Fast and easy methods for the detection of coliphages

Somatic Coliphages as an Operational Tool to Assess Loss of Bathing Water Quality after Heavy Rain Events

Rapid population growth and coastal development has led to increased fecal contamination of coastal surface waters worldwide, enhancing the potential risk of waterborne human pathogens in bathing areas. More frequent heavy rainfall events, attributed to global warming, have further exacerbated the problem by causing sometimes sewer overflows into recreational waters. As traditional bacterial indicators have limited accuracy for predicting health risks associated with waterborne viruses, the additional use of viral indicators such as coliphages is recommended. In this study, we compared the behavior of bacterial and viral indicators of water quality at 10 Barcelona beaches during three bathing seasons, in dry conditions, and after four rainstorms that caused specific pollution events due to rain runoff with combined sewer overflows (CSO). Levels of all target indicators increased after the rainstorms, but compared to Escherichia coli and intestinal enterococci, somatic coliphages exhibited a slower decline and higher environmental persistence following a rain event. Daily continuous sampling carried out during the days following a rainstorm allowed not only the determination of the decay kinetics of each target indicator but also the day when the water quality recovered the values established in the current European regulation in approximately 2 -3 days after each CSO. These observations indicate that the combined use of bacterial and viral indicators can enhance the surveillance of microbial quality of bathing waters. Moreover, coliphages can swiftly provide insights into transient fecal pollution linked to rainfall episodes, thanks to available analytical techniques that enable same-day recommendations. The management of urban wastewater and recreational water regulations should consistently employ microbial indicators to address rainwater runoff or sewer overflows resulting from heavy rainfall.

Coliphages as viral indicators in municipal wastewater: A comparison between the ISO and the USEPA methods based on a systematic literature review

The use of traditional faecal indicator bacteria as surrogate organisms for pathogenic viruses in domestic wastewater has been noted as a problematic as concentrations and removal rates of bacteria and viruses do not seem to correlate. In this sense, bacteriophages (phages) emerge as potential viral indicators, as they are commonly found in wastewater in high levels, and can be quantified using simple, fast, low-cost methods. Somatic and F-specific coliphages comprise groups of phages commonly used as indicators of water quality. There are two internationally recognised methods to detect and enumerate coliphages in water samples, the International Standardization Organization (ISO) and the US Environmental Protection Agency (USEPA) methods. Both methods are based on the lysis of specific bacterial host strains infected by phages. Within this context, this systematic literature review aimed at gathering concentrations in raw and treated domestic wastewater (secondary, biological treatment systems and post-treatment systems), and removal efficiencies of somatic and F-specific coliphages obtained by ISO and USEPA methods, and then compare both methods. A total of 33 research papers were considered in this study. Results showed that the ISO method is more commonly applied than the USEPA method. Some discrepancies in terms of concentrations and removal efficiencies were observed between both methods. Higher removal rates were observed for both somatic and F-specific coliphages in activated sludge systems when using the USEPA method compared to the ISO method; in other secondary (biological) treatment systems, this was observed only for F-specific coliphages. The use of different standardised methods available might lead to difficulties in obtaining and comparing phage data in different conditions and locations. Future research comparing both ISO and USEPA methods as well as viral and bacterial pathogens and indicators in WWTP is recommended.

Quantification and fate of plasmid-specific bacteriophages in wastewater: Beyond the F-coliphages

