewater treatment plants. The wastewater samples were collected from two different treatment plants for E. coli isolation. The antibiotic sensitivity profile and occurrence of virulence and resistant genes were tested in 28 E. coli isolates. Phage ZCEC13 was selected based on its promising activity and host range to undergo identification and characterization. ZCEC13 was evaluated by transmission electron microscopy, genomic sequencing, in vitro lytic activity and tested for its stability under different conditions such as pH, Ultraviolet light exposure, and temperature. The results reported that ZCEC13 belongs to the Caudoviricetes class, with a high antibacterial dynamic. Phage ZCEC13 displayed high stability at different pH values ranging from 2 to 12, good tolerance to temperatures from -4 to 65°C, and high stability at UV exposure for 120 min. Respectively, the findings showed stability of the phage under several conditions and high efficiency in killing MDR bacteria isolated from the treatment plants. Further studies are encouraged to analyse the efficacy of phages as a microbial control agent in wastewater treatment plants.

Benefits and Challenges of Applying Bacteriophage Biocontrol in the Consumer Water Cycle

Bacteria (including disinfection- and antibiotic-resistant bacteria) are abundant in the consumer water cycle, where they may cause disease, and lead to biofouling and infrastructure damage in distributions systems, subsequently resulting in significant economic losses. Bacteriophages and their associated enzymes may then offer a biological control solution for application within the water sector. Lytic bacteriophages are of particular interest as biocontrol agents as their narrow host range can be exploited for the targeted removal of specific bacteria in a designated environment. Bacteriophages can also be used to improve processes such as wastewater treatment, while bacteriophage-derived enzymes can be applied to combat biofouling based on their effectiveness against preformed biofilms. However, the host range, environmental stability, bacteriophage resistance and biosafety risks are some of the factors that need to be considered prior to the large-scale application of these bacterial viruses. Characteristics of bacteriophages that highlight their potential as biocontrol agents are thus outlined in this review, as well as the potential application of bacteriophage biocontrol throughout the consumer water cycle. Additionally, the limitations of bacteriophage biocontrol and corresponding mitigation strategies are outlined, including the use of engineered bacteriophages for improved host ranges, environmental stability and the antimicrobial re-sensitisation of bacteria. Finally, the potential public and environmental risks associated with large-scale bacteriophage biocontrol application are considered, and alternative applications of bacteriophages to enhance the functioning of the consumer water cycle, including their use as water quality or treatment indicators and microbial source tracking markers, are discussed.

Phage phylogeny, molecular signaling, and auxiliary antimicrobial resistance in aerobic and anaerobic membrane bioreactors

Phage emit communication signals that inform their lytic and lysogenic life cycles. However, little is known regarding the abundance and diversity of the genes associated with phage communication systems in wastewater treatment microbial communities. This study focused on phage communities within two distinct biochemical wastewater environments, specifically aerobic membrane bioreactors (AeMBRs) and anaerobic membrane bioreactors (AnMBRs) exposed to varying antibiotic concentrations. Metagenomic data from the bench-scale systems were analyzed to explore phage phylogeny, life cycles, and genetic capacity for antimicrobial resistance and quorum sensing. Two dominant phage families, Schitoviridae and Peduoviridae, exhibited redox-dependent dynamics. Schitoviridae prevailed in anaerobic conditions, while Peduoviridae dominated in aerobic conditions. Notably, the abundance of lytic and lysogenic proteins varied across conditions, suggesting the coexistence of both life cycles. Furthermore, the presence of antibiotic resistance genes (ARGs) within viral contigs highlighted the potential for phage to transfer ARGs in AeMBRs. Finally, quorum sensing genes in the virome of AeMBRs indicated possible molecular signaling between phage and bacteria. Overall, this study provides insights into the dynamics of viral communities across varied redox conditions in MBRs. These findings shed light on phage life cycles, and auxiliary genetic capacity such as antibiotic resistance and bacterial quorum sensing within wastewater treatment microbial communities.

Bacteriophages of Thermophilic 'Bacillus Group' Bacteria-A Systematic Review, 2023 Update

Bacteriophages associated with thermophiles are gaining increased attention due to their pivotal roles in various biogeochemical and ecological processes, as well as their applications in biotechnology and bionanotechnology. Although thermophages are not suitable for controlling bacterial infections in humans or animals, their individual components, such as enzymes and capsid proteins, can be employed in molecular biology and significantly contribute to the enhancement of human and animal health. Despite their significance, thermophages still remain underrepresented in the known prokaryotic virosphere, primarily due to limited in-depth investigations. However, due to their unique properties, thermophages are currently attracting increasing interest, as evidenced by several newly discovered phages belonging to this group. This review offers an updated compilation of thermophages characterized to date, focusing on species infecting the thermophilic bacilli. Moreover, it presents experimental findings, including novel proteomic data (39 proteins) concerning the model TP-84 bacteriophage, along with the first announcement of 6 recently discovered thermophages infecting Geobacillus thermodenitrificans: PK5.2, PK2.1, NIIg10.1, NIIg2.1, NIIg2.2, and NIIg2.3. This review serves as an update to our previous publication in 2021.

Two novel bacteriophages isolated from the environment that can help control activated sludge foaming

Nocardia spp., which belongs to one of the Nocardio-form filamentous bacteria, is usually surface hydrophobic and when overproduced attaches to the surface of bubbles under the action of surfactants, allowing the stable presence of foam on the surface of aeration tanks, leading to the occurrence of sludge-foaming events. Two novel phages, P69 and KYD2, were isolated from the environment, and their hosts were Nocardia transvalensis and Nocardia carnea, respectively. These two phages are Siphophages-like with long tails. An aeration tank pilot plant was constructed in the laboratory to simulate sludge foaming, and these two strains of phage were applied. Compared with the reactor not dosed with phage, the application of phage could reduce the host level in the reactor, resulting in the highest decrease in turbidity by more than 68% and sludge volume index by more than 25%. The time for surface foam disappearance was 9 h earlier than that of the control group (the group with the same concentration of Nocardia carnea but no bacteriophage applied), significantly improving water quality. The phage can effectively inhibit the propagation of Nocardia in the actual sludge-foaming event, control the sludge foaming, and improve the effluent quality. It provides a novel and relatively economical solution for controlling sludge foaming in sewage treatment plants in the future, shows that the phages have potential application value in the prevention and control of Nocardia, and provides another way to control the sludge-foaming event caused by the excessive reproduction of Nocardia in the future.

Flow Virometry: A Fluorescence-Based Approach to Enumerate Bacteriophages in Liquid Samples

Correctly designed flow cytometry (virometry) assays allow accurate detection and enumeration of viruses in water. However, rigorous controls and calibrators are needed to obtain quality data. In the absence of proper controls, the use of fluorescent dyes for virus enumeration can produce false positive signals and lead to the wrong estimation of total virus counts by misreporting colloid particles as virions. Here we describe a protocol that addresses the problems that might potentially confound virometry data accuracy.

Bacteriophages: Vectors of or weapons against the transmission of antibiotic resistance genes in hospital wastewater systems?

