CrAssphage May Be Viable Markers of Contamination in Pristine and Contaminated River Water

Mafumo, Nyasha; Bezuidt, Oliver; Roux, Wouter le; Makhalanyane, Thulani P.

doi:10.1128/msystems.01282-22

Cited by 5 publications

(5 citation statements)

References 87 publications

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“…The negative samples in the current study may contain lower concentrations of crAssphage below the limits of detection. Lastly, new research has demonstrated the great diversity of crAss-like phages that can affect the detection of target genes using PCR [ 45 , 46 ].…”

Section: Discussionmentioning

confidence: 99%

Prevalence and Genetic Diversity of Cross-Assembly Phages in Wastewater Treatment Plants in Riyadh, Saudi Arabia

Alotaibi,

Eifan,

Hanif

et al. 2023

Microorganisms

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The most common DNA virus found in wastewaters globally is the cross-assembly phage (crAssphage). King Saud University wastewater treatment plant (KSU-WWTP); Manfoha wastewater treatment plant (MN-WWTP); and the Embassy wastewater treatment plant (EMB-WWTP) in Riyadh, Saudi Arabia were selected, and 36 untreated sewage water samples during the year 2022 were used in the current study. The meteorological impact on crAssphage prevalence was investigated. CrAssphage prevalence was recorded using PCR and Sanger sequencing. The molecular diversity of crAssphage sequences was studied for viral gene segments from the major capsid protein (MCP) and membrane protein containing the peptidoglycan-binding domain (MP-PBD). KSU-WWTP and EMB-WWTP showed a higher prevalence of crAssphage (83.3%) than MN-WWTP (75%). Phylogenetic analysis of MCP and MP-PBD segments depicted a close relationship to the Japanese isolates. The MCP gene from the current study’s isolate WW/2M/SA/2022 depicted zero evolutionary divergence from 3057_98020, 2683_104905, and 4238_99953 isolates (d = 0.000) from Japan. A significant influence of temporal variations on the prevalence of crAssphage was detected in the three WWTPs. CrAssphage displayed the highest prevalence at high temperatures (33–44 °C), low relative humidity (6–14%), and moderate wind speed (16–21 Km/h). The findings provided pioneering insights into crAssphage prevalence and its genetic diversity in WWTPs in Riyadh, Saudi Arabia.

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Section: Discussionmentioning

confidence: 99%

Prevalence and Genetic Diversity of Cross-Assembly Phages in Wastewater Treatment Plants in Riyadh, Saudi Arabia

Alotaibi,

Eifan,

Hanif

et al. 2023

Microorganisms

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“…A specific group of bacteriophages named crAssphages have been proposed as potential universal human feces viral indicators in water bodies (Farkas et al, 2019;Mafumo et al, 2023). CrAssphages were described by Dutilh et al (2014) as the most abundant phages in the human gut virome.…”

Section: Bacteriophages As Pollution Indicators In Watermentioning

confidence: 99%

“…Further studies identified that crAssphages are highly specific and abundant to human feces (Sabar et al, 2022), highly prevalent in sewage samples (Stachler et al, 2017), and maintain correlation to the presence of human enteric viruses in water (Jennings et al, 2020). Given the previous characteristics, crAssphages have been preconized in favor of currently used fecal indicator bacteria (FIB), which poorly explain viral pathogen dynamics in water and have low host specificity, making difficult the identification of the source of contamination (Ward et al, 2020;Toribio-Avedillo et al, 2021;Mafumo et al, 2023). CrAssphage applicability has been evaluated in several countries (Crank et al, 2020;Ward et al, 2020;Sangkaew et al, 2021;Nam et al, 2022) and shows promising possibilities for human fecal contamination detection in freshwater.…”

Section: Bacteriophages As Pollution Indicators In Watermentioning

confidence: 99%

Tools and methodology to in silico phage discovery in freshwater environments

Dantas,

Martins,

Nogueira

et al. 2024

Front. Microbiol.