Plasmid-specific bacteriophages specifically infect bacteria carrying conjugal plasmids. While wastewater has been used as isolation source for such phages, to date, only the distribution and ecology of RNA phages specific to the F plasmid have been described, because they serve as a water quality indicator. Yet, several other plasmid classes have higher clinical and ecological relevance, and the distribution, fate, and ecology of the phages that target them remain uncharacterized. We aimed to (i) provide an experimental platform to quantify the abundance of plasmid-specific phages applicable to several different conjugal plasmid classes, (ii) describe the distribution of such phages in wastewater systems, and (iii) relate their abundance to plasmid abundance and to municipal wastewater treatment processes. We introduced four model conjugal plasmids, belonging to incompatibility groups IncP-1, IncN, IncHI1, or IncF into an avirulent Salmonella enterica strain, for which somatic phages are at low abundance in wastewater. These strains were used in double layer agar assays with waters from contrasting sources. Plasmid-specific phages were common in wastewater but rare in river water. Hospital wastewater contained significantly more IncP-1-, but fewer IncF- and IncN- specific phages than domestic wastewater. This pattern did not match that of plasmid abundance estimated by Inc group targeting high-throughput quantitative PCR. The comparison between influent and effluent of wastewater treatment plants revealed a reduction in phage concentration by ca. 2 log, without significant contribution of primary settling. Overall, the ubiquity of these phages hints at their importance for plasmid ecology, and can provide opportunities in water quality monitoring and in ecological management of mobile resistance genes.

Comparison of methods for the enumeration of coliphages in 100 mL water samples

In the last decade coliphages have been included in many water quality regulations as viral faecal indicators. However, the standardised methods used to detect and quantify coliphages differ in bacterial host strains, culture media and techniques. In this comparative study, 100 mL samples of mineral drinking water, river water and wastewater were analysed with International Organization for Standardization (ISO) standard methods, with United States-Environmental Protection Agency (U.S. EPA) based methods as well as commercial kits combining a single agar layer (SAL) assay with ISO bacterial host strains. The three methods gave similar counts (p-value>0.05) for somatic and total coliphages in the matrices with less than 100 PFU/100 mL, whereas for F-specific coliphages, the U.S. EPA method provided statistically significant lower numbers (p-value<0.05) than the other two protocols, possibly because it uses a different bacterial host strain (Escherichia coli HS (pFamp) R vs. the ISO strain Salmonella enterica serovar Typhimurium WG49). In samples with more than 100 PFU/100 mL, the ISO method yielded higher counts of somatic coliphages than the other two protocols (p-value<0.05). As the three methods provided similar results in clean water, the approach combining a SAL assay with the ISO bacterial host strain could be a useful option for coliphage analysis in this type of sample, as it does not require a concentration step.

Decay of infectious SARS-CoV-2 and surrogates in aquatic environments

The introduction of SARS-CoV-2 containing human stool and sewage into water bodies may raise public health concerns. However, assessment of public health risks by faecally contaminated water is limited by a lack of knowledge regarding the persistence of infectious SARS-CoV-2 in water. In the present study the decay rates of viable infectious SARS-CoV-2 and SARS-CoV-2 RNA were determined in river and seawater at 4 and 20°C. These decay rates were compared to S. typhimurium bacteriophage MS2 and pepper mild mottle virus (PMMoV). Persistence of viable SARS-CoV-2 was temperature dependent, remaining infectious for significantly longer periods of time in both freshwater and seawater at 4°C than at 20°C. T₉₀ for infectious SARS-CoV-2 in river water was 2.3 days and 3.8 days at 20°C and 4°C, respectively. The T₉₀ values were 1.1 days and 2.2 days in seawater at 20°C and 4°C, respectively. In contrast to the rapid inactivation of infectious SARS-CoV-2 in river and sea water, viral RNA was relatively stable. The RNA decay rates were increased in non-sterilised river and seawater, presumably due to the presence of microbiota. The decay rates of infectious MS2, MS2 RNA and PMMoV RNA differed significantly from the decay rate of SARS-CoV-2 RNA, suggesting that their use as surrogate markers for the persistence of SARS-CoV-2 in the environment is limited.

Bacteriophages as Fecal Pollution Indicators

Bacteriophages are promising tools for the detection of fecal pollution in different environments, and particularly for viral pathogen risk assessment. Having similar morphological and biological characteristics, bacteriophages mimic the fate and transport of enteric viruses. Enteric bacteriophages, especially phages infecting Escherichia coli (coliphages), have been proposed as alternatives or complements to fecal indicator bacteria. Here, we provide a general overview of the potential use of enteric bacteriophages as fecal and viral indicators in different environments, as well as the available methods for their detection and enumeration, and the regulations for their application.