Antimicrobial resistance poses a serious threat to human health and is responsible for the death of millions of people annually. Hospital wastewater is an important hotspot for antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). However, little is known about the relationship between phages and ARGs in hospital wastewater systems (HWS). In the present study, the viral diversity of 12 HWSs using data from public metagenomic databases was investigated. Viruses were widely found in both the influent and effluent of each HWS. A total of 45 unique ARGs were carried by 85 viral contigs, which accounted for only 0.14% of the total viral populations, implying that ARGs were not commonly present in phages. Three efflux pump genes were identified as shared between phages and bacterial genomes. However, the predominant types of ARGs in HWS such as aminoglycoside- and beta-lactam-resistance genes were rarely found in phages. Based on CRISPR spacer and tRNA matches, interactions between 171 viral contigs and 60 antibiotic-resistant genomes were predicted, including interactions involving phages and vancomycin-resistant Enterococcus_B faecium or beta-lactam-resistant Klebsiella pneumoniae. More than half (56.1%) of these viral contigs indicated lytic and none of them carried ARGs. As the vOTUs in this study had few ARGs and were primarily lytic, HWS may be a valuable source for phage discovery. Future studies will be able to experimentally validate these sequence-based results to confirm the suitability of HWS phages for pathogen control measures in wastewater.

Phage for drug delivery vehicles

Viruses being the natural carriers of gene have been widely used as drug delivery systems. However, the commonly used eukaryotic viruses such as adenoviruses, retroviruses, and lentiviruses, besides efficiently targeting the cells, can also stimulate immunological response or disrupt tumour suppressor genes leading to cancer. Consequently, there has been an increase interest in the scientific fraternity towards exploring other alternatives, which are safer and equally efficient for drug delivery. Bacteriophages, in this context have been at the forefront as an efficient, reliable, and safer choice. Novel phage dependent technologies led the foundation of peptide libraries and provides way to recognising abilities and targeting of specific ligands. Hybridisation of phage with inorganic complexes could be an appropriate strategy for the construction of carrying bioinorganic carriers. In this chapter, we have tried to cover major advances in the phage species that can be used as drug delivery vehicles.

Bacteriophages in Infectious Diseases and Beyond-A Narrative Review

The discovery of antibiotics has revolutionized medicine and has changed medical practice, enabling successful fighting of infection. However, quickly after the start of the antibiotic era, therapeutics for infectious diseases started having limitations due to the development of antimicrobial resistance. Since the antibiotic pipeline has largely slowed down, with few new compounds being produced in the last decades and with most of them belonging to already-existing classes, the discovery of new ways to treat pathogens that are resistant to antibiotics is becoming an urgent need. To that end, bacteriophages (phages), which are already used in some countries in agriculture, aquaculture, food safety, and wastewater plant treatments, could be also used in clinical practice against bacterial pathogens. Their discovery one century ago was followed by some clinical studies that showed optimistic results that were limited, however, by some notable obstacles. However, the rise of antibiotics during the next decades left phage research in an inactive status. In the last decades, new studies on phages have shown encouraging results in animals. Hence, further studies in humans are needed to confirm their potential for effective and safe treatment in cases where there are few or no other viable therapeutic options. This study reviews the biology and applications of phages for medical and non-medical uses in a narrative manner.

Bacteriophage-based biocontrol technology to enhance the efficiency of wastewater treatment and reduce targeted bacterial biofilms

Wastewater treatment is an essential process for public health and a sustainable ecosystem. Inadequate wastewater treatment can lead to the release of organic and inorganic pollutants and pathogenic bacteria into the receiving waters which could be further utilized for recreation purposes. The interaction between bacteriophage and bacteria in a wastewater treatment plant plays a major role in maintaining the treatment process. Phage therapy has been proposed as an alternative to conventional treatment methods as bacteriophages can be used on specific targets and leave useful bacteria unharmed. The bacterial species, which are responsible for bulking, foaming, and biofilm formation in a wastewater treatment plant (WWTP) have been identified and their respective phages are isolated to control their growth. Phages with lytic life cycles are preferred to lysogenic. Lytic phages can kill the specific target as they lyse the cell, infect most of the hosts, and have an immediate effect on controlling problems caused by bacteria in a WWTP. The bacteriophages such as T7, SPI1, GTE7, PhaxI, MAG1, MAG2, ϕPh_Se01, ϕPh_Se02, and Bxb1 have been investigated for the removal of bacterial biofilms from wastewater. Novel experimental setups have improved the efficiency of phage therapy in small-scale and pilot-scale experiments. Much more in-depth knowledge of the microbial community and their interaction would help promote the usage of phage therapy in large-scale wastewater treatments. This paper has covered the recent advancements in phage therapy as an effective biocontrol of pathogenic bacteria in the wastewater treatment process and has looked at certain shortcomings that have to be improved.

Phages against killer superbugs: An enticing strategy against antibiotics-resistant pathogens

The emerging resistivity of antibiotic resistance superbugs desire the need to resolve the global problem of antibiotic resistance. Among several other methods currently being adopted, one possible solution may be the development of supplemental therapies for antibiotics. The use of the normal and advanced bactericidal properties of bacteriophages (bacteriophage therapy) may be one of the viable infection control options. It is evident, however, that the safe and regulated application of phage treatment will need extensive knowledge of the characteristics and behaviour of certain phage-bacterium systems. This mini review offers an overview of the potential for phage therapy as well as the constraints and obstacles it faces in becoming a commonly accepted infection management strategy.

The role of microbial ecology in improving the performance of anaerobic digestion of sewage sludge

The use of next-generation diagnostic tools to optimise the anaerobic digestion of municipal sewage sludge has the potential to increase renewable natural gas recovery, improve the reuse of biosolid fertilisers and help operators expand circular economies globally. This review aims to provide perspectives on the role of microbial ecology in improving digester performance in wastewater treatment plants, highlighting that a systems biology approach is fundamental for monitoring mesophilic anaerobic sewage sludge in continuously stirred reactor tanks. We further highlight the potential applications arising from investigations into sludge ecology. The principal limitation for improvements in methane recoveries or in process stability of anaerobic digestion, especially after pre-treatment or during co-digestion, are ecological knowledge gaps related to the front-end metabolism (hydrolysis and fermentation). Operational problems such as stable biological foaming are a key problem, for which ecological markers are a suitable approach. However, no biomarkers exist yet to assist in monitoring and management of clade-specific foaming potentials along with other risks, such as pollutants and pathogens. Fundamental ecological principles apply to anaerobic digestion, which presents opportunities to predict and manipulate reactor functions. The path ahead for mapping ecological markers on process endpoints and risk factors of anaerobic digestion will involve numerical ecology, an expanding field that employs metrics derived from alpha, beta, phylogenetic, taxonomic, and functional diversity, as well as from phenotypes or life strategies derived from genetic potentials. In contrast to addressing operational issues (as noted above), which are effectively addressed by whole population or individual biomarkers, broad improvement and optimisation of function will require enhancement of hydrolysis and acidogenic processes. This will require a discovery-based approach, which will involve integrative research involving the proteome and metabolome. This will utilise, but overcome current limitations of DNA-centric approaches, and likely have broad application outside the specific field of anaerobic digestion.

