Next-generation sequencing provides new insights into the diversity and structure of bacterial communities, as well as the fate of pathogens in wastewater treatment systems. In this study, the bacterial community structure and the presence of pathogenic bacteria in three wastewater treatment plants across Gauteng province in South Africa were studied. The physicochemical results indicated that the quality of wastewater varies considerably from one plant to the others. Proteobacteria, Actinobacteria, Firmicutes, and Chloroflexi were the dominant phyla across the three wastewater treatment plants, while Alphaproteobacteria, Actinobacteria, Bacilli, and Clostridia were the dominant classes. The dominant bacterial functions were highly associated with carbohydrate, energy, and amino acid metabolism. In addition, potential pathogenic bacterial members identified from the influent/effluent samples included Roseomonas, Bacillus, Pseudomonas, Clostridium, Mycobacterium, Methylobacterium, and Aeromonas. The results of linear discriminant analysis (LDA) effect size analysis also confirmed that these bacterial pathogens were significantly abundant in the wastewater treatment systems. Further, the results of this study highlighted that the presence of bacterial pathogens in treated effluent pose a potential contamination risk, transmitted through soil, agriculture, water, or sediments. There is thus a need for continuous monitoring of potential pathogens in wastewater treatment plants (WWTPs) in order to minimize public health risk.

There has been an increase in the quest for metagenomics as an approach for the identification and study of the diversity of human viruses found in aquatic systems, both for their role as waterborne pathogens and as water quality indicators. In the last few years, environmental viral metagenomics has grown significantly and has enabled the identification, diversity and entire genome sequencing of viruses in environmental and clinical samples extensively. Prior to the arrival of metagenomics, traditional molecular procedures such as the polymerase chain reaction (PCR) and sequencing, were mostly used to identify and classify enteric viral species in different environmental milieu. After the advent of metagenomics, more detailed reports have emerged about the important waterborne viruses identified in wastewater treatment plant effluents and surface water. This paper provides a review of methods that have been used for the concentration, detection and identification of viral species from different environmental matrices. The review also takes into consideration where metagenomics has been explored in different African countries, as well as the limitations and challenges facing the approach. Procedures including sample processing, experimental design, sequencing technology, and bioinformatics analysis are discussed. The review concludes by summarising the current thinking and practices in the field and lays bare key issues that those venturing into this field need to consider and address.

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Waterborne pathogens are still considered a threat to human health. Wastewater treatment plants (WWTPs), contain a high populace and diversity of viruses that can significantly affect the aquatic ecosystem. Subsequently, the occurrence and recurrence of viral pathogens are alarming that exist in human populations, which are potentially discharged into sewage systems. This study investigated the distribution and diversity of the viral communities from three WWTPs in Gauteng Province, South Africa using next-generation sequencing technology. The results uncovered that most of the viral populaces in the wastewater plants belong to the families Siphoviridae, Microviridae, and Myoviridae of the order Caudovirales. Other families including Baculoviridae, Partitiviridae, Virgaviridae, and Tymoviridae were likewise recorded. On the other hand, enteric pathogens detected were Astroviridae, Reoviridae, and Coronaviridae. The predicted functional features for the viromes revealed that the DNA metabolism was the major function within the community followed by carbohydrate and amino acid metabolism, suggesting that the treatment plants provide a rich biological environment for the growth of diverse viral species and other processes. The overall results in this study highlight the biological significance of WWTPs as a hotspot for some viral agents. The contamination routes of these viral agents are needed for efficient and cost-effective management strategies in water systems. Further, viral metagenomics ought to be considered as a key approach for revealing the diversity and early warning of emerging disease outbreaks.

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