Coliphages as a Complementary Tool to Improve the Management of Urban Wastewater Treatments and Minimize Health Risks in Receiving Waters

Even in countries with extensive sanitation systems, outbreaks of waterborne infectious diseases are being reported. Current tendencies, such as the growing concentration of populations in large urban conurbations, climate change, aging of existing infrastructures, and emerging pathogens, indicate that the management of water resources will become increasingly challenging in the near future. In this context, there is an urgent need to control the fate of fecal microorganisms in wastewater to avoid the negative health consequences of releasing treated effluents into surface waters (rivers, lakes, etc.) or marine coastal water. On the other hand, the measurement of bacterial indicators yields insufficient information to gauge the human health risk associated with viral infections. It would therefore seem advisable to include a viral indicator—for example, somatic coliphages—to monitor the functioning of wastewater treatments. As indicated in the studies reviewed herein, the concentrations of somatic coliphages in raw sewage remain consistently high throughout the year worldwide, as occurs with bacterial indicators. The removal process for bacterial indicators and coliphages in traditional sewage treatments is similar, the concentrations in secondary effluents remaining sufficiently high for enumeration, without the need for cumbersome and costly concentration procedures. Additionally, according to the available data on indicator behavior, which is still limited for sewers but abundant for surface waters, coliphages persist longer than bacterial indicators once outside the gut. Based on these data, coliphages can be recommended as indicators to assess the efficiency of wastewater management procedures with the aim of minimizing the health impact of urban wastewater release in surface waters.

Variable fecal source prioritization in recreational waters routinely monitored with viral and bacterial general indicators

Somatic and F+ coliphage methods are under consideration as potential routine surface water quality monitoring tools to identify unsafe levels of fecal pollution in recreational waters. However, little is known about the cooccurrence of these virus-based fecal indicators and host-associated genetic markers used to prioritize key pollution sources for remediation. In this study, paired measurements of cultivated coliphage (somatic and F+) and bacterial (E. coli and enterococci) general fecal indicators and genetic markers indicative of human (HF183/BacR287 and HumM2), ruminant (Rum2Bac), canine (DG3), and avian (GFD) fecal pollution sources were assessed in 365 water samples collected from six Great Lakes Basin beach and river sites over a 15-week recreational season. Water samples were organized into groups based on defined viral and bacterial fecal indicator water quality thresholds and average log10 host-associated genetic marker fecal score ratios were estimated to compare pollutant source inferences based on variable routine water quality monitoring practices. Eligible log10 fecal score ratios ranged from -0.051 (F+ coliphage, GFD) to 2.08 (enterococci, Rum2Bac). Using a fecal score ratio approach, findings suggest that general fecal indicator selection for routine water quality monitoring can influence the interpretation of host-associated genetic marker measurements, in some cases, prioritizing different pollutant sources for remediation. Variable trends were also observed between Great Lake beach and river sites suggesting disparate management practices may be useful for each water type.

Phages as a Cohesive Prophylactic and Therapeutic Approach in Aquaculture Systems

Facing antibiotic resistance has provoked a continuously growing focus on phage therapy. Although the greatest emphasis has always been placed on phage treatment in humans, behind phage application lies a complex approach that can be usefully adopted by the food industry, from hatcheries and croplands to ready-to-eat products. Such diverse businesses require an efficient method for combating highly pathogenic bacteria since antibiotic resistance concerns every aspect of human life. Despite the vast abundance of phages on Earth, the aquatic environment has been considered their most natural habitat. Water favors multidirectional Brownian motion and increases the possibility of contact between phage particles and their bacterial hosts. As the global production of aquatic organisms has rapidly grown over the past decades, phage treatment of bacterial infections seems to be an obvious and promising solution in this market sector. Pathogenic bacteria, such as Aeromonas and Vibrio, have already proved to be responsible for mass mortalities in aquatic systems, resulting in economic losses. The main objective of this work is to summarize, from a scientific and industry perspective, the recent data regarding phage application in the form of targeted probiotics and therapeutic agents in aquaculture niches.