Bacteriophages in wastewater treatment: can they be an approach to optimize biological treatment processes?

In this paper, we explore the applications of bacteriophages and the advantages of using these viruses to control undesirable organisms in wastewater treatment plants. Based on this, this paper reviewed the literature on the subject by performing a bibliometric and scientometric analysis of articles published in peer-reviewed journals through 2021. We obtained 806 publications, of which 40% were published in the last 5 years, demonstrating an increase in interest in the subject. These articles analyzed, bacteriophages in treatment plants were strongly linked to bacteria such as Escherichia coli and related to disinfection, inactivation, sewage, and wastewater, in addition, biocontrol studies have gained prominence in recent years, particularly due to the resistance of microorganisms to antibiotics. Studies have shown that bacteriophages have great potential for application in treatment systems to control unwanted processes and act as valuable economic and environmental tools to improve the efficiency of various treatment technologies. Although these viruses have already been studied in various applications to optimize treatment plant processes, technology transfer remains a challenge due to the limitations of the technique-such as physicochemical factors related to the environment-and the complexity of biological systems. The research focusing on application strategies in conjunction with molecular biology techniques can expand this study area, enabling the discovery of new bacteriophages.

Escherichia coli ST155 as a production-host of three different polyvalent phages and their characterisation with a prospect for wastewater disinfection

Bacteriophages are generally specific, and a cocktail of phages is needed to combat different bacterial targets. Their production usually requires pathogenic isolation hosts. We identified a novel strain, Escherichia coli ST155, that could serve as a production host for three different polyvalent phages (ϕPh_SE03, ϕPh_SD01, and ϕPh_EC01), thus superseding the use of individual isolation hosts. Upon propagation in E. coli ST155, the phages demonstrated differential intergeneric infectivity against Salmonella enterica, E. coli OP50, Shigella dysenteriae, E. coli MDR, and Acinetobacter baumannii. Phages were characterised based on morphology, latent period, burst size, the efficiency of plating, and restriction enzyme profile. Survival assay on Caenorhabditis elegans, the absence of Shiga toxin, and enterotoxigenic E. coli virulence genes indicated that E. coli ST155 could be non-pathogenic. Lack of antibiotic resistance and absence of functional prophages rendered the host suitable for environmental applications. As a proof-of-concept, phage ϕPh_SE03 was produced in ST155 by employing a unique Bacteriophage Amplification Reactor-Lytics Broadcasting System and was simultaneously disseminated into S. enterica augmented wastewater, which resulted in a 3-log reduction in 24 h. The study establishes the potential of E. coli ST155 as a phage production host thereby minimising the possibility of accidental release of pathogenic hosts into wastewater.

Strategies and progresses for enhancing targeted antibiotic delivery

Antibiotic resistance is a global health issue and a potential risk for society. Antibiotics administered through conventional formulations are devoid of targeting effect and often spread to various undesired body sites, leading to sub-lethal concentrations at the site of action and thus resulting in emergence of resistance, as well as side effects. Moreover, we have a very slim antibiotic pipeline. Drug-delivery systems have been designed to control the rate, time, and site of drug release, and innovative approaches for antibiotic delivery provide a glint of hope for addressing these issues. This review elaborates different delivery strategies and approaches employed to overcome the limitations of conventional antibiotic therapy. These include antibiotic conjugates, prodrugs, and nanocarriers for local and targeted antibiotic release. In addition, a wide range of stimuli-responsive nanocarriers and biological carriers for targeted antibiotic delivery are discussed. The potential advantages and limitations of targeted antibiotic delivery strategies are described along with possible solutions to avoid these limitations. A number of antibiotics successfully delivered through these approaches with attained outcomes and potentials are reviewed.

The Specific Properties of Phusang Hot Spring Water: Safety and Benefits

Phusang warm pond or Phusang hot spring (Thailand) has a temperature of approximately 36–38 °C and may be suitable for bacterial growth. However, data on the microbiota and effectiveness of this water remain obscure. Therefore, this study aimed to evaluate the characteristics of Phusang hot spring water by clarifying the microorganisms and viral pathogens present. Cytotoxicity, irritation, liposome uptake, antimicrobial and anti-inflammatory effects were evaluated. The levels of trace elements such as sodium (Na), calcium (Ca), and strontium (Sr) were confirmed. Phusang hot spring water was nontoxic to L-929 cells and HDFa cells and was nonirritating to human phototypes I to IV at 48 h. The antimicrobial effects of Phusang hot spring water on S. aureus, S. epidermidis, B. subtilis and E. coli were not detected using the agar well diffusion assay. Phusang hot spring water decreased interleukin-6 (IL-6) expression at 24 h compared with (PBS) and untreated controls, as measured using semi qRT‒PCR and ELISA. Phusang hot spring water combined with curcumin-loaded liposomes exerted antiaging effects, suggesting their benefits for application in cosmetic products. The bacteriophage families Myoviridae, Siphoviridae and Podoviridae were detected, but not HPV or EBV. Trace elements such as Na and Ca were present. Therefore, the importance of this study is that Phusang hot spring water exerts anti-inflammatory effects via IL-6, is nontoxic and nonirritating, and might be used for balneotherapy or as a cosmetic ingredient under sterile conditions.

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.

Bacteriophages Can Make a Difference in Water Quality: Evidence From a Community-Based Study From North India

Background and objectives

Diarrhoea is a preventable and treatable faecal-oral disease. Despite significant inputs from the health and non-health sector in the treatment and prevention of diarrhoea, it remains a significant contributor to under-five-years children mortality and exerts profound effects on their growth and development. Bacteriophage has the potential to prevent diarrhoea. Bacteriophage status may influence the extent of diarrhoea. The objectives of the study were a) to assess the bacteriophage status and quality of water based on the Most Probable Number (MPN) count in the drinking water of under-five years children, and b) to find the association of the extent of diarrhoea with the bacteriophage status and quality of drinking water of under-five-years children in rural areas of Varanasi.

Methods

This is a community-based cross-sectional study done in the Chiraigaon community development block in a rural area of Varanasi. Water samples were collected and analysed in the Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi.

Results

The result of the study was that bacteriophage is present in 118 samples of water, whereas bacteriophage for Escherichia coli (E. coli), Klebsiella, and Vibrio were present in the drinking water of 81.1%, 53.8%, and 25.8% of under-five-years children, respectively. The water quality was highly satisfactory in 41.7% of samples and unsatisfactory in 15.2% of samples (p<0.004). All samples with highly satisfactory water quality had bacteriophages. Diarrhoea was present in 57.14% of samples without bacteriophage and 24.5% in samples with bacteriophage (p<0.01). The unadjusted odds ratio is 4.09.

Interpretation and conclusions

The odds of diarrhoea are four times higher in the water sample without bacteriophage than in the water sample in which bacteriophage is present. Bacteriophage study in preventing diarrhoea in children under five and health risk assessment call for focus.

