Molecular Diagnostic Tools Applied for Assessing Microbial Water Quality

Abstract

Microbial water quality is of vital importance for human, animal, and environmental health. Notably, pathogenically contaminated water can result in serious health problems, such as waterborne outbreaks, which have caused huge economic and social losses. In this context, the prompt detection of microbial contamination becomes essential to enable early warning and timely reaction with proper interventions. Recently, molecular diagnostics have been increasingly employed for the rapid and robust assessment of microbial water quality implicated by various microbial pollutants, e.g., waterborne pathogens and antibiotic-resistance genes (ARGs), imposing the most critical health threats to humans and the environment. Continuous technological advances have led to constant improvements and expansions of molecular methods, such as conventional end-point PCR, DNA microarray, real-time quantitative PCR (qPCR), multiplex qPCR (mqPCR), loop-mediated isothermal amplification (LAMP), digital droplet PCR (ddPCR), and high-throughput next-generation DNA sequencing (HT-NGS). These state-of-the-art molecular approaches largely facilitate the surveillance of microbial water quality in diverse aquatic systems and wastewater. This review provides an up-to-date overview of the advancement of the key molecular tools frequently employed for microbial water quality assessment, with future perspectives on their applications.

Aligning monitoring of virus barriers in potable reuse with unit process treatment mechanisms and time scales: A critical review and research needs

“…These methods can be adapted to any pathogen whose genetic sequence is known, and future development is expected to detect other common waterborne enteric viruses. Molecular methods are considered the most likely avenue for future development of viral monitoring due to rapid, robust, and precise detection of virus (Paruch, 2022). Other techniques like flow cytometry and cell counts, while best established for bacteria and protozoa, are more difficult to apply to viruses due to their smaller size and are therefore a topic of potential research interest (Huang et al, 2016).…”

FlashPCR: Revolutionising qPCR by Accelerating Amplification through Low ∆T Protocols

“…This approach is clearly unsuitable for PoC applications, particularly in infectious disease diagnosis, where quick and accurate identification of the causative agent is crucial for effective treatment and containment. Additionally, in fields such as environmental monitoring [ 17 ], food safety [ 18 ], and forensic analysis [ 19 ], reliable and rapid detection is crucial for timely decision-making and intervention. Whilst sample preparation remains a bottleneck within the PCR workflow, this issue is being addressed [ 20 , 21 , 22 , 23 , 24 , 25 , 26 ], making it even more important to address the PCR step itself.…”

Evaluation of a Tetracycline-Resistant E. coli Enumeration Method for Correctly Classifying E. coli in Environmental Waters in Kentucky, USA

“…The focus of this study is assessing the validity of culture-based method results for tetracycline-resistant E. coli, while recognizing molecular approaches in general are preferred for future methodological monitoring standards [ 15 ]. Among these methods, qPCR is one expected to be among future gold-standard molecular methods for quantifying fecal indicator markers and pathogens [ 16 ]. Regarding qPCR, while tremendous progress has been made in reducing equipment, software, and consumable costs for fecal indicators and pathogens in water, molecular methods including qPCR present major obstacles for limited resource environments including high costs, specialized instruments, and training/personnel costs [ 16 ].…”

“…Among these methods, qPCR is one expected to be among future gold-standard molecular methods for quantifying fecal indicator markers and pathogens [ 16 ]. Regarding qPCR, while tremendous progress has been made in reducing equipment, software, and consumable costs for fecal indicators and pathogens in water, molecular methods including qPCR present major obstacles for limited resource environments including high costs, specialized instruments, and training/personnel costs [ 16 ]. Thus, culture-based methods have some advantages in resource-limited environments with respect to the 20 characteristics identified by Bain et al [ 17 ].…”