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Freshwater availability is essential, and its maintenance has become an enormous challenge. Due to population growth and climate changes, freshwater sources are becoming scarce, imposing the need for strategies for its reuse. Currently, the constant discharge of waste into water bodies from human activities leads to the dissemination of pathogenic bacteria, negatively impacting water quality from the source to the infrastructure required for treatment, such as the accumulation of biofilms. Current water treatment methods cannot keep pace with bacterial evolution, which increasingly exhibits a profile of multidrug resistance to antibiotics. Furthermore, using more powerful disinfectants may affect the balance of aquatic ecosystems. Therefore, there is a need to explore sustainable ways to control the spreading of pathogenic bacteria. Bacteriophages can infect bacteria and archaea, hijacking their host machinery to favor their replication. They are widely abundant globally and provide a biological alternative to bacterial treatment with antibiotics. In contrast to common disinfectants and antibiotics, bacteriophages are highly specific, minimizing adverse effects on aquatic microbial communities and offering a lower cost–benefit ratio in production compared to antibiotics. However, due to the difficulty involving cultivating and identifying environmental bacteriophages, alternative approaches using NGS metagenomics in combination with some bioinformatic tools can help identify new bacteriophages that can be useful as an alternative treatment against resistant bacteria. In this review, we discuss advances in exploring the virome of freshwater, as well as current applications of bacteriophages in freshwater treatment, along with current challenges and future perspectives.

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“…Even though treated water samples tested negative for the presence of E. coli and total coliforms, these outbreaks raised questions about the sole usefulness of the current microbial standards of aquatic health for routine wastewater quality testing. Aside from Norovirus outbreaks, there are many other reports on Rotavirus, crAssphage, and Adenovirus prevalence in freshwaters (Hellmer et al, 2014; Garcia et al, 2022; Mafumo et al, 2023).…”

Section: Introductionmentioning

confidence: 99%

Seasonal Patterns of Viromes in Urban Aquatic Environments of Manitoba

Francis,

Uyaguari

2024

Preprint

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Although wastewater and treatment plants harbor many pathogenic organisms' traditional methods that monitor the microbial quality of wastewater have not changed since the early 1900s and often disregard the presence of other types of significant waterborne pathogens such as viruses. Using advanced technology, our study aims to characterize the taxonomy, functional profiling and seasonal patterns of viral DNA and RNA community structures using metagenomics and quantitative-PCR, for the purpose of establishing the virome distribution in aquatic environment’s receiving wastewater discharge. Environmental water samples were collected at 11 locations in Winnipeg, Manitoba along the Red and Assiniboine Rivers during the Spring, Summer and Fall 2021. Samples were filtered and underwent skimmed milk flocculation for viral concentration. The taxonomic classification of DNA viruses identified from the RefSeq database (available from MG-RAST) and Kraken 2 Viral Genome database were predominately DNA bacteriophages(Myoviridae, PodoviridaeandSiphoviridae) which accounted for approximately 90% of each aquatic sample location along the Red and Assiniboine Rivers. Phage related functionalities such as phage tail fiber proteins, phage replication, and phage packaging machinery accounted for 40% of each aquatic samples collected which possibly correspond to the DNA phages that were previously identified. RNA phages such asCystoviridaeandLeviviridaewere identified to a lesser extent accounting for approximately 3 % of each aquatic sample collected, while other viruses such asVirgaviridae, Retroviridae, PicobirnaviridaeandPartiviridaeaccounted for 7%–100% of aquatic samples. The functionalities of RNA viruses were primarily related to metabolic pathways such as potassium homeostasis, respiratory complexes and sialic acid metabolism, essential for RNA viruses to survive in their host.

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CrAssphage May Be Viable Markers of Contamination in Pristine and Contaminated River Water

Abstract: Rivers support substantial populations and provide important ecosystem services. Despite the application of fecal coliform tests and other markers, we lack rapid and reproducible approaches for determining fecal contamination in rivers.

Cited by 5 publications

References 87 publications

Prevalence and Genetic Diversity of Cross-Assembly Phages in Wastewater Treatment Plants in Riyadh, Saudi Arabia

Prevalence and Genetic Diversity of Cross-Assembly Phages in Wastewater Treatment Plants in Riyadh, Saudi Arabia

Tools and methodology to in silico phage discovery in freshwater environments

Seasonal Patterns of Viromes in Urban Aquatic Environments of Manitoba

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