Exploring the design implications of bacteriophages in mixed suspensions by considering attachment and break-up

The validity and usefulness of implementing bacteriophages into water treatment systems as agents of targeted bacterial inactivation is yet to be determined. While some concerns are still more purely biological in nature other concerns are still chiefly rooted in design feasibility. This work investigated bacteriophage heteroaggregation, a process whereby phages attach to non-host background particles, to explore different design options for water quality engineers, especially tuning mixing velocity. This was done by adapting batch/mixing assays, originally developed to study inert particle heteroaggregation, to characterize bacteriophage and kaolinite heteroaggregation using modified Smoluchowski parameters under different ionic strength conditions. This work found that regardless of the ionic strength or the tested phage to kaolinite ratios heteroaggregation occurred rapidly and was likely driven by extended DLVO forces. A model of bacteriophage-kaolinite heteroaggregation was generated and showed promising correspondence with observed laboratory data. This model, along with other findings, suggests that should bacteriophages be utilized as agents of host inactivation they ought to be used following particle separation processes to reduce the likelihood of phage scavenging through attachment to particulate matter rather than the targeted bacteria.

Renaissance for Phage-Based Bacterial Control

Bacteriophages (phages) are an underutilized biological resource with vast potential for pathogen control and microbiome editing. Phage research and commercialization have increased rapidly in biomedical and agricultural industries, but adoption has been limited elsewhere. Nevertheless, converging advances in DNA sequencing, bioinformatics, microbial ecology, and synthetic biology are now poised to broaden phage applications beyond pathogen control toward the manipulation of microbial communities for defined functional improvements. Enhancements in sequencing combined with network analysis make it now feasible to identify and disrupt microbial associations to elicit desirable shifts in community structure or function, indirectly modulate species abundance, and target hub or keystone species to achieve broad functional shifts. Sequencing and bioinformatic advancements are also facilitating the use of temperate phages for safe gene delivery applications. Finally, integration of synthetic biology stands to create novel phage chassis and modular genetic components. While some fundamental, regulatory, and commercialization barriers to widespread phage use remain, many major challenges that have impeded the field now have workable solutions. Thus, a new dawn for phage-based (chemical-free) precise biocontrol and microbiome editing is on the horizon to enhance, suppress, or modulate microbial activities important for public health, food security, and more sustainable energy production and water reuse.

Lytics broadcasting system: A novel approach to disseminate bacteriophages for disinfection and biogenic hydrogen sulphide removal tested in synthetic sewage

Owing to their selective nature, bacteriophages are prospective in targeted wastewater disinfection. Other potential applications include the removal of biogenic malodour and the mitigation of corrosion in sewerage pipelines. Nevertheless, its applications are ridden with challenges, the most prominent of which is scaling up. Towards that end, effective methodologies are required for dispersing phages into wastewater. The study describes a device arbitrarily named Lytics Broadcasting System. In principle, the device contains phages that can be continuously dispersed into wastewater. The modified version is called Bacteriophage Amplification Reactor, which operates with both phages and their respective hosts, ensuring continual production and dissemination of phages. Both prototypes utilize 0.22 μm cellulose membranes as an interface through which phage diffuse passively and selectively owing to its smaller size and established through membrane-overlay method. In the study, previously reported bacteriophage φPh_Se01 and Salmonella enterica were used. A reduction of 3-4 log was achieved with both the prototypes after 48 h of operation in 1 L of augmented synthetic sewage. Subsequently, the biogenic H₂S produced by Salmonella enterica was reduced by 64-74% indicating its utility for targeted disinfection and malodour mitigation of wastewater. This study aims to provide a framework for the development of scalable prototypes of Lytic Broadcasting Systems for real-world wastewater applications.

Use of bacteriophage to inactivate pathogenic bacteria from wastewater

The aim of this study was to enhance the rhizobacterium potential in horizontal subsurface flow constructed wetland (CW) system planted by Phragmites australis using specific and lytic phages. The bioinoculation of specific bacteriophage for target bacteria; Salmonella typhi, and the monitoring of bacterial inactivation under different conditions showed the effectiveness of this methodology to enhance bacteria reduction and consequentially ameliorate purification performance of this studied biological treatment system. The injection of the phage at a concentration equal to 10³ UFP/mL within the rhizosphere of the inoculated filter (F) was allowed 1 U-Log₁₀ of improvement of bacterial inactivation compared to the control filter (T) nearly 1 logarithmic unit thus, a 90% improvement of bacteria reduction. When we increased the phage titer (10⁵ UFP/mL), the bacterial reduction equal to 2.75 U-Log₁₀ (N/N₀) was registered that corresponds to a decrease of nearly 99.9%. According to the first-order model, the inactivation coefficient is equal to 2.29 min^-1 (0.88 min^-1 for the first experiment) and the bacterial reduction rate is 5 times higher than that determined for the control filter. This results show the positive impact of the phage in the bacterial inactivation and the improvement of water treatment of the biofilter C.

Bacteriophages in the Control of Aeromonas sp. in Aquaculture Systems: An Integrative View

Aeromonas species often cause disease in farmed fish and are responsible for causing significant economic losses worldwide. Although vaccination is the ideal method to prevent infectious diseases, there are still very few vaccines commercially available in the aquaculture field. Currently, aquaculture production relies heavily on antibiotics, contributing to the global issue of the emergence of antimicrobial-resistant bacteria and resistance genes. Therefore, it is essential to develop effective alternatives to antibiotics to reduce their use in aquaculture systems. Bacteriophage (or phage) therapy is a promising approach to control pathogenic bacteria in farmed fish that requires a heavy understanding of certain factors such as the selection of phages, the multiplicity of infection that produces the best bacterial inactivation, bacterial resistance, safety, the host’s immune response, administration route, phage stability and influence. This review focuses on the need to advance phage therapy research in aquaculture, its efficiency as an antimicrobial strategy and the critical aspects to successfully apply this therapy to control Aeromonas infection in fish.

Monitoring the Viral Transmission of SARS-CoV-2 in Still Waterbodies Using a Lanthanide-Doped Carbon Nanoparticle-Based Sensor Array

The latest epidemic of extremely infectious coronavirus disease 2019 (COVID-19) has created a significant public health concern. Despite substantial efforts to contain severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within a specific location, shortcomings in the surveillance of predominantly asymptomatic infections constrain attempts to identify the epidemiological spread of the virus. Continuous surveillance of wastewater streams, including sewage, offers opportunities to track the spread of SARS-CoV-2, which is believed to be found in fecal waste. To demonstrate the feasibility of SARS-CoV-2 detection in wastewater systems, we herein present a novel facilely constructed fluorescence sensing array based on a panel of three different lanthanide-doped carbon nanoparticles (LnCNPs). The differential fluorescence response pattern due to the counterion-ligand interactions allowed us to employ powerful pattern recognition to effectively detect SARS-CoV-2 and differentiate it from other viruses or bacteria. The sensor results were benchmarked to the gold standard RT-qPCR, and the sensor showed excellent sensitivity (1.5 copies/μL) and a short sample-to-results time of 15 min. This differential response of the sensor array was also explained from the differential mode of binding of the LnCNPs with the surface proteins of the studied bacteria and viruses. Therefore, the developed sensor array provides a cost-effective, community diagnostic tool that could be potentially used as a novel epidemiologic surveillance approach to mitigate the spread of COVID-19.

The challenges of monitoring and manipulating anaerobic microbial communities

Mixed anaerobic microbial communities are a key component in valorization of waste biomass via anaerobic digestion. Similar microbial communities are important as soil and animal microbiomes and have played a critical role in shaping the planet as it is today. Understanding how individual species within communities interact with others and their environment is important for improving performance and potential applications of an inherently green technology. Here, the challenges associated with making measurements critical to assessing the status of anaerobic microbial communities are considered. How these measurements could be incorporated into control philosophies and augment the potential of anaerobic microbial communities to produce different and higher value products from waste materials are discussed. The benefits and pitfalls of current genetic and molecular approaches to measuring and manipulating anaerobic microbial communities and the challenges which should be addressed to realise the potential of this exciting technology are explored.

Bacteriophages in Biological Wastewater Treatment Systems: Occurrence, Characterization, and Function

Phage bacteria interactions can affect structure, dynamics, and function of microbial communities. In the context of biological wastewater treatment (BWT), the presence of phages can alter the efficiency of the treatment process and influence the quality of the treated effluent. The active role of phages in BWT has been demonstrated, but many questions remain unanswered regarding the diversity of phages in these engineered environments, the dynamics of infection, the determination of bacterial hosts, and the impact of their activity in full-scale processes. A deeper understanding of the phage ecology in BWT can lead the improvement of process monitoring and control, promote higher influent quality, and potentiate the use of phages as biocontrol agents. In this review, we highlight suitable methods for studying phages in wastewater adapted from other research fields, provide a critical overview on the current state of knowledge on the effect of phages on structure and function of BWT bacterial communities, and highlight gaps, opportunities, and priority questions to be addressed in future research.

Shotgun metagenomics assessment of the resistome, mobilome, pathogen dynamics and their ecological control modes in full-scale urban wastewater treatment plants

The conventional activated sludge (CAS) process has limited capacity to remove pathogenic microorganisms and antibiotic resistance genes (ARGs), compared to membrane bioreactors (MBRs). However, the full extent of pathogenic microbial fraction, resistome (antibiotic and biocide resistance genes, ARGs and BRGs) and mobilome (mobile genetic elements, MGE) of urban wastewater treatment plant (UWTP) influents and effluents remains unknown. Thus, the fate of putative pathogenic bacteria, ARGs and potential co-occurrence patterns with BRGs, MGEs and bacterial-predatory microorganisms was determined in two full-scale UWTPs, a MBR and a CAS system, using shotgun metagenomics. Both UWTPs significantly reduced the BOD₅ (99.4-99.9%), COD (97.6-99.4%) and TSS (98.9-99.9%). MBR was more effective in reducing the abundance and diversity of pathogen-containing taxa, with 4 and 30 taxa enriched in MBR and CAS effluents, respectively. MBR treatment favored resistance genes associated with triclosan, whereas CAS effluents contained ARGs associated with antibiotics of clinical importance. Correlations between putative pathogenic bacteria, ARG/BRGs/MGEs and bacterial-predatory microorganisms suggested that: (i) opportunistic pathogens (Clostridia, Nocardia) may acquire ARGs against first-line treatments and (ii) bacteriophages may act as a biogenic mechanism of pathogen removal. These findings reinforce the MBR capacity to retain pathogenic components, hence reducing potential health risks associated with treated wastewater reuse.

Elimination of SARS-CoV-2 along wastewater and sludge treatment processes

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is shed in the feces of infected people. As a consequence, genomic RNA of the virus can be detected in wastewater. Although the presence of viral RNA does not inform on the infectivity of the virus, this presence of genetic material raised the question of the effectiveness of treatment processes in reducing the virus in wastewater and sludge. In this work, treatment lines of 16 wastewater treatment plants were monitored to evaluate the removal of SARS-CoV-2 RNA in raw, processed waters and sludge, from March to May 2020. Viral RNA copies were enumerated using reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) in 5 different laboratories. These laboratories participated in proficiency testing scheme and their results demonstrated the reliability and comparability of the results obtained for each one. SARS-CoV-2 RNA was found in 50.5% of the 101 influent wastewater samples characterized. Positive results were detected more frequently in those regions with a COVID-19 incidence higher than 100 cases per 100,000 inhabitants. Wastewater treatment plants (WWTPs) significantly reduced the occurrence of virus RNA along the water treatment lines. Secondary treatment effluents showed an occurrence of SARS-CoV-2 RNA in 23.3% of the samples and no positive results were found after MBR and chlorination. Non-treated sludge (from primary and secondary treatments) presented a higher occurrence of SARS-CoV-2 RNA than the corresponding water samples, demonstrating the affinity of virus particles for solids. Furthermore, SARS-CoV-2 RNA was detected in treated sludge after thickening and anaerobic digestion, whereas viral RNA was completely eliminated from sludge only when thermal hydrolysis was applied. Finally, co-analysis of SARS-CoV-2 and F-specific RNA bacteriophages was done in the same water and sludge samples in order to investigate the potential use of these bacteriophages as indicators of SARS-CoV-2 fate and reduction along the wastewater treatment.

Foaming mechanisms and control strategies during the anaerobic digestion of organic waste: A critical review

Foaming is a problem that affects the efficient and stable operation of the anaerobic digestion process. Characterizing foaming mechanisms and developing early warning and foaming control methods is thus critically important. This review summarizes the correlation of process parameters, state parameters, and microbial communities with foaming in anaerobic digesters; discusses the applicability of the above-mentioned multi-scale parameters and foaming potential evaluation methods for the prediction of foaming risk; and introduces the principles and practical applications of antifoaming and defoaming methods. Multiple causes of foaming in anaerobic digestion systems have been identified, but a generalizable foaming mechanism has yet to be described. Further study of the correlation between extracellular polymeric substances and soluble microbial products and foaming may provide new insights into foaming mechanisms. Monitoring the foaming potential (including the volume expansion potential) is an effective approach for estimating the risk of foaming. An in-situ monitoring system for determining the foaming potential in anaerobic digestion sites could provide an early warning of foaming risk. Antifoaming methods based on operating parameter management and process regulation help prevent foaming from the source, and biological defoaming methods are highly targeted and efficient, which is a promising research direction. Clarifying foaming mechanisms will aid the development of active antifoaming methods and efficient biological defoaming methods.

Bacteriophage ecology in biological wastewater treatment systems

Biological wastewater treatment (BWT) is currently the most widely applied approach for treating wastewater. The performance of BWT systems depends on the complex microbial communities they support. Although bacteriophages (phages), which are the viruses that infect prokaryotes, are recognized as the most abundant life entities, understanding of their ecological roles in BWT systems remains limited. Here, we review recent progress in phage-associated researches in BWT systems, including the interactions between phage and host, polyvalent phages, the influence of phage activity on BWT performance, and the potential applications of phage-based control for sludge bulking/foaming and pathogens. The challenges and perspectives of phage ecology are also outlined, which are expected to provide implications for future research and applications.Key points• Phage-host interactions in BWT systems are summarized• Impacts of phage activities on BWT performance• Potential applications of phages in BWT systems.

Measuring reproducibility of virus metagenomics analyses using bootstrap samples from FASTQ-files

MOTIVATION

High-throughput sequencing data can be affected by different technical errors, e.g. from probe preparation or false base calling. As a consequence, reproducibility of experiments can be weakened. In virus metagenomics, technical errors can result in falsely identified viruses in samples from infected hosts. We present a new resampling approach based on bootstrap sampling of sequencing reads from FASTQ-files in order to generate artificial replicates of sequencing runs which can help to judge the robustness of an analysis. In addition, we evaluate a mixture model on the distribution of read counts per virus to identify potentially false positive findings.

RESULTS

The evaluation of our approach on an artificially generated dataset with known viral sequence content shows in general a high reproducibility of uncovering viruses in sequencing data, i.e. the correlation between original and mean bootstrap read count was highly correlated. However, the bootstrap read counts can also indicate reduced or increased evidence for the presence of a virus in the biological sample. We also found that the mixture-model fits well to the read counts, and furthermore, it provides a higher accuracy on the original or on the bootstrap read counts than on the difference between both. The usefulness of our methods is further demonstrated on two freely available real-world datasets from harbor seals.

AVAILABILITY AND IMPLEMENTATION

We provide a Phyton tool, called RESEQ, available from https://github.com/babaksaremi/RESEQ that allows efficient generation of bootstrap reads from an original FASTQ-file.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

The first sequenced Sphaerotilus natans bacteriophage- characterization and potential to control its filamentous bacterium host

Bacteriophages (phages) are ubiquitous entities present in every conceivable habitat as a result of their bacterial parasitism. Their prevalence and impact in the ecology of bacterial communities and their ability to control pathogens make their characterization essential, particularly of new phages, improving knowledge and potential application. The isolation and characterization of a new lytic phage against Sphaerotilus natans strain DSM 6575, named vB_SnaP-R1 (SnaR1), is here described. Besides being the first sequenced genome of a Sphaerotilus natans infecting phage, 99% of its 41507 bp genome lacks homology with any other sequenced phage, revealing its uniqueness and previous lack of knowledge. Moreover, SnaR1 is the first Podoviridae phage described infecting this bacterium. Sphaerotilus natans is an important filamentous bacterium due to its deleterious effect on wastewater treatment plants (WWTP) and thus, phages may play a role as novel biotechnological tools against filamentous overgrowth in WWTP. The lytic spectrum of SnaR1 was restricted to its host strain, infecting only one out of three S. natans strains and infection assays revealed its ability to reduce bacterial loads. Results suggest SnaR1 as the prototype of a new phage genus and demonstrates its potential as a non-chemical alternative to reduce S. natans DSM 6575 cells.

Current challenges and future opportunities of phage therapy

Antibiotic resistance is a major public health challenge worldwide, whose implications for global health might be devastating if novel antibacterial strategies are not quickly developed. As natural predators of bacteria, (bacterio)phages may play an essential role in escaping such a dreadful future. The rising problem of antibiotic resistance has revived the interest in phage therapy and important developments have been achieved over the last years. But where do we stand today and what can we expect from phage therapy in the future? This is the question we set to answer in this review. Here, we scour the outcomes of human phage therapy clinical trials and case reports, and address the major barriers that stand in the way of using phages in clinical settings. We particularly address the potential of phage resistance to hinder phage therapy and discuss future avenues to explore the full capacity of phage therapy.

New benzo(a)pyrene-degrading strains of the Burkholderia cepacia complex prospected from activated sludge in a petrochemical wastewater treatment plant

The prospection of bacteria that are resistant to polyaromatic hydrocarbons (PAH) of activated sludge from a Petrochemical Wastewater Treatment Plant (WWTP) allows investigating potential biodegraders of PAH. For this purpose, sludge samples were cultured with benzo(a)pyrene and/or naphthalene as carbon sources. The recovered isolates were characterized by biochemical methods and identified based on the analysis of the sequence of three genes: 16S, recA and gyrB. The isolated strains were shown to be capable of producing surfactants, which are important for compound degradation. The ability to reduce benzo(a)pyrene in vitro was tested by gas chromatography. After 20 days of experiment, the consortium that was enriched with 1 mg/L of benzo(a)pyrene was able to reduce 30% of the compound when compared to a control without bacteria. The four isolated strains that significantly reduced benzo(a)pyrene belong to the Burkholderia cepacia complex and were identified within the consortium as the species B. cenocepacia IIIa, B. vietnamiensis, B. cepacia, and B. multivorans. This finding demonstrates the biotechnological potential of the B. cepacia complex strains for use in wastewater treatment and bioremediation. Previous studies on hydrocarbon-degrading strains focused mainly on contaminated soil or marine areas. In this work, the strains were prospected from activated sludge in a WWTP and showed the potential of indigenous samples to be used in both improving treatment systems and bioremediation of areas contaminated with petrochemical waste.

Bacteriophages as a Potential 360-Degree Pathogen Control Strategy

Bacteriophages are viruses that exclusively kill bacteria and are the most ubiquitous organisms on the planet. Since their discovery, bacteriophages have been considered an important weapon to fight human and animal infections of bacterial origin due to their specific ability to attack the associated target bacteria. With the discovery of antibiotics, phage treatment was progressively abandoned in Western countries. However, due to the recent emergence of growing antimicrobial resistance (AMR) to antibiotics, interest in phage use in human therapy has once again grown. Similarly, at the environmental level, the extensive use of disinfectants based on chemicals, including biocides in agriculture, has been associated with the emergence of resistance against disinfectants themselves, besides having a high environmental impact. Due to these issues, the applications of phages with biocontrol purposes have become an interesting option in several fields, including farms, food industry, agriculture, aquaculture and wastewater plants. Notably, phage action is maintained even when the target bacteria are multidrug resistant (MDR), rendering this option extremely interesting in counteracting AMR emergence both for therapeutical and decontamination purposes. Based on this, bacteriophages have been interestingly proposed as environmental routine sanitizers in hospitals, to counteract the spread of the pathogenic MDR bacteria that persistently contaminate hard surfaces. This review summarizes the studies aimed at evaluating the potential use of phages as decontaminants, with a special focus on hospital sanitation.

Phage therapy as a potential approach in the biocontrol of pathogenic bacteria associated with shellfish consumption

Infectious human diseases acquired from bivalve shellfish consumption constitute a public health threat. These health threats are largely related to the filter-feeding phenomenon, by which bivalve organisms retain and concentrate pathogenic bacteria from their surrounding waters. Even after depuration, bivalve shellfish are still involved in outbreaks caused by pathogenic bacteria, which increases the demand for new and efficient strategies to control transmission of shellfish infection. Bacteriophage (or phage) therapy represents a promising, tailor-made approach to control human pathogens in bivalves, but its success depends on a deep understanding of several factors that include the bacterial communities present in the harvesting waters, the appropriate selection of phage particles, the multiplicity of infection that produces the best bacterial inactivation, chemical and physical factors, the emergence of phage-resistant bacterial mutants and the life cycle of bivalves. This review discusses the need to advance phage therapy research for bivalve decontamination, highlighting their efficiency as an antimicrobial strategy and identifying critical aspects to successfully apply this therapy to control human pathogens associated with bivalve consumption.

Recent Insights into Aeromonas salmonicida and Its Bacteriophages in Aquaculture: A Comprehensive Review

The emergence and spread of antimicrobial resistance in pathogenic bacteria of fish and shellfish have caused serious concerns in the aquaculture industry, owing to the potential health risks to humans and animals. Among these bacteria, Aeromonas salmonicida, which is one of the most important primary pathogens in salmonids, is responsible for significant economic losses in the global aquaculture industry, especially in salmonid farming because of its severe infectivity and acquisition of antimicrobial resistance. Therefore, interest in the use of alternative approaches to prevent and control A. salmonicida infections has increased in recent years, and several applications of bacteriophages (phages) have provided promising results. For several decades, A. salmonicida and phages infecting this fish pathogen have been thoroughly investigated in various research areas including aquaculture. The general overview of phage usage to control bacterial diseases in aquaculture, including the general advantages of this strategy, has been clearly described in previous reviews. Therefore, this review specifically focuses on providing insights into the phages infecting A. salmonicida, from basic research to biotechnological application in aquaculture, as well as recent advances in the study of A. salmonicida.

Molecular Insights into Bacteriophage Evolution toward Its Host

Bacteriophages (phages), viruses that infect bacteria, are considered to be highly host-specific. To add to the knowledge about the evolution and development of bacteriophage speciation toward its host, we conducted a 21-day experiment with the broad host-range bacteriophage Aquamicrobium phage P14. We incubated the phage, which was previously isolated and enriched with the Alphaproteobacteria Aquamicrobium H14, with the Betaproteobacteria Alcaligenaceae H5. During the experiment, we observed an increase in the phage's predation efficacy towards Alcaligenaceae H5. Furthermore, genome analysis and the comparison of the bacteriophage's whole genome indicated that rather than being scattered evenly along the genome, mutations occur in specific regions. In total, 67% of the mutations with a frequency higher than 30% were located in genes that encode tail proteins, which are essential for host recognition and attachment. As control, we incubated the phage with the Alphaproteobacteria Aquamicrobium H8. In both experiments, most of the mutations appeared in the gene encoding the tail fiber protein. However, mutations in the gene encoding the tail tubular protein B were only observed when the phage was incubated with Alcaligenaceae H5. This highlights the phage's tail as a key player in its adaptation to different hosts. We conclude that mutations in the phage's genome were mainly located in tail-related regions. Further investigation is needed to fully characterize the adaptation mechanisms of the Aquamicrobium phage P14.

Profile of the Spatial Distribution Patterns of the Human and Bacteriophage Virome in a Wastewater Treatment Plant Located in the South of Spain

In wastewater treatment plants, most microbial characterization has focused on bacterial, archaeal, and fungal populations. Due to the difficult isolation, quantification, and identification of viruses, only a limited number of virome studies associated with wastewater treatment plants have been carried out. However, the virus populations play an important role in the microbial dynamics in wastewater treatment systems and the biosafety of effluents. In this work, the viral members present in influent wastewater, mixed liquor (aerobic bioreactor), excess sludge, and effluent water of a conventional activated sludge system for the treatment of urban wastewater were identified. Viral members were observed by transmission electron microscopy and studied through next-generation sequencing studies. The results showed the dominance of bacteriophages in the viral community in all samples, with the dominant viral phylotype classified as Escherichia coli O157 typing phage 7. Moreover, different human viruses, such as Cynomolgus cytomegalovirus and Gammaherpesvirus, were also detected.

Removal of antibiotic resistance genes in various water resources recovery facilities

Water resources recovery facilities (WWTPs) are hotspots for antibiotic resistance genes (ARGs) and pose a significant threat to environments. Therefore, ARG removal efficiencies of WWTPs are of great importance. In this study, conventional activated sludge (CAS), biological nutrient removal (BNR), sequencing batch reactor (SBR), membrane bioreactor (MBR), package MBR, and WWTP with coagulation-flocculation and UV disinfection units were investigated in terms of their removal efficiencies on overall bacterial genes with 16S rDNA and seven ARGs including the genes aadA, bla_CTX-M , cmlA, ermB, sul1, tetA, and qnrS corresponding to commonly used antibiotics aminoglycosides, β-lactams, amphenicols, macrolides-lincosamides-streptogramins, sulfonamides-trimethoprim, tetracyclines, and quinolones, respectively. Seasonal abundance of overall genes and ARGs in influents and effluents of each WWTPs was determined by quantitative polymerase chain reaction. Membrane bioreactor and package MBR systems showed the highest removal efficiency up to 5-log reductions. Seasonal changes affected ARG removal efficiencies of BNR and CAS significantly (p < 0.05). The lowest log reductions were determined in summer for BNR and in both autumn and winter for CAS. The abundance of the genes increased in sludge treatment of CAS. In all WWTPs tested, ARG removal rates were correlated with the 16S rDNA gene removal (p > 0.05). The results elucidated that the removal mechanism was not ARG-specific. PRACTITIONER POINTS: Removal of genes in WWTPs was found to be not ARG-specific. MBR and package MBR systems had the highest gene removal efficiencies. Effluents of the MBR systems still retained up to 10⁴  gene copy number/ml. Removal of genes in CAS and BNR systems showed seasonal variations. The copy numbers of the genes increased in the sludge of CAS.

Identification of a newly isolated lytic bacteriophage against K24 capsular type, carbapenem resistant Klebsiella pneumoniae isolates

The increasing incidence of carbapenemase-producing K. pneumoniae strains (CP-Kps) in the last decade has become a serious global healthcare problem. Therapeutic options for the treatment of emerging hospital clones have drastically narrowed and therefore novel approaches must be considered. Here we have isolated and characterized a lytic bacteriophage, named vB_KpnS_Kp13, that was effective against all Verona integron-encoded metallo-β-lactamase (VIM) producing K. pneumoniae isolates originating from hospital samples (urine, blood, sputum and faeces), belonging to the ST15 clonal lineage and expressing the K24 capsule. Morphological characterization of vB_KpnS_Kp13 showed that the newly identified phage belonged to the Siphoviridae family, and phylogenetic analysis showed that it is part of a distinct clade of the Tunavirinae subfamily. Functional analysis revealed that vB_KpnS_Kp13 had relatively short latent period times (18 minutes) compared to other K. pneumoniae bacteriophages and could degrade biofilm by more than 50% and 70% in 24 and 48 hours respectively. Complete in vivo rescue potential of the new phage was revealed in an intraperitoneal mouse model where phages were administered intraperitoneally 10 minutes after bacterial challenge. Our findings could potentially be used to develop specific anti-CP-Kps bacteriophage-based therapeutic strategies against major clonal lineages and serotypes.

Defining and combating antibiotic resistance from One Health and Global Health perspectives

Several interconnected human, animal and environmental habitats can contribute to the emergence, evolution and spread of antibiotic resistance, and the health of these contiguous habitats (the focus of the One Health approach) may represent a risk to human health. Additionally, the expansion of resistant clones and antibiotic resistance determinants among human-associated, animal-associated and environmental microbiomes have the potential to alter bacterial population genetics at local and global levels, thereby modifying the structure, and eventually the productivity, of microbiomes where antibiotic-resistant bacteria can expand. Conversely, any change in these habitats (including pollution by antibiotics or by antibiotic-resistant organisms) may influence the structures of their associated bacterial populations, which might affect the spread of antibiotic resistance to, and among, the above-mentioned microbiomes. Besides local transmission among connected habitats-the focus of studies under the One Health concept-the transmission of resistant microorganisms might occur on a broader (even worldwide) scale, requiring coordinated Global Health actions. This Review provides updated information on the elements involved in the evolution and spread of antibiotic resistance at local and global levels, and proposes studies to be performed and strategies to be followed that may help reduce the burden of antibiotic resistance as well as its impact on human and planetary health.

Presence of bacteria and bacteriophages in full-scale trickling filters and an aerated constructed wetland

Aerated Constructed Wetlands are a state-of-the-art design that provides a different physical and chemical environment (compared to traditional passive wetland designs) for the wastewater treatment processes and, thus, may have different pathogen removal characteristics. In order to establish the fate of bacterial and viral indicators, a field study was carried out at a Sewage Treatment Works (STW) in the UK (serving 20,000 pe). The STW consists of primary and secondary sedimentation tanks and trickling filters (TF) as the biological stage. A large (1,160 m²) pilot aerated Vertical Flow Constructed Wetland (AVFCW) was constructed at the STW as tertiary stage receiving ¼ of the total flow rate, i.e., 1250 m³/day. Effluent quality of the AVFCW complied with national and international standards for environmental discharge and reuse. For the first time, two sets of bacterial (Faecal coliforms, E.coli and intestinal enterococci) and viral indicators (Somatic coliphages, F-RNA specific bacteriophages and human-specific B. fragilis GB124 phages) were simultaneously investigated in an AVFCW and TF. High elimination rates were detected (up to 3.7 and 2.2 log reduction for bacteria indicators and phages, respectively) and strong correlations between the two sets were found. The superior efficiency of the aerated Constructed Wetlands in microbiological contamination removal compared to passive wetland systems was established for the first time, which may have implications for process selection for wastewater reuse. This field study therefore provides new evidence on the fate of bacteriophages and a first indication of their potential use for performance evaluation in TF and aerated Constructed Wetlands. It also demonstrates that the combination of TF with aerated constructed wetlands could be a novel and effective treatment scheme for new STW or for the upgrade of existing STW.

Isolation and Genomic Characterization of an Acinetobacter johnsonii Bacteriophage AJO2 From Bulking Activated Sludge

A novel Podoviridae lytic phage AJO2, specifically infecting Acinetobacter johnsonii, was isolated from bulking activated sludge. The one-step growth experiment showed that the latent period and burst size of AJO2 were estimated to be 30 min and 78.1 phages per infected cell, respectively. The viability test indicated that neutral conditions (pH 6-8) were table for AJO2 survival, while it was sensitive to high temperature (≥60°C) and ultraviolet treatment (254 nm). Genomic sequencing revealed that the AJO2 had a linearly permuted, double-stranded (ds) DNA consisting of 38,124 bp, with the G+C content of 41 mol%. A total of 58 putative open reading frames (ORFs), 11 pairs of repeats and 11 promoters were identified. The AJO2 genome had a modular gene structure which shared some similarities to those of A. baumanii phages. However, genomic comparative analysis revealed many differences among them, and novel genes were identified in the AJO2 genome. These results contribute to subsequent researches on the interaction between bacteriophages and hosts in wastewater treatment, especially during the bulking period. Additionally, the newly isolated phage could be a good candidate as a therapeutic agent to control nosocomial infections caused by A. johnsonii.

Treatment modalities for the reuse of produced waste from oil and gas development

Unconventional oil and gas development is achieved through a series of sub-processes, which utilize large amounts of water, proppant, and chemical additives to retrieve sequestered hydrocarbons from low permeability petroliferous strata. As a result, a large amount of wastewater is produced, which is traditionally disposed of via subsurface injection into non-productive stratum throughout the country. However, this method of waste management has been linked to the induction of seismic events in a number of regions across North America, calling into question the environmental stewardship and sustainability of subsurface waste disposal. Advancements in water treatment technologies have improved the efficacy and financial viability of produced water recycling for beneficial reuse in the oil and gas sector. This review will cover the various treatment options that are currently being utilized in shale energy basins to remove organic, inorganic, and biological constituents, as well as some emerging technologies that are designed to remove pertinent contaminants that would otherwise preclude the reuse of produced water for production well stimulation.

Computational Modelling of Large Scale Phage Production Using a Two-Stage Batch Process

Cost effective and scalable methods for phage production are required to meet an increasing demand for phage, as an alternative to antibiotics. Computational models can assist the optimization of such production processes. A model is developed here that can simulate the dynamics of phage population growth and production in a two-stage, self-cycling process. The model incorporates variable infection parameters as a function of bacterial growth rate and employs ordinary differential equations, allowing application to a setup with multiple reactors. The model provides simple cost estimates as a function of key operational parameters including substrate concentration, feed volume and cycling times. For the phage and bacteria pairing examined, costs and productivity varied by three orders of magnitude, with the lowest cost found to be most sensitive to the influent substrate concentration and low level setting in the first vessel. An example case study of phage production is also presented, showing how parameter values affect the production costs and estimating production times. The approach presented is flexible and can be used to optimize phage production at laboratory or factory scale by minimizing costs or maximizing productivity.

Complete genome sequence of SRT8, a novel T1-like Escherichia coli bacteriophage

In this study, an Escherichia coli virulent phage, SRT8, was isolated from sewage sludge samples collected from Jinan, Shandong Province, China. The genome of phage SRT8 consists of 49,579 bp with 47.83% G+C content. The phage genome contains 84 putative protein-coding genes, and no rRNA or tRNA genes. Comparative genomics analysis showed that the E. coli phage SRT8 is a member of a new species and belongs to the subfamily Tunavirinae, which includes T1-like phages.

Computational Modeling of Bacteriophage Production for Process Optimization

Computational models can be used to optimize the production of bacteriophages. Here a model is described for production in a two-stage self-cycling process. Theoretical and practical considerations for modeling bacteriophage production are first introduced. The key experimental protocols required to estimate key kinetic parameters for the model, including determining variable infection rates as a function of substrate concentration, are described. ppSim is an open-source R-script that can simulate bacteriophage production to optimize productivity or minimize costs. The steps included to run the simulation using the experimentally determined infection parameters are described. An example is also presented, where a level sensor and cycle time are optimized to maximize bacteriophage productivity in two sequential 1-L bioreactors, resulting in a production rate of 4.46 × 10¹⁰ bacteriophage particles/hour. The protocols and programs described here will allow users to potentially optimize production of their own bacteriophage-bacteria pairing by effectively applying bacteriophage modeling.